Warning: Permanently added '2620:52:3:1:dead:beef:cafe:c1d6' (ED25519) to the list of known hosts. You can reproduce this build on your computer by running: sudo dnf install copr-rpmbuild /usr/bin/copr-rpmbuild --verbose --drop-resultdir --task-url https://copr.fedorainfracloud.org/backend/get-build-task/6941749-fedora-39-x86_64 --chroot fedora-39-x86_64 Version: 0.70 PID: 174205 Logging PID: 174206 Task: {'appstream': False, 'background': True, 'build_id': 6941749, 'buildroot_pkgs': [], 'chroot': 'fedora-39-x86_64', 'enable_net': False, 'fedora_review': False, 'git_hash': '51fba3fe7209564c4c610615aa1f44865d83ef32', 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/torsava/automatic-obsoletes/apbs', 'isolation': 'default', 'memory_reqs': 2048, 'package_name': 'apbs', 'package_version': '3.0.0-22', 'project_dirname': 'automatic-obsoletes', 'project_name': 'automatic-obsoletes', 'project_owner': 'torsava', 'repo_priority': None, 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/torsava/automatic-obsoletes/fedora-39-x86_64/', 'id': 'copr_base', 'name': 'Copr repository', 'priority': None}], 'sandbox': 'torsava/automatic-obsoletes--https://src.fedoraproject.org/user/releng', 'source_json': {}, 'source_type': None, 'submitter': 'https://src.fedoraproject.org/user/releng', 'tags': [], 'task_id': '6941749-fedora-39-x86_64', 'timeout': 18000, 'uses_devel_repo': False, 'with_opts': [], 'without_opts': []} Running: git clone https://copr-dist-git.fedorainfracloud.org/git/torsava/automatic-obsoletes/apbs /var/lib/copr-rpmbuild/workspace/workdir-nr35hko_/apbs --depth 500 --no-single-branch --recursive cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/torsava/automatic-obsoletes/apbs', '/var/lib/copr-rpmbuild/workspace/workdir-nr35hko_/apbs', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-nr35hko_/apbs'... Running: git checkout 51fba3fe7209564c4c610615aa1f44865d83ef32 -- cmd: ['git', 'checkout', '51fba3fe7209564c4c610615aa1f44865d83ef32', '--'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-nr35hko_/apbs rc: 0 stdout: stderr: Note: switching to '51fba3fe7209564c4c610615aa1f44865d83ef32'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by switching back to a branch. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -c with the switch command. Example: git switch -c Or undo this operation with: git switch - Turn off this advice by setting config variable advice.detachedHead to false HEAD is now at 51fba3f automatic import of apbs Running: copr-distgit-client sources cmd: ['copr-distgit-client', 'sources'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-nr35hko_/apbs rc: 0 stdout: /usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated stderr: INFO: Reading stdout from command: git rev-parse --abbrev-ref HEAD INFO: Reading stdout from command: git rev-parse HEAD INFO: Reading sources specification file: sources INFO: Downloading apbs-3.0.0.tar.gz INFO: Reading stdout from command: curl --help all INFO: Calling: curl -H Pragma: -o apbs-3.0.0.tar.gz --location --connect-timeout 60 --retry 3 --retry-delay 10 --remote-time --show-error --fail --retry-all-errors https://copr-dist-git.fedorainfracloud.org/repo/pkgs/torsava/automatic-obsoletes/apbs/apbs-3.0.0.tar.gz/md5/f54dff1a670e1dc766d5ad3f775b5de8/apbs-3.0.0.tar.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 25.9M 100 25.9M 0 0 40.8M 0 --:--:-- --:--:-- --:--:-- 40.8M INFO: Reading stdout from command: md5sum apbs-3.0.0.tar.gz Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-nr35hko_/apbs/apbs.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-nr35hko_/apbs --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1705965440.204976 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 5.4 starting (python version = 3.11.3, NVR = mock-5.4-1.fc38), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-nr35hko_/apbs/apbs.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-nr35hko_/apbs --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1705965440.204976 -r /var/lib/copr-rpmbuild/results/configs/child.cfg Start(bootstrap): init plugins INFO: tmpfs initialized INFO: selinux enabled INFO: chroot_scan: initialized INFO: compress_logs: initialized Finish(bootstrap): init plugins Start: init plugins INFO: tmpfs initialized INFO: selinux enabled INFO: chroot_scan: initialized INFO: compress_logs: initialized Finish: init plugins INFO: Signal handler active Start: run INFO: Start(/var/lib/copr-rpmbuild/workspace/workdir-nr35hko_/apbs/apbs.spec) Config(fedora-39-x86_64) Start: clean chroot Finish: clean chroot Mock Version: 5.4 INFO: Mock Version: 5.4 Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-39-x86_64-bootstrap-1705965440.204976/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata INFO: Guessed host environment type: unknown INFO: Using bootstrap image: registry.fedoraproject.org/fedora:39 INFO: Pulling image: registry.fedoraproject.org/fedora:39 INFO: Copy content of container registry.fedoraproject.org/fedora:39 to /var/lib/mock/fedora-39-x86_64-bootstrap-1705965440.204976/root INFO: Checking that registry.fedoraproject.org/fedora:39 image matches host's architecture INFO: mounting registry.fedoraproject.org/fedora:39 with podman image mount INFO: image registry.fedoraproject.org/fedora:39 as /var/lib/containers/storage/overlay/8ff7ad910417a7b8a49019008335921d2aac0e3304a19ce258deabf431e59801/merged INFO: umounting image registry.fedoraproject.org/fedora:39 (/var/lib/containers/storage/overlay/8ff7ad910417a7b8a49019008335921d2aac0e3304a19ce258deabf431e59801/merged) with podman image umount INFO: Package manager dnf detected and used (fallback) INFO: Bootstrap image not marked ready Start(bootstrap): installing dnf tooling No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 28 MB/s | 18 MB 00:00 fedora 24 MB/s | 89 MB 00:03 updates 12 MB/s | 29 MB 00:02 Last metadata expiration check: 0:00:04 ago on Mon Jan 22 23:17:49 2024. Package python3-dnf-4.18.1-2.fc39.noarch is already installed. Dependencies resolved. ================================================================================ Package Arch Version Repository Size ================================================================================ Installing: python3-dnf-plugins-core noarch 4.4.4-2.fc39 copr_base 302 k Upgrading: dnf noarch 4.18.2-2.fc39 copr_base 496 k dnf-data noarch 4.18.2-2.fc39 copr_base 40 k python3-dnf noarch 4.18.2-2.fc39 copr_base 550 k yum noarch 4.18.2-2.fc39 copr_base 38 k Installing dependencies: dbus-libs x86_64 1:1.14.10-1.fc39 fedora 156 k python3-dateutil noarch 1:2.8.2-12.fc39 copr_base 345 k python3-dbus x86_64 1.3.2-5.fc39 copr_base 147 k python3-distro noarch 1.9.0-2.fc39 copr_base 46 k python3-six noarch 1.16.0-13.fc39 copr_base 41 k python3-systemd x86_64 235-6.fc39 copr_base 101 k Transaction Summary ================================================================================ Install 7 Packages Upgrade 4 Packages Total download size: 2.2 M Downloading Packages: (1/11): python3-distro-1.9.0-2.fc39.noarch.rpm 975 kB/s | 46 kB 00:00 (2/11): python3-dbus-1.3.2-5.fc39.x86_64.rpm 3.0 MB/s | 147 kB 00:00 (3/11): python3-dateutil-2.8.2-12.fc39.noarch.r 4.9 MB/s | 345 kB 00:00 (4/11): python3-dnf-plugins-core-4.4.4-2.fc39.n 11 MB/s | 302 kB 00:00 (5/11): python3-six-1.16.0-13.fc39.noarch.rpm 1.5 MB/s | 41 kB 00:00 (6/11): python3-systemd-235-6.fc39.x86_64.rpm 9.9 MB/s | 101 kB 00:00 (7/11): dnf-4.18.2-2.fc39.noarch.rpm 30 MB/s | 496 kB 00:00 (8/11): dnf-data-4.18.2-2.fc39.noarch.rpm 2.8 MB/s | 40 kB 00:00 (9/11): python3-dnf-4.18.2-2.fc39.noarch.rpm 35 MB/s | 550 kB 00:00 (10/11): yum-4.18.2-2.fc39.noarch.rpm 2.4 MB/s | 38 kB 00:00 (11/11): dbus-libs-1.14.10-1.fc39.x86_64.rpm 479 kB/s | 156 kB 00:00 -------------------------------------------------------------------------------- Total 5.1 MB/s | 2.2 MB 00:00 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Upgrading : dnf-data-4.18.2-2.fc39.noarch 1/15 Upgrading : python3-dnf-4.18.2-2.fc39.noarch 2/15 Upgrading : dnf-4.18.2-2.fc39.noarch 3/15 Running scriptlet: dnf-4.18.2-2.fc39.noarch 3/15 Installing : dbus-libs-1:1.14.10-1.fc39.x86_64 4/15 Installing : python3-dbus-1.3.2-5.fc39.x86_64 5/15 Installing : python3-systemd-235-6.fc39.x86_64 6/15 Installing : python3-six-1.16.0-13.fc39.noarch 7/15 Installing : python3-dateutil-1:2.8.2-12.fc39.noarch 8/15 Installing : python3-distro-1.9.0-2.fc39.noarch 9/15 Installing : python3-dnf-plugins-core-4.4.4-2.fc39.noarch 10/15 Upgrading : yum-4.18.2-2.fc39.noarch 11/15 Cleanup : yum-4.18.1-2.fc39.noarch 12/15 Running scriptlet: dnf-4.18.1-2.fc39.noarch 13/15 Cleanup : dnf-4.18.1-2.fc39.noarch 13/15 Running scriptlet: dnf-4.18.1-2.fc39.noarch 13/15 Cleanup : python3-dnf-4.18.1-2.fc39.noarch 14/15 Cleanup : dnf-data-4.18.1-2.fc39.noarch 15/15 Running scriptlet: dnf-data-4.18.1-2.fc39.noarch 15/15 Verifying : python3-dateutil-1:2.8.2-12.fc39.noarch 1/15 Verifying : python3-dbus-1.3.2-5.fc39.x86_64 2/15 Verifying : python3-distro-1.9.0-2.fc39.noarch 3/15 Verifying : python3-dnf-plugins-core-4.4.4-2.fc39.noarch 4/15 Verifying : python3-six-1.16.0-13.fc39.noarch 5/15 Verifying : python3-systemd-235-6.fc39.x86_64 6/15 Verifying : dbus-libs-1:1.14.10-1.fc39.x86_64 7/15 Verifying : dnf-4.18.2-2.fc39.noarch 8/15 Verifying : dnf-4.18.1-2.fc39.noarch 9/15 Verifying : dnf-data-4.18.2-2.fc39.noarch 10/15 Verifying : dnf-data-4.18.1-2.fc39.noarch 11/15 Verifying : python3-dnf-4.18.2-2.fc39.noarch 12/15 Verifying : python3-dnf-4.18.1-2.fc39.noarch 13/15 Verifying : yum-4.18.2-2.fc39.noarch 14/15 Verifying : yum-4.18.1-2.fc39.noarch 15/15 Upgraded: dnf-4.18.2-2.fc39.noarch dnf-data-4.18.2-2.fc39.noarch python3-dnf-4.18.2-2.fc39.noarch yum-4.18.2-2.fc39.noarch Installed: dbus-libs-1:1.14.10-1.fc39.x86_64 python3-dateutil-1:2.8.2-12.fc39.noarch python3-dbus-1.3.2-5.fc39.x86_64 python3-distro-1.9.0-2.fc39.noarch python3-dnf-plugins-core-4.4.4-2.fc39.noarch python3-six-1.16.0-13.fc39.noarch python3-systemd-235-6.fc39.x86_64 Complete! Finish(bootstrap): installing dnf tooling Start(bootstrap): creating root cache Finish(bootstrap): creating root cache Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-39-x86_64-1705965440.204976/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin INFO: Package manager dnf detected and used (direct choice) INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-4.19.0-1.fc39.x86_64 rpm-sequoia-1.5.0-1.fc39.x86_64 python3-dnf-4.18.2-2.fc39.noarch python3-dnf-plugins-core-4.4.4-2.fc39.noarch yum-4.18.2-2.fc39.noarch Start: installing minimal buildroot with dnf No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 44 kB/s | 1.5 kB 00:00 Copr repository 61 MB/s | 18 MB 00:00 fedora 743 kB/s | 24 kB 00:00 updates 663 kB/s | 23 kB 00:00 Dependencies resolved. ================================================================================ Package Arch Version Repo Size ================================================================================ Installing group/module packages: bash x86_64 5.2.21-1.fc39 updates 1.8 M bzip2 x86_64 1.0.8-16.fc39 fedora 52 k coreutils x86_64 9.3-4.fc39 fedora 1.1 M cpio x86_64 2.14-4.fc39 fedora 279 k diffutils x86_64 3.10-3.fc39 fedora 398 k fedora-release-common noarch 39-34 updates 19 k findutils x86_64 1:4.9.0-5.fc39 fedora 492 k gawk x86_64 5.2.2-2.fc39 fedora 1.1 M glibc-minimal-langpack x86_64 2.38-14.fc39 updates 70 k grep x86_64 3.11-3.fc39 fedora 298 k gzip x86_64 1.12-6.fc39 fedora 166 k info x86_64 7.0.3-3.fc39 fedora 182 k patch x86_64 2.7.6-22.fc39 fedora 125 k redhat-rpm-config noarch 262-1.fc39 fedora 84 k rpm-build x86_64 4.19.1-3.fc39 copr_base 72 k sed x86_64 4.8-14.fc39 fedora 306 k shadow-utils x86_64 2:4.14.0-2.fc39 updates 1.3 M tar x86_64 2:1.35-2.fc39 fedora 864 k unzip x86_64 6.0-62.fc39 fedora 184 k util-linux x86_64 2.39.3-2.fc39 copr_base 1.1 M which x86_64 2.21-40.fc39 fedora 42 k xz x86_64 5.4.4-1.fc39 fedora 556 k Installing dependencies: alternatives x86_64 1.25-1.fc39 fedora 39 k ansible-srpm-macros noarch 1-11.fc39 fedora 21 k audit-libs x86_64 4.0-2.fc39 copr_base 119 k authselect x86_64 1.4.3-1.fc39 fedora 149 k authselect-libs x86_64 1.4.3-1.fc39 fedora 249 k basesystem noarch 11-18.fc39 fedora 7.2 k binutils x86_64 2.40-13.fc39 fedora 5.6 M binutils-gold x86_64 2.40-13.fc39 fedora 797 k bzip2-libs x86_64 1.0.8-16.fc39 fedora 41 k ca-certificates noarch 2023.2.60_v7.0.306-2.fc39 fedora 837 k coreutils-common x86_64 9.3-4.fc39 fedora 2.1 M cracklib x86_64 2.9.11-2.fc39 fedora 94 k crypto-policies noarch 20231204-1.git1e3a2e4.fc39 updates 100 k curl x86_64 8.2.1-4.fc39 updates 345 k cyrus-sasl-lib x86_64 2.1.28-11.fc39 fedora 793 k debugedit x86_64 5.0-12.fc39 updates 79 k dwz x86_64 0.15-3.fc39 fedora 134 k ed x86_64 1.19-4.fc39 fedora 79 k efi-srpm-macros noarch 5-9.fc39 fedora 22 k elfutils x86_64 0.190-4.fc39 updates 551 k elfutils-debuginfod-client x86_64 0.190-4.fc39 updates 38 k elfutils-default-yama-scope noarch 0.190-4.fc39 updates 13 k elfutils-libelf x86_64 0.190-4.fc39 updates 194 k elfutils-libs x86_64 0.190-4.fc39 updates 260 k fedora-gpg-keys noarch 39-1 fedora 130 k fedora-release noarch 39-34 updates 8.4 k fedora-release-identity-basic noarch 39-34 updates 9.2 k fedora-repos noarch 39-1 fedora 9.3 k file x86_64 5.45-2.fc39 copr_base 50 k file-libs x86_64 5.45-2.fc39 copr_base 764 k filesystem x86_64 3.18-6.fc39 fedora 1.1 M fonts-srpm-macros noarch 1:2.0.5-12.fc39 fedora 26 k fpc-srpm-macros noarch 1.3-8.fc39 fedora 7.4 k gdb-minimal x86_64 14.1-2.fc39 updates 4.3 M gdbm-libs x86_64 1:1.23-4.fc39 fedora 56 k ghc-srpm-macros noarch 1.6.1-2.fc39 fedora 7.8 k glibc x86_64 2.38-14.fc39 updates 2.2 M glibc-common x86_64 2.38-14.fc39 updates 352 k glibc-gconv-extra x86_64 2.38-14.fc39 updates 1.6 M gmp x86_64 1:6.2.1-5.fc39 fedora 313 k gnat-srpm-macros noarch 6-3.fc39 fedora 8.8 k go-srpm-macros noarch 3.3.1-1.fc39 updates 28 k jansson x86_64 2.13.1-7.fc39 fedora 44 k kernel-srpm-macros noarch 1.0-20.fc39 fedora 10 k keyutils-libs x86_64 1.6.1-7.fc39 fedora 31 k krb5-libs x86_64 1.21.2-2.fc39 updates 764 k libacl x86_64 2.3.1-9.fc39 updates 23 k libarchive x86_64 3.7.1-1.fc39 fedora 408 k libattr x86_64 2.5.1-8.fc39 fedora 18 k libblkid x86_64 2.39.3-2.fc39 copr_base 117 k libbrotli x86_64 1.1.0-2.fc39 copr_base 336 k libcap x86_64 2.48-9.fc39 updates 68 k libcap-ng x86_64 0.8.4-3.fc39 copr_base 33 k libcom_err x86_64 1.47.0-2.fc39 fedora 26 k libcurl x86_64 8.2.1-4.fc39 updates 323 k libdb x86_64 5.3.28-56.fc39 fedora 760 k libeconf x86_64 0.5.2-1.fc39 fedora 30 k libevent x86_64 2.1.12-9.fc39 fedora 258 k libfdisk x86_64 2.39.3-2.fc39 copr_base 163 k libffi x86_64 3.4.4-4.fc39 fedora 40 k libgcc x86_64 13.2.1-6.fc39 updates 112 k libgomp x86_64 13.2.1-6.fc39 updates 322 k libidn2 x86_64 2.3.4-3.fc39 fedora 117 k libmount x86_64 2.39.3-2.fc39 copr_base 155 k libnghttp2 x86_64 1.55.1-4.fc39 updates 76 k libnsl2 x86_64 2.0.0-6.fc39 fedora 30 k libpkgconf x86_64 1.9.5-2.fc39 fedora 38 k libpsl x86_64 0.21.2-4.fc39 fedora 63 k libpwquality x86_64 1.4.5-8.fc39 copr_base 108 k libselinux x86_64 3.5-5.fc39 copr_base 87 k libsemanage x86_64 3.5-4.fc39 copr_base 120 k libsepol x86_64 3.5-2.fc39 fedora 324 k libsigsegv x86_64 2.14-5.fc39 fedora 27 k libsmartcols x86_64 2.39.3-2.fc39 copr_base 68 k libssh x86_64 0.10.6-2.fc39 updates 212 k libssh-config noarch 0.10.6-2.fc39 updates 9.0 k libstdc++ x86_64 13.2.1-6.fc39 updates 865 k libtasn1 x86_64 4.19.0-3.fc39 fedora 74 k libtirpc x86_64 1.3.4-0.rc2.fc39 updates 94 k libunistring x86_64 1.1-5.fc39 fedora 543 k libutempter x86_64 1.2.1-10.fc39 fedora 26 k libuuid x86_64 2.39.3-2.fc39 copr_base 29 k libverto x86_64 0.3.2-6.fc39 fedora 20 k libxcrypt x86_64 4.4.36-2.fc39 fedora 119 k libxml2 x86_64 2.12.4-2.fc39 copr_base 694 k libzstd x86_64 1.5.5-4.fc39 fedora 309 k lua-libs x86_64 5.4.6-3.fc39 fedora 133 k lua-srpm-macros noarch 1-9.fc39 fedora 8.6 k lz4-libs x86_64 1.9.4-4.fc39 fedora 67 k mpfr x86_64 4.2.0-3.fc39 fedora 344 k ncurses-base noarch 6.4-7.20230520.fc39 fedora 88 k ncurses-libs x86_64 6.4-7.20230520.fc39 fedora 336 k ocaml-srpm-macros noarch 8-2.fc39 fedora 14 k openblas-srpm-macros noarch 2-14.fc39 fedora 7.5 k openldap x86_64 2.6.6-1.fc39 fedora 255 k openssl-libs x86_64 1:3.1.1-4.fc39 fedora 2.2 M p11-kit x86_64 0.25.3-1.fc39 updates 520 k p11-kit-trust x86_64 0.25.3-1.fc39 updates 140 k package-notes-srpm-macros noarch 0.5-9.fc39 fedora 11 k pam x86_64 1.5.3-3.fc39 updates 542 k pam-libs x86_64 1.5.3-3.fc39 updates 56 k pcre2 x86_64 10.42-1.fc39.2 fedora 233 k pcre2-syntax noarch 10.42-1.fc39.2 fedora 143 k perl-srpm-macros noarch 1-51.fc39 fedora 8.0 k pkgconf x86_64 1.9.5-2.fc39 fedora 42 k pkgconf-m4 noarch 1.9.5-2.fc39 fedora 14 k pkgconf-pkg-config x86_64 1.9.5-2.fc39 fedora 9.6 k popt x86_64 1.19-3.fc39 fedora 66 k publicsuffix-list-dafsa noarch 20240107-1.fc39 updates 58 k pyproject-srpm-macros noarch 1.11.0-1.fc39 updates 15 k python-srpm-macros noarch 3.12-4.fc39 fedora 25 k qt5-srpm-macros noarch 5.15.11-1.fc39 updates 8.3 k qt6-srpm-macros noarch 6.6.0-1.fc39 updates 8.6 k readline x86_64 8.2-4.fc39 fedora 213 k rpm x86_64 4.19.1-3.fc39 copr_base 511 k rpm-build-libs x86_64 4.19.1-3.fc39 copr_base 96 k rpm-libs x86_64 4.19.1-3.fc39 copr_base 313 k rpm-sequoia x86_64 1.5.0-2.fc39 updates 878 k rpmautospec-rpm-macros noarch 0.4.1-2.fc39 copr_base 9.8 k rust-srpm-macros noarch 25.2-2.fc39 copr_base 13 k setup noarch 2.14.4-1.fc39 fedora 154 k sqlite-libs x86_64 3.42.0-7.fc39 fedora 678 k systemd-libs x86_64 254.7-1.fc39 updates 689 k util-linux-core x86_64 2.39.3-2.fc39 copr_base 493 k xxhash-libs x86_64 0.8.2-1.fc39 fedora 37 k xz-libs x86_64 5.4.4-1.fc39 fedora 108 k zip x86_64 3.0-39.fc39 fedora 266 k zlib x86_64 1.2.13-4.fc39 fedora 94 k zstd x86_64 1.5.5-4.fc39 fedora 482 k Installing Groups: Buildsystem building group Transaction Summary ================================================================================ Install 151 Packages Total size: 52 M Installed size: 179 M Downloading Packages: [SKIPPED] audit-libs-4.0-2.fc39.x86_64.rpm: Already downloaded [SKIPPED] file-5.45-2.fc39.x86_64.rpm: Already downloaded [SKIPPED] file-libs-5.45-2.fc39.x86_64.rpm: Already downloaded [SKIPPED] libblkid-2.39.3-2.fc39.x86_64.rpm: Already downloaded [SKIPPED] libbrotli-1.1.0-2.fc39.x86_64.rpm: Already downloaded [SKIPPED] libcap-ng-0.8.4-3.fc39.x86_64.rpm: Already downloaded [SKIPPED] libfdisk-2.39.3-2.fc39.x86_64.rpm: Already downloaded [SKIPPED] libmount-2.39.3-2.fc39.x86_64.rpm: Already downloaded [SKIPPED] libpwquality-1.4.5-8.fc39.x86_64.rpm: Already downloaded [SKIPPED] libselinux-3.5-5.fc39.x86_64.rpm: Already downloaded [SKIPPED] libsemanage-3.5-4.fc39.x86_64.rpm: Already downloaded [SKIPPED] libsmartcols-2.39.3-2.fc39.x86_64.rpm: Already downloaded [SKIPPED] libuuid-2.39.3-2.fc39.x86_64.rpm: Already downloaded [SKIPPED] libxml2-2.12.4-2.fc39.x86_64.rpm: Already downloaded [SKIPPED] 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systemd-libs-254.7-1.fc39.x86_64.rpm: Already downloaded fedora 1.6 MB/s | 1.6 kB 00:00 Importing GPG key 0x18B8E74C: Userid : "Fedora (39) " Fingerprint: E8F2 3996 F232 1864 0CB4 4CBE 75CF 5AC4 18B8 E74C From : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-39-primary Key imported successfully Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Running scriptlet: filesystem-3.18-6.fc39.x86_64 1/1 Preparing : 1/1 Installing : libgcc-13.2.1-6.fc39.x86_64 1/151 Running scriptlet: libgcc-13.2.1-6.fc39.x86_64 1/151 Installing : crypto-policies-20231204-1.git1e3a2e4.fc39.noarc 2/151 Running scriptlet: crypto-policies-20231204-1.git1e3a2e4.fc39.noarc 2/151 Installing : fedora-release-identity-basic-39-34.noarch 3/151 Installing : fedora-gpg-keys-39-1.noarch 4/151 Installing : fedora-repos-39-1.noarch 5/151 Installing : fedora-release-common-39-34.noarch 6/151 Installing : fedora-release-39-34.noarch 7/151 Installing : setup-2.14.4-1.fc39.noarch 8/151 warning: /etc/hosts created as /etc/hosts.rpmnew Running scriptlet: setup-2.14.4-1.fc39.noarch 8/151 Installing : filesystem-3.18-6.fc39.x86_64 9/151 Installing : basesystem-11-18.fc39.noarch 10/151 Installing : qt6-srpm-macros-6.6.0-1.fc39.noarch 11/151 Installing : qt5-srpm-macros-5.15.11-1.fc39.noarch 12/151 Installing : 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gdbm-libs-1:1.23-4.fc39.x86_64 87/151 Installing : cyrus-sasl-lib-2.1.28-11.fc39.x86_64 88/151 Installing : keyutils-libs-1.6.1-7.fc39.x86_64 89/151 Installing : libdb-5.3.28-56.fc39.x86_64 90/151 Installing : libffi-3.4.4-4.fc39.x86_64 91/151 Installing : p11-kit-0.25.3-1.fc39.x86_64 92/151 Installing : p11-kit-trust-0.25.3-1.fc39.x86_64 93/151 Running scriptlet: p11-kit-trust-0.25.3-1.fc39.x86_64 93/151 Installing : libpkgconf-1.9.5-2.fc39.x86_64 94/151 Installing : pkgconf-1.9.5-2.fc39.x86_64 95/151 Installing : pkgconf-pkg-config-1.9.5-2.fc39.x86_64 96/151 Installing : libsigsegv-2.14-5.fc39.x86_64 97/151 Installing : gawk-5.2.2-2.fc39.x86_64 98/151 Installing : libverto-0.3.2-6.fc39.x86_64 99/151 Installing : xxhash-libs-0.8.2-1.fc39.x86_64 100/151 Installing : libgomp-13.2.1-6.fc39.x86_64 101/151 Installing : libnghttp2-1.55.1-4.fc39.x86_64 102/151 Installing : elfutils-default-yama-scope-0.190-4.fc39.noarch 103/151 Running scriptlet: elfutils-default-yama-scope-0.190-4.fc39.noarch 103/151 Installing : kernel-srpm-macros-1.0-20.fc39.noarch 104/151 Installing : gnat-srpm-macros-6-3.fc39.noarch 105/151 Installing : ghc-srpm-macros-1.6.1-2.fc39.noarch 106/151 Installing : fpc-srpm-macros-1.3-8.fc39.noarch 107/151 Installing : coreutils-common-9.3-4.fc39.x86_64 108/151 Installing : openssl-libs-1:3.1.1-4.fc39.x86_64 109/151 Installing : coreutils-9.3-4.fc39.x86_64 110/151 Running scriptlet: ca-certificates-2023.2.60_v7.0.306-2.fc39.noarch 111/151 Installing : ca-certificates-2023.2.60_v7.0.306-2.fc39.noarch 111/151 Running scriptlet: ca-certificates-2023.2.60_v7.0.306-2.fc39.noarch 111/151 Installing : krb5-libs-1.21.2-2.fc39.x86_64 112/151 Installing : libtirpc-1.3.4-0.rc2.fc39.x86_64 113/151 Running scriptlet: authselect-libs-1.4.3-1.fc39.x86_64 114/151 Installing : authselect-libs-1.4.3-1.fc39.x86_64 114/151 Installing : gzip-1.12-6.fc39.x86_64 115/151 Installing : cracklib-2.9.11-2.fc39.x86_64 116/151 Installing : libpwquality-1.4.5-8.fc39.x86_64 117/151 Installing : authselect-1.4.3-1.fc39.x86_64 118/151 Installing : libnsl2-2.0.0-6.fc39.x86_64 119/151 Installing : pam-1.5.3-3.fc39.x86_64 120/151 Installing : libssh-0.10.6-2.fc39.x86_64 121/151 Installing : libarchive-3.7.1-1.fc39.x86_64 122/151 Installing : libevent-2.1.12-9.fc39.x86_64 123/151 Installing : openldap-2.6.6-1.fc39.x86_64 124/151 Installing : libcurl-8.2.1-4.fc39.x86_64 125/151 Installing : elfutils-libs-0.190-4.fc39.x86_64 126/151 Installing : elfutils-debuginfod-client-0.190-4.fc39.x86_64 127/151 Installing : binutils-gold-2.40-13.fc39.x86_64 128/151 Running scriptlet: binutils-gold-2.40-13.fc39.x86_64 128/151 Installing : binutils-2.40-13.fc39.x86_64 129/151 Running scriptlet: binutils-2.40-13.fc39.x86_64 129/151 Installing : elfutils-0.190-4.fc39.x86_64 130/151 Installing : gdb-minimal-14.1-2.fc39.x86_64 131/151 Installing : debugedit-5.0-12.fc39.x86_64 132/151 Installing : curl-8.2.1-4.fc39.x86_64 133/151 Installing : rpm-sequoia-1.5.0-2.fc39.x86_64 134/151 Installing : rpm-libs-4.19.1-3.fc39.x86_64 135/151 Running scriptlet: rpm-4.19.1-3.fc39.x86_64 136/151 Installing : rpm-4.19.1-3.fc39.x86_64 136/151 Installing : rpmautospec-rpm-macros-0.4.1-2.fc39.noarch 137/151 Installing : efi-srpm-macros-5-9.fc39.noarch 138/151 Installing : lua-srpm-macros-1-9.fc39.noarch 139/151 Installing : rpm-build-libs-4.19.1-3.fc39.x86_64 140/151 Installing : ansible-srpm-macros-1-11.fc39.noarch 141/151 Installing : rust-srpm-macros-25.2-2.fc39.noarch 142/151 Installing : pyproject-srpm-macros-1.11.0-1.fc39.noarch 143/151 Installing : rpm-build-4.19.1-3.fc39.x86_64 144/151 Installing : fonts-srpm-macros-1:2.0.5-12.fc39.noarch 145/151 Installing : python-srpm-macros-3.12-4.fc39.noarch 146/151 Installing : go-srpm-macros-3.3.1-1.fc39.noarch 147/151 Installing : redhat-rpm-config-262-1.fc39.noarch 148/151 Installing : util-linux-2.39.3-2.fc39.x86_64 149/151 Installing : which-2.21-40.fc39.x86_64 150/151 Installing : info-7.0.3-3.fc39.x86_64 151/151 Running scriptlet: filesystem-3.18-6.fc39.x86_64 151/151 Running scriptlet: ca-certificates-2023.2.60_v7.0.306-2.fc39.noarch 151/151 Running scriptlet: authselect-libs-1.4.3-1.fc39.x86_64 151/151 Running scriptlet: rpm-4.19.1-3.fc39.x86_64 151/151 Running scriptlet: info-7.0.3-3.fc39.x86_64 151/151 Installed: alternatives-1.25-1.fc39.x86_64 ansible-srpm-macros-1-11.fc39.noarch audit-libs-4.0-2.fc39.x86_64 authselect-1.4.3-1.fc39.x86_64 authselect-libs-1.4.3-1.fc39.x86_64 basesystem-11-18.fc39.noarch bash-5.2.21-1.fc39.x86_64 binutils-2.40-13.fc39.x86_64 binutils-gold-2.40-13.fc39.x86_64 bzip2-1.0.8-16.fc39.x86_64 bzip2-libs-1.0.8-16.fc39.x86_64 ca-certificates-2023.2.60_v7.0.306-2.fc39.noarch coreutils-9.3-4.fc39.x86_64 coreutils-common-9.3-4.fc39.x86_64 cpio-2.14-4.fc39.x86_64 cracklib-2.9.11-2.fc39.x86_64 crypto-policies-20231204-1.git1e3a2e4.fc39.noarch curl-8.2.1-4.fc39.x86_64 cyrus-sasl-lib-2.1.28-11.fc39.x86_64 debugedit-5.0-12.fc39.x86_64 diffutils-3.10-3.fc39.x86_64 dwz-0.15-3.fc39.x86_64 ed-1.19-4.fc39.x86_64 efi-srpm-macros-5-9.fc39.noarch elfutils-0.190-4.fc39.x86_64 elfutils-debuginfod-client-0.190-4.fc39.x86_64 elfutils-default-yama-scope-0.190-4.fc39.noarch elfutils-libelf-0.190-4.fc39.x86_64 elfutils-libs-0.190-4.fc39.x86_64 fedora-gpg-keys-39-1.noarch fedora-release-39-34.noarch fedora-release-common-39-34.noarch fedora-release-identity-basic-39-34.noarch fedora-repos-39-1.noarch file-5.45-2.fc39.x86_64 file-libs-5.45-2.fc39.x86_64 filesystem-3.18-6.fc39.x86_64 findutils-1:4.9.0-5.fc39.x86_64 fonts-srpm-macros-1:2.0.5-12.fc39.noarch fpc-srpm-macros-1.3-8.fc39.noarch gawk-5.2.2-2.fc39.x86_64 gdb-minimal-14.1-2.fc39.x86_64 gdbm-libs-1:1.23-4.fc39.x86_64 ghc-srpm-macros-1.6.1-2.fc39.noarch glibc-2.38-14.fc39.x86_64 glibc-common-2.38-14.fc39.x86_64 glibc-gconv-extra-2.38-14.fc39.x86_64 glibc-minimal-langpack-2.38-14.fc39.x86_64 gmp-1:6.2.1-5.fc39.x86_64 gnat-srpm-macros-6-3.fc39.noarch go-srpm-macros-3.3.1-1.fc39.noarch grep-3.11-3.fc39.x86_64 gzip-1.12-6.fc39.x86_64 info-7.0.3-3.fc39.x86_64 jansson-2.13.1-7.fc39.x86_64 kernel-srpm-macros-1.0-20.fc39.noarch keyutils-libs-1.6.1-7.fc39.x86_64 krb5-libs-1.21.2-2.fc39.x86_64 libacl-2.3.1-9.fc39.x86_64 libarchive-3.7.1-1.fc39.x86_64 libattr-2.5.1-8.fc39.x86_64 libblkid-2.39.3-2.fc39.x86_64 libbrotli-1.1.0-2.fc39.x86_64 libcap-2.48-9.fc39.x86_64 libcap-ng-0.8.4-3.fc39.x86_64 libcom_err-1.47.0-2.fc39.x86_64 libcurl-8.2.1-4.fc39.x86_64 libdb-5.3.28-56.fc39.x86_64 libeconf-0.5.2-1.fc39.x86_64 libevent-2.1.12-9.fc39.x86_64 libfdisk-2.39.3-2.fc39.x86_64 libffi-3.4.4-4.fc39.x86_64 libgcc-13.2.1-6.fc39.x86_64 libgomp-13.2.1-6.fc39.x86_64 libidn2-2.3.4-3.fc39.x86_64 libmount-2.39.3-2.fc39.x86_64 libnghttp2-1.55.1-4.fc39.x86_64 libnsl2-2.0.0-6.fc39.x86_64 libpkgconf-1.9.5-2.fc39.x86_64 libpsl-0.21.2-4.fc39.x86_64 libpwquality-1.4.5-8.fc39.x86_64 libselinux-3.5-5.fc39.x86_64 libsemanage-3.5-4.fc39.x86_64 libsepol-3.5-2.fc39.x86_64 libsigsegv-2.14-5.fc39.x86_64 libsmartcols-2.39.3-2.fc39.x86_64 libssh-0.10.6-2.fc39.x86_64 libssh-config-0.10.6-2.fc39.noarch libstdc++-13.2.1-6.fc39.x86_64 libtasn1-4.19.0-3.fc39.x86_64 libtirpc-1.3.4-0.rc2.fc39.x86_64 libunistring-1.1-5.fc39.x86_64 libutempter-1.2.1-10.fc39.x86_64 libuuid-2.39.3-2.fc39.x86_64 libverto-0.3.2-6.fc39.x86_64 libxcrypt-4.4.36-2.fc39.x86_64 libxml2-2.12.4-2.fc39.x86_64 libzstd-1.5.5-4.fc39.x86_64 lua-libs-5.4.6-3.fc39.x86_64 lua-srpm-macros-1-9.fc39.noarch lz4-libs-1.9.4-4.fc39.x86_64 mpfr-4.2.0-3.fc39.x86_64 ncurses-base-6.4-7.20230520.fc39.noarch ncurses-libs-6.4-7.20230520.fc39.x86_64 ocaml-srpm-macros-8-2.fc39.noarch openblas-srpm-macros-2-14.fc39.noarch openldap-2.6.6-1.fc39.x86_64 openssl-libs-1:3.1.1-4.fc39.x86_64 p11-kit-0.25.3-1.fc39.x86_64 p11-kit-trust-0.25.3-1.fc39.x86_64 package-notes-srpm-macros-0.5-9.fc39.noarch pam-1.5.3-3.fc39.x86_64 pam-libs-1.5.3-3.fc39.x86_64 patch-2.7.6-22.fc39.x86_64 pcre2-10.42-1.fc39.2.x86_64 pcre2-syntax-10.42-1.fc39.2.noarch perl-srpm-macros-1-51.fc39.noarch pkgconf-1.9.5-2.fc39.x86_64 pkgconf-m4-1.9.5-2.fc39.noarch pkgconf-pkg-config-1.9.5-2.fc39.x86_64 popt-1.19-3.fc39.x86_64 publicsuffix-list-dafsa-20240107-1.fc39.noarch pyproject-srpm-macros-1.11.0-1.fc39.noarch python-srpm-macros-3.12-4.fc39.noarch qt5-srpm-macros-5.15.11-1.fc39.noarch qt6-srpm-macros-6.6.0-1.fc39.noarch readline-8.2-4.fc39.x86_64 redhat-rpm-config-262-1.fc39.noarch rpm-4.19.1-3.fc39.x86_64 rpm-build-4.19.1-3.fc39.x86_64 rpm-build-libs-4.19.1-3.fc39.x86_64 rpm-libs-4.19.1-3.fc39.x86_64 rpm-sequoia-1.5.0-2.fc39.x86_64 rpmautospec-rpm-macros-0.4.1-2.fc39.noarch rust-srpm-macros-25.2-2.fc39.noarch sed-4.8-14.fc39.x86_64 setup-2.14.4-1.fc39.noarch shadow-utils-2:4.14.0-2.fc39.x86_64 sqlite-libs-3.42.0-7.fc39.x86_64 systemd-libs-254.7-1.fc39.x86_64 tar-2:1.35-2.fc39.x86_64 unzip-6.0-62.fc39.x86_64 util-linux-2.39.3-2.fc39.x86_64 util-linux-core-2.39.3-2.fc39.x86_64 which-2.21-40.fc39.x86_64 xxhash-libs-0.8.2-1.fc39.x86_64 xz-5.4.4-1.fc39.x86_64 xz-libs-5.4.4-1.fc39.x86_64 zip-3.0-39.fc39.x86_64 zlib-1.2.13-4.fc39.x86_64 zstd-1.5.5-4.fc39.x86_64 Complete! Finish: installing minimal buildroot with dnf Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: alternatives-1.25-1.fc39.x86_64 ansible-srpm-macros-1-11.fc39.noarch audit-libs-4.0-2.fc39.x86_64 authselect-1.4.3-1.fc39.x86_64 authselect-libs-1.4.3-1.fc39.x86_64 basesystem-11-18.fc39.noarch bash-5.2.21-1.fc39.x86_64 binutils-2.40-13.fc39.x86_64 binutils-gold-2.40-13.fc39.x86_64 bzip2-1.0.8-16.fc39.x86_64 bzip2-libs-1.0.8-16.fc39.x86_64 ca-certificates-2023.2.60_v7.0.306-2.fc39.noarch coreutils-9.3-4.fc39.x86_64 coreutils-common-9.3-4.fc39.x86_64 cpio-2.14-4.fc39.x86_64 cracklib-2.9.11-2.fc39.x86_64 crypto-policies-20231204-1.git1e3a2e4.fc39.noarch curl-8.2.1-4.fc39.x86_64 cyrus-sasl-lib-2.1.28-11.fc39.x86_64 debugedit-5.0-12.fc39.x86_64 diffutils-3.10-3.fc39.x86_64 dwz-0.15-3.fc39.x86_64 ed-1.19-4.fc39.x86_64 efi-srpm-macros-5-9.fc39.noarch elfutils-0.190-4.fc39.x86_64 elfutils-debuginfod-client-0.190-4.fc39.x86_64 elfutils-default-yama-scope-0.190-4.fc39.noarch elfutils-libelf-0.190-4.fc39.x86_64 elfutils-libs-0.190-4.fc39.x86_64 fedora-gpg-keys-39-1.noarch fedora-release-39-34.noarch fedora-release-common-39-34.noarch fedora-release-identity-basic-39-34.noarch fedora-repos-39-1.noarch file-5.45-2.fc39.x86_64 file-libs-5.45-2.fc39.x86_64 filesystem-3.18-6.fc39.x86_64 findutils-4.9.0-5.fc39.x86_64 fonts-srpm-macros-2.0.5-12.fc39.noarch fpc-srpm-macros-1.3-8.fc39.noarch gawk-5.2.2-2.fc39.x86_64 gdb-minimal-14.1-2.fc39.x86_64 gdbm-libs-1.23-4.fc39.x86_64 ghc-srpm-macros-1.6.1-2.fc39.noarch glibc-2.38-14.fc39.x86_64 glibc-common-2.38-14.fc39.x86_64 glibc-gconv-extra-2.38-14.fc39.x86_64 glibc-minimal-langpack-2.38-14.fc39.x86_64 gmp-6.2.1-5.fc39.x86_64 gnat-srpm-macros-6-3.fc39.noarch go-srpm-macros-3.3.1-1.fc39.noarch gpg-pubkey-18b8e74c-62f2920f grep-3.11-3.fc39.x86_64 gzip-1.12-6.fc39.x86_64 info-7.0.3-3.fc39.x86_64 jansson-2.13.1-7.fc39.x86_64 kernel-srpm-macros-1.0-20.fc39.noarch keyutils-libs-1.6.1-7.fc39.x86_64 krb5-libs-1.21.2-2.fc39.x86_64 libacl-2.3.1-9.fc39.x86_64 libarchive-3.7.1-1.fc39.x86_64 libattr-2.5.1-8.fc39.x86_64 libblkid-2.39.3-2.fc39.x86_64 libbrotli-1.1.0-2.fc39.x86_64 libcap-2.48-9.fc39.x86_64 libcap-ng-0.8.4-3.fc39.x86_64 libcom_err-1.47.0-2.fc39.x86_64 libcurl-8.2.1-4.fc39.x86_64 libdb-5.3.28-56.fc39.x86_64 libeconf-0.5.2-1.fc39.x86_64 libevent-2.1.12-9.fc39.x86_64 libfdisk-2.39.3-2.fc39.x86_64 libffi-3.4.4-4.fc39.x86_64 libgcc-13.2.1-6.fc39.x86_64 libgomp-13.2.1-6.fc39.x86_64 libidn2-2.3.4-3.fc39.x86_64 libmount-2.39.3-2.fc39.x86_64 libnghttp2-1.55.1-4.fc39.x86_64 libnsl2-2.0.0-6.fc39.x86_64 libpkgconf-1.9.5-2.fc39.x86_64 libpsl-0.21.2-4.fc39.x86_64 libpwquality-1.4.5-8.fc39.x86_64 libselinux-3.5-5.fc39.x86_64 libsemanage-3.5-4.fc39.x86_64 libsepol-3.5-2.fc39.x86_64 libsigsegv-2.14-5.fc39.x86_64 libsmartcols-2.39.3-2.fc39.x86_64 libssh-0.10.6-2.fc39.x86_64 libssh-config-0.10.6-2.fc39.noarch libstdc++-13.2.1-6.fc39.x86_64 libtasn1-4.19.0-3.fc39.x86_64 libtirpc-1.3.4-0.rc2.fc39.x86_64 libunistring-1.1-5.fc39.x86_64 libutempter-1.2.1-10.fc39.x86_64 libuuid-2.39.3-2.fc39.x86_64 libverto-0.3.2-6.fc39.x86_64 libxcrypt-4.4.36-2.fc39.x86_64 libxml2-2.12.4-2.fc39.x86_64 libzstd-1.5.5-4.fc39.x86_64 lua-libs-5.4.6-3.fc39.x86_64 lua-srpm-macros-1-9.fc39.noarch lz4-libs-1.9.4-4.fc39.x86_64 mpfr-4.2.0-3.fc39.x86_64 ncurses-base-6.4-7.20230520.fc39.noarch ncurses-libs-6.4-7.20230520.fc39.x86_64 ocaml-srpm-macros-8-2.fc39.noarch openblas-srpm-macros-2-14.fc39.noarch openldap-2.6.6-1.fc39.x86_64 openssl-libs-3.1.1-4.fc39.x86_64 p11-kit-0.25.3-1.fc39.x86_64 p11-kit-trust-0.25.3-1.fc39.x86_64 package-notes-srpm-macros-0.5-9.fc39.noarch pam-1.5.3-3.fc39.x86_64 pam-libs-1.5.3-3.fc39.x86_64 patch-2.7.6-22.fc39.x86_64 pcre2-10.42-1.fc39.2.x86_64 pcre2-syntax-10.42-1.fc39.2.noarch perl-srpm-macros-1-51.fc39.noarch pkgconf-1.9.5-2.fc39.x86_64 pkgconf-m4-1.9.5-2.fc39.noarch pkgconf-pkg-config-1.9.5-2.fc39.x86_64 popt-1.19-3.fc39.x86_64 publicsuffix-list-dafsa-20240107-1.fc39.noarch pyproject-srpm-macros-1.11.0-1.fc39.noarch python-srpm-macros-3.12-4.fc39.noarch qt5-srpm-macros-5.15.11-1.fc39.noarch qt6-srpm-macros-6.6.0-1.fc39.noarch readline-8.2-4.fc39.x86_64 redhat-rpm-config-262-1.fc39.noarch rpm-4.19.1-3.fc39.x86_64 rpm-build-4.19.1-3.fc39.x86_64 rpm-build-libs-4.19.1-3.fc39.x86_64 rpm-libs-4.19.1-3.fc39.x86_64 rpm-sequoia-1.5.0-2.fc39.x86_64 rpmautospec-rpm-macros-0.4.1-2.fc39.noarch rust-srpm-macros-25.2-2.fc39.noarch sed-4.8-14.fc39.x86_64 setup-2.14.4-1.fc39.noarch shadow-utils-4.14.0-2.fc39.x86_64 sqlite-libs-3.42.0-7.fc39.x86_64 systemd-libs-254.7-1.fc39.x86_64 tar-1.35-2.fc39.x86_64 unzip-6.0-62.fc39.x86_64 util-linux-2.39.3-2.fc39.x86_64 util-linux-core-2.39.3-2.fc39.x86_64 which-2.21-40.fc39.x86_64 xxhash-libs-0.8.2-1.fc39.x86_64 xz-5.4.4-1.fc39.x86_64 xz-libs-5.4.4-1.fc39.x86_64 zip-3.0-39.fc39.x86_64 zlib-1.2.13-4.fc39.x86_64 zstd-1.5.5-4.fc39.x86_64 Start: buildsrpm Start: rpmbuild -bs warning: %patchN is deprecated (3 usages found), use %patch N (or %patch -P N) Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1705881600 Wrote: /builddir/build/SRPMS/apbs-3.0.0-22.fc39.src.rpm RPM build warnings: %patchN is deprecated (3 usages found), use %patch N (or %patch -P N) Finish: rpmbuild -bs INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-39-x86_64-1705965440.204976/root/var/log/dnf.rpm.log /var/lib/mock/fedora-39-x86_64-1705965440.204976/root/var/log/dnf.librepo.log /var/lib/mock/fedora-39-x86_64-1705965440.204976/root/var/log/dnf.log Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-nr35hko_/apbs/apbs.spec) Config(child) 1 minutes 2 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot INFO: Start(/var/lib/copr-rpmbuild/results/apbs-3.0.0-22.fc39.src.rpm) Config(fedora-39-x86_64) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-39-x86_64-bootstrap-1705965440.204976/root. INFO: reusing tmpfs at /var/lib/mock/fedora-39-x86_64-bootstrap-1705965440.204976/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-39-x86_64-1705965440.204976/root. INFO: calling preinit hooks INFO: enabled root cache Start: unpacking root cache Finish: unpacking root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-4.19.0-1.fc39.x86_64 rpm-sequoia-1.5.0-1.fc39.x86_64 python3-dnf-4.18.2-2.fc39.noarch python3-dnf-plugins-core-4.4.4-2.fc39.noarch yum-4.18.2-2.fc39.noarch Finish: chroot init Start: build phase for apbs-3.0.0-22.fc39.src.rpm Start: build setup for apbs-3.0.0-22.fc39.src.rpm warning: %patchN is deprecated (3 usages found), use %patch N (or %patch -P N) Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1705881600 Wrote: /builddir/build/SRPMS/apbs-3.0.0-22.fc39.src.rpm RPM build warnings: %patchN is deprecated (3 usages found), use %patch N (or %patch -P N) No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 31 kB/s | 1.5 kB 00:00 fedora 713 kB/s | 24 kB 00:00 updates 725 kB/s | 23 kB 00:00 Dependencies resolved. ============================================================================================ Package Arch Version Repo Size ============================================================================================ Installing: chrpath x86_64 0.16-21.fc39 fedora 30 k cmake x86_64 3.27.7-1.fc39 fedora 8.0 M doxygen x86_64 2:1.9.7-3.fc39 fedora 5.0 M gcc-c++ x86_64 13.2.1-6.fc39 updates 13 M graphviz x86_64 9.0.0-8.fc39 copr_base 5.0 M make x86_64 1:4.4.1-2.fc39 fedora 589 k maloc-devel x86_64 1.5-28.fc39 fedora 1.4 M python3-devel x86_64 3.12.1-2.fc39 updates 312 k python3-numpy x86_64 1:1.26.2-3.fc39 copr_base 7.2 M python3-sphinx noarch 1:7.2.6-5.fc39 copr_base 2.5 M swig x86_64 4.1.1-9.fc39 fedora 1.6 M texlive-adjustbox noarch 11:svn64967-69.fc39 fedora 31 k texlive-collection-latexrecommended noarch 11:svn65512-69.fc39 fedora 12 k texlive-etoc noarch 11:svn66299-69.fc39 fedora 29 k texlive-hanging noarch 11:svn15878.1.2b-69.fc39 fedora 19 k texlive-multirow noarch 11:svn58396-69.fc39 fedora 17 k texlive-newunicodechar noarch 11:svn47382-69.fc39 fedora 19 k texlive-sectsty noarch 11:svn15878.2.0.2-69.fc39 fedora 19 k texlive-stackengine noarch 11:svn60019-69.fc39 fedora 22 k texlive-tocloft noarch 11:svn53364-69.fc39 fedora 23 k texlive-ulem noarch 11:svn53365-69.fc39 fedora 17 k texlive-wasy noarch 11:svn53533-69.fc39 fedora 44 k texlive-wasysym noarch 11:svn54080-69.fc39 fedora 18 k zlib-devel x86_64 1.2.13-4.fc39 fedora 45 k Installing dependencies: abattis-cantarell-vf-fonts noarch 0.301-10.fc39 fedora 121 k adobe-mappings-cmap noarch 20230622-1.fc39 fedora 2.1 M adobe-mappings-cmap-deprecated noarch 20230622-1.fc39 fedora 113 k adobe-mappings-pdf noarch 20190401-5.fc39 fedora 698 k annobin-docs noarch 12.35-1.fc39 updates 90 k annobin-plugin-gcc x86_64 12.35-1.fc39 updates 957 k avahi-libs x86_64 0.8-24.fc39 fedora 67 k biber noarch 2.19-3.fc39 fedora 292 k cairo x86_64 1.18.0-1.fc39 fedora 710 k cairo-gobject x86_64 1.18.0-1.fc39 fedora 19 k clang16-libs x86_64 16.0.6-3.fc39 fedora 22 M clang16-resource-filesystem x86_64 16.0.6-3.fc39 fedora 13 k cmake-data noarch 3.27.7-1.fc39 fedora 2.2 M cmake-filesystem x86_64 3.27.7-1.fc39 fedora 19 k cmake-rpm-macros noarch 3.27.7-1.fc39 fedora 18 k cpp x86_64 13.2.1-6.fc39 updates 11 M crypto-policies-scripts noarch 20231204-1.git1e3a2e4.fc39 updates 117 k cups-libs x86_64 1:2.4.7-5.fc39 updates 268 k dbus-libs x86_64 1:1.14.10-1.fc39 fedora 156 k default-fonts-core-sans noarch 4.0-9.fc39 fedora 32 k emacs-filesystem noarch 1:29.1-2.fc39 fedora 7.1 k expat x86_64 2.5.0-3.fc39 fedora 110 k flexiblas x86_64 3.4.1-1.fc39 updates 25 k flexiblas-netlib x86_64 3.4.1-1.fc39 updates 3.1 M flexiblas-openblas-openmp x86_64 3.4.1-1.fc39 updates 17 k fontconfig x86_64 2.14.2-5.fc39 fedora 297 k fonts-filesystem noarch 1:2.0.5-12.fc39 fedora 8.2 k freetype x86_64 2.13.1-2.fc39 fedora 414 k fribidi x86_64 1.0.13-2.fc39 fedora 91 k gc x86_64 8.2.2-4.fc39 fedora 110 k gcc x86_64 13.2.1-6.fc39 updates 34 M gcc-plugin-annobin x86_64 13.2.1-6.fc39 updates 50 k gd x86_64 2.3.3-12.fc39 fedora 139 k gdk-pixbuf2 x86_64 2.42.10-5.fc39 fedora 484 k ghostscript x86_64 10.02.1-2.fc39 updates 37 k ghostscript-tools-fonts x86_64 10.02.1-2.fc39 updates 12 k ghostscript-tools-printing x86_64 10.02.1-2.fc39 updates 13 k glib2 x86_64 2.78.3-1.fc39 updates 2.8 M glibc-devel x86_64 2.38-14.fc39 updates 84 k glibc-headers-x86 noarch 2.38-14.fc39 updates 568 k gnutls x86_64 3.8.2-2.fc39 updates 1.1 M google-droid-sans-fonts noarch 20200215-17.fc39 fedora 2.7 M google-noto-fonts-common noarch 20230801-4.fc39 updates 17 k google-noto-sans-vf-fonts noarch 20230801-4.fc39 updates 583 k graphite2 x86_64 1.3.14-12.fc39 fedora 95 k groff-base x86_64 1.23.0-3.fc39 updates 1.1 M gts x86_64 0.7.6-46.20121130.fc39 fedora 240 k guile22 x86_64 2.2.7-9.fc39 fedora 6.5 M harfbuzz x86_64 8.2.1-2.fc39 fedora 975 k highway x86_64 1.0.7-1.fc39 fedora 478 k jbig2dec-libs x86_64 0.19-10.fc39 fedora 73 k jbigkit-libs x86_64 2.1-26.fc39 fedora 53 k jsoncpp x86_64 1.9.5-5.fc39 fedora 99 k kernel-headers x86_64 6.6.3-200.fc39 updates 1.6 M lasi x86_64 1.1.3-11.fc39 fedora 54 k lcms2 x86_64 2.15-2.fc39 fedora 177 k libICE x86_64 1.0.10-11.fc39 fedora 70 k libSM x86_64 1.2.3-13.fc39 fedora 41 k libX11 x86_64 1.8.7-1.fc39 fedora 650 k libX11-common noarch 1.8.7-1.fc39 fedora 176 k libXau x86_64 1.0.11-3.fc39 fedora 31 k libXaw x86_64 1.0.14-5.fc39 fedora 202 k libXext x86_64 1.3.5-3.fc39 fedora 39 k libXft x86_64 2.3.8-3.fc39 fedora 72 k libXi x86_64 1.8.1-2.fc39 fedora 40 k libXmu x86_64 1.1.4-3.fc39 fedora 76 k libXpm x86_64 3.5.17-1.fc39 updates 65 k libXrender x86_64 0.9.11-3.fc39 fedora 27 k libXt x86_64 1.2.1-5.fc39 fedora 178 k libaom x86_64 3.8.0-1.fc39 updates 1.8 M libavif x86_64 0.11.1-11.fc39 fedora 84 k libb2 x86_64 0.98.1-9.fc39 fedora 25 k libdatrie x86_64 0.2.13-7.fc39 fedora 32 k libdav1d x86_64 1.2.1-2.fc39 fedora 618 k libedit x86_64 3.1-48.20230828cvs.fc39 fedora 107 k libgfortran x86_64 13.2.1-6.fc39 updates 907 k libgs x86_64 10.02.1-2.fc39 updates 3.4 M libicu x86_64 73.2-2.fc39 fedora 11 M libijs x86_64 0.35-19.fc39 fedora 29 k libimagequant x86_64 4.0.3-2.fc39 updates 318 k libjpeg-turbo x86_64 2.1.4-3.fc39 fedora 183 k libjxl x86_64 1:0.8.2-3.fc39 fedora 1.2 M liblerc x86_64 4.0.0-4.fc39 fedora 201 k libmpc x86_64 1.3.1-3.fc39 fedora 70 k libpaper x86_64 1:2.1.1-1.fc39 fedora 27 k libpng x86_64 2:1.6.37-15.fc39 fedora 119 k libquadmath x86_64 13.2.1-6.fc39 updates 197 k librsvg2 x86_64 2.57.1-1.fc39 updates 1.6 M libstdc++-devel x86_64 13.2.1-6.fc39 updates 2.6 M libthai x86_64 0.1.29-6.fc39 fedora 213 k libtiff x86_64 4.4.0-8.fc39 fedora 202 k libtool-ltdl x86_64 2.4.7-7.fc39 fedora 36 k libuv x86_64 1:1.47.0-3.fc39 updates 250 k libvmaf x86_64 2.3.0-6.fc39 fedora 180 k libwebp x86_64 1.3.2-2.fc39 fedora 284 k libxcb x86_64 1.13.1-12.fc39 fedora 233 k libxcrypt-devel x86_64 4.4.36-2.fc39 fedora 30 k libxslt x86_64 1.1.39-1.fc39 updates 187 k llvm16-libs x86_64 16.0.6-5.fc39 fedora 27 M mailcap noarch 2.1.54-2.fc39 fedora 34 k maloc x86_64 1.5-28.fc39 fedora 99 k mpdecimal x86_64 2.5.1-7.fc39 fedora 89 k ncurses x86_64 6.4-7.20230520.fc39 fedora 416 k netpbm x86_64 11.02.00-2.fc39 fedora 185 k nettle x86_64 3.9.1-2.fc39 fedora 425 k nspr x86_64 4.35.0-16.fc39 updates 138 k nss x86_64 3.96.1-1.fc39 updates 696 k nss-softokn x86_64 3.96.1-1.fc39 updates 414 k nss-softokn-freebl x86_64 3.96.1-1.fc39 updates 351 k nss-sysinit x86_64 3.96.1-1.fc39 updates 18 k nss-util x86_64 3.96.1-1.fc39 updates 87 k openblas x86_64 0.3.21-6.fc39 fedora 35 k openblas-openmp x86_64 0.3.21-6.fc39 fedora 4.9 M openjpeg2 x86_64 2.5.0-5.fc39 fedora 178 k pango x86_64 1.51.0-1.fc39 fedora 343 k perl-Authen-SASL noarch 2.1700-1.fc39 fedora 62 k perl-AutoLoader noarch 5.74-502.fc39 updates 21 k perl-B x86_64 1.88-502.fc39 updates 177 k perl-B-Hooks-EndOfScope noarch 0.26-7.fc39 fedora 43 k perl-Business-ISBN noarch 3.008-2.fc39 fedora 32 k perl-Business-ISBN-Data noarch 20230926.001-1.fc39 updates 38 k perl-Business-ISMN noarch 1.203-2.fc39 fedora 25 k perl-Business-ISSN noarch 1.005-8.fc39 fedora 18 k perl-Carp noarch 1.54-500.fc39 fedora 29 k perl-Class-Accessor noarch 0.51-18.fc39 fedora 28 k perl-Class-Data-Inheritable noarch 0.09-6.fc39 fedora 13 k perl-Class-Inspector noarch 1.36-14.fc39 fedora 30 k perl-Class-Method-Modifiers noarch 2.15-2.fc39 fedora 50 k perl-Class-Singleton noarch 1.6-9.fc39 fedora 25 k perl-Class-Struct noarch 0.68-502.fc39 updates 22 k perl-Clone x86_64 0.46-4.fc39 fedora 22 k perl-Compress-Raw-Bzip2 x86_64 2.206-1.fc39 fedora 35 k perl-Compress-Raw-Zlib x86_64 2.206-1.fc39 fedora 64 k perl-Convert-ASN1 noarch 0.34-1.fc39 fedora 59 k perl-Data-Compare noarch 1.29-2.fc39 fedora 34 k perl-Data-Dump noarch 1.25-8.fc39 fedora 32 k perl-Data-Dumper x86_64 2.188-501.fc39 fedora 56 k perl-Data-OptList noarch 0.114-2.fc39 fedora 27 k perl-Data-Uniqid noarch 0.12-31.fc39 fedora 12 k perl-Date-ISO8601 noarch 0.005-18.fc39 fedora 19 k perl-Date-Manip noarch 6.93-1.fc39 updates 1.1 M perl-DateTime x86_64 2:1.59-5.fc39 fedora 132 k perl-DateTime-Calendar-Julian noarch 0.107-5.fc39 fedora 23 k perl-DateTime-Format-Builder noarch 0.8300-11.fc39 fedora 93 k perl-DateTime-Format-Strptime noarch 1:1.79-8.fc39 fedora 41 k perl-DateTime-Locale noarch 1.39-2.fc39 fedora 3.7 M perl-DateTime-TimeZone noarch 2.61-1.fc39 updates 398 k perl-DateTime-TimeZone-SystemV noarch 0.010-19.fc39 fedora 22 k perl-DateTime-TimeZone-Tzfile noarch 0.011-19.fc39 fedora 19 k perl-Devel-CallChecker x86_64 0.009-3.fc39 fedora 24 k perl-Devel-Caller x86_64 2.07-3.fc39 fedora 19 k perl-Devel-GlobalDestruction noarch 0.14-22.fc39 fedora 17 k perl-Devel-LexAlias x86_64 0.05-34.fc39 fedora 16 k perl-Devel-StackTrace noarch 1:2.04-16.fc39 fedora 30 k perl-Digest noarch 1.20-500.fc39 fedora 25 k perl-Digest-HMAC noarch 1.04-8.fc39 fedora 22 k perl-Digest-MD5 x86_64 2.58-500.fc39 fedora 35 k perl-Digest-SHA x86_64 1:6.04-501.fc39 fedora 61 k perl-Dist-CheckConflicts noarch 0.11-28.fc39 fedora 23 k perl-DynaLoader x86_64 1.54-502.fc39 updates 26 k perl-DynaLoader-Functions noarch 0.004-2.fc39 fedora 19 k perl-Email-Date-Format noarch 1.008-2.fc39 fedora 18 k perl-Encode x86_64 4:3.19-500.fc39 fedora 1.7 M perl-Encode-Locale noarch 1.05-27.fc39 fedora 18 k perl-English noarch 1.11-502.fc39 updates 14 k perl-Errno x86_64 1.37-502.fc39 updates 15 k perl-Eval-Closure noarch 0.14-21.fc39 fedora 24 k perl-Exception-Class noarch 1.45-8.fc39 fedora 43 k perl-Exporter noarch 5.77-500.fc39 fedora 31 k perl-ExtUtils-MM-Utils noarch 2:7.70-501.fc39 fedora 11 k perl-Fcntl x86_64 1.15-502.fc39 updates 21 k perl-File-Basename noarch 2.86-502.fc39 updates 17 k perl-File-Compare noarch 1.100.700-502.fc39 updates 13 k perl-File-Copy noarch 2.41-502.fc39 updates 20 k perl-File-Find noarch 1.43-502.fc39 updates 25 k perl-File-Find-Rule noarch 0.34-26.fc39 fedora 32 k perl-File-Listing noarch 6.16-1.fc39 fedora 25 k perl-File-Path noarch 2.18-500.fc39 fedora 35 k perl-File-ShareDir noarch 1.118-9.fc39 fedora 29 k perl-File-Slurper noarch 0.014-3.fc39 fedora 21 k perl-File-Temp noarch 1:0.231.100-500.fc39 fedora 58 k perl-File-stat noarch 1.13-502.fc39 updates 17 k perl-FileHandle noarch 2.05-502.fc39 updates 16 k perl-Filter x86_64 2:1.64-501.fc39 fedora 87 k perl-GSSAPI x86_64 0.28-43.fc39 fedora 55 k perl-Getopt-Long noarch 1:2.54-500.fc39 fedora 60 k perl-Getopt-Std noarch 1.13-502.fc39 updates 16 k perl-HTML-Parser x86_64 3.81-3.fc39 fedora 124 k perl-HTML-Tagset noarch 3.20-54.fc39 fedora 18 k perl-HTTP-Cookies noarch 6.10-10.fc39 fedora 37 k perl-HTTP-Date noarch 6.06-2.fc39 fedora 24 k perl-HTTP-Message noarch 6.44-3.fc39 fedora 101 k perl-HTTP-Negotiate noarch 6.01-36.fc39 fedora 19 k perl-HTTP-Tiny noarch 0.088-3.fc39 fedora 56 k perl-Hash-Util-FieldHash x86_64 1.26-502.fc39 updates 38 k perl-I18N-LangTags noarch 0.45-502.fc39 updates 53 k perl-I18N-Langinfo x86_64 0.22-502.fc39 updates 22 k perl-IO x86_64 1.52-502.fc39 updates 82 k perl-IO-Compress noarch 2.206-1.fc39 fedora 272 k perl-IO-HTML noarch 1.004-11.fc39 fedora 28 k perl-IO-Socket-IP noarch 0.42-1.fc39 fedora 42 k perl-IO-Socket-SSL noarch 2.083-3.fc39 fedora 225 k perl-IO-String noarch 1.08-48.fc39 fedora 17 k perl-IPC-Cmd noarch 2:1.04-501.fc39 fedora 39 k perl-IPC-Open3 noarch 1.22-502.fc39 updates 22 k perl-IPC-Run3 noarch 0.048-29.fc39 fedora 38 k perl-IPC-SysV x86_64 2.09-501.fc39 fedora 41 k perl-IPC-System-Simple noarch 1.30-11.fc39 fedora 39 k perl-JSON noarch 4.10-3.fc39 fedora 95 k perl-LDAP noarch 1:0.68-11.fc39 fedora 384 k perl-LWP-MediaTypes noarch 6.04-15.fc39 fedora 33 k perl-LWP-Protocol-https noarch 6.11-1.fc39 fedora 20 k perl-Lingua-Translit noarch 0.29-4.fc39 fedora 33 k perl-List-AllUtils noarch 0.19-10.fc39 fedora 48 k perl-List-SomeUtils noarch 0.59-3.fc39 fedora 45 k perl-List-UtilsBy noarch 0.12-7.fc39 fedora 28 k perl-Locale-Maketext noarch 1.33-501.fc39 fedora 94 k perl-Locale-Maketext-Simple noarch 1:0.21-502.fc39 updates 18 k perl-Log-Dispatch noarch 2.71-2.fc39 fedora 84 k perl-Log-Dispatch-FileRotate noarch 1.38-7.fc39 fedora 32 k perl-Log-Log4perl noarch 1.57-3.fc39 fedora 360 k perl-MIME-Base64 x86_64 3.16-500.fc39 fedora 29 k perl-MIME-Charset noarch 1.013.1-3.fc39 fedora 48 k perl-MIME-Lite noarch 3.033-8.fc39 fedora 94 k perl-MIME-Types noarch 2.24-3.fc39 fedora 69 k perl-MRO-Compat noarch 0.15-7.fc39 fedora 25 k perl-Mail-Sender noarch 1:0.903-22.fc39 fedora 50 k perl-Mail-Sendmail noarch 0.80-18.fc39 fedora 36 k perl-MailTools noarch 2.21-14.fc39 fedora 108 k perl-Math-BigInt noarch 1:1.9998.39-2.fc39 fedora 203 k perl-Math-BigRat noarch 0.2624-500.fc39 fedora 41 k perl-Math-Complex noarch 1.62-502.fc39 updates 46 k perl-Module-CoreList noarch 1:5.20231230-1.fc39 updates 88 k perl-Module-Implementation noarch 0.09-37.fc39 fedora 19 k perl-Module-Load noarch 1:0.36-500.fc39 fedora 17 k perl-Module-Load-Conditional noarch 0.74-500.fc39 fedora 22 k perl-Module-Metadata noarch 1.000038-3.fc39 fedora 35 k perl-Module-Runtime noarch 0.016-20.fc39 fedora 23 k perl-Mozilla-CA noarch 20230801-1.fc39 fedora 13 k perl-NTLM noarch 1.09-36.fc39 fedora 22 k perl-Net-HTTP noarch 6.23-2.fc39 fedora 39 k perl-Net-SMTP-SSL noarch 1.04-21.fc39 fedora 11 k perl-Net-SSLeay x86_64 1.92-10.fc39 fedora 360 k perl-Number-Compare noarch 0.03-36.fc39 fedora 12 k perl-Opcode x86_64 1.64-502.fc39 updates 36 k perl-POSIX x86_64 2.13-502.fc39 updates 97 k perl-Package-Generator noarch 1.106-29.fc39 fedora 22 k perl-Package-Stash noarch 0.40-5.fc39 fedora 33 k perl-Package-Stash-XS x86_64 0.30-5.fc39 fedora 35 k perl-PadWalker x86_64 2.5-10.fc39 fedora 27 k perl-Params-Check noarch 1:0.38-500.fc39 fedora 22 k perl-Params-Classify x86_64 0.015-20.fc39 fedora 31 k perl-Params-Util x86_64 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k texlive-pst-text noarch 11:svn49542-69.fc39 fedora 19 k texlive-pst-tools noarch 11:svn60621-69.fc39 fedora 21 k texlive-pst-tree noarch 11:svn60421-69.fc39 fedora 21 k texlive-pstricks noarch 11:svn65346-69.fc39 fedora 117 k texlive-pstricks-add noarch 11:svn65067-69.fc39 fedora 37 k texlive-ragged2e noarch 11:svn66152-69.fc39 fedora 682 k texlive-rcs noarch 11:svn15878.0-69.fc39 fedora 28 k texlive-realscripts noarch 11:svn56594-69.fc39 fedora 19 k texlive-refcount noarch 11:svn53164-69.fc39 fedora 335 k texlive-rerunfilecheck noarch 11:svn63869-69.fc39 fedora 341 k texlive-rsfs noarch 11:svn15878.0-69.fc39 fedora 73 k texlive-sansmath noarch 11:svn17997.1.1-69.fc39 fedora 14 k texlive-sansmathaccent noarch 11:svn53628-69.fc39 fedora 36 k texlive-sauerj noarch 11:svn15878.0-69.fc39 fedora 20 k texlive-section noarch 11:svn20180.0-69.fc39 fedora 24 k texlive-seminar noarch 11:svn59801-69.fc39 fedora 52 k texlive-sepnum noarch 11:svn20186.2.0-69.fc39 fedora 17 k texlive-setspace noarch 11:svn65206-69.fc39 fedora 18 k texlive-showexpl noarch 11:svn57414-69.fc39 fedora 18 k texlive-stringenc noarch 11:svn52982-69.fc39 fedora 702 k texlive-subfig noarch 11:svn15878.1.3-69.fc39 fedora 21 k texlive-symbol noarch 11:svn61719-69.fc39 fedora 54 k texlive-tex x86_64 11:svn66186-77.fc39 fedora 212 k texlive-tex-ini-files noarch 11:svn40533-69.fc39 fedora 15 k texlive-texlive-common-doc noarch 11:svn54176-69.fc39 fedora 158 k texlive-texlive-en noarch 11:svn66572-77.fc39 fedora 2.0 M texlive-texlive-msg-translations noarch 11:svn66593-69.fc39 fedora 165 k texlive-texlive-scripts noarch 11:svn66584-77.fc39 fedora 122 k texlive-texlive.infra noarch 11:svn66512-77.fc39 fedora 295 k texlive-textcase noarch 11:svn63868-69.fc39 fedora 16 k texlive-thumbpdf noarch 11:svn62518-77.fc39 fedora 41 k texlive-times noarch 11:svn61719-69.fc39 fedora 368 k texlive-tipa noarch 11:svn29349.1.3-69.fc39 fedora 2.8 M texlive-titlesec noarch 11:svn59845-69.fc39 fedora 34 k texlive-tools noarch 11:svn64892-69.fc39 fedora 75 k texlive-translator noarch 11:svn59412-69.fc39 fedora 296 k texlive-transparent noarch 11:svn64852-69.fc39 fedora 286 k texlive-typehtml noarch 11:svn17134.0-69.fc39 fedora 21 k texlive-ucharcat noarch 11:svn38907-69.fc39 fedora 15 k texlive-ucs noarch 11:svn64114-69.fc39 fedora 423 k texlive-underscore noarch 11:svn18261.0-69.fc39 fedora 19 k texlive-unicode-data noarch 11:svn64423-69.fc39 fedora 371 k texlive-unicode-math noarch 11:svn61719-69.fc39 fedora 63 k texlive-uniquecounter noarch 11:svn53162-69.fc39 fedora 300 k texlive-url noarch 11:svn32528.3.4-69.fc39 fedora 20 k texlive-utopia noarch 11:svn15878.0-69.fc39 fedora 239 k texlive-varwidth noarch 11:svn24104.0.92-69.fc39 fedora 18 k texlive-xcolor noarch 11:svn63563-69.fc39 fedora 32 k texlive-xdvi x86_64 11:svn62387-77.fc39 fedora 351 k texlive-xetex x86_64 11:svn66203-77.fc39 fedora 1.3 M texlive-xetexconfig noarch 11:svn45845-69.fc39 fedora 11 k texlive-xifthen noarch 11:svn38929-69.fc39 fedora 16 k texlive-xkeyval noarch 11:svn63616-69.fc39 fedora 27 k texlive-xltxtra noarch 11:svn56594-69.fc39 fedora 17 k texlive-xpatch noarch 11:svn54563-69.fc39 fedora 19 k texlive-xstring noarch 11:svn65551-69.fc39 fedora 25 k texlive-xunicode noarch 11:svn30466.0.981-69.fc39 fedora 44 k texlive-zapfding noarch 11:svn61719-69.fc39 fedora 64 k texlive-zref noarch 11:svn62977-69.fc39 fedora 688 k tzdata noarch 2023d-1.fc39 updates 718 k urw-base35-bookman-fonts noarch 20200910-18.fc39 fedora 847 k urw-base35-c059-fonts noarch 20200910-18.fc39 fedora 874 k urw-base35-d050000l-fonts noarch 20200910-18.fc39 fedora 76 k urw-base35-fonts noarch 20200910-18.fc39 fedora 10 k urw-base35-fonts-common noarch 20200910-18.fc39 fedora 21 k urw-base35-gothic-fonts noarch 20200910-18.fc39 fedora 643 k urw-base35-nimbus-mono-ps-fonts noarch 20200910-18.fc39 fedora 795 k urw-base35-nimbus-roman-fonts noarch 20200910-18.fc39 fedora 856 k urw-base35-nimbus-sans-fonts noarch 20200910-18.fc39 fedora 1.3 M urw-base35-p052-fonts noarch 20200910-18.fc39 fedora 974 k urw-base35-standard-symbols-ps-fonts noarch 20200910-18.fc39 fedora 42 k urw-base35-z003-fonts noarch 20200910-18.fc39 fedora 276 k vim-filesystem noarch 2:9.1.031-1.fc39 updates 17 k xapian-core-libs x86_64 1.4.23-1.fc39 fedora 771 k xml-common noarch 0.6.3-61.fc39 fedora 31 k xpdf-libs x86_64 1:4.04-10.fc39 fedora 647 k zziplib x86_64 0.13.72-5.fc39 fedora 86 k Transaction Summary ============================================================================================ Install 682 Packages Total size: 468 M Total download size: 454 M Installed size: 1.4 G Downloading Packages: [SKIPPED] python-pip-wheel-23.3.1-4.fc39.noarch.rpm: Already downloaded [SKIPPED] python3-jinja2-3.1.3-2.fc39.noarch.rpm: Already downloaded [SKIPPED] python3-markupsafe-2.1.3-3.fc39.x86_64.rpm: Already downloaded [SKIPPED] python3-packaging-23.2-3.fc39.noarch.rpm: Already downloaded [SKIPPED] python3-setuptools-68.2.2-2.fc39.noarch.rpm: Already downloaded [SKIPPED] expat-2.5.0-3.fc39.x86_64.rpm: Already downloaded [SKIPPED] libb2-0.98.1-9.fc39.x86_64.rpm: Already downloaded [SKIPPED] mpdecimal-2.5.1-7.fc39.x86_64.rpm: Already downloaded [SKIPPED] python-rpm-macros-3.12-4.fc39.noarch.rpm: Already downloaded [SKIPPED] python3-rpm-generators-14-7.fc39.noarch.rpm: Already downloaded [SKIPPED] python3-rpm-macros-3.12-4.fc39.noarch.rpm: Already downloaded [SKIPPED] pyproject-rpm-macros-1.11.0-1.fc39.noarch.rpm: Already downloaded [SKIPPED] python3-3.12.1-2.fc39.x86_64.rpm: Already downloaded [SKIPPED] python3-devel-3.12.1-2.fc39.x86_64.rpm: Already downloaded [SKIPPED] python3-libs-3.12.1-2.fc39.x86_64.rpm: Already downloaded [SKIPPED] tzdata-2023d-1.fc39.noarch.rpm: Already downloaded (17/682): python3-charset-normalizer-3.3.2-1.fc 1.6 MB/s | 99 kB 00:00 (18/682): graphviz-9.0.0-8.fc39.x86_64.rpm 25 MB/s | 5.0 MB 00:00 (19/682): python3-docutils-0.20.1-2.fc39.noarch 6.9 MB/s | 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freetype-2.13.1-2.fc39.x86_64.rpm 236 kB/s | 414 kB 00:01 (49/682): fribidi-1.0.13-2.fc39.x86_64.rpm 380 kB/s | 91 kB 00:00 (50/682): gc-8.2.2-4.fc39.x86_64.rpm 465 kB/s | 110 kB 00:00 (51/682): gd-2.3.3-12.fc39.x86_64.rpm 584 kB/s | 139 kB 00:00 (52/682): gdk-pixbuf2-2.42.10-5.fc39.x86_64.rpm 674 kB/s | 484 kB 00:00 (53/682): cmake-3.27.7-1.fc39.x86_64.rpm 485 kB/s | 8.0 MB 00:16 (54/682): graphite2-1.3.14-12.fc39.x86_64.rpm 587 kB/s | 95 kB 00:00 (55/682): gts-0.7.6-46.20121130.fc39.x86_64.rpm 757 kB/s | 240 kB 00:00 (56/682): google-droid-sans-fonts-20200215-17.f 792 kB/s | 2.7 MB 00:03 (57/682): harfbuzz-8.2.1-2.fc39.x86_64.rpm 768 kB/s | 975 kB 00:01 (58/682): highway-1.0.7-1.fc39.x86_64.rpm 751 kB/s | 478 kB 00:00 (59/682): jbig2dec-libs-0.19-10.fc39.x86_64.rpm 462 kB/s | 73 kB 00:00 (60/682): jbigkit-libs-2.1-26.fc39.x86_64.rpm 662 kB/s | 53 kB 00:00 (61/682): jsoncpp-1.9.5-5.fc39.x86_64.rpm 618 kB/s | 99 kB 00:00 (62/682): lasi-1.1.3-11.fc39.x86_64.rpm 619 kB/s | 54 kB 00:00 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libdatrie-0.2.13-7.fc39.x86_64.rpm 366 kB/s | 32 kB 00:00 (79/682): libedit-3.1-48.20230828cvs.fc39.x86_6 664 kB/s | 107 kB 00:00 (80/682): libdav1d-1.2.1-2.fc39.x86_64.rpm 781 kB/s | 618 kB 00:00 (81/682): libijs-0.35-19.fc39.x86_64.rpm 337 kB/s | 29 kB 00:00 (82/682): libjpeg-turbo-2.1.4-3.fc39.x86_64.rpm 768 kB/s | 183 kB 00:00 (83/682): libjxl-0.8.2-3.fc39.x86_64.rpm 725 kB/s | 1.2 MB 00:01 (84/682): liblerc-4.0.0-4.fc39.x86_64.rpm 597 kB/s | 201 kB 00:00 (85/682): libmpc-1.3.1-3.fc39.x86_64.rpm 435 kB/s | 70 kB 00:00 (86/682): libpaper-2.1.1-1.fc39.x86_64.rpm 333 kB/s | 27 kB 00:00 (87/682): libpng-1.6.37-15.fc39.x86_64.rpm 749 kB/s | 119 kB 00:00 (88/682): libthai-0.1.29-6.fc39.x86_64.rpm 673 kB/s | 213 kB 00:00 (89/682): libtiff-4.4.0-8.fc39.x86_64.rpm 608 kB/s | 202 kB 00:00 (90/682): libtool-ltdl-2.4.7-7.fc39.x86_64.rpm 453 kB/s | 36 kB 00:00 (91/682): libvmaf-2.3.0-6.fc39.x86_64.rpm 730 kB/s | 180 kB 00:00 (92/682): clang16-libs-16.0.6-3.fc39.x86_64.rpm 729 kB/s | 22 MB 00:31 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-------------------------------------------------------------------------------- Total 2.6 MB/s | 454 MB 02:57 Running transaction check Transaction check succeeded. 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texlive-oberdiek-11:svn65521-77.fc39.noarch 595/682 Installing : texlive-pdfpages-11:svn65319-69.fc39.noarch 596/682 Installing : texlive-sansmathaccent-11:svn53628-69.fc39.noarc 597/682 Installing : texlive-ae-11:svn15878.1.4-69.fc39.noarch 598/682 Installing : texlive-extsizes-11:svn17263.1.4a-69.fc39.noarch 599/682 Installing : texlive-jknapltx-11:svn19440.0-69.fc39.noarch 600/682 Installing : texlive-minitoc-11:svn61719-69.fc39.noarch 601/682 Installing : texlive-ltxmisc-11:svn21927.0-69.fc39.noarch 602/682 Installing : texlive-mnsymbol-11:svn18651.1.4-69.fc39.noarch 603/682 Installing : texlive-mathspec-11:svn42773-69.fc39.noarch 604/682 Installing : texlive-typehtml-11:svn17134.0-69.fc39.noarch 605/682 Installing : texlive-ucs-11:svn64114-69.fc39.noarch 606/682 Installing : texlive-beamer-11:svn65984-69.fc39.noarch 607/682 Installing : texlive-breqn-11:svn60881-69.fc39.noarch 608/682 Installing : texlive-l3experimental-11:svn65621-69.fc39.noarc 609/682 Installing : texlive-realscripts-11:svn56594-69.fc39.noarch 610/682 Installing : texlive-xltxtra-11:svn56594-69.fc39.noarch 611/682 Installing : fribidi-1.0.13-2.fc39.x86_64 612/682 Installing : pango-1.51.0-1.fc39.x86_64 613/682 Installing : librsvg2-2.57.1-1.fc39.x86_64 614/682 Installing : rsvg-pixbuf-loader-2.57.1-1.fc39.x86_64 615/682 Installing : lasi-1.1.3-11.fc39.x86_64 616/682 Installing : emacs-filesystem-1:29.1-2.fc39.noarch 617/682 Installing : dbus-libs-1:1.14.10-1.fc39.x86_64 618/682 Installing : avahi-libs-0.8-24.fc39.x86_64 619/682 Installing : cups-libs-1:2.4.7-5.fc39.x86_64 620/682 Installing : clang16-resource-filesystem-16.0.6-3.fc39.x86_64 621/682 Installing : clang16-libs-16.0.6-3.fc39.x86_64 622/682 Installing : adobe-mappings-pdf-20190401-5.fc39.noarch 623/682 Installing : libgs-10.02.1-2.fc39.x86_64 624/682 Installing : ghostscript-tools-fonts-10.02.1-2.fc39.x86_64 625/682 Installing : ghostscript-tools-printing-10.02.1-2.fc39.x86_64 626/682 Installing : ghostscript-10.02.1-2.fc39.x86_64 627/682 Installing : texlive-thumbpdf-11:svn62518-77.fc39.noarch 628/682 Installing : texlive-collection-latex-11:svn63515-69.fc39.noa 629/682 Installing : texlive-collection-latexrecommended-11:svn65512- 630/682 Installing : texlive-collection-basic-11:svn59159-69.fc39.noa 631/682 Installing : texlive-dvipdfmx-11:svn66203-77.fc39.x86_64 632/682 Installing : texlive-xetex-11:svn66203-77.fc39.x86_64 633/682 Installing : python-pip-wheel-23.3.1-4.fc39.noarch 634/682 Installing : python3-3.12.1-2.fc39.x86_64 635/682 Installing : python3-libs-3.12.1-2.fc39.x86_64 636/682 Installing : python3-idna-3.6-2.fc39.noarch 637/682 Installing : python3-packaging-23.2-3.fc39.noarch 638/682 Installing : cmake-rpm-macros-3.27.7-1.fc39.noarch 639/682 Installing : cmake-3.27.7-1.fc39.x86_64 640/682 Installing : cmake-data-3.27.7-1.fc39.noarch 641/682 Installing : python3-rpm-generators-14-7.fc39.noarch 642/682 Installing : python3-urllib3-1.26.18-2.fc39.noarch 643/682 Installing : python3-charset-normalizer-3.3.2-1.fc39.noarch 644/682 Installing : python3-requests-2.31.0-2.fc39.noarch 645/682 Installing : python3-docutils-0.20.1-2.fc39.noarch 646/682 Installing : python3-imagesize-1.4.1-6.fc39.noarch 647/682 Installing : python3-markupsafe-2.1.3-3.fc39.x86_64 648/682 Installing : python3-jinja2-3.1.3-2.fc39.noarch 649/682 Installing : python3-pygments-2.17.2-2.fc39.noarch 650/682 Installing : python3-setuptools-68.2.2-2.fc39.noarch 651/682 Installing : python3-babel-2.13.1-2.fc39.noarch 652/682 Installing : python3-sphinx-theme-alabaster-0.7.16-2.fc39.noa 653/682 Installing : python3-snowballstemmer-2.2.0-7.fc39.noarch 654/682 Installing : crypto-policies-scripts-20231204-1.git1e3a2e4.fc 655/682 Installing : nss-sysinit-3.96.1-1.fc39.x86_64 656/682 Installing : nss-3.96.1-1.fc39.x86_64 657/682 Running scriptlet: nss-3.96.1-1.fc39.x86_64 657/682 Installing : poppler-23.08.0-1.fc39.x86_64 658/682 Installing : poppler-glib-23.08.0-1.fc39.x86_64 659/682 Installing : graphviz-9.0.0-8.fc39.x86_64 660/682 Installing : python3-sphinx-1:7.2.6-5.fc39.noarch 661/682 Installing : doxygen-2:1.9.7-3.fc39.x86_64 662/682 Installing : python3-devel-3.12.1-2.fc39.x86_64 663/682 Installing : python3-numpy-1:1.26.2-3.fc39.x86_64 664/682 Installing : texlive-adjustbox-11:svn64967-69.fc39.noarch 665/682 Installing : texlive-stackengine-11:svn60019-69.fc39.noarch 666/682 Installing : texlive-etoc-11:svn66299-69.fc39.noarch 667/682 Installing : texlive-hanging-11:svn15878.1.2b-69.fc39.noarch 668/682 Installing : texlive-multirow-11:svn58396-69.fc39.noarch 669/682 Installing : texlive-newunicodechar-11:svn47382-69.fc39.noarc 670/682 Installing : texlive-sectsty-11:svn15878.2.0.2-69.fc39.noarch 671/682 Installing : texlive-tocloft-11:svn53364-69.fc39.noarch 672/682 Installing : texlive-ulem-11:svn53365-69.fc39.noarch 673/682 Installing : texlive-wasy-11:svn53533-69.fc39.noarch 674/682 Installing : texlive-wasysym-11:svn54080-69.fc39.noarch 675/682 Installing : annobin-plugin-gcc-12.35-1.fc39.x86_64 676/682 Running scriptlet: annobin-plugin-gcc-12.35-1.fc39.x86_64 676/682 Installing : gcc-c++-13.2.1-6.fc39.x86_64 677/682 Installing : gcc-plugin-annobin-13.2.1-6.fc39.x86_64 678/682 Running scriptlet: gcc-plugin-annobin-13.2.1-6.fc39.x86_64 678/682 Installing : maloc-devel-1.5-28.fc39.x86_64 679/682 Installing : zlib-devel-1.2.13-4.fc39.x86_64 680/682 Installing : swig-4.1.1-9.fc39.x86_64 681/682 Installing : chrpath-0.16-21.fc39.x86_64 682/682 Running scriptlet: texlive-base-11:20230311-77.fc39.x86_64 682/682 Running scriptlet: urw-base35-bookman-fonts-20200910-18.fc39.noarch 682/682 Running scriptlet: urw-base35-c059-fonts-20200910-18.fc39.noarch 682/682 Running scriptlet: urw-base35-d050000l-fonts-20200910-18.fc39.noarc 682/682 Running scriptlet: urw-base35-gothic-fonts-20200910-18.fc39.noarch 682/682 Running scriptlet: urw-base35-nimbus-mono-ps-fonts-20200910-18.fc39 682/682 Running scriptlet: urw-base35-nimbus-roman-fonts-20200910-18.fc39.n 682/682 Running scriptlet: urw-base35-nimbus-sans-fonts-20200910-18.fc39.no 682/682 Running scriptlet: urw-base35-p052-fonts-20200910-18.fc39.noarch 682/682 Running scriptlet: urw-base35-standard-symbols-ps-fonts-20200910-18 682/682 Running scriptlet: urw-base35-z003-fonts-20200910-18.fc39.noarch 682/682 Running scriptlet: fontconfig-2.14.2-5.fc39.x86_64 682/682 Running scriptlet: crypto-policies-scripts-20231204-1.git1e3a2e4.fc 682/682 Running scriptlet: nss-3.96.1-1.fc39.x86_64 682/682 Running scriptlet: chrpath-0.16-21.fc39.x86_64 682/682 Installed: abattis-cantarell-vf-fonts-0.301-10.fc39.noarch adobe-mappings-cmap-20230622-1.fc39.noarch adobe-mappings-cmap-deprecated-20230622-1.fc39.noarch adobe-mappings-pdf-20190401-5.fc39.noarch annobin-docs-12.35-1.fc39.noarch annobin-plugin-gcc-12.35-1.fc39.x86_64 avahi-libs-0.8-24.fc39.x86_64 biber-2.19-3.fc39.noarch cairo-1.18.0-1.fc39.x86_64 cairo-gobject-1.18.0-1.fc39.x86_64 chrpath-0.16-21.fc39.x86_64 clang16-libs-16.0.6-3.fc39.x86_64 clang16-resource-filesystem-16.0.6-3.fc39.x86_64 cmake-3.27.7-1.fc39.x86_64 cmake-data-3.27.7-1.fc39.noarch cmake-filesystem-3.27.7-1.fc39.x86_64 cmake-rpm-macros-3.27.7-1.fc39.noarch cpp-13.2.1-6.fc39.x86_64 crypto-policies-scripts-20231204-1.git1e3a2e4.fc39.noarch cups-libs-1:2.4.7-5.fc39.x86_64 dbus-libs-1:1.14.10-1.fc39.x86_64 default-fonts-core-sans-4.0-9.fc39.noarch doxygen-2:1.9.7-3.fc39.x86_64 emacs-filesystem-1:29.1-2.fc39.noarch expat-2.5.0-3.fc39.x86_64 flexiblas-3.4.1-1.fc39.x86_64 flexiblas-netlib-3.4.1-1.fc39.x86_64 flexiblas-openblas-openmp-3.4.1-1.fc39.x86_64 fontconfig-2.14.2-5.fc39.x86_64 fonts-filesystem-1:2.0.5-12.fc39.noarch freetype-2.13.1-2.fc39.x86_64 fribidi-1.0.13-2.fc39.x86_64 gc-8.2.2-4.fc39.x86_64 gcc-13.2.1-6.fc39.x86_64 gcc-c++-13.2.1-6.fc39.x86_64 gcc-plugin-annobin-13.2.1-6.fc39.x86_64 gd-2.3.3-12.fc39.x86_64 gdk-pixbuf2-2.42.10-5.fc39.x86_64 ghostscript-10.02.1-2.fc39.x86_64 ghostscript-tools-fonts-10.02.1-2.fc39.x86_64 ghostscript-tools-printing-10.02.1-2.fc39.x86_64 glib2-2.78.3-1.fc39.x86_64 glibc-devel-2.38-14.fc39.x86_64 glibc-headers-x86-2.38-14.fc39.noarch gnutls-3.8.2-2.fc39.x86_64 google-droid-sans-fonts-20200215-17.fc39.noarch google-noto-fonts-common-20230801-4.fc39.noarch google-noto-sans-vf-fonts-20230801-4.fc39.noarch graphite2-1.3.14-12.fc39.x86_64 graphviz-9.0.0-8.fc39.x86_64 groff-base-1.23.0-3.fc39.x86_64 gts-0.7.6-46.20121130.fc39.x86_64 guile22-2.2.7-9.fc39.x86_64 harfbuzz-8.2.1-2.fc39.x86_64 highway-1.0.7-1.fc39.x86_64 jbig2dec-libs-0.19-10.fc39.x86_64 jbigkit-libs-2.1-26.fc39.x86_64 jsoncpp-1.9.5-5.fc39.x86_64 kernel-headers-6.6.3-200.fc39.x86_64 lasi-1.1.3-11.fc39.x86_64 lcms2-2.15-2.fc39.x86_64 libICE-1.0.10-11.fc39.x86_64 libSM-1.2.3-13.fc39.x86_64 libX11-1.8.7-1.fc39.x86_64 libX11-common-1.8.7-1.fc39.noarch libXau-1.0.11-3.fc39.x86_64 libXaw-1.0.14-5.fc39.x86_64 libXext-1.3.5-3.fc39.x86_64 libXft-2.3.8-3.fc39.x86_64 libXi-1.8.1-2.fc39.x86_64 libXmu-1.1.4-3.fc39.x86_64 libXpm-3.5.17-1.fc39.x86_64 libXrender-0.9.11-3.fc39.x86_64 libXt-1.2.1-5.fc39.x86_64 libaom-3.8.0-1.fc39.x86_64 libavif-0.11.1-11.fc39.x86_64 libb2-0.98.1-9.fc39.x86_64 libdatrie-0.2.13-7.fc39.x86_64 libdav1d-1.2.1-2.fc39.x86_64 libedit-3.1-48.20230828cvs.fc39.x86_64 libgfortran-13.2.1-6.fc39.x86_64 libgs-10.02.1-2.fc39.x86_64 libicu-73.2-2.fc39.x86_64 libijs-0.35-19.fc39.x86_64 libimagequant-4.0.3-2.fc39.x86_64 libjpeg-turbo-2.1.4-3.fc39.x86_64 libjxl-1:0.8.2-3.fc39.x86_64 liblerc-4.0.0-4.fc39.x86_64 libmpc-1.3.1-3.fc39.x86_64 libpaper-1:2.1.1-1.fc39.x86_64 libpng-2:1.6.37-15.fc39.x86_64 libquadmath-13.2.1-6.fc39.x86_64 librsvg2-2.57.1-1.fc39.x86_64 libstdc++-devel-13.2.1-6.fc39.x86_64 libthai-0.1.29-6.fc39.x86_64 libtiff-4.4.0-8.fc39.x86_64 libtool-ltdl-2.4.7-7.fc39.x86_64 libuv-1:1.47.0-3.fc39.x86_64 libvmaf-2.3.0-6.fc39.x86_64 libwebp-1.3.2-2.fc39.x86_64 libxcb-1.13.1-12.fc39.x86_64 libxcrypt-devel-4.4.36-2.fc39.x86_64 libxslt-1.1.39-1.fc39.x86_64 llvm16-libs-16.0.6-5.fc39.x86_64 mailcap-2.1.54-2.fc39.noarch make-1:4.4.1-2.fc39.x86_64 maloc-1.5-28.fc39.x86_64 maloc-devel-1.5-28.fc39.x86_64 mpdecimal-2.5.1-7.fc39.x86_64 ncurses-6.4-7.20230520.fc39.x86_64 netpbm-11.02.00-2.fc39.x86_64 nettle-3.9.1-2.fc39.x86_64 nspr-4.35.0-16.fc39.x86_64 nss-3.96.1-1.fc39.x86_64 nss-softokn-3.96.1-1.fc39.x86_64 nss-softokn-freebl-3.96.1-1.fc39.x86_64 nss-sysinit-3.96.1-1.fc39.x86_64 nss-util-3.96.1-1.fc39.x86_64 openblas-0.3.21-6.fc39.x86_64 openblas-openmp-0.3.21-6.fc39.x86_64 openjpeg2-2.5.0-5.fc39.x86_64 pango-1.51.0-1.fc39.x86_64 perl-Authen-SASL-2.1700-1.fc39.noarch perl-AutoLoader-5.74-502.fc39.noarch perl-B-1.88-502.fc39.x86_64 perl-B-Hooks-EndOfScope-0.26-7.fc39.noarch perl-Business-ISBN-3.008-2.fc39.noarch perl-Business-ISBN-Data-20230926.001-1.fc39.noarch perl-Business-ISMN-1.203-2.fc39.noarch perl-Business-ISSN-1.005-8.fc39.noarch perl-Carp-1.54-500.fc39.noarch perl-Class-Accessor-0.51-18.fc39.noarch perl-Class-Data-Inheritable-0.09-6.fc39.noarch perl-Class-Inspector-1.36-14.fc39.noarch perl-Class-Method-Modifiers-2.15-2.fc39.noarch perl-Class-Singleton-1.6-9.fc39.noarch perl-Class-Struct-0.68-502.fc39.noarch perl-Clone-0.46-4.fc39.x86_64 perl-Compress-Raw-Bzip2-2.206-1.fc39.x86_64 perl-Compress-Raw-Zlib-2.206-1.fc39.x86_64 perl-Convert-ASN1-0.34-1.fc39.noarch perl-Data-Compare-1.29-2.fc39.noarch perl-Data-Dump-1.25-8.fc39.noarch perl-Data-Dumper-2.188-501.fc39.x86_64 perl-Data-OptList-0.114-2.fc39.noarch perl-Data-Uniqid-0.12-31.fc39.noarch perl-Date-ISO8601-0.005-18.fc39.noarch perl-Date-Manip-6.93-1.fc39.noarch perl-DateTime-2:1.59-5.fc39.x86_64 perl-DateTime-Calendar-Julian-0.107-5.fc39.noarch perl-DateTime-Format-Builder-0.8300-11.fc39.noarch perl-DateTime-Format-Strptime-1:1.79-8.fc39.noarch perl-DateTime-Locale-1.39-2.fc39.noarch perl-DateTime-TimeZone-2.61-1.fc39.noarch perl-DateTime-TimeZone-SystemV-0.010-19.fc39.noarch perl-DateTime-TimeZone-Tzfile-0.011-19.fc39.noarch perl-Devel-CallChecker-0.009-3.fc39.x86_64 perl-Devel-Caller-2.07-3.fc39.x86_64 perl-Devel-GlobalDestruction-0.14-22.fc39.noarch perl-Devel-LexAlias-0.05-34.fc39.x86_64 perl-Devel-StackTrace-1:2.04-16.fc39.noarch perl-Digest-1.20-500.fc39.noarch perl-Digest-HMAC-1.04-8.fc39.noarch perl-Digest-MD5-2.58-500.fc39.x86_64 perl-Digest-SHA-1:6.04-501.fc39.x86_64 perl-Dist-CheckConflicts-0.11-28.fc39.noarch perl-DynaLoader-1.54-502.fc39.x86_64 perl-DynaLoader-Functions-0.004-2.fc39.noarch perl-Email-Date-Format-1.008-2.fc39.noarch perl-Encode-4:3.19-500.fc39.x86_64 perl-Encode-Locale-1.05-27.fc39.noarch perl-English-1.11-502.fc39.noarch perl-Errno-1.37-502.fc39.x86_64 perl-Eval-Closure-0.14-21.fc39.noarch perl-Exception-Class-1.45-8.fc39.noarch perl-Exporter-5.77-500.fc39.noarch perl-ExtUtils-MM-Utils-2:7.70-501.fc39.noarch perl-Fcntl-1.15-502.fc39.x86_64 perl-File-Basename-2.86-502.fc39.noarch perl-File-Compare-1.100.700-502.fc39.noarch perl-File-Copy-2.41-502.fc39.noarch perl-File-Find-1.43-502.fc39.noarch perl-File-Find-Rule-0.34-26.fc39.noarch perl-File-Listing-6.16-1.fc39.noarch perl-File-Path-2.18-500.fc39.noarch perl-File-ShareDir-1.118-9.fc39.noarch perl-File-Slurper-0.014-3.fc39.noarch perl-File-Temp-1:0.231.100-500.fc39.noarch perl-File-stat-1.13-502.fc39.noarch perl-FileHandle-2.05-502.fc39.noarch perl-Filter-2:1.64-501.fc39.x86_64 perl-GSSAPI-0.28-43.fc39.x86_64 perl-Getopt-Long-1:2.54-500.fc39.noarch perl-Getopt-Std-1.13-502.fc39.noarch perl-HTML-Parser-3.81-3.fc39.x86_64 perl-HTML-Tagset-3.20-54.fc39.noarch perl-HTTP-Cookies-6.10-10.fc39.noarch perl-HTTP-Date-6.06-2.fc39.noarch perl-HTTP-Message-6.44-3.fc39.noarch perl-HTTP-Negotiate-6.01-36.fc39.noarch perl-HTTP-Tiny-0.088-3.fc39.noarch perl-Hash-Util-FieldHash-1.26-502.fc39.x86_64 perl-I18N-LangTags-0.45-502.fc39.noarch perl-I18N-Langinfo-0.22-502.fc39.x86_64 perl-IO-1.52-502.fc39.x86_64 perl-IO-Compress-2.206-1.fc39.noarch perl-IO-HTML-1.004-11.fc39.noarch perl-IO-Socket-IP-0.42-1.fc39.noarch perl-IO-Socket-SSL-2.083-3.fc39.noarch perl-IO-String-1.08-48.fc39.noarch perl-IPC-Cmd-2:1.04-501.fc39.noarch perl-IPC-Open3-1.22-502.fc39.noarch perl-IPC-Run3-0.048-29.fc39.noarch perl-IPC-SysV-2.09-501.fc39.x86_64 perl-IPC-System-Simple-1.30-11.fc39.noarch perl-JSON-4.10-3.fc39.noarch perl-LDAP-1:0.68-11.fc39.noarch perl-LWP-MediaTypes-6.04-15.fc39.noarch perl-LWP-Protocol-https-6.11-1.fc39.noarch perl-Lingua-Translit-0.29-4.fc39.noarch perl-List-AllUtils-0.19-10.fc39.noarch perl-List-SomeUtils-0.59-3.fc39.noarch perl-List-UtilsBy-0.12-7.fc39.noarch perl-Locale-Maketext-1.33-501.fc39.noarch perl-Locale-Maketext-Simple-1:0.21-502.fc39.noarch perl-Log-Dispatch-2.71-2.fc39.noarch perl-Log-Dispatch-FileRotate-1.38-7.fc39.noarch perl-Log-Log4perl-1.57-3.fc39.noarch perl-MIME-Base64-3.16-500.fc39.x86_64 perl-MIME-Charset-1.013.1-3.fc39.noarch perl-MIME-Lite-3.033-8.fc39.noarch perl-MIME-Types-2.24-3.fc39.noarch perl-MRO-Compat-0.15-7.fc39.noarch perl-Mail-Sender-1:0.903-22.fc39.noarch perl-Mail-Sendmail-0.80-18.fc39.noarch perl-MailTools-2.21-14.fc39.noarch perl-Math-BigInt-1:1.9998.39-2.fc39.noarch perl-Math-BigRat-0.2624-500.fc39.noarch perl-Math-Complex-1.62-502.fc39.noarch perl-Module-CoreList-1:5.20231230-1.fc39.noarch perl-Module-Implementation-0.09-37.fc39.noarch perl-Module-Load-1:0.36-500.fc39.noarch perl-Module-Load-Conditional-0.74-500.fc39.noarch perl-Module-Metadata-1.000038-3.fc39.noarch perl-Module-Runtime-0.016-20.fc39.noarch perl-Mozilla-CA-20230801-1.fc39.noarch perl-NTLM-1.09-36.fc39.noarch perl-Net-HTTP-6.23-2.fc39.noarch perl-Net-SMTP-SSL-1.04-21.fc39.noarch perl-Net-SSLeay-1.92-10.fc39.x86_64 perl-Number-Compare-0.03-36.fc39.noarch perl-Opcode-1.64-502.fc39.x86_64 perl-POSIX-2.13-502.fc39.x86_64 perl-Package-Generator-1.106-29.fc39.noarch perl-Package-Stash-0.40-5.fc39.noarch perl-Package-Stash-XS-0.30-5.fc39.x86_64 perl-PadWalker-2.5-10.fc39.x86_64 perl-Params-Check-1:0.38-500.fc39.noarch perl-Params-Classify-0.015-20.fc39.x86_64 perl-Params-Util-1.102-12.fc39.x86_64 perl-Params-Validate-1.31-5.fc39.x86_64 perl-Params-ValidationCompiler-0.31-3.fc39.noarch perl-Parse-RecDescent-1.967015-20.fc39.noarch perl-PathTools-3.89-500.fc39.x86_64 perl-Pod-Escapes-1:1.07-500.fc39.noarch perl-Pod-Html-1.34-502.fc39.noarch perl-Pod-Perldoc-3.28.01-501.fc39.noarch perl-Pod-Simple-1:3.45-4.fc39.noarch perl-Pod-Usage-4:2.03-500.fc39.noarch perl-Ref-Util-0.204-18.fc39.noarch perl-Ref-Util-XS-0.117-20.fc39.x86_64 perl-Regexp-Common-2017060201-22.fc39.noarch perl-Role-Tiny-2.002004-9.fc39.noarch perl-Safe-2.44-502.fc39.noarch perl-Scalar-List-Utils-5:1.63-500.fc39.x86_64 perl-SelectSaver-1.02-502.fc39.noarch perl-Socket-4:2.037-3.fc39.x86_64 perl-Sort-Key-1.33-28.fc39.x86_64 perl-Specio-0.48-4.fc39.noarch perl-Storable-1:3.32-500.fc39.x86_64 perl-Sub-Exporter-0.990-1.fc39.noarch perl-Sub-Exporter-Progressive-0.001013-22.fc39.noarch perl-Sub-Identify-0.14-24.fc39.x86_64 perl-Sub-Install-0.929-3.fc39.noarch perl-Symbol-1.09-502.fc39.noarch perl-Sys-Hostname-1.25-502.fc39.x86_64 perl-Sys-Syslog-0.36-501.fc39.x86_64 perl-Term-ANSIColor-5.01-501.fc39.noarch perl-Term-Cap-1.18-500.fc39.noarch perl-Text-Balanced-2.06-500.fc39.noarch perl-Text-BibTeX-0.89-3.fc39.x86_64 perl-Text-CSV-2.02-3.fc39.noarch perl-Text-Glob-0.11-21.fc39.noarch perl-Text-ParseWords-3.31-500.fc39.noarch perl-Text-Roman-3.5-25.fc39.noarch perl-Text-Soundex-3.05-28.fc39.x86_64 perl-Text-Tabs+Wrap-2023.0511-3.fc39.noarch perl-Text-Unidecode-1.30-22.fc39.noarch perl-Tie-4.6-502.fc39.noarch perl-Tie-Cycle-1.227-9.fc39.noarch perl-Tie-RefHash-1.40-500.fc39.noarch perl-Time-HiRes-4:1.9775-500.fc39.x86_64 perl-Time-Local-2:1.350-3.fc39.noarch perl-TimeDate-1:2.33-11.fc39.noarch perl-Try-Tiny-0.31-6.fc39.noarch perl-URI-5.21-1.fc39.noarch perl-Unicode-Collate-1.31-500.fc39.x86_64 perl-Unicode-LineBreak-2019.001-18.fc39.x86_64 perl-Unicode-Normalize-1.32-500.fc39.x86_64 perl-Unicode-UCD-0.78-502.fc39.noarch perl-Variable-Magic-0.63-4.fc39.x86_64 perl-WWW-RobotRules-6.02-37.fc39.noarch perl-XML-LibXML-1:2.0209-2.fc39.x86_64 perl-XML-LibXML-Simple-1.01-12.fc39.noarch perl-XML-LibXSLT-2.002.001-3.fc39.x86_64 perl-XML-NamespaceSupport-1.12-20.fc39.noarch perl-XML-Parser-2.46-15.fc39.x86_64 perl-XML-SAX-1.02-13.fc39.noarch perl-XML-SAX-Base-1.09-20.fc39.noarch perl-XML-Writer-0.900-12.fc39.noarch perl-XML-XPath-1.48-4.fc39.noarch perl-XString-0.005-10.fc39.x86_64 perl-autodie-2.36-501.fc39.noarch perl-autovivification-0.18-20.fc39.x86_64 perl-base-2.27-502.fc39.noarch perl-constant-1.33-501.fc39.noarch perl-deprecate-0.04-502.fc39.noarch perl-encoding-4:3.00-500.fc39.x86_64 perl-if-0.61.000-502.fc39.noarch perl-interpreter-4:5.38.2-502.fc39.x86_64 perl-libnet-3.15-501.fc39.noarch perl-libs-4:5.38.2-502.fc39.x86_64 perl-libwww-perl-6.72-1.fc39.noarch perl-locale-1.10-502.fc39.noarch perl-meta-notation-5.38.2-502.fc39.noarch perl-mro-1.28-502.fc39.x86_64 perl-namespace-autoclean-0.29-16.fc39.noarch perl-namespace-clean-0.27-24.fc39.noarch perl-open-1.13-502.fc39.noarch perl-overload-1.37-502.fc39.noarch perl-overloading-0.02-502.fc39.noarch perl-parent-1:0.241-500.fc39.noarch perl-podlators-1:5.01-500.fc39.noarch perl-sigtrap-1.10-502.fc39.noarch perl-subs-1.04-502.fc39.noarch perl-vars-1.05-502.fc39.noarch perl-version-8:0.99.30-1.fc39.x86_64 perltidy-20230912-1.fc39.noarch pixman-0.42.2-2.fc39.x86_64 poppler-23.08.0-1.fc39.x86_64 poppler-data-0.4.11-5.fc39.noarch poppler-glib-23.08.0-1.fc39.x86_64 pyproject-rpm-macros-1.11.0-1.fc39.noarch python-pip-wheel-23.3.1-4.fc39.noarch python-rpm-macros-3.12-4.fc39.noarch python3-3.12.1-2.fc39.x86_64 python3-babel-2.13.1-2.fc39.noarch python3-charset-normalizer-3.3.2-1.fc39.noarch python3-devel-3.12.1-2.fc39.x86_64 python3-docutils-0.20.1-2.fc39.noarch python3-idna-3.6-2.fc39.noarch python3-imagesize-1.4.1-6.fc39.noarch python3-jinja2-3.1.3-2.fc39.noarch python3-libs-3.12.1-2.fc39.x86_64 python3-markupsafe-2.1.3-3.fc39.x86_64 python3-numpy-1:1.26.2-3.fc39.x86_64 python3-packaging-23.2-3.fc39.noarch python3-pygments-2.17.2-2.fc39.noarch python3-requests-2.31.0-2.fc39.noarch python3-rpm-generators-14-7.fc39.noarch python3-rpm-macros-3.12-4.fc39.noarch python3-setuptools-68.2.2-2.fc39.noarch python3-snowballstemmer-2.2.0-7.fc39.noarch python3-sphinx-1:7.2.6-5.fc39.noarch python3-sphinx-theme-alabaster-0.7.16-2.fc39.noarch python3-urllib3-1.26.18-2.fc39.noarch rav1e-libs-0.6.6-4.fc39.x86_64 rhash-1.4.3-3.fc39.x86_64 rsvg-pixbuf-loader-2.57.1-1.fc39.x86_64 shared-mime-info-2.2-4.fc39.x86_64 sombok-2.4.0-20.fc39.x86_64 svt-av1-libs-1.4.1-3.fc39.x86_64 swig-4.1.1-9.fc39.x86_64 teckit-2.5.12-1.fc39.x86_64 texlive-adjustbox-11:svn64967-69.fc39.noarch texlive-ae-11:svn15878.1.4-69.fc39.noarch texlive-algorithms-11:svn42428-69.fc39.noarch texlive-alphalph-11:svn53087-69.fc39.noarch texlive-amscls-11:svn55378-69.fc39.noarch texlive-amsfonts-11:svn61937-69.fc39.noarch texlive-amsmath-11:svn63514-69.fc39.noarch texlive-anysize-11:svn15878.0-69.fc39.noarch texlive-atbegshi-11:svn53051-69.fc39.noarch texlive-attachfile-11:svn42099-69.fc39.noarch texlive-attachfile2-11:svn57959-77.fc39.noarch texlive-atveryend-11:svn53108-69.fc39.noarch texlive-auto-pst-pdf-11:svn56596-69.fc39.noarch texlive-auxhook-11:svn53173-69.fc39.noarch texlive-avantgar-11:svn61983-69.fc39.noarch texlive-babel-11:svn65823-69.fc39.noarch texlive-babel-english-11:svn44495-69.fc39.noarch texlive-babelbib-11:svn57349-69.fc39.noarch texlive-base-11:20230311-77.fc39.x86_64 texlive-beamer-11:svn65984-69.fc39.noarch texlive-bera-11:svn20031.0-69.fc39.noarch texlive-beton-11:svn15878.0-69.fc39.noarch texlive-biblatex-11:svn66403-69.fc39.noarch texlive-bibtex-11:svn66186-77.fc39.x86_64 texlive-bidi-11:svn65572-69.fc39.noarch texlive-bigintcalc-11:svn53172-69.fc39.noarch texlive-bitset-11:svn53837-69.fc39.noarch texlive-bookman-11:svn61719-69.fc39.noarch texlive-bookmark-11:svn56885-69.fc39.noarch texlive-booktabs-11:svn53402-69.fc39.noarch texlive-breakurl-11:svn29901.1.40-69.fc39.noarch texlive-breqn-11:svn60881-69.fc39.noarch texlive-caption-11:svn66580-69.fc39.noarch texlive-carlisle-11:svn59577-69.fc39.noarch texlive-catchfile-11:svn53084-69.fc39.noarch texlive-changepage-11:svn15878.1.0c-69.fc39.noarch texlive-charter-11:svn15878.0-69.fc39.noarch texlive-cite-11:svn36428.5.5-69.fc39.noarch texlive-cm-11:svn57963-69.fc39.noarch texlive-cm-super-11:svn15878.0-69.fc39.noarch texlive-cmap-11:svn57640-69.fc39.noarch texlive-collectbox-11:svn64967-69.fc39.noarch texlive-collection-basic-11:svn59159-69.fc39.noarch texlive-collection-latex-11:svn63515-69.fc39.noarch texlive-collection-latexrecommended-11:svn65512-69.fc39.noarch texlive-colorprofiles-11:svn49086-69.fc39.noarch texlive-colortbl-11:svn64015-69.fc39.noarch texlive-courier-11:svn61719-69.fc39.noarch texlive-crop-11:svn55424-69.fc39.noarch texlive-csquotes-11:svn64389-69.fc39.noarch texlive-ctable-11:svn38672-69.fc39.noarch texlive-ctablestack-11:svn38514-69.fc39.noarch texlive-currfile-11:svn64673-69.fc39.noarch texlive-dehyph-11:svn48599-69.fc39.noarch texlive-dvipdfmx-11:svn66203-77.fc39.x86_64 texlive-dvips-11:svn66203-77.fc39.x86_64 texlive-ec-11:svn25033.1.0-69.fc39.noarch texlive-enctex-11:svn34957.0-69.fc39.noarch texlive-enumitem-11:svn51423-69.fc39.noarch texlive-epstopdf-11:svn66461-77.fc39.noarch texlive-epstopdf-pkg-11:svn53546-69.fc39.noarch texlive-eso-pic-11:svn56658-69.fc39.noarch texlive-etex-11:svn66203-69.fc39.noarch texlive-etex-pkg-11:svn41784-69.fc39.noarch texlive-etexcmds-11:svn53171-69.fc39.noarch texlive-etoc-11:svn66299-69.fc39.noarch texlive-etoolbox-11:svn56554-69.fc39.noarch texlive-euenc-11:svn19795.0.1h-69.fc39.noarch texlive-euler-11:svn42428-69.fc39.noarch texlive-everysel-11:svn57489-69.fc39.noarch texlive-everyshi-11:svn57001-69.fc39.noarch texlive-extsizes-11:svn17263.1.4a-69.fc39.noarch texlive-fancybox-11:svn18304.1.4-69.fc39.noarch texlive-fancyhdr-11:svn64977-69.fc39.noarch texlive-fancyref-11:svn15878.0.9c-69.fc39.noarch texlive-fancyvrb-11:svn65585-69.fc39.noarch texlive-filecontents-11:svn52142-69.fc39.noarch texlive-filehook-11:svn64822-69.fc39.noarch texlive-finstrut-11:svn21719.0.5-69.fc39.noarch texlive-firstaid-11:svn64892-69.fc39.noarch texlive-fix2col-11:svn38770-69.fc39.noarch texlive-float-11:svn15878.1.3d-69.fc39.noarch texlive-fontspec-11:svn63386-69.fc39.noarch texlive-footmisc-11:svn62524-69.fc39.noarch texlive-footnotehyper-11:svn60374-69.fc39.noarch texlive-fp-11:svn49719-69.fc39.noarch texlive-fpl-11:svn54512-69.fc39.noarch texlive-geometry-11:svn61719-69.fc39.noarch texlive-gettitlestring-11:svn53170-69.fc39.noarch texlive-glyphlist-11:svn54074-77.fc39.noarch texlive-graphics-11:svn66204-69.fc39.noarch texlive-graphics-cfg-11:svn41448-69.fc39.noarch texlive-graphics-def-11:svn64487-69.fc39.noarch texlive-grfext-11:svn53024-69.fc39.noarch texlive-grffile-11:svn52756-69.fc39.noarch texlive-gsftopk-11:svn52851-77.fc39.x86_64 texlive-hanging-11:svn15878.1.2b-69.fc39.noarch texlive-helvetic-11:svn61719-69.fc39.noarch texlive-hobsub-11:svn52810-69.fc39.noarch texlive-hologo-11:svn61719-69.fc39.noarch texlive-hopatch-11:svn65491-69.fc39.noarch texlive-hycolor-11:svn53584-69.fc39.noarch texlive-hypdoc-11:svn65678-69.fc39.noarch texlive-hyperref-11:svn65758-69.fc39.noarch texlive-hyph-utf8-11:svn61719-69.fc39.noarch texlive-hyphen-base-11:svn66413-69.fc39.noarch texlive-hyphenex-11:svn57387-69.fc39.noarch texlive-ifmtarg-11:svn47544-69.fc39.noarch texlive-ifoddpage-11:svn64967-69.fc39.noarch texlive-ifplatform-11:svn45533-69.fc39.noarch texlive-iftex-11:svn61910-69.fc39.noarch texlive-index-11:svn24099.4.1beta-69.fc39.noarch texlive-infwarerr-11:svn53023-69.fc39.noarch texlive-intcalc-11:svn53168-69.fc39.noarch texlive-jknapltx-11:svn19440.0-69.fc39.noarch texlive-kastrup-11:svn15878.0-69.fc39.noarch texlive-knuth-lib-11:svn57963-69.fc39.noarch texlive-knuth-local-11:svn57963-69.fc39.noarch texlive-koma-script-11:svn64685-69.fc39.noarch texlive-kpathsea-11:svn66209-77.fc39.x86_64 texlive-kvdefinekeys-11:svn53193-69.fc39.noarch texlive-kvoptions-11:svn63622-69.fc39.noarch texlive-kvsetkeys-11:svn64632-69.fc39.noarch texlive-l3backend-11:svn65573-69.fc39.noarch texlive-l3experimental-11:svn65621-69.fc39.noarch texlive-l3kernel-11:svn66094-69.fc39.noarch texlive-l3packages-11:svn65722-69.fc39.noarch texlive-latex-11:svn65161-77.fc39.noarch texlive-latex-fonts-11:svn28888.0-69.fc39.noarch texlive-latex-lab-11:svn64892-69.fc39.noarch texlive-latexbug-11:svn63596-69.fc39.noarch texlive-latexconfig-11:svn53525-69.fc39.noarch texlive-letltxmacro-11:svn53022-69.fc39.noarch texlive-lib-11:20230311-77.fc39.x86_64 texlive-lineno-11:svn65586-69.fc39.noarch texlive-listings-11:svn66222-69.fc39.noarch texlive-listofitems-11:svn51923-69.fc39.noarch texlive-lm-11:svn65956-69.fc39.noarch texlive-lm-math-11:svn36915.1.959-69.fc39.noarch texlive-logreq-11:svn53003-69.fc39.noarch texlive-ltabptch-11:svn17533.1.74d-69.fc39.noarch texlive-ltxcmds-11:svn56421-69.fc39.noarch texlive-ltxmisc-11:svn21927.0-69.fc39.noarch texlive-lua-alt-getopt-11:svn56414-69.fc39.noarch texlive-lua-uni-algos-11:svn62204-69.fc39.noarch texlive-luabidi-11:svn54512-69.fc39.noarch texlive-luahbtex-11:svn66186-77.fc39.x86_64 texlive-lualatex-math-11:svn61464-69.fc39.noarch texlive-lualibs-11:svn64615-69.fc39.noarch texlive-luaotfload-11:svn64616-77.fc39.noarch texlive-luatex-11:svn66967-77.fc39.x86_64 texlive-luatexbase-11:svn52663-69.fc39.noarch texlive-lwarp-11:svn66259-77.fc39.noarch texlive-makecmds-11:svn15878.0-69.fc39.noarch texlive-makeindex-11:svn62517-77.fc39.x86_64 texlive-marginnote-11:svn48383-69.fc39.noarch texlive-marvosym-11:svn29349.2.2a-69.fc39.noarch texlive-mathpazo-11:svn52663-69.fc39.noarch texlive-mathspec-11:svn42773-69.fc39.noarch texlive-mathtools-11:svn63767-69.fc39.noarch texlive-mdwtools-11:svn15878.1.05.4-69.fc39.noarch texlive-memoir-11:svn65040-69.fc39.noarch texlive-metafont-11:svn66186-77.fc39.x86_64 texlive-metalogo-11:svn18611.0.12-69.fc39.noarch texlive-mflogo-11:svn42428-69.fc39.noarch texlive-mfnfss-11:svn46036-69.fc39.noarch texlive-mfware-11:svn66186-77.fc39.x86_64 texlive-microtype-11:svn66587-69.fc39.noarch texlive-minitoc-11:svn61719-69.fc39.noarch texlive-mnsymbol-11:svn18651.1.4-69.fc39.noarch texlive-modes-11:svn61719-69.fc39.noarch texlive-mparhack-11:svn59066-69.fc39.noarch texlive-mptopdf-11:svn65952-77.fc39.noarch texlive-ms-11:svn57473-69.fc39.noarch texlive-multido-11:svn18302.1.42-69.fc39.noarch texlive-multirow-11:svn58396-69.fc39.noarch texlive-natbib-11:svn20668.8.31b-69.fc39.noarch texlive-newfloat-11:svn52906-69.fc39.noarch texlive-newunicodechar-11:svn47382-69.fc39.noarch texlive-notoccite-11:svn18129.0-69.fc39.noarch texlive-ntgclass-11:svn65522-69.fc39.noarch texlive-oberdiek-11:svn65521-77.fc39.noarch texlive-pagesel-11:svn56105-69.fc39.noarch texlive-palatino-11:svn61719-69.fc39.noarch texlive-paralist-11:svn43021-69.fc39.noarch texlive-parallel-11:svn15878.0-69.fc39.noarch texlive-parskip-11:svn58358-69.fc39.noarch texlive-pdfcol-11:svn64469-69.fc39.noarch texlive-pdfcolfoot-11:svn65512-69.fc39.noarch texlive-pdfcolmk-11:svn52912-69.fc39.noarch texlive-pdfescape-11:svn53082-69.fc39.noarch texlive-pdflscape-11:svn64851-69.fc39.noarch texlive-pdfmanagement-testphase-11:svn66532-69.fc39.noarch texlive-pdfpages-11:svn65319-69.fc39.noarch texlive-pdftex-11:svn66243-77.fc39.x86_64 texlive-pdftexcmds-11:svn55777-69.fc39.noarch texlive-pgf-11:svn65553-69.fc39.noarch texlive-picture-11:svn54867-69.fc39.noarch texlive-placeins-11:svn19848.2.2-69.fc39.noarch texlive-plain-11:svn57963-69.fc39.noarch texlive-polyglossia-11:svn65792-69.fc39.noarch texlive-psfrag-11:svn15878.3.04-69.fc39.noarch texlive-pslatex-11:svn57434-69.fc39.noarch texlive-psnfss-11:svn54694-69.fc39.noarch texlive-pspicture-11:svn15878.0-69.fc39.noarch texlive-pst-3d-11:svn17257.1.10-69.fc39.noarch texlive-pst-coil-11:svn62977-69.fc39.noarch texlive-pst-eps-11:svn15878.1.0-69.fc39.noarch texlive-pst-fill-11:svn60671-69.fc39.noarch texlive-pst-grad-11:svn15878.1.06-69.fc39.noarch texlive-pst-math-11:svn64732-69.fc39.noarch texlive-pst-node-11:svn61838-69.fc39.noarch texlive-pst-ovl-11:svn54963-69.fc39.noarch texlive-pst-plot-11:svn65346-69.fc39.noarch texlive-pst-text-11:svn49542-69.fc39.noarch texlive-pst-tools-11:svn60621-69.fc39.noarch texlive-pst-tree-11:svn60421-69.fc39.noarch texlive-pstricks-11:svn65346-69.fc39.noarch texlive-pstricks-add-11:svn65067-69.fc39.noarch texlive-ragged2e-11:svn66152-69.fc39.noarch texlive-rcs-11:svn15878.0-69.fc39.noarch texlive-realscripts-11:svn56594-69.fc39.noarch texlive-refcount-11:svn53164-69.fc39.noarch texlive-rerunfilecheck-11:svn63869-69.fc39.noarch texlive-rsfs-11:svn15878.0-69.fc39.noarch texlive-sansmath-11:svn17997.1.1-69.fc39.noarch texlive-sansmathaccent-11:svn53628-69.fc39.noarch texlive-sauerj-11:svn15878.0-69.fc39.noarch texlive-section-11:svn20180.0-69.fc39.noarch texlive-sectsty-11:svn15878.2.0.2-69.fc39.noarch texlive-seminar-11:svn59801-69.fc39.noarch texlive-sepnum-11:svn20186.2.0-69.fc39.noarch texlive-setspace-11:svn65206-69.fc39.noarch texlive-showexpl-11:svn57414-69.fc39.noarch texlive-stackengine-11:svn60019-69.fc39.noarch texlive-stringenc-11:svn52982-69.fc39.noarch texlive-subfig-11:svn15878.1.3-69.fc39.noarch texlive-symbol-11:svn61719-69.fc39.noarch texlive-tex-11:svn66186-77.fc39.x86_64 texlive-tex-ini-files-11:svn40533-69.fc39.noarch texlive-texlive-common-doc-11:svn54176-69.fc39.noarch texlive-texlive-en-11:svn66572-77.fc39.noarch texlive-texlive-msg-translations-11:svn66593-69.fc39.noarch texlive-texlive-scripts-11:svn66584-77.fc39.noarch texlive-texlive.infra-11:svn66512-77.fc39.noarch texlive-textcase-11:svn63868-69.fc39.noarch texlive-thumbpdf-11:svn62518-77.fc39.noarch texlive-times-11:svn61719-69.fc39.noarch texlive-tipa-11:svn29349.1.3-69.fc39.noarch texlive-titlesec-11:svn59845-69.fc39.noarch texlive-tocloft-11:svn53364-69.fc39.noarch texlive-tools-11:svn64892-69.fc39.noarch texlive-translator-11:svn59412-69.fc39.noarch texlive-transparent-11:svn64852-69.fc39.noarch texlive-typehtml-11:svn17134.0-69.fc39.noarch texlive-ucharcat-11:svn38907-69.fc39.noarch texlive-ucs-11:svn64114-69.fc39.noarch texlive-ulem-11:svn53365-69.fc39.noarch texlive-underscore-11:svn18261.0-69.fc39.noarch texlive-unicode-data-11:svn64423-69.fc39.noarch texlive-unicode-math-11:svn61719-69.fc39.noarch texlive-uniquecounter-11:svn53162-69.fc39.noarch texlive-url-11:svn32528.3.4-69.fc39.noarch texlive-utopia-11:svn15878.0-69.fc39.noarch texlive-varwidth-11:svn24104.0.92-69.fc39.noarch texlive-wasy-11:svn53533-69.fc39.noarch texlive-wasysym-11:svn54080-69.fc39.noarch texlive-xcolor-11:svn63563-69.fc39.noarch texlive-xdvi-11:svn62387-77.fc39.x86_64 texlive-xetex-11:svn66203-77.fc39.x86_64 texlive-xetexconfig-11:svn45845-69.fc39.noarch texlive-xifthen-11:svn38929-69.fc39.noarch texlive-xkeyval-11:svn63616-69.fc39.noarch texlive-xltxtra-11:svn56594-69.fc39.noarch texlive-xpatch-11:svn54563-69.fc39.noarch texlive-xstring-11:svn65551-69.fc39.noarch texlive-xunicode-11:svn30466.0.981-69.fc39.noarch texlive-zapfding-11:svn61719-69.fc39.noarch texlive-zref-11:svn62977-69.fc39.noarch tzdata-2023d-1.fc39.noarch urw-base35-bookman-fonts-20200910-18.fc39.noarch urw-base35-c059-fonts-20200910-18.fc39.noarch urw-base35-d050000l-fonts-20200910-18.fc39.noarch urw-base35-fonts-20200910-18.fc39.noarch urw-base35-fonts-common-20200910-18.fc39.noarch urw-base35-gothic-fonts-20200910-18.fc39.noarch urw-base35-nimbus-mono-ps-fonts-20200910-18.fc39.noarch urw-base35-nimbus-roman-fonts-20200910-18.fc39.noarch urw-base35-nimbus-sans-fonts-20200910-18.fc39.noarch urw-base35-p052-fonts-20200910-18.fc39.noarch urw-base35-standard-symbols-ps-fonts-20200910-18.fc39.noarch urw-base35-z003-fonts-20200910-18.fc39.noarch vim-filesystem-2:9.1.031-1.fc39.noarch xapian-core-libs-1.4.23-1.fc39.x86_64 xml-common-0.6.3-61.fc39.noarch xpdf-libs-1:4.04-10.fc39.x86_64 zlib-devel-1.2.13-4.fc39.x86_64 zziplib-0.13.72-5.fc39.x86_64 Complete! Finish: build setup for apbs-3.0.0-22.fc39.src.rpm Start: rpmbuild apbs-3.0.0-22.fc39.src.rpm warning: %patchN is deprecated (4 usages found), use %patch N (or %patch -P N) Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1705881600 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.keYuJG + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf apbs-3.0.0 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/apbs-3.0.0.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + cd apbs-3.0.0 + rm -rf /builddir/build/BUILD/apbs-3.0.0-SPECPARTS + /usr/bin/mkdir -p /builddir/build/BUILD/apbs-3.0.0-SPECPARTS + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . Patch #0 (apbs-cmake.patch): + echo 'Patch #0 (apbs-cmake.patch):' + /usr/bin/patch --no-backup-if-mismatch -f -p2 -b --suffix .apbs-cmake --fuzz=0 patching file CMakeLists.txt patching file src/CMakeLists.txt patching file tools/manip/CMakeLists.txt patching file tools/mesh/CMakeLists.txt Patch #1 (apbs-exclude_tests.patch): + echo 'Patch #1 (apbs-exclude_tests.patch):' + /usr/bin/patch --no-backup-if-mismatch -f -p1 -b --suffix .exclude_tests --fuzz=0 patching file tests/test_cases.cfg Patch #2 (apbs-python311.patch): + echo 'Patch #2 (apbs-python311.patch):' + /usr/bin/patch --no-backup-if-mismatch -f -p1 -b --suffix .python311 --fuzz=0 patching file tools/manip/inputgen.py Patch #3 (apbs-c99.patch): + echo 'Patch #3 (apbs-c99.patch):' + /usr/bin/patch --no-backup-if-mismatch -f -p1 --fuzz=0 patching file contrib/iapbs/src/apbs_driver.c + cp -p contrib/iapbs/COPYING contrib/iapbs/iapbs-COPYING + cp -p /builddir/build/SOURCES/apbs-LGPL_V2 contrib/iapbs/iapbs-LGPLv2 + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.8hWxzL + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd apbs-3.0.0 + export 'CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fopenmp -lm' + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fopenmp -lm' + export 'CXXFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fopenmp -lm' + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fopenmp -lm' + mkdir -p build + cmake -S . -B build -DCMAKE_BUILD_TYPE:STRING=Release -DENABLE_iAPBS:BOOL=ON -DENABLE_OPENMP:BOOL=ON -DENABLE_VERBOSE_DEBUG:BOOL=OFF -DENABLE_FETK:BOOL=OFF '-DCMAKE_C_FLAGS:STRING=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fopenmp -lm -DNDEBUG' '-DCMAKE_CXX_FLAGS:STRING=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fopenmp -lm -DNDEBUG' -DBUILD_SHARED_LIBS:BOOL=OFF -DENABLE_PYTHON:BOOL=ON -DBUILD_DOC:BOOL=ON -DBUILD_TESTING:BOOL=ON -DENABLE_TESTS:BOOL=ON -DCMAKE_INSTALL_PREFIX:PATH=/usr -DINCLUDE_INSTALL_DIR:PATH=/usr/include -DLIB_INSTALL_DIR:PATH=/usr/lib64 -DSHARE_INSTALL_PREFIX:PATH=/usr/share CMake Deprecation Warning at CMakeLists.txt:11 (cmake_policy): The OLD behavior for policy CMP0054 will be removed from a future version of CMake. The cmake-policies(7) manual explains that the OLD behaviors of all policies are deprecated and that a policy should be set to OLD only under specific short-term circumstances. Projects should be ported to the NEW behavior and not rely on setting a policy to OLD. -- The C compiler identification is GNU 13.2.1 -- The CXX compiler identification is GNU 13.2.1 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Setting project paths -- Setting lookup paths for headers and libraries -- Computing machine epsilon values -- Floating point epsilon is 2.220446e-16 -- Double precision epsilon is 2.220446e-16 -- Looking for time -- Looking for time - found -- Looking for rand -- Looking for rand - found -- Looking for srand -- Looking for srand - found -- Inline functions enabled -- Checking for OpenMP -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- OpenMP support enabled CMake Deprecation Warning at src/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Adding apbs_generic -- With source files nosh.c;mgparm.c;femparm.c;pbamparm.c;pbsamparm.c;pbeparm.c;bemparm.c;geoflowparm.c;apolparm.c;vacc.c;valist.c;vatom.c;vpbe.c;vcap.c;vclist.c;vstring.c;vparam.c;vgreen.c -- With external header files nosh.h;mgparm.h;femparm.h;pbamparm.h;pbsamparm.h;pbeparm.h;bemparm.h;geoflowparm.h;apolparm.h;vacc.h;valist.h;vatom.h;vpbe.h;vcap.h;vclist.h;vstring.h;vparam.h;vgreen.h;vmatrix.h;vhal.h;vunit.h -- With internal header files -- With library dependencies m;stdc++;maloc;-fopenmp -- Added apbs_generic -- Adding apbs_pmgc -- With source files buildAd.c;buildBd.c;buildGd.c;buildPd.c;cgd.c;gsd.c;matvecd.c;mgcsd.c;mgdrvd.c;mgsubd.c;mikpckd.c;mlinpckd.c;mypdec.c;newtond.c;newdrvd.c;powerd.c;smoothd.c;mgfasd.c -- With external header files buildAd.h;buildBd.h;buildGd.h;buildPd.h;cgd.h;gsd.h;matvecd.h;mgcsd.h;mgdrvd.h;mgsubd.h;mikpckd.h;mlinpckd.h;mypdec.h;newtond.h;newdrvd.h;powerd.h;smoothd.h;mgfasd.h -- With internal header files -- With library dependencies m;stdc++;maloc;-fopenmp -- Added apbs_pmgc -- Adding apbs_mg -- With source files vgrid.c;vmgrid.c;vopot.c;vpmg.c;vpmgp.c -- With external header files vgrid.h;vmgrid.h;vopot.h;vpmg.h;vpmgp.h -- With internal header files -- With library dependencies m;stdc++;maloc;-fopenmp;apbs_generic;apbs_pmgc -- Added apbs_mg -- Adding apbs_routines -- With source files routines.c -- With external header files -- With internal header files -- With library dependencies m;stdc++;maloc;-fopenmp -- Added apbs_routines -- External Headers: -- -- APBS Libraries: m;stdc++;maloc;-fopenmp -- Internal Libraries: apbs_generic;apbs_pmgc;apbs_mg;apbs_routines -- -- -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fopenmp -lm -DNDEBUG -fPIC -- Building documentation enabled -- Found Doxygen: /usr/bin/doxygen (found version "1.9.7") found components: doxygen dot -- Supplemental tools enabled -- Building mesh -- libraries: apbs -- Building manip -- libraries: apbs CMake Deprecation Warning at tools/python/CMakeLists.txt:2 (CMAKE_POLICY): The OLD behavior for policy CMP0078 will be removed from a future version of CMake. The cmake-policies(7) manual explains that the OLD behaviors of all policies are deprecated and that a policy should be set to OLD only under specific short-term circumstances. Projects should be ported to the NEW behavior and not rely on setting a policy to OLD. CMake Deprecation Warning at tools/python/CMakeLists.txt:3 (CMAKE_POLICY): The OLD behavior for policy CMP0086 will be removed from a future version of CMake. The cmake-policies(7) manual explains that the OLD behaviors of all policies are deprecated and that a policy should be set to OLD only under specific short-term circumstances. Projects should be ported to the NEW behavior and not rely on setting a policy to OLD. -- Found SWIG: /usr/bin/swig (found version "4.1.1") -- Found Python3: /usr/bin/python3.12 (found version "3.12.1") found components: Interpreter Development Development.Module Development.Embed -- ******* Python3 FOUND -- ***** Python3 include path is: /usr/include/python3.12 -- ***** Python3 library path is: /usr/lib64/libpython3.12.so -- ***** Python3 library dir is: /usr/lib64 -- Building of iAPBS interface enabled -- Found Python3: /usr/bin/python3.12 (found version "3.12.1") found components: Interpreter -- ******* Python3 FOUND /usr/bin/python3.12 -- TEST born_test COMMAND /usr/bin/python3.12 /builddir/build/BUILD/apbs-3.0.0/tests/apbs_tester.py -c /builddir/build/BUILD/apbs-3.0.0/tests/test_cases.cfg -e /builddir/build/BUILD/apbs-3.0.0/build/apbs -t born -- TEST actin-dimer-auto_test COMMAND /usr/bin/python3.12 /builddir/build/BUILD/apbs-3.0.0/tests/apbs_tester.py -c /builddir/build/BUILD/apbs-3.0.0/tests/test_cases.cfg -e /builddir/build/BUILD/apbs-3.0.0/build/apbs -t actin-dimer-auto -- TEST actin-dimer-parallel_test COMMAND /usr/bin/python3.12 /builddir/build/BUILD/apbs-3.0.0/tests/apbs_tester.py -c /builddir/build/BUILD/apbs-3.0.0/tests/test_cases.cfg -e /builddir/build/BUILD/apbs-3.0.0/build/apbs -t actin-dimer-parallel -- TEST alkanes_test COMMAND /usr/bin/python3.12 /builddir/build/BUILD/apbs-3.0.0/tests/apbs_tester.py -c /builddir/build/BUILD/apbs-3.0.0/tests/test_cases.cfg -e /builddir/build/BUILD/apbs-3.0.0/build/apbs -t alkanes -- TEST FKBP_test COMMAND /usr/bin/python3.12 /builddir/build/BUILD/apbs-3.0.0/tests/apbs_tester.py -c /builddir/build/BUILD/apbs-3.0.0/tests/test_cases.cfg -e /builddir/build/BUILD/apbs-3.0.0/build/apbs -t FKBP -- TEST hca-bind_test COMMAND /usr/bin/python3.12 /builddir/build/BUILD/apbs-3.0.0/tests/apbs_tester.py -c /builddir/build/BUILD/apbs-3.0.0/tests/test_cases.cfg -e /builddir/build/BUILD/apbs-3.0.0/build/apbs -t hca-bind -- TEST ionize_test COMMAND /usr/bin/python3.12 /builddir/build/BUILD/apbs-3.0.0/tests/apbs_tester.py -c /builddir/build/BUILD/apbs-3.0.0/tests/test_cases.cfg -e /builddir/build/BUILD/apbs-3.0.0/build/apbs -t ionize -- TEST ion-pmf_test COMMAND /usr/bin/python3.12 /builddir/build/BUILD/apbs-3.0.0/tests/apbs_tester.py -c /builddir/build/BUILD/apbs-3.0.0/tests/test_cases.cfg -e /builddir/build/BUILD/apbs-3.0.0/build/apbs -t ion-pmf -- TEST ion-protein_test COMMAND /usr/bin/python3.12 /builddir/build/BUILD/apbs-3.0.0/tests/apbs_tester.py -c /builddir/build/BUILD/apbs-3.0.0/tests/test_cases.cfg -e /builddir/build/BUILD/apbs-3.0.0/build/apbs -t ion-protein -- TEST pka-lig_test COMMAND /usr/bin/python3.12 /builddir/build/BUILD/apbs-3.0.0/tests/apbs_tester.py -c /builddir/build/BUILD/apbs-3.0.0/tests/test_cases.cfg -e /builddir/build/BUILD/apbs-3.0.0/build/apbs -t pka-lig -- TEST point-pmf_test COMMAND /usr/bin/python3.12 /builddir/build/BUILD/apbs-3.0.0/tests/apbs_tester.py -c /builddir/build/BUILD/apbs-3.0.0/tests/test_cases.cfg -e /builddir/build/BUILD/apbs-3.0.0/build/apbs -t point-pmf -- TEST solv_test COMMAND /usr/bin/python3.12 /builddir/build/BUILD/apbs-3.0.0/tests/apbs_tester.py -c /builddir/build/BUILD/apbs-3.0.0/tests/test_cases.cfg -e /builddir/build/BUILD/apbs-3.0.0/build/apbs -t solv -- Configuring done (2.1s) -- Generating done (0.0s) -- Build files have been written to: /builddir/build/BUILD/apbs-3.0.0/build + make -O -j1 V=1 -C build make: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 1%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vgrid.c.o /builddir/build/BUILD/apbs-3.0.0/src/mg/vgrid.c: In function ‘Vgrid_readDXBIN’: /builddir/build/BUILD/apbs-3.0.0/src/mg/vgrid.c:816:13: warning: variable ‘isBinary’ set but not used [-Wunused-but-set-variable] 816 | int isBinary = 0; | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vgrid.c:813:25: warning: unused variable ‘itmp’ [-Wunused-variable] 813 | size_t i, j, k, itmp, u; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vgrid.c: In function ‘Vgrid_writeUHBD’: /builddir/build/BUILD/apbs-3.0.0/src/mg/vgrid.c:1697:36: warning: variable ‘hy’ set but not used [-Wunused-but-set-variable] 1697 | double xmin, ymin, zmin, hzed, hy, hx; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vgrid.c:1697:30: warning: variable ‘hzed’ set but not used [-Wunused-but-set-variable] 1697 | double xmin, ymin, zmin, hzed, hy, hx; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vgrid.c: In function ‘Vgrid_readDXBIN’: /builddir/build/BUILD/apbs-3.0.0/src/mg/vgrid.c:853:17: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 853 | fgets(tok, VMAX_BUFSIZE, fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vgrid.c:831:17: warning: argument 1 null where non-null expected [-Wnonnull] 831 | fclose(fd); | ^~~~~~~~~~ In file included from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /builddir/build/BUILD/apbs-3.0.0/src/mg/vgrid.h:67, from /builddir/build/BUILD/apbs-3.0.0/src/mg/vgrid.c:57: /usr/include/stdio.h:183:12: note: in a call to function ‘fclose’ declared ‘nonnull’ 183 | extern int fclose (FILE *__stream) __nonnull ((1)); | ^~~~~~ [ 2%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vmgrid.c.o /builddir/build/BUILD/apbs-3.0.0/src/mg/vmgrid.c: In function ‘Vmgrid_addGrid’: /builddir/build/BUILD/apbs-3.0.0/src/mg/vmgrid.c:198:12: warning: unused variable ‘tgrad’ [-Wunused-variable] 198 | double tgrad[3]; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vmgrid.c:197:15: warning: unused variable ‘rc’ [-Wunused-variable] 197 | int i, j, rc; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vmgrid.c:197:12: warning: unused variable ‘j’ [-Wunused-variable] 197 | int i, j, rc; | ^ /builddir/build/BUILD/apbs-3.0.0/src/mg/vmgrid.c:197:9: warning: unused variable ‘i’ [-Wunused-variable] 197 | int i, j, rc; | ^ [ 3%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vopot.c.o /builddir/build/BUILD/apbs-3.0.0/src/mg/vopot.c: In function ‘Vopot_curvature’: /builddir/build/BUILD/apbs-3.0.0/src/mg/vopot.c:219:26: warning: variable ‘eps_w’ set but not used [-Wunused-but-set-variable] 219 | double u, T, charge, eps_w, xkappa, dist, size, val, *position, zkappa2; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vopot.c:219:18: warning: variable ‘charge’ set but not used [-Wunused-but-set-variable] 219 | double u, T, charge, eps_w, xkappa, dist, size, val, *position, zkappa2; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vopot.c:219:15: warning: variable ‘T’ set but not used [-Wunused-but-set-variable] 219 | double u, T, charge, eps_w, xkappa, dist, size, val, *position, zkappa2; | ^ [ 4%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vpmg.c.o /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function ‘Vpmg_ctor2’: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:157:61: warning: variable ‘zkappa2’ set but not used [-Wunused-but-set-variable] 157 | double ionConc[MAXION], ionQ[MAXION], ionRadii[MAXION], zkappa2, zks2; | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function ‘Vpmg_qmEnergySMPBE’: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:1503:12: warning: variable ‘zks2’ set but not used [-Wunused-but-set-variable] 1503 | zks2; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function ‘Vpmg_qfEnergyPoint’: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:1712:13: warning: variable ‘pvec’ set but not used [-Wunused-but-set-variable] 1712 | double *pvec; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:1709:24: warning: variable ‘zmax’ set but not used [-Wunused-but-set-variable] 1709 | double xmax, ymax, zmax, xmin, ymin, zmin, hx, hy, hzed, ifloat, jfloat; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:1709:18: warning: variable ‘ymax’ set but not used [-Wunused-but-set-variable] 1709 | double xmax, ymax, zmax, xmin, ymin, zmin, hx, hy, hzed, ifloat, jfloat; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:1709:12: warning: variable ‘xmax’ set but not used [-Wunused-but-set-variable] 1709 | double xmax, ymax, zmax, xmin, ymin, zmin, hx, hy, hzed, ifloat, jfloat; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function ‘Vpmg_qfAtomEnergy’: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:1794:36: warning: variable ‘zmax’ set but not used [-Wunused-but-set-variable] 1794 | double xmax, xmin, ymax, ymin, zmax, zmin, hx, hy, hzed, ifloat, jfloat; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:1794:24: warning: variable ‘ymax’ set but not used [-Wunused-but-set-variable] 1794 | double xmax, xmin, ymax, ymin, zmax, zmin, hx, hy, hzed, ifloat, jfloat; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:1794:12: warning: variable ‘xmax’ set but not used [-Wunused-but-set-variable] 1794 | double xmax, xmin, ymax, ymin, zmax, zmin, hx, hy, hzed, ifloat, jfloat; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function ‘focusFillBound’: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:1953:12: warning: variable ‘charge’ set but not used [-Wunused-but-set-variable] 1953 | charge, | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:1952:13: warning: variable ‘apos’ set but not used [-Wunused-but-set-variable] 1952 | *apos, | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:1951:12: warning: variable ‘size’ set but not used [-Wunused-but-set-variable] 1951 | size, | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:1950:12: warning: variable ‘xkappa’ set but not used [-Wunused-but-set-variable] 1950 | xkappa, | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function ‘bcfl2’: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:2668:40: warning: variable ‘qzy’ set but not used [-Wunused-but-set-variable] 2668 | double qxx,qxy,qxz,qyx,qyy,qyz,qzx,qzy,qzz; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:2668:36: warning: variable ‘qzx’ set but not used [-Wunused-but-set-variable] 2668 | double qxx,qxy,qxz,qyx,qyy,qyz,qzx,qzy,qzz; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:2668:24: warning: variable ‘qyx’ set but not used [-Wunused-but-set-variable] 2668 | double qxx,qxy,qxz,qyx,qyy,qyz,qzx,qzy,qzz; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function ‘bcCalcOrig’: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:2832:34: warning: unused variable ‘debye’ [-Wunused-variable] 2832 | double *dipole, *quadrupole, debye, eps_p; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:2832:22: warning: variable ‘quadrupole’ set but not used [-Wunused-but-set-variable] 2832 | double *dipole, *quadrupole, debye, eps_p; | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:2832:13: warning: variable ‘dipole’ set but not used [-Wunused-but-set-variable] 2832 | double *dipole, *quadrupole, debye, eps_p; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function ‘bcflnew’: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3415:31: warning: variable ‘eps_p’ set but not used [-Wunused-but-set-variable] 3415 | double dist, pre1, eps_w, eps_p, T, xkappa; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3410:29: warning: unused variable ‘z1’ [-Wunused-variable] 3410 | int x0, x1, y0, y1, z0, z1; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3410:25: warning: unused variable ‘z0’ [-Wunused-variable] 3410 | int x0, x1, y0, y1, z0, z1; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3410:21: warning: unused variable ‘y1’ [-Wunused-variable] 3410 | int x0, x1, y0, y1, z0, z1; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3410:17: warning: unused variable ‘y0’ [-Wunused-variable] 3410 | int x0, x1, y0, y1, z0, z1; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3410:13: warning: unused variable ‘x1’ [-Wunused-variable] 3410 | int x0, x1, y0, y1, z0, z1; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3410:9: warning: unused variable ‘x0’ [-Wunused-variable] 3410 | int x0, x1, y0, y1, z0, z1; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3409:13: warning: unused variable ‘k’ [-Wunused-variable] 3409 | int i,j,k, iatom, igrid; | ^ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3409:11: warning: unused variable ‘j’ [-Wunused-variable] 3409 | int i,j,k, iatom, igrid; | ^ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3409:9: warning: unused variable ‘i’ [-Wunused-variable] 3409 | int i,j,k, iatom, igrid; | ^ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function ‘multipolebc’: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3492:19: warning: variable ‘kr3’ set but not used [-Wunused-but-set-variable] 3492 | double kr,kr2,kr3; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function ‘bcfl_sdh’: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3608:40: warning: variable ‘qzy’ set but not used [-Wunused-but-set-variable] 3608 | double qxx,qxy,qxz,qyx,qyy,qyz,qzx,qzy,qzz; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3608:36: warning: variable ‘qzx’ set but not used [-Wunused-but-set-variable] 3608 | double qxx,qxy,qxz,qyx,qyy,qyz,qzx,qzy,qzz; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3608:24: warning: variable ‘qyx’ set but not used [-Wunused-but-set-variable] 3608 | double qxx,qxy,qxz,qyx,qyy,qyz,qzx,qzy,qzz; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3604:22: warning: unused variable ‘quadrupole’ [-Wunused-variable] 3604 | double *dipole, *quadrupole; | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3604:13: warning: unused variable ‘dipole’ [-Wunused-variable] 3604 | double *dipole, *quadrupole; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function ‘bcfl_mdh’: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3875:41: warning: variable ‘eps_p’ set but not used [-Wunused-but-set-variable] 3875 | double size, charge, xkappa, eps_w, eps_p, T, pre1, dist; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3874:22: warning: unused variable ‘quadrupole’ [-Wunused-variable] 3874 | double *dipole, *quadrupole; | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3874:13: warning: unused variable ‘dipole’ [-Wunused-variable] 3874 | double *dipole, *quadrupole; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function ‘bcfl_mem’: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:4008:24: warning: unused variable ‘edge_L’ [-Wunused-variable] 4008 | double A, B, C, D, edge_L, l; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:4007:38: warning: unused variable ‘z_shift’ [-Wunused-variable] 4007 | double dist, val, z_low, z_high, z_shift; | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:4007:12: warning: unused variable ‘dist’ [-Wunused-variable] 4007 | double dist, val, z_low, z_high, z_shift; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function ‘bcfl_map’: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:4177:38: warning: variable ‘hzed’ set but not used [-Wunused-but-set-variable] 4177 | double position[3], pot, hx, hy, hzed; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:4177:34: warning: variable ‘hy’ set but not used [-Wunused-but-set-variable] 4177 | double position[3], pot, hx, hy, hzed; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:4177:30: warning: variable ‘hx’ set but not used [-Wunused-but-set-variable] 4177 | double position[3], pot, hx, hy, hzed; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:4176:11: warning: unused variable ‘pbe’ [-Wunused-variable] 4176 | Vpbe *pbe; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function ‘fillcoCoefMap’: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:4492:46: warning: unused variable ‘pot’ [-Wunused-variable] 4492 | double ionstr, position[3], tkappa, eps, pot, hx, hy, hzed; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function ‘fillcoCoefMolIon’: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:4638:16: warning: variable ‘surfMeth’ set but not used [-Wunused-but-set-variable] 4638 | Vsurf_Meth surfMeth; | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:4630:11: warning: variable ‘acc’ set but not used [-Wunused-but-set-variable] 4630 | Vacc *acc; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function ‘fillcoCoefMolDielNoSmooth’: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:4746:30: warning: unused variable ‘deps’ [-Wunused-variable] 4746 | double srad, epsw, epsp, deps, area; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function ‘fillcoCoefSpline’: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:5031:47: warning: variable ‘rtot2’ set but not used [-Wunused-but-set-variable] 5031 | double dx2, dy2, dz2, stot2, itot2, rtot, rtot2, splineWin, w3i; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function ‘fillcoCharge’: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:5289:15: warning: unused variable ‘rc’ [-Wunused-variable] 5289 | Vrc_Codes rc; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function ‘fillcoChargeMap’: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:5346:49: warning: variable ‘hzed’ set but not used [-Wunused-but-set-variable] 5346 | double position[3], charge, zmagic, hx, hy, hzed; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:5346:45: warning: variable ‘hy’ set but not used [-Wunused-but-set-variable] 5346 | double position[3], charge, zmagic, hx, hy, hzed; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:5346:41: warning: variable ‘hx’ set but not used [-Wunused-but-set-variable] 5346 | double position[3], charge, zmagic, hx, hy, hzed; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function ‘Vpmg_force’: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:5829:12: warning: unused variable ‘npF’ [-Wunused-variable] 5829 | double npF[3]; /* Non-polar boundary force */ | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function ‘Vpmg_ibForce’: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:5854:24: warning: variable ‘zlen’ set but not used [-Wunused-but-set-variable] 5854 | double xlen, ylen, zlen, xmin, ymin, zmin, xmax, ymax, zmax, rtot2; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:5854:18: warning: variable ‘ylen’ set but not used [-Wunused-but-set-variable] 5854 | double xlen, ylen, zlen, xmin, ymin, zmin, xmax, ymax, zmax, rtot2; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:5854:12: warning: variable ‘xlen’ set but not used [-Wunused-but-set-variable] 5854 | double xlen, ylen, zlen, xmin, ymin, zmin, xmax, ymax, zmax, rtot2; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:5848:13: warning: variable ‘alist’ set but not used [-Wunused-but-set-variable] 5848 | Valist *alist; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function ‘Vpmg_dbForce’: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:6019:55: warning: variable ‘kT’ set but not used [-Wunused-but-set-variable] 6019 | double rtot, dx, gpos[3], tgrad[3], dbFmag, epsw, kT; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:6019:18: warning: variable ‘dx’ set but not used [-Wunused-but-set-variable] 6019 | double rtot, dx, gpos[3], tgrad[3], dbFmag, epsw, kT; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:6018:66: warning: variable ‘rtot2’ set but not used [-Wunused-but-set-variable] 6018 | double xlen, ylen, zlen, xmin, ymin, zmin, xmax, ymax, zmax, rtot2, epsp; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:6018:24: warning: variable ‘zlen’ set but not used [-Wunused-but-set-variable] 6018 | double xlen, ylen, zlen, xmin, ymin, zmin, xmax, ymax, zmax, rtot2, epsp; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:6018:18: warning: variable ‘ylen’ set but not used [-Wunused-but-set-variable] 6018 | double xlen, ylen, zlen, xmin, ymin, zmin, xmax, ymax, zmax, rtot2, epsp; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:6018:12: warning: variable ‘xlen’ set but not used [-Wunused-but-set-variable] 6018 | double xlen, ylen, zlen, xmin, ymin, zmin, xmax, ymax, zmax, rtot2, epsp; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function ‘qfForceSpline2’: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:6453:24: warning: variable ‘zlen’ set but not used [-Wunused-but-set-variable] 6453 | double xlen, ylen, zlen, xmin, ymin, zmin, xmax, ymax, zmax; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:6453:18: warning: variable ‘ylen’ set but not used [-Wunused-but-set-variable] 6453 | double xlen, ylen, zlen, xmin, ymin, zmin, xmax, ymax, zmax; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:6453:12: warning: variable ‘xlen’ set but not used [-Wunused-but-set-variable] 6453 | double xlen, ylen, zlen, xmin, ymin, zmin, xmax, ymax, zmax; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function ‘qfForceSpline4’: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:6576:15: warning: unused variable ‘k’ [-Wunused-variable] 6576 | int i, j, k, ii, jj, kk; | ^ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:6576:12: warning: unused variable ‘j’ [-Wunused-variable] 6576 | int i, j, k, ii, jj, kk; | ^ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:6568:24: warning: variable ‘zlen’ set but not used [-Wunused-but-set-variable] 6568 | double xlen, ylen, zlen, xmin, ymin, zmin, xmax, ymax, zmax; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:6568:18: warning: variable ‘ylen’ set but not used [-Wunused-but-set-variable] 6568 | double xlen, ylen, zlen, xmin, ymin, zmin, xmax, ymax, zmax; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:6568:12: warning: variable ‘xlen’ set but not used [-Wunused-but-set-variable] 6568 | double xlen, ylen, zlen, xmin, ymin, zmin, xmax, ymax, zmax; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function ‘markFrac’: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:6692:39: warning: variable ‘a000’ set but not used [-Wunused-but-set-variable] 6692 | double dx, dx2, dy, dy2, dz, dz2, a000, a001, a010, a100, r2; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function ‘zlapSolve’: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:6912:12: warning: unused variable ‘norm’ [-Wunused-variable] 6912 | double norm, coef, proj, eigx, eigy, eigz; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function ‘Vpmg_solveLaplace’: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7044:35: warning: variable ‘n’ set but not used [-Wunused-but-set-variable] 7044 | int i, j, k, ijk, nx, ny, nz, n, dilo, dihi, djlo, djhi, dklo, dkhi; | ^ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7044:18: warning: unused variable ‘ijk’ [-Wunused-variable] 7044 | int i, j, k, ijk, nx, ny, nz, n, dilo, dihi, djlo, djhi, dklo, dkhi; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function ‘fillcoPermanentMultipole’: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7263:58: warning: unused variable ‘mqzz’ [-Wunused-variable] 7263 | double debye,mc,mux,muy,muz,mqxx,mqyx,mqyy,mqzx,mqzy,mqzz; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7263:53: warning: unused variable ‘mqzy’ [-Wunused-variable] 7263 | double debye,mc,mux,muy,muz,mqxx,mqyx,mqyy,mqzx,mqzy,mqzz; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7263:48: warning: unused variable ‘mqzx’ [-Wunused-variable] 7263 | double debye,mc,mux,muy,muz,mqxx,mqyx,mqyy,mqzx,mqzy,mqzz; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7263:43: warning: unused variable ‘mqyy’ [-Wunused-variable] 7263 | double debye,mc,mux,muy,muz,mqxx,mqyx,mqyy,mqzx,mqzy,mqzz; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7263:38: warning: unused variable ‘mqyx’ [-Wunused-variable] 7263 | double debye,mc,mux,muy,muz,mqxx,mqyx,mqyy,mqzx,mqzy,mqzz; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7263:33: warning: unused variable ‘mqxx’ [-Wunused-variable] 7263 | double debye,mc,mux,muy,muz,mqxx,mqyx,mqyy,mqzx,mqzy,mqzz; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7263:29: warning: unused variable ‘muz’ [-Wunused-variable] 7263 | double debye,mc,mux,muy,muz,mqxx,mqyx,mqyy,mqzx,mqzy,mqzz; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7263:25: warning: unused variable ‘muy’ [-Wunused-variable] 7263 | double debye,mc,mux,muy,muz,mqxx,mqyx,mqyy,mqzx,mqzy,mqzz; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7263:21: warning: unused variable ‘mux’ [-Wunused-variable] 7263 | double debye,mc,mux,muy,muz,mqxx,mqyx,mqyy,mqzx,mqzy,mqzz; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7263:18: warning: unused variable ‘mc’ [-Wunused-variable] 7263 | double debye,mc,mux,muy,muz,mqxx,mqyx,mqyy,mqzx,mqzy,mqzz; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7263:12: warning: unused variable ‘debye’ [-Wunused-variable] 7263 | double debye,mc,mux,muy,muz,mqxx,mqyx,mqyy,mqzx,mqzy,mqzz; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7262:24: warning: unused variable ‘mr2’ [-Wunused-variable] 7262 | double mir,mjr,mkr,mr2; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7262:20: warning: unused variable ‘mkr’ [-Wunused-variable] 7262 | double mir,mjr,mkr,mr2; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7262:16: warning: unused variable ‘mjr’ [-Wunused-variable] 7262 | double mir,mjr,mkr,mr2; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7262:12: warning: unused variable ‘mir’ [-Wunused-variable] 7262 | double mir,mjr,mkr,mr2; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7258:9: warning: unused variable ‘i’ [-Wunused-variable] 7258 | int i, ii, jj, kk, nx, ny, nz, iatom; | ^ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7253:47: warning: unused variable ‘qave’ [-Wunused-variable] 7253 | double c,ux,uy,uz,qxx,qyx,qyy,qzx,qzy,qzz,qave; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7252:29: warning: unused variable ‘quad’ [-Wunused-variable] 7252 | double charge, *dipole,*quad; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7252:21: warning: unused variable ‘dipole’ [-Wunused-variable] 7252 | double charge, *dipole,*quad; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function ‘fillcoCoefSpline4’: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:9948:47: warning: variable ‘rtot2’ set but not used [-Wunused-but-set-variable] 9948 | double dx2, dy2, dz2, stot2, itot2, rtot, rtot2, splineWin; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:9946:42: warning: unused variable ‘w2i’ [-Wunused-variable] 9946 | double irad, dx, dy, dz, epsw, epsp, w2i; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function ‘fillcoPermanentInduced’: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10278:9: warning: unused variable ‘i’ [-Wunused-variable] 10278 | int i, ii, jj, kk, nx, ny, nz, iatom; | ^ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10273:47: warning: unused variable ‘qave’ [-Wunused-variable] 10273 | double c,ux,uy,uz,qxx,qyx,qyy,qzx,qzy,qzz,qave; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10272:29: warning: unused variable ‘quad’ [-Wunused-variable] 10272 | double charge, *dipole,*quad; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10272:21: warning: unused variable ‘dipole’ [-Wunused-variable] 10272 | double charge, *dipole,*quad; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function ‘fillcoCoefSpline3’: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10441:27: warning: variable ‘e5’ set but not used [-Wunused-but-set-variable] 10441 | double e, e2, e3, e4, e5; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10439:47: warning: variable ‘rtot2’ set but not used [-Wunused-but-set-variable] 10439 | double dx2, dy2, dz2, stot2, itot2, rtot, rtot2, splineWin; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10437:42: warning: unused variable ‘w2i’ [-Wunused-variable] 10437 | double irad, dx, dy, dz, epsw, epsp, w2i; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function ‘bcolcomp’: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10746:55: warning: variable ‘mxlv’ set but not used [-Wunused-but-set-variable] 10746 | int nrwk, niwk, nx, ny, nz, nlev, ierror, maxlev, mxlv; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10746:47: warning: unused variable ‘maxlev’ [-Wunused-variable] 10746 | int nrwk, niwk, nx, ny, nz, nlev, ierror, maxlev, mxlv; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10746:39: warning: unused variable ‘ierror’ [-Wunused-variable] 10746 | int nrwk, niwk, nx, ny, nz, nlev, ierror, maxlev, mxlv; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10746:15: warning: variable ‘niwk’ set but not used [-Wunused-but-set-variable] 10746 | int nrwk, niwk, nx, ny, nz, nlev, ierror, maxlev, mxlv; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10746:9: warning: variable ‘nrwk’ set but not used [-Wunused-but-set-variable] 10746 | int nrwk, niwk, nx, ny, nz, nlev, ierror, maxlev, mxlv; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10743:29: warning: unused variable ‘i’ [-Wunused-variable] 10743 | int nrow, ncol, nnzero, i; | ^ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10743:21: warning: unused variable ‘nnzero’ [-Wunused-variable] 10743 | int nrow, ncol, nnzero, i; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10743:15: warning: unused variable ‘ncol’ [-Wunused-variable] 10743 | int nrow, ncol, nnzero, i; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10743:9: warning: unused variable ‘nrow’ [-Wunused-variable] 10743 | int nrow, ncol, nnzero, i; | ^~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:93, from /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:73: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function ‘bcolcomp2’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_iz’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10804:5: note: in expansion of macro ‘MAT2’ 10804 | MAT2(iz, 50, nlev); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function ‘bcolcomp3’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_ac’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10836:5: note: in expansion of macro ‘MAT2’ 10836 | MAT2(ac, *nx * *ny * *nz, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function ‘bcolcomp4’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10874:5: note: in expansion of macro ‘MAT3’ 10874 | MAT3(oC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_cc’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10873:5: note: in expansion of macro ‘MAT3’ 10873 | MAT3(cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10872:5: note: in expansion of macro ‘MAT3’ 10872 | MAT3(uC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10871:5: note: in expansion of macro ‘MAT3’ 10871 | MAT3(oN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10870:5: note: in expansion of macro ‘MAT3’ 10870 | MAT3(oE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10866:27: warning: variable ‘nrow’ set but not used [-Wunused-but-set-variable] 10866 | int inonz, iirow, nn, nrow, ncol, nonz, irow, n; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h: At top level: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: ‘fillcoInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: ‘fillcoNLInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7229:16: warning: ‘d3bspline4’ defined but not used [-Wunused-function] 7229 | VPUBLIC double d3bspline4(double x) { | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:6684:15: warning: ‘markFrac’ defined but not used [-Wunused-function] 6684 | VPRIVATE void markFrac( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3868:15: warning: ‘bcfl_mdh’ defined but not used [-Wunused-function] 3868 | VPRIVATE void bcfl_mdh(Vpmg *thee){ | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:2828:15: warning: ‘bcCalcOrig’ defined but not used [-Wunused-function] 2828 | VPRIVATE void bcCalcOrig(Vpmg *thee) { | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:2547:17: warning: ‘bcfl1sp’ defined but not used [-Wunused-function] 2547 | VPRIVATE double bcfl1sp(double size, double *apos, double charge, | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:1148:17: warning: ‘Vpmg_polarizEnergy’ defined but not used [-Wunused-function] 1148 | VPRIVATE double Vpmg_polarizEnergy(Vpmg *thee, | ^~~~~~~~~~~~~~~~~~ [ 5%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vpmgp.c.o /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmgp.c: In function ‘Vpmgp_size’: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmgp.c:204:87: warning: unused variable ‘iretot’ [-Wunused-variable] 204 | int nxf, nyf, nzf, level, num_nf_oper, num_narrc_oper, n_band, nc_band, num_band, iretot; | ^~~~~~ [ 5%] Built target apbs_mg [ 6%] Building C object src/generic/CMakeFiles/apbs_generic.dir/nosh.c.o /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c: In function ‘NOsh_setupCalcGEOFLOWMANUAL’: /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:2683:15: warning: variable ‘apolparm’ set but not used [-Wunused-but-set-variable] 2683 | APOLparm *apolparm = VNULL; | ^~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:57: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h: At top level: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: ‘GEOFLOWparm_parseVDW’ declared ‘static’ but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: ‘GEOFLOWparm_parseETOL’ declared ‘static’ but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: ‘PBAMparm_parseSalt’ declared ‘static’ but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: ‘PBAMparm_parseRunType’ declared ‘static’ but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: ‘PBAMparm_parseRunName’ declared ‘static’ but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: ‘PBAMparm_parseRandorient’ declared ‘static’ but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: ‘PBAMparm_parsePBCS’ declared ‘static’ but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: ‘PBAMparm_parseUnits’ declared ‘static’ but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: ‘PBAMparm_parse3Dmap’ declared ‘static’ but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: ‘PBAMparm_parseGrid2D’ declared ‘static’ but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: ‘PBAMparm_parseDX’ declared ‘static’ but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: ‘PBAMparm_parseGridPts’ declared ‘static’ but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: ‘PBAMparm_parseTermcombine’ declared ‘static’ but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: ‘PBAMparm_parseDiff’ declared ‘static’ but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: ‘PBAMparm_parseXYZ’ declared ‘static’ but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: ‘PBSAMparm_parseTolsp’ declared ‘static’ but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: ‘PBSAMparm_parseSurf’ declared ‘static’ but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: ‘PBSAMparm_parseImat’ declared ‘static’ but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: ‘PBSAMparm_parseExp’ declared ‘static’ but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: ‘PBSAMparm_parseMSMS’ declared ‘static’ but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c: In function ‘NOsh_parsePBAM’: /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:3139:17: warning: ‘strncpy’ specified bound 1000 equals destination size [-Wstringop-truncation] 3139 | strncpy(parm->dxname, pbeparm->writestem[pbeparm->numwrite -1], CHR_MAXLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c: In function ‘NOsh_parsePBSAM’: /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:3268:17: warning: ‘strncpy’ specified bound 1000 equals destination size [-Wstringop-truncation] 3268 | strncpy(parm->dxname, pbeparm->writestem[pbeparm->numwrite - 1], CHR_MAXLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c: In function ‘NOsh_parseInput’: /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:1348:13: warning: ‘strncpy’ output may be truncated copying 1024 bytes from a string of length 8191 [-Wstringop-truncation] 1348 | strncpy(thee->apolname[thee->napol], tok, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:1222:13: warning: ‘__strncpy_chk’ output may be truncated copying 1024 bytes from a string of length 8191 [-Wstringop-truncation] 1222 | strncpy(thee->elecname[thee->nelec], tok, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:953:9: warning: ‘__strncpy_chk’ output may be truncated copying 1024 bytes from a string of length 8191 [-Wstringop-truncation] 953 | strncpy(thee->meshpath[thee->nmesh], tok, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:918:5: warning: ‘__strncpy_chk’ output may be truncated copying 1024 bytes from a string of length 8191 [-Wstringop-truncation] 918 | strncpy(thee->chargepath[thee->ncharge], tok, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:872:5: warning: ‘__strncpy_chk’ output may be truncated copying 1024 bytes from a string of length 8191 [-Wstringop-truncation] 872 | strncpy(thee->potpath[thee->npot], tok, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:827:5: warning: ‘__strncpy_chk’ output may be truncated copying 1024 bytes from a string of length 8191 [-Wstringop-truncation] 827 | strncpy(thee->kappapath[thee->nkappa], tok, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:772:5: warning: ‘__strncpy_chk’ output may be truncated copying 1024 bytes from a string of length 8191 [-Wstringop-truncation] 772 | strncpy(thee->dielXpath[thee->ndiel], tok, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:776:5: warning: ‘__strncpy_chk’ output may be truncated copying 1024 bytes from a string of length 8191 [-Wstringop-truncation] 776 | strncpy(thee->dielYpath[thee->ndiel], tok, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:780:5: warning: ‘__strncpy_chk’ output may be truncated copying 1024 bytes from a string of length 8191 [-Wstringop-truncation] 780 | strncpy(thee->dielZpath[thee->ndiel], tok, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:723:13: warning: ‘strncpy’ output may be truncated copying 1024 bytes from a string of length 8191 [-Wstringop-truncation] 723 | strncpy(thee->parmpath, tok, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:701:13: warning: ‘strncpy’ output may be truncated copying 1024 bytes from a string of length 8191 [-Wstringop-truncation] 701 | strncpy(thee->parmpath, tok, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:659:9: warning: ‘__strncpy_chk’ output may be truncated copying 1024 bytes from a string of length 8191 [-Wstringop-truncation] 659 | strncpy(thee->molpath[thee->nmol], tok, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:640:9: warning: ‘__strncpy_chk’ output may be truncated copying 1024 bytes from a string of length 8191 [-Wstringop-truncation] 640 | strncpy(thee->molpath[thee->nmol], tok, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:621:9: warning: ‘__strncpy_chk’ output may be truncated copying 1024 bytes from a string of length 8191 [-Wstringop-truncation] 621 | strncpy(thee->molpath[thee->nmol], tok, VMAX_ARGLEN); | ^ [ 8%] Building C object src/generic/CMakeFiles/apbs_generic.dir/mgparm.c.o [ 9%] Building C object src/generic/CMakeFiles/apbs_generic.dir/femparm.c.o [ 10%] Building C object src/generic/CMakeFiles/apbs_generic.dir/pbamparm.c.o /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c: In function ‘PBAMparm_parseRandorient’: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c:305:17: warning: unused variable ‘name’ [-Wunused-variable] 305 | const char* name = "randorient"; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c: In function ‘PBAMparm_parse3Dmap’: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c:373:10: warning: unused variable ‘tok’ [-Wunused-variable] 373 | char tok[VMAX_BUFSIZE]; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c:372:17: warning: unused variable ‘name’ [-Wunused-variable] 372 | const char* name = "3dmap"; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c: In function ‘PBAMparm_parseRunType’: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c:282:7: warning: ‘strncpy’ output may be truncated copying 1000 bytes from a string of length 8191 [-Wstringop-truncation] 282 | strncpy(thee->runtype, tok, CHR_MAXLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c: In function ‘PBAMparm_parseRunName’: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c:297:7: warning: ‘strncpy’ output may be truncated copying 1000 bytes from a string of length 8191 [-Wstringop-truncation] 297 | strncpy(thee->runname, tok, CHR_MAXLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c: In function ‘PBAMparm_parseUnits’: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c:344:7: warning: ‘strncpy’ output may be truncated copying 1000 bytes from a string of length 8191 [-Wstringop-truncation] 344 | strncpy(thee->units, tok, CHR_MAXLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c: In function ‘PBAMparm_parseTermcombine’: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c:452:7: warning: ‘strncpy’ output may be truncated copying 1000 bytes from a string of length 8191 [-Wstringop-truncation] 452 | strncpy(thee->termcombine, tok, CHR_MAXLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c: In function ‘PBAMparm_parseGrid2D’: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c:400:7: warning: ‘__strncpy_chk’ output may be truncated copying 1000 bytes from a string of length 8191 [-Wstringop-truncation] 400 | strncpy(thee->grid2Dname[thee->grid2Dct], tok, CHR_MAXLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c:408:7: warning: ‘__strncpy_chk’ output may be truncated copying 1000 bytes from a string of length 8191 [-Wstringop-truncation] 408 | strncpy(thee->grid2Dax[thee->grid2Dct], tok, CHR_MAXLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c: In function ‘PBAMparm_parseXYZ’: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c:656:8: warning: ‘__strncpy_chk’ output may be truncated copying 1000 bytes from a string of length 8191 [-Wstringop-truncation] 656 | strncpy(thee->xyzfil[mol][thee->xyzct[mol]], tok, CHR_MAXLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c: In function ‘PBAMparm_parseDiff’: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c:500:8: warning: ‘__strncpy_chk’ output may be truncated copying 1000 bytes from a string of length 8191 [-Wstringop-truncation] 500 | strncpy(thee->moveType[molind], tok, CHR_MAXLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c: In function ‘PBAMparm_parseTerm’: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c:563:12: warning: ‘__strncpy_chk’ output may be truncated copying 1000 bytes from a string of length 8191 [-Wstringop-truncation] 563 | strncpy(thee->termnam[thee->termct], tok, CHR_MAXLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c:573:11: warning: ‘__strncpy_chk’ output may be truncated copying 1000 bytes from a string of length 8191 [-Wstringop-truncation] 573 | strncpy(thee->confil[thee->confilct], tok, CHR_MAXLEN); | ^ [ 11%] Building C object src/generic/CMakeFiles/apbs_generic.dir/pbsamparm.c.o /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.c: In function ‘PBSAMparm_ctor2’: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.c:79:9: warning: unused variable ‘i’ [-Wunused-variable] 79 | int i; | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.c: In function ‘PBSAMparm_parseMSMS’: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.c:183:13: warning: unused variable ‘td’ [-Wunused-variable] 183 | int td; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.c: In function ‘PBSAMparm_parseSurf’: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.c:174:8: warning: ‘__strncpy_chk’ output may be truncated copying 1000 bytes from a string of length 8191 [-Wstringop-truncation] 174 | strncpy(thee->surffil[thee->surfct], tok, CHR_MAXLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.c: In function ‘PBSAMparm_parseImat’: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.c:211:8: warning: ‘__strncpy_chk’ output may be truncated copying 1000 bytes from a string of length 8191 [-Wstringop-truncation] 211 | strncpy(thee->imatfil[thee->imatct], tok, CHR_MAXLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.c: In function ‘PBSAMparm_parseExp’: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.c:226:8: warning: ‘strncpy’ output may be truncated copying 1000 bytes from a string of length 8191 [-Wstringop-truncation] 226 | strncpy(thee->expfil[thee->expct], tok, CHR_MAXLEN); | ^ [ 12%] Building C object src/generic/CMakeFiles/apbs_generic.dir/pbeparm.c.o /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c: In function ‘PBEparm_parseWRITE’: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:1163:9: warning: ‘__strncpy_chk’ output may be truncated copying 1024 bytes from a string of length 8191 [-Wstringop-truncation] 1163 | strncpy(thee->writestem[thee->numwrite], tok, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c: In function ‘PBEparm_parseWRITEMAT’: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:1204:5: warning: ‘strncpy’ output may be truncated copying 1024 bytes from a string of length 8191 [-Wstringop-truncation] 1204 | strncpy(thee->writematstem, tok, VMAX_ARGLEN); | ^ [ 13%] Building C object src/generic/CMakeFiles/apbs_generic.dir/bemparm.c.o /builddir/build/BUILD/apbs-3.0.0/src/generic/bemparm.c: In function ‘BEMparm_ctor2’: /builddir/build/BUILD/apbs-3.0.0/src/generic/bemparm.c:79:9: warning: unused variable ‘i’ [-Wunused-variable] 79 | int i; | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/bemparm.c: In function ‘BEMparm_check’: /builddir/build/BUILD/apbs-3.0.0/src/generic/bemparm.c:127:36: warning: unused variable ‘nlev’ [-Wunused-variable] 127 | int i, tdime[3], ti, tnlev[3], nlev; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/bemparm.c:127:26: warning: unused variable ‘tnlev’ [-Wunused-variable] 127 | int i, tdime[3], ti, tnlev[3], nlev; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/bemparm.c:127:22: warning: unused variable ‘ti’ [-Wunused-variable] 127 | int i, tdime[3], ti, tnlev[3], nlev; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/generic/bemparm.c:127:12: warning: unused variable ‘tdime’ [-Wunused-variable] 127 | int i, tdime[3], ti, tnlev[3], nlev; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/bemparm.c:127:9: warning: unused variable ‘i’ [-Wunused-variable] 127 | int i, tdime[3], ti, tnlev[3], nlev; | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/bemparm.c: In function ‘BEMparm_copy’: /builddir/build/BUILD/apbs-3.0.0/src/generic/bemparm.c:176:9: warning: unused variable ‘i’ [-Wunused-variable] 176 | int i; | ^ [ 14%] Building C object src/generic/CMakeFiles/apbs_generic.dir/geoflowparm.c.o /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.c: In function ‘GEOFLOWparm_ctor2’: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.c:79:9: warning: unused variable ‘i’ [-Wunused-variable] 79 | int i; | ^ [ 16%] Building C object src/generic/CMakeFiles/apbs_generic.dir/apolparm.c.o [ 17%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vacc.c.o /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c: In function ‘VaccSurf_dtor’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:841:11: warning: variable ‘mem’ set but not used [-Wunused-but-set-variable] 841 | Vmem *mem; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c: In function ‘Vacc_splineAccGradAtomNorm3’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:1104:27: warning: variable ‘e5’ set but not used [-Wunused-but-set-variable] 1104 | double e, e2, e3, e4, e5; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c: In function ‘Vacc_atomdSASA’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:1338:12: warning: variable ‘ts’ set but not used [-Wunused-but-set-variable] 1338 | time_t ts; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:1335:15: warning: variable ‘ref’ set but not used [-Wunused-but-set-variable] 1335 | VaccSurf *ref; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c: In function ‘Vacc_totalAtomdSASA’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:1395:15: warning: variable ‘ref’ set but not used [-Wunused-but-set-variable] 1395 | VaccSurf *ref; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:1392:23: warning: variable ‘tRad’ set but not used [-Wunused-but-set-variable] 1392 | double *temp_Pos, tRad; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:1391:9: warning: variable ‘iatom’ set but not used [-Wunused-but-set-variable] 1391 | int iatom; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c: In function ‘Vacc_totalAtomdSAV’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:1454:15: warning: variable ‘ref’ set but not used [-Wunused-but-set-variable] 1454 | VaccSurf *ref; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:1451:23: warning: variable ‘tRad’ set but not used [-Wunused-but-set-variable] 1451 | double *temp_Pos, tRad; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:1450:9: warning: variable ‘iatom’ set but not used [-Wunused-but-set-variable] 1450 | int iatom; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c: In function ‘Vacc_wcaEnergyAtom’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:1584:9: warning: variable ‘npts’ set but not used [-Wunused-but-set-variable] 1584 | int npts[3]; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c: In function ‘Vacc_wcaForceAtom’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:1807:12: warning: variable ‘ts’ set but not used [-Wunused-but-set-variable] 1807 | time_t ts; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:1764:9: warning: variable ‘npts’ set but not used [-Wunused-but-set-variable] 1764 | npts[3], | ^~~~ [ 18%] Building C object src/generic/CMakeFiles/apbs_generic.dir/valist.c.o /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c: In function ‘Valist_readPQR’: /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:618:10: warning: unused variable ‘chs’ [-Wunused-variable] 618 | char chs[VMAX_BUFSIZE]; | ^~~ [ 19%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vatom.c.o [ 20%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vpbe.c.o [ 21%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vcap.c.o [ 22%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vclist.c.o [ 24%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vstring.c.o [ 25%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vparam.c.o /builddir/build/BUILD/apbs-3.0.0/src/generic/vparam.c: In function ‘Vparam_readXMLFile’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vparam.c:412:22: warning: ‘natoms’ may be used uninitialized [-Wmaybe-uninitialized] 412 | for (i=0; ivmem, nalloc, sizeof(Vparam_AtomData), (void **)&(atoms)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vparam.c:309:26: note: ‘nalloc’ was declared here 309 | int i, ires, natoms, nalloc, ralloc; | ^~~~~~ [ 26%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vgreen.c.o /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c: In function ‘Vgreen_coulomb_direct’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:229:31: warning: unused variable ‘fz’ [-Wunused-variable] 229 | double *q, qtemp, fx, fy, fz; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:229:27: warning: unused variable ‘fy’ [-Wunused-variable] 229 | double *q, qtemp, fx, fy, fz; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:229:23: warning: unused variable ‘fx’ [-Wunused-variable] 229 | double *q, qtemp, fx, fy, fz; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:229:16: warning: unused variable ‘qtemp’ [-Wunused-variable] 229 | double *q, qtemp, fx, fy, fz; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:229:13: warning: unused variable ‘q’ [-Wunused-variable] 229 | double *q, qtemp, fx, fy, fz; | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c: In function ‘Vgreen_coulomb’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:264:9: warning: unused variable ‘iatom’ [-Wunused-variable] 264 | int iatom, ipos; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:263:31: warning: unused variable ‘fz’ [-Wunused-variable] 263 | double *q, qtemp, fx, fy, fz; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:263:27: warning: unused variable ‘fy’ [-Wunused-variable] 263 | double *q, qtemp, fx, fy, fz; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:263:23: warning: unused variable ‘fx’ [-Wunused-variable] 263 | double *q, qtemp, fx, fy, fz; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:263:16: warning: unused variable ‘qtemp’ [-Wunused-variable] 263 | double *q, qtemp, fx, fy, fz; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:263:13: warning: unused variable ‘q’ [-Wunused-variable] 263 | double *q, qtemp, fx, fy, fz; | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:262:45: warning: unused variable ‘scale’ [-Wunused-variable] 262 | double *apos, charge, dist, dx, dy, dz, scale; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:262:41: warning: unused variable ‘dz’ [-Wunused-variable] 262 | double *apos, charge, dist, dx, dy, dz, scale; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:262:37: warning: unused variable ‘dy’ [-Wunused-variable] 262 | double *apos, charge, dist, dx, dy, dz, scale; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:262:33: warning: unused variable ‘dx’ [-Wunused-variable] 262 | double *apos, charge, dist, dx, dy, dz, scale; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:262:27: warning: unused variable ‘dist’ [-Wunused-variable] 262 | double *apos, charge, dist, dx, dy, dz, scale; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:262:19: warning: unused variable ‘charge’ [-Wunused-variable] 262 | double *apos, charge, dist, dx, dy, dz, scale; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:262:13: warning: unused variable ‘apos’ [-Wunused-variable] 262 | double *apos, charge, dist, dx, dy, dz, scale; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:261:12: warning: unused variable ‘atom’ [-Wunused-variable] 261 | Vatom *atom; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c: In function ‘Vgreen_coulombD_direct’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:316:16: warning: unused variable ‘qtemp’ [-Wunused-variable] 316 | double *q, qtemp; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:316:13: warning: unused variable ‘q’ [-Wunused-variable] 316 | double *q, qtemp; | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c: In function ‘Vgreen_coulombD’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:368:9: warning: unused variable ‘iatom’ [-Wunused-variable] 368 | int iatom, ipos; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:367:16: warning: unused variable ‘qtemp’ [-Wunused-variable] 367 | double *q, qtemp; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:367:13: warning: unused variable ‘q’ [-Wunused-variable] 367 | double *q, qtemp; | ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:366:60: warning: unused variable ‘scale’ [-Wunused-variable] 366 | double *apos, charge, dist, dist2, idist3, dy, dz, dx, scale; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:366:56: warning: unused variable ‘dx’ [-Wunused-variable] 366 | double *apos, charge, dist, dist2, idist3, dy, dz, dx, scale; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:366:52: warning: unused variable ‘dz’ [-Wunused-variable] 366 | double *apos, charge, dist, dist2, idist3, dy, dz, dx, scale; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:366:48: warning: unused variable ‘dy’ [-Wunused-variable] 366 | double *apos, charge, dist, dist2, idist3, dy, dz, dx, scale; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:366:40: warning: unused variable ‘idist3’ [-Wunused-variable] 366 | double *apos, charge, dist, dist2, idist3, dy, dz, dx, scale; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:366:33: warning: unused variable ‘dist2’ [-Wunused-variable] 366 | double *apos, charge, dist, dist2, idist3, dy, dz, dx, scale; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:366:27: warning: unused variable ‘dist’ [-Wunused-variable] 366 | double *apos, charge, dist, dist2, idist3, dy, dz, dx, scale; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:366:19: warning: unused variable ‘charge’ [-Wunused-variable] 366 | double *apos, charge, dist, dist2, idist3, dy, dz, dx, scale; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:366:13: warning: unused variable ‘apos’ [-Wunused-variable] 366 | double *apos, charge, dist, dist2, idist3, dy, dz, dx, scale; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:365:12: warning: unused variable ‘atom’ [-Wunused-variable] 365 | Vatom *atom; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c: At top level: /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:525:14: warning: ‘treecalc’ defined but not used [-Wunused-function] 525 | VPRIVATE int treecalc(Vgreen *thee, double *xtar, double *ytar, double *ztar, | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:505:14: warning: ‘treecleanup’ defined but not used [-Wunused-function] 505 | VPRIVATE int treecleanup(Vgreen *thee) { | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:425:14: warning: ‘treesetup’ defined but not used [-Wunused-function] 425 | VPRIVATE int treesetup(Vgreen *thee) { | ^~~~~~~~~ [ 26%] Built target apbs_generic [ 27%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildAd.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.h:57, from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c:55: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c: In function ‘VbuildA’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_ac’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c:66:5: note: in expansion of macro ‘MAT2’ 66 | MAT2(ac, *nx * *ny * *nz, 14); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c: In function ‘VbuildA_fv’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_gzcf’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c:167:5: note: in expansion of macro ‘MAT3’ 167 | MAT3(gzcf, *nx, *ny, 2); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_gycf’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c:166:5: note: in expansion of macro ‘MAT3’ 166 | MAT3(gycf, *nx, *nz, 2); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_gxcf’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c:165:5: note: in expansion of macro ‘MAT3’ 165 | MAT3(gxcf, *ny, *nz, 2); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c:164:5: note: in expansion of macro ‘MAT3’ 164 | MAT3( oE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c:163:5: note: in expansion of macro ‘MAT3’ 163 | MAT3( oN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c:162:5: note: in expansion of macro ‘MAT3’ 162 | MAT3( uC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_a3cf’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c:161:5: note: in expansion of macro ‘MAT3’ 161 | MAT3(a3cf, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_a2cf’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c:160:5: note: in expansion of macro ‘MAT3’ 160 | MAT3(a2cf, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_a1cf’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c:159:5: note: in expansion of macro ‘MAT3’ 159 | MAT3(a1cf, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c:158:5: note: in expansion of macro ‘MAT3’ 158 | MAT3( oC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_ccf’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c:157:5: note: in expansion of macro ‘MAT3’ 157 | MAT3( ccf, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_cc’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c:156:5: note: in expansion of macro ‘MAT3’ 156 | MAT3( cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_fcf’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c:155:5: note: in expansion of macro ‘MAT3’ 155 | MAT3( fcf, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_fc’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c:154:5: note: in expansion of macro ‘MAT3’ 154 | MAT3( fc, *nx, *ny, *nz); | ^~~~ [ 28%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildBd.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.h:57, from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:55: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c: In function ‘Vbuildband’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_ac’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:65:5: note: in expansion of macro ‘MAT2’ 65 | MAT2(ac, *nx * *ny * *nz, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c: In function ‘Vbuildband1_7’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:133:5: note: in expansion of macro ‘MAT3’ 133 | MAT3(uC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:132:5: note: in expansion of macro ‘MAT3’ 132 | MAT3(oN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:131:5: note: in expansion of macro ‘MAT3’ 131 | MAT3(oE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:130:5: note: in expansion of macro ‘MAT3’ 130 | MAT3(oC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_acB’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:128:5: note: in expansion of macro ‘MAT2’ 128 | MAT2(acB, *lda, *ny-1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c: In function ‘Vbuildband1_27’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:213:5: note: in expansion of macro ‘MAT3’ 213 | MAT3(uSW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:212:5: note: in expansion of macro ‘MAT3’ 212 | MAT3(uSE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:211:5: note: in expansion of macro ‘MAT3’ 211 | MAT3(uNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:210:5: note: in expansion of macro ‘MAT3’ 210 | MAT3(uNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:208:5: note: in expansion of macro ‘MAT3’ 208 | MAT3( uS, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:207:5: note: in expansion of macro ‘MAT3’ 207 | MAT3( uN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:206:5: note: in expansion of macro ‘MAT3’ 206 | MAT3( uW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:205:5: note: in expansion of macro ‘MAT3’ 205 | MAT3( uE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:203:5: note: in expansion of macro ‘MAT3’ 203 | MAT3(oNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:202:5: note: in expansion of macro ‘MAT3’ 202 | MAT3(oNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:200:5: note: in expansion of macro ‘MAT3’ 200 | MAT3( uC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:199:5: note: in expansion of macro ‘MAT3’ 199 | MAT3( oN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:198:5: note: in expansion of macro ‘MAT3’ 198 | MAT3( oE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:197:5: note: in expansion of macro ‘MAT3’ 197 | MAT3( oC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_acB’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:195:5: note: in expansion of macro ‘MAT2’ 195 | MAT2(acB, *lda, *ny-1); | ^~~~ [ 29%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildGd.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.h:57, from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:55: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c: In function ‘VbuildG’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_ac’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:64:5: note: in expansion of macro ‘MAT2’ 64 | MAT2( ac, *nxc * *nyc * *nzc, 27); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_acFF’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:63:5: note: in expansion of macro ‘MAT2’ 63 | MAT2(acFF, *nxf * *nyf * *nzf, 27); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_pcFF’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:62:5: note: in expansion of macro ‘MAT2’ 62 | MAT2(pcFF, *nxc * *nyc * *nzc, 27); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c: In function ‘VbuildG_1’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:216:5: note: in expansion of macro ‘MAT3’ 216 | MAT3(dPSW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:215:5: note: in expansion of macro ‘MAT3’ 215 | MAT3(dPSE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:214:5: note: in expansion of macro ‘MAT3’ 214 | MAT3(dPNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:213:5: note: in expansion of macro ‘MAT3’ 213 | MAT3(dPNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:212:5: note: in expansion of macro ‘MAT3’ 212 | MAT3( dPW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:211:5: note: in expansion of macro ‘MAT3’ 211 | MAT3( dPE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:210:5: note: in expansion of macro ‘MAT3’ 210 | MAT3( dPS, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:209:5: note: in expansion of macro ‘MAT3’ 209 | MAT3( dPN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:208:5: note: in expansion of macro ‘MAT3’ 208 | MAT3( dPC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:206:5: note: in expansion of macro ‘MAT3’ 206 | MAT3(uPSW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:205:5: note: in expansion of macro ‘MAT3’ 205 | MAT3(uPSE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:204:5: note: in expansion of macro ‘MAT3’ 204 | MAT3(uPNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:203:5: note: in expansion of macro ‘MAT3’ 203 | MAT3(uPNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:202:5: note: in expansion of macro ‘MAT3’ 202 | MAT3( uPW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:201:5: note: in expansion of macro ‘MAT3’ 201 | MAT3( uPE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:200:5: note: in expansion of macro ‘MAT3’ 200 | MAT3( uPS, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:199:5: note: in expansion of macro ‘MAT3’ 199 | MAT3( uPN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:198:5: note: in expansion of macro ‘MAT3’ 198 | MAT3( uPC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:196:5: note: in expansion of macro ‘MAT3’ 196 | MAT3(oPSW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:195:5: note: in expansion of macro ‘MAT3’ 195 | MAT3(oPSE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:194:5: note: in expansion of macro ‘MAT3’ 194 | MAT3(oPNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:193:5: note: in expansion of macro ‘MAT3’ 193 | MAT3(oPNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:192:5: note: in expansion of macro ‘MAT3’ 192 | MAT3( oPW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:191:5: note: in expansion of macro ‘MAT3’ 191 | MAT3( oPE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:190:5: note: in expansion of macro ‘MAT3’ 190 | MAT3( oPS, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:189:5: note: in expansion of macro ‘MAT3’ 189 | MAT3( oPN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:188:5: note: in expansion of macro ‘MAT3’ 188 | MAT3( oPC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XuSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:186:5: note: in expansion of macro ‘MAT3’ 186 | MAT3(XuSW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XuSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:185:5: note: in expansion of macro ‘MAT3’ 185 | MAT3(XuSE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XuNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:184:5: note: in expansion of macro ‘MAT3’ 184 | MAT3(XuNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XuNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:183:5: note: in expansion of macro ‘MAT3’ 183 | MAT3(XuNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XuS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:182:5: note: in expansion of macro ‘MAT3’ 182 | MAT3( XuS, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XuN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:181:5: note: in expansion of macro ‘MAT3’ 181 | MAT3( XuN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XuW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:180:5: note: in expansion of macro ‘MAT3’ 180 | MAT3( XuW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XuE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:179:5: note: in expansion of macro ‘MAT3’ 179 | MAT3( XuE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XoNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:177:5: note: in expansion of macro ‘MAT3’ 177 | MAT3(XoNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XoNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:176:5: note: in expansion of macro ‘MAT3’ 176 | MAT3(XoNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XuC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:174:5: note: in expansion of macro ‘MAT3’ 174 | MAT3( XuC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XoN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:172:5: note: in expansion of macro ‘MAT3’ 172 | MAT3( XoN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XoE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:171:5: note: in expansion of macro ‘MAT3’ 171 | MAT3( XoE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XoC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:170:5: note: in expansion of macro ‘MAT3’ 170 | MAT3( XoC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:168:5: note: in expansion of macro ‘MAT3’ 168 | MAT3( oC, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:164:21: warning: variable ‘nzm1’ set but not used [-Wunused-but-set-variable] 164 | int nxm1, nym1, nzm1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:164:15: warning: variable ‘nym1’ set but not used [-Wunused-but-set-variable] 164 | int nxm1, nym1, nzm1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:164:9: warning: variable ‘nxm1’ set but not used [-Wunused-but-set-variable] 164 | int nxm1, nym1, nzm1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:163:33: warning: variable ‘kkm1’ set but not used [-Wunused-but-set-variable] 163 | int iim1, iip1, jjm1, jjp1, kkm1, kkp1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c: In function ‘VbuildG_7’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:532:5: note: in expansion of macro ‘MAT3’ 532 | MAT3(dPSW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:531:5: note: in expansion of macro ‘MAT3’ 531 | MAT3(dPSE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:530:5: note: in expansion of macro ‘MAT3’ 530 | MAT3(dPNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:529:5: note: in expansion of macro ‘MAT3’ 529 | MAT3(dPNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:528:5: note: in expansion of macro ‘MAT3’ 528 | MAT3( dPW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:527:5: note: in expansion of macro ‘MAT3’ 527 | MAT3( dPE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:526:5: note: in expansion of macro ‘MAT3’ 526 | MAT3( dPS, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:525:5: note: in expansion of macro ‘MAT3’ 525 | MAT3( dPN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:524:5: note: in expansion of macro ‘MAT3’ 524 | MAT3( dPC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:522:5: note: in expansion of macro ‘MAT3’ 522 | MAT3(uPSW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:521:5: note: in expansion of macro ‘MAT3’ 521 | MAT3(uPSE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:520:5: note: in expansion of macro ‘MAT3’ 520 | MAT3(uPNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:519:5: note: in expansion of macro ‘MAT3’ 519 | MAT3(uPNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:518:5: note: in expansion of macro ‘MAT3’ 518 | MAT3( uPW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:517:5: note: in expansion of macro ‘MAT3’ 517 | MAT3( uPE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:516:5: note: in expansion of macro ‘MAT3’ 516 | MAT3( uPS, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:515:5: note: in expansion of macro ‘MAT3’ 515 | MAT3( uPN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:514:5: note: in expansion of macro ‘MAT3’ 514 | MAT3( uPC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:512:5: note: in expansion of macro ‘MAT3’ 512 | MAT3(oPSW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:511:5: note: in expansion of macro ‘MAT3’ 511 | MAT3(oPSE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:510:5: note: in expansion of macro ‘MAT3’ 510 | MAT3(oPNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:509:5: note: in expansion of macro ‘MAT3’ 509 | MAT3(oPNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:508:5: note: in expansion of macro ‘MAT3’ 508 | MAT3( oPW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:507:5: note: in expansion of macro ‘MAT3’ 507 | MAT3( oPE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:506:5: note: in expansion of macro ‘MAT3’ 506 | MAT3( oPS, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:505:5: note: in expansion of macro ‘MAT3’ 505 | MAT3( oPN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:504:5: note: in expansion of macro ‘MAT3’ 504 | MAT3( oPC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XuSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:502:5: note: in expansion of macro ‘MAT3’ 502 | MAT3(XuSW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XuSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:501:5: note: in expansion of macro ‘MAT3’ 501 | MAT3(XuSE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XuNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:500:5: note: in expansion of macro ‘MAT3’ 500 | MAT3(XuNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XuNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:499:5: note: in expansion of macro ‘MAT3’ 499 | MAT3(XuNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XuS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:498:5: note: in expansion of macro ‘MAT3’ 498 | MAT3( XuS, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XuN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:497:5: note: in expansion of macro ‘MAT3’ 497 | MAT3( XuN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XuW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:496:5: note: in expansion of macro ‘MAT3’ 496 | MAT3( XuW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XuE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:495:5: note: in expansion of macro ‘MAT3’ 495 | MAT3( XuE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XuC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:494:5: note: in expansion of macro ‘MAT3’ 494 | MAT3( XuC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XoNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:492:5: note: in expansion of macro ‘MAT3’ 492 | MAT3(XoNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XoNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:491:5: note: in expansion of macro ‘MAT3’ 491 | MAT3(XoNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XoN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:490:5: note: in expansion of macro ‘MAT3’ 490 | MAT3( XoN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XoE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:489:5: note: in expansion of macro ‘MAT3’ 489 | MAT3( XoE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XoC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:488:5: note: in expansion of macro ‘MAT3’ 488 | MAT3( XoC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:486:5: note: in expansion of macro ‘MAT3’ 486 | MAT3( uC, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:484:5: note: in expansion of macro ‘MAT3’ 484 | MAT3( oN, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:483:5: note: in expansion of macro ‘MAT3’ 483 | MAT3( oE, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:482:5: note: in expansion of macro ‘MAT3’ 482 | MAT3( oC, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:473:21: warning: variable ‘nzm1’ set but not used [-Wunused-but-set-variable] 473 | int nxm1, nym1, nzm1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:473:15: warning: variable ‘nym1’ set but not used [-Wunused-but-set-variable] 473 | int nxm1, nym1, nzm1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:473:9: warning: variable ‘nxm1’ set but not used [-Wunused-but-set-variable] 473 | int nxm1, nym1, nzm1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:472:9: warning: variable ‘kkm1’ set but not used [-Wunused-but-set-variable] 472 | int kkm1, kkp1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:469:28: warning: variable ‘kp2’ set but not used [-Wunused-but-set-variable] 469 | int km1, kp1, km2, kp2; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:469:22: warning: variable ‘km2’ set but not used [-Wunused-but-set-variable] 469 | int km1, kp1, km2, kp2; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:468:28: warning: variable ‘jp2’ set but not used [-Wunused-but-set-variable] 468 | int jm1, jp1, jm2, jp2; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:467:28: warning: variable ‘ip2’ set but not used [-Wunused-but-set-variable] 467 | int im1, ip1, im2, ip2; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c: In function ‘VbuildG_27’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1380:5: note: in expansion of macro ‘MAT3’ 1380 | MAT3(dPSW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1379:5: note: in expansion of macro ‘MAT3’ 1379 | MAT3(dPSE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1378:5: note: in expansion of macro ‘MAT3’ 1378 | MAT3(dPNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1377:5: note: in expansion of macro ‘MAT3’ 1377 | MAT3(dPNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1376:5: note: in expansion of macro ‘MAT3’ 1376 | MAT3( dPW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1375:5: note: in expansion of macro ‘MAT3’ 1375 | MAT3( dPE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1374:5: note: in expansion of macro ‘MAT3’ 1374 | MAT3( dPS, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1373:5: note: in expansion of macro ‘MAT3’ 1373 | MAT3( dPN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1372:5: note: in expansion of macro ‘MAT3’ 1372 | MAT3( dPC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1370:5: note: in expansion of macro ‘MAT3’ 1370 | MAT3(uPSW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1369:5: note: in expansion of macro ‘MAT3’ 1369 | MAT3(uPSE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1368:5: note: in expansion of macro ‘MAT3’ 1368 | MAT3(uPNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1367:5: note: in expansion of macro ‘MAT3’ 1367 | MAT3(uPNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1366:5: note: in expansion of macro ‘MAT3’ 1366 | MAT3( uPW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1365:5: note: in expansion of macro ‘MAT3’ 1365 | MAT3( uPE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1364:5: note: in expansion of macro ‘MAT3’ 1364 | MAT3( uPS, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1363:5: note: in expansion of macro ‘MAT3’ 1363 | MAT3( uPN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1362:5: note: in expansion of macro ‘MAT3’ 1362 | MAT3( uPC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1360:5: note: in expansion of macro ‘MAT3’ 1360 | MAT3(oPSW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1359:5: note: in expansion of macro ‘MAT3’ 1359 | MAT3(oPSE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1358:5: note: in expansion of macro ‘MAT3’ 1358 | MAT3(oPNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1357:5: note: in expansion of macro ‘MAT3’ 1357 | MAT3(oPNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1356:5: note: in expansion of macro ‘MAT3’ 1356 | MAT3( oPW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1355:5: note: in expansion of macro ‘MAT3’ 1355 | MAT3( oPE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1354:5: note: in expansion of macro ‘MAT3’ 1354 | MAT3( oPS, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1353:5: note: in expansion of macro ‘MAT3’ 1353 | MAT3( oPN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1352:5: note: in expansion of macro ‘MAT3’ 1352 | MAT3( oPC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XuSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1350:5: note: in expansion of macro ‘MAT3’ 1350 | MAT3(XuSW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XuSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1349:5: note: in expansion of macro ‘MAT3’ 1349 | MAT3(XuSE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XuNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1348:5: note: in expansion of macro ‘MAT3’ 1348 | MAT3(XuNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XuNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1347:5: note: in expansion of macro ‘MAT3’ 1347 | MAT3(XuNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XuS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1346:5: note: in expansion of macro ‘MAT3’ 1346 | MAT3( XuS, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XuN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1345:5: note: in expansion of macro ‘MAT3’ 1345 | MAT3( XuN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XuW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1344:5: note: in expansion of macro ‘MAT3’ 1344 | MAT3( XuW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XuE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1343:5: note: in expansion of macro ‘MAT3’ 1343 | MAT3( XuE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XuC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1342:5: note: in expansion of macro ‘MAT3’ 1342 | MAT3( XuC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XoNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1340:5: note: in expansion of macro ‘MAT3’ 1340 | MAT3(XoNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XoNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1339:5: note: in expansion of macro ‘MAT3’ 1339 | MAT3(XoNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XoN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1338:5: note: in expansion of macro ‘MAT3’ 1338 | MAT3( XoN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XoE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1337:5: note: in expansion of macro ‘MAT3’ 1337 | MAT3( XoE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XoC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1336:5: note: in expansion of macro ‘MAT3’ 1336 | MAT3( XoC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1334:5: note: in expansion of macro ‘MAT3’ 1334 | MAT3( uSW, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1333:5: note: in expansion of macro ‘MAT3’ 1333 | MAT3( uSE, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1332:5: note: in expansion of macro ‘MAT3’ 1332 | MAT3( uNW, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1331:5: note: in expansion of macro ‘MAT3’ 1331 | MAT3( uNE, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1330:5: note: in expansion of macro ‘MAT3’ 1330 | MAT3( uS, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1329:5: note: in expansion of macro ‘MAT3’ 1329 | MAT3( uN, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1328:5: note: in expansion of macro ‘MAT3’ 1328 | MAT3( uW, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1327:5: note: in expansion of macro ‘MAT3’ 1327 | MAT3( uE, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1326:5: note: in expansion of macro ‘MAT3’ 1326 | MAT3( uC, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1324:5: note: in expansion of macro ‘MAT3’ 1324 | MAT3( oNW, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1323:5: note: in expansion of macro ‘MAT3’ 1323 | MAT3( oNE, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1322:5: note: in expansion of macro ‘MAT3’ 1322 | MAT3( oN, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1321:5: note: in expansion of macro ‘MAT3’ 1321 | MAT3( oE, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1320:5: note: in expansion of macro ‘MAT3’ 1320 | MAT3( oC, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1277:21: warning: variable ‘nzm1’ set but not used [-Wunused-but-set-variable] 1277 | int nxm1, nym1, nzm1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1277:15: warning: variable ‘nym1’ set but not used [-Wunused-but-set-variable] 1277 | int nxm1, nym1, nzm1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1277:9: warning: variable ‘nxm1’ set but not used [-Wunused-but-set-variable] 1277 | int nxm1, nym1, nzm1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1276:9: warning: variable ‘kkm1’ set but not used [-Wunused-but-set-variable] 1276 | int kkm1, kkp1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1273:28: warning: variable ‘kp2’ set but not used [-Wunused-but-set-variable] 1273 | int km1, kp1, km2, kp2; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1273:22: warning: variable ‘km2’ set but not used [-Wunused-but-set-variable] 1273 | int km1, kp1, km2, kp2; | ^~~ [ 31%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildPd.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.h:58, from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:55: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c: In function ‘VbuildP’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_ac’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:67:5: note: in expansion of macro ‘MAT2’ 67 | MAT2(ac, *nxf * *nyf * *nzf, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_pc’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:66:5: note: in expansion of macro ‘MAT2’ 66 | MAT2(pc, *nxc * *nyc * *nzc, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c: In function ‘VbuildP_trilin’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_pc’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:101:5: note: in expansion of macro ‘MAT2’ 101 | MAT2(pc, *nxc * *nyc * *nzc, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c: In function ‘VbuildPb_trilin’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:163:5: note: in expansion of macro ‘MAT3’ 163 | MAT3(dPSW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:162:5: note: in expansion of macro ‘MAT3’ 162 | MAT3(dPSE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:161:5: note: in expansion of macro ‘MAT3’ 161 | MAT3(dPNW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:160:5: note: in expansion of macro ‘MAT3’ 160 | MAT3(dPNE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:158:5: note: in expansion of macro ‘MAT3’ 158 | MAT3( dPW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:157:5: note: in expansion of macro ‘MAT3’ 157 | MAT3( dPE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:156:5: note: in expansion of macro ‘MAT3’ 156 | MAT3( dPS, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:155:5: note: in expansion of macro ‘MAT3’ 155 | MAT3( dPN, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:154:5: note: in expansion of macro ‘MAT3’ 154 | MAT3( dPC, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:152:5: note: in expansion of macro ‘MAT3’ 152 | MAT3(uPSW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:151:5: note: in expansion of macro ‘MAT3’ 151 | MAT3(uPSE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:150:5: note: in expansion of macro ‘MAT3’ 150 | MAT3(uPNW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:149:5: note: in expansion of macro ‘MAT3’ 149 | MAT3(uPNE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:147:5: note: in expansion of macro ‘MAT3’ 147 | MAT3( uPW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:146:5: note: in expansion of macro ‘MAT3’ 146 | MAT3( uPE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:145:5: note: in expansion of macro ‘MAT3’ 145 | MAT3( uPS, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:144:5: note: in expansion of macro ‘MAT3’ 144 | MAT3( uPN, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:143:5: note: in expansion of macro ‘MAT3’ 143 | MAT3( uPC, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:141:5: note: in expansion of macro ‘MAT3’ 141 | MAT3(oPSW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:140:5: note: in expansion of macro ‘MAT3’ 140 | MAT3(oPSE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:139:5: note: in expansion of macro ‘MAT3’ 139 | MAT3(oPNW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:138:5: note: in expansion of macro ‘MAT3’ 138 | MAT3(oPNE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:136:5: note: in expansion of macro ‘MAT3’ 136 | MAT3( oPW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:135:5: note: in expansion of macro ‘MAT3’ 135 | MAT3( oPE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:134:5: note: in expansion of macro ‘MAT3’ 134 | MAT3( oPS, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:133:5: note: in expansion of macro ‘MAT3’ 133 | MAT3( oPN, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:132:5: note: in expansion of macro ‘MAT3’ 132 | MAT3( oPC, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c: In function ‘VbuildP_op7’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_pc’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:212:5: note: in expansion of macro ‘MAT2’ 212 | MAT2(pc, *nxc * *nyc * *nzc, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_ac’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:211:5: note: in expansion of macro ‘MAT2’ 211 | MAT2(ac, *nxf * *nyf * *nzf, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c: In function ‘VbuildPb_op7’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:287:5: note: in expansion of macro ‘MAT3’ 287 | MAT3(dPSW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:286:5: note: in expansion of macro ‘MAT3’ 286 | MAT3(dPSE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:285:5: note: in expansion of macro ‘MAT3’ 285 | MAT3(dPNW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:284:5: note: in expansion of macro ‘MAT3’ 284 | MAT3(dPNE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:283:5: note: in expansion of macro ‘MAT3’ 283 | MAT3( dPW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:282:5: note: in expansion of macro ‘MAT3’ 282 | MAT3( dPE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:281:5: note: in expansion of macro ‘MAT3’ 281 | MAT3( dPS, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:280:5: note: in expansion of macro ‘MAT3’ 280 | MAT3( dPN, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:279:5: note: in expansion of macro ‘MAT3’ 279 | MAT3( dPC, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:278:5: note: in expansion of macro ‘MAT3’ 278 | MAT3(uPSW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:277:5: note: in expansion of macro ‘MAT3’ 277 | MAT3(uPSE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:276:5: note: in expansion of macro ‘MAT3’ 276 | MAT3(uPNW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:275:5: note: in expansion of macro ‘MAT3’ 275 | MAT3(uPNE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:274:5: note: in expansion of macro ‘MAT3’ 274 | MAT3( uPW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:273:5: note: in expansion of macro ‘MAT3’ 273 | MAT3( uPE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:272:5: note: in expansion of macro ‘MAT3’ 272 | MAT3( uPS, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:271:5: note: in expansion of macro ‘MAT3’ 271 | MAT3( uPN, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:270:5: note: in expansion of macro ‘MAT3’ 270 | MAT3( uPC, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:269:5: note: in expansion of macro ‘MAT3’ 269 | MAT3(oPSW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:268:5: note: in expansion of macro ‘MAT3’ 268 | MAT3(oPSE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:267:5: note: in expansion of macro ‘MAT3’ 267 | MAT3(oPNW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:266:5: note: in expansion of macro ‘MAT3’ 266 | MAT3(oPNE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:265:5: note: in expansion of macro ‘MAT3’ 265 | MAT3( oPW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:264:5: note: in expansion of macro ‘MAT3’ 264 | MAT3( oPE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:263:5: note: in expansion of macro ‘MAT3’ 263 | MAT3( oPS, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:262:5: note: in expansion of macro ‘MAT3’ 262 | MAT3( oPN, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:261:5: note: in expansion of macro ‘MAT3’ 261 | MAT3( oPC, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:260:5: note: in expansion of macro ‘MAT3’ 260 | MAT3( uC, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:259:5: note: in expansion of macro ‘MAT3’ 259 | MAT3( oN, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:258:5: note: in expansion of macro ‘MAT3’ 258 | MAT3( oE, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:257:5: note: in expansion of macro ‘MAT3’ 257 | MAT3( oC, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:255:32: warning: variable ‘eighth’ set but not used [-Wunused-but-set-variable] 255 | double won, half, quarter, eighth; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:255:23: warning: variable ‘quarter’ set but not used [-Wunused-but-set-variable] 255 | double won, half, quarter, eighth; | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:255:17: warning: variable ‘half’ set but not used [-Wunused-but-set-variable] 255 | double won, half, quarter, eighth; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:253:15: warning: variable ‘kkp1’ set but not used [-Wunused-but-set-variable] 253 | int kkm1, kkp1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:253:9: warning: variable ‘kkm1’ set but not used [-Wunused-but-set-variable] 253 | int kkm1, kkp1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:252:15: warning: variable ‘jjp1’ set but not used [-Wunused-but-set-variable] 252 | int jjm1, jjp1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:252:9: warning: variable ‘jjm1’ set but not used [-Wunused-but-set-variable] 252 | int jjm1, jjp1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:251:15: warning: variable ‘iip1’ set but not used [-Wunused-but-set-variable] 251 | int iim1, iip1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:251:9: warning: variable ‘iim1’ set but not used [-Wunused-but-set-variable] 251 | int iim1, iip1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:250:16: warning: variable ‘kp2’ set but not used [-Wunused-but-set-variable] 250 | int km2, kp2; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:250:10: warning: variable ‘km2’ set but not used [-Wunused-but-set-variable] 250 | int km2, kp2; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:248:16: warning: variable ‘jp2’ set but not used [-Wunused-but-set-variable] 248 | int jm2, jp2; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:248:10: warning: variable ‘jm2’ set but not used [-Wunused-but-set-variable] 248 | int jm2, jp2; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:246:16: warning: variable ‘ip2’ set but not used [-Wunused-but-set-variable] 246 | int im2, ip2; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:246:10: warning: variable ‘im2’ set but not used [-Wunused-but-set-variable] 246 | int im2, ip2; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c: In function ‘VbuildP_op27’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_pc’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:728:5: note: in expansion of macro ‘MAT2’ 728 | MAT2(pc, *nxc * *nyc * *nzc, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_ac’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:727:5: note: in expansion of macro ‘MAT2’ 727 | MAT2(ac, *nxf * *nyf * *nzf, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c: In function ‘VbuildPb_op27’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:818:7: note: in expansion of macro ‘MAT3’ 818 | MAT3(dPSW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:817:7: note: in expansion of macro ‘MAT3’ 817 | MAT3(dPSE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:816:7: note: in expansion of macro ‘MAT3’ 816 | MAT3(dPNW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:815:7: note: in expansion of macro ‘MAT3’ 815 | MAT3(dPNE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:814:7: note: in expansion of macro ‘MAT3’ 814 | MAT3( dPW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:813:7: note: in expansion of macro ‘MAT3’ 813 | MAT3( dPE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:812:7: note: in expansion of macro ‘MAT3’ 812 | MAT3( dPS, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:811:7: note: in expansion of macro ‘MAT3’ 811 | MAT3( dPN, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:810:7: note: in expansion of macro ‘MAT3’ 810 | MAT3( dPC, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:809:7: note: in expansion of macro ‘MAT3’ 809 | MAT3(uPSW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:808:7: note: in expansion of macro ‘MAT3’ 808 | MAT3(uPSE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:807:7: note: in expansion of macro ‘MAT3’ 807 | MAT3(uPNW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:806:7: note: in expansion of macro ‘MAT3’ 806 | MAT3(uPNE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:805:7: note: in expansion of macro ‘MAT3’ 805 | MAT3( uPW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:804:7: note: in expansion of macro ‘MAT3’ 804 | MAT3( uPE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:803:7: note: in expansion of macro ‘MAT3’ 803 | MAT3( uPS, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:802:7: note: in expansion of macro ‘MAT3’ 802 | MAT3( uPN, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:801:7: note: in expansion of macro ‘MAT3’ 801 | MAT3( uPC, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:800:7: note: in expansion of macro ‘MAT3’ 800 | MAT3(oPSW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:799:7: note: in expansion of macro ‘MAT3’ 799 | MAT3(oPSE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:798:7: note: in expansion of macro ‘MAT3’ 798 | MAT3(oPNW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:797:7: note: in expansion of macro ‘MAT3’ 797 | MAT3(oPNE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:796:7: note: in expansion of macro ‘MAT3’ 796 | MAT3( oPW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:795:7: note: in expansion of macro ‘MAT3’ 795 | MAT3( oPE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:794:7: note: in expansion of macro ‘MAT3’ 794 | MAT3( oPS, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:793:7: note: in expansion of macro ‘MAT3’ 793 | MAT3( oPN, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:792:7: note: in expansion of macro ‘MAT3’ 792 | MAT3( oPC, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:791:7: note: in expansion of macro ‘MAT3’ 791 | MAT3( uSW, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:790:7: note: in expansion of macro ‘MAT3’ 790 | MAT3( uSE, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:789:7: note: in expansion of macro ‘MAT3’ 789 | MAT3( uNW, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:788:7: note: in expansion of macro ‘MAT3’ 788 | MAT3( uNE, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:787:7: note: in expansion of macro ‘MAT3’ 787 | MAT3( uS, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:786:7: note: in expansion of macro ‘MAT3’ 786 | MAT3( uN, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:785:7: note: in expansion of macro ‘MAT3’ 785 | MAT3( uW, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:784:7: note: in expansion of macro ‘MAT3’ 784 | MAT3( uE, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:783:7: note: in expansion of macro ‘MAT3’ 783 | MAT3( oNW, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:782:7: note: in expansion of macro ‘MAT3’ 782 | MAT3( oNE, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:781:7: note: in expansion of macro ‘MAT3’ 781 | MAT3( uC, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:780:7: note: in expansion of macro ‘MAT3’ 780 | MAT3( oN, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:779:7: note: in expansion of macro ‘MAT3’ 779 | MAT3( oE, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:778:7: note: in expansion of macro ‘MAT3’ 778 | MAT3( oC, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:776:34: warning: variable ‘eighth’ set but not used [-Wunused-but-set-variable] 776 | double won, half, quarter, eighth; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:776:25: warning: variable ‘quarter’ set but not used [-Wunused-but-set-variable] 776 | double won, half, quarter, eighth; | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:776:19: warning: variable ‘half’ set but not used [-Wunused-but-set-variable] 776 | double won, half, quarter, eighth; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:774:17: warning: variable ‘kkp1’ set but not used [-Wunused-but-set-variable] 774 | int kkm1, kkp1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:774:11: warning: variable ‘kkm1’ set but not used [-Wunused-but-set-variable] 774 | int kkm1, kkp1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:773:17: warning: variable ‘jjp1’ set but not used [-Wunused-but-set-variable] 773 | int jjm1, jjp1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:773:11: warning: variable ‘jjm1’ set but not used [-Wunused-but-set-variable] 773 | int jjm1, jjp1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:772:17: warning: variable ‘iip1’ set but not used [-Wunused-but-set-variable] 772 | int iim1, iip1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:772:11: warning: variable ‘iim1’ set but not used [-Wunused-but-set-variable] 772 | int iim1, iip1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:771:18: warning: variable ‘kp2’ set but not used [-Wunused-but-set-variable] 771 | int km2, kp2; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:771:12: warning: variable ‘km2’ set but not used [-Wunused-but-set-variable] 771 | int km2, kp2; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:769:18: warning: variable ‘jp2’ set but not used [-Wunused-but-set-variable] 769 | int jm2, jp2; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:769:12: warning: variable ‘jm2’ set but not used [-Wunused-but-set-variable] 769 | int jm2, jp2; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:767:18: warning: variable ‘ip2’ set but not used [-Wunused-but-set-variable] 767 | int im2, ip2; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:767:12: warning: variable ‘im2’ set but not used [-Wunused-but-set-variable] 767 | int im2, ip2; | ^~~ [ 32%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/cgd.c.o /builddir/build/BUILD/apbs-3.0.0/src/pmgc/cgd.c: In function ‘Vcghs’: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/cgd.c:99:24: warning: ‘rhok1’ may be used uninitialized [-Wmaybe-uninitialized] 99 | beta = rhok2 / rhok1; | ~~~~~~^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/cgd.c:66:12: note: ‘rhok1’ was declared here 66 | double rhok1, rhok2, alpha, beta; | ^~~~~ [ 33%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/gsd.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.h:57, from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:55: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c: In function ‘Vgsrb’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_ac’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:67:5: note: in expansion of macro ‘MAT2’ 67 | MAT2(ac, *nx * *ny * *nz, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c: In function ‘Vgsrb7x’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:116:5: note: in expansion of macro ‘MAT3’ 116 | MAT3(oC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:115:5: note: in expansion of macro ‘MAT3’ 115 | MAT3(uC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:114:5: note: in expansion of macro ‘MAT3’ 114 | MAT3(oN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:113:5: note: in expansion of macro ‘MAT3’ 113 | MAT3(oE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_r’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:111:5: note: in expansion of macro ‘MAT3’ 111 | MAT3( r, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:78:9: warning: unused variable ‘dy_r’ [-Wunused-variable] 78 | int dy_##mat = dy; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:111:5: note: in expansion of macro ‘MAT3’ 111 | MAT3( r, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:77:9: warning: unused variable ‘dx_r’ [-Wunused-variable] 77 | int dx_##mat = dx; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:111:5: note: in expansion of macro ‘MAT3’ 111 | MAT3( r, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_w2’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:110:5: note: in expansion of macro ‘MAT3’ 110 | MAT3(w2, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:78:9: warning: unused variable ‘dy_w2’ [-Wunused-variable] 78 | int dy_##mat = dy; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:110:5: note: in expansion of macro ‘MAT3’ 110 | MAT3(w2, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:77:9: warning: unused variable ‘dx_w2’ [-Wunused-variable] 77 | int dx_##mat = dx; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:110:5: note: in expansion of macro ‘MAT3’ 110 | MAT3(w2, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_w1’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:109:5: note: in expansion of macro ‘MAT3’ 109 | MAT3(w1, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:78:9: warning: unused variable ‘dy_w1’ [-Wunused-variable] 78 | int dy_##mat = dy; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:109:5: note: in expansion of macro ‘MAT3’ 109 | MAT3(w1, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:77:9: warning: unused variable ‘dx_w1’ [-Wunused-variable] 77 | int dx_##mat = dx; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:109:5: note: in expansion of macro ‘MAT3’ 109 | MAT3(w1, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_x’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:108:5: note: in expansion of macro ‘MAT3’ 108 | MAT3( x, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_fc’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:107:5: note: in expansion of macro ‘MAT3’ 107 | MAT3(fc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_cc’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:106:5: note: in expansion of macro ‘MAT3’ 106 | MAT3(cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c: In function ‘Vgsrb27x’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:208:5: note: in expansion of macro ‘MAT3’ 208 | MAT3(uSW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:207:5: note: in expansion of macro ‘MAT3’ 207 | MAT3(uSE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:206:5: note: in expansion of macro ‘MAT3’ 206 | MAT3(uNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:205:5: note: in expansion of macro ‘MAT3’ 205 | MAT3(uNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:204:5: note: in expansion of macro ‘MAT3’ 204 | MAT3( uS, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:203:5: note: in expansion of macro ‘MAT3’ 203 | MAT3( uN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:202:5: note: in expansion of macro ‘MAT3’ 202 | MAT3( uW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:201:5: note: in expansion of macro ‘MAT3’ 201 | MAT3( uE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:199:5: note: in expansion of macro ‘MAT3’ 199 | MAT3(oNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:198:5: note: in expansion of macro ‘MAT3’ 198 | MAT3(oNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:196:5: note: in expansion of macro ‘MAT3’ 196 | MAT3(oC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:195:5: note: in expansion of macro ‘MAT3’ 195 | MAT3(uC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:194:5: note: in expansion of macro ‘MAT3’ 194 | MAT3(oN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:193:5: note: in expansion of macro ‘MAT3’ 193 | MAT3(oE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_r’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:191:5: note: in expansion of macro ‘MAT3’ 191 | MAT3( r, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:78:9: warning: unused variable ‘dy_r’ [-Wunused-variable] 78 | int dy_##mat = dy; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:191:5: note: in expansion of macro ‘MAT3’ 191 | MAT3( r, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:77:9: warning: unused variable ‘dx_r’ [-Wunused-variable] 77 | int dx_##mat = dx; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:191:5: note: in expansion of macro ‘MAT3’ 191 | MAT3( r, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_w2’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:190:5: note: in expansion of macro ‘MAT3’ 190 | MAT3(w2, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:78:9: warning: unused variable ‘dy_w2’ [-Wunused-variable] 78 | int dy_##mat = dy; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:190:5: note: in expansion of macro ‘MAT3’ 190 | MAT3(w2, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:77:9: warning: unused variable ‘dx_w2’ [-Wunused-variable] 77 | int dx_##mat = dx; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:190:5: note: in expansion of macro ‘MAT3’ 190 | MAT3(w2, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_w1’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:189:5: note: in expansion of macro ‘MAT3’ 189 | MAT3(w1, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:78:9: warning: unused variable ‘dy_w1’ [-Wunused-variable] 78 | int dy_##mat = dy; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:189:5: note: in expansion of macro ‘MAT3’ 189 | MAT3(w1, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:77:9: warning: unused variable ‘dx_w1’ [-Wunused-variable] 77 | int dx_##mat = dx; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:189:5: note: in expansion of macro ‘MAT3’ 189 | MAT3(w1, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_x’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:188:5: note: in expansion of macro ‘MAT3’ 188 | MAT3( x, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_fc’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:187:5: note: in expansion of macro ‘MAT3’ 187 | MAT3(fc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_cc’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:186:5: note: in expansion of macro ‘MAT3’ 186 | MAT3( cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:182:9: warning: variable ‘istep’ set but not used [-Wunused-but-set-variable] 182 | int istep; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:180:17: warning: variable ‘k2’ set but not used [-Wunused-but-set-variable] 180 | int i2, j2, k2; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:180:13: warning: variable ‘j2’ set but not used [-Wunused-but-set-variable] 180 | int i2, j2, k2; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:180:9: warning: variable ‘i2’ set but not used [-Wunused-but-set-variable] 180 | int i2, j2, k2; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:179:17: warning: variable ‘k1’ set but not used [-Wunused-but-set-variable] 179 | int i1, j1, k1; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:179:13: warning: variable ‘j1’ set but not used [-Wunused-but-set-variable] 179 | int i1, j1, k1; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:179:9: warning: variable ‘i1’ set but not used [-Wunused-but-set-variable] 179 | int i1, j1, k1; | ^~ [ 34%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/matvecd.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.h:55, from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:55: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function ‘Vmatvec7’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_ac’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:87:5: note: in expansion of macro ‘MAT2’ 87 | MAT2(ac, *nx * *ny * *nz, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function ‘Vmatvec7_1s’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_y’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:112:5: note: in expansion of macro ‘MAT3’ 112 | MAT3(y, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_x’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:111:5: note: in expansion of macro ‘MAT3’ 111 | MAT3(x, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:110:5: note: in expansion of macro ‘MAT3’ 110 | MAT3(oC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_cc’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:109:5: note: in expansion of macro ‘MAT3’ 109 | MAT3(cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:108:5: note: in expansion of macro ‘MAT3’ 108 | MAT3(uC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:107:5: note: in expansion of macro ‘MAT3’ 107 | MAT3(oN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:106:5: note: in expansion of macro ‘MAT3’ 106 | MAT3(oE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function ‘Vmatvec27’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_ac’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:139:5: note: in expansion of macro ‘MAT2’ 139 | MAT2(ac, *nx * *ny * *nz, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function ‘Vmatvec27_1s’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:184:5: note: in expansion of macro ‘MAT3’ 184 | MAT3(uSW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:183:5: note: in expansion of macro ‘MAT3’ 183 | MAT3(uSE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:182:5: note: in expansion of macro ‘MAT3’ 182 | MAT3(uNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:181:5: note: in expansion of macro ‘MAT3’ 181 | MAT3(uNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:180:5: note: in expansion of macro ‘MAT3’ 180 | MAT3(uS, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:179:5: note: in expansion of macro ‘MAT3’ 179 | MAT3(uN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:178:5: note: in expansion of macro ‘MAT3’ 178 | MAT3(uW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:177:5: note: in expansion of macro ‘MAT3’ 177 | MAT3(uE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:176:5: note: in expansion of macro ‘MAT3’ 176 | MAT3(uC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:174:5: note: in expansion of macro ‘MAT3’ 174 | MAT3(oNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:173:5: note: in expansion of macro ‘MAT3’ 173 | MAT3(oNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:172:5: note: in expansion of macro ‘MAT3’ 172 | MAT3(oN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:171:5: note: in expansion of macro ‘MAT3’ 171 | MAT3(oE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:170:5: note: in expansion of macro ‘MAT3’ 170 | MAT3(oC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_y’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:168:5: note: in expansion of macro ‘MAT3’ 168 | MAT3(y, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_x’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:167:5: note: in expansion of macro ‘MAT3’ 167 | MAT3(x, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_cc’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:166:5: note: in expansion of macro ‘MAT3’ 166 | MAT3(cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function ‘Vnmatvec7’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_ac’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:263:5: note: in expansion of macro ‘MAT2’ 263 | MAT2(ac, *nx * *ny * *nz, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function ‘Vnmatvecd7_1s’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_w1’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:292:5: note: in expansion of macro ‘MAT3’ 292 | MAT3(w1, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_y’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:291:5: note: in expansion of macro ‘MAT3’ 291 | MAT3( y, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_x’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:290:5: note: in expansion of macro ‘MAT3’ 290 | MAT3( x, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:289:5: note: in expansion of macro ‘MAT3’ 289 | MAT3(oC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_cc’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:288:5: note: in expansion of macro ‘MAT3’ 288 | MAT3(cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:78:9: warning: unused variable ‘dy_cc’ [-Wunused-variable] 78 | int dy_##mat = dy; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:288:5: note: in expansion of macro ‘MAT3’ 288 | MAT3(cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:77:9: warning: unused variable ‘dx_cc’ [-Wunused-variable] 77 | int dx_##mat = dx; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:288:5: note: in expansion of macro ‘MAT3’ 288 | MAT3(cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:287:5: note: in expansion of macro ‘MAT3’ 287 | MAT3(uC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:286:5: note: in expansion of macro ‘MAT3’ 286 | MAT3(oN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:285:5: note: in expansion of macro ‘MAT3’ 285 | MAT3(oE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function ‘Vnmatvec27’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_ac’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:322:5: note: in expansion of macro ‘MAT2’ 322 | MAT2(ac, *nx * *ny * *nz, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function ‘Vnmatvecd27_1s’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_w1’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:370:5: note: in expansion of macro ‘MAT3’ 370 | MAT3( w1, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_y’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:369:5: note: in expansion of macro ‘MAT3’ 369 | MAT3( y, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_x’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:368:5: note: in expansion of macro ‘MAT3’ 368 | MAT3( x, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:367:5: note: in expansion of macro ‘MAT3’ 367 | MAT3( oC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_cc’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:366:5: note: in expansion of macro ‘MAT3’ 366 | MAT3( cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:78:9: warning: unused variable ‘dy_cc’ [-Wunused-variable] 78 | int dy_##mat = dy; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:366:5: note: in expansion of macro ‘MAT3’ 366 | MAT3( cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:77:9: warning: unused variable ‘dx_cc’ [-Wunused-variable] 77 | int dx_##mat = dx; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:366:5: note: in expansion of macro ‘MAT3’ 366 | MAT3( cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:365:5: note: in expansion of macro ‘MAT3’ 365 | MAT3(uSW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:364:5: note: in expansion of macro ‘MAT3’ 364 | MAT3(uSE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:363:5: note: in expansion of macro ‘MAT3’ 363 | MAT3(uNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:362:5: note: in expansion of macro ‘MAT3’ 362 | MAT3(uNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:361:5: note: in expansion of macro ‘MAT3’ 361 | MAT3( uS, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:360:5: note: in expansion of macro ‘MAT3’ 360 | MAT3( uN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:359:5: note: in expansion of macro ‘MAT3’ 359 | MAT3( uW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:358:5: note: in expansion of macro ‘MAT3’ 358 | MAT3( uE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:357:5: note: in expansion of macro ‘MAT3’ 357 | MAT3(oNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:356:5: note: in expansion of macro ‘MAT3’ 356 | MAT3(oNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:355:5: note: in expansion of macro ‘MAT3’ 355 | MAT3( uC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:354:5: note: in expansion of macro ‘MAT3’ 354 | MAT3( oN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:353:5: note: in expansion of macro ‘MAT3’ 353 | MAT3( oE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function ‘Vmresid7’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_ac’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:451:5: note: in expansion of macro ‘MAT2’ 451 | MAT2(ac, *nx * *ny * *nz, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function ‘Vmresid7_1s’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_r’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:476:5: note: in expansion of macro ‘MAT3’ 476 | MAT3(r, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_x’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:475:5: note: in expansion of macro ‘MAT3’ 475 | MAT3(x, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:474:5: note: in expansion of macro ‘MAT3’ 474 | MAT3(oC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_fc’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:473:5: note: in expansion of macro ‘MAT3’ 473 | MAT3(fc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_cc’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:472:5: note: in expansion of macro ‘MAT3’ 472 | MAT3(cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:471:5: note: in expansion of macro ‘MAT3’ 471 | MAT3(uC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:470:5: note: in expansion of macro ‘MAT3’ 470 | MAT3(oN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:469:5: note: in expansion of macro ‘MAT3’ 469 | MAT3(oE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function ‘Vmresid27’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_ac’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:503:5: note: in expansion of macro ‘MAT2’ 503 | MAT2(ac, *nx * *ny * *nz, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function ‘Vmresid27_1s’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:550:5: note: in expansion of macro ‘MAT3’ 550 | MAT3(uSW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:549:5: note: in expansion of macro ‘MAT3’ 549 | MAT3(uSE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:548:5: note: in expansion of macro ‘MAT3’ 548 | MAT3(uNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:547:5: note: in expansion of macro ‘MAT3’ 547 | MAT3(uNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:546:5: note: in expansion of macro ‘MAT3’ 546 | MAT3(uS, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:545:5: note: in expansion of macro ‘MAT3’ 545 | MAT3(uN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:544:5: note: in expansion of macro ‘MAT3’ 544 | MAT3(uW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:543:5: note: in expansion of macro ‘MAT3’ 543 | MAT3(uE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:542:5: note: in expansion of macro ‘MAT3’ 542 | MAT3(uC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:540:5: note: in expansion of macro ‘MAT3’ 540 | MAT3(oNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:539:5: note: in expansion of macro ‘MAT3’ 539 | MAT3(oNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:538:5: note: in expansion of macro ‘MAT3’ 538 | MAT3(oN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:537:5: note: in expansion of macro ‘MAT3’ 537 | MAT3(oE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:536:5: note: in expansion of macro ‘MAT3’ 536 | MAT3(oC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_r’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:534:5: note: in expansion of macro ‘MAT3’ 534 | MAT3(r, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_x’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:533:5: note: in expansion of macro ‘MAT3’ 533 | MAT3(x, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_fc’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:532:5: note: in expansion of macro ‘MAT3’ 532 | MAT3(fc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_cc’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:531:5: note: in expansion of macro ‘MAT3’ 531 | MAT3(cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function ‘Vnmresid7’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_ac’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:623:5: note: in expansion of macro ‘MAT2’ 623 | MAT2(ac, *nx * *ny * *nz, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function ‘Vnmresid7_1s’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_w1’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:650:5: note: in expansion of macro ‘MAT3’ 650 | MAT3(w1, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_r’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:649:5: note: in expansion of macro ‘MAT3’ 649 | MAT3( r, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_x’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:648:5: note: in expansion of macro ‘MAT3’ 648 | MAT3( x, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:647:5: note: in expansion of macro ‘MAT3’ 647 | MAT3(oC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_fc’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:646:5: note: in expansion of macro ‘MAT3’ 646 | MAT3(fc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_cc’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:645:5: note: in expansion of macro ‘MAT3’ 645 | MAT3(cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:78:9: warning: unused variable ‘dy_cc’ [-Wunused-variable] 78 | int dy_##mat = dy; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:645:5: note: in expansion of macro ‘MAT3’ 645 | MAT3(cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:77:9: warning: unused variable ‘dx_cc’ [-Wunused-variable] 77 | int dx_##mat = dx; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:645:5: note: in expansion of macro ‘MAT3’ 645 | MAT3(cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:644:5: note: in expansion of macro ‘MAT3’ 644 | MAT3(uC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:643:5: note: in expansion of macro ‘MAT3’ 643 | MAT3(oN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:642:5: note: in expansion of macro ‘MAT3’ 642 | MAT3(oE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function ‘Vnmresid27’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_ac’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:681:5: note: in expansion of macro ‘MAT2’ 681 | MAT2(ac, *nx * *ny * *nz, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function ‘Vnmresid27_1s’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_w1’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:727:5: note: in expansion of macro ‘MAT3’ 727 | MAT3( w1, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_r’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:726:5: note: in expansion of macro ‘MAT3’ 726 | MAT3( r, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_x’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:725:5: note: in expansion of macro ‘MAT3’ 725 | MAT3( x, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:724:5: note: in expansion of macro ‘MAT3’ 724 | MAT3(uSW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:723:5: note: in expansion of macro ‘MAT3’ 723 | MAT3(uSE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:722:5: note: in expansion of macro ‘MAT3’ 722 | MAT3(uNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:721:5: note: in expansion of macro ‘MAT3’ 721 | MAT3(uNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:720:5: note: in expansion of macro ‘MAT3’ 720 | MAT3( uS, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:719:5: note: in expansion of macro ‘MAT3’ 719 | MAT3( uN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:718:5: note: in expansion of macro ‘MAT3’ 718 | MAT3( uW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:717:5: note: in expansion of macro ‘MAT3’ 717 | MAT3( uE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:716:5: note: in expansion of macro ‘MAT3’ 716 | MAT3(oNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:715:5: note: in expansion of macro ‘MAT3’ 715 | MAT3(oNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:714:5: note: in expansion of macro ‘MAT3’ 714 | MAT3( uC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:713:5: note: in expansion of macro ‘MAT3’ 713 | MAT3( oN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:712:5: note: in expansion of macro ‘MAT3’ 712 | MAT3( oE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_fc’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:711:5: note: in expansion of macro ‘MAT3’ 711 | MAT3( fc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_cc’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:710:5: note: in expansion of macro ‘MAT3’ 710 | MAT3( cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:78:9: warning: unused variable ‘dy_cc’ [-Wunused-variable] 78 | int dy_##mat = dy; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:710:5: note: in expansion of macro ‘MAT3’ 710 | MAT3( cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:77:9: warning: unused variable ‘dx_cc’ [-Wunused-variable] 77 | int dx_##mat = dx; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:710:5: note: in expansion of macro ‘MAT3’ 710 | MAT3( cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:709:5: note: in expansion of macro ‘MAT3’ 709 | MAT3( oC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function ‘Vrestrc’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_pc’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:786:5: note: in expansion of macro ‘MAT2’ 786 | MAT2(pc, *nxc * *nyc * *nzc, 1 ); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function ‘Vrestrc2’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:852:5: note: in expansion of macro ‘MAT3’ 852 | MAT3(dPSW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:851:5: note: in expansion of macro ‘MAT3’ 851 | MAT3(dPSE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:850:5: note: in expansion of macro ‘MAT3’ 850 | MAT3(dPNW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:849:5: note: in expansion of macro ‘MAT3’ 849 | MAT3(dPNE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:847:5: note: in expansion of macro ‘MAT3’ 847 | MAT3(dPW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:846:5: note: in expansion of macro ‘MAT3’ 846 | MAT3(dPE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:845:5: note: in expansion of macro ‘MAT3’ 845 | MAT3(dPS, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:844:5: note: in expansion of macro ‘MAT3’ 844 | MAT3(dPN, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:843:5: note: in expansion of macro ‘MAT3’ 843 | MAT3(dPC, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:841:5: note: in expansion of macro ‘MAT3’ 841 | MAT3(uPSW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:840:5: note: in expansion of macro ‘MAT3’ 840 | MAT3(uPSE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:839:5: note: in expansion of macro ‘MAT3’ 839 | MAT3(uPNW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:838:5: note: in expansion of macro ‘MAT3’ 838 | MAT3(uPNE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:836:5: note: in expansion of macro ‘MAT3’ 836 | MAT3(uPW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:835:5: note: in expansion of macro ‘MAT3’ 835 | MAT3(uPE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:834:5: note: in expansion of macro ‘MAT3’ 834 | MAT3(uPS, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:833:5: note: in expansion of macro ‘MAT3’ 833 | MAT3(uPN, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:832:5: note: in expansion of macro ‘MAT3’ 832 | MAT3(uPC, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:830:5: note: in expansion of macro ‘MAT3’ 830 | MAT3(oPSW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:829:5: note: in expansion of macro ‘MAT3’ 829 | MAT3(oPSE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:828:5: note: in expansion of macro ‘MAT3’ 828 | MAT3(oPNW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:827:5: note: in expansion of macro ‘MAT3’ 827 | MAT3(oPNE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:825:5: note: in expansion of macro ‘MAT3’ 825 | MAT3(oPW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:824:5: note: in expansion of macro ‘MAT3’ 824 | MAT3(oPE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:823:5: note: in expansion of macro ‘MAT3’ 823 | MAT3(oPS, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:822:5: note: in expansion of macro ‘MAT3’ 822 | MAT3(oPN, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:821:5: note: in expansion of macro ‘MAT3’ 821 | MAT3(oPC, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_xout’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:819:5: note: in expansion of macro ‘MAT3’ 819 | MAT3(xout, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_xin’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:818:5: note: in expansion of macro ‘MAT3’ 818 | MAT3(xin, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:816:12: warning: variable ‘dimfac’ set but not used [-Wunused-but-set-variable] 816 | double dimfac; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function ‘VinterpPMG’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_pc’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:920:5: note: in expansion of macro ‘MAT2’ 920 | MAT2(pc, *nxc * *nyc * *nzc, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function ‘VinterpPMG2’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:982:5: note: in expansion of macro ‘MAT3’ 982 | MAT3(dPSW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:981:5: note: in expansion of macro ‘MAT3’ 981 | MAT3(dPSE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:980:5: note: in expansion of macro ‘MAT3’ 980 | MAT3(dPNW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:979:5: note: in expansion of macro ‘MAT3’ 979 | MAT3(dPNE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:977:5: note: in expansion of macro ‘MAT3’ 977 | MAT3( dPW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:976:5: note: in expansion of macro ‘MAT3’ 976 | MAT3( dPE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:975:5: note: in expansion of macro ‘MAT3’ 975 | MAT3( dPS, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:974:5: note: in expansion of macro ‘MAT3’ 974 | MAT3( dPN, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:973:5: note: in expansion of macro ‘MAT3’ 973 | MAT3( dPC, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:971:5: note: in expansion of macro ‘MAT3’ 971 | MAT3(uPSW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:970:5: note: in expansion of macro ‘MAT3’ 970 | MAT3(uPSE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:969:5: note: in expansion of macro ‘MAT3’ 969 | MAT3(uPNW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:968:5: note: in expansion of macro ‘MAT3’ 968 | MAT3(uPNE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:966:5: note: in expansion of macro ‘MAT3’ 966 | MAT3( uPW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:965:5: note: in expansion of macro ‘MAT3’ 965 | MAT3( uPE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:964:5: note: in expansion of macro ‘MAT3’ 964 | MAT3( uPS, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:963:5: note: in expansion of macro ‘MAT3’ 963 | MAT3( uPN, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:962:5: note: in expansion of macro ‘MAT3’ 962 | MAT3( uPC, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:960:5: note: in expansion of macro ‘MAT3’ 960 | MAT3(oPSW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:959:5: note: in expansion of macro ‘MAT3’ 959 | MAT3(oPSE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:958:5: note: in expansion of macro ‘MAT3’ 958 | MAT3(oPNW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:957:5: note: in expansion of macro ‘MAT3’ 957 | MAT3(oPNE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:955:5: note: in expansion of macro ‘MAT3’ 955 | MAT3( oPW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:954:5: note: in expansion of macro ‘MAT3’ 954 | MAT3( oPE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:953:5: note: in expansion of macro ‘MAT3’ 953 | MAT3( oPS, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:952:5: note: in expansion of macro ‘MAT3’ 952 | MAT3( oPN, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:951:5: note: in expansion of macro ‘MAT3’ 951 | MAT3( oPC, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:78:9: warning: unused variable ‘dy_oPC’ [-Wunused-variable] 78 | int dy_##mat = dy; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:951:5: note: in expansion of macro ‘MAT3’ 951 | MAT3( oPC, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:77:9: warning: unused variable ‘dx_oPC’ [-Wunused-variable] 77 | int dx_##mat = dx; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:951:5: note: in expansion of macro ‘MAT3’ 951 | MAT3( oPC, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_xout’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:949:5: note: in expansion of macro ‘MAT3’ 949 | MAT3(xout, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_xin’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:948:5: note: in expansion of macro ‘MAT3’ 948 | MAT3( xin, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function ‘Vextrac’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_xout’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:1086:5: note: in expansion of macro ‘MAT3’ 1086 | MAT3(xout, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_xin’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:1085:5: note: in expansion of macro ‘MAT3’ 1085 | MAT3( xin, *nxf, *nyf, *nzf); | ^~~~ [ 35%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgcsd.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgcsd.h:58, from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgcsd.c:55: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgcsd.c: In function ‘Vmvcs’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_iz’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgcsd.c:99:5: note: in expansion of macro ‘MAT2’ 99 | MAT2(iz, 50, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgcsd.c:560:13: warning: ‘rsden’ may be used uninitialized [-Wmaybe-uninitialized] 560 | Vprtstp(*iok, *iters, rsnrm, rsden, orsnrm); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgcsd.c:88:12: note: ‘rsden’ was declared here 88 | double rsden; // @todo: doc | ^~~~~ [ 36%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgdrvd.c.o /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.c: In function ‘Vmgdriv’: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.c:85:9: warning: unused variable ‘ierror’ [-Wunused-variable] 85 | int ierror = 0; | ^~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.h:62, from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.c:55: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.c: In function ‘Vmgdriv2’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_iz’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.c:267:5: note: in expansion of macro ‘MAT2’ 267 | MAT2(iz, 50, nlev); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.c:234:12: warning: unused variable ‘tsolve’ [-Wunused-variable] 234 | double tsolve = 0.0; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.c:233:12: warning: unused variable ‘tsetupc’ [-Wunused-variable] 233 | double tsetupc = 0.0; | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.c:232:12: warning: unused variable ‘tsetupf’ [-Wunused-variable] 232 | double tsetupf = 0.0; | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.c:231:12: warning: unused variable ‘oh’ [-Wunused-variable] 231 | double oh = 0.0; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.c:230:12: warning: unused variable ‘bf’ [-Wunused-variable] 230 | double bf = 0.0; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.c:226:12: warning: unused variable ‘epsmac’ [-Wunused-variable] 226 | double epsmac = 0.0; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.c: In function ‘Vmgsz’: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.c:655:26: warning: ‘num_narrc_oper’ may be used uninitialized [-Wmaybe-uninitialized] 655 | + (num_narrc + num_narrc_oper) * *narrc | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.c:580:22: note: ‘num_narrc_oper’ was declared here 580 | int num_nf_oper, num_narrc_oper; | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.c:654:41: warning: ‘num_nf_oper’ may be used uninitialized [-Wmaybe-uninitialized] 654 | + (num_nf + num_nf_oper) * *nf | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.c:580:9: note: ‘num_nf_oper’ was declared here 580 | int num_nf_oper, num_narrc_oper; | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.c:656:13: warning: ‘n_band’ may be used uninitialized [-Wmaybe-uninitialized] 653 | *iretot = num_narr * *narr | ~~~~~~~~~~~~~~~~ 654 | + (num_nf + num_nf_oper) * *nf | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 655 | + (num_narrc + num_narrc_oper) * *narrc | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 656 | + n_band | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.c:577:28: note: ‘n_band’ was declared here 577 | int nc_band, num_band, n_band; | ^~~~~~ [ 37%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgsubd.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.h:58, from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:55: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c: In function ‘Vbuildops’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_iz’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:83:5: note: in expansion of macro ‘MAT2’ 83 | MAT2(iz, 50, *nlev); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c: In function ‘Vbuildstr’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_iz’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:266:5: note: in expansion of macro ‘MAT2’ 266 | MAT2(iz, 50, *nlev); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c: In function ‘Vbuildcopy0’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_fcf’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:628:5: note: in expansion of macro ‘MAT3’ 628 | MAT3( fcf, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_ccf’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:627:5: note: in expansion of macro ‘MAT3’ 627 | MAT3( ccf, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_tcf’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:626:5: note: in expansion of macro ‘MAT3’ 626 | MAT3( tcf, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_a3cf’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:625:5: note: in expansion of macro ‘MAT3’ 625 | MAT3(a3cf, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_a2cf’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:624:5: note: in expansion of macro ‘MAT3’ 624 | MAT3(a2cf, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_a1cf’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:623:5: note: in expansion of macro ‘MAT3’ 623 | MAT3(a1cf, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_gzcf’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:622:5: note: in expansion of macro ‘MAT3’ 622 | MAT3(gzcf, *nxf, *nyf, 4); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_gycf’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:621:5: note: in expansion of macro ‘MAT3’ 621 | MAT3(gycf, *nxf, *nzf, 4); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_gxcf’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:620:5: note: in expansion of macro ‘MAT3’ 620 | MAT3(gxcf, *nyf, *nzf, 4); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_tc’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:619:5: note: in expansion of macro ‘MAT3’ 619 | MAT3( tc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_fc’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:618:5: note: in expansion of macro ‘MAT3’ 618 | MAT3( fc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_cc’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:617:5: note: in expansion of macro ‘MAT3’ 617 | MAT3( cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_a3c’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:616:5: note: in expansion of macro ‘MAT3’ 616 | MAT3( a3c, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_a2c’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:615:5: note: in expansion of macro ‘MAT3’ 615 | MAT3( a2c, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_a1c’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:614:5: note: in expansion of macro ‘MAT3’ 614 | MAT3( a1c, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_gzc’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:613:5: note: in expansion of macro ‘MAT3’ 613 | MAT3( gzc, *nx, *ny, 4); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_gyc’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:612:5: note: in expansion of macro ‘MAT3’ 612 | MAT3( gyc, *nx, *nz, 4); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_gxc’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:611:5: note: in expansion of macro ‘MAT3’ 611 | MAT3( gxc, *ny, *nz, 4); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c: In function ‘Vbuildalg’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_iz’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:914:5: note: in expansion of macro ‘MAT2’ 914 | MAT2(iz, 50, *nlev); | ^~~~ [ 39%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mikpckd.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.h:58, from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:55: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c: In function ‘Vxcopy’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_y’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:60:5: note: in expansion of macro ‘MAT3’ 60 | MAT3(y, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_x’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:59:5: note: in expansion of macro ‘MAT3’ 59 | MAT3(x, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c: In function ‘Vxcopy_small’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_y’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:78:5: note: in expansion of macro ‘MAT3’ 78 | MAT3(y, *nx - 2, *ny - 2, *nz - 2); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_x’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:77:5: note: in expansion of macro ‘MAT3’ 77 | MAT3(x, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c: In function ‘Vxcopy_large’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_y’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:99:5: note: in expansion of macro ‘MAT3’ 99 | MAT3(y, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_x’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:98:5: note: in expansion of macro ‘MAT3’ 98 | MAT3(x, *nx - 2, *ny - 2, *nz - 2); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c: In function ‘Vxaxpy’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_y’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:117:5: note: in expansion of macro ‘MAT3’ 117 | MAT3(y, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_x’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:116:5: note: in expansion of macro ‘MAT3’ 116 | MAT3(x, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c: In function ‘Vxnrm1’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_x’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:136:5: note: in expansion of macro ‘MAT3’ 136 | MAT3(x, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c: In function ‘Vxnrm2’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_x’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:157:5: note: in expansion of macro ‘MAT3’ 157 | MAT3(x, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c: In function ‘Vxdot’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_y’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:182:5: note: in expansion of macro ‘MAT3’ 182 | MAT3(y, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_x’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:181:5: note: in expansion of macro ‘MAT3’ 181 | MAT3(x, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c: In function ‘Vazeros’: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:198:9: warning: unused variable ‘nproc’ [-Wunused-variable] 198 | int nproc = 1; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c: In function ‘VfboundPMG’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_gzc’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:218:5: note: in expansion of macro ‘MAT3’ 218 | MAT3(gzc, *nx, *ny, 2); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_gyc’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:217:5: note: in expansion of macro ‘MAT3’ 217 | MAT3(gyc, *nx, *nz, 2); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_gxc’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:216:5: note: in expansion of macro ‘MAT3’ 216 | MAT3(gxc, *ny, *nz, 2); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_x’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:215:5: note: in expansion of macro ‘MAT3’ 215 | MAT3( x, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c: In function ‘VfboundPMG00’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_x’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:262:5: note: in expansion of macro ‘MAT3’ 262 | MAT3( x, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c: In function ‘Vaxrand’: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:295:12: warning: variable ‘xdum’ set but not used [-Wunused-but-set-variable] 295 | double xdum; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:293:33: warning: variable ‘iflag’ set but not used [-Wunused-but-set-variable] 293 | int n, i, ii, ipara, ivect, iflag; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:293:26: warning: variable ‘ivect’ set but not used [-Wunused-but-set-variable] 293 | int n, i, ii, ipara, ivect, iflag; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c: In function ‘Vxscal’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_x’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:322:5: note: in expansion of macro ‘MAT3’ 322 | MAT3(x, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c: In function ‘Vprtmatd’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_ac’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:337:5: note: in expansion of macro ‘MAT2’ 337 | MAT2(ac, *nx * *ny * *nz, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c: In function ‘Vprtmatd7’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:370:5: note: in expansion of macro ‘MAT3’ 370 | MAT3(uC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:369:5: note: in expansion of macro ‘MAT3’ 369 | MAT3(oN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:368:5: note: in expansion of macro ‘MAT3’ 368 | MAT3(oE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:367:5: note: in expansion of macro ‘MAT3’ 367 | MAT3(oC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c: In function ‘Vprtmatd27’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:415:5: note: in expansion of macro ‘MAT3’ 415 | MAT3(uSW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:414:5: note: in expansion of macro ‘MAT3’ 414 | MAT3(uSE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:413:5: note: in expansion of macro ‘MAT3’ 413 | MAT3(uNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:412:5: note: in expansion of macro ‘MAT3’ 412 | MAT3(uNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:411:5: note: in expansion of macro ‘MAT3’ 411 | MAT3( uS, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:410:5: note: in expansion of macro ‘MAT3’ 410 | MAT3( uN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:409:5: note: in expansion of macro ‘MAT3’ 409 | MAT3( uW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:408:5: note: in expansion of macro ‘MAT3’ 408 | MAT3( uE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:407:5: note: in expansion of macro ‘MAT3’ 407 | MAT3(oNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:406:5: note: in expansion of macro ‘MAT3’ 406 | MAT3(oNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:405:5: note: in expansion of macro ‘MAT3’ 405 | MAT3( uC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:404:5: note: in expansion of macro ‘MAT3’ 404 | MAT3( oN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:403:5: note: in expansion of macro ‘MAT3’ 403 | MAT3( oE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:402:5: note: in expansion of macro ‘MAT3’ 402 | MAT3( oC, *nx, *ny, *nz); | ^~~~ [ 40%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mlinpckd.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mlinpckd.h:57, from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mlinpckd.c:55: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mlinpckd.c: In function ‘Vdpbsl’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_abd’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mlinpckd.c:62:5: note: in expansion of macro ‘MAT2’ 62 | MAT2(abd, *lda, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mlinpckd.c: In function ‘Vdpbfa’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_abd’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mlinpckd.c:199:5: note: in expansion of macro ‘MAT2’ 199 | MAT2(abd, *lda, 1); | ^~~~ [ 41%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mypdec.c.o /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c: In function ‘Vmypdefinitsmpbe’: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:96:9: warning: unused variable ‘i’ [-Wunused-variable] 96 | int i; | ^ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c: In function ‘Vc_vecsmpbe’: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:223:26: warning: variable ‘ivect’ set but not used [-Wunused-but-set-variable] 223 | int n, i, ii, ipara, ivect; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:223:19: warning: variable ‘ipara’ set but not used [-Wunused-but-set-variable] 223 | int n, i, ii, ipara, ivect; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:223:15: warning: unused variable ‘ii’ [-Wunused-variable] 223 | int n, i, ii, ipara, ivect; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:222:9: warning: unused variable ‘iion’ [-Wunused-variable] 222 | int iion; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:219:28: warning: unused variable ‘fact’ [-Wunused-variable] 219 | double argument, poly, fact; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:219:22: warning: unused variable ‘poly’ [-Wunused-variable] 219 | double argument, poly, fact; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:219:12: warning: unused variable ‘argument’ [-Wunused-variable] 219 | double argument, poly, fact; | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:218:29: warning: unused variable ‘am_pos’ [-Wunused-variable] 218 | double am_zero, am_neg, am_pos; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:218:21: warning: unused variable ‘am_neg’ [-Wunused-variable] 218 | double am_zero, am_neg, am_pos; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:217:18: warning: unused variable ‘zu2’ [-Wunused-variable] 217 | double zcf2, zu2; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:217:12: warning: unused variable ‘zcf2’ [-Wunused-variable] 217 | double zcf2, zu2; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:216:9: warning: unused variable ‘ideg’ [-Wunused-variable] 216 | int ideg; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c: In function ‘Vdc_vec’: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:345:9: warning: unused variable ‘n’ [-Wunused-variable] 345 | int n = *nx * *ny * *nz; | ^ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:344:9: warning: unused variable ‘i’ [-Wunused-variable] 344 | int i; | ^ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c: In function ‘Vdc_vecpmg’: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:360:28: warning: unused variable ‘fact’ [-Wunused-variable] 360 | double argument, poly, fact; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:360:22: warning: unused variable ‘poly’ [-Wunused-variable] 360 | double argument, poly, fact; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:357:9: warning: unused variable ‘ideg’ [-Wunused-variable] 357 | int ideg, iion; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c: In function ‘Vdc_vecsmpbe’: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:433:16: warning: variable ‘ivect’ set but not used [-Wunused-but-set-variable] 433 | int ipara, ivect; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:433:9: warning: variable ‘ipara’ set but not used [-Wunused-but-set-variable] 433 | int ipara, ivect; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:432:15: warning: unused variable ‘ii’ [-Wunused-variable] 432 | int n, i, ii; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:429:28: warning: unused variable ‘fact’ [-Wunused-variable] 429 | double argument, poly, fact; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:429:22: warning: unused variable ‘poly’ [-Wunused-variable] 429 | double argument, poly, fact; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:429:12: warning: unused variable ‘argument’ [-Wunused-variable] 429 | double argument, poly, fact; | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:428:29: warning: unused variable ‘am_pos’ [-Wunused-variable] 428 | double am_zero, am_neg, am_pos; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:428:21: warning: unused variable ‘am_neg’ [-Wunused-variable] 428 | double am_zero, am_neg, am_pos; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:427:18: warning: unused variable ‘zu2’ [-Wunused-variable] 427 | double zcf2, zu2; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:427:12: warning: unused variable ‘zcf2’ [-Wunused-variable] 427 | double zcf2, zu2; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:426:15: warning: unused variable ‘iion’ [-Wunused-variable] 426 | int ideg, iion; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:426:9: warning: unused variable ‘ideg’ [-Wunused-variable] 426 | int ideg, iion; | ^~~~ [ 42%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/newtond.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newtond.h:57, from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newtond.c:56: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newtond.c: In function ‘Vfnewton’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_iz’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newtond.c:77:5: note: in expansion of macro ‘MAT2’ 77 | MAT2( iz, 50, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newtond.c: In function ‘Vnewton’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_iz’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newtond.c:187:5: note: in expansion of macro ‘MAT2’ 187 | MAT2(iz, 50, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newtond.c: In function ‘Vgetjac’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_iz’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newtond.c:560:5: note: in expansion of macro ‘MAT2’ 560 | MAT2(iz, 50, 1); | ^~~~ [ 43%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/newdrvd.c.o /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c: In function ‘Vnewdriv’: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c:86:9: warning: unused variable ‘maxlev’ [-Wunused-variable] 86 | int maxlev; /// @todo: Doc | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c:85:9: warning: unused variable ‘ierror’ [-Wunused-variable] 85 | int ierror; /// @todo: Doc | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c: In function ‘Vnewdriv2’: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c:223:9: warning: unused variable ‘i’ [-Wunused-variable] 223 | int i; | ^ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c:221:12: warning: unused variable ‘orsnrm_t’ [-Wunused-variable] 221 | double orsnrm_t; | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c:220:12: warning: unused variable ‘rsden_t’ [-Wunused-variable] 220 | double rsden_t; | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c:219:12: warning: unused variable ‘rsnrm_t’ [-Wunused-variable] 219 | double rsnrm_t; | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c:218:9: warning: unused variable ‘iters_t’ [-Wunused-variable] 218 | int iters_t; | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c:217:9: warning: unused variable ‘iok_t’ [-Wunused-variable] 217 | int iok_t; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c:215:9: warning: unused variable ‘numlev’ [-Wunused-variable] 215 | int numlev; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c:210:12: warning: unused variable ‘tsolve’ [-Wunused-variable] 210 | double tsolve; /// @todo: Doc | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c:209:12: warning: unused variable ‘tsetupc’ [-Wunused-variable] 209 | double tsetupc; /// @todo: Doc | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c:208:12: warning: unused variable ‘tsetupf’ [-Wunused-variable] 208 | double tsetupf; /// @todo: Doc | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c:207:12: warning: unused variable ‘oh’ [-Wunused-variable] 207 | double oh; /// @todo: Doc | ^~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c:206:12: warning: unused variable ‘bf’ [-Wunused-variable] 206 | double bf; /// @todo: Doc | ^~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c:204:12: warning: variable ‘omegal’ set but not used [-Wunused-but-set-variable] 204 | double omegal; /// @todo: Doc | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c:202:12: warning: unused variable ‘epsmac’ [-Wunused-variable] 202 | double epsmac; /// @todo: Doc | ^~~~~~ [ 44%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/powerd.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/powerd.h:57, from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/powerd.c:55: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/powerd.c: In function ‘Vpower’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_iz’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/powerd.c:74:5: note: in expansion of macro ‘MAT2’ 74 | MAT2(iz, 50, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/powerd.c:71:9: warning: unused variable ‘skipIters’ [-Wunused-variable] 71 | int skipIters = 0; | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/powerd.c: In function ‘Vipower’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_iz’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/powerd.c:188:5: note: in expansion of macro ‘MAT2’ 188 | MAT2(iz, 50, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/powerd.c: In function ‘Vmpower’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_iz’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/powerd.c:311:5: note: in expansion of macro ‘MAT2’ 311 | MAT2(iz, 50, 1); | ^~~~ [ 45%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/smoothd.c.o [ 47%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgfasd.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/smoothd.h:57, from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgfasd.h:57, from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgfasd.c:55: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgfasd.c: In function ‘Vfmvfas’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_iz’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgfasd.c:79:5: note: in expansion of macro ‘MAT2’ 79 | MAT2(iz, 50, *nlev); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgfasd.c:74:12: warning: variable ‘errd’ set but not used [-Wunused-but-set-variable] 74 | double errd; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgfasd.c: In function ‘Vmvfas’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_iz’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgfasd.c:182:5: note: in expansion of macro ‘MAT2’ 182 | MAT2(iz, 50, *nlev); | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgfasd.c:171:33: warning: unused variable ‘ivariv’ [-Wunused-variable] 171 | int itmax_s, iters_s, nuuu, ivariv, mgsmoo_s, iresid; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgfasd.c:254:13: warning: ‘rsden’ may be used uninitialized [-Wmaybe-uninitialized] 254 | if (rsden == 0.0) { | ^ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgfasd.c:176:12: note: ‘rsden’ was declared here 176 | double rsden, rsnrm, orsnrm; | ^~~~~ [ 47%] Built target apbs_pmgc [ 48%] Linking C shared library ../lib/libapbs.so [ 48%] Built target apbs [ 49%] Building C object src/CMakeFiles/apbs_routines.dir/routines.c.o /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function ‘loadDielMaps’: /builddir/build/BUILD/apbs-3.0.0/src/routines.c:296:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 296 | for (ii=0; ii<(nx*ny*nz); ii++) | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:298:21: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 298 | sum = sum*hx*hy*hzed; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:331:9: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 331 | for (ii=0; ii<(nx*ny*nz); ii++) | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:333:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 333 | sum = sum*hx*hy*hzed; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:420:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 420 | for (ii=0; ii<(nx*ny*nz); ii++) | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:422:21: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 422 | sum = sum*hx*hy*hzed; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:454:9: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 454 | for (ii=0; ii<(nx*ny*nz); ii++) | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:456:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 456 | sum = sum*hx*hy*hzed; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function ‘initMG’: /builddir/build/BUILD/apbs-3.0.0/src/routines.c:1234:12: warning: variable ‘iparm’ set but not used [-Wunused-but-set-variable] 1234 | iparm, | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function ‘energyMG’: /builddir/build/BUILD/apbs-3.0.0/src/routines.c:1584:13: warning: variable ‘mgparm’ set but not used [-Wunused-but-set-variable] 1584 | MGparm *mgparm; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function ‘writematMG’: /builddir/build/BUILD/apbs-3.0.0/src/routines.c:1803:10: warning: variable ‘mxtype’ set but not used [-Wunused-but-set-variable] 1803 | char mxtype[3]; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function ‘printApolForce’: /builddir/build/BUILD/apbs-3.0.0/src/routines.c:3485:12: warning: variable ‘scalar’ set but not used [-Wunused-but-set-variable] 3485 | scalar, | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:3484:12: warning: variable ‘temp’ set but not used [-Wunused-but-set-variable] 3484 | double temp, | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function ‘initAPOL’: /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4496:12: warning: variable ‘sav’ set but not used [-Wunused-but-set-variable] 4496 | sav, /**< @todo document */ | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4495:12: warning: variable ‘sasa’ set but not used [-Wunused-but-set-variable] 4495 | double sasa, /**< @todo document */ | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4489:12: warning: unused variable ‘ts’ [-Wunused-variable] 4489 | time_t ts; /**< Temporary timing variable for debugging (PCE) */ | ^~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function ‘forceAPOL’: /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4753:13: warning: unused variable ‘apos’ [-Wunused-variable] 4753 | *apos; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4737:46: warning: unused variable ‘ts_sub’ [-Wunused-variable] 4737 | time_t ts, ts_main, ts_sub; | ^~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/src/routines.h:64, from /builddir/build/BUILD/apbs-3.0.0/src/routines.c:54: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h: At top level: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: ‘GEOFLOWparm_parseVDW’ declared ‘static’ but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: ‘GEOFLOWparm_parseETOL’ declared ‘static’ but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: ‘PBAMparm_parseSalt’ declared ‘static’ but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: ‘PBAMparm_parseRunType’ declared ‘static’ but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: ‘PBAMparm_parseRunName’ declared ‘static’ but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: ‘PBAMparm_parseRandorient’ declared ‘static’ but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: ‘PBAMparm_parsePBCS’ declared ‘static’ but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: ‘PBAMparm_parseUnits’ declared ‘static’ but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: ‘PBAMparm_parse3Dmap’ declared ‘static’ but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: ‘PBAMparm_parseGrid2D’ declared ‘static’ but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: ‘PBAMparm_parseDX’ declared ‘static’ but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: ‘PBAMparm_parseGridPts’ declared ‘static’ but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: ‘PBAMparm_parseTermcombine’ declared ‘static’ but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: ‘PBAMparm_parseDiff’ declared ‘static’ but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: ‘PBAMparm_parseXYZ’ declared ‘static’ but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: ‘PBSAMparm_parseTolsp’ declared ‘static’ but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: ‘PBSAMparm_parseSurf’ declared ‘static’ but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: ‘PBSAMparm_parseImat’ declared ‘static’ but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: ‘PBSAMparm_parseExp’ declared ‘static’ but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: ‘PBSAMparm_parseMSMS’ declared ‘static’ but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: ‘bcolcomp’ declared ‘static’ but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: ‘bcolcomp2’ declared ‘static’ but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: ‘bcolcomp3’ declared ‘static’ but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: ‘bcolcomp4’ declared ‘static’ but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: ‘pcolcomp’ declared ‘static’ but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: ‘bspline2’ declared ‘static’ but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: ‘dbspline2’ declared ‘static’ but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: ‘VFCHI4’ declared ‘static’ but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: ‘bspline4’ declared ‘static’ but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: ‘dbspline4’ declared ‘static’ but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: ‘d2bspline4’ declared ‘static’ but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: ‘d3bspline4’ declared ‘static’ but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: ‘Vpmg_polarizEnergy’ declared ‘static’ but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: ‘Vpmg_qfEnergyPoint’ declared ‘static’ but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: ‘Vpmg_qfEnergyVolume’ declared ‘static’ but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: ‘Vpmg_splineSelect’ declared ‘static’ but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: ‘focusFillBound’ declared ‘static’ but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: ‘bcfl1’ declared ‘static’ but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: ‘bcfl2’ declared ‘static’ but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: ‘multipolebc’ declared ‘static’ but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: ‘bcfl1sp’ declared ‘static’ but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: ‘bcCalc’ declared ‘static’ but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: ‘fillcoCoef’ declared ‘static’ but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: ‘fillcoCoefMap’ declared ‘static’ but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: ‘fillcoCoefMol’ declared ‘static’ but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: ‘fillcoCoefMolIon’ declared ‘static’ but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: ‘fillcoCoefMolDiel’ declared ‘static’ but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: ‘fillcoCoefMolDielNoSmooth’ declared ‘static’ but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: ‘fillcoCoefMolDielSmooth’ declared ‘static’ but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: ‘fillcoCoefSpline’ declared ‘static’ but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: ‘fillcoCoefSpline3’ declared ‘static’ but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: ‘fillcoCoefSpline4’ declared ‘static’ but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: ‘fillcoCharge’ declared ‘static’ but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: ‘fillcoChargeMap’ declared ‘static’ but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: ‘fillcoChargeSpline1’ declared ‘static’ but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: ‘fillcoChargeSpline2’ declared ‘static’ but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: ‘fillcoPermanentMultipole’ declared ‘static’ but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: ‘fillcoInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: ‘fillcoNLInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: ‘extEnergy’ declared ‘static’ but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: ‘qfForceSpline1’ declared ‘static’ but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: ‘qfForceSpline2’ declared ‘static’ but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: ‘qfForceSpline4’ declared ‘static’ but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: ‘zlapSolve’ declared ‘static’ but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: ‘markSphere’ declared ‘static’ but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: ‘Vpmg_qmEnergySMPBE’ declared ‘static’ but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: ‘Vpmg_qmEnergyNONLIN’ declared ‘static’ but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function ‘initAPOL’: /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4590:20: warning: ‘Vparam_getAtomData’ accessing 1024 bytes in a region of size 4 [-Wstringop-overflow=] 4590 | atomData = Vparam_getAtomData(param, "WAT", "OW"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4590:20: note: referencing argument 2 of type ‘char[1024]’ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4590:20: warning: ‘Vparam_getAtomData’ accessing 1024 bytes in a region of size 3 [-Wstringop-overflow=] /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4590:20: note: referencing argument 3 of type ‘char[1024]’ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/apolparm.h:73, from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:73: /builddir/build/BUILD/apbs-3.0.0/src/generic/vparam.h:304:27: note: in a call to function ‘Vparam_getAtomData’ 304 | VEXTERNC Vparam_AtomData* Vparam_getAtomData(Vparam *thee, | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4591:43: warning: ‘Vparam_getAtomData’ accessing 1024 bytes in a region of size 4 [-Wstringop-overflow=] 4591 | if (atomData == VNULL) atomData = Vparam_getAtomData(param, "WAT", "O"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4591:43: note: referencing argument 2 of type ‘char[1024]’ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4591:43: warning: ‘Vparam_getAtomData’ accessing 1024 bytes in a region of size 2 [-Wstringop-overflow=] /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4591:43: note: referencing argument 3 of type ‘char[1024]’ /builddir/build/BUILD/apbs-3.0.0/src/generic/vparam.h:304:27: note: in a call to function ‘Vparam_getAtomData’ 304 | VEXTERNC Vparam_AtomData* Vparam_getAtomData(Vparam *thee, | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function ‘writematMG’: /builddir/build/BUILD/apbs-3.0.0/src/routines.c:1826:34: warning: ‘-PE’ directive writing 3 bytes into a region of size between 1 and 1024 [-Wformat-overflow=] 1826 | sprintf(writematstem, "%s-PE%d", pbeparm->writematstem,nosh->proc_rank); | ^~~ In file included from /usr/include/stdio.h:964, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:67: In function ‘sprintf’, inlined from ‘writematMG’ at /builddir/build/BUILD/apbs-3.0.0/src/routines.c:1826:9: /usr/include/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 1038 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function ‘writematMG’: /builddir/build/BUILD/apbs-3.0.0/src/routines.c:1840:30: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 1840 | sprintf(outpath, "%s.%s", writematstem, "mat"); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘writematMG’ at /builddir/build/BUILD/apbs-3.0.0/src/routines.c:1840:9: /usr/include/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 1028 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function ‘writedataFlat’: /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2105:33: warning: ‘scalar’ may be used uninitialized [-Wmaybe-uninitialized] 2105 | ltenergy += (scalar * Vunit_kb * (1e-3) * Vunit_Na * /builddir/build/BUILD/apbs-3.0.0/src/routines.c:1906:44: note: ‘scalar’ was declared here 1906 | double conversion, ltenergy, gtenergy, scalar; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function ‘writedataXML’: /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2363:33: warning: ‘scalar’ may be used uninitialized [-Wmaybe-uninitialized] 2363 | ltenergy += (scalar * Vunit_kb * (1e-3) * Vunit_Na * /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2140:44: note: ‘scalar’ was declared here 2140 | double conversion, ltenergy, gtenergy, scalar; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function ‘writedataMG’: /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2676:30: warning: ‘%s’ directive writing 5 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2676 | sprintf(outpath, "%s.%s", writestem, "dxbin"); | ^~ ~~~~~~~ In function ‘sprintf’, inlined from ‘writedataMG’ at /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2676:9: /usr/include/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 7 and 1030 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function ‘writedataMG’: /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2720:38: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2720 | sprintf(outpath, "%s.%s", writestem, "txt"); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘writedataMG’ at /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2720:17: /usr/include/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 1028 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function ‘writedataMG’: /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2711:38: warning: ‘%s’ directive writing 5 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2711 | sprintf(outpath, "%s.%s", writestem, "dx.gz"); | ^~ ~~~~~~~ In function ‘sprintf’, inlined from ‘writedataMG’ at /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2711:17: /usr/include/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 7 and 1030 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function ‘writedataMG’: /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2694:38: warning: ‘%s’ directive writing 4 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2694 | sprintf(outpath, "%s.%s", writestem, "mcsf"); | ^~ ~~~~~~ In function ‘sprintf’, inlined from ‘writedataMG’ at /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2694:17: /usr/include/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 6 and 1029 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function ‘writedataMG’: /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2687:38: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2687 | sprintf(outpath, "%s.%s", writestem, "ucd"); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘writedataMG’ at /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2687:17: /usr/include/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 1028 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function ‘writedataMG’: /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2701:38: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2701 | sprintf(outpath, "%s.%s", writestem, "grd"); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘writedataMG’ at /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2701:17: /usr/include/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 1028 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function ‘writedataMG’: /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2666:38: warning: ‘%s’ directive writing 2 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2666 | sprintf(outpath, "%s.%s", writestem, "dx"); | ^~ ~~~~ In function ‘sprintf’, inlined from ‘writedataMG’ at /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2666:17: /usr/include/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 4 and 1027 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function ‘returnEnergy’: /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2778:29: warning: ‘scalar’ may be used uninitialized [-Wmaybe-uninitialized] 2778 | ltenergy += (scalar * Vunit_kb * (1e-3) * Vunit_Na * /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2762:12: note: ‘scalar’ was declared here 2762 | scalar; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function ‘printEnergy’: /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2839:29: warning: ‘scalar’ may be used uninitialized [-Wmaybe-uninitialized] 2839 | ltenergy += (scalar * Vunit_kb * (1e-3) * Vunit_Na * /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2795:12: note: ‘scalar’ was declared here 2795 | scalar; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function ‘printElecEnergy’: /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2904:29: warning: ‘scalar’ may be used uninitialized [-Wmaybe-uninitialized] 2904 | ltenergy += (scalar * Vunit_kb * (1e-3) * Vunit_Na * /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2863:12: note: ‘scalar’ was declared here 2863 | scalar; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function ‘printApolEnergy’: /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2970:29: warning: ‘scalar’ may be used uninitialized [-Wmaybe-uninitialized] 2970 | gtenergy += (scalar * ((apolparm->gamma*apolparm->sasa) + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2971 | (apolparm->press*apolparm->sav) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2972 | (apolparm->wcaEnergy))); | ~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2925:12: note: ‘scalar’ was declared here 2925 | scalar; | ^~~~~~ [ 49%] Built target apbs_routines [ 50%] Building C object src/CMakeFiles/apbs-bin.dir/main.c.o /builddir/build/BUILD/apbs-3.0.0/src/main.c: In function ‘main’: /builddir/build/BUILD/apbs-3.0.0/src/main.c:117:11: warning: unused variable ‘gm’ [-Wunused-variable] 117 | void *gm[NOSH_MAXMOL]; | ^~ /builddir/build/BUILD/apbs-3.0.0/src/main.c:116:11: warning: variable ‘fetk’ set but not used [-Wunused-but-set-variable] 116 | void *fetk[NOSH_MAXCALC]; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/main.c:96:18: warning: unused variable ‘geoflowparm’ [-Wunused-variable] 96 | GEOFLOWparm *geoflowparm = VNULL; | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/main.c:92:14: warning: unused variable ‘feparm’ [-Wunused-variable] 92 | FEMparm *feparm = VNULL; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/main.c:86:17: warning: unused variable ‘te’ [-Wunused-variable] 86 | clock_t ts, te; | ^~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/src/routines.h:64, from /builddir/build/BUILD/apbs-3.0.0/src/main.c:70: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h: At top level: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: ‘GEOFLOWparm_parseVDW’ declared ‘static’ but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: ‘GEOFLOWparm_parseETOL’ declared ‘static’ but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: ‘PBAMparm_parseSalt’ declared ‘static’ but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: ‘PBAMparm_parseRunType’ declared ‘static’ but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: ‘PBAMparm_parseRunName’ declared ‘static’ but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: ‘PBAMparm_parseRandorient’ declared ‘static’ but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: ‘PBAMparm_parsePBCS’ declared ‘static’ but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: ‘PBAMparm_parseUnits’ declared ‘static’ but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: ‘PBAMparm_parse3Dmap’ declared ‘static’ but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: ‘PBAMparm_parseGrid2D’ declared ‘static’ but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: ‘PBAMparm_parseDX’ declared ‘static’ but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: ‘PBAMparm_parseGridPts’ declared ‘static’ but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: ‘PBAMparm_parseTermcombine’ declared ‘static’ but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: ‘PBAMparm_parseDiff’ declared ‘static’ but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: ‘PBAMparm_parseXYZ’ declared ‘static’ but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: ‘PBSAMparm_parseTolsp’ declared ‘static’ but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: ‘PBSAMparm_parseSurf’ declared ‘static’ but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: ‘PBSAMparm_parseImat’ declared ‘static’ but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: ‘PBSAMparm_parseExp’ declared ‘static’ but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: ‘PBSAMparm_parseMSMS’ declared ‘static’ but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: ‘bcolcomp’ declared ‘static’ but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: ‘bcolcomp2’ declared ‘static’ but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: ‘bcolcomp3’ declared ‘static’ but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: ‘bcolcomp4’ declared ‘static’ but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: ‘pcolcomp’ declared ‘static’ but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: ‘bspline2’ declared ‘static’ but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: ‘dbspline2’ declared ‘static’ but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: ‘VFCHI4’ declared ‘static’ but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: ‘bspline4’ declared ‘static’ but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: ‘dbspline4’ declared ‘static’ but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: ‘d2bspline4’ declared ‘static’ but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: ‘d3bspline4’ declared ‘static’ but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: ‘Vpmg_polarizEnergy’ declared ‘static’ but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: ‘Vpmg_qfEnergyPoint’ declared ‘static’ but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: ‘Vpmg_qfEnergyVolume’ declared ‘static’ but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: ‘Vpmg_splineSelect’ declared ‘static’ but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: ‘focusFillBound’ declared ‘static’ but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: ‘bcfl1’ declared ‘static’ but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: ‘bcfl2’ declared ‘static’ but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: ‘multipolebc’ declared ‘static’ but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: ‘bcfl1sp’ declared ‘static’ but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: ‘bcCalc’ declared ‘static’ but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: ‘fillcoCoef’ declared ‘static’ but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: ‘fillcoCoefMap’ declared ‘static’ but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: ‘fillcoCoefMol’ declared ‘static’ but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: ‘fillcoCoefMolIon’ declared ‘static’ but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: ‘fillcoCoefMolDiel’ declared ‘static’ but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: ‘fillcoCoefMolDielNoSmooth’ declared ‘static’ but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: ‘fillcoCoefMolDielSmooth’ declared ‘static’ but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: ‘fillcoCoefSpline’ declared ‘static’ but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: ‘fillcoCoefSpline3’ declared ‘static’ but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: ‘fillcoCoefSpline4’ declared ‘static’ but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: ‘fillcoCharge’ declared ‘static’ but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: ‘fillcoChargeMap’ declared ‘static’ but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: ‘fillcoChargeSpline1’ declared ‘static’ but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: ‘fillcoChargeSpline2’ declared ‘static’ but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: ‘fillcoPermanentMultipole’ declared ‘static’ but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: ‘fillcoInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: ‘fillcoNLInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: ‘extEnergy’ declared ‘static’ but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: ‘qfForceSpline1’ declared ‘static’ but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: ‘qfForceSpline2’ declared ‘static’ but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: ‘qfForceSpline4’ declared ‘static’ but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: ‘zlapSolve’ declared ‘static’ but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: ‘markSphere’ declared ‘static’ but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: ‘Vpmg_qmEnergySMPBE’ declared ‘static’ but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: ‘Vpmg_qmEnergyNONLIN’ declared ‘static’ but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ [ 51%] Building C object src/CMakeFiles/apbs-bin.dir/routines.c.o /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function ‘loadDielMaps’: /builddir/build/BUILD/apbs-3.0.0/src/routines.c:296:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 296 | for (ii=0; ii<(nx*ny*nz); ii++) | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:298:21: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 298 | sum = sum*hx*hy*hzed; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:331:9: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 331 | for (ii=0; ii<(nx*ny*nz); ii++) | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:333:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 333 | sum = sum*hx*hy*hzed; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:420:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 420 | for (ii=0; ii<(nx*ny*nz); ii++) | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:422:21: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 422 | sum = sum*hx*hy*hzed; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:454:9: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 454 | for (ii=0; ii<(nx*ny*nz); ii++) | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:456:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 456 | sum = sum*hx*hy*hzed; | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function ‘initMG’: /builddir/build/BUILD/apbs-3.0.0/src/routines.c:1234:12: warning: variable ‘iparm’ set but not used [-Wunused-but-set-variable] 1234 | iparm, | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function ‘energyMG’: /builddir/build/BUILD/apbs-3.0.0/src/routines.c:1584:13: warning: variable ‘mgparm’ set but not used [-Wunused-but-set-variable] 1584 | MGparm *mgparm; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function ‘writematMG’: /builddir/build/BUILD/apbs-3.0.0/src/routines.c:1803:10: warning: variable ‘mxtype’ set but not used [-Wunused-but-set-variable] 1803 | char mxtype[3]; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function ‘printApolForce’: /builddir/build/BUILD/apbs-3.0.0/src/routines.c:3485:12: warning: variable ‘scalar’ set but not used [-Wunused-but-set-variable] 3485 | scalar, | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:3484:12: warning: variable ‘temp’ set but not used [-Wunused-but-set-variable] 3484 | double temp, | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function ‘initAPOL’: /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4496:12: warning: variable ‘sav’ set but not used [-Wunused-but-set-variable] 4496 | sav, /**< @todo document */ | ^~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4495:12: warning: variable ‘sasa’ set but not used [-Wunused-but-set-variable] 4495 | double sasa, /**< @todo document */ | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4489:12: warning: unused variable ‘ts’ [-Wunused-variable] 4489 | time_t ts; /**< Temporary timing variable for debugging (PCE) */ | ^~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function ‘forceAPOL’: /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4753:13: warning: unused variable ‘apos’ [-Wunused-variable] 4753 | *apos; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4737:46: warning: unused variable ‘ts_sub’ [-Wunused-variable] 4737 | time_t ts, ts_main, ts_sub; | ^~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/src/routines.h:64, from /builddir/build/BUILD/apbs-3.0.0/src/routines.c:54: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h: At top level: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: ‘GEOFLOWparm_parseVDW’ declared ‘static’ but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: ‘GEOFLOWparm_parseETOL’ declared ‘static’ but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: ‘PBAMparm_parseSalt’ declared ‘static’ but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: ‘PBAMparm_parseRunType’ declared ‘static’ but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: ‘PBAMparm_parseRunName’ declared ‘static’ but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: ‘PBAMparm_parseRandorient’ declared ‘static’ but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: ‘PBAMparm_parsePBCS’ declared ‘static’ but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: ‘PBAMparm_parseUnits’ declared ‘static’ but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: ‘PBAMparm_parse3Dmap’ declared ‘static’ but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: ‘PBAMparm_parseGrid2D’ declared ‘static’ but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: ‘PBAMparm_parseDX’ declared ‘static’ but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: ‘PBAMparm_parseGridPts’ declared ‘static’ but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: ‘PBAMparm_parseTermcombine’ declared ‘static’ but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: ‘PBAMparm_parseDiff’ declared ‘static’ but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: ‘PBAMparm_parseXYZ’ declared ‘static’ but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: ‘PBSAMparm_parseTolsp’ declared ‘static’ but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: ‘PBSAMparm_parseSurf’ declared ‘static’ but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: ‘PBSAMparm_parseImat’ declared ‘static’ but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: ‘PBSAMparm_parseExp’ declared ‘static’ but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: ‘PBSAMparm_parseMSMS’ declared ‘static’ but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: ‘bcolcomp’ declared ‘static’ but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: ‘bcolcomp2’ declared ‘static’ but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: ‘bcolcomp3’ declared ‘static’ but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: ‘bcolcomp4’ declared ‘static’ but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: ‘pcolcomp’ declared ‘static’ but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: ‘bspline2’ declared ‘static’ but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: ‘dbspline2’ declared ‘static’ but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: ‘VFCHI4’ declared ‘static’ but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: ‘bspline4’ declared ‘static’ but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: ‘dbspline4’ declared ‘static’ but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: ‘d2bspline4’ declared ‘static’ but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: ‘d3bspline4’ declared ‘static’ but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: ‘Vpmg_polarizEnergy’ declared ‘static’ but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: ‘Vpmg_qfEnergyPoint’ declared ‘static’ but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: ‘Vpmg_qfEnergyVolume’ declared ‘static’ but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: ‘Vpmg_splineSelect’ declared ‘static’ but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: ‘focusFillBound’ declared ‘static’ but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: ‘bcfl1’ declared ‘static’ but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: ‘bcfl2’ declared ‘static’ but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: ‘multipolebc’ declared ‘static’ but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: ‘bcfl1sp’ declared ‘static’ but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: ‘bcCalc’ declared ‘static’ but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: ‘fillcoCoef’ declared ‘static’ but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: ‘fillcoCoefMap’ declared ‘static’ but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: ‘fillcoCoefMol’ declared ‘static’ but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: ‘fillcoCoefMolIon’ declared ‘static’ but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: ‘fillcoCoefMolDiel’ declared ‘static’ but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: ‘fillcoCoefMolDielNoSmooth’ declared ‘static’ but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: ‘fillcoCoefMolDielSmooth’ declared ‘static’ but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: ‘fillcoCoefSpline’ declared ‘static’ but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: ‘fillcoCoefSpline3’ declared ‘static’ but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: ‘fillcoCoefSpline4’ declared ‘static’ but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: ‘fillcoCharge’ declared ‘static’ but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: ‘fillcoChargeMap’ declared ‘static’ but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: ‘fillcoChargeSpline1’ declared ‘static’ but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: ‘fillcoChargeSpline2’ declared ‘static’ but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: ‘fillcoPermanentMultipole’ declared ‘static’ but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: ‘fillcoInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: ‘fillcoNLInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: ‘extEnergy’ declared ‘static’ but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: ‘qfForceSpline1’ declared ‘static’ but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: ‘qfForceSpline2’ declared ‘static’ but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: ‘qfForceSpline4’ declared ‘static’ but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: ‘zlapSolve’ declared ‘static’ but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: ‘markSphere’ declared ‘static’ but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: ‘Vpmg_qmEnergySMPBE’ declared ‘static’ but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: ‘Vpmg_qmEnergyNONLIN’ declared ‘static’ but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function ‘initAPOL’: /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4590:20: warning: ‘Vparam_getAtomData’ accessing 1024 bytes in a region of size 4 [-Wstringop-overflow=] 4590 | atomData = Vparam_getAtomData(param, "WAT", "OW"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4590:20: note: referencing argument 2 of type ‘char[1024]’ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4590:20: warning: ‘Vparam_getAtomData’ accessing 1024 bytes in a region of size 3 [-Wstringop-overflow=] /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4590:20: note: referencing argument 3 of type ‘char[1024]’ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/apolparm.h:73, from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:73: /builddir/build/BUILD/apbs-3.0.0/src/generic/vparam.h:304:27: note: in a call to function ‘Vparam_getAtomData’ 304 | VEXTERNC Vparam_AtomData* Vparam_getAtomData(Vparam *thee, | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4591:43: warning: ‘Vparam_getAtomData’ accessing 1024 bytes in a region of size 4 [-Wstringop-overflow=] 4591 | if (atomData == VNULL) atomData = Vparam_getAtomData(param, "WAT", "O"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4591:43: note: referencing argument 2 of type ‘char[1024]’ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4591:43: warning: ‘Vparam_getAtomData’ accessing 1024 bytes in a region of size 2 [-Wstringop-overflow=] /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4591:43: note: referencing argument 3 of type ‘char[1024]’ /builddir/build/BUILD/apbs-3.0.0/src/generic/vparam.h:304:27: note: in a call to function ‘Vparam_getAtomData’ 304 | VEXTERNC Vparam_AtomData* Vparam_getAtomData(Vparam *thee, | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function ‘writematMG’: /builddir/build/BUILD/apbs-3.0.0/src/routines.c:1826:34: warning: ‘-PE’ directive writing 3 bytes into a region of size between 1 and 1024 [-Wformat-overflow=] 1826 | sprintf(writematstem, "%s-PE%d", pbeparm->writematstem,nosh->proc_rank); | ^~~ In file included from /usr/include/stdio.h:964, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:67: In function ‘sprintf’, inlined from ‘writematMG’ at /builddir/build/BUILD/apbs-3.0.0/src/routines.c:1826:9: /usr/include/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 1038 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function ‘writematMG’: /builddir/build/BUILD/apbs-3.0.0/src/routines.c:1840:30: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 1840 | sprintf(outpath, "%s.%s", writematstem, "mat"); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘writematMG’ at /builddir/build/BUILD/apbs-3.0.0/src/routines.c:1840:9: /usr/include/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 1028 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function ‘writedataFlat’: /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2105:33: warning: ‘scalar’ may be used uninitialized [-Wmaybe-uninitialized] 2105 | ltenergy += (scalar * Vunit_kb * (1e-3) * Vunit_Na * /builddir/build/BUILD/apbs-3.0.0/src/routines.c:1906:44: note: ‘scalar’ was declared here 1906 | double conversion, ltenergy, gtenergy, scalar; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function ‘writedataXML’: /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2363:33: warning: ‘scalar’ may be used uninitialized [-Wmaybe-uninitialized] 2363 | ltenergy += (scalar * Vunit_kb * (1e-3) * Vunit_Na * /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2140:44: note: ‘scalar’ was declared here 2140 | double conversion, ltenergy, gtenergy, scalar; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function ‘writedataMG’: /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2676:30: warning: ‘%s’ directive writing 5 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2676 | sprintf(outpath, "%s.%s", writestem, "dxbin"); | ^~ ~~~~~~~ In function ‘sprintf’, inlined from ‘writedataMG’ at /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2676:9: /usr/include/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 7 and 1030 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function ‘writedataMG’: /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2720:38: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2720 | sprintf(outpath, "%s.%s", writestem, "txt"); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘writedataMG’ at /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2720:17: /usr/include/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 1028 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function ‘writedataMG’: /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2711:38: warning: ‘%s’ directive writing 5 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2711 | sprintf(outpath, "%s.%s", writestem, "dx.gz"); | ^~ ~~~~~~~ In function ‘sprintf’, inlined from ‘writedataMG’ at /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2711:17: /usr/include/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 7 and 1030 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function ‘writedataMG’: /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2694:38: warning: ‘%s’ directive writing 4 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2694 | sprintf(outpath, "%s.%s", writestem, "mcsf"); | ^~ ~~~~~~ In function ‘sprintf’, inlined from ‘writedataMG’ at /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2694:17: /usr/include/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 6 and 1029 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function ‘writedataMG’: /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2687:38: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2687 | sprintf(outpath, "%s.%s", writestem, "ucd"); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘writedataMG’ at /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2687:17: /usr/include/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 1028 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function ‘writedataMG’: /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2701:38: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2701 | sprintf(outpath, "%s.%s", writestem, "grd"); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘writedataMG’ at /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2701:17: /usr/include/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 1028 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function ‘writedataMG’: /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2666:38: warning: ‘%s’ directive writing 2 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2666 | sprintf(outpath, "%s.%s", writestem, "dx"); | ^~ ~~~~ In function ‘sprintf’, inlined from ‘writedataMG’ at /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2666:17: /usr/include/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 4 and 1027 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function ‘returnEnergy’: /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2778:29: warning: ‘scalar’ may be used uninitialized [-Wmaybe-uninitialized] 2778 | ltenergy += (scalar * Vunit_kb * (1e-3) * Vunit_Na * /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2762:12: note: ‘scalar’ was declared here 2762 | scalar; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function ‘printEnergy’: /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2839:29: warning: ‘scalar’ may be used uninitialized [-Wmaybe-uninitialized] 2839 | ltenergy += (scalar * Vunit_kb * (1e-3) * Vunit_Na * /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2795:12: note: ‘scalar’ was declared here 2795 | scalar; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function ‘printElecEnergy’: /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2904:29: warning: ‘scalar’ may be used uninitialized [-Wmaybe-uninitialized] 2904 | ltenergy += (scalar * Vunit_kb * (1e-3) * Vunit_Na * /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2863:12: note: ‘scalar’ was declared here 2863 | scalar; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function ‘printApolEnergy’: /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2970:29: warning: ‘scalar’ may be used uninitialized [-Wmaybe-uninitialized] 2970 | gtenergy += (scalar * ((apolparm->gamma*apolparm->sasa) + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2971 | (apolparm->press*apolparm->sav) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2972 | (apolparm->wcaEnergy))); | ~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2925:12: note: ‘scalar’ was declared here 2925 | scalar; | ^~~~~~ [ 52%] Linking C executable ../bin/apbs [ 52%] Built target apbs-bin [ 54%] Generating documentation with Doxygen warning: Tag 'TCL_SUBST' at line 213 of file '/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'COLS_IN_ALPHA_INDEX' at line 857 of file '/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'HTML_TIMESTAMP' at line 953 of file '/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'FORMULA_TRANSPARENT' at line 1175 of file '/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'LATEX_SOURCE_CODE' at line 1313 of file '/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'PERL_PATH' at line 1565 of file '/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'CLASS_DIAGRAMS' at line 1577 of file '/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'MSCGEN_PATH' at line 1586 of file '/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'DOT_FONTNAME' at line 1616 of file '/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'DOT_FONTSIZE' at line 1621 of file '/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'DOT_TRANSPARENT' at line 1770 of file '/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: tag INPUT: input source '/builddir/build/BUILD/apbs-3.0.0/doc/license/LICENSE.txt' does not exist warning: source '/builddir/build/BUILD/apbs-3.0.0/doc/license/LICENSE.txt' is not a readable file or directory... skipping. Doxygen version used: 1.9.7 Searching for include files... Searching for example files... Searching for images... Searching for dot files... Searching for msc files... Searching for dia files... Searching for files to exclude Searching INPUT for files to process... Searching for files in directory /builddir/build/BUILD/apbs-3.0.0/src Searching for files in directory /builddir/build/BUILD/apbs-3.0.0/src/pmgc Searching for files in directory /builddir/build/BUILD/apbs-3.0.0/src/mg Searching for files in directory /builddir/build/BUILD/apbs-3.0.0/src/generic Searching for files in directory /builddir/build/BUILD/apbs-3.0.0/src/fem Reading and parsing tag files Parsing files Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/apbs.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/apbs.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/fem/vcsm.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/fem/vcsm.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/fem/vcsm.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/fem/vcsm.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c... 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Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgfasd.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgfasd.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgfasd.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgfasd.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mlinpckd.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mlinpckd.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mlinpckd.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mlinpckd.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/myp/builddir/build/BUILD/apbs-3.0.0/src/generic/bemparm.h:7: warning: the name 'beparm.h' supplied as the argument in the \file statement is not an input file dec.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newtond.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newtond.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newtond.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newtond.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/powerd.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/powerd.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/powerd.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/powerd.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/smoothd.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/smoothd.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/smoothd.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/smoothd.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/routines.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/routines.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/routines.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/routines.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/mainpage.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/mainpage.h... Building macro definition list... Building group list... Building directory list... Building namespace list... Building file list... Building class list... Building concept list... Computing nesting relations for classes... Associating documentation with classes... Associating documentation with concepts... Building example list... Searching for enumerations... Searching for documented typedefs... Searching for members imported via using declarations... Searching for included using directives... Searching for documented variables... Building interface member list... Building member list... Searching for friends... Searching for documented defines... Computing class inheritance relations... Computing class usage relations... Flushing cached template relations that have become invalid... Computing class relations... Add enum values to enums... Searching for member function documentation... Creating members for template instances... Building page list... Search for main page... Computing page relations... Determining the scope of groups... Sorting lists... Determining which enums are documented Computing member relations... Building full member lists recursively... Adding members to member groups. Computing member references... Inheriting documentation... Generating disk names... Adding source references... Adding xrefitems... Sorting member lists... Setting anonymous enum type... Computing dependencies between directories... Generating citations page... Counting members... Counting data structures... Resolving user defined references... Finding anchors and sections in the documentation... Transferring function references... Combining using relations... Adding members to index pages... Correcting members for VHDL... Computing tooltip texts... Generating style sheet... Generating search indices... Generating images for formulas in HTML... Generating image form_0.png for formula Generating image form_1.png for formula Generating image form_2.png for formula Generating image form_3.png for formula Generating image form_4.png for formula Generating image form_5.png for formula Generating image form_6.png for formula Generating image form_7.png for formula Generating image form_8.png for formula Generating image form_9.png for formula Generating image form_10.png for formula Generating image form_11.png for formula Generating image form_12.png for formula Generating image form_13.png for formula Generating image form_14.png for formula Generating image form_15.png for formula Generating image form_16.png for formula Generating image form_17.png for formula Generating image form_18.png for formula Generating image form_19.png for formula Generating image form_20.png for formula Generating image form_21.png for formula Generating image form_22.png for formula Generating image form_23.png for formula Generating image form_24.png for formula Generating image form_25.png for formula Generating image form_26.png for formula Generating image form_27.png for formula Generating image form_28.png for formula Generating image form_29.png for formula Generating image form_30.png for formula Generating image form_31.png for formula Generating image form_32.png for formula Generating image form_33.png for formula Generating image form_34.png for formula Generating image form_35.png for formula Generating image form_36.png for formula Generating image form_37.png for formula Generating image form_38.png for formula Generating image form_39.png for formula Generating image form_40.png for formula Generating image form_41.png for formula Generating image form_42.png for formula Generating image form_43.png for formula Generating image form_44.png for formula Generating image form_45.png for formula Generating image form_46.png for formula Generating image form_47.png for formula Generating image form_48.png for formula Generating image form_49.png for formula Generating image form_50.png for formula Generating image form_51.png for formula Generating image form_52.png for formula Generating image form_53.png for formula Generating image form_54.png for formula Generating image form_55.png for formula Generating image form_56.png for formula Generating image form_57.png for formula Generating image form_58.png for formula Generating image form_59.png for formula Generating image form_60.png for formula Generating image form_61.png for formula Generating image form_62.png for formula Generating image form_63.png for formula Generating image form_64.png for formula Generating image form_0_dark.png for formula Generating image form_1_dark.png for formula Generating image form_2_dark.png for formula Generating image form_3_dark.png for formula Generating image form_4_dark.png for formula Generating image form_5_dark.png for formula Generating image form_6_dark.png for formula Generating image form_7_dark.png for formula Generating image form_8_dark.png for formula Generating image form_9_dark.png for formula Generating image form_10_dark.png for formula Generating image form_11_dark.png for formula Generating image form_12_dark.png for formula Generating image form_13_dark.png for formula Generating image form_14_dark.png for formula Generating image form_15_dark.png for formula Generating image form_16_dark.png for formula Generating image form_17_dark.png for formula Generating image form_18_dark.png for formula Generating image form_19_dark.png for formula Generating image form_20_dark.png for formula Generating image form_21_dark.png for formula Generating image form_22_dark.png for formula Generating image form_23_dark.png for formula Generating image form_24_dark.png for formula Generating image form_25_dark.png for formula Generating image form_26_dark.png for formula Generating image form_27_dark.png for formula Generating image form_28_dark.png for formula Generating image form_29_dark.png for formula Generating image form_30_dark.png for formula Generating image form_31_dark.png for formula Generating image form_32_dark.png for formula Generating image form_33_dark.png for formula Generating image form_34_dark.png for formula Generating image form_35_dark.png for formula Generating image form_36_dark.png for formula Generating image form_37_dark.png for formula Generating image form_38_dark.png for formula Generating image form_39_dark.png for formula Generating image form_40_dark.png for formula Generating image form_41_dark.png for formula Generating image form_42_dark.png for formula Generating image form_43_dark.png for formula Generating image form_44_dark.png for formula Generating image form_45_dark.png for formula Generating image form_46_dark.png for formula Generating image form_47_dark.png for formula Generating image form_48_dark.png for formula Generating image form_49_dark.png for formula Generating image form_50_dark.png for formula Generating image form_51_dark.png for formula Generating image form_52_dark.png for formula Generating image form_53_dark.png for formula Generating image form_54_dark.png for formula Generating image form_55_dark.png for formula Generating image form_56_dark.png for formula Generating image form_57_dark.png for formula Generating image form_58_dark.png for formula Generating image form_59_dark.png for formula Generating image form_60_dark.png for formula Generating image form_61_dark.png for formula Generating image form_62_dark.png for formula Generating image form_63_dark.png for formula Generating image form_64_dark.png for formula Generating example documentation... Generating file sources... Generating code for file doc/programmer/mainpage.h... Generating code for file src/apbs.h... Generating code for file src/fem/vcsm.c... Generating code for file src/fem/vcsm.h... Generating code for file src/fem/vfetk.c... Generating code for file src/fem/vfetk.h... Generating code for file src/fem/vpee.c... Generating code for file src/fem/vpee.h... Generating code for file src/generic/apolparm.c... Generating code for file src/generic/apolparm.h... Generating code for file src/generic/bemparm.c... Generating code for file src/generic/bemparm.h... Generating code for file src/generic/femparm.c... Generating code for file src/generic/femparm.h... Generating code for file src/generic/geoflowparm.c... Generating code for file src/generic/geoflowparm.h... Generating code for file src/generic/mgparm.c... Generating code for file src/generic/mgparm.h... Generating code for file src/generic/nosh.c... Generating code for file src/generic/nosh.h... Generating code for file src/generic/pbamparm.c... Generating code for file src/generic/pbamparm.h... Generating code for file src/generic/pbeparm.c... Generating code for file src/generic/pbeparm.h... Generating code for file src/generic/pbsamparm.c... Generating code for file src/generic/pbsamparm.h... Generating code for file src/generic/vacc.c... Generating code for file src/generic/vacc.h... Generating code for file src/generic/valist.c... Generating code for file src/generic/valist.h... Generating code for file src/generic/vatom.c... Generating code for file src/generic/vatom.h... Generating code for file src/generic/vcap.c... Generating code for file src/generic/vcap.h... Generating code for file src/generic/vclist.c... Generating code for file src/generic/vclist.h... Generating code for file src/generic/vgreen.c... Generating code for file src/generic/vgreen.h... Generating code for file src/generic/vhal.h... Generating code for file src/generic/vmatrix.h... Generating code for file src/generic/vparam.c... Generating code for file src/generic/vparam.h... Generating code for file src/generic/vpbe.c... Generating code for file src/generic/vpbe.h... Generating code for file src/generic/vstring.c... Generating code for file src/generic/vstring.h... Generating code for file src/generic/vunit.h... Generating code for file src/main.c... Generating code for file src/mg/vgrid.c... Generating code for file src/mg/vgrid.h... Generating code for file src/mg/vmgrid.c... Generating code for file src/mg/vmgrid.h... Generating code for file src/mg/vopot.c... Generating code for file src/mg/vopot.h... Generating code for file src/mg/vpmg.c... Generating code for file src/mg/vpmg.h... Generating code for file src/mg/vpmgp.c... Generating code for file src/mg/vpmgp.h... Generating code for file src/pmgc/buildAd.c... Generating code for file src/pmgc/buildAd.h... Generating code for file src/pmgc/buildBd.c... Generating code for file src/pmgc/buildBd.h... Generating code for file src/pmgc/buildGd.c... Generating code for file src/pmgc/buildGd.h... Generating code for file src/pmgc/buildPd.c... Generating code for file src/pmgc/buildPd.h... Generating code for file src/pmgc/cgd.c... Generating code for file src/pmgc/cgd/builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:2095: warning: Member polyEval(int numP, double p[], double c[][VMAXP], double xv[]) (function) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:1528: warning: Member Vfetk_PDE_initElement(PDE *thee, int elementType, int chart, double tvx[][3], void *data) (function) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:1571: warning: Member Vfetk_PDE_initPoint(PDE *thee, int pointType, int chart, double txq[], double tU[], double tdU[][3]) (function) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:1741: warning: Member Vfetk_PDE_DFu_wv(PDE *thee, int key, double W[], double dW[][VAPBS_DIM], double V[], double dV[][3]) (function) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:1902: warning: Member Vfetk_PDE_bisectEdge(int dim, int dimII, int edgeType, int chart[], double vx[][3]) (function) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:1912: warning: Member Vfetk_PDE_mapBoundary(int dim, int dimII, int vertexType, int chart, double vx[3]) (function) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:1917: warning: Member Vfetk_PDE_markSimplex(int dim, int dimII, int simplexType, int faceType[VAPBS_NVS], int vertexType[VAPBS_NVS], int chart[], double vx[][3], void *simplex) (function) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:1998: warning: Member Vfetk_PDE_oneChart(int dim, int dimII, int objType, int chart[], double vx[][3], int dimV) (function) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:86: warning: Member var (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:93: warning: Member diriCubeString (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:130: warning: Member neumCubeString (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:366: warning: Member dim_2DP1 (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:386: warning: Member lgr_2DP1[3][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:395: warning: Member lgr_2DP1x[3][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:402: warning: Member lgr_2DP1y[3][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:409: warning: Member lgr_2DP1z[3][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:437: warning: Member dim_3DP1 (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:438: warning: Member lgr_3DP1[VAPBS_NVS][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:446: warning: Member lgr_3DP1x[VAPBS_NVS][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:454: warning: Member lgr_3DP1y[VAPBS_NVS][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:462: warning: Member lgr_3DP1z[VAPBS_NVS][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:476: warning: Member P_DEG (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:482: warning: Member numP (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:483: warning: Member c[VMAXP][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:484: warning: Member cx[VMAXP][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:485: warning: Member cy[VMAXP][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:486: warning: Member cz[VMAXP][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.h:207: warning: Member Vfetk (typedef) of file vfetk.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vpee.c:498: warning: Member Vpee_userDefined(Vpee *thee, SS *sm) (function) of file vpee.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vpee.c:532: warning: Member Vpee_ourSimp(Vpee *thee, SS *sm, int rcol) (function) of file vpee.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vpee.c:66: warning: Member Aprx_estNonlinResid(Aprx *thee, SS *sm, Bvec *u, Bvec *ud, Bvec *f) (function) of file vpee.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vpee.c:72: warning: Member Aprx_estLocalProblem(Aprx *thee, SS *sm, Bvec *u, Bvec *ud, Bvec *f) (function) of file vpee.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vpee.c:77: warning: Member Aprx_estDualProblem(Aprx *thee, SS *sm, Bvec *u, Bvec *ud, Bvec *f) (function) of file vpee.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/apolparm.c:237: warning: Member APOLparm_parseGRID(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/apolparm.c:268: warning: Member APOLparm_parseMOL(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/apolparm.c:287: warning: Member APOLparm_parseSRFM(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/apolparm.c:309: warning: Member APOLparm_parseSRAD(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/apolparm.c:328: warning: Member APOLparm_parseSWIN(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/apolparm.c:347: warning: Member APOLparm_parseTEMP(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/apolparm.c:366: warning: Member APOLparm_parseGAMMA(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/apolparm.c:385: warning: Member APOLparm_parseCALCENERGY(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/apolparm.c:438: warning: Member APOLparm_parseCALCFORCE(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/apolparm.c:491: warning: Member APOLparm_parseBCONC(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/apolparm.c:510: warning: Member APOLparm_parseSDENS(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/apolparm.c:529: warning: Member APOLparm_parseDPOS(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/apolparm.c:558: warning: Member APOLparm_parsePRESS(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/bemparm.c:210: warning: Member BEMparm_parseTREE_ORDER(BEMparm *thee, Vio *sock) (function) of file bemparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/bemparm.c:233: warning: Member BEMparm_parseTREE_N0(BEMparm *thee, Vio *sock) (function) of file bemparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/bemparm.c:256: warning: Member BEMparm_parseMAC(BEMparm *thee, Vio *sock) (function) of file bemparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/bemparm.c:279: warning: Member BEMparm_parseMESH(BEMparm *thee, Vio *sock) (function) of file bemparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/bemparm.c:308: warning: Member BEMparm_parseOUTDATA(BEMparm *thee, Vio *sock) (function) of file bemparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/femparm.c:196: warning: Member FEMparm_parseDOMAINLENGTH(FEMparm *thee, Vio *sock) (function) of file femparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/femparm.c:221: warning: Member FEMparm_parseETOL(FEMparm *thee, Vio *sock) (function) of file femparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/femparm.c:244: warning: Member FEMparm_parseEKEY(FEMparm *thee, Vio *sock) (function) of file femparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/femparm.c:276: warning: Member FEMparm_parseAKEYPRE(FEMparm *thee, Vio *sock) (function) of file femparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/femparm.c:303: warning: Member FEMparm_parseAKEYSOLVE(FEMparm *thee, Vio *sock) (function) of file femparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/femparm.c:333: warning: Member FEMparm_parseTARGETNUM(FEMparm *thee, Vio *sock) (function) of file femparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/femparm.c:352: warning: Member FEMparm_parseTARGETRES(FEMparm *thee, Vio *sock) (function) of file femparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/femparm.c:372: warning: Member FEMparm_parseMAXSOLVE(FEMparm *thee, Vio *sock) (function) of file femparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/femparm.c:391: warning: Member FEMparm_parseMAXVERT(FEMparm *thee, Vio *sock) (function) of file femparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/femparm.c:411: warning: Member FEMparm_parseUSEMESH(FEMparm *thee, Vio *sock) (function) of file femparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/femparm.h:182: warning: Member FEMparm (typedef) of file femparm.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.c:138: warning: Member FUBAR(const char *name) (function) of file geoflowparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.c:143: warning: Member parseNonNeg(double *tf, double def, int *set, char *name, Vio *sock) (function) of file geoflowparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.c:164: warning: Member GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock) (function) of file geoflowparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.c:186: warning: Member GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock) (function) of file geoflowparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169: warning: Member GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock) (function) of file geoflowparm.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171: warning: Member GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock) (function) of file geoflowparm.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:415: warning: Member MGparm_parseDIME(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:446: warning: Member MGparm_parseCHGM(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:497: warning: Member MGparm_parseNLEV(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:516: warning: Member MGparm_parseETOL(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:539: warning: Member MGparm_parseGRID(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:570: warning: Member MGparm_parseGLEN(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:601: warning: Member MGparm_parseGAMMA(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:616: warning: Member MGparm_parseGCENT(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:668: warning: Member MGparm_parseCGLEN(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:699: warning: Member MGparm_parseFGLEN(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:730: warning: Member MGparm_parseCGCENT(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:782: warning: Member MGparm_parseFGCENT(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:834: warning: Member MGparm_parsePDIME(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:872: warning: Member MGparm_parseOFRAC(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:892: warning: Member MGparm_parseASYNC(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:912: warning: Member MGparm_parseUSEAQUA(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.h:203: warning: Member MGparm (typedef) of file mgparm.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:970: warning: Member NOsh_parseREAD(NOsh *thee, Vio *sock) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:1021: warning: Member NOsh_parsePRINT(NOsh *thee, Vio *sock) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:1187: warning: Member NOsh_parseELEC(NOsh *thee, Vio *sock) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:1313: warning: Member NOsh_parseAPOLAR(NOsh *thee, Vio *sock) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:2385: warning: Member NOsh_parseFEM(NOsh *thee, Vio *sock, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:1510: warning: Member NOsh_parseMG(NOsh *thee, Vio *sock, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:2845: warning: Member NOsh_parseBEM(NOsh *thee, Vio *sock, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:2934: warning: Member NOsh_parseGEOFLOW(NOsh *thee, Vio *sock, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:3048: warning: Member NOsh_parsePBAM(NOsh *thee, Vio *sock, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:3166: warning: Member NOsh_parsePBSAM(NOsh *thee, Vio *sock, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:2508: warning: Member NOsh_parseAPOL(NOsh *thee, Vio *sock, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:1603: warning: Member NOsh_setupCalcMG(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:1815: warning: Member NOsh_setupCalcMGAUTO(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:1747: warning: Member NOsh_setupCalcMGMANUAL(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:2090: warning: Member NOsh_setupCalcMGPARA(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:1722: warning: Member NOsh_setupCalcFEM(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:2471: warning: Member NOsh_setupCalcFEMANUAL(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:1638: warning: Member NOsh_setupCalcBEM(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:1666: warning: Member NOsh_setupCalcGEOFLOW(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:1686: warning: Member NOsh_setupCalcPBAM(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:1704: warning: Member NOsh_setupCalcPBSAM(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:2612: warning: Member NOsh_setupCalcBEMMANUAL(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:2677: warning: Member NOsh_setupCalcGEOFLOWMANUAL(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:2735: warning: Member NOsh_setupCalcPBAMAUTO(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:2786: warning: Member NOsh_setupCalcPBSAMAUTO(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:2581: warning: Member NOsh_setupCalcAPOL(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:598: warning: Member NOsh_parseREAD_MOL(NOsh *thee, Vio *sock) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:675: warning: Member NOsh_parseREAD_PARM(NOsh *thee, Vio *sock) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:739: warning: Member NOsh_parseREAD_DIEL(NOsh *thee, Vio *sock) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:793: warning: Member NOsh_parseREAD_KAPPA(NOsh *thee, Vio *sock) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:839: warning: Member NOsh_parseREAD_POTENTIAL(NOsh *thee, Vio *sock) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:884: warning: Member NOsh_parseREAD_CHARGE(NOsh *thee, Vio *sock) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:930: warning: Member NOsh_parseREAD_MESH(NOsh *thee, Vio *sock) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:188: warning: Member NOsh_calc (typedef) of file nosh.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c:458: warning: Member PBAMparm_parseNtraj(PBAMparm *thee, Vio *sock) (function) of file pbamparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c:549: warning: Member PBAMparm_parseTerm(PBAMparm *thee, Vio *sock) (function) of file pbamparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:77: warning: Member PBAMPARM_MAXWRITE (macro definition) of file pbamparm.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:78: warning: Member PBAMPARM_MAXMOL (macro definition) of file pbamparm.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:87: warning: Member PBEparm_getzmem(PBEparm *thee) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:91: warning: Member PBEparm_getLmem(PBEparm *thee) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:95: warning: Member PBEparm_getmembraneDiel(PBEparm *thee) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:99: warning: Member PBEparm_getmemv(PBEparm *thee) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:368: warning: Member PBEparm_parseLPBE(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:375: warning: Member PBEparm_parseNPBE(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:382: warning: Member PBEparm_parseMOL(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:401: warning: Member PBEparm_parseLRPBE(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:408: warning: Member PBEparm_parseNRPBE(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:415: warning: Member PBEparm_parseSMPBE(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:474: warning: Member PBEparm_parseBCFL(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:555: warning: Member PBEparm_parseION(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:652: warning: Member PBEparm_parsePDIE(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:671: warning: Member PBEparm_parseSDENS(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:690: warning: Member PBEparm_parseSDIE(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:709: warning: Member PBEparm_parseSRFM(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:780: warning: Member PBEparm_parseSRAD(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:799: warning: Member PBEparm_parseSWIN(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:818: warning: Member PBEparm_parseTEMP(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:837: warning: Member PBEparm_parseUSEMAP(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:895: warning: Member PBEparm_parseCALCENERGY(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:948: warning: Member PBEparm_parseCALCFORCE(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:1005: warning: Member PBEparm_parseZMEM(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:1025: warning: Member PBEparm_parseLMEM(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:1044: warning: Member PBEparm_parseMDIE(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:1063: warning: Member PBEparm_parseMEMV(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:1084: warning: Member PBEparm_parseWRITE(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:1178: warning: Member PBEparm_parseWRITEMAT(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:77: warning: Member PBSAMPARM_MAXWRITE (macro definition) of file pbsamparm.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:78: warning: Member PBSAMPARM_MAXMOL (macro definition) of file pbsamparm.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:277: warning: Member Vacc_vdwAcc(Vacc *thee, double center[3]) (function) of file vacc.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:307: warning: Member Vacc_ivdwAcc(Vacc *thee, double center[3], double radius) (function) of file vacc.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:679: warning: Member Vacc_writeGMV(Vacc *thee, double radius, int meth, Gem *gm, char *iodev, char *iofmt, char *iohost, char *iofile) (function) of file vacc.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:1252: warning: Member Vacc_SASAPos(Vacc *thee, double radius) (function) of file vacc.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:1277: warning: Member Vacc_atomSASAPos(Vacc *thee, double radius, Vatom *atom, int mode) (function) of file vacc.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:76: warning: The following parameter of ivdwAccExclus(Vacc *thee, double center[3], double radius, int atomID) is not documented: parameter 'thee' /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:490: warning: The following parameter of splineAcc(Vacc *thee, double center[VAPBS_DIM], double win, double infrad, VclistCell *cell) is not documented: parameter 'thee' /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:186: warning: Member Valist_readPDBSerial(Valist *thee, Vio *sock, int *serial) (function) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:206: warning: Member Valist_readPDBAtomName(Valist *thee, Vio *sock, char atomName[VMAX_ARGLEN]) (function) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:224: warning: Member Valist_readPDBResidueName(Valist *thee, Vio *sock, char resName[VMAX_ARGLEN]) (function) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:242: warning: Member Valist_readPDBResidueNumber(Valist *thee, Vio *sock, int *resSeq) (function) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:298: warning: Member Valist_readPDBAtomCoord(Valist *thee, Vio *sock, double *coord) (function) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:316: warning: Member Valist_readPDBChargeRadius(Valist *thee, Vio *sock, double *charge, double *radius) (function) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:344: warning: Member Valist_readPDB_throughXYZ(Valist *thee, Vio *sock, int *serial, char atomName[VMAX_ARGLEN], char resName[VMAX_ARGLEN], int *resSeq, double *x, double *y, double *z) (function) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:424: warning: Member Valist_getAtomStorage(Valist *thee, Vatom **plist, int *pnlist, int *pnatoms) (function) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:480: warning: Member Valist_setAtomArray(Valist *thee, Vatom **plist, int nlist, int natoms) (function) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:60: warning: Member Valist_whiteChars (variable) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:61: warning: Member Valist_commChars (variable) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:62: warning: Member Valist_xmlwhiteChars (variable) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vclist.c:128: warning: Member VCLIST_INFLATE (macro definition) of file vclist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vclist.c:90: warning: Member Vclist_getMolDims(Vclist *thee, double lower_corner[VAPBS_DIM], double upper_corner[VAPBS_DIM], double *r_max) (function) of file vclist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vclist.c:125: warning: Member Vclist_setupGrid(Vclist *thee) (function) of file vclist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vclist.c:174: warning: Member Vclist_storeParms(Vclist *thee, Valist *alist, double max_radius, int npts[VAPBS_DIM], Vclist_DomainMode mode, double lower_corner[VAPBS_DIM], double upper_corner[VAPBS_DIM]) (function) of file vclist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vclist.c:231: warning: Member Vclist_gridSpan(Vclist *thee, Vatom *atom, int imin[VAPBS_DIM], int imax[VAPBS_DIM]) (function) of file vclist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vclist.c:262: warning: Member Vclist_arrayIndex(Vclist *thee, int i, int j, int k) (function) of file vclist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vclist.c:270: warning: Member Vclist_assignAtoms(Vclist *thee) (function) of file vclist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vclist.h:94: warning: Member Vclist_DomainMode (typedef) of file vclist.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:425: warning: Member treesetup(Vgreen *thee) (function) of file vgreen.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:505: warning: Member treecleanup(Vgreen *thee) (function) of file vgreen.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:525: warning: Member treecalc(Vgreen *thee, double *xtar, double *ytar, double *ztar, double *qtar, int numtars, double *tpengtar, double *x, double *y, double *z, double *q, int numpars, double *fx, double *fy, double *fz, int iflag, int farrdim, int arrdim) (function) of file vgreen.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:458: warning: Member MAX_HASH_DIM (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:572: warning: Member OS_SEP_STR (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:573: warning: Member OS_SEP_CHAR (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:600: warning: Member ANNOUNCE_FUNCTION (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:601: warning: Member WARN_UNTESTED (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:602: warning: Member WARN_PARTTESTED (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:653: warning: Member VCHANNELEDMESSAGE0(channel, msg) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:658: warning: Member VCHANNELEDMESSAGE1(channel, msg, arg0) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:665: warning: Member VCHANNELEDMESSAGE2(channel, msg, arg0, arg1) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:672: warning: Member VCHANNELEDMESSAGE3(channel, msg, arg0, arg1, arg2) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:679: warning: Member VMESSAGE0(msg) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:680: warning: Member VMESSAGE1(msg, arg0) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:681: warning: Member VMESSAGE2(msg, arg0, arg1) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:682: warning: Member VMESSAGE3(msg, arg0, arg1, arg2) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:684: warning: Member VERRMSG0(msg) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:685: warning: Member VERRMSG1(msg, arg0) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:686: warning: Member VERRMSG2(msg, arg0, arg1) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:687: warning: Member VERRMSG3(msg, arg0, arg1, arg2) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:731: warning: Member VASSERT_MSG0(cnd, msg) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:741: warning: Member VASSERT_MSG1(cnd, msg, arg) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:753: warning: Member VASSERT_MSG2(cnd, msg, arg0, arg1) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:825: warning: Member VWARN_MSG0(cnd, msg) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:838: warning: Member VWARN_MSG1(cnd, msg, arg0) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:853: warning: Member VWARN_MSG2(cnd, msg, arg0, arg1) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:899: warning: Member VABORT_MSG0(msg) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:907: warning: Member VABORT_MSG1(msg, arg) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:917: warning: Member VABORT_MSG2(msg, arg0, arg1) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:944: warning: Member PRINT_INT(expr) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:945: warning: Member PRINT_DBL(expr) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:948: warning: Member VMALLOC(vmem, n, type) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:950: warning: Member VFREE(vmem, n, type, ptr) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:952: warning: Member VFILL(vec, n, val) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:959: warning: Member VCOPY(srcvec, dstvec, i, n) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:968: warning: Member VAT(array, i) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:969: warning: Member RAT(array, i) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:73: warning: Member Vrc_Codes (typedef) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:95: warning: Member Vsol_Meth (typedef) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:133: warning: Member Vsurf_Meth (typedef) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:244: warning: Member Vchrg_Meth (typedef) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:262: warning: Member Vchrg_Src (typedef) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:302: warning: Member Vdata_Type (typedef) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:323: warning: Member Vdata_Format (typedef) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:966: warning: Member wrap_text(char *str, int right_margin, int left_padding) (function) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:64: warning: Member MAT2(mat, dx, dy) (macro definition) of file vmatrix.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:68: warning: Member RAT2(mat, x, y) (macro definition) of file vmatrix.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:71: warning: Member VAT2(mat, x, y) (macro definition) of file vmatrix.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:76: warning: Member MAT3(mat, dx, dy, dz) (macro definition) of file vmatrix.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:81: warning: Member RAT3(mat, x, y, z) (macro definition) of file vmatrix.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:84: warning: Member VAT3(mat, x, y, z) (macro definition) of file vmatrix.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vparam.h:127: warning: Member Vparam_ResData (typedef) of file vparam.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vparam.h:147: warning: Member Vparam (typedef) of file vparam.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vpbe.c:62: warning: Member MAX_SPLINE_WINDOW (macro definition) of file vpbe.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vgrid.c:67: warning: Member IJK(i, j, k) (macro definition) of file vgrid.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vgrid.c:77: warning: Member MCwhiteChars (variable) of file vgrid.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vgrid.c:78: warning: Member MCcommChars (variable) of file vgrid.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vgrid.c:79: warning: Member Vcompare (variable) of file vgrid.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vgrid.c:80: warning: Member Vprecision[26] (variable) of file vgrid.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vopot.c:113: warning: Member IJK(i, j, k) (macro definition) of file vopot.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:1401: warning: Member Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:2828: warning: Member bcCalcOrig(Vpmg *thee) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3130: warning: Member gridPointIsValid(int i, int j, int k, int nx, int ny, int nz) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3313: warning: Member packAtoms(double *ax, double *ay, double *az, double *charge, double *size, Vpmg *thee) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3338: warning: Member packUnpack(int nx, int ny, int nz, int ngrid, double *gx, double *gy, double *gz, double *value, Vpmg *thee, int pack) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3407: warning: Member bcflnew(Vpmg *thee) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3597: warning: Member bcfl_sdh(Vpmg *thee) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3868: warning: Member bcfl_mdh(Vpmg *thee) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3995: warning: Member bcfl_mem(double zmem, double L, double eps_m, double eps_w, double V, double xkappa, double *gxcf, double *gycf, double *gzcf, double *xf, double *yf, double *zf, int nx, int ny, int nz) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:4174: warning: Member bcfl_map(Vpmg *thee) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:6684: warning: Member markFrac(double rtot, double *tpos, int nx, int ny, int nz, double hx, double hy, double hzed, double xmin, double ymin, double zmin, double *xarray, double *yarray, double *zarray) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10260: warning: Member fillcoPermanentInduced(Vpmg *thee) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1056: warning: The following parameter of bcfl1(double size, double *apos, double charge, double xkappa, double pre1, double *gxcf, double *gycf, double *gzcf, double *xf, double *yf, double *zf, int nx, int ny, int nz) is not documented: parameter 'size' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1362: warning: argument 'hz' of command @param is not found in the argument list of markSphere(double rtot, double *tpos, int nx, int ny, int nz, double hx, double hy, double hzed, double xmin, double ymin, double zmin, double *array, double markVal) /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1362: warning: The following parameter of markSphere(double rtot, double *tpos, int nx, int ny, int nz, double hx, double hy, double hzed, double xmin, double ymin, double zmin, double *array, double markVal) is not documented: parameter 'rtot' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1105: warning: The following parameter of multipolebc(double r, double kappa, double eps_p, double eps_w, double rad, double tsr[3]) is not documented: parameter 'r' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1315: warning: The following parameters of qfForceSpline1(Vpmg *thee, double *force, int atomID) are not documented: parameter 'thee' parameter 'force' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1325: warning: The following parameters of qfForceSpline2(Vpmg *thee, double *force, int atomID) are not documented: parameter 'thee' parameter 'force' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1335: warning: The following parameters of qfForceSpline4(Vpmg *thee, double *force, int atomID) are not documented: parameter 'thee' parameter 'force' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:995: warning: The following parameter of Vpmg_polarizEnergy(Vpmg *thee, int extFlag) is not documented: parameter 'thee' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1006: warning: The following parameter of Vpmg_qfEnergyPoint(Vpmg *thee, int extFlag) is not documented: parameter 'thee' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1017: warning: The following parameter of Vpmg_qfEnergyVolume(Vpmg *thee, int extFlag) is not documented: parameter 'thee' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1029: warning: The following parameter of Vpmg_splineSelect(int srfm, Vacc *acc, double *gpos, double win, double infrad, Vatom *atom, double *force) is not documented: parameter 'srfm' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1348: warning: The following parameters of zlapSolve(Vpmg *thee, double **solution, double **source, double **work1) are not documented: parameter 'thee' parameter 'solution' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:105: warning: Member VPMGMAXPART (macro definition) of file vpmg.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1392: warning: Member VCUB(x) (macro definition) of file vpmg.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1393: warning: Member VLOG(x) (macro definition) of file vpmg.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1395: warning: Member IJK(i, j, k) (macro definition) of file vpmg.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1396: warning: Member IJKx(j, k, i) (macro definition) of file vpmg.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1397: warning: Member IJKy(i, k, j) (macro definition) of file vpmg.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1398: warning: Member IJKz(i, j, k) (macro definition) of file vpmg.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1399: warning: Member VFCHI(iint, iflt) (macro definition) of file vpmg.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385: warning: Member Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag) (function) of file vpmg.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1056: warning: The following parameter of bcfl1(double size, double *apos, double charge, double xkappa, double pre1, double *gxcf, double *gycf, double *gzcf, double *xf, double *yf, double *zf, int nx, int ny, int nz) is not documented: parameter 'size' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1362: warning: The following parameter of markSphere(double rtot, double *tpos, int nx, int ny, int nz, double hx, double hy, double hzed, double xmin, double ymin, double zmin, double *array, double markVal) is not documented: parameter 'rtot' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1105: warning: The following parameter of multipolebc(double r, double kappa, double eps_p, double eps_w, double rad, double tsr[3]) is not documented: parameter 'r' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1315: warning: The following parameters of qfForceSpline1(Vpmg *thee, double *force, int atomID) are not documented: parameter 'thee' parameter 'force' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1325: warning: The following parameters of qfForceSpline2(Vpmg *thee, double *force, int atomID) are not documented: parameter 'thee' parameter 'force' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1335: warning: The following parameters of qfForceSpline4(Vpmg *thee, double *force, int atomID) are not documented: parameter 'thee' parameter 'force' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:995: warning: The following parameter of Vpmg_polarizEnergy(Vpmg *thee, int extFlag) is not documented: parameter 'thee' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1006: warning: The following parameter of Vpmg_qfEnergyPoint(Vpmg *thee, int extFlag) is not documented: parameter 'thee' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1017: warning: The following parameter of Vpmg_qfEnergyVolume(Vpmg *thee, int extFlag) is not documented: parameter 'thee' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1029: warning: The following parameter of Vpmg_splineSelect(int srfm, Vacc *acc, double *gpos, double win, double infrad, Vatom *atom, double *force) is not documented: parameter 'srfm' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1348: warning: The following parameters of zlapSolve(Vpmg *thee, double **solution, double **source, double **work1) are not documented: parameter 'thee' parameter 'solution' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmgp.c:294: warning: Member coarsenThis(int nOld) (function) of file vpmgp.c is not documented. .h... Generating code for file src/pmgc/gsd.c... Generating code for file src/pmgc/gsd.h... Generating code for file src/pmgc/matvecd.c... Generating code for file src/pmgc/matvecd.h... Generating code for file src/pmgc/mgcsd.c... Generating code for file src/pmgc/mgcsd.h... Generating code for file src/pmgc/mgdrvd.c... Generating code for file src/pmgc/mgdrvd.h... Generating code for file src/pmgc/mgfasd.c... Generating code for file src/pmgc/mgfasd.h... Generating code for file src/pmgc/mgsubd.c... Generating code for file src/pmgc/mgsubd.h... Generating code for file src/pmgc/mikpckd.c... Generating code for file src/pmgc/mikpckd.h... Generating code for file src/pmgc/mlinpckd.c... Generating code for file src/pmgc/mlinpckd.h... Generating code for file src/pmgc/mypdec.c... Generating code for file src/pmgc/mypdec.h... Generating code for file src/pmgc/newdrvd.c... Generating code for file src/pmgc/newdrvd.h... Generating code for file src/pmgc/newtond.c... Generating code for file src/pmgc/newtond.h... Generating code for file src/pmgc/powerd.c... Generating code for file src/pmgc/powerd.h... Generating code for file src/pmgc/smoothd.c... Generating code for file src/pmgc/smoothd.h... Generating code for file src/routines.c... Generating code for file src/routines.h... Generating file documentation... Generating docs for file src/apbs.h... Generating docs for file src/fem/vcsm.c... Generating docs for file src/fem/vcsm.h... Generating docs for file src/fem/vfetk.c... Generating docs for file src/fem/vfetk.h... Generating docs for file src/fem/vpee.c... Generating docs for file src/fem/vpee.h... Generating docs for file src/generic/apolparm.c... Generating docs for file src/generic/bemparm.c... Generating docs for file src/generic/femparm.c... Generating docs for file src/generic/femparm.h... Generating docs for file src/generic/geoflowparm.c... Generating docs for file src/generic/geoflowparm.h... Generating docs for file src/generic/mgparm.c... Generating docs for file src/generic/mgparm.h... Generating docs for file src/generic/nosh.c... Generating docs for file src/generic/nosh.h... Generating docs for file src/generic/pbamparm.c... Generating docs for file src/generic/pbamparm.h... Generating docs for file src/generic/pbeparm.c... Generating docs for file src/generic/pbeparm.h... Generating docs for file src/generic/pbsamparm.c... Generating docs for file src/generic/pbsamparm.h... Generating docs for file src/generic/vacc.c... Generating docs for file src/generic/vacc.h... Generating docs for file src/generic/valist.c... Generating docs for file src/generic/valist.h... Generating docs for file src/generic/vatom.c... Generating docs for file src/generic/vatom.h... Generating docs for file src/generic/vcap.c... Generating docs for file src/generic/vcap.h... Generating docs for file src/generic/vclist.c... Generating docs for file src/generic/vclist.h... Generating docs for file src/generic/vgreen.c... Generating docs for file src/generic/vgreen.h... Generating docs for file src/generic/vhal.h... Generating docs for file src/generic/vmatrix.h... Generating docs for file src/generic/vparam.c... Generating docs for file src/generic/vparam.h... Generating docs for file src/generic/vpbe.c... Generating docs for file src/generic/vpbe.h... Generating docs for file src/generic/vstring.c... Generating docs for file src/generic/vstring.h... Generating docs for file src/generic/vunit.h... Generating docs for file src/main.c... Generating docs for file src/mg/vgrid.c... Generating docs for file src/mg/vgrid.h... Generating docs for file src/mg/vmgrid.c... Generating docs for file src/mg/vmgrid.h... Generating docs for file src/mg/vopot.c... Generating docs for file src/mg/vopot.h... Generating docs for file src/mg/vpmg.c... Generating docs for file src/mg/vpmg.h... Generating docs for file src/mg/vpmgp.c... Generating docs for file src/mg/vpmgp.h... Generating docs for file src/routines.c... Generating docs for file src/routines.h... Generating page documentation... Generating docs for page bug... Generating docs for page dep/builddir/build/BUILD/apbs-3.0.0/src/fem/vpee.h:17: warning: end of comment block while expecting command /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:247: warning: argument 'parm' of command @param is not found in the argument list of PBAMparm_parseSalt(PBAMparm *thee, Vio *sock) /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:247: warning: The following parameter of PBAMparm_parseSalt(PBAMparm *thee, Vio *sock) is not documented: parameter 'sock' /builddir/build/BUILD/apbs-3.0.0/src/routines.h:513: warning: The following parameter of energyAPOL(APOLparm *apolparm, double sasa, double sav, double atomsasa[], double atomwcaEnergy[], int numatoms) is not documented: parameter 'apolparm' /builddir/build/BUILD/apbs-3.0.0/src/routines.h:610: warning: The following parameter of killFE(NOsh *nosh, Vpbe *pbe[NOSH_MAXCALC], Vfetk *fetk[NOSH_MAXCALC], Gem *gem[NOSH_MAXMOL]) is not documented: parameter 'nosh' /builddir/build/BUILD/apbs-3.0.0/src/routines.h:262: warning: The following parameter of killMG(NOsh *nosh, Vpbe *pbe[NOSH_MAXCALC], Vpmgp *pmgp[NOSH_MAXCALC], Vpmg *pmg[NOSH_MAXCALC]) is not documented: parameter 'nosh' /builddir/build/BUILD/apbs-3.0.0/src/routines.c:882: warning: argument 'charge' of command @param is not found in the argument list of loadChargeMaps(NOsh *nosh, Vgrid *map[NOSH_MAXMOL]) /builddir/build/BUILD/apbs-3.0.0/src/routines.c:882: warning: The following parameter of loadChargeMaps(NOsh *nosh, Vgrid *map[NOSH_MAXMOL]) is not documented: parameter 'map' /builddir/build/BUILD/apbs-3.0.0/src/routines.c:662: warning: argument 'kappa' of command @param is not found in the argument list of loadKappaMaps(NOsh *nosh, Vgrid *map[NOSH_MAXMOL]) /builddir/build/BUILD/apbs-3.0.0/src/routines.c:662: warning: The following parameter of loadKappaMaps(NOsh *nosh, Vgrid *map[NOSH_MAXMOL]) is not documented: parameter 'map' /builddir/build/BUILD/apbs-3.0.0/src/routines.c:791: warning: argument 'pot' of command @param is not found in the argument list of loadPotMaps(NOsh *nosh, Vgrid *map[NOSH_MAXMOL]) /builddir/build/BUILD/apbs-3.0.0/src/routines.c:791: warning: The following parameter of loadPotMaps(NOsh *nosh, Vgrid *map[NOSH_MAXMOL]) is not documented: parameter 'map' /builddir/build/BUILD/apbs-3.0.0/src/routines.h:622: warning: argument 'nosh' of command @param is not found in the argument list of preRefineFE(int i, FEMparm *feparm, Vfetk *fetk[NOSH_MAXCALC]) /builddir/build/BUILD/apbs-3.0.0/src/routines.h:494: warning: The following parameter of printApolForce(Vcom *com, NOsh *nosh, int nforce[NOSH_MAXCALC], AtomForce *atomForce[NOSH_MAXCALC], int i) is not documented: parameter 'com' /builddir/build/BUILD/apbs-3.0.0/src/routines.h:445: warning: The following parameter of printElecEnergy(Vcom *com, NOsh *nosh, double totEnergy[NOSH_MAXCALC], int iprint) is not documented: parameter 'com' /builddir/build/BUILD/apbs-3.0.0/src/routines.h:481: warning: The following parameter of printElecForce(Vcom *com, NOsh *nosh, int nforce[NOSH_MAXCALC], AtomForce *atomForce[NOSH_MAXCALC], int i) is not documented: parameter 'com' /builddir/build/BUILD/apbs-3.0.0/src/routines.h:432: warning: The following parameter of printEnergy(Vcom *com, NOsh *nosh, double totEnergy[NOSH_MAXCALC], int iprint) is not documented: parameter 'com' /builddir/build/BUILD/apbs-3.0.0/src/routines.h:468: warning: The following parameter of printForce(Vcom *com, NOsh *nosh, int nforce[NOSH_MAXCALC], AtomForce *atomForce[NOSH_MAXCALC], int i) is not documented: parameter 'com' /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4125: warning: argument 'i' of command @param is not found in the argument list of solveFE(int icalc, PBEparm *pbeparm, FEMparm *feparm, Vfetk *fetk[NOSH_MAXCALC]) /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:104: warning: Member vdw (variable) of struct sGEOFLOWparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:105: warning: Member setvdw (variable) of struct sGEOFLOWparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:111: warning: Member salt (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:112: warning: Member setsalt (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:115: warning: Member runtype[CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:116: warning: Member setruntype (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:119: warning: Member runname[CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:120: warning: Member setrunname (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:123: warning: Member setrandorient (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:126: warning: Member pbcboxlen (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:127: warning: Member setpbcs (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:130: warning: Member units[CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:131: warning: Member setunits (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:137: warning: Member gridpt (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:138: warning: Member setgridpt (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:141: warning: Member map3dname[CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:142: warning: Member set3dmap (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:145: warning: Member grid2Dname[PBAMPARM_MAXWRITE][CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:146: warning: Member grid2Dax[PBAMPARM_MAXWRITE][CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:147: warning: Member grid2Dloc[PBAMPARM_MAXWRITE] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:148: warning: Member grid2Dct (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:149: warning: Member setgrid2Dname (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:152: warning: Member dxname[CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:153: warning: Member setdxname (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:158: warning: Member ntraj (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:159: warning: Member setntraj (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:161: warning: Member termcombine[CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:162: warning: Member settermcombine (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:164: warning: Member diffct (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:165: warning: Member moveType[PBAMPARM_MAXMOL][CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:166: warning: Member transDiff[PBAMPARM_MAXMOL] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:167: warning: Member rotDiff[PBAMPARM_MAXMOL] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:169: warning: Member termct (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:170: warning: Member setterm (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:172: warning: Member termnam[PBAMPARM_MAXWRITE][CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:173: warning: Member termnu[PBAMPARM_MAXWRITE][1] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:174: warning: Member termVal[PBAMPARM_MAXWRITE] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:175: warning: Member confil[PBAMPARM_MAXWRITE][CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:176: warning: Member conpad[PBAMPARM_MAXWRITE] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:177: warning: Member confilct (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:179: warning: Member setxyz (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:180: warning: Member xyzct[PBAMPARM_MAXMOL] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:181: warning: Member xyzfil[PBAMPARM_MAXMOL][PBAMPARM_MAXWRITE][CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.h:202: warning: Member pbam_3dmapstem[VMAX_ARGLEN] (variable) of struct sPBEparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.h:203: warning: Member pbam_3dmapflag (variable) of struct sPBEparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:112: warning: Member settolsp (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:113: warning: Member tolsp (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:115: warning: Member setmsms (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:116: warning: Member probe_radius (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:117: warning: Member density (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:119: warning: Member setsurf (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:120: warning: Member surfct (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:121: warning: Member surffil[PBSAMPARM_MAXMOL][CHR_MAXLEN] (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:123: warning: Member setimat (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:124: warning: Member imatct (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:125: warning: Member imatfil[PBSAMPARM_MAXMOL][CHR_MAXLEN] (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:127: warning: Member setexp (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:128: warning: Member expct (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:129: warning: Member expfil[PBSAMPARM_MAXMOL][CHR_MAXLEN] (variable) of struct sPBSAMparm is not documented. recated... Generating group documentation... Generating class documentation... Generating docs for compound AtomForce... Generating docs for compound sAPOLparm... Generating docs for compound sBEMparm... Generating docs for compound sFEMparm... Generating docs for compound sGEOFLOWparm... Generating docs for compound sMGparm... Generating docs for compound sNOsh... Generating docs for compound sNOsh_calc... Generating docs for compound sPBAMparm... Generating docs for compound sPBEparm... Generating docs for compound sPBSAMparm... Generating docs for compound sVacc... Generating docs for compound sVaccSurf... Generating docs for compound sValist... Generating docs for compound sVatom... Generating docs for compound sVclist... Generating docs for compound sVclistCell... Generating docs for compound sVcsm... Generating docs for compound sVfetk... Generating docs for compound sVfetk_LocalVar... Generating docs for compound sVgreen... Generating docs for compound sVgrid... Generating docs for compound sVmgrid... Generating docs for compound sVopot... Generating docs for compound sVparam_AtomData... Generating docs for compound sVpbe... Generating docs for compound sVpee... Generating docs for compound sVpmg... Generating docs for compound sVpmgp... Generating docs for compound Vparam... Generating docs for compound Vparam_ResData... Generating concept documentation... Generating namespace documentation... Generating graph info page... Generating directory documentation... Generating dependency graph for directory src/fem Generating dependency graph for directory src/generic Generating dependency graph for directory src/mg Generating dependency graph for directory src/pmgc Generating dependency graph for directory doc/programmer Generating dependency graph for directory src Generating index page... Generating main page... Generating page index... Generating module index... Generating namespace index... Generating namespace member index... Generating concept index... Generating annotated compound index... Generating alphabetical compound index... Generating hierarchical class index... Generating graphical class hierarchy... Generating member index... Generating file index... Generating file member index... Generating example index... finalizing index lists... writing tag file... Running plantuml with JAVA... Running dot... Generating dot graphs using 3 parallel threads... 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LaTeX Warning: Reference `newtond_8c_source' on page 18 undefined on input line 93. LaTeX Warning: Reference `newtond_8h_source' on page 18 undefined on input line 94. LaTeX Warning: Reference `powerd_8c_source' on page 18 undefined on input line 95. LaTeX Warning: Reference `powerd_8h_source' on page 18 undefined on input line 96. LaTeX Warning: Reference `smoothd_8c_source' on page 18 undefined on input line 97. LaTeX Warning: Reference `smoothd_8h_source' on page 18 undefined on input line 98. ) [18] Chapter 7. (./group___header.tex) (./group___vcsm.tex [19] Underfull \hbox (badness 10000) detected at line 93 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.1 on input line 102. [20] Underfull \hbox (badness 10000) detected at line 113 [][][] Underfull \hbox (badness 10000) detected at line 116 [][][] Underfull \hbox (badness 10000) detected at line 121 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.2 on input line 130. Underfull \hbox (badness 10000) detected at line 145 [][][] Underfull \hbox (badness 10000) detected at line 148 [][][] Underfull \hbox (badness 10000) detected at line 153 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.3 on input line 164. [21] Underfull \hbox (badness 10000) detected at line 179 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.4 on input line 186. Underfull \hbox (badness 10000) detected at line 201 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.5 on input line 208. 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Underfull \hbox (badness 10000) detected at line 1881 [][][] Underfull \hbox (badness 10000) detected at line 1886 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.68 on input line 1905. ) (./group___vpee.tex [56] Underfull \hbox (badness 849) in paragraph at lines 45--46 \T1/phv/m/n/10 Holst par-al-lel re-fine-ment rou-tine es-sen-tially re-duces th e er-ror out-side the \T1/pcr/m/n/10 local^^D partition to zero. Underfull \hbox (badness 10000) in paragraph at lines 45--46 \T1/pcr/m/n/10 However, this leads to the need for a few final overlapping Schw arz solves to Underfull \hbox (badness 10000) in paragraph at lines 45--46 \T1/pcr/m/n/10 smooth out the errors near partition boundaries. Supposedly, if the region in Underfull \hbox (badness 10000) in paragraph at lines 45--46 \T1/pcr/m/n/10 which we allow error-based refinement includes the$\OML/cmm/m/it /10 <$\T1/pcr/m/n/10 /tt$\OML/cmm/m/it/10 >$\T1/pcr/m/n/10 local^^D partition a nd an Underfull \hbox (badness 10000) in paragraph at lines 45--46 \T1/pcr/m/n/10 external buffer zone approximately equal in size to the local re gion, then the Underfull \hbox (badness 10000) in paragraph at lines 45--46 \T1/pcr/m/n/10 solution will asymptotically approach the solution obtained via more typical Underfull \hbox (badness 10000) in paragraph at lines 45--46 \T1/pcr/m/n/10 methods. This is essentially a more flexible parallel implementa tion of MC\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 s [57] Underfull \hbox (badness 10000) detected at line 75 [][][] Underfull \hbox (badness 10000) detected at line 78 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.69 on input line 93. 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Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 198 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.103 on input line 207. Underfull \hbox (badness 10000) detected at line 208 [][][] [76] Underfull \hbox (badness 10000) detected at line 225 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.104 on input line 232. Underfull \hbox (badness 10000) detected at line 247 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.105 on input line 254. Underfull \hbox (badness 10000) detected at line 269 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.106 on input line 280. [77] Underfull \hbox (badness 10000) detected at line 281 [][][] ) (./group___m_gparm.tex [78] [79] Package longtable Warning: Column widths have changed (longtable) in table 7.107 on input line 159. Package longtable Warning: Column widths have changed (longtable) in table 7.108 on input line 187. Underfull \hbox (badness 10000) detected at line 205 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.109 on input line 216. [80] Underfull \hbox (badness 10000) detected at line 217 [][][] Underfull \hbox (badness 10000) detected at line 234 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.110 on input line 245. Underfull \hbox (badness 10000) detected at line 246 [][][] Underfull \hbox (badness 10000) detected at line 263 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.111 on input line 270. Underfull \hbox (badness 10000) detected at line 271 [][][] [81] Underfull \hbox (badness 10000) detected at line 288 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.112 on input line 297. Underfull \hbox (badness 10000) detected at line 312 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.113 on input line 319. Underfull \hbox (badness 10000) detected at line 320 [][][] Underfull \hbox (badness 10000) detected at line 337 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.114 on input line 346. Underfull \hbox (badness 10000) detected at line 347 [][][] [82] Underfull \hbox (badness 10000) detected at line 364 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.115 on input line 371. Underfull \hbox (badness 10000) detected at line 386 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.116 on input line 393. Underfull \hbox (badness 10000) detected at line 408 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.117 on input line 415. Underfull \hbox (badness 10000) detected at line 416 [][][] [83] Underfull \hbox (badness 10000) detected at line 433 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.118 on input line 440. Underfull \hbox (badness 10000) detected at line 441 [][][] Underfull \hbox (badness 10000) detected at line 458 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.119 on input line 465. Underfull \hbox (badness 10000) detected at line 466 [][][] Underfull \hbox (badness 10000) detected at line 483 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.120 on input line 490. Underfull \hbox (badness 10000) detected at line 491 [][][] [84] Underfull \hbox (badness 10000) detected at line 508 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.121 on input line 515. Underfull \hbox (badness 10000) detected at line 516 [][][] Underfull \hbox (badness 10000) detected at line 533 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.122 on input line 540. Underfull \hbox (badness 10000) detected at line 541 [][][] Underfull \hbox (badness 10000) detected at line 558 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.123 on input line 565. [85] Underfull \hbox (badness 10000) detected at line 566 [][][] Underfull \hbox (badness 10000) detected at line 583 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.124 on input line 590. Underfull \hbox (badness 10000) detected at line 591 [][][] Underfull \hbox (badness 10000) detected at line 608 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.125 on input line 615. Underfull \hbox (badness 10000) detected at line 616 [][][] Underfull \hbox (badness 10000) detected at line 633 [][][] [86] Package longtable Warning: Column widths have changed (longtable) in table 7.126 on input line 644. Underfull \hbox (badness 10000) detected at line 645 [][][] Underfull \hbox (badness 10000) detected at line 662 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.127 on input line 671. Underfull \hbox (badness 10000) detected at line 686 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.128 on input line 695. [87] Underfull \hbox (badness 10000) detected at line 710 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.129 on input line 719. ) (./group___n_osh.tex [88] [89] [90] Package longtable Warning: Column widths have changed (longtable) in table 7.130 on input line 321. [91] Package longtable Warning: Column widths have changed (longtable) in table 7.131 on input line 349. Package longtable Warning: Column widths have changed (longtable) in table 7.132 on input line 373. Package longtable Warning: Column widths have changed (longtable) in table 7.133 on input line 413. [92] Underfull \hbox (badness 10000) detected at line 431 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.134 on input line 440. Underfull \hbox (badness 10000) detected at line 441 [][][] Underfull \hbox (badness 10000) detected at line 458 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.135 on input line 467. Underfull \hbox (badness 10000) detected at line 482 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.136 on input line 489. [93] Underfull \hbox (badness 10000) detected at line 490 [][][] Underfull \hbox (badness 10000) detected at line 507 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.137 on input line 514. Underfull \hbox (badness 10000) detected at line 529 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.138 on input line 538. Underfull \hbox (badness 10000) detected at line 539 [][][] Underfull \hbox (badness 10000) detected at line 556 [][][] [94] Package longtable Warning: Column widths have changed (longtable) in table 7.139 on input line 567. Underfull \hbox (badness 10000) detected at line 568 [][][] Underfull \hbox (badness 10000) detected at line 585 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.140 on input line 592. Underfull \hbox (badness 10000) detected at line 607 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.141 on input line 614. Underfull \hbox (badness 10000) detected at line 629 [][][] [95] Package longtable Warning: Column widths have changed (longtable) in table 7.142 on input line 638. Underfull \hbox (badness 10000) detected at line 639 [][][] Underfull \hbox (badness 10000) detected at line 656 [][][] Underfull \hbox (badness 10000) detected at line 659 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.143 on input line 668. Underfull \hbox (badness 10000) detected at line 669 [][][] Underfull \hbox (badness 10000) detected at line 672 [][][] Underfull \hbox (badness 10000) detected at line 689 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.144 on input line 698. Overfull \vbox (15.28305pt too high) has occurred while \output is active [96] Underfull \hbox (badness 10000) detected at line 699 [][][] Underfull \hbox (badness 10000) detected at line 716 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.145 on input line 725. Underfull \hbox (badness 10000) detected at line 726 [][][] Underfull \hbox (badness 10000) detected at line 743 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.146 on input line 752. Underfull \hbox (badness 10000) detected at line 753 [][][] [97] Underfull \hbox (badness 10000) detected at line 770 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.147 on input line 779. Underfull \hbox (badness 10000) detected at line 780 [][][] Underfull \hbox (badness 10000) detected at line 797 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.148 on input line 806. Underfull \hbox (badness 10000) detected at line 807 [][][] Underfull \hbox (badness 10000) detected at line 824 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.149 on input line 833. [98] Underfull \hbox (badness 10000) detected at line 834 [][][] Underfull \hbox (badness 10000) detected at line 851 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.150 on input line 860. Underfull \hbox (badness 10000) detected at line 861 [][][] Underfull \hbox (badness 10000) detected at line 878 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.151 on input line 887. Underfull \hbox (badness 10000) detected at line 888 [][][] [99] Underfull \hbox (badness 10000) detected at line 905 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.152 on input line 914. Underfull \hbox (badness 10000) detected at line 915 [][][] Underfull \hbox (badness 10000) detected at line 932 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.153 on input line 941. Underfull \hbox (badness 10000) detected at line 942 [][][] Underfull \hbox (badness 10000) detected at line 959 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.154 on input line 968. [100] Underfull \hbox (badness 10000) detected at line 969 [][][] Underfull \hbox (badness 10000) detected at line 986 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.155 on input line 995. Underfull \hbox (badness 10000) detected at line 996 [][][] Underfull \hbox (badness 10000) detected at line 1013 [][][] Underfull \hbox (badness 10000) detected at line 1016 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.156 on input line 1025. Underfull \hbox (badness 10000) detected at line 1026 [][][] [101] Underfull \hbox (badness 10000) detected at line 1043 [][][] Underfull \hbox (badness 10000) detected at line 1048 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.157 on input line 1057. Underfull \hbox (badness 10000) detected at line 1058 [][][] Underfull \hbox (badness 10000) detected at line 1075 [][][] Underfull \hbox (badness 10000) detected at line 1078 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.158 on input line 1089. [102] Underfull \hbox (badness 10000) detected at line 1090 [][][] Underfull \hbox (badness 10000) detected at line 1093 [][][] Underfull \hbox (badness 10000) detected at line 1110 [][][] Underfull \hbox (badness 10000) detected at line 1113 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.159 on input line 1122. Underfull \hbox (badness 10000) detected at line 1123 [][][] Underfull \hbox (badness 10000) detected at line 1126 [][][] Underfull \hbox (badness 10000) detected at line 1143 [][][] Underfull \hbox (badness 10000) detected at line 1146 [][][] [103] Package longtable Warning: Column widths have changed (longtable) in table 7.160 on input line 1157. Underfull \hbox (badness 10000) detected at line 1158 [][][] Underfull \hbox (badness 10000) detected at line 1161 [][][] Underfull \hbox (badness 10000) detected at line 1178 [][][] Underfull \hbox (badness 10000) detected at line 1181 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.161 on input line 1190. Underfull \hbox (badness 10000) detected at line 1191 [][][] Underfull \hbox (badness 10000) detected at line 1194 [][][] Underfull \hbox (badness 10000) detected at line 1211 [][][] [104] Underfull \hbox (badness 10000) detected at line 1214 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.162 on input line 1223. Underfull \hbox (badness 10000) detected at line 1224 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.163 on input line 1233. Underfull \hbox (badness 10000) detected at line 1248 [][][] Underfull \hbox (badness 10000) detected at line 1251 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.164 on input line 1260. Underfull \hbox (badness 10000) detected at line 1261 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.165 on input line 1270. Overfull \vbox (3.94589pt too high) has occurred while \output is active [105]) (./group___p_b_a_mparm.tex [106] Underfull \hbox (badness 10000) detected at line 116 [][][] Underfull \hbox (badness 10000) detected at line 119 [][][] [107] Package longtable Warning: Column widths have changed (longtable) in table 7.166 on input line 154. Underfull \hbox (badness 10000) detected at line 172 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.167 on input line 179. Underfull \hbox (badness 10000) detected at line 180 [][][] Underfull \hbox (badness 10000) detected at line 197 [][][] [108] Package longtable Warning: Column widths have changed (longtable) in table 7.168 on input line 206. Underfull \hbox (badness 10000) detected at line 221 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.169 on input line 228. Underfull \hbox (badness 10000) detected at line 229 [][][] Underfull \hbox (badness 10000) detected at line 246 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.170 on input line 255. Underfull \hbox (badness 10000) detected at line 256 [][][] [109] Underfull \hbox (badness 10000) detected at line 273 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.171 on input line 280. Underfull \hbox (badness 10000) detected at line 295 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.172 on input line 302. Underfull \hbox (badness 10000) detected at line 317 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.173 on input line 326. Underfull \hbox (badness 10000) detected at line 341 [][][] [110] Package longtable Warning: Column widths have changed (longtable) in table 7.174 on input line 350. Underfull \hbox (badness 10000) detected at line 365 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.175 on input line 374. Underfull \hbox (badness 10000) detected at line 389 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.176 on input line 398. Underfull \hbox (badness 10000) detected at line 413 [][][] [111] Package longtable Warning: Column widths have changed (longtable) in table 7.177 on input line 422. Underfull \hbox (badness 10000) detected at line 437 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.178 on input line 446. Underfull \hbox (badness 10000) detected at line 461 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.179 on input line 470. Underfull \hbox (badness 10000) detected at line 485 [][][] [112] Package longtable Warning: Column widths have changed (longtable) in table 7.180 on input line 494. Underfull \hbox (badness 10000) detected at line 509 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.181 on input line 518. Underfull \hbox (badness 10000) detected at line 533 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.182 on input line 542. Underfull \hbox (badness 10000) detected at line 557 [][][] [113] Package longtable Warning: Column widths have changed (longtable) in table 7.183 on input line 566. Underfull \hbox (badness 10000) detected at line 581 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.184 on input line 592. Underfull \hbox (badness 10000) detected at line 593 [][][] Underfull \hbox (badness 10000) detected at line 610 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.185 on input line 619. [114] Underfull \hbox (badness 10000) detected at line 634 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.186 on input line 643. ) (./group___p_b_eparm.tex [115] [116] Package longtable Warning: Column widths have changed (longtable) in table 7.187 on input line 163. Package longtable Warning: Column widths have changed (longtable) in table 7.188 on input line 191. Underfull \hbox (badness 10000) detected at line 209 [][][] Underfull \hbox (badness 10000) detected at line 212 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.189 on input line 219. [117] Underfull \hbox (badness 10000) detected at line 234 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.190 on input line 243. Underfull \hbox (badness 10000) detected at line 258 [][][] Underfull \hbox (badness 10000) detected at line 261 [][][] Underfull \hbox (badness 10000) detected at line 278 [][][] Underfull \hbox (badness 10000) detected at line 281 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.191 on input line 288. [118] Underfull \hbox (badness 10000) detected at line 303 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.192 on input line 310. Underfull \hbox (badness 10000) detected at line 325 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.193 on input line 332. Underfull \hbox (badness 10000) detected at line 347 [][][] Underfull \hbox (badness 10000) detected at line 350 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.194 on input line 359. [119] Underfull \hbox (badness 10000) detected at line 374 [][][] Underfull \hbox (badness 10000) detected at line 377 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.195 on input line 386. Underfull \hbox (badness 10000) detected at line 401 [][][] Underfull \hbox (badness 10000) detected at line 404 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.196 on input line 413. Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 431 [][][] [120] Package longtable Warning: Column widths have changed (longtable) in table 7.197 on input line 442. ) (./group___p_b_s_a_mparm.tex [121] Underfull \hbox (badness 10000) detected at line 100 [][][] Underfull \hbox (badness 10000) detected at line 103 [][][] [122] Package longtable Warning: Column widths have changed (longtable) in table 7.198 on input line 138. Underfull \hbox (badness 10000) detected at line 156 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.199 on input line 163. Underfull \hbox (badness 10000) detected at line 164 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.200 on input line 190. [123] Underfull \hbox (badness 10000) detected at line 205 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.201 on input line 212. Underfull \hbox (badness 10000) detected at line 213 [][][] Underfull \hbox (badness 10000) detected at line 230 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.202 on input line 239. Underfull \hbox (badness 10000) detected at line 240 [][][] Underfull \hbox (badness 10000) detected at line 257 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.203 on input line 264. Overfull \vbox (0.37224pt too high) has occurred while \output is active [124] Underfull \hbox (badness 10000) detected at line 279 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.204 on input line 286. Underfull \hbox (badness 10000) detected at line 301 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.205 on input line 310. Underfull \hbox (badness 10000) detected at line 325 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.206 on input line 334. [125] Underfull \hbox (badness 10000) detected at line 349 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.207 on input line 358. Underfull \hbox (badness 10000) detected at line 373 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.208 on input line 382. Underfull \hbox (badness 10000) detected at line 397 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.209 on input line 408. [126] Underfull \hbox (badness 10000) detected at line 409 [][][] Underfull \hbox (badness 10000) detected at line 426 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.210 on input line 435. ) (./group___vacc.tex [127] [128] [129] Underfull \hbox (badness 10000) detected at line 149 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.211 on input line 164. Underfull \hbox (badness 10000) detected at line 179 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.212 on input line 192. [130] Underfull \hbox (badness 10000) detected at line 207 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] Underfull \hbox (badness 10000) detected at line 213 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.213 on input line 224. Underfull \hbox (badness 10000) detected at line 239 [][][] Underfull \hbox (badness 10000) detected at line 242 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.214 on input line 253. [131] Underfull \hbox (badness 10000) detected at line 268 [][][] Underfull \hbox (badness 10000) detected at line 271 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.215 on input line 282. Underfull \hbox (badness 10000) detected at line 283 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.216 on input line 290. Underfull \hbox (badness 10000) detected at line 305 [][][] Underfull \hbox (badness 10000) detected at line 308 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.217 on input line 319. [132] Underfull \hbox (badness 10000) detected at line 334 [][][] Underfull \hbox (badness 10000) detected at line 337 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.218 on input line 350. Underfull \hbox (badness 10000) detected at line 365 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.219 on input line 372. Underfull \hbox (badness 10000) detected at line 387 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.220 on input line 394. [133] Underfull \hbox (badness 10000) detected at line 411 [][][] Underfull \hbox (badness 10000) detected at line 414 [][][] Underfull \hbox (badness 10000) detected at line 417 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.221 on input line 430. Underfull \hbox (badness 10000) detected at line 447 [][][] Underfull \hbox (badness 10000) detected at line 450 [][][] [134] Package longtable Warning: Column widths have changed (longtable) in table 7.222 on input line 461. Underfull \hbox (badness 10000) detected at line 472 [][][] Underfull \hbox (badness 10000) detected at line 475 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.223 on input line 482. Underfull \hbox (badness 10000) detected at line 499 [][][] Underfull \hbox (badness 10000) detected at line 502 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.224 on input line 515. [135] Underfull \hbox (badness 10000) detected at line 530 [][][] Underfull \hbox (badness 10000) detected at line 533 [][][] Underfull \hbox (badness 10000) detected at line 536 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.225 on input line 545. Underfull \hbox (badness 10000) detected at line 562 [][][] Underfull \hbox (badness 10000) detected at line 565 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.226 on input line 578. [136] Underfull \hbox (badness 10000) detected at line 595 [][][] Underfull \hbox (badness 10000) detected at line 598 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.227 on input line 613. Underfull \hbox (badness 10000) detected at line 628 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.228 on input line 643. [137] Underfull \hbox (badness 10000) detected at line 660 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.229 on input line 677. Underfull \hbox (badness 10000) detected at line 692 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.230 on input line 709. [138] Underfull \hbox (badness 10000) detected at line 724 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.231 on input line 741. Underfull \hbox (badness 10000) detected at line 758 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.232 on input line 775. [139] Underfull \hbox (badness 10000) detected at line 790 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.233 on input line 805. Underfull \hbox (badness 10000) detected at line 820 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.234 on input line 837. [140] Underfull \hbox (badness 10000) detected at line 852 [][][] Underfull \hbox (badness 10000) detected at line 855 [][][] Underfull \hbox (badness 10000) detected at line 858 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.235 on input line 867. Underfull \hbox (badness 10000) detected at line 882 [][][] Underfull \hbox (badness 10000) detected at line 885 [][][] Underfull \hbox (badness 10000) detected at line 888 [][][] [141] Package longtable Warning: Column widths have changed (longtable) in table 7.236 on input line 901. Underfull \hbox (badness 10000) detected at line 918 [][][] Underfull \hbox (badness 10000) detected at line 921 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.237 on input line 930. Underfull \hbox (badness 10000) detected at line 941 [][][] Underfull \hbox (badness 10000) detected at line 944 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.238 on input line 957. Overfull \vbox (21.5778pt too high) has occurred while \output is active [142] Underfull \hbox (badness 10000) detected at line 972 [][][] Underfull \hbox (badness 10000) detected at line 975 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.239 on input line 992. Underfull \hbox (badness 10000) detected at line 1007 [][][] Underfull \hbox (badness 10000) detected at line 1010 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.240 on input line 1025. [143] Underfull \hbox (badness 10000) detected at line 1040 [][][] Underfull \hbox (badness 10000) detected at line 1043 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.241 on input line 1054. Underfull \hbox (badness 10000) detected at line 1069 [][][] Underfull \hbox (badness 10000) detected at line 1072 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.242 on input line 1085. Overfull \vbox (18.93095pt too high) has occurred while \output is active [144] Underfull \hbox (badness 10000) detected at line 1100 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.243 on input line 1107. Underfull \hbox (badness 10000) detected at line 1122 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.244 on input line 1129. Underfull \hbox (badness 10000) detected at line 1146 [][][] Underfull \hbox (badness 10000) detected at line 1149 [][][] Underfull \hbox (badness 10000) detected at line 1152 [][][] [145] Package longtable Warning: Column widths have changed (longtable) in table 7.245 on input line 1161. ) (./group___valist.tex [146] Underfull \hbox (badness 10000) detected at line 91 [][][] Underfull \hbox (badness 10000) detected at line 94 [][][] Underfull \hbox (badness 10000) detected at line 111 [][][] Underfull \hbox (badness 10000) detected at line 114 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.246 on input line 121. Overfull \vbox (3.49948pt too high) has occurred while \output is active [147] Underfull \hbox (badness 10000) detected at line 136 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.247 on input line 143. Underfull \hbox (badness 10000) detected at line 158 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.248 on input line 165. Underfull \hbox (badness 10000) detected at line 180 [][][] Underfull \hbox (badness 10000) detected at line 183 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.249 on input line 192. [148] Underfull \hbox (badness 10000) detected at line 207 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.250 on input line 217. Underfull \hbox (badness 10000) detected at line 232 [][][] Underfull \hbox (badness 10000) detected at line 235 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.251 on input line 242. Underfull \hbox (badness 10000) detected at line 257 [][][] Underfull \hbox (badness 10000) detected at line 260 [][][] [149] Package longtable Warning: Column widths have changed (longtable) in table 7.252 on input line 267. Underfull \hbox (badness 10000) detected at line 282 [][][] Underfull \hbox (badness 10000) detected at line 285 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.253 on input line 292. Underfull \hbox (badness 10000) detected at line 307 [][][] Underfull \hbox (badness 10000) detected at line 310 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.254 on input line 317. Underfull \hbox (badness 10000) detected at line 332 [][][] [150] Underfull \hbox (badness 10000) detected at line 335 [][][] Underfull \hbox (badness 10000) detected at line 352 [][][] Underfull \hbox (badness 10000) detected at line 355 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.255 on input line 362. Underfull \hbox (badness 10000) detected at line 377 [][][] Underfull \hbox (badness 10000) detected at line 380 [][][] Underfull \hbox (badness 10000) detected at line 383 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.256 on input line 394. [151] Underfull \hbox (badness 10000) detected at line 409 [][][] Underfull \hbox (badness 10000) detected at line 412 [][][] Underfull \hbox (badness 10000) detected at line 415 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.257 on input line 428. Underfull \hbox (badness 10000) detected at line 443 [][][] Underfull \hbox (badness 10000) detected at line 446 [][][] Underfull \hbox (badness 10000) detected at line 449 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.258 on input line 462. Overfull \vbox (15.85518pt too high) has occurred while \output is active [152]) (./group___vatom.tex [153] Underfull \hbox (badness 10000) detected at line 97 [][][] [154] Underfull \hbox (badness 10000) detected at line 134 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.259 on input line 143. Underfull \hbox (badness 10000) detected at line 158 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.260 on input line 167. Underfull \hbox (badness 10000) detected at line 182 [][][] Underfull \hbox (badness 10000) detected at line 185 [][][] [155] Underfull \hbox (badness 10000) detected at line 202 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.261 on input line 209. Underfull \hbox (badness 10000) detected at line 210 [][][] Underfull \hbox (badness 10000) detected at line 227 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.262 on input line 234. Underfull \hbox (badness 10000) detected at line 249 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.263 on input line 256. Underfull \hbox (badness 10000) detected at line 271 [][][] [156] Package longtable Warning: Column widths have changed (longtable) in table 7.264 on input line 278. Underfull \hbox (badness 10000) detected at line 279 [][][] Underfull \hbox (badness 10000) detected at line 296 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.265 on input line 305. Underfull \hbox (badness 10000) detected at line 320 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.266 on input line 327. Underfull \hbox (badness 10000) detected at line 328 [][][] [157] Underfull \hbox (badness 10000) detected at line 345 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.267 on input line 352. Underfull \hbox (badness 10000) detected at line 353 [][][] Underfull \hbox (badness 10000) detected at line 370 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.268 on input line 377. Underfull \hbox (badness 10000) detected at line 378 [][][] Underfull \hbox (badness 10000) detected at line 395 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.269 on input line 402. Underfull \hbox (badness 10000) detected at line 403 [][][] [158] Underfull \hbox (badness 10000) detected at line 420 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.270 on input line 427. Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 445 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.271 on input line 454. Underfull \hbox (badness 10000) detected at line 469 [][][] [159] Package longtable Warning: Column widths have changed (longtable) in table 7.272 on input line 476. Underfull \hbox (badness 10000) detected at line 477 [][][] Underfull \hbox (badness 10000) detected at line 494 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.273 on input line 503. Underfull \hbox (badness 10000) detected at line 518 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.274 on input line 527. [160] Underfull \hbox (badness 10000) detected at line 542 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.275 on input line 551. Underfull \hbox (badness 10000) detected at line 566 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.276 on input line 575. Underfull \hbox (badness 10000) detected at line 590 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.277 on input line 599. [161] Underfull \hbox (badness 10000) detected at line 614 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.278 on input line 623. Underfull \hbox (badness 10000) detected at line 638 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.279 on input line 647. Underfull \hbox (badness 10000) detected at line 662 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.280 on input line 671. ) (./group___vcap.tex [162] Underfull \hbox (badness 10000) detected at line 36 [][][] [163] Underfull \hbox (badness 10000) detected at line 86 [][][] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 92 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.281 on input line 101. Underfull \hbox (badness 10000) detected at line 119 [][][] Underfull \hbox (badness 10000) detected at line 122 [][][] Underfull \hbox (badness 10000) detected at line 125 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.282 on input line 134. [164] Underfull \hbox (badness 10000) detected at line 152 [][][] Underfull \hbox (badness 10000) detected at line 155 [][][] Underfull \hbox (badness 10000) detected at line 158 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.283 on input line 167. ) (./group___vclist.tex [165] [166] Underfull \hbox (badness 10000) detected at line 110 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.284 on input line 122. Underfull \hbox (badness 10000) detected at line 140 [][][] Underfull \hbox (badness 10000) detected at line 143 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.285 on input line 160. [167] Underfull \hbox (badness 10000) detected at line 175 [][][] Underfull \hbox (badness 10000) detected at line 178 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.286 on input line 197. Underfull \hbox (badness 10000) detected at line 212 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.287 on input line 219. [168] Underfull \hbox (badness 10000) detected at line 234 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.288 on input line 241. Underfull \hbox (badness 10000) detected at line 256 [][][] Underfull \hbox (badness 10000) detected at line 259 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.289 on input line 268. Underfull \hbox (badness 10000) detected at line 283 [][][] Underfull \hbox (badness 10000) detected at line 286 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.290 on input line 293. [169] Underfull \hbox (badness 10000) detected at line 308 [][][] Underfull \hbox (badness 10000) detected at line 311 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.291 on input line 318. Underfull \hbox (badness 10000) detected at line 333 [][][] Underfull \hbox (badness 10000) detected at line 336 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.292 on input line 343. Underfull \hbox (badness 10000) detected at line 358 [][][] Underfull \hbox (badness 10000) detected at line 361 [][][] [170] Package longtable Warning: Column widths have changed (longtable) in table 7.293 on input line 370. Underfull \hbox (badness 10000) detected at line 385 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.294 on input line 392. Underfull \hbox (badness 10000) detected at line 407 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.295 on input line 414. ) (./group___vgreen.tex [171] Underfull \hbox (badness 10000) detected at line 57 [][][] Underfull \hbox (badness 10000) detected at line 60 [][][] [172] [173] Underfull \hbox (badness 10000) detected at line 141 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.296 on input line 158. Underfull \hbox (badness 10000) detected at line 159 [][][] Underfull \hbox (badness 10000) detected at line 178 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.297 on input line 195. [174] Underfull \hbox (badness 10000) detected at line 196 [][][] Underfull \hbox (badness 10000) detected at line 215 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.298 on input line 238. [175] Underfull \hbox (badness 10000) detected at line 239 [][][] Underfull \hbox (badness 10000) detected at line 258 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.299 on input line 281. Underfull \hbox (badness 10000) detected at line 282 [][][] [176] Underfull \hbox (badness 10000) detected at line 299 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.300 on input line 306. Underfull \hbox (badness 10000) detected at line 307 [][][] Underfull \hbox (badness 10000) detected at line 324 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.301 on input line 333. Underfull \hbox (badness 10000) detected at line 334 [][][] Underfull \hbox (badness 10000) detected at line 351 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.302 on input line 358. [177] Underfull \hbox (badness 10000) detected at line 373 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.303 on input line 380. Underfull \hbox (badness 10000) detected at line 395 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.304 on input line 402. Underfull \hbox (badness 10000) detected at line 403 [][][] Underfull \hbox (badness 10000) detected at line 424 [][][] [178] Underfull \hbox (badness 10000) detected at line 429 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.305 on input line 448. Underfull \hbox (badness 10000) detected at line 449 [][][] Underfull \hbox (badness 10000) detected at line 471 [][][] Underfull \hbox (badness 10000) detected at line 476 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.306 on input line 499. [179] Underfull \hbox (badness 10000) detected at line 500 [][][] Underfull \hbox (badness 10000) detected at line 517 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.307 on input line 524. Underfull \hbox (badness 10000) detected at line 525 [][][] ) (./group___vhal.tex [180] [181] [182] [183] Underfull \hbox (badness 10000) detected at line 380 [][][] Underfull \hbox (badness 10000) detected at line 411 [][][] [184] Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 445 [][][] Underfull \hbox (badness 10000) detected at line 476 [][][] Underfull \hbox (badness 10000) detected at line 493 [][][] Underfull \hbox (badness 10000) detected at line 516 [][][] [185] Underfull \hbox (badness 10000) detected at line 547 [][][] [186] Underfull \hbox (badness 10000) detected at line 682 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.308 on input line 714. Underfull \hbox (badness 10000) detected at line 729 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.309 on input line 745. [187] Underfull \hbox (badness 10000) detected at line 760 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.310 on input line 780. Underfull \hbox (badness 10000) detected at line 795 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.311 on input line 827. Underfull \hbox (badness 10000) detected at line 842 [][][] Missing character: There is no Å in font cmr10! Missing character: There is no Å in font cmr10! LaTeX Warning: Command \r invalid in math mode on input line 58. Missing character: There is no Å in font cmr10! Package longtable Warning: Column widths have changed (longtable) in table 7.312 on input line 906. [188] Package longtable Warning: Column widths have changed (longtable) in table 7.313 on input line 934. Package longtable Warning: Column widths have changed (longtable) in table 7.314 on input line 980. [189] Package longtable Warning: Column widths have changed (longtable) in table 7.315 on input line 1004. Underfull \hbox (badness 10000) detected at line 1019 [][][] Underfull \hbox (badness 10000) detected at line 1022 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.316 on input line 1035. Underfull \hbox (badness 10000) detected at line 1050 [][][] Underfull \hbox (badness 10000) detected at line 1053 [][][] Underfull \hbox (badness 10000) detected at line 1070 [][][] [190] Package longtable Warning: Column widths have changed (longtable) in table 7.317 on input line 1095. ) (./group___vmatrix.tex) (./group___vparam.tex [191] [192] Underfull \hbox (badness 10000) detected at line 120 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.318 on input line 129. Underfull \hbox (badness 10000) detected at line 130 [][][] [193] Underfull \hbox (badness 10000) detected at line 147 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.319 on input line 156. Underfull \hbox (badness 10000) detected at line 157 [][][] Underfull \hbox (badness 10000) detected at line 174 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.320 on input line 183. Underfull \hbox (badness 10000) detected at line 198 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.321 on input line 207. [194] Underfull \hbox (badness 10000) detected at line 222 [][][] Underfull \hbox (badness 10000) detected at line 225 [][][] Underfull \hbox (badness 10000) detected at line 242 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.322 on input line 249. Underfull \hbox (badness 10000) detected at line 250 [][][] Underfull \hbox (badness 10000) detected at line 267 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.323 on input line 274. [195] Underfull \hbox (badness 10000) detected at line 289 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.324 on input line 296. Underfull \hbox (badness 10000) detected at line 311 [][][] Underfull \hbox (badness 10000) detected at line 314 [][][] Underfull \hbox (badness 10000) detected at line 331 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.325 on input line 338. Underfull \hbox (badness 10000) detected at line 339 [][][] Underfull \hbox (badness 10000) detected at line 356 [][][] [196] Package longtable Warning: Column widths have changed (longtable) in table 7.326 on input line 363. Underfull \hbox (badness 10000) detected at line 378 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.327 on input line 385. Underfull \hbox (badness 10000) detected at line 400 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.328 on input line 411. Underfull \hbox (badness 10000) detected at line 412 [][][] Underfull \hbox (badness 10000) detected at line 415 [][][] Underfull \hbox (badness 10000) detected at line 418 [][][] [197] Underfull \hbox (badness 10000) detected at line 435 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.329 on input line 444. Underfull \hbox (badness 10000) detected at line 445 [][][] Underfull \hbox (badness 10000) detected at line 448 [][][] Underfull \hbox (badness 10000) detected at line 451 [][][] Underfull \hbox (badness 10000) detected at line 468 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.330 on input line 475. Underfull \hbox (badness 10000) detected at line 476 [][][] [198] Underfull \hbox (badness 10000) detected at line 493 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.331 on input line 508. Underfull \hbox (badness 10000) detected at line 509 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Underfull \hbox (badness 10000) detected at line 537 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.332 on input line 552. [199] Underfull \hbox (badness 10000) detected at line 553 [][][] Underfull \hbox (badness 10000) detected at line 570 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.333 on input line 579. Underfull \hbox (badness 10000) detected at line 594 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.334 on input line 601. Underfull \hbox (badness 10000) detected at line 602 [][][] [200] Underfull \hbox (badness 10000) detected at line 619 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.335 on input line 628. Underfull \hbox (badness 10000) detected at line 629 [][][] Underfull \hbox (badness 10000) detected at line 646 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.336 on input line 653. Underfull \hbox (badness 10000) detected at line 668 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.337 on input line 675. [201]) (./group___vpbe.tex [202] [203] Underfull \hbox (badness 10000) detected at line 128 [][][] Underfull \hbox (badness 10000) detected at line 131 [][][] LaTeX Warning: Command \r invalid in math mode on input line 133. Missing character: There is no Å in font cmr10! LaTeX Warning: Command \r invalid in math mode on input line 133. Missing character: There is no Å in font cmr10! [204] Underfull \hbox (badness 10000) detected at line 136 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.338 on input line 171. [205] Underfull \hbox (badness 10000) detected at line 186 [][][] Underfull \hbox (badness 10000) detected at line 189 [][][] LaTeX Warning: Command \r invalid in math mode on input line 190. Missing character: There is no Å in font cmr10! LaTeX Warning: Command \r invalid in math mode on input line 190. Missing character: There is no Å in font cmr10! Underfull \hbox (badness 10000) detected at line 195 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.339 on input line 232. Overfull \vbox (21.60152pt too high) has occurred while \output is active [206] Underfull \hbox (badness 10000) detected at line 247 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.340 on input line 254. Underfull \hbox (badness 10000) detected at line 269 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.341 on input line 276. Underfull \hbox (badness 10000) detected at line 291 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.342 on input line 298. Underfull \hbox (badness 10000) detected at line 299 [][][] [207] Overfull \hbox (151.96916pt too wide) in paragraph at lines 318--318 [] \T1/p cr/m/n/8 permittivity equal to the protein interior) and zero ionic[] Underfull \hbox (badness 10000) detected at line 325 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.343 on input line 332. Underfull \hbox (badness 10000) detected at line 333 [][][] Underfull \hbox (badness 10000) detected at line 350 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.344 on input line 357. Underfull \hbox (badness 10000) detected at line 358 [][][] [208] Underfull \hbox (badness 10000) detected at line 375 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.345 on input line 382. Underfull \hbox (badness 10000) detected at line 383 [][][] Underfull \hbox (badness 10000) detected at line 396 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.346 on input line 411. Underfull \hbox (badness 10000) detected at line 412 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.347 on input line 435. [209] Underfull \hbox (badness 10000) detected at line 436 [][][] Underfull \hbox (badness 10000) detected at line 453 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.348 on input line 460. Underfull \hbox (badness 10000) detected at line 461 [][][] Underfull \hbox (badness 10000) detected at line 478 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.349 on input line 485. Underfull \hbox (badness 10000) detected at line 486 [][][] Underfull \hbox (badness 10000) detected at line 503 [][][] [210] Package longtable Warning: Column widths have changed (longtable) in table 7.350 on input line 510. Underfull \hbox (badness 10000) detected at line 525 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.351 on input line 532. Underfull \hbox (badness 10000) detected at line 533 [][][] Underfull \hbox (badness 10000) detected at line 550 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.352 on input line 557. Underfull \hbox (badness 10000) detected at line 558 [][][] Underfull \hbox (badness 10000) detected at line 575 [][][] [211] Package longtable Warning: Column widths have changed (longtable) in table 7.353 on input line 582. Underfull \hbox (badness 10000) detected at line 583 [][][] Underfull \hbox (badness 10000) detected at line 600 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.354 on input line 607. Underfull \hbox (badness 10000) detected at line 608 [][][] Underfull \hbox (badness 10000) detected at line 625 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.355 on input line 632. Underfull \hbox (badness 10000) detected at line 633 [][][] [212] Underfull \hbox (badness 10000) detected at line 650 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.356 on input line 657. Underfull \hbox (badness 10000) detected at line 658 [][][] Underfull \hbox (badness 10000) detected at line 675 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.357 on input line 682. Underfull \hbox (badness 10000) detected at line 683 [][][] Underfull \hbox (badness 10000) detected at line 700 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.358 on input line 707. Underfull \hbox (badness 10000) detected at line 708 [][][] [213] Underfull \hbox (badness 10000) detected at line 725 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.359 on input line 732. Underfull \hbox (badness 10000) detected at line 733 [][][] Underfull \hbox (badness 10000) detected at line 750 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.360 on input line 757. Underfull \hbox (badness 10000) detected at line 758 [][][] Underfull \hbox (badness 10000) detected at line 775 [][][] [214] Package longtable Warning: Column widths have changed (longtable) in table 7.361 on input line 782. Underfull \hbox (badness 10000) detected at line 783 [][][] Underfull \hbox (badness 10000) detected at line 800 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.362 on input line 807. Underfull \hbox (badness 10000) detected at line 808 [][][] Underfull \hbox (badness 10000) detected at line 825 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.363 on input line 832. Underfull \hbox (badness 10000) detected at line 833 [][][] [215] Underfull \hbox (badness 10000) detected at line 850 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.364 on input line 857. Underfull \hbox (badness 10000) detected at line 858 [][][] LaTeX Warning: Command \r invalid in math mode on input line 859. Missing character: There is no Å in font cmr10! Underfull \hbox (badness 10000) detected at line 875 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.365 on input line 882. Underfull \hbox (badness 10000) detected at line 883 [][][] Underfull \hbox (badness 10000) detected at line 900 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.366 on input line 907. Underfull \hbox (badness 10000) detected at line 908 [][][] [216] Underfull \hbox (badness 10000) detected at line 925 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.367 on input line 932. Underfull \hbox (badness 10000) detected at line 933 [][][] ) (./group___vstring.tex [217] Underfull \hbox (badness 10000) detected at line 42 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.368 on input line 49. Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 67 [][][] Underfull \hbox (badness 10000) detected at line 70 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.369 on input line 79. Underfull \hbox (badness 10000) detected at line 80 [][][] Underfull \hbox (badness 10000) detected at line 93 [][][] [218] Underfull \hbox (badness 10000) detected at line 96 [][][] Underfull \hbox (badness 10000) detected at line 99 [][][] Underfull \hbox (badness 10000) detected at line 102 [][][] Underfull \hbox (badness 10000) detected at line 105 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.370 on input line 116. ) (./group___vunit.tex [219] LaTeX Warning: Command \r invalid in math mode on input line 39. Missing character: There is no Å in font cmr9! [220] LaTeX Warning: Command \r invalid in math mode on input line 142. Missing character: There is no Å in font cmr10! ) (./group___vgrid.tex [221] [222] [223] Underfull \hbox (badness 10000) detected at line 125 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.371 on input line 150. Underfull \hbox (badness 10000) detected at line 151 [][][] Underfull \hbox (badness 10000) detected at line 168 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.372 on input line 195. [224] Underfull \hbox (badness 10000) detected at line 196 [][][] Underfull \hbox (badness 10000) detected at line 213 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.373 on input line 228. Underfull \hbox (badness 10000) detected at line 229 [][][] [225] Underfull \hbox (badness 10000) detected at line 246 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.374 on input line 253. Underfull \hbox (badness 10000) detected at line 268 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.375 on input line 275. Underfull \hbox (badness 10000) detected at line 290 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.376 on input line 301. Underfull \hbox (badness 10000) detected at line 302 [][][] [226] Underfull \hbox (badness 10000) detected at line 319 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.377 on input line 326. Underfull \hbox (badness 10000) detected at line 327 [][][] Underfull \hbox (badness 10000) detected at line 344 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.378 on input line 351. Underfull \hbox (badness 10000) detected at line 352 [][][] Underfull \hbox (badness 10000) detected at line 369 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.379 on input line 376. Underfull \hbox (badness 10000) detected at line 377 [][][] [227] Underfull \hbox (badness 10000) detected at line 395 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.380 on input line 402. Underfull \hbox (badness 10000) detected at line 403 [][][] Underfull \hbox (badness 10000) detected at line 420 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.381 on input line 427. Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 445 [][][] [228] Package longtable Warning: Column widths have changed (longtable) in table 7.382 on input line 452. Underfull \hbox (badness 10000) detected at line 453 [][][] Underfull \hbox (badness 10000) detected at line 470 [][][] Underfull \hbox (badness 10000) detected at line 473 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.383 on input line 488. Underfull \hbox (badness 10000) detected at line 489 [][][] Underfull \hbox (badness 10000) detected at line 492 [][][] [229] Underfull \hbox (badness 10000) detected at line 509 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.384 on input line 527. Underfull \hbox (badness 10000) detected at line 528 [][][] Underfull \hbox (badness 10000) detected at line 531 [][][] Underfull \hbox (badness 10000) detected at line 548 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.385 on input line 560. [230] Underfull \hbox (badness 10000) detected at line 575 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.386 on input line 582. Underfull \hbox (badness 10000) detected at line 583 [][][] Underfull \hbox (badness 10000) detected at line 600 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.387 on input line 611. Underfull \hbox (badness 10000) detected at line 612 [][][] [231] Underfull \hbox (badness 10000) detected at line 629 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.388 on input line 648. Underfull \hbox (badness 10000) detected at line 663 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.389 on input line 682. [232] Underfull \hbox (badness 10000) detected at line 697 [][][] Underfull \hbox (badness 10000) detected at line 702 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.390 on input line 721. ) (./group___vmgrid.tex [233] [234] Underfull \hbox (badness 10000) detected at line 105 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.391 on input line 114. Underfull \hbox (badness 10000) detected at line 115 [][][] Underfull \hbox (badness 10000) detected at line 132 [][][] Underfull \hbox (badness 10000) detected at line 135 [][][] Underfull \hbox (badness 10000) detected at line 152 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.392 on input line 159. [235] Underfull \hbox (badness 10000) detected at line 160 [][][] Underfull \hbox (badness 10000) detected at line 177 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.393 on input line 192. Underfull \hbox (badness 10000) detected at line 193 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.394 on input line 217. [236] Underfull \hbox (badness 10000) detected at line 232 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.395 on input line 239. Underfull \hbox (badness 10000) detected at line 254 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.396 on input line 263. Underfull \hbox (badness 10000) detected at line 264 [][][] Underfull \hbox (badness 10000) detected at line 277 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.397 on input line 286. [237] Underfull \hbox (badness 10000) detected at line 287 [][][] Underfull \hbox (badness 10000) detected at line 300 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.398 on input line 311. Underfull \hbox (badness 10000) detected at line 312 [][][] Underfull \hbox (badness 10000) detected at line 329 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.399 on input line 340. Underfull \hbox (badness 10000) detected at line 341 [][][] ) (./group___vopot.tex [238] [239] Underfull \hbox (badness 10000) detected at line 77 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.400 on input line 88. Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 106 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.401 on input line 119. [240] Underfull \hbox (badness 10000) detected at line 120 [][][] Underfull \hbox (badness 10000) detected at line 137 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.402 on input line 152. Underfull \hbox (badness 10000) detected at line 153 [][][] Underfull \hbox (badness 10000) detected at line 170 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.403 on input line 177. [241] Underfull \hbox (badness 10000) detected at line 192 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.404 on input line 199. Underfull \hbox (badness 10000) detected at line 214 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.405 on input line 225. Underfull \hbox (badness 10000) detected at line 226 [][][] Underfull \hbox (badness 10000) detected at line 243 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.406 on input line 254. Overfull \vbox (28.1848pt too high) has occurred while \output is active [242] Underfull \hbox (badness 10000) detected at line 255 [][][] ) (./group___vpmg.tex [243] [244] [245] Underfull \hbox (badness 10000) detected at line 117 [][][] Underfull \hbox (badness 10000) detected at line 150 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.407 on input line 171. [246] Underfull \hbox (badness 10000) detected at line 186 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.408 on input line 219. [247] Underfull \hbox (badness 10000) detected at line 234 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.409 on input line 261. Underfull \hbox (badness 10000) detected at line 276 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.410 on input line 309. [248] Underfull \hbox (badness 10000) detected at line 324 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.411 on input line 347. [249] Underfull \hbox (badness 10000) detected at line 362 [][][] Underfull \hbox (badness 10000) detected at line 381 [][][] Underfull \hbox (badness 10000) detected at line 384 [][][] [250] Package longtable Warning: Column widths have changed (longtable) in table 7.412 on input line 401. Underfull \hbox (badness 10000) detected at line 416 [][][] Underfull \hbox (badness 10000) detected at line 419 [][][] Underfull \hbox (badness 10000) detected at line 422 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.413 on input line 443. [251] Underfull \hbox (badness 10000) detected at line 458 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.414 on input line 473. Underfull \hbox (badness 10000) detected at line 484 [][][] Underfull \hbox (badness 10000) detected at line 487 [][][] Underfull \hbox (badness 10000) detected at line 492 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.415 on input line 505. Overfull \vbox (1.11014pt too high) has occurred while \output is active [252] Underfull \hbox (badness 10000) detected at line 520 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.416 on input line 535. Underfull \hbox (badness 10000) detected at line 546 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.417 on input line 561. [253] Underfull \hbox (badness 10000) detected at line 572 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.418 on input line 583. Underfull \hbox (badness 10000) detected at line 604 [][][] Underfull \hbox (badness 10000) detected at line 607 [][][] Underfull \hbox (badness 10000) detected at line 610 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.419 on input line 619. [254] Underfull \hbox (badness 10000) detected at line 643 [][][] Underfull \hbox (badness 10000) detected at line 646 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.420 on input line 653. Underfull \hbox (badness 10000) detected at line 668 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.421 on input line 675. Underfull \hbox (badness 10000) detected at line 690 [][][] [255] Package longtable Warning: Column widths have changed (longtable) in table 7.422 on input line 697. Underfull \hbox (badness 10000) detected at line 712 [][][] Underfull \hbox (badness 10000) detected at line 715 [][][] Underfull \hbox (badness 10000) detected at line 718 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.423 on input line 727. Underfull \hbox (badness 10000) detected at line 742 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.424 on input line 753. [256] Underfull \hbox (badness 10000) detected at line 764 [][][] Underfull \hbox (badness 10000) detected at line 767 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.425 on input line 784. Underfull \hbox (badness 10000) detected at line 799 [][][] [257] Underfull \hbox (badness 10000) detected at line 802 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.426 on input line 841. Underfull \hbox (badness 10000) detected at line 856 [][][] Underfull \hbox (badness 10000) detected at line 859 [][][] Underfull \hbox (badness 10000) detected at line 864 [][][] [258] Package longtable Warning: Column widths have changed (longtable) in table 7.427 on input line 879. Underfull \hbox (badness 10000) detected at line 894 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.428 on input line 909. Underfull \hbox (badness 10000) detected at line 920 [][][] Underfull \hbox (badness 10000) detected at line 923 [][][] [259] Underfull \hbox (badness 10000) detected at line 928 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.429 on input line 941. Underfull \hbox (badness 10000) detected at line 956 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.430 on input line 971. Underfull \hbox (badness 10000) detected at line 982 [][][] [260] Package longtable Warning: Column widths have changed (longtable) in table 7.431 on input line 997. Underfull \hbox (badness 10000) detected at line 1008 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.432 on input line 1019. Underfull \hbox (badness 10000) detected at line 1030 [][][] Underfull \hbox (badness 10000) detected at line 1033 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.433 on input line 1040. [261] Underfull \hbox (badness 10000) detected at line 1055 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.434 on input line 1076. Underfull \hbox (badness 10000) detected at line 1093 [][][] Underfull \hbox (badness 10000) detected at line 1096 [][][] [262] Underfull \hbox (badness 10000) detected at line 1099 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.435 on input line 1108. Underfull \hbox (badness 10000) detected at line 1123 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.436 on input line 1140. Underfull \hbox (badness 10000) detected at line 1160 [][][] [263] Underfull \hbox (badness 10000) detected at line 1163 [][][] Underfull \hbox (badness 10000) detected at line 1166 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.437 on input line 1175. Underfull \hbox (badness 10000) detected at line 1190 [][][] Underfull \hbox (badness 10000) detected at line 1193 [][][] Underfull \hbox (badness 10000) detected at line 1198 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.438 on input line 1211. [264] Underfull \hbox (badness 10000) detected at line 1226 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.439 on input line 1241. Underfull \hbox (badness 10000) detected at line 1252 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.440 on input line 1269. [265] Underfull \hbox (badness 10000) detected at line 1280 [][][] Underfull \hbox (badness 10000) detected at line 1283 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.441 on input line 1292. Underfull \hbox (badness 10000) detected at line 1303 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.442 on input line 1316. [266] Underfull \hbox (badness 10000) detected at line 1343 [][][] Underfull \hbox (badness 10000) detected at line 1346 [][][] Underfull \hbox (badness 10000) detected at line 1349 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.443 on input line 1358. Underfull \hbox (badness 10000) detected at line 1373 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.444 on input line 1386. [267] Underfull \hbox (badness 10000) detected at line 1401 [][][] Underfull \hbox (badness 10000) detected at line 1404 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.445 on input line 1411. Underfull \hbox (badness 10000) detected at line 1426 [][][] Underfull \hbox (badness 10000) detected at line 1429 [][][] Underfull \hbox (badness 10000) detected at line 1432 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.446 on input line 1439. Underfull \hbox (badness 10000) detected at line 1454 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.447 on input line 1461. ) (./group___vpmgp.tex [268] Underfull \hbox (badness 10000) detected at line 45 [][][] [269] Underfull \hbox (badness 10000) detected at line 78 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.448 on input line 85. Underfull \hbox (badness 10000) detected at line 86 [][][] Underfull \hbox (badness 10000) detected at line 103 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.449 on input line 112. Underfull \hbox (badness 10000) detected at line 113 [][][] Underfull \hbox (badness 10000) detected at line 130 [][][] [270] Package longtable Warning: Column widths have changed (longtable) in table 7.450 on input line 137. Underfull \hbox (badness 10000) detected at line 152 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.451 on input line 159. Underfull \hbox (badness 10000) detected at line 174 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.452 on input line 193. [271] Underfull \hbox (badness 10000) detected at line 208 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.453 on input line 215. ) (./group___p_m_g_c.tex [272] [273] [274] [275] Underfull \hbox (badness 10000) detected at line 150 [][][] Underfull \hbox (badness 10000) detected at line 153 [][][] Underfull \hbox (badness 10000) detected at line 156 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 165--165 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [276] Underfull \hbox (badness 10000) detected at line 212 [][][] Underfull \hbox (badness 10000) detected at line 215 [][][] Underfull \hbox (badness 10000) detected at line 218 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 227--227 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [277] Underfull \hbox (badness 10000) detected at line 277 [][][] Underfull \hbox (badness 10000) detected at line 280 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.454 on input line 293. [278] Underfull \hbox (badness 10000) detected at line 308 [][][] Underfull \hbox (badness 10000) detected at line 311 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.455 on input line 324. Underfull \hbox (badness 10000) detected at line 339 [][][] Underfull \hbox (badness 10000) detected at line 342 [][][] Underfull \hbox (badness 10000) detected at line 345 [][][] [279] Overfull \hbox (304.08286pt too wide) in paragraph at lines 355--355 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 392 [][][] Underfull \hbox (badness 10000) detected at line 395 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 404--404 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [280] Underfull \hbox (badness 10000) detected at line 439 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.456 on input line 488. [281] Underfull \hbox (badness 10000) detected at line 503 [][][] Underfull \hbox (badness 10000) detected at line 506 [][][] Underfull \hbox (badness 10000) detected at line 509 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 518--518 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [282] Underfull \hbox (badness 10000) detected at line 556 [][][] Underfull \hbox (badness 10000) detected at line 559 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 568--568 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 603 [][][] Underfull \hbox (badness 10000) detected at line 606 [][][] [283] Package longtable Warning: Column widths have changed (longtable) in table 7.457 on input line 631. Underfull \hbox (badness 10000) detected at line 646 [][][] Underfull \hbox (badness 10000) detected at line 649 [][][] [284] Package longtable Warning: Column widths have changed (longtable) in table 7.458 on input line 704. [285] Underfull \hbox (badness 10000) detected at line 719 [][][] Underfull \hbox (badness 10000) detected at line 722 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.459 on input line 757. Underfull \hbox (badness 10000) detected at line 772 [][][] Underfull \hbox (badness 10000) detected at line 775 [][][] Underfull \hbox (badness 10000) detected at line 778 [][][] [286] Overfull \hbox (304.08286pt too wide) in paragraph at lines 788--788 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 825 [][][] Underfull \hbox (badness 10000) detected at line 828 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 837--837 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [287] Package longtable Warning: Column widths have changed (longtable) in table 7.460 on input line 892. [288] Underfull \hbox (badness 10000) detected at line 907 [][][] Underfull \hbox (badness 10000) detected at line 910 [][][] [289] Package longtable Warning: Column widths have changed (longtable) in table 7.461 on input line 1035. [290] [291] Underfull \hbox (badness 10000) detected at line 1050 [][][] Underfull \hbox (badness 10000) detected at line 1053 [][][] [292] Package longtable Warning: Column widths have changed (longtable) in table 7.462 on input line 1214. [293] [294] Underfull \hbox (badness 10000) detected at line 1229 [][][] Underfull \hbox (badness 10000) detected at line 1232 [][][] [295] Package longtable Warning: Column widths have changed (longtable) in table 7.463 on input line 1367. [296] Underfull \hbox (badness 10000) detected at line 1382 [][][] Underfull \hbox (badness 10000) detected at line 1385 [][][] Underfull \hbox (badness 10000) detected at line 1388 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.464 on input line 1431. [297] [298] Underfull \hbox (badness 10000) detected at line 1446 [][][] Underfull \hbox (badness 10000) detected at line 1449 [][][] Underfull \hbox (badness 10000) detected at line 1452 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 1462--1462 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 1501 [][][] Underfull \hbox (badness 10000) detected at line 1504 [][][] [299] Package longtable Warning: Column widths have changed (longtable) in table 7.465 on input line 1569. [300] Underfull \hbox (badness 10000) detected at line 1584 [][][] Underfull \hbox (badness 10000) detected at line 1587 [][][] Underfull \hbox (badness 10000) detected at line 1590 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 1600--1600 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 1637 [][][] Underfull \hbox (badness 10000) detected at line 1640 [][][] [301] Underfull \hbox (badness 10000) detected at line 1643 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 1652--1652 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Package longtable Warning: Column widths have changed (longtable) in table 7.466 on input line 1715. Overfull \vbox (9.44278pt too high) has occurred while \output is active [302] Underfull \hbox (badness 10000) detected at line 1730 [][][] Underfull \hbox (badness 10000) detected at line 1735 [][][] Underfull \hbox (badness 10000) detected at line 1738 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.467 on input line 1753. Underfull \hbox (badness 10000) detected at line 1768 [][][] Underfull \hbox (badness 10000) detected at line 1771 [][][] [303] Package longtable Warning: Column widths have changed (longtable) in table 7.468 on input line 1790. Underfull \hbox (badness 10000) detected at line 1805 [][][] Underfull \hbox (badness 10000) detected at line 1808 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.469 on input line 1827. [304] Underfull \hbox (badness 10000) detected at line 1842 [][][] Underfull \hbox (badness 10000) detected at line 1845 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.470 on input line 1864. Underfull \hbox (badness 10000) detected at line 1879 [][][] Underfull \hbox (badness 10000) detected at line 1882 [][][] [305] Underfull \hbox (badness 10000) detected at line 1885 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 1895--1895 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 1932 [][][] Underfull \hbox (badness 10000) detected at line 1935 [][][] Underfull \hbox (badness 10000) detected at line 1938 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 1947--1947 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [306] Package longtable Warning: Column widths have changed (longtable) in table 7.471 on input line 2018. [307] Underfull \hbox (badness 10000) detected at line 2033 [][][] Underfull \hbox (badness 10000) detected at line 2036 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.472 on input line 2055. Underfull \hbox (badness 10000) detected at line 2070 [][][] Underfull \hbox (badness 10000) detected at line 2073 [][][] Underfull \hbox (badness 10000) detected at line 2076 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 2086--2086 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [308] Underfull \hbox (badness 10000) detected at line 2123 [][][] Underfull \hbox (badness 10000) detected at line 2126 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2135--2135 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [309] Underfull \hbox (badness 10000) detected at line 2170 [][][] Underfull \hbox (badness 10000) detected at line 2173 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.473 on input line 2190. Underfull \hbox (badness 10000) detected at line 2205 [][][] [310] Underfull \hbox (badness 10000) detected at line 2208 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.474 on input line 2229. Underfull \hbox (badness 10000) detected at line 2244 [][][] Underfull \hbox (badness 10000) detected at line 2247 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.475 on input line 2268. [311] Underfull \hbox (badness 10000) detected at line 2283 [][][] Underfull \hbox (badness 10000) detected at line 2286 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.476 on input line 2299. [312] Underfull \hbox (badness 10000) detected at line 2314 [][][] Underfull \hbox (badness 10000) detected at line 2317 [][][] Underfull \hbox (badness 10000) detected at line 2320 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 2330--2330 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [313] Underfull \hbox (badness 10000) detected at line 2367 [][][] Underfull \hbox (badness 10000) detected at line 2370 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2379--2379 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 2414 [][][] Underfull \hbox (badness 10000) detected at line 2417 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.477 on input line 2488. [314] [315] Underfull \hbox (badness 10000) detected at line 2503 [][][] Underfull \hbox (badness 10000) detected at line 2506 [][][] Underfull \hbox (badness 10000) detected at line 2509 [][][] [316] Underfull \hbox (badness 10000) detected at line 2557 [][][] Underfull \hbox (badness 10000) detected at line 2560 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2569--2569 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [317] Underfull \hbox (badness 10000) detected at line 2604 [][][] Underfull \hbox (badness 10000) detected at line 2607 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.478 on input line 2682. [318] Underfull \hbox (badness 10000) detected at line 2697 [][][] Underfull \hbox (badness 10000) detected at line 2700 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.479 on input line 2731. [319] Underfull \hbox (badness 10000) detected at line 2746 [][][] Underfull \hbox (badness 10000) detected at line 2749 [][][] Underfull \hbox (badness 10000) detected at line 2752 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 2762--2762 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [320] Underfull \hbox (badness 10000) detected at line 2799 [][][] Underfull \hbox (badness 10000) detected at line 2802 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2811--2811 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 2846 [][][] Underfull \hbox (badness 10000) detected at line 2849 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.480 on input line 2890. [321] Underfull \hbox (badness 10000) detected at line 2905 [][][] Underfull \hbox (badness 10000) detected at line 2908 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.481 on input line 2931. Overfull \vbox (18.98318pt too high) has occurred while \output is active [322] Underfull \hbox (badness 10000) detected at line 2946 [][][] Underfull \hbox (badness 10000) detected at line 2957 [][][] [323] Underfull \hbox (badness 10000) detected at line 2960 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.482 on input line 3031. [324] Underfull \hbox (badness 10000) detected at line 3046 [][][] Underfull \hbox (badness 10000) detected at line 3049 [][][] Underfull \hbox (badness 10000) detected at line 3052 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3062--3062 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 3099 [][][] Underfull \hbox (badness 10000) detected at line 3102 [][][] [325] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 3111--3111 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 3146 [][][] Underfull \hbox (badness 10000) detected at line 3149 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.483 on input line 3172. [326] Underfull \hbox (badness 10000) detected at line 3187 [][][] Underfull \hbox (badness 10000) detected at line 3190 [][][] Underfull \hbox (badness 10000) detected at line 3193 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3203--3203 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [327] Underfull \hbox (badness 10000) detected at line 3240 [][][] Underfull \hbox (badness 10000) detected at line 3243 [][][] Underfull \hbox (badness 10000) detected at line 3246 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 3255--3255 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [328] Underfull \hbox (badness 10000) detected at line 3288 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.484 on input line 3327. [329] Underfull \hbox (badness 10000) detected at line 3342 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.485 on input line 3418. [330] [331] Underfull \hbox (badness 10000) detected at line 3484 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.486 on input line 3527. [332] Underfull \hbox (badness 10000) detected at line 3542 [][][] Underfull \hbox (badness 10000) detected at line 3545 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.487 on input line 3570. [333] Underfull \hbox (badness 10000) detected at line 3585 [][][] Underfull \hbox (badness 10000) detected at line 3588 [][][] Underfull \hbox (badness 10000) detected at line 3591 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3601--3601 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [334] Underfull \hbox (badness 10000) detected at line 3638 [][][] Underfull \hbox (badness 10000) detected at line 3641 [][][] Underfull \hbox (badness 10000) detected at line 3644 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 3653--3653 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [335] Underfull \hbox (badness 10000) detected at line 3702 [][][] Underfull \hbox (badness 10000) detected at line 3705 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.488 on input line 3774. [336] [337] Underfull \hbox (badness 10000) detected at line 3789 [][][] Underfull \hbox (badness 10000) detected at line 3792 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.489 on input line 3875. [338] Underfull \hbox (badness 10000) detected at line 3890 [][][] Underfull \hbox (badness 10000) detected at line 3893 [][][] Underfull \hbox (badness 10000) detected at line 3896 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3906--3906 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [339] Underfull \hbox (badness 10000) detected at line 3943 [][][] Underfull \hbox (badness 10000) detected at line 3946 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.490 on input line 3957. Underfull \hbox (badness 10000) detected at line 3972 [][][] Underfull \hbox (badness 10000) detected at line 3975 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.491 on input line 3986. [340] Underfull \hbox (badness 10000) detected at line 4001 [][][] Underfull \hbox (badness 10000) detected at line 4004 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.492 on input line 4019. [341] Underfull \hbox (badness 10000) detected at line 4034 [][][] Underfull \hbox (badness 10000) detected at line 4037 [][][] Underfull \hbox (badness 10000) detected at line 4040 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 4050--4050 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 4087 [][][] [342] Underfull \hbox (badness 10000) detected at line 4090 [][][] Underfull \hbox (badness 10000) detected at line 4093 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 4102--4102 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 4137 [][][] Underfull \hbox (badness 10000) detected at line 4140 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.493 on input line 4179. [343] Underfull \hbox (badness 10000) detected at line 4194 [][][] [344] Underfull \hbox (badness 10000) detected at line 4216 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.494 on input line 4275. Overfull \vbox (38.14133pt too high) has occurred while \output is active [345] Underfull \hbox (badness 10000) detected at line 4290 [][][] Underfull \hbox (badness 10000) detected at line 4293 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.495 on input line 4368. [346] [347] Underfull \hbox (badness 10000) detected at line 4383 [][][] Underfull \hbox (badness 10000) detected at line 4386 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.496 on input line 4411. Underfull \hbox (badness 10000) detected at line 4426 [][][] Underfull \hbox (badness 10000) detected at line 4429 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.497 on input line 4456. [348] Underfull \hbox (badness 10000) detected at line 4471 [][][] Underfull \hbox (badness 10000) detected at line 4474 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.498 on input line 4517. [349] Underfull \hbox (badness 10000) detected at line 4532 [][][] Underfull \hbox (badness 10000) detected at line 4535 [][][] Underfull \hbox (badness 10000) detected at line 4538 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 4548--4548 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [350] Underfull \hbox (badness 10000) detected at line 4585 [][][] Underfull \hbox (badness 10000) detected at line 4588 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 4597--4597 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [351] Underfull \hbox (badness 10000) detected at line 4630 [][][] Underfull \hbox (badness 10000) detected at line 4633 [][][] Underfull \hbox (badness 10000) detected at line 4636 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.499 on input line 4681. [352] Underfull \hbox (badness 10000) detected at line 4692 [][][] Underfull \hbox (badness 10000) detected at line 4695 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.500 on input line 4712. Underfull \hbox (badness 10000) detected at line 4727 [][][] Underfull \hbox (badness 10000) detected at line 4730 [][][] [353] Package longtable Warning: Column widths have changed (longtable) in table 7.501 on input line 4753. Underfull \hbox (badness 10000) detected at line 4768 [][][] Underfull \hbox (badness 10000) detected at line 4771 [][][] Underfull \hbox (badness 10000) detected at line 4774 [][][] Overfull \hbox (20.88268pt too wide) in paragraph at lines 4784--4784 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute,[] [354] Underfull \hbox (badness 10000) detected at line 4822 [][][] Underfull \hbox (badness 10000) detected at line 4825 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 4834--4834 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [355] Underfull \hbox (badness 10000) detected at line 4869 [][][] Underfull \hbox (badness 10000) detected at line 4872 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.502 on input line 4915. [356] Underfull \hbox (badness 10000) detected at line 4930 [][][] Underfull \hbox (badness 10000) detected at line 4933 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.503 on input line 4950. Underfull \hbox (badness 10000) detected at line 4965 [][][] Underfull \hbox (badness 10000) detected at line 4968 [][][] Underfull \hbox (badness 10000) detected at line 4971 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 4981--4981 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [357] Underfull \hbox (badness 10000) detected at line 5018 [][][] Underfull \hbox (badness 10000) detected at line 5021 [][][] Underfull \hbox (badness 10000) detected at line 5024 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 5033--5033 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [358] Underfull \hbox (badness 10000) detected at line 5068 [][][] Underfull \hbox (badness 10000) detected at line 5071 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.504 on input line 5086. Underfull \hbox (badness 10000) detected at line 5101 [][][] Underfull \hbox (badness 10000) detected at line 5104 [][][] Underfull \hbox (badness 10000) detected at line 5107 [][][] [359] Package longtable Warning: Column widths have changed (longtable) in table 7.505 on input line 5122. Underfull \hbox (badness 10000) detected at line 5137 [][][] Underfull \hbox (badness 10000) detected at line 5140 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.506 on input line 5155. Underfull \hbox (badness 10000) detected at line 5170 [][][] [360] Underfull \hbox (badness 10000) detected at line 5173 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.507 on input line 5188. Underfull \hbox (badness 10000) detected at line 5203 [][][] Underfull \hbox (badness 10000) detected at line 5206 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.508 on input line 5219. Underfull \hbox (badness 10000) detected at line 5234 [][][] [361] Underfull \hbox (badness 10000) detected at line 5237 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.509 on input line 5250. Underfull \hbox (badness 10000) detected at line 5265 [][][] Underfull \hbox (badness 10000) detected at line 5268 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.510 on input line 5283. ) (./group___frontend.tex [362] Underfull \hbox (badness 2495) in paragraph at lines 32--33 []\T1/phv/m/n/10 VPUBLIC Vrc[]_[][]Codes [] (int icalc, [] $\OMS/cmsy/m/n/10 ^^ C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 feparm, [] $\OMS /cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbeparm, [] Overfull \hbox (16.65858pt too wide) in paragraph at lines 40--41 []\T1/phv/m/n/10 VEXTERNC int [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], Overfull \hbox (16.91972pt too wide) in paragraph at lines 42--43 []\T1/phv/m/n/10 VEXTERNC void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh , [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/1 0 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], Underfull \hbox (badness 1910) in paragraph at lines 60--61 [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1 /phv/m/n/10 alist[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][] [], [] Underfull \hbox (badness 1237) in paragraph at lines 60--61 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 charge[]Map[][][], [] $\OMS/cmsy/m/n/10 ^^C $\T1/phv/m/n/10 pmgp[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pmg[][][], [] [363] Underfull \hbox (badness 5817) in paragraph at lines 78--79 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], Underfull \hbox (badness 5817) in paragraph at lines 80--81 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], [364] [365] Underfull \hbox (badness 10000) detected at line 178 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.511 on input line 196. Underfull \hbox (badness 10000) detected at line 211 [][][] [366] Package longtable Warning: Column widths have changed (longtable) in table 7.512 on input line 232. Underfull \hbox (badness 10000) detected at line 235 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.513 on input line 260. [367] Underfull \hbox (badness 10000) detected at line 275 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.514 on input line 296. Underfull \hbox (badness 10000) detected at line 297 [][][] Underfull \hbox (badness 10000) detected at line 314 [][][] Underfull \hbox (badness 10000) detected at line 317 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.515 on input line 336. [368] Underfull \hbox (badness 10000) detected at line 351 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.516 on input line 372. Underfull \hbox (badness 10000) detected at line 373 [][][] Underfull \hbox (badness 10000) detected at line 390 [][][] Underfull \hbox (badness 10000) detected at line 393 [][][] [369] Package longtable Warning: Column widths have changed (longtable) in table 7.517 on input line 480. [370] Underfull \hbox (badness 10000) detected at line 495 [][][] Underfull \hbox (badness 10000) detected at line 502 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.518 on input line 557. [371] Underfull \hbox (badness 10000) detected at line 572 [][][] Underfull \hbox (badness 10000) detected at line 575 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.519 on input line 610. [372] Underfull \hbox (badness 10000) detected at line 625 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.520 on input line 634. Underfull \hbox (badness 10000) detected at line 649 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.521 on input line 662. Underfull \hbox (badness 10000) detected at line 677 [][][] [373] Underfull \hbox (badness 10000) detected at line 694 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.522 on input line 705. Underfull \hbox (badness 10000) detected at line 720 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.523 on input line 733. Underfull \hbox (badness 10000) detected at line 748 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.524 on input line 757. [374] Underfull \hbox (badness 10000) detected at line 772 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.525 on input line 781. Underfull \hbox (badness 10000) detected at line 792 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.526 on input line 803. Underfull \hbox (badness 10000) detected at line 818 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.527 on input line 827. [375] Underfull \hbox (badness 10000) detected at line 842 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.528 on input line 851. Underfull \hbox (badness 10000) detected at line 866 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.529 on input line 875. Underfull \hbox (badness 10000) detected at line 876 [][][] Underfull \hbox (badness 10000) detected at line 895 [][][] [376] Package longtable Warning: Column widths have changed (longtable) in table 7.530 on input line 908. Underfull \hbox (badness 10000) detected at line 909 [][][] Underfull \hbox (badness 10000) detected at line 912 [][][] Underfull \hbox (badness 10000) detected at line 929 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.531 on input line 938. Underfull \hbox (badness 10000) detected at line 939 [][][] Underfull \hbox (badness 10000) detected at line 958 [][][] Underfull \hbox (badness 10000) detected at line 961 [][][] [377] Package longtable Warning: Column widths have changed (longtable) in table 7.532 on input line 970. Underfull \hbox (badness 10000) detected at line 981 [][][] Underfull \hbox (badness 10000) detected at line 984 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.533 on input line 995. Underfull \hbox (badness 10000) detected at line 1010 [][][] Underfull \hbox (badness 10000) detected at line 1013 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.534 on input line 1020. [378] Underfull \hbox (badness 10000) detected at line 1035 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.535 on input line 1044. Underfull \hbox (badness 10000) detected at line 1045 [][][] Underfull \hbox (badness 10000) detected at line 1064 [][][] Underfull \hbox (badness 10000) detected at line 1067 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.536 on input line 1076. Underfull \hbox (badness 10000) detected at line 1091 [][][] [379] Package longtable Warning: Column widths have changed (longtable) in table 7.537 on input line 1104. Underfull \hbox (badness 10000) detected at line 1105 [][][] Underfull \hbox (badness 10000) detected at line 1122 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.538 on input line 1133. Underfull \hbox (badness 10000) detected at line 1134 [][][] Underfull \hbox (badness 10000) in paragraph at lines 1135--1136 Underfull \hbox (badness 10000) detected at line 1138 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.539 on input line 1151. [380] Underfull \hbox (badness 10000) detected at line 1166 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.540 on input line 1179. Underfull \hbox (badness 10000) detected at line 1180 [][][] Underfull \hbox (badness 10000) detected at line 1201 [][][] Underfull \hbox (badness 10000) detected at line 1204 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.541 on input line 1213. [381] Underfull \hbox (badness 10000) detected at line 1228 [][][] Underfull \hbox (badness 10000) detected at line 1231 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.542 on input line 1244. Underfull \hbox (badness 10000) detected at line 1259 [][][] Underfull \hbox (badness 10000) detected at line 1262 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.543 on input line 1273. [382] Underfull \hbox (badness 10000) detected at line 1288 [][][] Underfull \hbox (badness 10000) detected at line 1291 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.544 on input line 1304. Underfull \hbox (badness 10000) detected at line 1319 [][][] Underfull \hbox (badness 10000) detected at line 1322 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.545 on input line 1333. [383] Underfull \hbox (badness 10000) detected at line 1348 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.546 on input line 1362. Underfull \hbox (badness 10000) detected at line 1377 [][][] Underfull \hbox (badness 10000) detected at line 1380 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.547 on input line 1393. Underfull \hbox (badness 10000) detected at line 1408 [][][] [384] Package longtable Warning: Column widths have changed (longtable) in table 7.548 on input line 1417. Underfull \hbox (badness 10000) detected at line 1432 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.549 on input line 1439. Underfull \hbox (badness 10000) detected at line 1454 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.550 on input line 1467. Underfull \hbox (badness 10000) detected at line 1468 [][][] [385] Underfull \hbox (badness 10000) detected at line 1485 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.551 on input line 1496. Underfull \hbox (badness 10000) detected at line 1497 [][][] Underfull \hbox (badness 10000) detected at line 1514 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.552 on input line 1527. Underfull \hbox (badness 10000) detected at line 1528 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.553 on input line 1547. [386] Underfull \hbox (badness 10000) detected at line 1562 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.554 on input line 1573. Underfull \hbox (badness 10000) detected at line 1574 [][][] Underfull \hbox (badness 10000) detected at line 1591 [][][] Underfull \hbox (badness 10000) detected at line 1608 [][][] [387] Package longtable Warning: Column widths have changed (longtable) in table 7.555 on input line 1621. Underfull \hbox (badness 10000) detected at line 1636 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.556 on input line 1649. Underfull \hbox (badness 10000) detected at line 1650 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.557 on input line 1673. [388] Underfull \hbox (badness 10000) detected at line 1688 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.558 on input line 1715. Underfull \hbox (badness 10000) detected at line 1716 [][][] Underfull \hbox (badness 10000) detected at line 1733 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.559 on input line 1746. [389] Underfull \hbox (badness 10000) detected at line 1747 [][][] Underfull \hbox (badness 10000) detected at line 1764 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.560 on input line 1791. Underfull \hbox (badness 10000) detected at line 1792 [][][] [390] Underfull \hbox (badness 10000) detected at line 1809 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.561 on input line 1822. Underfull \hbox (badness 10000) detected at line 1823 [][][] ) [391] [392] Chapter 8. (./struct_atom_force.tex Underfull \hbox (badness 10000) detected at line 32 [][][] [393]) (./structs_a_p_o_lparm.tex [394] Underfull \hbox (badness 10000) detected at line 88 [][][] [395] Underfull \hbox (badness 10000) detected at line 224 [][][] [396] Underfull \hbox (badness 10000) detected at line 237 [][][] Underfull \hbox (badness 10000) detected at line 250 [][][] Underfull \hbox (badness 10000) detected at line 263 [][][] Underfull \hbox (badness 10000) detected at line 276 [][][] Underfull \hbox (badness 10000) detected at line 289 [][][] Underfull \hbox (badness 10000) detected at line 302 [][][] [397] Underfull \hbox (badness 10000) detected at line 315 [][][] Underfull \hbox (badness 10000) detected at line 328 [][][] Underfull \hbox (badness 10000) detected at line 341 [][][] Underfull \hbox (badness 10000) detected at line 354 [][][] Underfull \hbox (badness 10000) detected at line 367 [][][] Underfull \hbox (badness 10000) detected at line 380 [][][] [398]) (./structs_b_e_mparm.tex [399] Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 53 [][][] [400] Underfull \hbox (badness 10000) detected at line 129 [][][] Underfull \hbox (badness 10000) detected at line 142 [][][] Underfull \hbox (badness 10000) detected at line 155 [][][] [401] Underfull \hbox (badness 10000) detected at line 168 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 194 [][][] ) (./structs_f_e_mparm.tex [402] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) in paragraph at lines 84--85 [403] [404] [405]) (./structs_g_e_o_f_l_o_wparm.tex Underfull \hbox (badness 10000) detected at line 30 [][][] Underfull \hbox (badness 10000) detected at line 33 [][][] [406]) (./structs_m_gparm.tex [407] Underfull \hbox (badness 10000) detected at line 120 [][][] Underfull \hbox (badness 10000) detected at line 123 [][][] [408] Underfull \hbox (badness 10000) in paragraph at lines 149--150 Underfull \hbox (badness 10000) in paragraph at lines 180--181 [409] Underfull \hbox (badness 10000) in paragraph at lines 261--262 [410] [411] Underfull \hbox (badness 10000) detected at line 434 [][][] Underfull \hbox (badness 10000) detected at line 447 [][][] Underfull \hbox (badness 10000) detected at line 460 [][][] Underfull \hbox (badness 10000) detected at line 473 [][][] [412] Underfull \hbox (badness 10000) detected at line 486 [][][] Underfull \hbox (badness 10000) detected at line 499 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] Underfull \hbox (badness 10000) detected at line 538 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] [413] Underfull \hbox (badness 10000) detected at line 564 [][][] Underfull \hbox (badness 10000) detected at line 577 [][][] Underfull \hbox (badness 10000) detected at line 590 [][][] Underfull \hbox (badness 10000) detected at line 603 [][][] Underfull \hbox (badness 10000) detected at line 616 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] [414] Underfull \hbox (badness 10000) detected at line 642 [][][] Underfull \hbox (badness 10000) detected at line 655 [][][] Underfull \hbox (badness 10000) detected at line 668 [][][] ) (./structs_n_osh.tex [415] Underfull \hbox (badness 10000) detected at line 108 [][][] [416] [417] [418] [419] [420]) (./structs_n_osh__calc.tex [421] Underfull \hbox (badness 10000) detected at line 38 [][][] [422]) (./structs_p_b_a_mparm.tex [423] Underfull \hbox (badness 10000) detected at line 106 [][][] Underfull \hbox (badness 10000) detected at line 109 [][][] [424] [425] [426] [427]) (./structs_p_b_eparm.tex [428] [429] Underfull \hbox (badness 10000) detected at line 142 [][][] Underfull \hbox (badness 10000) detected at line 145 [][][] [430] [431] [432] Underfull \hbox (badness 10000) detected at line 391 [][][] Underfull \hbox (badness 10000) detected at line 404 [][][] Underfull \hbox (badness 10000) detected at line 417 [][][] Underfull \hbox (badness 10000) detected at line 430 [][][] [433] Underfull \hbox (badness 10000) detected at line 473 [][][] Underfull \hbox (badness 10000) detected at line 486 [][][] Underfull \hbox (badness 10000) detected at line 499 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] [434] Underfull \hbox (badness 10000) detected at line 538 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] Underfull \hbox (badness 10000) detected at line 564 [][][] Underfull \hbox (badness 10000) detected at line 577 [][][] Underfull \hbox (badness 10000) detected at line 590 [][][] Underfull \hbox (badness 10000) detected at line 603 [][][] [435] Underfull \hbox (badness 10000) detected at line 616 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] [436] [437]) (./structs_p_b_s_a_mparm.tex [438] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] [439]) (./structs_vacc.tex [440] Underfull \hbox (badness 10000) detected at line 36 [][][] [441]) (./structs_vacc_surf.tex Underfull \hbox (badness 10000) detected at line 36 [][][] [442]) (./structs_valist.tex [443] Underfull \hbox (badness 10000) detected at line 36 [][][] [444]) (./structs_vatom.tex Underfull \hbox (badness 10000) detected at line 36 [][][] Underfull \hbox (badness 10000) in paragraph at lines 62--63 [445] Underfull \hbox (badness 10000) in paragraph at lines 93--94 Underfull \hbox (badness 10000) in paragraph at lines 114--115 ) (./structs_vclist.tex [446] Underfull \hbox (badness 10000) detected at line 40 [][][] [447]) (./structs_vclist_cell.tex Underfull \hbox (badness 10000) detected at line 24 [][][] ) (./structs_vcsm.tex [448] Underfull \hbox (badness 10000) detected at line 42 [][][] [449]) (./structs_vfetk.tex [450] Underfull \hbox (badness 10000) detected at line 60 [][][] [451] Underfull \hbox (badness 10000) in paragraph at lines 116--117 [452]) (./structs_vfetk___local_var.tex [453] Underfull \hbox (badness 10000) detected at line 86 [][][] [454] [455] [456] [457]) (./structs_vgreen.tex Underfull \hbox (badness 10000) detected at line 34 [][][] [458]) (./structs_vgrid.tex [459] Underfull \hbox (badness 10000) detected at line 52 [][][] [460] [461]) (./structs_vmgrid.tex Underfull \hbox (badness 10000) detected at line 24 [][][] ) (./structs_vopot.tex [462] Underfull \hbox (badness 10000) detected at line 26 [][][] ) (./structs_vparam___atom_data.tex [463] Underfull \hbox (badness 10000) detected at line 30 [][][] Underfull \hbox (badness 10000) detected at line 33 [][][] ) (./structs_vpbe.tex [464] Underfull \hbox (badness 10000) detected at line 86 [][][] [465] [466] [467] [468]) (./structs_vpee.tex [469] Underfull \hbox (badness 10000) detected at line 34 [][][] ) (./structs_vpmg.tex [470] [471] Underfull \hbox (badness 10000) detected at line 116 [][][] [472] [473] [474] [475] [476]) (./structs_vpmgp.tex [477] Underfull \hbox (badness 10000) detected at line 126 [][][] [478] Underfull \hbox (badness 10000) in paragraph at lines 164--165 Underfull \hbox (badness 10000) in paragraph at lines 175--176 Underfull \hbox (badness 10000) in paragraph at lines 186--187 [479] Underfull \hbox (badness 10000) in paragraph at lines 234--235 [480] [481] [482] [483] Underfull \hbox (badness 10000) in paragraph at lines 506--507 Underfull \hbox (badness 10000) in paragraph at lines 527--528 [484] Underfull \hbox (badness 10000) in paragraph at lines 548--549 Underfull \hbox (badness 10000) in paragraph at lines 589--590 [485] Underfull \hbox (badness 10000) in paragraph at lines 630--631 Underfull \hbox (badness 10000) in paragraph at lines 671--672 ) (./struct_vparam.tex [486] Underfull \hbox (badness 10000) detected at line 26 [][][] ) (./struct_vparam___res_data.tex [487] Underfull \hbox (badness 10000) detected at line 28 [][][] ) [488] Chapter 9. (./mainpage_8h_source.tex) (./apbs_8h.tex <./apbs_8h__incl.pdf> <./apbs_8h__dep __incl.pdf> [489] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] Underfull \hbox (badness 10000) detected at line 58 [][][] [490]) (./apbs_8h_source.tex) (./vcsm_8c.tex [491] <./vcsm_8c__incl.pdf> [492] Underfull \hbox (badness 10000) detected at line 53 [][][] Underfull \hbox (badness 10000) detected at line 56 [][][] Underfull \hbox (badness 10000) detected at line 59 [][][] [493]) (./vcsm_8c_source.tex [494] [495] [496] [497] [498] [499]) (./vcsm_8h.tex <./vcsm_8h__incl.pdf> <./vcsm_8h__dep__incl.pdf> [500] [501] Underfull \hbox (badness 10000) detected at line 77 [][][] Underfull \hbox (badness 10000) detected at line 80 [][][] Underfull \hbox (badness 10000) detected at line 83 [][][] [502]) (./vcsm_8h_source.tex [503]) (./vfetk_8c.tex [504] <./vfetk_8c__incl.pdf > [505] [506] Underfull \hbox (badness 10000) detected at line 163 [][][] Underfull \hbox (badness 10000) detected at line 166 [][][] [507] Underfull \hbox (badness 10000) detected at line 169 [][][] [508] [509] [510] [511]) (./vfetk_8c_source.tex [512] [513] [514] [515] [516] [517] [518] [519] [520] [521] [522] [523] [524] [525] [526] [527] [528] [529] [530] [531] [532] [533] [534] [535] [536] [537] [538] [539] [540] [541]) (./vfetk_8h.tex [542] <./vfetk_8h__incl.pdf> <./vfetk_8h__dep__inc l.pdf> [543] [544] [545] Underfull \hbox (badness 10000) detected at line 189 [][][] [546] Underfull \hbox (badness 10000) detected at line 192 [][][] Underfull \hbox (badness 10000) detected at line 195 [][][] ) (./vfetk_8h_source.tex [547] [548] [549] [550] [551] [552]) (./vpee_8c.tex <. /vpee_8c__incl.pdf> [553] Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 53 [][][] Underfull \hbox (badness 10000) detected at line 56 [][][] [554]) (./vpee_8c_source.tex [555] [556] [557] [558] [559] [560]) (./vpee_8h.tex [561] <./vpee_8h__incl.pdf> <./vpee_8h__dep__incl.pdf> [562] Underfull \hbox (badness 10000) detected at line 57 [][][] Underfull \hbox (badness 10000) detected at line 60 [][][] Underfull \hbox (badness 10000) detected at line 63 [][][] [563]) (./vpee_8h_source.tex [564]) (./apolparm_8c.tex <./apolparm_8c__incl.pdf > [565] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) detected at line 71 [][][] [566] [567]) (./apolparm_8c_source.tex [568] [569] [570] [571] [572] [573] [574] [575]) (./apolparm_8h_source.tex [576]) (./bemparm_8c.tex <./bemparm_8c__ incl.pdf> [577] [578] Underfull \hbox (badness 10000) detected at line 49 [][][] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] [579] Underfull \hbox (badness 10000) detected at line 121 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.1 on input line 130. ) (./bemparm_8c_source.tex [580] [581] [582] [583]) (./bemparm_8h_source.tex [584]) (./femparm_8c.tex <./femparm_8c__incl.pdf> [585] [586] Underfull \hbox (badness 10000) detected at line 59 [][][] Underfull \hbox (badness 10000) detected at line 62 [][][] Underfull \hbox (badness 10000) detected at line 65 [][][] [587] [588]) (./femparm_8c_source.tex [589] [590] [591] [592] [593]) (./femparm_8h.tex <./femparm_8h__incl.pdf> [594] <./femparm_8h__dep__incl.pdf> [595] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 92 [][][] Underfull \hbox (badness 10000) detected at line 95 [][][] [596]) (./femparm_8h_source.tex [597]) (./geoflowparm_8c.tex [598] <./geoflowpa rm_8c__incl.pdf> [599] Underfull \hbox (badness 10000) detected at line 47 [][][] Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 53 [][][] [600]) (./geoflowparm_8c_source.tex [601] [602]) (./geoflowparm_8h.tex [603] <. /geoflowparm_8h__incl.pdf> <./geoflowparm_8h__dep__incl.pdf> [604] [605] Underfull \hbox (badness 10000) detected at line 71 [][][] Underfull \hbox (badness 10000) detected at line 74 [][][] Underfull \hbox (badness 10000) detected at line 77 [][][] [606]) (./geoflowparm_8h_source.tex [607]) (./mgparm_8c.tex <./mgparm_8c__incl. pdf> [608] [609] Underfull \hbox (badness 10000) detected at line 95 [][][] Underfull \hbox (badness 10000) detected at line 98 [][][] Underfull \hbox (badness 10000) detected at line 101 [][][] [610] [611]) (./mgparm_8c_source.tex [612] [613] [614] [615] [616] [617] [618] [619] [620] [621] [622] [623]) (./mgparm_8h.tex <./mgparm_8h__incl.pdf> [624] <./mgparm_8h__dep__incl.pdf> [625] [626] Underfull \hbox (badness 10000) detected at line 104 [][][] Underfull \hbox (badness 10000) detected at line 107 [][][] Underfull \hbox (badness 10000) detected at line 110 [][][] [627]) (./mgparm_8h_source.tex [628]) (./nosh_8c.tex <./nosh_8c__incl.pdf> [629] [630] [631] Underfull \hbox (badness 10000) detected at line 151 [][][] Underfull \hbox (badness 10000) detected at line 154 [][][] Underfull \hbox (badness 10000) detected at line 157 [][][] [632] [633] [634] [635] [636]) (./nosh_8c_source.tex [637] [638] [639] [640] [641] [642] [643] [644] [645] [646] [647] [648] [649] [650] [651] [652] [653] [654] [655] [656] [657] [658] [659] [660] [661] [662] [663] [664] [665] [666] [667] [668] [669] [670] [671] [672] [673] [674] [675] [676]) (./nosh_8h.tex <./nosh_8h__incl.pdf> [677] <./nosh_8h__dep__incl.pdf> [678] [679] [680] Underfull \hbox (badness 10000) detected at line 171 [][][] Underfull \hbox (badness 10000) detected at line 174 [][][] Underfull \hbox (badness 10000) detected at line 177 [][][] ) (./nosh_8h_source.tex [681] [682] [683]) (./pbamparm_8c.tex <./pbamparm_8c__i ncl.pdf> [684] [685] Underfull \hbox (badness 10000) detected at line 69 [][][] Underfull \hbox (badness 10000) detected at line 72 [][][] Underfull \hbox (badness 10000) detected at line 75 [][][] [686]) (./pbamparm_8c_source.tex [687] [688] [689] [690] [691] [692] [693] [694] [695]) (./pbamparm_8h.tex <./pbamparm_8h__incl.pdf> <./pbamparm_8h__dep__ incl.pdf> [696] [697] Underfull \hbox (badness 10000) detected at line 102 [][][] [698] Underfull \hbox (badness 10000) detected at line 105 [][][] Underfull \hbox (badness 10000) detected at line 108 [][][] [699]) (./pbamparm_8h_source.tex [700]) (./pbeparm_8c.tex [701] <./pbeparm_8c__ incl.pdf> [702] Underfull \hbox (badness 10000) detected at line 101 [][][] Underfull \hbox (badness 10000) detected at line 104 [][][] Underfull \hbox (badness 10000) detected at line 107 [][][] [703] [704] [705] [706] [707]) (./pbeparm_8c_source.tex [708] [709] [710] [711] [712] [713] [714] [715] [716] [717] [718] [719] [720] [721] [722]) (./pbeparm_8h.tex <./pbeparm_8h__incl.pdf> [723] <./pbeparm_8h__dep__incl.pdf> [724] Underfull \hbox (badness 10000) detected at line 88 [][][] Underfull \hbox (badness 10000) detected at line 91 [][][] Underfull \hbox (badness 10000) detected at line 94 [][][] [725]) (./pbeparm_8h_source.tex [726] [727]) (./pbsamparm_8c.tex <./pbsamparm_8 c__incl.pdf> [728] [729] Underfull \hbox (badness 10000) detected at line 49 [][][] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] [730]) (./pbsamparm_8c_source.tex [731] [732]) (./pbsamparm_8h.tex [733] <./pbs amparm_8h__incl.pdf> <./pbsamparm_8h__dep__incl.pdf> [734] [735] Underfull \hbox (badness 10000) detected at line 86 [][][] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 92 [][][] [736]) (./pbsamparm_8h_source.tex [737]) (./vacc_8c.tex <./vacc_8c__incl.pdf> [738] [739] [740] Underfull \hbox (badness 10000) detected at line 107 [][][] Underfull \hbox (badness 10000) detected at line 110 [][][] Underfull \hbox (badness 10000) detected at line 113 [][][] [741] Underfull \hbox (badness 10000) detected at line 179 [][][] Underfull \hbox (badness 10000) detected at line 182 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.2 on input line 193. Underfull \hbox (badness 10000) detected at line 208 [][][] Underfull \hbox (badness 10000) detected at line 211 [][][] [742] Package longtable Warning: Column widths have changed (longtable) in table 9.3 on input line 224. [743]) (./vacc_8c_source.tex [744] [745] [746] [747] [748] [749] [750] [751] [752] [753] [754] [755] [756] [757] [758] [759] [760] [761] [762] [763] [764] [765] [766]) (./vacc_8h.tex <./vacc_8h__incl.pdf> <./vacc_8h__dep__incl.p df> [767] [768] [769] Underfull \hbox (badness 10000) detected at line 123 [][][] Underfull \hbox (badness 10000) detected at line 126 [][][] Underfull \hbox (badness 10000) detected at line 129 [][][] [770]) (./vacc_8h_source.tex [771] [772] [773]) (./valist_8c.tex <./valist_8c__ incl.pdf> [774] [775] Underfull \hbox (badness 2293) in paragraph at lines 54--56 []\T1/phv/m/n/10 VPRIVATE Vrc[]_[][]Codes [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/ m/n/10 thee, Vio $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 sock, int $\OMS/cmsy/m/n/ 10 ^^C$\T1/phv/m/n/10 serial, char atom[] Underfull \hbox (badness 10000) detected at line 82 [][][] Underfull \hbox (badness 10000) detected at line 85 [][][] Underfull \hbox (badness 10000) detected at line 88 [][][] [776] [777] [778]) (./valist_8c_source.tex [779] [780] [781] [782] [783] [784] [785] [786] [787] [788]) (./valist_8h.tex [789] <./valist_8h__incl.pdf> < ./valist_8h__dep__incl.pdf> [790] Underfull \hbox (badness 10000) detected at line 77 [][][] Underfull \hbox (badness 10000) detected at line 80 [][][] Underfull \hbox (badness 10000) detected at line 83 [][][] [791]) (./valist_8h_source.tex [792] [793]) (./vatom_8c.tex <./vatom_8c__incl.p df> [794] Underfull \hbox (badness 10000) detected at line 71 [][][] Underfull \hbox (badness 10000) detected at line 74 [][][] Underfull \hbox (badness 10000) detected at line 77 [][][] [795]) (./vatom_8c_source.tex [796] [797] [798]) (./vatom_8h.tex <./vatom_8h__i ncl.pdf> [799] <./vatom_8h__dep__incl.pdf> [800] [801] Underfull \hbox (badness 10000) detected at line 96 [][][] Underfull \hbox (badness 10000) detected at line 99 [][][] Underfull \hbox (badness 10000) detected at line 102 [][][] ) (./vatom_8h_source.tex [802] [803]) (./vcap_8c.tex <./vcap_8c__incl.pdf> [804] Underfull \hbox (badness 10000) detected at line 31 [][][] Underfull \hbox (badness 10000) detected at line 34 [][][] Underfull \hbox (badness 10000) detected at line 37 [][][] [805]) (./vcap_8c_source.tex [806]) (./vcap_8h.tex <./vcap_8h__incl.pdf> <./vca p_8h__dep__incl.pdf> [807] Underfull \hbox (badness 10000) detected at line 47 [][][] Underfull \hbox (badness 10000) detected at line 50 [][][] [808] Underfull \hbox (badness 10000) detected at line 53 [][][] ) (./vcap_8h_source.tex [809]) (./vclist_8c.tex <./vclist_8c__incl.pdf> Underfull \hbox (badness 4060) in paragraph at lines 32--34 []\T1/phv/m/n/10 VPRIVATE void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 thee , dou-ble lower[]_[]corner[][][], dou-ble upper[]_[] [810] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) detected at line 71 [][][] [811] [812]) (./vclist_8c_source.tex [813] [814] [815] [816] [817]) (./vclist_8h.tex [818] <./vclist_8h__incl.pdf> <./vclist_8h__dep__incl.pdf> [819] [820] Underfull \hbox (badness 10000) detected at line 84 [][][] Underfull \hbox (badness 10000) detected at line 87 [][][] Underfull \hbox (badness 10000) detected at line 90 [][][] [821]) (./vclist_8h_source.tex [822]) (./vgreen_8c.tex [823] <./vgreen_8c__incl .pdf> [824] Underfull \hbox (badness 10000) detected at line 55 [][][] Underfull \hbox (badness 10000) detected at line 58 [][][] Underfull \hbox (badness 10000) detected at line 61 [][][] [825]) (./vgreen_8c_source.tex [826] [827] [828] [829] [830] [831]) (./vgreen_8h.tex <./vgreen_8h__incl.pdf> [832] <./vgreen_8h__dep__incl.pdf> [833] Underfull \hbox (badness 10000) detected at line 72 [][][] Underfull \hbox (badness 10000) detected at line 75 [][][] ) (./vgreen_8h_source.tex [834]) (./vhal_8h.tex [835] <./vhal_8h__incl.pdf> <./ vhal_8h__dep__incl.pdf> [836] [837] [838] [839] Underfull \hbox (badness 10000) detected at line 303 [][][] Underfull \hbox (badness 10000) detected at line 306 [][][] Underfull \hbox (badness 10000) detected at line 309 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 318--318 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [840] [841] [842] [843] [844] [845] [846]) (./vhal_8h_source.tex [847] [848] [849] [850] [851] [852] [853] [854]) (./vmatrix_8h.tex [855] <./vmatrix_8h__dep __incl.pdf> Underfull \hbox (badness 10000) detected at line 36 [][][] Underfull \hbox (badness 10000) detected at line 39 [][][] Underfull \hbox (badness 10000) detected at line 42 [][][] [856] [857]) (./vmatrix_8h_source.tex [858]) (./vparam_8c.tex <./vparam_8c__inc l.pdf> [859] Underfull \hbox (badness 10000) detected at line 78 [][][] Underfull \hbox (badness 10000) detected at line 81 [][][] [860] Underfull \hbox (badness 10000) detected at line 84 [][][] ) (./vparam_8c_source.tex [861] [862] [863] [864] [865] [866] [867] [868]) (./vparam_8h.tex [869] <./vparam_8h__incl.pdf> <./vparam_8h__dep__incl.pdf> [870] [871] Underfull \hbox (badness 10000) detected at line 96 [][][] Underfull \hbox (badness 10000) detected at line 99 [][][] Underfull \hbox (badness 10000) detected at line 102 [][][] [872]) (./vparam_8h_source.tex [873]) (./vpbe_8c.tex <./vpbe_8c__incl.pdf> [874] [875] Underfull \hbox (badness 10000) detected at line 90 [][][] Underfull \hbox (badness 10000) detected at line 93 [][][] [876] Underfull \hbox (badness 10000) detected at line 96 [][][] ) (./vpbe_8c_source.tex [877] [878] [879] [880] [881] [882] [883]) (./vpbe_8h.tex <./vpbe_8h__incl.pdf> <./vpbe_8h__dep__incl.pdf> [884] [885] Underfull \hbox (badness 10000) detected at line 111 [][][] Underfull \hbox (badness 10000) detected at line 114 [][][] Underfull \hbox (badness 10000) detected at line 117 [][][] [886]) (./vpbe_8h_source.tex [887] [888] [889]) (./vstring_8c.tex <./vstring_8c __incl.pdf> [890] Underfull \hbox (badness 10000) detected at line 31 [][][] Underfull \hbox (badness 10000) detected at line 34 [][][] Underfull \hbox (badness 10000) detected at line 37 [][][] ) (./vstring_8c_source.tex [891] [892] [893]) (./vstring_8h.tex <./vstring_8h__ incl.pdf> <./vstring_8h__dep__incl.pdf> [894] Underfull \hbox (badness 10000) detected at line 41 [][][] Underfull \hbox (badness 10000) detected at line 44 [][][] Underfull \hbox (badness 10000) detected at line 47 [][][] [895]) (./vstring_8h_source.tex) (./vunit_8h.tex <./vunit_8h__dep__incl.pdf> [896] LaTeX Warning: Command \r invalid in math mode on input line 42. Missing character: There is no Å in font cmr9! Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] Underfull \hbox (badness 10000) detected at line 58 [][][] [897]) (./vunit_8h_source.tex) (./main_8c.tex [898] <./main_8c__incl.pdf> Underfull \hbox (badness 10000) detected at line 28 [][][] Underfull \hbox (badness 10000) detected at line 41 [][][] Underfull \hbox (badness 10000) detected at line 44 [][][] [899]) (./main_8c_source.tex [900] [901] [902] [903] [904] [905] [906] [907] [908] [909] [910]) (./vgrid_8c.tex <./vgrid_8c__incl.pdf> [911] [912] Underfull \hbox (badness 10000) detected at line 84 [][][] Underfull \hbox (badness 10000) detected at line 87 [][][] Underfull \hbox (badness 10000) detected at line 90 [][][] [913] Underfull \hbox (badness 10000) detected at line 169 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.4 on input line 188. [914]) (./vgrid_8c_source.tex [915] [916] [917] [918] [919] [920] [921] [922] [923] [924] [925] [926] [927] [928] [929] [930] [931] [932] [933] [934] [935] [936] [937]) (./vgrid_8h.tex [938] <./vgrid_8h__incl.pdf> <./vgrid_ 8h__dep__incl.pdf> [939] [940] Underfull \hbox (badness 10000) detected at line 93 [][][] [941] Underfull \hbox (badness 10000) detected at line 96 [][][] Underfull \hbox (badness 10000) detected at line 99 [][][] [942] Underfull \hbox (badness 10000) detected at line 165 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.5 on input line 184. ) (./vgrid_8h_source.tex [943]) (./vmgrid_8c.tex [944] <./vmgrid_8c__incl.pdf> [945] Underfull \hbox (badness 10000) detected at line 41 [][][] Underfull \hbox (badness 10000) detected at line 44 [][][] Underfull \hbox (badness 10000) detected at line 47 [][][] Underfull \hbox (badness 10000) detected at line 50 [][][] Overfull \hbox (1024.08331pt too wide) in paragraph at lines 59--59 []\T1/pcr/m/n/8 * Copyright (c) 2010, Pacific Northwest National Laboratory. Portions Copyright (c) 2002-2020, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2020, T he Regents of the University of California. Portions Copyright (c) 1995, Michae l Holst.[] ) (./vmgrid_8c_source.tex [946] [947] [948]) (./vmgrid_8h.tex <./vmgrid_8h__inc l.pdf> <./vmgrid_8h__dep__incl.pdf> [949] [950] Underfull \hbox (badness 10000) detected at line 71 [][][] Underfull \hbox (badness 10000) detected at line 74 [][][] Underfull \hbox (badness 10000) detected at line 77 [][][] [951]) (./vmgrid_8h_source.tex) (./vopot_8c.tex [952] <./vopot_8c__incl.pdf> Underfull \hbox (badness 10000) detected at line 44 [][][] Underfull \hbox (badness 10000) detected at line 47 [][][] Underfull \hbox (badness 10000) detected at line 50 [][][] [953]) (./vopot_8c_source.tex [954] [955] [956] [957] [958]) (./vopot_8h.tex <. /vopot_8h__incl.pdf> <./vopot_8h__dep__incl.pdf> [959] [960] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) detected at line 71 [][][] ) (./vopot_8h_source.tex [961]) (./vpmg_8c.tex <./vpmg_8c__incl.pdf> [962] [963] [964] [965] Underfull \hbox (badness 10000) detected at line 173 [][][] Underfull \hbox (badness 10000) detected at line 176 [][][] Underfull \hbox (badness 10000) detected at line 179 [][][] [966] Underfull \hbox (badness 10000) detected at line 261 [][][] [967] Underfull \hbox (badness 10000) detected at line 288 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.6 on input line 319. [968] Underfull \hbox (badness 10000) detected at line 384 [][][] Underfull \hbox (badness 10000) detected at line 387 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.7 on input line 394. Underfull \hbox (badness 10000) detected at line 409 [][][] Underfull \hbox (badness 10000) detected at line 412 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.8 on input line 419. [969] Underfull \hbox (badness 10000) detected at line 434 [][][] Underfull \hbox (badness 10000) detected at line 437 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.9 on input line 444. Underfull \hbox (badness 10000) detected at line 459 [][][] Underfull \hbox (badness 10000) detected at line 462 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.10 on input line 469. Underfull \hbox (badness 10000) detected at line 484 [][][] Underfull \hbox (badness 10000) detected at line 487 [][][] [970] Package longtable Warning: Column widths have changed (longtable) in table 9.11 on input line 494. Underfull \hbox (badness 10000) detected at line 509 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.12 on input line 519. Underfull \hbox (badness 10000) detected at line 534 [][][] Underfull \hbox (badness 10000) detected at line 537 [][][] Underfull \hbox (badness 10000) detected at line 554 [][][] Underfull \hbox (badness 10000) detected at line 557 [][][] [971] Underfull \hbox (badness 10000) detected at line 574 [][][] Underfull \hbox (badness 10000) detected at line 591 [][][] Underfull \hbox (badness 10000) detected at line 608 [][][] Underfull \hbox (badness 10000) detected at line 625 [][][] Underfull \hbox (badness 10000) detected at line 642 [][][] [972] Underfull \hbox (badness 10000) detected at line 659 [][][] Underfull \hbox (badness 10000) detected at line 676 [][][] Underfull \hbox (badness 10000) detected at line 697 [][][] Underfull \hbox (badness 10000) detected at line 700 [][][] Underfull \hbox (badness 10000) detected at line 717 [][][] [973] Underfull \hbox (badness 10000) detected at line 734 [][][] Underfull \hbox (badness 10000) detected at line 751 [][][] Underfull \hbox (badness 10000) detected at line 768 [][][] Underfull \hbox (badness 10000) detected at line 795 [][][] [974] Underfull \hbox (badness 10000) detected at line 832 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.13 on input line 861. [975] Underfull \hbox (badness 10000) detected at line 876 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.14 on input line 891. [976] Underfull \hbox (badness 10000) detected at line 926 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.15 on input line 933. Underfull \hbox (badness 10000) detected at line 948 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.16 on input line 955. [977] Underfull \hbox (badness 10000) detected at line 970 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.17 on input line 977. Underfull \hbox (badness 10000) detected at line 992 [][][] Underfull \hbox (badness 10000) detected at line 995 [][][] Underfull \hbox (badness 10000) detected at line 1012 [][][] Underfull \hbox (badness 10000) detected at line 1015 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.18 on input line 1022. [978] Underfull \hbox (badness 10000) detected at line 1037 [][][] Underfull \hbox (badness 10000) detected at line 1040 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.19 on input line 1047. Underfull \hbox (badness 10000) detected at line 1062 [][][] Underfull \hbox (badness 10000) detected at line 1065 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.20 on input line 1072. Underfull \hbox (badness 10000) detected at line 1097 [][][] [979] Underfull \hbox (badness 10000) detected at line 1114 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.21 on input line 1131. Underfull \hbox (badness 10000) detected at line 1146 [][][] Underfull \hbox (badness 10000) detected at line 1149 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.22 on input line 1158. ) (./vpmg_8c_source.tex [980] [981] [982] [983] [984] [985] [986] [987] [988] [989] [990] [991] [992] [993] [994] [995] [996] [997] [998] [999] [1000] [1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008] [1009] [1010] [1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] [1021] [1022] [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] [1033] [1034] [1035] [1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] [1090] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112] [1113] [1114] [1115] [1116]) (./vpmg_8h.tex <./vpmg_8h__in cl.pdf> <./vpmg_8h__dep__incl.pdf> [1117] [1118] [1119] [1120] [1121] [1122] Underfull \hbox (badness 10000) detected at line 235 [][][] Underfull \hbox (badness 10000) detected at line 238 [][][] Underfull \hbox (badness 10000) detected at line 241 [][][] [1123] [1124] Underfull \hbox (badness 10000) detected at line 406 [][][] Underfull \hbox (badness 10000) detected at line 423 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.23 on input line 454. [1125] Underfull \hbox (badness 10000) detected at line 469 [][][] Underfull \hbox (badness 10000) detected at line 472 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.24 on input line 479. Underfull \hbox (badness 10000) detected at line 494 [][][] Underfull \hbox (badness 10000) detected at line 497 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.25 on input line 504. [1126] Underfull \hbox (badness 10000) detected at line 519 [][][] Underfull \hbox (badness 10000) detected at line 522 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.26 on input line 529. Underfull \hbox (badness 10000) detected at line 544 [][][] Underfull \hbox (badness 10000) detected at line 547 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.27 on input line 554. Underfull \hbox (badness 10000) detected at line 569 [][][] Underfull \hbox (badness 10000) detected at line 572 [][][] [1127] Package longtable Warning: Column widths have changed (longtable) in table 9.28 on input line 579. Underfull \hbox (badness 10000) detected at line 594 [][][] Underfull \hbox (badness 10000) detected at line 597 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.29 on input line 604. Underfull \hbox (badness 10000) detected at line 619 [][][] Underfull \hbox (badness 10000) detected at line 622 [][][] Underfull \hbox (badness 10000) detected at line 639 [][][] Underfull \hbox (badness 10000) detected at line 642 [][][] [1128] Underfull \hbox (badness 10000) detected at line 659 [][][] Underfull \hbox (badness 10000) detected at line 676 [][][] Underfull \hbox (badness 10000) detected at line 693 [][][] Underfull \hbox (badness 10000) detected at line 710 [][][] Underfull \hbox (badness 10000) detected at line 727 [][][] [1129] Underfull \hbox (badness 10000) detected at line 744 [][][] Underfull \hbox (badness 10000) detected at line 761 [][][] Underfull \hbox (badness 10000) detected at line 782 [][][] Underfull \hbox (badness 10000) detected at line 785 [][][] Underfull \hbox (badness 10000) detected at line 802 [][][] [1130] Underfull \hbox (badness 10000) detected at line 819 [][][] Underfull \hbox (badness 10000) detected at line 836 [][][] Underfull \hbox (badness 10000) detected at line 853 [][][] Underfull \hbox (badness 10000) detected at line 870 [][][] Underfull \hbox (badness 10000) detected at line 883 [][][] [1131] Underfull \hbox (badness 10000) detected at line 896 [][][] Underfull \hbox (badness 10000) detected at line 913 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.30 on input line 942. [1132] Underfull \hbox (badness 10000) detected at line 957 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.31 on input line 972. Underfull \hbox (badness 10000) detected at line 987 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.32 on input line 994. [1133] Underfull \hbox (badness 10000) detected at line 1009 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.33 on input line 1016. Underfull \hbox (badness 10000) detected at line 1031 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.34 on input line 1038. Underfull \hbox (badness 10000) detected at line 1053 [][][] Underfull \hbox (badness 10000) detected at line 1056 [][][] Underfull \hbox (badness 10000) detected at line 1073 [][][] [1134] Underfull \hbox (badness 10000) detected at line 1076 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.35 on input line 1083. Underfull \hbox (badness 10000) detected at line 1098 [][][] Underfull \hbox (badness 10000) detected at line 1101 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.36 on input line 1108. Underfull \hbox (badness 10000) detected at line 1123 [][][] Underfull \hbox (badness 10000) detected at line 1126 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.37 on input line 1133. [1135] Underfull \hbox (badness 10000) detected at line 1158 [][][] Underfull \hbox (badness 10000) detected at line 1175 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.38 on input line 1192. [1136] Underfull \hbox (badness 10000) detected at line 1207 [][][] Underfull \hbox (badness 10000) detected at line 1210 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.39 on input line 1219. ) (./vpmg_8h_source.tex [1137] [1138] [1139] [1140] [1141] [1142] [1143] [1144]) (./vpmgp_8c.tex <./vpmgp_8c__incl.pdf> [1145] [1146] Underfull \hbox (badness 10000) detected at line 39 [][][] Underfull \hbox (badness 10000) detected at line 42 [][][] Underfull \hbox (badness 10000) detected at line 45 [][][] [1147]) (./vpmgp_8c_source.tex [1148] [1149] [1150]) (./vpmgp_8h.tex <./vpmgp_8 h__incl.pdf> [1151] <./vpmgp_8h__dep__incl.pdf> [1152] [1153] Underfull \hbox (badness 10000) detected at line 58 [][][] Underfull \hbox (badness 10000) detected at line 61 [][][] Underfull \hbox (badness 10000) detected at line 64 [][][] Underfull \hbox (badness 10000) detected at line 67 [][][] [1154]) (./vpmgp_8h_source.tex [1155]) (./build_ad_8c_source.tex [1156] [1157] [1158]) (./build_ad_8h_source.tex [1159]) (./build_bd_8c_source.tex [1160] [1161] [1162] [1163]) (./build_bd_8h_source.tex [1164]) (./build_gd_8c_source.tex [1165] [1166] [1167] [1168] [1169] [1170] [1171] [1172] [1173] [1174] [1175] [1176] [1177] [1178] [1179] [1180] [1181] [1182] [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] [1191] [1192] [1193] [1194] [1195] [1196] [1197] [1198] [1199] [1200] [1201] [1202]) (./build_gd_8h_source.tex [1203] [1204]) (./build_pd_8c_source.tex [1205] [1206] [1207] [1208] [1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216] [1217] [1218] [1219] [1220] [1221] [1222] [1223]) (./build_pd_8h_source.tex [1224] [1225] [1226]) (./cgd_8c_source.tex) (./cgd_8h_source.tex [1227]) (./gsd_8c_source.tex [1228] [1229] [1230] [1231]) (./gsd_8h_source.tex [1232]) (./matvecd_8c_source.tex [1233] [1234] [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242] [1243] [1244] [1245]) (./matvecd_8h_source.tex [1246] [1247] [1248] [1249] [1250] [1251]) 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(./powerd_8h_source.tex [1326]) (./smoothd_8c_source.tex [1327]) (./smoothd_8h_source.tex [1328]) (./routines_8c.tex <./routines_8c__incl.pdf> [1329] Underfull \hbox (badness 776) in paragraph at lines 48--49 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv /m/n/10 alist[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[] Underfull \hbox (badness 2856) in paragraph at lines 48--49 \T1/phv/m/n/10 YMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]ZMap[] [][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 kappa[]Map[][][], [] Underfull \hbox (badness 1237) in paragraph at lines 48--49 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 charge[]Map[][][], [] $\OMS/cmsy/m/n/10 ^^C $\T1/phv/m/n/10 pmgp[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pmg[][][], [] Underfull \hbox (badness 905) in paragraph at lines 62--63 []\T1/phv/m/n/10 VPUBLIC void [] (Vmem $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 mem , [] 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<./routines_8h__dep__incl.pdf> [1401] Overfull \hbox (16.65858pt too wide) in paragraph at lines 52--53 []\T1/phv/m/n/10 VEXTERNC int [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], Overfull \hbox (16.91972pt too wide) in paragraph at lines 54--55 []\T1/phv/m/n/10 VEXTERNC void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh , [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/1 0 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], Underfull \hbox (badness 1910) in paragraph at lines 72--73 [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1 /phv/m/n/10 alist[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][] [], [] Underfull \hbox (badness 1237) in paragraph at lines 72--73 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 charge[]Map[][][], [] $\OMS/cmsy/m/n/10 ^^C $\T1/phv/m/n/10 pmgp[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pmg[][][], [] [1402] Underfull \hbox (badness 5817) in paragraph at lines 90--91 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], Underfull \hbox (badness 5817) in paragraph at lines 92--93 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], [1403] Underfull \hbox (badness 2495) in paragraph at lines 124--125 []\T1/phv/m/n/10 VPUBLIC Vrc[]_[][]Codes [] (int icalc, [] $\OMS/cmsy/m/n/10 ^^ C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 feparm, [] $\OMS /cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbeparm, [] Underfull \hbox (badness 10000) detected at line 147 [][][] Underfull \hbox (badness 10000) detected at line 150 [][][] Underfull \hbox (badness 10000) detected at line 153 [][][] [1404]) (./routines_8h_source.tex [1405] [1406] [1407] [1408] [1409]) [1410] No file refman.ind. 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(./group___header.tex) (./group___vcsm.tex [19] Underfull \hbox (badness 10000) detected at line 93 [][][] [20] Underfull \hbox (badness 10000) detected at line 113 [][][] Underfull \hbox (badness 10000) detected at line 116 [][][] Underfull \hbox (badness 10000) detected at line 121 [][][] Underfull \hbox (badness 10000) detected at line 145 [][][] Underfull \hbox (badness 10000) detected at line 148 [][][] Underfull \hbox (badness 10000) detected at line 153 [][][] [21] Underfull \hbox (badness 10000) detected at line 179 [][][] Underfull \hbox (badness 10000) detected at line 201 [][][] Underfull \hbox (badness 10000) detected at line 223 [][][] Underfull \hbox (badness 10000) detected at line 226 [][][] Overfull \vbox (4.57304pt too high) has occurred while \output is active [22] Underfull \hbox (badness 10000) detected at line 252 [][][] Underfull \hbox (badness 10000) detected at line 255 [][][] Underfull \hbox (badness 10000) detected at line 281 [][][] Underfull \hbox (badness 10000) detected at line 284 [][][] [23] Underfull \hbox (badness 10000) detected at line 308 [][][] Underfull \hbox (badness 10000) detected at line 311 [][][] Underfull \hbox (badness 10000) detected at line 335 [][][] Underfull \hbox (badness 10000) detected at line 338 [][][] Underfull \hbox (badness 10000) detected at line 364 [][][] Underfull \hbox (badness 10000) detected at line 367 [][][] [24] Underfull \hbox (badness 10000) detected at line 393 [][][] Underfull \hbox (badness 10000) detected at line 396 [][][] Underfull \hbox (badness 10000) detected at line 418 [][][] Underfull \hbox (badness 10000) detected at line 421 [][][] [25] Underfull \hbox (badness 10000) detected at line 443 [][][] Underfull \hbox (badness 10000) detected at line 446 [][][] Underfull \hbox (badness 10000) detected at line 468 [][][] Underfull \hbox (badness 10000) detected at line 471 [][][] ) (./group___vfetk.tex [26] [27] [28] [29] [30] Underfull \hbox (badness 10000) detected at line 304 [][][] Underfull \hbox (badness 10000) detected at line 335 [][][] [31] Underfull \hbox (badness 10000) detected at line 398 [][][] Underfull \hbox (badness 10000) detected at line 429 [][][] Underfull \hbox (badness 10000) detected at line 463 [][][] Underfull \hbox (badness 10000) detected at line 466 [][][] [32] Underfull \hbox (badness 10000) detected at line 492 [][][] Underfull \hbox (badness 10000) detected at line 495 [][][] Underfull \hbox (badness 10000) detected at line 498 [][][] Underfull \hbox (badness 10000) detected at line 522 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] Underfull \hbox (badness 10000) detected at line 528 [][][] [33] Underfull \hbox (badness 10000) detected at line 559 [][][] Underfull \hbox (badness 10000) detected at line 569 [][][] [34] Underfull \hbox (badness 10000) detected at line 593 [][][] Underfull \hbox (badness 10000) detected at line 615 [][][] Underfull \hbox (badness 10000) detected at line 637 [][][] [35] Underfull \hbox (badness 10000) detected at line 658 [][][] Underfull \hbox (badness 10000) detected at line 661 [][][] Underfull \hbox (badness 10000) detected at line 668 [][][] Underfull \hbox (badness 10000) detected at line 671 [][][] Underfull \hbox (badness 10000) detected at line 701 [][][] [36] Underfull \hbox (badness 10000) detected at line 727 [][][] Underfull \hbox (badness 10000) detected at line 730 [][][] Underfull \hbox (badness 10000) detected at line 735 [][][] Underfull \hbox (badness 10000) detected at line 761 [][][] [37] Underfull \hbox (badness 10000) detected at line 789 [][][] Underfull \hbox (badness 10000) detected at line 792 [][][] Underfull \hbox (badness 10000) detected at line 814 [][][] Underfull \hbox (badness 10000) detected at line 817 [][][] Underfull \hbox (badness 10000) detected at line 820 [][][] [38] Underfull \hbox (badness 10000) detected at line 844 [][][] Underfull \hbox (badness 10000) detected at line 847 [][][] Underfull \hbox (badness 10000) detected at line 869 [][][] Underfull \hbox (badness 10000) detected at line 872 [][][] Underfull \hbox (badness 10000) detected at line 875 [][][] Underfull \hbox (badness 10000) detected at line 899 [][][] Underfull \hbox (badness 10000) detected at line 902 [][][] [39] Underfull \hbox (badness 10000) detected at line 924 [][][] Underfull \hbox (badness 10000) detected at line 927 [][][] Underfull \hbox (badness 10000) detected at line 949 [][][] [40] Underfull \hbox (badness 10000) detected at line 969 [][][] Underfull \hbox (badness 10000) detected at line 999 [][][] Underfull \hbox (badness 10000) detected at line 1002 [][][] Underfull \hbox (badness 10000) detected at line 1024 [][][] Underfull \hbox (badness 10000) detected at line 1027 [][][] [41] Underfull \hbox (badness 10000) detected at line 1053 [][][] Underfull \hbox (badness 10000) detected at line 1056 [][][] Underfull \hbox (badness 10000) detected at line 1080 [][][] Underfull \hbox (badness 10000) detected at line 1083 [][][] [42] Underfull \hbox (badness 10000) detected at line 1109 [][][] Underfull \hbox (badness 10000) detected at line 1146 [][][] Underfull \hbox (badness 10000) detected at line 1149 [][][] [43] Underfull \hbox (badness 10000) detected at line 1179 [][][] Underfull \hbox (badness 10000) detected at line 1182 [][][] Underfull \hbox (badness 10000) detected at line 1204 [][][] Underfull \hbox (badness 10000) detected at line 1207 [][][] [44] Underfull \hbox (badness 10000) detected at line 1232 [][][] Underfull \hbox (badness 10000) detected at line 1265 [][][] Underfull \hbox (badness 10000) detected at line 1268 [][][] [45] Underfull \hbox (badness 10000) detected at line 1298 [][][] Underfull \hbox (badness 10000) detected at line 1301 [][][] Underfull \hbox (badness 10000) detected at line 1327 [][][] [46] Underfull \hbox (badness 10000) detected at line 1355 [][][] Underfull \hbox (badness 10000) detected at line 1385 [][][] [47] Underfull \hbox (badness 10000) detected at line 1419 [][][] Underfull \hbox (badness 10000) detected at line 1422 [][][] Underfull \hbox (badness 10000) detected at line 1448 [][][] Underfull \hbox (badness 10000) detected at line 1451 [][][] [48] Underfull \hbox (badness 10000) detected at line 1477 [][][] Underfull \hbox (badness 10000) detected at line 1480 [][][] [49] Underfull \hbox (badness 10000) detected at line 1514 [][][] Underfull \hbox (badness 10000) detected at line 1517 [][][] Underfull \hbox (badness 10000) detected at line 1545 [][][] [50] Underfull \hbox (badness 10000) detected at line 1579 [][][] Underfull \hbox (badness 10000) detected at line 1582 [][][] [51] [52] Underfull \hbox (badness 10000) detected at line 1665 [][][] Underfull \hbox (badness 10000) detected at line 1699 [][][] Underfull \hbox (badness 10000) detected at line 1702 [][][] [53] Underfull \hbox (badness 10000) detected at line 1745 [][][] Underfull \hbox (badness 10000) detected at line 1755 [][][] Underfull \hbox (badness 10000) detected at line 1779 [][][] Underfull \hbox (badness 10000) detected at line 1782 [][][] Underfull \hbox (badness 10000) detected at line 1785 [][][] [54] Underfull \hbox (badness 10000) detected at line 1807 [][][] Underfull \hbox (badness 10000) detected at line 1810 [][][] Underfull \hbox (badness 10000) detected at line 1813 [][][] Underfull \hbox (badness 10000) detected at line 1835 [][][] [55] Underfull \hbox (badness 10000) detected at line 1861 [][][] Underfull \hbox (badness 10000) detected at line 1881 [][][] Underfull \hbox (badness 10000) detected at line 1886 [][][] ) (./group___vpee.tex [56] Underfull \hbox (badness 849) in paragraph at lines 45--46 \T1/phv/m/n/10 Holst par-al-lel re-fine-ment rou-tine es-sen-tially re-duces th e er-ror out-side the \T1/pcr/m/n/10 local^^D partition to zero. Underfull \hbox (badness 10000) in paragraph at lines 45--46 \T1/pcr/m/n/10 However, this leads to the need for a few final overlapping Schw arz solves to Underfull \hbox (badness 10000) in paragraph at lines 45--46 \T1/pcr/m/n/10 smooth out the errors near partition boundaries. Supposedly, if the region in Underfull \hbox (badness 10000) in paragraph at lines 45--46 \T1/pcr/m/n/10 which we allow error-based refinement includes the$\OML/cmm/m/it /10 <$\T1/pcr/m/n/10 /tt$\OML/cmm/m/it/10 >$\T1/pcr/m/n/10 local^^D partition a nd an Underfull \hbox (badness 10000) in paragraph at lines 45--46 \T1/pcr/m/n/10 external buffer zone approximately equal in size to the local re gion, then the Underfull \hbox (badness 10000) in paragraph at lines 45--46 \T1/pcr/m/n/10 solution will asymptotically approach the solution obtained via more typical Underfull \hbox (badness 10000) in paragraph at lines 45--46 \T1/pcr/m/n/10 methods. This is essentially a more flexible parallel implementa tion of MC\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 s [57] Underfull \hbox (badness 10000) detected at line 75 [][][] Underfull \hbox (badness 10000) detected at line 78 [][][] Underfull \hbox (badness 10000) detected at line 94 [][][] Underfull \hbox (badness 10000) detected at line 111 [][][] [58] Underfull \hbox (badness 10000) detected at line 114 [][][] Underfull \hbox (badness 10000) detected at line 132 [][][] Underfull \hbox (badness 10000) detected at line 149 [][][] Underfull \hbox (badness 10000) detected at line 171 [][][] [59] Underfull \hbox (badness 10000) detected at line 195 [][][] Underfull \hbox (badness 10000) detected at line 198 [][][] Underfull \hbox (badness 10000) detected at line 201 [][][] Overfull \vbox (42.60027pt too high) has occurred while \output is active [60] Underfull \hbox (badness 10000) detected at line 241 [][][] Underfull \hbox (badness 10000) detected at line 244 [][][] ) (./group___a_p_o_lparm.tex [61] Overfull \vbox (22.62613pt too high) has occurred while \output is active [62] Underfull \hbox (badness 10000) detected at line 212 [][][] Underfull \hbox (badness 10000) detected at line 220 [][][] [63] Underfull \hbox (badness 10000) detected at line 237 [][][] Underfull \hbox (badness 10000) detected at line 261 [][][] Underfull \hbox (badness 10000) detected at line 264 [][][] Underfull \hbox (badness 10000) detected at line 281 [][][] Underfull \hbox (badness 10000) detected at line 289 [][][] [64] Underfull \hbox (badness 10000) detected at line 306 [][][] Underfull \hbox (badness 10000) detected at line 328 [][][] ) (./group___b_e_mparm.tex [65] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] [66] Underfull \hbox (badness 10000) detected at line 125 [][][] Underfull \hbox (badness 10000) detected at line 133 [][][] Underfull \hbox (badness 10000) detected at line 150 [][][] Underfull \hbox (badness 10000) detected at line 158 [][][] Underfull \hbox (badness 10000) detected at line 175 [][][] [67] Underfull \hbox (badness 10000) detected at line 185 [][][] Underfull \hbox (badness 10000) detected at line 202 [][][] Underfull \hbox (badness 10000) detected at line 224 [][][] Underfull \hbox (badness 10000) detected at line 246 [][][] [68] Underfull \hbox (badness 10000) detected at line 258 [][][] ) (./group___f_e_mparm.tex [69] Underfull \hbox (badness 10000) detected at line 111 [][][] [70] Underfull \hbox (badness 10000) detected at line 155 [][][] Underfull \hbox (badness 10000) detected at line 158 [][][] Underfull \hbox (badness 10000) detected at line 197 [][][] Underfull \hbox (badness 10000) detected at line 231 [][][] [71] Underfull \hbox (badness 10000) detected at line 239 [][][] Underfull \hbox (badness 10000) detected at line 256 [][][] Underfull \hbox (badness 10000) detected at line 280 [][][] Underfull \hbox (badness 10000) detected at line 288 [][][] [72] Underfull \hbox (badness 10000) detected at line 305 [][][] Underfull \hbox (badness 10000) detected at line 315 [][][] Underfull \hbox (badness 10000) detected at line 332 [][][] Underfull \hbox (badness 10000) detected at line 354 [][][] ) (./group___g_e_o_f_l_o_wparm.tex [73] Underfull \hbox (badness 10000) detected at line 68 [][][] [74] Underfull \hbox (badness 10000) detected at line 71 [][][] Underfull \hbox (badness 10000) detected at line 124 [][][] Underfull \hbox (badness 10000) detected at line 132 [][][] [75] Underfull \hbox (badness 10000) detected at line 149 [][][] Underfull \hbox (badness 10000) detected at line 173 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 198 [][][] Underfull \hbox (badness 10000) detected at line 208 [][][] [76] Underfull \hbox (badness 10000) detected at line 225 [][][] Underfull \hbox (badness 10000) detected at line 247 [][][] Underfull \hbox (badness 10000) detected at line 269 [][][] [77] Underfull \hbox (badness 10000) detected at line 281 [][][] ) (./group___m_gparm.tex [78] [79] Underfull \hbox (badness 10000) detected at line 205 [][][] [80] Underfull \hbox (badness 10000) detected at line 217 [][][] Underfull \hbox (badness 10000) detected at line 234 [][][] Underfull \hbox (badness 10000) detected at line 246 [][][] Underfull \hbox (badness 10000) detected at line 263 [][][] Underfull \hbox (badness 10000) detected at line 271 [][][] [81] Underfull \hbox (badness 10000) detected at line 288 [][][] Underfull \hbox (badness 10000) detected at line 312 [][][] Underfull \hbox (badness 10000) detected at line 320 [][][] Underfull \hbox (badness 10000) detected at line 337 [][][] Underfull \hbox (badness 10000) detected at line 347 [][][] [82] Underfull \hbox (badness 10000) detected at line 364 [][][] Underfull \hbox (badness 10000) detected at line 386 [][][] Underfull \hbox (badness 10000) detected at line 408 [][][] Underfull \hbox (badness 10000) detected at line 416 [][][] [83] Underfull \hbox (badness 10000) detected at line 433 [][][] Underfull \hbox (badness 10000) detected at line 441 [][][] Underfull \hbox (badness 10000) detected at line 458 [][][] Underfull \hbox (badness 10000) detected at line 466 [][][] Underfull \hbox (badness 10000) detected at line 483 [][][] Underfull \hbox (badness 10000) detected at line 491 [][][] [84] Underfull \hbox (badness 10000) detected at line 508 [][][] Underfull \hbox (badness 10000) detected at line 516 [][][] Underfull \hbox (badness 10000) detected at line 533 [][][] Underfull \hbox (badness 10000) detected at line 541 [][][] Underfull \hbox (badness 10000) detected at line 558 [][][] [85] Underfull \hbox (badness 10000) detected at line 566 [][][] Underfull \hbox (badness 10000) detected at line 583 [][][] Underfull \hbox (badness 10000) detected at line 591 [][][] Underfull \hbox (badness 10000) detected at line 608 [][][] Underfull \hbox (badness 10000) detected at line 616 [][][] Underfull \hbox (badness 10000) detected at line 633 [][][] [86] Underfull \hbox (badness 10000) detected at line 645 [][][] Underfull \hbox (badness 10000) detected at line 662 [][][] Underfull \hbox (badness 10000) detected at line 686 [][][] [87] Underfull \hbox (badness 10000) detected at line 710 [][][] ) (./group___n_osh.tex [88] [89] [90] [91] [92] Underfull \hbox (badness 10000) detected at line 431 [][][] Underfull \hbox (badness 10000) detected at line 441 [][][] Underfull \hbox (badness 10000) detected at line 458 [][][] Underfull \hbox (badness 10000) detected at line 482 [][][] [93] Underfull \hbox (badness 10000) detected at line 490 [][][] Underfull \hbox (badness 10000) detected at line 507 [][][] Underfull \hbox (badness 10000) detected at line 529 [][][] Underfull \hbox (badness 10000) detected at line 539 [][][] Underfull \hbox (badness 10000) detected at line 556 [][][] [94] Underfull \hbox (badness 10000) detected at line 568 [][][] Underfull \hbox (badness 10000) detected at line 585 [][][] Underfull \hbox (badness 10000) detected at line 607 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] [95] Underfull \hbox (badness 10000) detected at line 639 [][][] Underfull \hbox (badness 10000) detected at line 656 [][][] Underfull \hbox (badness 10000) detected at line 659 [][][] Underfull \hbox (badness 10000) detected at line 669 [][][] Underfull \hbox (badness 10000) detected at line 672 [][][] Underfull \hbox (badness 10000) detected at line 689 [][][] Overfull \vbox (15.28305pt too high) has occurred while \output is active [96] Underfull \hbox (badness 10000) detected at line 699 [][][] Underfull \hbox (badness 10000) detected at line 716 [][][] Underfull \hbox (badness 10000) detected at line 726 [][][] Underfull \hbox (badness 10000) detected at line 743 [][][] Underfull \hbox (badness 10000) detected at line 753 [][][] [97] Underfull \hbox (badness 10000) detected at line 770 [][][] Underfull \hbox (badness 10000) detected at line 780 [][][] Underfull \hbox (badness 10000) detected at line 797 [][][] Underfull \hbox (badness 10000) detected at line 807 [][][] Underfull \hbox (badness 10000) detected at line 824 [][][] [98] Underfull \hbox (badness 10000) detected at line 834 [][][] Underfull \hbox (badness 10000) detected at line 851 [][][] Underfull \hbox (badness 10000) detected at line 861 [][][] Underfull \hbox (badness 10000) detected at line 878 [][][] Underfull \hbox (badness 10000) detected at line 888 [][][] [99] Underfull \hbox (badness 10000) detected at line 905 [][][] Underfull \hbox (badness 10000) detected at line 915 [][][] Underfull \hbox (badness 10000) detected at line 932 [][][] Underfull \hbox (badness 10000) detected at line 942 [][][] Underfull \hbox (badness 10000) detected at line 959 [][][] [100] Underfull \hbox (badness 10000) detected at line 969 [][][] Underfull \hbox (badness 10000) detected at line 986 [][][] Underfull \hbox (badness 10000) detected at line 996 [][][] Underfull \hbox (badness 10000) detected at line 1013 [][][] Underfull \hbox (badness 10000) detected at line 1016 [][][] Underfull \hbox (badness 10000) detected at line 1026 [][][] [101] Underfull \hbox (badness 10000) detected at line 1043 [][][] Underfull \hbox (badness 10000) detected at line 1048 [][][] Underfull \hbox (badness 10000) detected at line 1058 [][][] Underfull \hbox (badness 10000) detected at line 1075 [][][] Underfull \hbox (badness 10000) detected at line 1078 [][][] [102] Underfull \hbox (badness 10000) detected at line 1090 [][][] Underfull \hbox (badness 10000) detected at line 1093 [][][] Underfull \hbox (badness 10000) detected at line 1110 [][][] Underfull \hbox (badness 10000) detected at line 1113 [][][] Underfull \hbox (badness 10000) detected at line 1123 [][][] Underfull \hbox (badness 10000) detected at line 1126 [][][] Underfull \hbox (badness 10000) detected at line 1143 [][][] Underfull \hbox (badness 10000) detected at line 1146 [][][] [103] Underfull \hbox (badness 10000) detected at line 1158 [][][] Underfull \hbox (badness 10000) detected at line 1161 [][][] Underfull \hbox (badness 10000) detected at line 1178 [][][] Underfull \hbox (badness 10000) detected at line 1181 [][][] Underfull \hbox (badness 10000) detected at line 1191 [][][] Underfull \hbox (badness 10000) detected at line 1194 [][][] Underfull \hbox (badness 10000) detected at line 1211 [][][] [104] Underfull \hbox (badness 10000) detected at line 1214 [][][] Underfull \hbox (badness 10000) detected at line 1224 [][][] Underfull \hbox (badness 10000) detected at line 1248 [][][] Underfull \hbox (badness 10000) detected at line 1251 [][][] Underfull \hbox (badness 10000) detected at line 1261 [][][] Overfull \vbox (3.94589pt too high) has occurred while \output is active [105]) (./group___p_b_a_mparm.tex [106] Underfull \hbox (badness 10000) detected at line 116 [][][] Underfull \hbox (badness 10000) detected at line 119 [][][] [107] Underfull \hbox (badness 10000) detected at line 172 [][][] Underfull \hbox (badness 10000) detected at line 180 [][][] Underfull \hbox (badness 10000) detected at line 197 [][][] [108] Underfull \hbox (badness 10000) detected at line 221 [][][] Underfull \hbox (badness 10000) detected at line 229 [][][] Underfull \hbox (badness 10000) detected at line 246 [][][] Underfull \hbox (badness 10000) detected at line 256 [][][] [109] Underfull \hbox (badness 10000) detected at line 273 [][][] Underfull \hbox (badness 10000) detected at line 295 [][][] Underfull \hbox (badness 10000) detected at line 317 [][][] Underfull \hbox (badness 10000) detected at line 341 [][][] [110] Underfull \hbox (badness 10000) detected at line 365 [][][] Underfull \hbox (badness 10000) detected at line 389 [][][] Underfull \hbox (badness 10000) detected at line 413 [][][] [111] Underfull \hbox (badness 10000) detected at line 437 [][][] Underfull \hbox (badness 10000) detected at line 461 [][][] Underfull \hbox (badness 10000) detected at line 485 [][][] [112] Underfull \hbox (badness 10000) detected at line 509 [][][] Underfull \hbox (badness 10000) detected at line 533 [][][] Underfull \hbox (badness 10000) detected at line 557 [][][] [113] Underfull \hbox (badness 10000) detected at line 581 [][][] Underfull \hbox (badness 10000) detected at line 593 [][][] Underfull \hbox (badness 10000) detected at line 610 [][][] [114] Underfull \hbox (badness 10000) detected at line 634 [][][] ) (./group___p_b_eparm.tex [115] [116] Underfull \hbox (badness 10000) detected at line 209 [][][] Underfull \hbox (badness 10000) detected at line 212 [][][] [117] Underfull \hbox (badness 10000) detected at line 234 [][][] Underfull \hbox (badness 10000) detected at line 258 [][][] Underfull \hbox (badness 10000) detected at line 261 [][][] Underfull \hbox (badness 10000) detected at line 278 [][][] Underfull \hbox (badness 10000) detected at line 281 [][][] [118] Underfull \hbox (badness 10000) detected at line 303 [][][] Underfull \hbox (badness 10000) detected at line 325 [][][] Underfull \hbox (badness 10000) detected at line 347 [][][] Underfull \hbox (badness 10000) detected at line 350 [][][] [119] Underfull \hbox (badness 10000) detected at line 374 [][][] Underfull \hbox (badness 10000) detected at line 377 [][][] Underfull \hbox (badness 10000) detected at line 401 [][][] Underfull \hbox (badness 10000) detected at line 404 [][][] Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 431 [][][] [120]) (./group___p_b_s_a_mparm.tex [121] Underfull \hbox (badness 10000) detected at line 100 [][][] Underfull \hbox (badness 10000) detected at line 103 [][][] [122] Underfull \hbox (badness 10000) detected at line 156 [][][] Underfull \hbox (badness 10000) detected at line 164 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] [123] Underfull \hbox (badness 10000) detected at line 205 [][][] Underfull \hbox (badness 10000) detected at line 213 [][][] Underfull \hbox (badness 10000) detected at line 230 [][][] Underfull \hbox (badness 10000) detected at line 240 [][][] Underfull \hbox (badness 10000) detected at line 257 [][][] Overfull \vbox (0.37224pt too high) has occurred while \output is active [124] Underfull \hbox (badness 10000) detected at line 279 [][][] Underfull \hbox (badness 10000) detected at line 301 [][][] Underfull \hbox (badness 10000) detected at line 325 [][][] [125] Underfull \hbox (badness 10000) detected at line 349 [][][] Underfull \hbox (badness 10000) detected at line 373 [][][] Underfull \hbox (badness 10000) detected at line 397 [][][] [126] Underfull \hbox (badness 10000) detected at line 409 [][][] Underfull \hbox (badness 10000) detected at line 426 [][][] ) (./group___vacc.tex [127] [128] [129] Underfull \hbox (badness 10000) detected at line 149 [][][] Underfull \hbox (badness 10000) detected at line 179 [][][] [130] Underfull \hbox (badness 10000) detected at line 207 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] Underfull \hbox (badness 10000) detected at line 213 [][][] Underfull \hbox (badness 10000) detected at line 239 [][][] Underfull \hbox (badness 10000) detected at line 242 [][][] [131] Underfull \hbox (badness 10000) detected at line 268 [][][] Underfull \hbox (badness 10000) detected at line 271 [][][] Underfull \hbox (badness 10000) detected at line 283 [][][] Underfull \hbox (badness 10000) detected at line 305 [][][] Underfull \hbox (badness 10000) detected at line 308 [][][] [132] Underfull \hbox (badness 10000) detected at line 334 [][][] Underfull \hbox (badness 10000) detected at line 337 [][][] Underfull \hbox (badness 10000) detected at line 365 [][][] Underfull \hbox (badness 10000) detected at line 387 [][][] [133] Underfull \hbox (badness 10000) detected at line 411 [][][] Underfull \hbox (badness 10000) detected at line 414 [][][] Underfull \hbox (badness 10000) detected at line 417 [][][] Underfull \hbox (badness 10000) detected at line 447 [][][] Underfull \hbox (badness 10000) detected at line 450 [][][] [134] Underfull \hbox (badness 10000) detected at line 472 [][][] Underfull \hbox (badness 10000) detected at line 475 [][][] Underfull \hbox (badness 10000) detected at line 499 [][][] Underfull \hbox (badness 10000) detected at line 502 [][][] [135] Underfull \hbox (badness 10000) detected at line 530 [][][] Underfull \hbox (badness 10000) detected at line 533 [][][] Underfull \hbox (badness 10000) detected at line 536 [][][] Underfull \hbox (badness 10000) detected at line 562 [][][] Underfull \hbox (badness 10000) detected at line 565 [][][] [136] Underfull \hbox (badness 10000) detected at line 595 [][][] Underfull \hbox (badness 10000) detected at line 598 [][][] Underfull \hbox (badness 10000) detected at line 628 [][][] [137] Underfull \hbox (badness 10000) detected at line 660 [][][] Underfull \hbox (badness 10000) detected at line 692 [][][] [138] Underfull \hbox (badness 10000) detected at line 724 [][][] Underfull \hbox (badness 10000) detected at line 758 [][][] [139] Underfull \hbox (badness 10000) detected at line 790 [][][] Underfull \hbox (badness 10000) detected at line 820 [][][] [140] Underfull \hbox (badness 10000) detected at line 852 [][][] Underfull \hbox (badness 10000) detected at line 855 [][][] Underfull \hbox (badness 10000) detected at line 858 [][][] Underfull \hbox (badness 10000) detected at line 882 [][][] Underfull \hbox (badness 10000) detected at line 885 [][][] Underfull \hbox (badness 10000) detected at line 888 [][][] [141] Underfull \hbox (badness 10000) detected at line 918 [][][] Underfull \hbox (badness 10000) detected at line 921 [][][] Underfull \hbox (badness 10000) detected at line 941 [][][] Underfull \hbox (badness 10000) detected at line 944 [][][] Overfull \vbox (21.5778pt too high) has occurred while \output is active [142] Underfull \hbox (badness 10000) detected at line 972 [][][] Underfull \hbox (badness 10000) detected at line 975 [][][] Underfull \hbox (badness 10000) detected at line 1007 [][][] Underfull \hbox (badness 10000) detected at line 1010 [][][] [143] Underfull \hbox (badness 10000) detected at line 1040 [][][] Underfull \hbox (badness 10000) detected at line 1043 [][][] Underfull \hbox (badness 10000) detected at line 1069 [][][] Underfull \hbox (badness 10000) detected at line 1072 [][][] Overfull \vbox (18.93095pt too high) has occurred while \output is active [144] Underfull \hbox (badness 10000) detected at line 1100 [][][] Underfull \hbox (badness 10000) detected at line 1122 [][][] Underfull \hbox (badness 10000) detected at line 1146 [][][] Underfull \hbox (badness 10000) detected at line 1149 [][][] Underfull \hbox (badness 10000) detected at line 1152 [][][] [145]) (./group___valist.tex [146] Underfull \hbox (badness 10000) detected at line 91 [][][] Underfull \hbox (badness 10000) detected at line 94 [][][] Underfull \hbox (badness 10000) detected at line 111 [][][] Underfull \hbox (badness 10000) detected at line 114 [][][] Overfull \vbox (3.49948pt too high) has occurred while \output is active [147] Underfull \hbox (badness 10000) detected at line 136 [][][] Underfull \hbox (badness 10000) detected at line 158 [][][] Underfull \hbox (badness 10000) detected at line 180 [][][] Underfull \hbox (badness 10000) detected at line 183 [][][] [148] Underfull \hbox (badness 10000) detected at line 207 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] Underfull \hbox (badness 10000) detected at line 232 [][][] Underfull \hbox (badness 10000) detected at line 235 [][][] Underfull \hbox (badness 10000) detected at line 257 [][][] Underfull \hbox (badness 10000) detected at line 260 [][][] [149] Underfull \hbox (badness 10000) detected at line 282 [][][] Underfull \hbox (badness 10000) detected at line 285 [][][] Underfull \hbox (badness 10000) detected at line 307 [][][] Underfull \hbox (badness 10000) detected at line 310 [][][] Underfull \hbox (badness 10000) detected at line 332 [][][] [150] Underfull \hbox (badness 10000) detected at line 335 [][][] Underfull \hbox (badness 10000) detected at line 352 [][][] Underfull \hbox (badness 10000) detected at line 355 [][][] Underfull \hbox (badness 10000) detected at line 377 [][][] Underfull \hbox (badness 10000) detected at line 380 [][][] Underfull \hbox (badness 10000) detected at line 383 [][][] [151] Underfull \hbox (badness 10000) detected at line 409 [][][] Underfull \hbox (badness 10000) detected at line 412 [][][] Underfull \hbox (badness 10000) detected at line 415 [][][] Underfull \hbox (badness 10000) detected at line 443 [][][] Underfull \hbox (badness 10000) detected at line 446 [][][] Underfull \hbox (badness 10000) detected at line 449 [][][] Overfull \vbox (15.85518pt too high) has occurred while \output is active [152]) (./group___vatom.tex [153] Underfull \hbox (badness 10000) detected at line 97 [][][] [154] Underfull \hbox (badness 10000) detected at line 134 [][][] Underfull \hbox (badness 10000) detected at line 158 [][][] Underfull \hbox (badness 10000) detected at line 182 [][][] Underfull \hbox (badness 10000) detected at line 185 [][][] [155] Underfull \hbox (badness 10000) detected at line 202 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] Underfull \hbox (badness 10000) detected at line 227 [][][] Underfull \hbox (badness 10000) detected at line 249 [][][] Underfull \hbox (badness 10000) detected at line 271 [][][] [156] Underfull \hbox (badness 10000) detected at line 279 [][][] Underfull \hbox (badness 10000) detected at line 296 [][][] Underfull \hbox (badness 10000) detected at line 320 [][][] Underfull \hbox (badness 10000) detected at line 328 [][][] [157] Underfull \hbox (badness 10000) detected at line 345 [][][] Underfull \hbox (badness 10000) detected at line 353 [][][] Underfull \hbox (badness 10000) detected at line 370 [][][] Underfull \hbox (badness 10000) detected at line 378 [][][] Underfull \hbox (badness 10000) detected at line 395 [][][] Underfull \hbox (badness 10000) detected at line 403 [][][] [158] Underfull \hbox (badness 10000) detected at line 420 [][][] Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 445 [][][] Underfull \hbox (badness 10000) detected at line 469 [][][] [159] Underfull \hbox (badness 10000) detected at line 477 [][][] Underfull \hbox (badness 10000) detected at line 494 [][][] Underfull \hbox (badness 10000) detected at line 518 [][][] [160] Underfull \hbox (badness 10000) detected at line 542 [][][] Underfull \hbox (badness 10000) detected at line 566 [][][] Underfull \hbox (badness 10000) detected at line 590 [][][] [161] Underfull \hbox (badness 10000) detected at line 614 [][][] Underfull \hbox (badness 10000) detected at line 638 [][][] Underfull \hbox (badness 10000) detected at line 662 [][][] ) (./group___vcap.tex [162] Underfull \hbox (badness 10000) detected at line 36 [][][] [163] Underfull \hbox (badness 10000) detected at line 86 [][][] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 92 [][][] Underfull \hbox (badness 10000) detected at line 119 [][][] Underfull \hbox (badness 10000) detected at line 122 [][][] Underfull \hbox (badness 10000) detected at line 125 [][][] [164] Underfull \hbox (badness 10000) detected at line 152 [][][] Underfull \hbox (badness 10000) detected at line 155 [][][] Underfull \hbox (badness 10000) detected at line 158 [][][] ) (./group___vclist.tex [165] [166] Underfull \hbox (badness 10000) detected at line 110 [][][] Underfull \hbox (badness 10000) detected at line 140 [][][] Underfull \hbox (badness 10000) detected at line 143 [][][] [167] Underfull \hbox (badness 10000) detected at line 175 [][][] Underfull \hbox (badness 10000) detected at line 178 [][][] Underfull \hbox (badness 10000) detected at line 212 [][][] [168] Underfull \hbox (badness 10000) detected at line 234 [][][] Underfull \hbox (badness 10000) detected at line 256 [][][] Underfull \hbox (badness 10000) detected at line 259 [][][] Underfull \hbox (badness 10000) detected at line 283 [][][] Underfull \hbox (badness 10000) detected at line 286 [][][] [169] Underfull \hbox (badness 10000) detected at line 308 [][][] Underfull \hbox (badness 10000) detected at line 311 [][][] Underfull \hbox (badness 10000) detected at line 333 [][][] Underfull \hbox (badness 10000) detected at line 336 [][][] Underfull \hbox (badness 10000) detected at line 358 [][][] Underfull \hbox (badness 10000) detected at line 361 [][][] [170] Underfull \hbox (badness 10000) detected at line 385 [][][] Underfull \hbox (badness 10000) detected at line 407 [][][] ) (./group___vgreen.tex [171] Underfull \hbox (badness 10000) detected at line 57 [][][] Underfull \hbox (badness 10000) detected at line 60 [][][] [172] [173] Underfull \hbox (badness 10000) detected at line 141 [][][] Underfull \hbox (badness 10000) detected at line 159 [][][] Underfull \hbox (badness 10000) detected at line 178 [][][] [174] Underfull \hbox (badness 10000) detected at line 196 [][][] Underfull \hbox (badness 10000) detected at line 215 [][][] [175] Underfull \hbox (badness 10000) detected at line 239 [][][] Underfull \hbox (badness 10000) detected at line 258 [][][] Underfull \hbox (badness 10000) detected at line 282 [][][] [176] Underfull \hbox (badness 10000) detected at line 299 [][][] Underfull \hbox (badness 10000) detected at line 307 [][][] Underfull \hbox (badness 10000) detected at line 324 [][][] Underfull \hbox (badness 10000) detected at line 334 [][][] Underfull \hbox (badness 10000) detected at line 351 [][][] [177] Underfull \hbox (badness 10000) detected at line 373 [][][] Underfull \hbox (badness 10000) detected at line 395 [][][] Underfull \hbox (badness 10000) detected at line 403 [][][] Underfull \hbox (badness 10000) detected at line 424 [][][] [178] Underfull \hbox (badness 10000) detected at line 429 [][][] Underfull \hbox (badness 10000) detected at line 449 [][][] Underfull \hbox (badness 10000) detected at line 471 [][][] Underfull \hbox (badness 10000) detected at line 476 [][][] [179] Underfull \hbox (badness 10000) detected at line 500 [][][] Underfull \hbox (badness 10000) detected at line 517 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] ) (./group___vhal.tex [180] [181] [182] [183] Underfull \hbox (badness 10000) detected at line 380 [][][] Underfull \hbox (badness 10000) detected at line 411 [][][] [184] Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 445 [][][] Underfull \hbox (badness 10000) detected at line 476 [][][] Underfull \hbox (badness 10000) detected at line 493 [][][] Underfull \hbox (badness 10000) detected at line 516 [][][] [185] Underfull \hbox (badness 10000) detected at line 547 [][][] [186] Underfull \hbox (badness 10000) detected at line 682 [][][] Underfull \hbox (badness 10000) detected at line 729 [][][] [187] Underfull \hbox (badness 10000) detected at line 760 [][][] Underfull \hbox (badness 10000) detected at line 795 [][][] Underfull \hbox (badness 10000) detected at line 842 [][][] Missing character: There is no Å in font cmr10! Missing character: There is no Å in font cmr10! LaTeX Warning: Command \r invalid in math mode on input line 58. Missing character: There is no Å in font cmr10! [188] [189] Underfull \hbox (badness 10000) detected at line 1019 [][][] Underfull \hbox (badness 10000) detected at line 1022 [][][] Underfull \hbox (badness 10000) detected at line 1050 [][][] Underfull \hbox (badness 10000) detected at line 1053 [][][] Underfull \hbox (badness 10000) detected at line 1070 [][][] [190]) (./group___vmatrix.tex) (./group___vparam.tex [191] [192] Underfull \hbox (badness 10000) detected at line 120 [][][] Underfull \hbox (badness 10000) detected at line 130 [][][] [193] Underfull \hbox (badness 10000) detected at line 147 [][][] Underfull \hbox (badness 10000) detected at line 157 [][][] Underfull \hbox (badness 10000) detected at line 174 [][][] Underfull \hbox (badness 10000) detected at line 198 [][][] [194] Underfull \hbox (badness 10000) detected at line 222 [][][] Underfull \hbox (badness 10000) detected at line 225 [][][] Underfull \hbox (badness 10000) detected at line 242 [][][] Underfull \hbox (badness 10000) detected at line 250 [][][] Underfull \hbox (badness 10000) detected at line 267 [][][] [195] Underfull \hbox (badness 10000) detected at line 289 [][][] Underfull \hbox (badness 10000) detected at line 311 [][][] Underfull \hbox (badness 10000) detected at line 314 [][][] Underfull \hbox (badness 10000) detected at line 331 [][][] Underfull \hbox (badness 10000) detected at line 339 [][][] Underfull \hbox (badness 10000) detected at line 356 [][][] [196] Underfull \hbox (badness 10000) detected at line 378 [][][] Underfull \hbox (badness 10000) detected at line 400 [][][] Underfull \hbox (badness 10000) detected at line 412 [][][] Underfull \hbox (badness 10000) detected at line 415 [][][] Underfull \hbox (badness 10000) detected at line 418 [][][] [197] Underfull \hbox (badness 10000) detected at line 435 [][][] Underfull \hbox (badness 10000) detected at line 445 [][][] Underfull \hbox (badness 10000) detected at line 448 [][][] Underfull \hbox (badness 10000) detected at line 451 [][][] Underfull \hbox (badness 10000) detected at line 468 [][][] Underfull \hbox (badness 10000) detected at line 476 [][][] [198] Underfull \hbox (badness 10000) detected at line 493 [][][] Underfull \hbox (badness 10000) detected at line 509 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Underfull \hbox (badness 10000) detected at line 537 [][][] [199] Underfull \hbox (badness 10000) detected at line 553 [][][] Underfull \hbox (badness 10000) detected at line 570 [][][] Underfull \hbox (badness 10000) detected at line 594 [][][] Underfull \hbox (badness 10000) detected at line 602 [][][] [200] Underfull \hbox (badness 10000) detected at line 619 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] Underfull \hbox (badness 10000) detected at line 646 [][][] Underfull \hbox (badness 10000) detected at line 668 [][][] [201]) (./group___vpbe.tex [202] [203] Underfull \hbox (badness 10000) detected at line 128 [][][] Underfull \hbox (badness 10000) detected at line 131 [][][] LaTeX Warning: Command \r invalid in math mode on input line 133. Missing character: There is no Å in font cmr10! LaTeX Warning: Command \r invalid in math mode on input line 133. Missing character: There is no Å in font cmr10! [204] Underfull \hbox (badness 10000) detected at line 136 [][][] [205] Underfull \hbox (badness 10000) detected at line 186 [][][] Underfull \hbox (badness 10000) detected at line 189 [][][] LaTeX Warning: Command \r invalid in math mode on input line 190. Missing character: There is no Å in font cmr10! LaTeX Warning: Command \r invalid in math mode on input line 190. Missing character: There is no Å in font cmr10! Underfull \hbox (badness 10000) detected at line 195 [][][] Overfull \vbox (21.60152pt too high) has occurred while \output is active [206] Underfull \hbox (badness 10000) detected at line 247 [][][] Underfull \hbox (badness 10000) detected at line 269 [][][] Underfull \hbox (badness 10000) detected at line 291 [][][] Underfull \hbox (badness 10000) detected at line 299 [][][] [207] Overfull \hbox (151.96916pt too wide) in paragraph at lines 318--318 [] \T1/p cr/m/n/8 permittivity equal to the protein interior) and zero ionic[] Underfull \hbox (badness 10000) detected at line 325 [][][] Underfull \hbox (badness 10000) detected at line 333 [][][] Underfull \hbox (badness 10000) detected at line 350 [][][] Underfull \hbox (badness 10000) detected at line 358 [][][] [208] Underfull \hbox (badness 10000) detected at line 375 [][][] Underfull \hbox (badness 10000) detected at line 383 [][][] Underfull \hbox (badness 10000) detected at line 396 [][][] Underfull \hbox (badness 10000) detected at line 412 [][][] [209] Underfull \hbox (badness 10000) detected at line 436 [][][] Underfull \hbox (badness 10000) detected at line 453 [][][] Underfull \hbox (badness 10000) detected at line 461 [][][] Underfull \hbox (badness 10000) detected at line 478 [][][] Underfull \hbox (badness 10000) detected at line 486 [][][] Underfull \hbox (badness 10000) detected at line 503 [][][] [210] Underfull \hbox (badness 10000) detected at line 525 [][][] Underfull \hbox (badness 10000) detected at line 533 [][][] Underfull \hbox (badness 10000) detected at line 550 [][][] Underfull \hbox (badness 10000) detected at line 558 [][][] Underfull \hbox (badness 10000) detected at line 575 [][][] [211] Underfull \hbox (badness 10000) detected at line 583 [][][] Underfull \hbox (badness 10000) detected at line 600 [][][] Underfull \hbox (badness 10000) detected at line 608 [][][] Underfull \hbox (badness 10000) detected at line 625 [][][] Underfull \hbox (badness 10000) detected at line 633 [][][] [212] Underfull \hbox (badness 10000) detected at line 650 [][][] Underfull \hbox (badness 10000) detected at line 658 [][][] Underfull \hbox (badness 10000) detected at line 675 [][][] Underfull \hbox (badness 10000) detected at line 683 [][][] Underfull \hbox (badness 10000) detected at line 700 [][][] Underfull \hbox (badness 10000) detected at line 708 [][][] [213] Underfull \hbox (badness 10000) detected at line 725 [][][] Underfull \hbox (badness 10000) detected at line 733 [][][] Underfull \hbox (badness 10000) detected at line 750 [][][] Underfull \hbox (badness 10000) detected at line 758 [][][] Underfull \hbox (badness 10000) detected at line 775 [][][] [214] Underfull \hbox (badness 10000) detected at line 783 [][][] Underfull \hbox (badness 10000) detected at line 800 [][][] Underfull \hbox (badness 10000) detected at line 808 [][][] Underfull \hbox (badness 10000) detected at line 825 [][][] Underfull \hbox (badness 10000) detected at line 833 [][][] [215] Underfull \hbox (badness 10000) detected at line 850 [][][] Underfull \hbox (badness 10000) detected at line 858 [][][] LaTeX Warning: Command \r invalid in math mode on input line 859. Missing character: There is no Å in font cmr10! Underfull \hbox (badness 10000) detected at line 875 [][][] Underfull \hbox (badness 10000) detected at line 883 [][][] Underfull \hbox (badness 10000) detected at line 900 [][][] Underfull \hbox (badness 10000) detected at line 908 [][][] [216] Underfull \hbox (badness 10000) detected at line 925 [][][] Underfull \hbox (badness 10000) detected at line 933 [][][] ) (./group___vstring.tex [217] Underfull \hbox (badness 10000) detected at line 42 [][][] Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 67 [][][] Underfull \hbox (badness 10000) detected at line 70 [][][] Underfull \hbox (badness 10000) detected at line 80 [][][] Underfull \hbox (badness 10000) detected at line 93 [][][] [218] Underfull \hbox (badness 10000) detected at line 96 [][][] Underfull \hbox (badness 10000) detected at line 99 [][][] Underfull \hbox (badness 10000) detected at line 102 [][][] Underfull \hbox (badness 10000) detected at line 105 [][][] ) (./group___vunit.tex [219] LaTeX Warning: Command \r invalid in math mode on input line 39. Missing character: There is no Å in font cmr9! [220] LaTeX Warning: Command \r invalid in math mode on input line 142. Missing character: There is no Å in font cmr10! ) (./group___vgrid.tex [221] [222] [223] Underfull \hbox (badness 10000) detected at line 125 [][][] Underfull \hbox (badness 10000) detected at line 151 [][][] Underfull \hbox (badness 10000) detected at line 168 [][][] [224] Underfull \hbox (badness 10000) detected at line 196 [][][] Underfull \hbox (badness 10000) detected at line 213 [][][] Underfull \hbox (badness 10000) detected at line 229 [][][] [225] Underfull \hbox (badness 10000) detected at line 246 [][][] Underfull \hbox (badness 10000) detected at line 268 [][][] Underfull \hbox (badness 10000) detected at line 290 [][][] Underfull \hbox (badness 10000) detected at line 302 [][][] [226] Underfull \hbox (badness 10000) detected at line 319 [][][] Underfull \hbox (badness 10000) detected at line 327 [][][] Underfull \hbox (badness 10000) detected at line 344 [][][] Underfull \hbox (badness 10000) detected at line 352 [][][] Underfull \hbox (badness 10000) detected at line 369 [][][] Underfull \hbox (badness 10000) detected at line 377 [][][] [227] Underfull \hbox (badness 10000) detected at line 395 [][][] Underfull \hbox (badness 10000) detected at line 403 [][][] Underfull \hbox (badness 10000) detected at line 420 [][][] Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 445 [][][] [228] Underfull \hbox (badness 10000) detected at line 453 [][][] Underfull \hbox (badness 10000) detected at line 470 [][][] Underfull \hbox (badness 10000) detected at line 473 [][][] Underfull \hbox (badness 10000) detected at line 489 [][][] Underfull \hbox (badness 10000) detected at line 492 [][][] [229] Underfull \hbox (badness 10000) detected at line 509 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Underfull \hbox (badness 10000) detected at line 528 [][][] Underfull \hbox (badness 10000) detected at line 531 [][][] Underfull \hbox (badness 10000) detected at line 548 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] [230] Underfull \hbox (badness 10000) detected at line 575 [][][] Underfull \hbox (badness 10000) detected at line 583 [][][] Underfull \hbox (badness 10000) detected at line 600 [][][] Underfull \hbox (badness 10000) detected at line 612 [][][] [231] Underfull \hbox (badness 10000) detected at line 629 [][][] Underfull \hbox (badness 10000) detected at line 663 [][][] [232] Underfull \hbox (badness 10000) detected at line 697 [][][] Underfull \hbox (badness 10000) detected at line 702 [][][] ) (./group___vmgrid.tex [233] [234] Underfull \hbox (badness 10000) detected at line 105 [][][] Underfull \hbox (badness 10000) detected at line 115 [][][] Underfull \hbox (badness 10000) detected at line 132 [][][] Underfull \hbox (badness 10000) detected at line 135 [][][] Underfull \hbox (badness 10000) detected at line 152 [][][] [235] Underfull \hbox (badness 10000) detected at line 160 [][][] Underfull \hbox (badness 10000) detected at line 177 [][][] Underfull \hbox (badness 10000) detected at line 193 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] [236] Underfull \hbox (badness 10000) detected at line 232 [][][] Underfull \hbox (badness 10000) detected at line 254 [][][] Underfull \hbox (badness 10000) detected at line 264 [][][] Underfull \hbox (badness 10000) detected at line 277 [][][] [237] Underfull \hbox (badness 10000) detected at line 287 [][][] Underfull \hbox (badness 10000) detected at line 300 [][][] Underfull \hbox (badness 10000) detected at line 312 [][][] Underfull \hbox (badness 10000) detected at line 329 [][][] Underfull \hbox (badness 10000) detected at line 341 [][][] ) (./group___vopot.tex [238] [239] Underfull \hbox (badness 10000) detected at line 77 [][][] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 106 [][][] [240] Underfull \hbox (badness 10000) detected at line 120 [][][] Underfull \hbox (badness 10000) detected at line 137 [][][] Underfull \hbox (badness 10000) detected at line 153 [][][] Underfull \hbox (badness 10000) detected at line 170 [][][] [241] Underfull \hbox (badness 10000) detected at line 192 [][][] Underfull \hbox (badness 10000) detected at line 214 [][][] Underfull \hbox (badness 10000) detected at line 226 [][][] Underfull \hbox (badness 10000) detected at line 243 [][][] Overfull \vbox (28.1848pt too high) has occurred while \output is active [242] Underfull \hbox (badness 10000) detected at line 255 [][][] ) (./group___vpmg.tex [243] [244] [245] Underfull \hbox (badness 10000) detected at line 117 [][][] Underfull \hbox (badness 10000) detected at line 150 [][][] [246] Underfull \hbox (badness 10000) detected at line 186 [][][] [247] Underfull \hbox (badness 10000) detected at line 234 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.409 on input line 261. Underfull \hbox (badness 10000) detected at line 276 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.410 on input line 309. [248] Underfull \hbox (badness 10000) detected at line 324 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.411 on input line 347. [249] Underfull \hbox (badness 10000) detected at line 362 [][][] Underfull \hbox (badness 10000) detected at line 381 [][][] Underfull \hbox (badness 10000) detected at line 384 [][][] [250] Underfull \hbox (badness 10000) detected at line 416 [][][] Underfull \hbox (badness 10000) detected at line 419 [][][] Underfull \hbox (badness 10000) detected at line 422 [][][] [251] Underfull \hbox (badness 10000) detected at line 458 [][][] Underfull \hbox (badness 10000) detected at line 484 [][][] Underfull \hbox (badness 10000) detected at line 487 [][][] Underfull \hbox (badness 10000) detected at line 492 [][][] Overfull \vbox (1.11014pt too high) has occurred while \output is active [252] Underfull \hbox (badness 10000) detected at line 520 [][][] Underfull \hbox (badness 10000) detected at line 546 [][][] [253] Underfull \hbox (badness 10000) detected at line 572 [][][] Underfull \hbox (badness 10000) detected at line 604 [][][] Underfull \hbox (badness 10000) detected at line 607 [][][] Underfull \hbox (badness 10000) detected at line 610 [][][] [254] Underfull \hbox (badness 10000) detected at line 643 [][][] Underfull \hbox (badness 10000) detected at line 646 [][][] Underfull \hbox (badness 10000) detected at line 668 [][][] Underfull \hbox (badness 10000) detected at line 690 [][][] [255] Underfull \hbox (badness 10000) detected at line 712 [][][] Underfull \hbox (badness 10000) detected at line 715 [][][] Underfull \hbox (badness 10000) detected at line 718 [][][] Underfull \hbox (badness 10000) detected at line 742 [][][] [256] Underfull \hbox (badness 10000) detected at line 764 [][][] Underfull \hbox (badness 10000) detected at line 767 [][][] Underfull \hbox (badness 10000) detected at line 799 [][][] [257] Underfull \hbox (badness 10000) detected at line 802 [][][] Underfull \hbox (badness 10000) detected at line 856 [][][] Underfull \hbox (badness 10000) detected at line 859 [][][] Underfull \hbox (badness 10000) detected at line 864 [][][] [258] Underfull \hbox (badness 10000) detected at line 894 [][][] Underfull \hbox (badness 10000) detected at line 920 [][][] Underfull \hbox (badness 10000) detected at line 923 [][][] [259] Underfull \hbox (badness 10000) detected at line 928 [][][] Underfull \hbox (badness 10000) detected at line 956 [][][] Underfull \hbox (badness 10000) detected at line 982 [][][] [260] Underfull \hbox (badness 10000) detected at line 1008 [][][] Underfull \hbox (badness 10000) detected at line 1030 [][][] Underfull \hbox (badness 10000) detected at line 1033 [][][] [261] Underfull \hbox (badness 10000) detected at line 1055 [][][] Underfull \hbox (badness 10000) detected at line 1093 [][][] Underfull \hbox (badness 10000) detected at line 1096 [][][] [262] Underfull \hbox (badness 10000) detected at line 1099 [][][] Underfull \hbox (badness 10000) detected at line 1123 [][][] Underfull \hbox (badness 10000) detected at line 1160 [][][] [263] Underfull \hbox (badness 10000) detected at line 1163 [][][] Underfull \hbox (badness 10000) detected at line 1166 [][][] Underfull \hbox (badness 10000) detected at line 1190 [][][] Underfull \hbox (badness 10000) detected at line 1193 [][][] Underfull \hbox (badness 10000) detected at line 1198 [][][] [264] Underfull \hbox (badness 10000) detected at line 1226 [][][] Underfull \hbox (badness 10000) detected at line 1252 [][][] [265] Underfull \hbox (badness 10000) detected at line 1280 [][][] Underfull \hbox (badness 10000) detected at line 1283 [][][] Underfull \hbox (badness 10000) detected at line 1303 [][][] [266] Underfull \hbox (badness 10000) detected at line 1343 [][][] Underfull \hbox (badness 10000) detected at line 1346 [][][] Underfull \hbox (badness 10000) detected at line 1349 [][][] Underfull \hbox (badness 10000) detected at line 1373 [][][] [267] Underfull \hbox (badness 10000) detected at line 1401 [][][] Underfull \hbox (badness 10000) detected at line 1404 [][][] Underfull \hbox (badness 10000) detected at line 1426 [][][] Underfull \hbox (badness 10000) detected at line 1429 [][][] Underfull \hbox (badness 10000) detected at line 1432 [][][] Underfull \hbox (badness 10000) detected at line 1454 [][][] ) (./group___vpmgp.tex [268] Underfull \hbox (badness 10000) detected at line 45 [][][] [269] Underfull \hbox (badness 10000) detected at line 78 [][][] Underfull \hbox (badness 10000) detected at line 86 [][][] Underfull \hbox (badness 10000) detected at line 103 [][][] Underfull \hbox (badness 10000) detected at line 113 [][][] Underfull \hbox (badness 10000) detected at line 130 [][][] [270] Underfull \hbox (badness 10000) detected at line 152 [][][] Underfull \hbox (badness 10000) detected at line 174 [][][] [271] Underfull \hbox (badness 10000) detected at line 208 [][][] ) (./group___p_m_g_c.tex [272] [273] [274] [275] Underfull \hbox (badness 10000) detected at line 150 [][][] Underfull \hbox (badness 10000) detected at line 153 [][][] Underfull \hbox (badness 10000) detected at line 156 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 165--165 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [276] Underfull \hbox (badness 10000) detected at line 212 [][][] Underfull \hbox (badness 10000) detected at line 215 [][][] Underfull \hbox (badness 10000) detected at line 218 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 227--227 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [277] Underfull \hbox (badness 10000) detected at line 277 [][][] Underfull \hbox (badness 10000) detected at line 280 [][][] [278] Underfull \hbox (badness 10000) detected at line 308 [][][] Underfull \hbox (badness 10000) detected at line 311 [][][] Underfull \hbox (badness 10000) detected at line 339 [][][] Underfull \hbox (badness 10000) detected at line 342 [][][] Underfull \hbox (badness 10000) detected at line 345 [][][] [279] Overfull \hbox (304.08286pt too wide) in paragraph at lines 355--355 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 392 [][][] Underfull \hbox (badness 10000) detected at line 395 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 404--404 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [280] Underfull \hbox (badness 10000) detected at line 439 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.456 on input line 488. [281] Underfull \hbox (badness 10000) detected at line 503 [][][] Underfull \hbox (badness 10000) detected at line 506 [][][] Underfull \hbox (badness 10000) detected at line 509 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 518--518 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [282] Underfull \hbox (badness 10000) detected at line 556 [][][] Underfull \hbox (badness 10000) detected at line 559 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 568--568 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 603 [][][] Underfull \hbox (badness 10000) detected at line 606 [][][] [283] Underfull \hbox (badness 10000) detected at line 646 [][][] Underfull \hbox (badness 10000) detected at line 649 [][][] [284] [285] Underfull \hbox (badness 10000) detected at line 719 [][][] Underfull \hbox (badness 10000) detected at line 722 [][][] Underfull \hbox (badness 10000) detected at line 772 [][][] Underfull \hbox (badness 10000) detected at line 775 [][][] Underfull \hbox (badness 10000) detected at line 778 [][][] [286] Overfull \hbox (304.08286pt too wide) in paragraph at lines 788--788 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 825 [][][] Underfull \hbox (badness 10000) detected at line 828 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 837--837 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [287] Package longtable Warning: Column widths have changed (longtable) in table 7.460 on input line 892. [288] Underfull \hbox (badness 10000) detected at line 907 [][][] Underfull \hbox (badness 10000) detected at line 910 [][][] [289] Package longtable Warning: Column widths have changed (longtable) in table 7.461 on input line 1035. [290] [291] Underfull \hbox (badness 10000) detected at line 1050 [][][] Underfull \hbox (badness 10000) detected at line 1053 [][][] [292] Package longtable Warning: Column widths have changed (longtable) in table 7.462 on input line 1214. [293] [294] Underfull \hbox (badness 10000) detected at line 1229 [][][] Underfull \hbox (badness 10000) detected at line 1232 [][][] [295] Package longtable Warning: Column widths have changed (longtable) in table 7.463 on input line 1367. [296] Underfull \hbox (badness 10000) detected at line 1382 [][][] Underfull \hbox (badness 10000) detected at line 1385 [][][] Underfull \hbox (badness 10000) detected at line 1388 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.464 on input line 1431. [297] [298] Underfull \hbox (badness 10000) detected at line 1446 [][][] Underfull \hbox (badness 10000) detected at line 1449 [][][] Underfull \hbox (badness 10000) detected at line 1452 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 1462--1462 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 1501 [][][] Underfull \hbox (badness 10000) detected at line 1504 [][][] [299] Package longtable Warning: Column widths have changed (longtable) in table 7.465 on input line 1569. [300] Underfull \hbox (badness 10000) detected at line 1584 [][][] Underfull \hbox (badness 10000) detected at line 1587 [][][] Underfull \hbox (badness 10000) detected at line 1590 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 1600--1600 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 1637 [][][] Underfull \hbox (badness 10000) detected at line 1640 [][][] [301] Underfull \hbox (badness 10000) detected at line 1643 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 1652--1652 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Package longtable Warning: Column widths have changed (longtable) in table 7.466 on input line 1715. Overfull \vbox (9.44278pt too high) has occurred while \output is active [302] Underfull \hbox (badness 10000) detected at line 1730 [][][] Underfull \hbox (badness 10000) detected at line 1735 [][][] Underfull \hbox (badness 10000) detected at line 1738 [][][] Underfull \hbox (badness 10000) detected at line 1768 [][][] Underfull \hbox (badness 10000) detected at line 1771 [][][] [303] Underfull \hbox (badness 10000) detected at line 1805 [][][] Underfull \hbox (badness 10000) detected at line 1808 [][][] [304] Underfull \hbox (badness 10000) detected at line 1842 [][][] Underfull \hbox (badness 10000) detected at line 1845 [][][] Underfull \hbox (badness 10000) detected at line 1879 [][][] Underfull \hbox (badness 10000) detected at line 1882 [][][] [305] Underfull \hbox (badness 10000) detected at line 1885 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 1895--1895 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 1932 [][][] Underfull \hbox (badness 10000) detected at line 1935 [][][] Underfull \hbox (badness 10000) detected at line 1938 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 1947--1947 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [306] Package longtable Warning: Column widths have changed (longtable) in table 7.471 on input line 2018. [307] Underfull \hbox (badness 10000) detected at line 2033 [][][] Underfull \hbox (badness 10000) detected at line 2036 [][][] Underfull \hbox (badness 10000) detected at line 2070 [][][] Underfull \hbox (badness 10000) detected at line 2073 [][][] Underfull \hbox (badness 10000) detected at line 2076 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 2086--2086 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [308] Underfull \hbox (badness 10000) detected at line 2123 [][][] Underfull \hbox (badness 10000) detected at line 2126 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2135--2135 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [309] Underfull \hbox (badness 10000) detected at line 2170 [][][] Underfull \hbox (badness 10000) detected at line 2173 [][][] Underfull \hbox (badness 10000) detected at line 2205 [][][] [310] Underfull \hbox (badness 10000) detected at line 2208 [][][] Underfull \hbox (badness 10000) detected at line 2244 [][][] Underfull \hbox (badness 10000) detected at line 2247 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.475 on input line 2268. [311] Underfull \hbox (badness 10000) detected at line 2283 [][][] Underfull \hbox (badness 10000) detected at line 2286 [][][] [312] Underfull \hbox (badness 10000) detected at line 2314 [][][] Underfull \hbox (badness 10000) detected at line 2317 [][][] Underfull \hbox (badness 10000) detected at line 2320 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 2330--2330 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [313] Underfull \hbox (badness 10000) detected at line 2367 [][][] Underfull \hbox (badness 10000) detected at line 2370 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2379--2379 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 2414 [][][] Underfull \hbox (badness 10000) detected at line 2417 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.477 on input line 2488. [314] [315] Underfull \hbox (badness 10000) detected at line 2503 [][][] Underfull \hbox (badness 10000) detected at line 2506 [][][] Underfull \hbox (badness 10000) detected at line 2509 [][][] [316] Underfull \hbox (badness 10000) detected at line 2557 [][][] Underfull \hbox (badness 10000) detected at line 2560 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2569--2569 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [317] Underfull \hbox (badness 10000) detected at line 2604 [][][] Underfull \hbox (badness 10000) detected at line 2607 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.478 on input line 2682. [318] Underfull \hbox (badness 10000) detected at line 2697 [][][] Underfull \hbox (badness 10000) detected at line 2700 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.479 on input line 2731. [319] Underfull \hbox (badness 10000) detected at line 2746 [][][] Underfull \hbox (badness 10000) detected at line 2749 [][][] Underfull \hbox (badness 10000) detected at line 2752 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 2762--2762 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [320] Underfull \hbox (badness 10000) detected at line 2799 [][][] Underfull \hbox (badness 10000) detected at line 2802 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2811--2811 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 2846 [][][] Underfull \hbox (badness 10000) detected at line 2849 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.480 on input line 2890. [321] Underfull \hbox (badness 10000) detected at line 2905 [][][] Underfull \hbox (badness 10000) detected at line 2908 [][][] Overfull \vbox (18.98318pt too high) has occurred while \output is active [322] Underfull \hbox (badness 10000) detected at line 2946 [][][] Underfull \hbox (badness 10000) detected at line 2957 [][][] [323] Underfull \hbox (badness 10000) detected at line 2960 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.482 on input line 3031. [324] Underfull \hbox (badness 10000) detected at line 3046 [][][] Underfull \hbox (badness 10000) detected at line 3049 [][][] Underfull \hbox (badness 10000) detected at line 3052 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3062--3062 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 3099 [][][] Underfull \hbox (badness 10000) detected at line 3102 [][][] [325] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 3111--3111 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 3146 [][][] Underfull \hbox (badness 10000) detected at line 3149 [][][] [326] Underfull \hbox (badness 10000) detected at line 3187 [][][] Underfull \hbox (badness 10000) detected at line 3190 [][][] Underfull \hbox (badness 10000) detected at line 3193 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3203--3203 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [327] Underfull \hbox (badness 10000) detected at line 3240 [][][] Underfull \hbox (badness 10000) detected at line 3243 [][][] Underfull \hbox (badness 10000) detected at line 3246 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 3255--3255 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [328] Underfull \hbox (badness 10000) detected at line 3288 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.484 on input line 3327. [329] Underfull \hbox (badness 10000) detected at line 3342 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.485 on input line 3418. [330] [331] Underfull \hbox (badness 10000) detected at line 3484 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.486 on input line 3527. [332] Underfull \hbox (badness 10000) detected at line 3542 [][][] Underfull \hbox (badness 10000) detected at line 3545 [][][] [333] Underfull \hbox (badness 10000) detected at line 3585 [][][] Underfull \hbox (badness 10000) detected at line 3588 [][][] Underfull \hbox (badness 10000) detected at line 3591 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3601--3601 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [334] Underfull \hbox (badness 10000) detected at line 3638 [][][] Underfull \hbox (badness 10000) detected at line 3641 [][][] Underfull \hbox (badness 10000) detected at line 3644 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 3653--3653 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [335] Underfull \hbox (badness 10000) detected at line 3702 [][][] Underfull \hbox (badness 10000) detected at line 3705 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.488 on input line 3774. [336] [337] Underfull \hbox (badness 10000) detected at line 3789 [][][] Underfull \hbox (badness 10000) detected at line 3792 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.489 on input line 3875. [338] Underfull \hbox (badness 10000) detected at line 3890 [][][] Underfull \hbox (badness 10000) detected at line 3893 [][][] Underfull \hbox (badness 10000) detected at line 3896 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3906--3906 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [339] Underfull \hbox (badness 10000) detected at line 3943 [][][] Underfull \hbox (badness 10000) detected at line 3946 [][][] Underfull \hbox (badness 10000) detected at line 3972 [][][] Underfull \hbox (badness 10000) detected at line 3975 [][][] [340] Underfull \hbox (badness 10000) detected at line 4001 [][][] Underfull \hbox (badness 10000) detected at line 4004 [][][] [341] Underfull \hbox (badness 10000) detected at line 4034 [][][] Underfull \hbox (badness 10000) detected at line 4037 [][][] Underfull \hbox (badness 10000) detected at line 4040 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 4050--4050 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 4087 [][][] [342] Underfull \hbox (badness 10000) detected at line 4090 [][][] Underfull \hbox (badness 10000) detected at line 4093 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 4102--4102 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 4137 [][][] Underfull \hbox (badness 10000) detected at line 4140 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.493 on input line 4179. [343] Underfull \hbox (badness 10000) detected at line 4194 [][][] [344] Underfull \hbox (badness 10000) detected at line 4216 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.494 on input line 4275. Overfull \vbox (38.14133pt too high) has occurred while \output is active [345] Underfull \hbox (badness 10000) detected at line 4290 [][][] Underfull \hbox (badness 10000) detected at line 4293 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.495 on input line 4368. [346] [347] Underfull \hbox (badness 10000) detected at line 4383 [][][] Underfull \hbox (badness 10000) detected at line 4386 [][][] Underfull \hbox (badness 10000) detected at line 4426 [][][] Underfull \hbox (badness 10000) detected at line 4429 [][][] [348] Underfull \hbox (badness 10000) detected at line 4471 [][][] Underfull \hbox (badness 10000) detected at line 4474 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.498 on input line 4517. [349] Underfull \hbox (badness 10000) detected at line 4532 [][][] Underfull \hbox (badness 10000) detected at line 4535 [][][] Underfull \hbox (badness 10000) detected at line 4538 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 4548--4548 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [350] Underfull \hbox (badness 10000) detected at line 4585 [][][] Underfull \hbox (badness 10000) detected at line 4588 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 4597--4597 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [351] Underfull \hbox (badness 10000) detected at line 4630 [][][] Underfull \hbox (badness 10000) detected at line 4633 [][][] Underfull \hbox (badness 10000) detected at line 4636 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.499 on input line 4681. [352] Underfull \hbox (badness 10000) detected at line 4692 [][][] Underfull \hbox (badness 10000) detected at line 4695 [][][] Underfull \hbox (badness 10000) detected at line 4727 [][][] Underfull \hbox (badness 10000) detected at line 4730 [][][] [353] Underfull \hbox (badness 10000) detected at line 4768 [][][] Underfull \hbox (badness 10000) detected at line 4771 [][][] Underfull \hbox (badness 10000) detected at line 4774 [][][] Overfull \hbox (20.88268pt too wide) in paragraph at lines 4784--4784 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute,[] [354] Underfull \hbox (badness 10000) detected at line 4822 [][][] Underfull \hbox (badness 10000) detected at line 4825 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 4834--4834 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [355] Underfull \hbox (badness 10000) detected at line 4869 [][][] Underfull \hbox (badness 10000) detected at line 4872 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.502 on input line 4915. [356] Underfull \hbox (badness 10000) detected at line 4930 [][][] Underfull \hbox (badness 10000) detected at line 4933 [][][] Underfull \hbox (badness 10000) detected at line 4965 [][][] Underfull \hbox (badness 10000) detected at line 4968 [][][] Underfull \hbox (badness 10000) detected at line 4971 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 4981--4981 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [357] Underfull \hbox (badness 10000) detected at line 5018 [][][] Underfull \hbox (badness 10000) detected at line 5021 [][][] Underfull \hbox (badness 10000) detected at line 5024 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 5033--5033 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [358] Underfull \hbox (badness 10000) detected at line 5068 [][][] Underfull \hbox (badness 10000) detected at line 5071 [][][] Underfull \hbox (badness 10000) detected at line 5101 [][][] Underfull \hbox (badness 10000) detected at line 5104 [][][] Underfull \hbox (badness 10000) detected at line 5107 [][][] [359] Underfull \hbox (badness 10000) detected at line 5137 [][][] Underfull \hbox (badness 10000) detected at line 5140 [][][] Underfull \hbox (badness 10000) detected at line 5170 [][][] [360] Underfull \hbox (badness 10000) detected at line 5173 [][][] Underfull \hbox (badness 10000) detected at line 5203 [][][] Underfull \hbox (badness 10000) detected at line 5206 [][][] Underfull \hbox (badness 10000) detected at line 5234 [][][] [361] Underfull \hbox (badness 10000) detected at line 5237 [][][] Underfull \hbox (badness 10000) detected at line 5265 [][][] Underfull \hbox (badness 10000) detected at line 5268 [][][] ) (./group___frontend.tex [362] Underfull \hbox (badness 2495) in paragraph at lines 32--33 []\T1/phv/m/n/10 VPUBLIC Vrc[]_[][]Codes [] (int icalc, [] $\OMS/cmsy/m/n/10 ^^ C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 feparm, [] $\OMS /cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbeparm, [] Overfull \hbox (16.65858pt too wide) in paragraph at lines 40--41 []\T1/phv/m/n/10 VEXTERNC int [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], Overfull \hbox (16.91972pt too wide) in paragraph at lines 42--43 []\T1/phv/m/n/10 VEXTERNC void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh , [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/1 0 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], Underfull \hbox (badness 1910) in paragraph at lines 60--61 [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1 /phv/m/n/10 alist[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][] [], [] Underfull \hbox (badness 1237) in paragraph at lines 60--61 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 charge[]Map[][][], [] $\OMS/cmsy/m/n/10 ^^C $\T1/phv/m/n/10 pmgp[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pmg[][][], [] [363] Underfull \hbox (badness 5817) in paragraph at lines 78--79 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], Underfull \hbox (badness 5817) in paragraph at lines 80--81 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], [364] [365] Underfull \hbox (badness 10000) detected at line 178 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 211 [][][] [366] Underfull \hbox (badness 10000) detected at line 235 [][][] [367] Underfull \hbox (badness 10000) detected at line 275 [][][] Underfull \hbox (badness 10000) detected at line 297 [][][] Underfull \hbox (badness 10000) detected at line 314 [][][] Underfull \hbox (badness 10000) detected at line 317 [][][] [368] Underfull \hbox (badness 10000) detected at line 351 [][][] Underfull \hbox (badness 10000) detected at line 373 [][][] Underfull \hbox (badness 10000) detected at line 390 [][][] Underfull \hbox (badness 10000) detected at line 393 [][][] [369] [370] Underfull \hbox (badness 10000) detected at line 495 [][][] Underfull \hbox (badness 10000) detected at line 502 [][][] [371] Underfull \hbox (badness 10000) detected at line 572 [][][] Underfull \hbox (badness 10000) detected at line 575 [][][] [372] Underfull \hbox (badness 10000) detected at line 625 [][][] Underfull \hbox (badness 10000) detected at line 649 [][][] Underfull \hbox (badness 10000) detected at line 677 [][][] [373] Underfull \hbox (badness 10000) detected at line 694 [][][] Underfull \hbox (badness 10000) detected at line 720 [][][] Underfull \hbox (badness 10000) detected at line 748 [][][] [374] Underfull \hbox (badness 10000) detected at line 772 [][][] Underfull \hbox (badness 10000) detected at line 792 [][][] Underfull \hbox (badness 10000) detected at line 818 [][][] [375] Underfull \hbox (badness 10000) detected at line 842 [][][] Underfull \hbox (badness 10000) detected at line 866 [][][] Underfull \hbox (badness 10000) detected at line 876 [][][] Underfull \hbox (badness 10000) detected at line 895 [][][] [376] Underfull \hbox (badness 10000) detected at line 909 [][][] Underfull \hbox (badness 10000) detected at line 912 [][][] Underfull \hbox (badness 10000) detected at line 929 [][][] Underfull \hbox (badness 10000) detected at line 939 [][][] Underfull \hbox (badness 10000) detected at line 958 [][][] Underfull \hbox (badness 10000) detected at line 961 [][][] [377] Underfull \hbox (badness 10000) detected at line 981 [][][] Underfull \hbox (badness 10000) detected at line 984 [][][] Underfull \hbox (badness 10000) detected at line 1010 [][][] Underfull \hbox (badness 10000) detected at line 1013 [][][] [378] Underfull \hbox (badness 10000) detected at line 1035 [][][] Underfull \hbox (badness 10000) detected at line 1045 [][][] Underfull \hbox (badness 10000) detected at line 1064 [][][] Underfull \hbox (badness 10000) detected at line 1067 [][][] Underfull \hbox (badness 10000) detected at line 1091 [][][] [379] Underfull \hbox (badness 10000) detected at line 1105 [][][] Underfull \hbox (badness 10000) detected at line 1122 [][][] Underfull \hbox (badness 10000) detected at line 1134 [][][] Underfull \hbox (badness 10000) in paragraph at lines 1135--1136 Underfull \hbox (badness 10000) detected at line 1138 [][][] [380] Underfull \hbox (badness 10000) detected at line 1166 [][][] Underfull \hbox (badness 10000) detected at line 1180 [][][] Underfull \hbox (badness 10000) detected at line 1201 [][][] Underfull \hbox (badness 10000) detected at line 1204 [][][] [381] Underfull \hbox (badness 10000) detected at line 1228 [][][] Underfull \hbox (badness 10000) detected at line 1231 [][][] Underfull \hbox (badness 10000) detected at line 1259 [][][] Underfull \hbox (badness 10000) detected at line 1262 [][][] [382] Underfull \hbox (badness 10000) detected at line 1288 [][][] Underfull \hbox (badness 10000) detected at line 1291 [][][] Underfull \hbox (badness 10000) detected at line 1319 [][][] Underfull \hbox (badness 10000) detected at line 1322 [][][] [383] Underfull \hbox (badness 10000) detected at line 1348 [][][] Underfull \hbox (badness 10000) detected at line 1377 [][][] Underfull \hbox (badness 10000) detected at line 1380 [][][] Underfull \hbox (badness 10000) detected at line 1408 [][][] [384] Underfull \hbox (badness 10000) detected at line 1432 [][][] Underfull \hbox (badness 10000) detected at line 1454 [][][] Underfull \hbox (badness 10000) detected at line 1468 [][][] [385] Underfull \hbox (badness 10000) detected at line 1485 [][][] Underfull \hbox (badness 10000) detected at line 1497 [][][] Underfull \hbox (badness 10000) detected at line 1514 [][][] Underfull \hbox (badness 10000) detected at line 1528 [][][] [386] Underfull \hbox (badness 10000) detected at line 1562 [][][] Underfull \hbox (badness 10000) detected at line 1574 [][][] Underfull \hbox (badness 10000) detected at line 1591 [][][] Underfull \hbox (badness 10000) detected at line 1608 [][][] [387] Underfull \hbox (badness 10000) detected at line 1636 [][][] Underfull \hbox (badness 10000) detected at line 1650 [][][] [388] Underfull \hbox (badness 10000) detected at line 1688 [][][] Underfull \hbox (badness 10000) detected at line 1716 [][][] Underfull \hbox (badness 10000) detected at line 1733 [][][] [389] Underfull \hbox (badness 10000) detected at line 1747 [][][] Underfull \hbox (badness 10000) detected at line 1764 [][][] Underfull \hbox (badness 10000) detected at line 1792 [][][] [390] Underfull \hbox (badness 10000) detected at line 1809 [][][] Underfull \hbox (badness 10000) detected at line 1823 [][][] ) [391] [392] Chapter 8. (./struct_atom_force.tex Underfull \hbox (badness 10000) detected at line 32 [][][] [393]) (./structs_a_p_o_lparm.tex [394] Underfull \hbox (badness 10000) detected at line 88 [][][] [395] Underfull \hbox (badness 10000) detected at line 224 [][][] [396] Underfull \hbox (badness 10000) detected at line 237 [][][] Underfull \hbox (badness 10000) detected at line 250 [][][] Underfull \hbox (badness 10000) detected at line 263 [][][] Underfull \hbox (badness 10000) detected at line 276 [][][] Underfull \hbox (badness 10000) detected at line 289 [][][] Underfull \hbox (badness 10000) detected at line 302 [][][] [397] Underfull \hbox (badness 10000) detected at line 315 [][][] Underfull \hbox (badness 10000) detected at line 328 [][][] Underfull \hbox (badness 10000) detected at line 341 [][][] Underfull \hbox (badness 10000) detected at line 354 [][][] Underfull \hbox (badness 10000) detected at line 367 [][][] Underfull \hbox (badness 10000) detected at line 380 [][][] [398]) (./structs_b_e_mparm.tex [399] Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 53 [][][] [400] Underfull \hbox (badness 10000) detected at line 129 [][][] Underfull \hbox (badness 10000) detected at line 142 [][][] Underfull \hbox (badness 10000) detected at line 155 [][][] [401] Underfull \hbox (badness 10000) detected at line 168 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 194 [][][] ) (./structs_f_e_mparm.tex [402] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) in paragraph at lines 84--85 [403] [404] [405]) (./structs_g_e_o_f_l_o_wparm.tex Underfull \hbox (badness 10000) detected at line 30 [][][] Underfull \hbox (badness 10000) detected at line 33 [][][] [406]) (./structs_m_gparm.tex [407] Underfull \hbox (badness 10000) detected at line 120 [][][] Underfull \hbox (badness 10000) detected at line 123 [][][] [408] Underfull \hbox (badness 10000) in paragraph at lines 149--150 Underfull \hbox (badness 10000) in paragraph at lines 180--181 [409] Underfull \hbox (badness 10000) in paragraph at lines 261--262 [410] [411] Underfull \hbox (badness 10000) detected at line 434 [][][] Underfull \hbox (badness 10000) detected at line 447 [][][] Underfull \hbox (badness 10000) detected at line 460 [][][] Underfull \hbox (badness 10000) detected at line 473 [][][] [412] Underfull \hbox (badness 10000) detected at line 486 [][][] Underfull \hbox (badness 10000) detected at line 499 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] Underfull \hbox (badness 10000) detected at line 538 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] [413] Underfull \hbox (badness 10000) detected at line 564 [][][] Underfull \hbox (badness 10000) detected at line 577 [][][] Underfull \hbox (badness 10000) detected at line 590 [][][] Underfull \hbox (badness 10000) detected at line 603 [][][] Underfull \hbox (badness 10000) detected at line 616 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] [414] Underfull \hbox (badness 10000) detected at line 642 [][][] Underfull \hbox (badness 10000) detected at line 655 [][][] Underfull \hbox (badness 10000) detected at line 668 [][][] ) (./structs_n_osh.tex [415] Underfull \hbox (badness 10000) detected at line 108 [][][] [416] [417] [418] [419] [420]) (./structs_n_osh__calc.tex [421] Underfull \hbox (badness 10000) detected at line 38 [][][] [422]) (./structs_p_b_a_mparm.tex [423] Underfull \hbox (badness 10000) detected at line 106 [][][] Underfull \hbox (badness 10000) detected at line 109 [][][] [424] [425] [426] [427]) (./structs_p_b_eparm.tex [428] [429] Underfull \hbox (badness 10000) detected at line 142 [][][] Underfull \hbox (badness 10000) detected at line 145 [][][] [430] [431] [432] Underfull \hbox (badness 10000) detected at line 391 [][][] Underfull \hbox (badness 10000) detected at line 404 [][][] Underfull \hbox (badness 10000) detected at line 417 [][][] Underfull \hbox (badness 10000) detected at line 430 [][][] [433] Underfull \hbox (badness 10000) detected at line 473 [][][] Underfull \hbox (badness 10000) detected at line 486 [][][] Underfull \hbox (badness 10000) detected at line 499 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] [434] Underfull \hbox (badness 10000) detected at line 538 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] Underfull \hbox (badness 10000) detected at line 564 [][][] Underfull \hbox (badness 10000) detected at line 577 [][][] Underfull \hbox (badness 10000) detected at line 590 [][][] Underfull \hbox (badness 10000) detected at line 603 [][][] [435] Underfull \hbox (badness 10000) detected at line 616 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] [436] [437]) (./structs_p_b_s_a_mparm.tex [438] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] [439]) (./structs_vacc.tex [440] Underfull \hbox (badness 10000) detected at line 36 [][][] [441]) (./structs_vacc_surf.tex Underfull \hbox (badness 10000) detected at line 36 [][][] [442]) (./structs_valist.tex [443] Underfull \hbox (badness 10000) detected at line 36 [][][] [444]) (./structs_vatom.tex Underfull \hbox (badness 10000) detected at line 36 [][][] Underfull \hbox (badness 10000) in paragraph at lines 62--63 [445] Underfull \hbox (badness 10000) in paragraph at lines 93--94 Underfull \hbox (badness 10000) in paragraph at lines 114--115 ) (./structs_vclist.tex [446] Underfull \hbox (badness 10000) detected at line 40 [][][] [447]) (./structs_vclist_cell.tex Underfull \hbox (badness 10000) detected at line 24 [][][] ) (./structs_vcsm.tex [448] Underfull \hbox (badness 10000) detected at line 42 [][][] [449]) (./structs_vfetk.tex [450] Underfull \hbox (badness 10000) detected at line 60 [][][] [451] Underfull \hbox (badness 10000) in paragraph at lines 116--117 [452]) (./structs_vfetk___local_var.tex [453] Underfull \hbox (badness 10000) detected at line 86 [][][] [454] [455] [456] [457]) (./structs_vgreen.tex Underfull \hbox (badness 10000) detected at line 34 [][][] [458]) (./structs_vgrid.tex [459] Underfull \hbox (badness 10000) detected at line 52 [][][] [460] [461]) (./structs_vmgrid.tex Underfull \hbox (badness 10000) detected at line 24 [][][] ) (./structs_vopot.tex [462] Underfull \hbox (badness 10000) detected at line 26 [][][] ) (./structs_vparam___atom_data.tex [463] Underfull \hbox (badness 10000) detected at line 30 [][][] Underfull \hbox (badness 10000) detected at line 33 [][][] ) (./structs_vpbe.tex [464] Underfull \hbox (badness 10000) detected at line 86 [][][] [465] [466] [467] [468]) (./structs_vpee.tex [469] Underfull \hbox (badness 10000) detected at line 34 [][][] ) (./structs_vpmg.tex [470] [471] Underfull \hbox (badness 10000) detected at line 116 [][][] [472] [473] [474] [475] [476]) (./structs_vpmgp.tex [477] Underfull \hbox (badness 10000) detected at line 126 [][][] [478] Underfull \hbox (badness 10000) in paragraph at lines 164--165 Underfull \hbox (badness 10000) in paragraph at lines 175--176 Underfull \hbox (badness 10000) in paragraph at lines 186--187 [479] Underfull \hbox (badness 10000) in paragraph at lines 234--235 [480] [481] [482] [483] Underfull \hbox (badness 10000) in paragraph at lines 506--507 Underfull \hbox (badness 10000) in paragraph at lines 527--528 [484] Underfull \hbox (badness 10000) in paragraph at lines 548--549 Underfull \hbox (badness 10000) in paragraph at lines 589--590 [485] Underfull \hbox (badness 10000) in paragraph at lines 630--631 Underfull \hbox (badness 10000) in paragraph at lines 671--672 ) (./struct_vparam.tex [486] Underfull \hbox (badness 10000) detected at line 26 [][][] ) (./struct_vparam___res_data.tex [487] Underfull \hbox (badness 10000) detected at line 28 [][][] ) [488] Chapter 9. (./mainpage_8h_source.tex) (./apbs_8h.tex <./apbs_8h__incl.pdf> <./apbs_8h__dep __incl.pdf> [489] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] Underfull \hbox (badness 10000) detected at line 58 [][][] [490]) (./apbs_8h_source.tex) (./vcsm_8c.tex [491] <./vcsm_8c__incl.pdf> [492] Underfull \hbox (badness 10000) detected at line 53 [][][] Underfull \hbox (badness 10000) detected at line 56 [][][] Underfull \hbox (badness 10000) detected at line 59 [][][] [493]) (./vcsm_8c_source.tex [494] [495] [496] [497] [498] [499]) (./vcsm_8h.tex <./vcsm_8h__incl.pdf> <./vcsm_8h__dep__incl.pdf> [500] [501] Underfull \hbox (badness 10000) detected at line 77 [][][] Underfull \hbox (badness 10000) detected at line 80 [][][] Underfull \hbox (badness 10000) detected at line 83 [][][] [502]) (./vcsm_8h_source.tex [503]) (./vfetk_8c.tex [504] <./vfetk_8c__incl.pdf > [505] [506] Underfull \hbox (badness 10000) detected at line 163 [][][] Underfull \hbox (badness 10000) detected at line 166 [][][] [507] Underfull \hbox (badness 10000) detected at line 169 [][][] [508] [509] [510] [511]) (./vfetk_8c_source.tex [512] [513] [514] [515] [516] [517] [518] [519] [520] [521] [522] [523] [524] [525] [526] [527] [528] [529] [530] [531] [532] [533] [534] [535] [536] [537] [538] [539] [540] [541]) (./vfetk_8h.tex [542] <./vfetk_8h__incl.pdf> <./vfetk_8h__dep__inc l.pdf> [543] [544] [545] Underfull \hbox (badness 10000) detected at line 189 [][][] [546] Underfull \hbox (badness 10000) detected at line 192 [][][] Underfull \hbox (badness 10000) detected at line 195 [][][] ) (./vfetk_8h_source.tex [547] [548] [549] [550] [551] [552]) (./vpee_8c.tex <. /vpee_8c__incl.pdf> [553] Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 53 [][][] Underfull \hbox (badness 10000) detected at line 56 [][][] [554]) (./vpee_8c_source.tex [555] [556] [557] [558] [559] [560]) (./vpee_8h.tex [561] <./vpee_8h__incl.pdf> <./vpee_8h__dep__incl.pdf> [562] Underfull \hbox (badness 10000) detected at line 57 [][][] Underfull \hbox (badness 10000) detected at line 60 [][][] Underfull \hbox (badness 10000) detected at line 63 [][][] [563]) (./vpee_8h_source.tex [564]) (./apolparm_8c.tex <./apolparm_8c__incl.pdf > [565] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) detected at line 71 [][][] [566] [567]) (./apolparm_8c_source.tex [568] [569] [570] [571] [572] [573] [574] [575]) (./apolparm_8h_source.tex [576]) (./bemparm_8c.tex <./bemparm_8c__ incl.pdf> [577] [578] Underfull \hbox (badness 10000) detected at line 49 [][][] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] [579] Underfull \hbox (badness 10000) detected at line 121 [][][] ) (./bemparm_8c_source.tex [580] [581] [582] [583]) (./bemparm_8h_source.tex [584]) (./femparm_8c.tex <./femparm_8c__incl.pdf> [585] [586] Underfull \hbox (badness 10000) detected at line 59 [][][] Underfull \hbox (badness 10000) detected at line 62 [][][] Underfull \hbox (badness 10000) detected at line 65 [][][] [587] [588]) (./femparm_8c_source.tex [589] [590] [591] [592] [593]) (./femparm_8h.tex <./femparm_8h__incl.pdf> [594] <./femparm_8h__dep__incl.pdf> [595] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 92 [][][] Underfull \hbox (badness 10000) detected at line 95 [][][] [596]) (./femparm_8h_source.tex [597]) (./geoflowparm_8c.tex [598] <./geoflowpa rm_8c__incl.pdf> [599] Underfull \hbox (badness 10000) detected at line 47 [][][] Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 53 [][][] [600]) (./geoflowparm_8c_source.tex [601] [602]) (./geoflowparm_8h.tex [603] <. /geoflowparm_8h__incl.pdf> <./geoflowparm_8h__dep__incl.pdf> [604] [605] Underfull \hbox (badness 10000) detected at line 71 [][][] Underfull \hbox (badness 10000) detected at line 74 [][][] Underfull \hbox (badness 10000) detected at line 77 [][][] [606]) (./geoflowparm_8h_source.tex [607]) (./mgparm_8c.tex <./mgparm_8c__incl. pdf> [608] [609] Underfull \hbox (badness 10000) detected at line 95 [][][] Underfull \hbox (badness 10000) detected at line 98 [][][] Underfull \hbox (badness 10000) detected at line 101 [][][] [610] [611]) (./mgparm_8c_source.tex [612] [613] [614] [615] [616] [617] [618] [619] [620] [621] [622] [623]) (./mgparm_8h.tex <./mgparm_8h__incl.pdf> [624] <./mgparm_8h__dep__incl.pdf> [625] [626] Underfull \hbox (badness 10000) detected at line 104 [][][] Underfull \hbox (badness 10000) detected at line 107 [][][] Underfull \hbox (badness 10000) detected at line 110 [][][] [627]) (./mgparm_8h_source.tex [628]) (./nosh_8c.tex <./nosh_8c__incl.pdf> [629] [630] [631] Underfull \hbox (badness 10000) detected at line 151 [][][] Underfull \hbox (badness 10000) detected at line 154 [][][] Underfull \hbox (badness 10000) detected at line 157 [][][] [632] [633] [634] [635] [636]) (./nosh_8c_source.tex [637] [638] [639] [640] [641] [642] [643] [644] [645] [646] [647] [648] [649] [650] [651] [652] [653] [654] [655] [656] [657] [658] [659] [660] [661] [662] [663] [664] [665] [666] [667] [668] [669] [670] [671] [672] [673] [674] [675] [676]) (./nosh_8h.tex <./nosh_8h__incl.pdf> [677] <./nosh_8h__dep__incl.pdf> [678] [679] [680] Underfull \hbox (badness 10000) detected at line 171 [][][] Underfull \hbox (badness 10000) detected at line 174 [][][] Underfull \hbox (badness 10000) detected at line 177 [][][] ) (./nosh_8h_source.tex [681] [682] [683]) (./pbamparm_8c.tex <./pbamparm_8c__i ncl.pdf> [684] [685] Underfull \hbox (badness 10000) detected at line 69 [][][] Underfull \hbox (badness 10000) detected at line 72 [][][] Underfull \hbox (badness 10000) detected at line 75 [][][] [686]) (./pbamparm_8c_source.tex [687] [688] [689] [690] [691] [692] [693] [694] [695]) (./pbamparm_8h.tex <./pbamparm_8h__incl.pdf> <./pbamparm_8h__dep__ incl.pdf> [696] [697] Underfull \hbox (badness 10000) detected at line 102 [][][] [698] Underfull \hbox (badness 10000) detected at line 105 [][][] Underfull \hbox (badness 10000) detected at line 108 [][][] [699]) (./pbamparm_8h_source.tex [700]) (./pbeparm_8c.tex [701] <./pbeparm_8c__ incl.pdf> [702] Underfull \hbox (badness 10000) detected at line 101 [][][] Underfull \hbox (badness 10000) detected at line 104 [][][] Underfull \hbox (badness 10000) detected at line 107 [][][] [703] [704] [705] [706] [707]) (./pbeparm_8c_source.tex [708] [709] [710] [711] [712] [713] [714] [715] [716] [717] [718] [719] [720] [721] [722]) (./pbeparm_8h.tex <./pbeparm_8h__incl.pdf> [723] <./pbeparm_8h__dep__incl.pdf> [724] Underfull \hbox (badness 10000) detected at line 88 [][][] Underfull \hbox (badness 10000) detected at line 91 [][][] Underfull \hbox (badness 10000) detected at line 94 [][][] [725]) (./pbeparm_8h_source.tex [726] [727]) (./pbsamparm_8c.tex <./pbsamparm_8 c__incl.pdf> [728] [729] Underfull \hbox (badness 10000) detected at line 49 [][][] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] [730]) (./pbsamparm_8c_source.tex [731] [732]) (./pbsamparm_8h.tex [733] <./pbs amparm_8h__incl.pdf> <./pbsamparm_8h__dep__incl.pdf> [734] [735] Underfull \hbox (badness 10000) detected at line 86 [][][] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 92 [][][] [736]) (./pbsamparm_8h_source.tex [737]) (./vacc_8c.tex <./vacc_8c__incl.pdf> [738] [739] [740] Underfull \hbox (badness 10000) detected at line 107 [][][] Underfull \hbox (badness 10000) detected at line 110 [][][] Underfull \hbox (badness 10000) detected at line 113 [][][] [741] Underfull \hbox (badness 10000) detected at line 179 [][][] Underfull \hbox (badness 10000) detected at line 182 [][][] Underfull \hbox (badness 10000) detected at line 208 [][][] Underfull \hbox (badness 10000) detected at line 211 [][][] [742] [743]) (./vacc_8c_source.tex [744] [745] [746] [747] [748] [749] [750] [751] [752] [753] [754] [755] [756] [757] [758] [759] [760] [761] [762] [763] [764] [765] [766]) (./vacc_8h.tex <./vacc_8h__incl.pdf> <./vacc_8h__dep__ incl.pdf> [767] [768] [769] Underfull \hbox (badness 10000) detected at line 123 [][][] Underfull \hbox (badness 10000) detected at line 126 [][][] Underfull \hbox (badness 10000) detected at line 129 [][][] [770]) (./vacc_8h_source.tex [771] [772] [773]) (./valist_8c.tex <./valist_8c__ incl.pdf> [774] [775] Underfull \hbox (badness 2293) in paragraph at lines 54--56 []\T1/phv/m/n/10 VPRIVATE Vrc[]_[][]Codes [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/ m/n/10 thee, Vio $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 sock, int $\OMS/cmsy/m/n/ 10 ^^C$\T1/phv/m/n/10 serial, char atom[] Underfull \hbox (badness 10000) detected at line 82 [][][] Underfull \hbox (badness 10000) detected at line 85 [][][] Underfull \hbox (badness 10000) detected at line 88 [][][] [776] [777] [778]) (./valist_8c_source.tex [779] [780] [781] [782] [783] [784] [785] [786] [787] [788]) (./valist_8h.tex [789] <./valist_8h__incl.pdf> < ./valist_8h__dep__incl.pdf> [790] Underfull \hbox (badness 10000) detected at line 77 [][][] Underfull \hbox (badness 10000) detected at line 80 [][][] Underfull \hbox (badness 10000) detected at line 83 [][][] [791]) (./valist_8h_source.tex [792] [793]) (./vatom_8c.tex <./vatom_8c__incl.p df> [794] Underfull \hbox (badness 10000) detected at line 71 [][][] Underfull \hbox (badness 10000) detected at line 74 [][][] Underfull \hbox (badness 10000) detected at line 77 [][][] [795]) (./vatom_8c_source.tex [796] [797] [798]) (./vatom_8h.tex <./vatom_8h__i ncl.pdf> [799] <./vatom_8h__dep__incl.pdf> [800] [801] Underfull \hbox (badness 10000) detected at line 96 [][][] Underfull \hbox (badness 10000) detected at line 99 [][][] Underfull \hbox (badness 10000) detected at line 102 [][][] ) (./vatom_8h_source.tex [802] [803]) (./vcap_8c.tex <./vcap_8c__incl.pdf> [804] Underfull \hbox (badness 10000) detected at line 31 [][][] Underfull \hbox (badness 10000) detected at line 34 [][][] Underfull \hbox (badness 10000) detected at line 37 [][][] [805]) (./vcap_8c_source.tex [806]) (./vcap_8h.tex <./vcap_8h__incl.pdf> <./vca p_8h__dep__incl.pdf> [807] Underfull \hbox (badness 10000) detected at line 47 [][][] Underfull \hbox (badness 10000) detected at line 50 [][][] [808] Underfull \hbox (badness 10000) detected at line 53 [][][] ) (./vcap_8h_source.tex [809]) (./vclist_8c.tex <./vclist_8c__incl.pdf> Underfull \hbox (badness 4060) in paragraph at lines 32--34 []\T1/phv/m/n/10 VPRIVATE void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 thee , dou-ble lower[]_[]corner[][][], dou-ble upper[]_[] [810] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) detected at line 71 [][][] [811] [812]) (./vclist_8c_source.tex [813] [814] [815] [816] [817]) (./vclist_8h.tex [818] <./vclist_8h__incl.pdf> <./vclist_8h__dep__incl.pdf> [819] [820] Underfull \hbox (badness 10000) detected at line 84 [][][] Underfull \hbox (badness 10000) detected at line 87 [][][] Underfull \hbox (badness 10000) detected at line 90 [][][] [821]) (./vclist_8h_source.tex [822]) (./vgreen_8c.tex [823] <./vgreen_8c__incl .pdf> [824] Underfull \hbox (badness 10000) detected at line 55 [][][] Underfull \hbox (badness 10000) detected at line 58 [][][] Underfull \hbox (badness 10000) detected at line 61 [][][] [825]) (./vgreen_8c_source.tex [826] [827] [828] [829] [830] [831]) (./vgreen_8h.tex <./vgreen_8h__incl.pdf> [832] <./vgreen_8h__dep__incl.pdf> [833] Underfull \hbox (badness 10000) detected at line 72 [][][] Underfull \hbox (badness 10000) detected at line 75 [][][] ) (./vgreen_8h_source.tex [834]) (./vhal_8h.tex [835] <./vhal_8h__incl.pdf> <./ vhal_8h__dep__incl.pdf> [836] [837] [838] [839] Underfull \hbox (badness 10000) detected at line 303 [][][] Underfull \hbox (badness 10000) detected at line 306 [][][] Underfull \hbox (badness 10000) detected at line 309 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 318--318 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [840] [841] [842] [843] [844] [845] [846]) (./vhal_8h_source.tex [847] [848] [849] [850] [851] [852] [853] [854]) (./vmatrix_8h.tex [855] <./vmatrix_8h__dep __incl.pdf> Underfull \hbox (badness 10000) detected at line 36 [][][] Underfull \hbox (badness 10000) detected at line 39 [][][] Underfull \hbox (badness 10000) detected at line 42 [][][] [856] [857]) (./vmatrix_8h_source.tex [858]) (./vparam_8c.tex <./vparam_8c__inc l.pdf> [859] Underfull \hbox (badness 10000) detected at line 78 [][][] Underfull \hbox (badness 10000) detected at line 81 [][][] [860] Underfull \hbox (badness 10000) detected at line 84 [][][] ) (./vparam_8c_source.tex [861] [862] [863] [864] [865] [866] [867] [868]) (./vparam_8h.tex [869] <./vparam_8h__incl.pdf> <./vparam_8h__dep__incl.pdf> [870] [871] Underfull \hbox (badness 10000) detected at line 96 [][][] Underfull \hbox (badness 10000) detected at line 99 [][][] Underfull \hbox (badness 10000) detected at line 102 [][][] [872]) (./vparam_8h_source.tex [873]) (./vpbe_8c.tex <./vpbe_8c__incl.pdf> [874] [875] Underfull \hbox (badness 10000) detected at line 90 [][][] Underfull \hbox (badness 10000) detected at line 93 [][][] [876] Underfull \hbox (badness 10000) detected at line 96 [][][] ) (./vpbe_8c_source.tex [877] [878] [879] [880] [881] [882] [883]) (./vpbe_8h.tex <./vpbe_8h__incl.pdf> <./vpbe_8h__dep__incl.pdf> [884] [885] Underfull \hbox (badness 10000) detected at line 111 [][][] Underfull \hbox (badness 10000) detected at line 114 [][][] Underfull \hbox (badness 10000) detected at line 117 [][][] [886]) (./vpbe_8h_source.tex [887] [888] [889]) (./vstring_8c.tex <./vstring_8c __incl.pdf> [890] Underfull \hbox (badness 10000) detected at line 31 [][][] Underfull \hbox (badness 10000) detected at line 34 [][][] Underfull \hbox (badness 10000) detected at line 37 [][][] ) (./vstring_8c_source.tex [891] [892] [893]) (./vstring_8h.tex <./vstring_8h__ incl.pdf> <./vstring_8h__dep__incl.pdf> [894] Underfull \hbox (badness 10000) detected at line 41 [][][] Underfull \hbox (badness 10000) detected at line 44 [][][] Underfull \hbox (badness 10000) detected at line 47 [][][] [895]) (./vstring_8h_source.tex) (./vunit_8h.tex <./vunit_8h__dep__incl.pdf> [896] LaTeX Warning: Command \r invalid in math mode on input line 42. Missing character: There is no Å in font cmr9! Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] Underfull \hbox (badness 10000) detected at line 58 [][][] [897]) (./vunit_8h_source.tex) (./main_8c.tex [898] <./main_8c__incl.pdf> Underfull \hbox (badness 10000) detected at line 28 [][][] Underfull \hbox (badness 10000) detected at line 41 [][][] Underfull \hbox (badness 10000) detected at line 44 [][][] [899]) (./main_8c_source.tex [900] [901] [902] [903] [904] [905] [906] [907] [908] [909] [910]) (./vgrid_8c.tex <./vgrid_8c__incl.pdf> [911] [912] Underfull \hbox (badness 10000) detected at line 84 [][][] Underfull \hbox (badness 10000) detected at line 87 [][][] Underfull \hbox (badness 10000) detected at line 90 [][][] [913] Underfull \hbox (badness 10000) detected at line 169 [][][] [914]) (./vgrid_8c_source.tex [915] [916] [917] [918] [919] [920] [921] [922] [923] [924] [925] [926] [927] [928] [929] [930] [931] [932] [933] [934] [935] [936] [937]) (./vgrid_8h.tex [938] <./vgrid_8h__incl.pdf> <./vgrid_ 8h__dep__incl.pdf> [939] [940] Underfull \hbox (badness 10000) detected at line 93 [][][] [941] Underfull \hbox (badness 10000) detected at line 96 [][][] Underfull \hbox (badness 10000) detected at line 99 [][][] [942] Underfull \hbox (badness 10000) detected at line 165 [][][] ) (./vgrid_8h_source.tex [943]) (./vmgrid_8c.tex [944] <./vmgrid_8c__incl.pdf> [945] Underfull \hbox (badness 10000) detected at line 41 [][][] Underfull \hbox (badness 10000) detected at line 44 [][][] Underfull \hbox (badness 10000) detected at line 47 [][][] Underfull \hbox (badness 10000) detected at line 50 [][][] Overfull \hbox (1024.08331pt too wide) in paragraph at lines 59--59 []\T1/pcr/m/n/8 * Copyright (c) 2010, Pacific Northwest National Laboratory. Portions Copyright (c) 2002-2020, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2020, T he Regents of the University of California. Portions Copyright (c) 1995, Michae l Holst.[] ) (./vmgrid_8c_source.tex [946] [947] [948]) (./vmgrid_8h.tex <./vmgrid_8h__inc l.pdf> <./vmgrid_8h__dep__incl.pdf> [949] [950] Underfull \hbox (badness 10000) detected at line 71 [][][] Underfull \hbox (badness 10000) detected at line 74 [][][] Underfull \hbox (badness 10000) detected at line 77 [][][] [951]) (./vmgrid_8h_source.tex) (./vopot_8c.tex [952] <./vopot_8c__incl.pdf> Underfull \hbox (badness 10000) detected at line 44 [][][] Underfull \hbox (badness 10000) detected at line 47 [][][] Underfull \hbox (badness 10000) detected at line 50 [][][] [953]) (./vopot_8c_source.tex [954] [955] [956] [957] [958]) (./vopot_8h.tex <. /vopot_8h__incl.pdf> <./vopot_8h__dep__incl.pdf> [959] [960] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) detected at line 71 [][][] ) (./vopot_8h_source.tex [961]) (./vpmg_8c.tex <./vpmg_8c__incl.pdf> [962] [963] [964] [965] Underfull \hbox (badness 10000) detected at line 173 [][][] Underfull \hbox (badness 10000) detected at line 176 [][][] Underfull \hbox (badness 10000) detected at line 179 [][][] [966] Underfull \hbox (badness 10000) detected at line 261 [][][] [967] Underfull \hbox (badness 10000) detected at line 288 [][][] [968] Underfull \hbox (badness 10000) detected at line 384 [][][] Underfull \hbox (badness 10000) detected at line 387 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.7 on input line 394. Underfull \hbox (badness 10000) detected at line 409 [][][] Underfull \hbox (badness 10000) detected at line 412 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.8 on input line 419. [969] Underfull \hbox (badness 10000) detected at line 434 [][][] Underfull \hbox (badness 10000) detected at line 437 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.9 on input line 444. Underfull \hbox (badness 10000) detected at line 459 [][][] Underfull \hbox (badness 10000) detected at line 462 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.10 on input line 469. Underfull \hbox (badness 10000) detected at line 484 [][][] Underfull \hbox (badness 10000) detected at line 487 [][][] [970] Package longtable Warning: Column widths have changed (longtable) in table 9.11 on input line 494. Underfull \hbox (badness 10000) detected at line 509 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.12 on input line 519. Underfull \hbox (badness 10000) detected at line 534 [][][] Underfull \hbox (badness 10000) detected at line 537 [][][] Underfull \hbox (badness 10000) detected at line 554 [][][] Underfull \hbox (badness 10000) detected at line 557 [][][] [971] Underfull \hbox (badness 10000) detected at line 574 [][][] Underfull \hbox (badness 10000) detected at line 591 [][][] Underfull \hbox (badness 10000) detected at line 608 [][][] Underfull \hbox (badness 10000) detected at line 625 [][][] Underfull \hbox (badness 10000) detected at line 642 [][][] [972] Underfull \hbox (badness 10000) detected at line 659 [][][] Underfull \hbox (badness 10000) detected at line 676 [][][] Underfull \hbox (badness 10000) detected at line 697 [][][] Underfull \hbox (badness 10000) detected at line 700 [][][] Underfull \hbox (badness 10000) detected at line 717 [][][] [973] Underfull \hbox (badness 10000) detected at line 734 [][][] Underfull \hbox (badness 10000) detected at line 751 [][][] Underfull \hbox (badness 10000) detected at line 768 [][][] Underfull \hbox (badness 10000) detected at line 795 [][][] [974] Underfull \hbox (badness 10000) detected at line 832 [][][] [975] Underfull \hbox (badness 10000) detected at line 876 [][][] [976] Underfull \hbox (badness 10000) detected at line 926 [][][] Underfull \hbox (badness 10000) detected at line 948 [][][] [977] Underfull \hbox (badness 10000) detected at line 970 [][][] Underfull \hbox (badness 10000) detected at line 992 [][][] Underfull \hbox (badness 10000) detected at line 995 [][][] Underfull \hbox (badness 10000) detected at line 1012 [][][] Underfull \hbox (badness 10000) detected at line 1015 [][][] [978] Underfull \hbox (badness 10000) detected at line 1037 [][][] Underfull \hbox (badness 10000) detected at line 1040 [][][] Underfull \hbox (badness 10000) detected at line 1062 [][][] Underfull \hbox (badness 10000) detected at line 1065 [][][] Underfull \hbox (badness 10000) detected at line 1097 [][][] [979] Underfull \hbox (badness 10000) detected at line 1114 [][][] Underfull \hbox (badness 10000) detected at line 1146 [][][] Underfull \hbox (badness 10000) detected at line 1149 [][][] ) (./vpmg_8c_source.tex [980] [981] [982] [983] [984] [985] [986] [987] [988] [989] [990] [991] [992] [993] [994] [995] [996] [997] [998] [999] [1000] [1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008] [1009] [1010] [1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] [1021] [1022] [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] [1033] [1034] [1035] [1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] [1090] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112] [1113] [1114] [1115] [1116]) (./vpmg_8h.tex <./vpmg_8h__in cl.pdf> <./vpmg_8h__dep__incl.pdf> [1117] [1118] [1119] [1120] [1121] [1122] Underfull \hbox (badness 10000) detected at line 235 [][][] Underfull \hbox (badness 10000) detected at line 238 [][][] Underfull \hbox (badness 10000) detected at line 241 [][][] [1123] [1124] Underfull \hbox (badness 10000) detected at line 406 [][][] Underfull \hbox (badness 10000) detected at line 423 [][][] [1125] Underfull \hbox (badness 10000) detected at line 469 [][][] Underfull \hbox (badness 10000) detected at line 472 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.24 on input line 479. Underfull \hbox (badness 10000) detected at line 494 [][][] Underfull \hbox (badness 10000) detected at line 497 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.25 on input line 504. [1126] Underfull \hbox (badness 10000) detected at line 519 [][][] Underfull \hbox (badness 10000) detected at line 522 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.26 on input line 529. Underfull \hbox (badness 10000) detected at line 544 [][][] Underfull \hbox (badness 10000) detected at line 547 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.27 on input line 554. Underfull \hbox (badness 10000) detected at line 569 [][][] Underfull \hbox (badness 10000) detected at line 572 [][][] [1127] Package longtable Warning: Column widths have changed (longtable) in table 9.28 on input line 579. Underfull \hbox (badness 10000) detected at line 594 [][][] Underfull \hbox (badness 10000) detected at line 597 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.29 on input line 604. Underfull \hbox (badness 10000) detected at line 619 [][][] Underfull \hbox (badness 10000) detected at line 622 [][][] Underfull \hbox (badness 10000) detected at line 639 [][][] Underfull \hbox (badness 10000) detected at line 642 [][][] [1128] Underfull \hbox (badness 10000) detected at line 659 [][][] Underfull \hbox (badness 10000) detected at line 676 [][][] Underfull \hbox (badness 10000) detected at line 693 [][][] Underfull \hbox (badness 10000) detected at line 710 [][][] Underfull \hbox (badness 10000) detected at line 727 [][][] [1129] Underfull \hbox (badness 10000) detected at line 744 [][][] Underfull \hbox (badness 10000) detected at line 761 [][][] Underfull \hbox (badness 10000) detected at line 782 [][][] Underfull \hbox (badness 10000) detected at line 785 [][][] Underfull \hbox (badness 10000) detected at line 802 [][][] [1130] Underfull \hbox (badness 10000) detected at line 819 [][][] Underfull \hbox (badness 10000) detected at line 836 [][][] Underfull \hbox (badness 10000) detected at line 853 [][][] Underfull \hbox (badness 10000) detected at line 870 [][][] Underfull \hbox (badness 10000) detected at line 883 [][][] [1131] Underfull \hbox (badness 10000) detected at line 896 [][][] Underfull \hbox (badness 10000) detected at line 913 [][][] [1132] Underfull \hbox (badness 10000) detected at line 957 [][][] Underfull \hbox (badness 10000) detected at line 987 [][][] [1133] Underfull \hbox (badness 10000) detected at line 1009 [][][] Underfull \hbox (badness 10000) detected at line 1031 [][][] Underfull \hbox (badness 10000) detected at line 1053 [][][] Underfull \hbox (badness 10000) detected at line 1056 [][][] Underfull \hbox (badness 10000) detected at line 1073 [][][] [1134] Underfull \hbox (badness 10000) detected at line 1076 [][][] Underfull \hbox (badness 10000) detected at line 1098 [][][] Underfull \hbox (badness 10000) detected at line 1101 [][][] Underfull \hbox (badness 10000) detected at line 1123 [][][] Underfull \hbox (badness 10000) detected at line 1126 [][][] [1135] Underfull \hbox (badness 10000) detected at line 1158 [][][] Underfull \hbox (badness 10000) detected at line 1175 [][][] [1136] Underfull \hbox (badness 10000) detected at line 1207 [][][] Underfull \hbox (badness 10000) detected at line 1210 [][][] ) (./vpmg_8h_source.tex [1137] [1138] [1139] [1140] [1141] [1142] [1143] [1144]) (./vpmgp_8c.tex <./vpmgp_8c__incl.pdf> [1145] [1146] Underfull \hbox (badness 10000) detected at line 39 [][][] Underfull \hbox (badness 10000) detected at line 42 [][][] Underfull \hbox (badness 10000) detected at line 45 [][][] [1147]) (./vpmgp_8c_source.tex [1148] [1149] [1150]) (./vpmgp_8h.tex <./vpmgp_8 h__incl.pdf> [1151] <./vpmgp_8h__dep__incl.pdf> [1152] [1153] Underfull \hbox (badness 10000) detected at line 58 [][][] Underfull \hbox (badness 10000) detected at line 61 [][][] Underfull \hbox (badness 10000) detected at line 64 [][][] Underfull \hbox (badness 10000) detected at line 67 [][][] [1154]) (./vpmgp_8h_source.tex [1155]) (./build_ad_8c_source.tex [1156] [1157] [1158]) (./build_ad_8h_source.tex [1159]) (./build_bd_8c_source.tex [1160] [1161] [1162] [1163]) (./build_bd_8h_source.tex [1164]) (./build_gd_8c_source.tex [1165] [1166] [1167] [1168] [1169] [1170] [1171] [1172] [1173] [1174] [1175] [1176] [1177] [1178] [1179] [1180] [1181] [1182] [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] [1191] [1192] [1193] [1194] [1195] [1196] [1197] [1198] [1199] [1200] [1201] [1202]) (./build_gd_8h_source.tex [1203] [1204]) (./build_pd_8c_source.tex [1205] [1206] [1207] [1208] [1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216] [1217] [1218] [1219] [1220] [1221] [1222] [1223]) (./build_pd_8h_source.tex [1224] [1225] [1226]) (./cgd_8c_source.tex) (./cgd_8h_source.tex [1227]) (./gsd_8c_source.tex [1228] [1229] [1230] [1231]) (./gsd_8h_source.tex [1232]) (./matvecd_8c_source.tex [1233] [1234] [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242] [1243] [1244] [1245]) (./matvecd_8h_source.tex [1246] [1247] [1248] [1249] [1250] [1251]) (./mgcsd_8c_source.tex [1252] [1253] [1254] [1255] [1256] [1257]) (./mgcsd_8h_source.tex [1258]) (./mgdrvd_8c_source.tex [1259] [1260] [1261] [1262] [1263] [1264] [1265]) (./mgdrvd_8h_source.tex [1266] [1267]) (./mgfasd_8c_source.tex [1268] [1269] [1270] [1271] [1272] [1273]) (./mgfasd_8h_source.tex [1274] [1275]) (./mgsubd_8c_source.tex [1276] [1277] [1278] [1279] [1280] [1281] [1282] [1283] [1284] [1285] [1286]) (./mgsubd_8h_source.tex [1287] [1288] [1289] [1290]) (./mikpckd_8c_source.tex [1291] [1292] [1293] [1294]) (./mikpckd_8h_source.tex [1295] [1296] [1297]) (./mlinpckd_8c_source.tex [1298] [1299]) (./mlinpckd_8h_source.tex) (./mypdec_8c_source.tex [1300] [1301] [1302] [1303] [1304] [1305] [1306]) (./mypdec_8h_source.tex [1307]) (./newdrvd_8c_source.tex [1308] [1309] [1310] [1311]) (./newdrvd_8h_source.tex [1312]) (./newtond_8c_source.tex [1313] [1314] [1315] [1316] [1317] [1318] [1319]) (./newtond_8h_source.tex [1320]) (./powerd_8c_source.tex [1321] [1322] [1323] [1324] [1325]) (./powerd_8h_source.tex [1326]) (./smoothd_8c_source.tex [1327]) (./smoothd_8h_source.tex [1328]) (./routines_8c.tex <./routines_8c__incl.pdf> [1329] Underfull \hbox (badness 776) in paragraph at lines 48--49 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv /m/n/10 alist[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[] Underfull \hbox (badness 2856) in paragraph at lines 48--49 \T1/phv/m/n/10 YMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]ZMap[] [][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 kappa[]Map[][][], [] Underfull \hbox (badness 1237) in paragraph at lines 48--49 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 charge[]Map[][][], [] $\OMS/cmsy/m/n/10 ^^C $\T1/phv/m/n/10 pmgp[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pmg[][][], [] Underfull \hbox (badness 905) in paragraph at lines 62--63 []\T1/phv/m/n/10 VPUBLIC void [] (Vmem $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 mem , [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, int nforce[][][], [] $\OMS/cmsy /m/n/10 ^^C$\T1/phv/m/n/10 atom[] Underfull \hbox (badness 5817) in paragraph at lines 68--69 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], Underfull \hbox (badness 5817) in paragraph at lines 70--71 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], [1330] Underfull \hbox (badness 1442) in paragraph at lines 82--83 []\T1/phv/m/n/10 VPUBLIC int [] (Vcom $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 com, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, int nforce[][][], [] $\OMS/cmsy/ m/n/10 ^^C$\T1/phv/m/n/10 atom[] Underfull \hbox (badness 931) in paragraph at lines 88--89 []\T1/phv/m/n/10 VPUBLIC void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T 1/phv/m/n/10 fetk[][][], Gem Underfull \hbox (badness 2495) in paragraph at lines 90--91 []\T1/phv/m/n/10 VPUBLIC Vrc[]_[][]Codes [] (int icalc, [] $\OMS/cmsy/m/n/10 ^^ C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 feparm, [] $\OMS /cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbeparm, [] [1331] Underfull \hbox (badness 10000) detected at line 117 [][][] Underfull \hbox (badness 10000) detected at line 120 [][][] Underfull \hbox (badness 10000) detected at line 123 [][][] ) (./routines_8c_source.tex [1332] [1333] [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341] [1342] [1343] [1344] [1345] [1346] [1347] [1348] [1349] [1350] [1351] [1352] [1353] [1354] [1355] [1356] [1357] [1358] [1359] [1360] [1361] [1362] [1363] [1364] [1365] [1366] [1367] [1368] [1369] [1370] [1371] [1372] [1373] [1374] [1375] [1376] [1377] [1378] [1379] [1380] [1381] [1382] [1383] [1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] [1392] [1393] [1394] [1395] [1396] [1397] [1398] [1399] [1400]) (./routines_8h.tex <./routine s_8h__incl.pdf> <./routines_8h__dep__incl.pdf> [1401] Overfull \hbox (16.65858pt too wide) in paragraph at lines 52--53 []\T1/phv/m/n/10 VEXTERNC int [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], Overfull \hbox (16.91972pt too wide) in paragraph at lines 54--55 []\T1/phv/m/n/10 VEXTERNC void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh , [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/1 0 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], Underfull \hbox (badness 1910) in paragraph at lines 72--73 [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1 /phv/m/n/10 alist[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][] [], [] Underfull \hbox (badness 1237) in paragraph at lines 72--73 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 charge[]Map[][][], [] $\OMS/cmsy/m/n/10 ^^C $\T1/phv/m/n/10 pmgp[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pmg[][][], [] [1402] Underfull \hbox (badness 5817) in paragraph at lines 90--91 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], Underfull \hbox (badness 5817) in paragraph at lines 92--93 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], [1403] Underfull \hbox (badness 2495) in paragraph at lines 124--125 []\T1/phv/m/n/10 VPUBLIC Vrc[]_[][]Codes [] (int icalc, [] $\OMS/cmsy/m/n/10 ^^ C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 feparm, [] $\OMS /cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbeparm, [] Underfull \hbox (badness 10000) detected at line 147 [][][] Underfull \hbox (badness 10000) detected at line 150 [][][] Underfull \hbox (badness 10000) detected at line 153 [][][] [1404]) (./routines_8h_source.tex [1405] [1406] [1407] [1408] [1409]) [1410] (./refman.ind [1411] [1412] [1413] [1414] [1415] [1416] [1417] [1418] [1419] [1420] [1421] [1422] [1423] [1424] [1425] [1426] [1427] [1428] [1429] [1430] [1431] [1432] [1433] [1434] [1435] [1436] [1437] [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] [1449] [1450] [1451] [1452] [1453] [1454] [1455] [1456] [1457] [1458] [1459]) Package longtable Warning: Table widths have changed. Rerun LaTeX. (./refman.aux) Package rerunfilecheck Warning: File `refman.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information)< /usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrro8a.pfb> Output written on refman.pdf (1517 pages, 6286495 bytes). Transcript written on refman.log. Package longtable Warning: Table widths have changed. Rerun LaTeX. Rerunning latex.... 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(/usr/share/texlive/texmf-dist/tex/latex/wasysym/uwasy.fd) [1{/var/lib/texmf/fo nts/map/pdftex/updmap/pdftex.map}{/usr/share/texlive/texmf-dist/fonts/enc/dvips /base/8r.enc}] [2] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] (./index.tex Chapter 1. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1phv.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [1] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [2]) (./bug.tex [3] [4] Chapter 2. [5] [6]) (./deprecated.tex [7] [8] Chapter 3. ) [9] [10] Chapter 4. (./modules.tex) [11] [12] Chapter 5. (./annotated.tex [13]) [14] Chapter 6. (./files.tex [15] [16] [17]) [18] Chapter 7. (./group___header.tex) (./group___vcsm.tex [19] Underfull \hbox (badness 10000) detected at line 93 [][][] [20] Underfull \hbox (badness 10000) detected at line 113 [][][] Underfull \hbox (badness 10000) detected at line 116 [][][] Underfull \hbox (badness 10000) detected at line 121 [][][] Underfull \hbox (badness 10000) detected at line 145 [][][] Underfull \hbox (badness 10000) detected at line 148 [][][] Underfull \hbox (badness 10000) detected at line 153 [][][] [21] Underfull \hbox (badness 10000) detected at line 179 [][][] Underfull \hbox (badness 10000) detected at line 201 [][][] Underfull \hbox (badness 10000) detected at line 223 [][][] Underfull \hbox (badness 10000) detected at line 226 [][][] Overfull \vbox (4.57304pt too high) has occurred while \output is active [22] Underfull \hbox (badness 10000) detected at line 252 [][][] Underfull \hbox (badness 10000) detected at line 255 [][][] Underfull \hbox (badness 10000) detected at line 281 [][][] Underfull \hbox (badness 10000) detected at line 284 [][][] [23] Underfull \hbox (badness 10000) detected at line 308 [][][] Underfull \hbox (badness 10000) detected at line 311 [][][] Underfull \hbox (badness 10000) detected at line 335 [][][] Underfull \hbox (badness 10000) detected at line 338 [][][] Underfull \hbox (badness 10000) detected at line 364 [][][] Underfull \hbox (badness 10000) detected at line 367 [][][] [24] Underfull \hbox (badness 10000) detected at line 393 [][][] Underfull \hbox (badness 10000) detected at line 396 [][][] Underfull \hbox (badness 10000) detected at line 418 [][][] Underfull \hbox (badness 10000) detected at line 421 [][][] [25] Underfull \hbox (badness 10000) detected at line 443 [][][] Underfull \hbox (badness 10000) detected at line 446 [][][] Underfull \hbox (badness 10000) detected at line 468 [][][] Underfull \hbox (badness 10000) detected at line 471 [][][] ) (./group___vfetk.tex [26] [27] [28] [29] [30] Underfull \hbox (badness 10000) detected at line 304 [][][] Underfull \hbox (badness 10000) detected at line 335 [][][] [31] Underfull \hbox (badness 10000) detected at line 398 [][][] Underfull \hbox (badness 10000) detected at line 429 [][][] Underfull \hbox (badness 10000) detected at line 463 [][][] Underfull \hbox (badness 10000) detected at line 466 [][][] [32] Underfull \hbox (badness 10000) detected at line 492 [][][] Underfull \hbox (badness 10000) detected at line 495 [][][] Underfull \hbox (badness 10000) detected at line 498 [][][] Underfull \hbox (badness 10000) detected at line 522 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] Underfull \hbox (badness 10000) detected at line 528 [][][] [33] Underfull \hbox (badness 10000) detected at line 559 [][][] Underfull \hbox (badness 10000) detected at line 569 [][][] [34] Underfull \hbox (badness 10000) detected at line 593 [][][] Underfull \hbox (badness 10000) detected at line 615 [][][] Underfull \hbox (badness 10000) detected at line 637 [][][] [35] Underfull \hbox (badness 10000) detected at line 658 [][][] Underfull \hbox (badness 10000) detected at line 661 [][][] Underfull \hbox (badness 10000) detected at line 668 [][][] Underfull \hbox (badness 10000) detected at line 671 [][][] Underfull \hbox (badness 10000) detected at line 701 [][][] [36] Underfull \hbox (badness 10000) detected at line 727 [][][] Underfull \hbox (badness 10000) detected at line 730 [][][] Underfull \hbox (badness 10000) detected at line 735 [][][] Underfull \hbox (badness 10000) detected at line 761 [][][] [37] Underfull \hbox (badness 10000) detected at line 789 [][][] Underfull \hbox (badness 10000) detected at line 792 [][][] Underfull \hbox (badness 10000) detected at line 814 [][][] Underfull \hbox (badness 10000) detected at line 817 [][][] Underfull \hbox (badness 10000) detected at line 820 [][][] [38] Underfull \hbox (badness 10000) detected at line 844 [][][] Underfull \hbox (badness 10000) detected at line 847 [][][] Underfull \hbox (badness 10000) detected at line 869 [][][] Underfull \hbox (badness 10000) detected at line 872 [][][] Underfull \hbox (badness 10000) detected at line 875 [][][] Underfull \hbox (badness 10000) detected at line 899 [][][] Underfull \hbox (badness 10000) detected at line 902 [][][] [39] Underfull \hbox (badness 10000) detected at line 924 [][][] Underfull \hbox (badness 10000) detected at line 927 [][][] Underfull \hbox (badness 10000) detected at line 949 [][][] [40] Underfull \hbox (badness 10000) detected at line 969 [][][] Underfull \hbox (badness 10000) detected at line 999 [][][] Underfull \hbox (badness 10000) detected at line 1002 [][][] Underfull \hbox (badness 10000) detected at line 1024 [][][] Underfull \hbox (badness 10000) detected at line 1027 [][][] [41] Underfull \hbox (badness 10000) detected at line 1053 [][][] Underfull \hbox (badness 10000) detected at line 1056 [][][] Underfull \hbox (badness 10000) detected at line 1080 [][][] Underfull \hbox (badness 10000) detected at line 1083 [][][] [42] Underfull \hbox (badness 10000) detected at line 1109 [][][] Underfull \hbox (badness 10000) detected at line 1146 [][][] Underfull \hbox (badness 10000) detected at line 1149 [][][] [43] Underfull \hbox (badness 10000) detected at line 1179 [][][] Underfull \hbox (badness 10000) detected at line 1182 [][][] Underfull \hbox (badness 10000) detected at line 1204 [][][] Underfull \hbox (badness 10000) detected at line 1207 [][][] [44] Underfull \hbox (badness 10000) detected at line 1232 [][][] Underfull \hbox (badness 10000) detected at line 1265 [][][] Underfull \hbox (badness 10000) detected at line 1268 [][][] [45] Underfull \hbox (badness 10000) detected at line 1298 [][][] Underfull \hbox (badness 10000) detected at line 1301 [][][] Underfull \hbox (badness 10000) detected at line 1327 [][][] [46] Underfull \hbox (badness 10000) detected at line 1355 [][][] Underfull \hbox (badness 10000) detected at line 1385 [][][] [47] Underfull \hbox (badness 10000) detected at line 1419 [][][] Underfull \hbox (badness 10000) detected at line 1422 [][][] Underfull \hbox (badness 10000) detected at line 1448 [][][] Underfull \hbox (badness 10000) detected at line 1451 [][][] [48] Underfull \hbox (badness 10000) detected at line 1477 [][][] Underfull \hbox (badness 10000) detected at line 1480 [][][] [49] Underfull \hbox (badness 10000) detected at line 1514 [][][] Underfull \hbox (badness 10000) detected at line 1517 [][][] Underfull \hbox (badness 10000) detected at line 1545 [][][] [50] Underfull \hbox (badness 10000) detected at line 1579 [][][] Underfull \hbox (badness 10000) detected at line 1582 [][][] [51] [52] Underfull \hbox (badness 10000) detected at line 1665 [][][] Underfull \hbox (badness 10000) detected at line 1699 [][][] Underfull \hbox (badness 10000) detected at line 1702 [][][] [53] Underfull \hbox (badness 10000) detected at line 1745 [][][] Underfull \hbox (badness 10000) detected at line 1755 [][][] Underfull \hbox (badness 10000) detected at line 1779 [][][] Underfull \hbox (badness 10000) detected at line 1782 [][][] Underfull \hbox (badness 10000) detected at line 1785 [][][] [54] Underfull \hbox (badness 10000) detected at line 1807 [][][] Underfull \hbox (badness 10000) detected at line 1810 [][][] Underfull \hbox (badness 10000) detected at line 1813 [][][] Underfull \hbox (badness 10000) detected at line 1835 [][][] [55] Underfull \hbox (badness 10000) detected at line 1861 [][][] Underfull \hbox (badness 10000) detected at line 1881 [][][] Underfull \hbox (badness 10000) detected at line 1886 [][][] ) (./group___vpee.tex [56] Underfull \hbox (badness 849) in paragraph at lines 45--46 \T1/phv/m/n/10 Holst par-al-lel re-fine-ment rou-tine es-sen-tially re-duces th e er-ror out-side the \T1/pcr/m/n/10 local^^D partition to zero. Underfull \hbox (badness 10000) in paragraph at lines 45--46 \T1/pcr/m/n/10 However, this leads to the need for a few final overlapping Schw arz solves to Underfull \hbox (badness 10000) in paragraph at lines 45--46 \T1/pcr/m/n/10 smooth out the errors near partition boundaries. Supposedly, if the region in Underfull \hbox (badness 10000) in paragraph at lines 45--46 \T1/pcr/m/n/10 which we allow error-based refinement includes the$\OML/cmm/m/it /10 <$\T1/pcr/m/n/10 /tt$\OML/cmm/m/it/10 >$\T1/pcr/m/n/10 local^^D partition a nd an Underfull \hbox (badness 10000) in paragraph at lines 45--46 \T1/pcr/m/n/10 external buffer zone approximately equal in size to the local re gion, then the Underfull \hbox (badness 10000) in paragraph at lines 45--46 \T1/pcr/m/n/10 solution will asymptotically approach the solution obtained via more typical Underfull \hbox (badness 10000) in paragraph at lines 45--46 \T1/pcr/m/n/10 methods. This is essentially a more flexible parallel implementa tion of MC\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 s [57] Underfull \hbox (badness 10000) detected at line 75 [][][] Underfull \hbox (badness 10000) detected at line 78 [][][] Underfull \hbox (badness 10000) detected at line 94 [][][] Underfull \hbox (badness 10000) detected at line 111 [][][] [58] Underfull \hbox (badness 10000) detected at line 114 [][][] Underfull \hbox (badness 10000) detected at line 132 [][][] Underfull \hbox (badness 10000) detected at line 149 [][][] Underfull \hbox (badness 10000) detected at line 171 [][][] [59] Underfull \hbox (badness 10000) detected at line 195 [][][] Underfull \hbox (badness 10000) detected at line 198 [][][] Underfull \hbox (badness 10000) detected at line 201 [][][] Overfull \vbox (42.60027pt too high) has occurred while \output is active [60] Underfull \hbox (badness 10000) detected at line 241 [][][] Underfull \hbox (badness 10000) detected at line 244 [][][] ) (./group___a_p_o_lparm.tex [61] Overfull \vbox (22.62613pt too high) has occurred while \output is active [62] Underfull \hbox (badness 10000) detected at line 212 [][][] Underfull \hbox (badness 10000) detected at line 220 [][][] [63] Underfull \hbox (badness 10000) detected at line 237 [][][] Underfull \hbox (badness 10000) detected at line 261 [][][] Underfull \hbox (badness 10000) detected at line 264 [][][] Underfull \hbox (badness 10000) detected at line 281 [][][] Underfull \hbox (badness 10000) detected at line 289 [][][] [64] Underfull \hbox (badness 10000) detected at line 306 [][][] Underfull \hbox (badness 10000) detected at line 328 [][][] ) (./group___b_e_mparm.tex [65] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] [66] Underfull \hbox (badness 10000) detected at line 125 [][][] Underfull \hbox (badness 10000) detected at line 133 [][][] Underfull \hbox (badness 10000) detected at line 150 [][][] Underfull \hbox (badness 10000) detected at line 158 [][][] Underfull \hbox (badness 10000) detected at line 175 [][][] [67] Underfull \hbox (badness 10000) detected at line 185 [][][] Underfull \hbox (badness 10000) detected at line 202 [][][] Underfull \hbox (badness 10000) detected at line 224 [][][] Underfull \hbox (badness 10000) detected at line 246 [][][] [68] Underfull \hbox (badness 10000) detected at line 258 [][][] ) (./group___f_e_mparm.tex [69] Underfull \hbox (badness 10000) detected at line 111 [][][] [70] Underfull \hbox (badness 10000) detected at line 155 [][][] Underfull \hbox (badness 10000) detected at line 158 [][][] Underfull \hbox (badness 10000) detected at line 197 [][][] Underfull \hbox (badness 10000) detected at line 231 [][][] [71] Underfull \hbox (badness 10000) detected at line 239 [][][] Underfull \hbox (badness 10000) detected at line 256 [][][] Underfull \hbox (badness 10000) detected at line 280 [][][] Underfull \hbox (badness 10000) detected at line 288 [][][] [72] Underfull \hbox (badness 10000) detected at line 305 [][][] Underfull \hbox (badness 10000) detected at line 315 [][][] Underfull \hbox (badness 10000) detected at line 332 [][][] Underfull \hbox (badness 10000) detected at line 354 [][][] ) (./group___g_e_o_f_l_o_wparm.tex [73] Underfull \hbox (badness 10000) detected at line 68 [][][] [74] Underfull \hbox (badness 10000) detected at line 71 [][][] Underfull \hbox (badness 10000) detected at line 124 [][][] Underfull \hbox (badness 10000) detected at line 132 [][][] [75] Underfull \hbox (badness 10000) detected at line 149 [][][] Underfull \hbox (badness 10000) detected at line 173 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 198 [][][] Underfull \hbox (badness 10000) detected at line 208 [][][] [76] Underfull \hbox (badness 10000) detected at line 225 [][][] Underfull \hbox (badness 10000) detected at line 247 [][][] Underfull \hbox (badness 10000) detected at line 269 [][][] [77] Underfull \hbox (badness 10000) detected at line 281 [][][] ) (./group___m_gparm.tex [78] [79] Underfull \hbox (badness 10000) detected at line 205 [][][] [80] Underfull \hbox (badness 10000) detected at line 217 [][][] Underfull \hbox (badness 10000) detected at line 234 [][][] Underfull \hbox (badness 10000) detected at line 246 [][][] Underfull \hbox (badness 10000) detected at line 263 [][][] Underfull \hbox (badness 10000) detected at line 271 [][][] [81] Underfull \hbox (badness 10000) detected at line 288 [][][] Underfull \hbox (badness 10000) detected at line 312 [][][] Underfull \hbox (badness 10000) detected at line 320 [][][] Underfull \hbox (badness 10000) detected at line 337 [][][] Underfull \hbox (badness 10000) detected at line 347 [][][] [82] Underfull \hbox (badness 10000) detected at line 364 [][][] Underfull \hbox (badness 10000) detected at line 386 [][][] Underfull \hbox (badness 10000) detected at line 408 [][][] Underfull \hbox (badness 10000) detected at line 416 [][][] [83] Underfull \hbox (badness 10000) detected at line 433 [][][] Underfull \hbox (badness 10000) detected at line 441 [][][] Underfull \hbox (badness 10000) detected at line 458 [][][] Underfull \hbox (badness 10000) detected at line 466 [][][] Underfull \hbox (badness 10000) detected at line 483 [][][] Underfull \hbox (badness 10000) detected at line 491 [][][] [84] Underfull \hbox (badness 10000) detected at line 508 [][][] Underfull \hbox (badness 10000) detected at line 516 [][][] Underfull \hbox (badness 10000) detected at line 533 [][][] Underfull \hbox (badness 10000) detected at line 541 [][][] Underfull \hbox (badness 10000) detected at line 558 [][][] [85] Underfull \hbox (badness 10000) detected at line 566 [][][] Underfull \hbox (badness 10000) detected at line 583 [][][] Underfull \hbox (badness 10000) detected at line 591 [][][] Underfull \hbox (badness 10000) detected at line 608 [][][] Underfull \hbox (badness 10000) detected at line 616 [][][] Underfull \hbox (badness 10000) detected at line 633 [][][] [86] Underfull \hbox (badness 10000) detected at line 645 [][][] Underfull \hbox (badness 10000) detected at line 662 [][][] Underfull \hbox (badness 10000) detected at line 686 [][][] [87] Underfull \hbox (badness 10000) detected at line 710 [][][] ) (./group___n_osh.tex [88] [89] [90] [91] [92] Underfull \hbox (badness 10000) detected at line 431 [][][] Underfull \hbox (badness 10000) detected at line 441 [][][] Underfull \hbox (badness 10000) detected at line 458 [][][] Underfull \hbox (badness 10000) detected at line 482 [][][] [93] Underfull \hbox (badness 10000) detected at line 490 [][][] Underfull \hbox (badness 10000) detected at line 507 [][][] Underfull \hbox (badness 10000) detected at line 529 [][][] Underfull \hbox (badness 10000) detected at line 539 [][][] Underfull \hbox (badness 10000) detected at line 556 [][][] [94] Underfull \hbox (badness 10000) detected at line 568 [][][] Underfull \hbox (badness 10000) detected at line 585 [][][] Underfull \hbox (badness 10000) detected at line 607 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] [95] Underfull \hbox (badness 10000) detected at line 639 [][][] Underfull \hbox (badness 10000) detected at line 656 [][][] Underfull \hbox (badness 10000) detected at line 659 [][][] Underfull \hbox (badness 10000) detected at line 669 [][][] Underfull \hbox (badness 10000) detected at line 672 [][][] Underfull \hbox (badness 10000) detected at line 689 [][][] Overfull \vbox (15.28305pt too high) has occurred while \output is active [96] Underfull \hbox (badness 10000) detected at line 699 [][][] Underfull \hbox (badness 10000) detected at line 716 [][][] Underfull \hbox (badness 10000) detected at line 726 [][][] Underfull \hbox (badness 10000) detected at line 743 [][][] Underfull \hbox (badness 10000) detected at line 753 [][][] [97] Underfull \hbox (badness 10000) detected at line 770 [][][] Underfull \hbox (badness 10000) detected at line 780 [][][] Underfull \hbox (badness 10000) detected at line 797 [][][] Underfull \hbox (badness 10000) detected at line 807 [][][] Underfull \hbox (badness 10000) detected at line 824 [][][] [98] Underfull \hbox (badness 10000) detected at line 834 [][][] Underfull \hbox (badness 10000) detected at line 851 [][][] Underfull \hbox (badness 10000) detected at line 861 [][][] Underfull \hbox (badness 10000) detected at line 878 [][][] Underfull \hbox (badness 10000) detected at line 888 [][][] [99] Underfull \hbox (badness 10000) detected at line 905 [][][] Underfull \hbox (badness 10000) detected at line 915 [][][] Underfull \hbox (badness 10000) detected at line 932 [][][] Underfull \hbox (badness 10000) detected at line 942 [][][] Underfull \hbox (badness 10000) detected at line 959 [][][] [100] Underfull \hbox (badness 10000) detected at line 969 [][][] Underfull \hbox (badness 10000) detected at line 986 [][][] Underfull \hbox (badness 10000) detected at line 996 [][][] Underfull \hbox (badness 10000) detected at line 1013 [][][] Underfull \hbox (badness 10000) detected at line 1016 [][][] Underfull \hbox (badness 10000) detected at line 1026 [][][] [101] Underfull \hbox (badness 10000) detected at line 1043 [][][] Underfull \hbox (badness 10000) detected at line 1048 [][][] Underfull \hbox (badness 10000) detected at line 1058 [][][] Underfull \hbox (badness 10000) detected at line 1075 [][][] Underfull \hbox (badness 10000) detected at line 1078 [][][] [102] Underfull \hbox (badness 10000) detected at line 1090 [][][] Underfull \hbox (badness 10000) detected at line 1093 [][][] Underfull \hbox (badness 10000) detected at line 1110 [][][] Underfull \hbox (badness 10000) detected at line 1113 [][][] Underfull \hbox (badness 10000) detected at line 1123 [][][] Underfull \hbox (badness 10000) detected at line 1126 [][][] Underfull \hbox (badness 10000) detected at line 1143 [][][] Underfull \hbox (badness 10000) detected at line 1146 [][][] [103] Underfull \hbox (badness 10000) detected at line 1158 [][][] Underfull \hbox (badness 10000) detected at line 1161 [][][] Underfull \hbox (badness 10000) detected at line 1178 [][][] Underfull \hbox (badness 10000) detected at line 1181 [][][] Underfull \hbox (badness 10000) detected at line 1191 [][][] Underfull \hbox (badness 10000) detected at line 1194 [][][] Underfull \hbox (badness 10000) detected at line 1211 [][][] [104] Underfull \hbox (badness 10000) detected at line 1214 [][][] Underfull \hbox (badness 10000) detected at line 1224 [][][] Underfull \hbox (badness 10000) detected at line 1248 [][][] Underfull \hbox (badness 10000) detected at line 1251 [][][] Underfull \hbox (badness 10000) detected at line 1261 [][][] Overfull \vbox (3.94589pt too high) has occurred while \output is active [105]) (./group___p_b_a_mparm.tex [106] Underfull \hbox (badness 10000) detected at line 116 [][][] Underfull \hbox (badness 10000) detected at line 119 [][][] [107] Underfull \hbox (badness 10000) detected at line 172 [][][] Underfull \hbox (badness 10000) detected at line 180 [][][] Underfull \hbox (badness 10000) detected at line 197 [][][] [108] Underfull \hbox (badness 10000) detected at line 221 [][][] Underfull \hbox (badness 10000) detected at line 229 [][][] Underfull \hbox (badness 10000) detected at line 246 [][][] Underfull \hbox (badness 10000) detected at line 256 [][][] [109] Underfull \hbox (badness 10000) detected at line 273 [][][] Underfull \hbox (badness 10000) detected at line 295 [][][] Underfull \hbox (badness 10000) detected at line 317 [][][] Underfull \hbox (badness 10000) detected at line 341 [][][] [110] Underfull \hbox (badness 10000) detected at line 365 [][][] Underfull \hbox (badness 10000) detected at line 389 [][][] Underfull \hbox (badness 10000) detected at line 413 [][][] [111] Underfull \hbox (badness 10000) detected at line 437 [][][] Underfull \hbox (badness 10000) detected at line 461 [][][] Underfull \hbox (badness 10000) detected at line 485 [][][] [112] Underfull \hbox (badness 10000) detected at line 509 [][][] Underfull \hbox (badness 10000) detected at line 533 [][][] Underfull \hbox (badness 10000) detected at line 557 [][][] [113] Underfull \hbox (badness 10000) detected at line 581 [][][] Underfull \hbox (badness 10000) detected at line 593 [][][] Underfull \hbox (badness 10000) detected at line 610 [][][] [114] Underfull \hbox (badness 10000) detected at line 634 [][][] ) (./group___p_b_eparm.tex [115] [116] Underfull \hbox (badness 10000) detected at line 209 [][][] Underfull \hbox (badness 10000) detected at line 212 [][][] [117] Underfull \hbox (badness 10000) detected at line 234 [][][] Underfull \hbox (badness 10000) detected at line 258 [][][] Underfull \hbox (badness 10000) detected at line 261 [][][] Underfull \hbox (badness 10000) detected at line 278 [][][] Underfull \hbox (badness 10000) detected at line 281 [][][] [118] Underfull \hbox (badness 10000) detected at line 303 [][][] Underfull \hbox (badness 10000) detected at line 325 [][][] Underfull \hbox (badness 10000) detected at line 347 [][][] Underfull \hbox (badness 10000) detected at line 350 [][][] [119] Underfull \hbox (badness 10000) detected at line 374 [][][] Underfull \hbox (badness 10000) detected at line 377 [][][] Underfull \hbox (badness 10000) detected at line 401 [][][] Underfull \hbox (badness 10000) detected at line 404 [][][] Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 431 [][][] [120]) (./group___p_b_s_a_mparm.tex [121] Underfull \hbox (badness 10000) detected at line 100 [][][] Underfull \hbox (badness 10000) detected at line 103 [][][] [122] Underfull \hbox (badness 10000) detected at line 156 [][][] Underfull \hbox (badness 10000) detected at line 164 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] [123] Underfull \hbox (badness 10000) detected at line 205 [][][] Underfull \hbox (badness 10000) detected at line 213 [][][] Underfull \hbox (badness 10000) detected at line 230 [][][] Underfull \hbox (badness 10000) detected at line 240 [][][] Underfull \hbox (badness 10000) detected at line 257 [][][] Overfull \vbox (0.37224pt too high) has occurred while \output is active [124] Underfull \hbox (badness 10000) detected at line 279 [][][] Underfull \hbox (badness 10000) detected at line 301 [][][] Underfull \hbox (badness 10000) detected at line 325 [][][] [125] Underfull \hbox (badness 10000) detected at line 349 [][][] Underfull \hbox (badness 10000) detected at line 373 [][][] Underfull \hbox (badness 10000) detected at line 397 [][][] [126] Underfull \hbox (badness 10000) detected at line 409 [][][] Underfull \hbox (badness 10000) detected at line 426 [][][] ) (./group___vacc.tex [127] [128] [129] Underfull \hbox (badness 10000) detected at line 149 [][][] Underfull \hbox (badness 10000) detected at line 179 [][][] [130] Underfull \hbox (badness 10000) detected at line 207 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] Underfull \hbox (badness 10000) detected at line 213 [][][] Underfull \hbox (badness 10000) detected at line 239 [][][] Underfull \hbox (badness 10000) detected at line 242 [][][] [131] Underfull \hbox (badness 10000) detected at line 268 [][][] Underfull \hbox (badness 10000) detected at line 271 [][][] Underfull \hbox (badness 10000) detected at line 283 [][][] Underfull \hbox (badness 10000) detected at line 305 [][][] Underfull \hbox (badness 10000) detected at line 308 [][][] [132] Underfull \hbox (badness 10000) detected at line 334 [][][] Underfull \hbox (badness 10000) detected at line 337 [][][] Underfull \hbox (badness 10000) detected at line 365 [][][] Underfull \hbox (badness 10000) detected at line 387 [][][] [133] Underfull \hbox (badness 10000) detected at line 411 [][][] Underfull \hbox (badness 10000) detected at line 414 [][][] Underfull \hbox (badness 10000) detected at line 417 [][][] Underfull \hbox (badness 10000) detected at line 447 [][][] Underfull \hbox (badness 10000) detected at line 450 [][][] [134] Underfull \hbox (badness 10000) detected at line 472 [][][] Underfull \hbox (badness 10000) detected at line 475 [][][] Underfull \hbox (badness 10000) detected at line 499 [][][] Underfull \hbox (badness 10000) detected at line 502 [][][] [135] Underfull \hbox (badness 10000) detected at line 530 [][][] Underfull \hbox (badness 10000) detected at line 533 [][][] Underfull \hbox (badness 10000) detected at line 536 [][][] Underfull \hbox (badness 10000) detected at line 562 [][][] Underfull \hbox (badness 10000) detected at line 565 [][][] [136] Underfull \hbox (badness 10000) detected at line 595 [][][] Underfull \hbox (badness 10000) detected at line 598 [][][] Underfull \hbox (badness 10000) detected at line 628 [][][] [137] Underfull \hbox (badness 10000) detected at line 660 [][][] Underfull \hbox (badness 10000) detected at line 692 [][][] [138] Underfull \hbox (badness 10000) detected at line 724 [][][] Underfull \hbox (badness 10000) detected at line 758 [][][] [139] Underfull \hbox (badness 10000) detected at line 790 [][][] Underfull \hbox (badness 10000) detected at line 820 [][][] [140] Underfull \hbox (badness 10000) detected at line 852 [][][] Underfull \hbox (badness 10000) detected at line 855 [][][] Underfull \hbox (badness 10000) detected at line 858 [][][] Underfull \hbox (badness 10000) detected at line 882 [][][] Underfull \hbox (badness 10000) detected at line 885 [][][] Underfull \hbox (badness 10000) detected at line 888 [][][] [141] Underfull \hbox (badness 10000) detected at line 918 [][][] Underfull \hbox (badness 10000) detected at line 921 [][][] Underfull \hbox (badness 10000) detected at line 941 [][][] Underfull \hbox (badness 10000) detected at line 944 [][][] Overfull \vbox (21.5778pt too high) has occurred while \output is active [142] Underfull \hbox (badness 10000) detected at line 972 [][][] Underfull \hbox (badness 10000) detected at line 975 [][][] Underfull \hbox (badness 10000) detected at line 1007 [][][] Underfull \hbox (badness 10000) detected at line 1010 [][][] [143] Underfull \hbox (badness 10000) detected at line 1040 [][][] Underfull \hbox (badness 10000) detected at line 1043 [][][] Underfull \hbox (badness 10000) detected at line 1069 [][][] Underfull \hbox (badness 10000) detected at line 1072 [][][] Overfull \vbox (18.93095pt too high) has occurred while \output is active [144] Underfull \hbox (badness 10000) detected at line 1100 [][][] Underfull \hbox (badness 10000) detected at line 1122 [][][] Underfull \hbox (badness 10000) detected at line 1146 [][][] Underfull \hbox (badness 10000) detected at line 1149 [][][] Underfull \hbox (badness 10000) detected at line 1152 [][][] [145]) (./group___valist.tex [146] Underfull \hbox (badness 10000) detected at line 91 [][][] Underfull \hbox (badness 10000) detected at line 94 [][][] Underfull \hbox (badness 10000) detected at line 111 [][][] Underfull \hbox (badness 10000) detected at line 114 [][][] Overfull \vbox (3.49948pt too high) has occurred while \output is active [147] Underfull \hbox (badness 10000) detected at line 136 [][][] Underfull \hbox (badness 10000) detected at line 158 [][][] Underfull \hbox (badness 10000) detected at line 180 [][][] Underfull \hbox (badness 10000) detected at line 183 [][][] [148] Underfull \hbox (badness 10000) detected at line 207 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] Underfull \hbox (badness 10000) detected at line 232 [][][] Underfull \hbox (badness 10000) detected at line 235 [][][] Underfull \hbox (badness 10000) detected at line 257 [][][] Underfull \hbox (badness 10000) detected at line 260 [][][] [149] Underfull \hbox (badness 10000) detected at line 282 [][][] Underfull \hbox (badness 10000) detected at line 285 [][][] Underfull \hbox (badness 10000) detected at line 307 [][][] Underfull \hbox (badness 10000) detected at line 310 [][][] Underfull \hbox (badness 10000) detected at line 332 [][][] [150] Underfull \hbox (badness 10000) detected at line 335 [][][] Underfull \hbox (badness 10000) detected at line 352 [][][] Underfull \hbox (badness 10000) detected at line 355 [][][] Underfull \hbox (badness 10000) detected at line 377 [][][] Underfull \hbox (badness 10000) detected at line 380 [][][] Underfull \hbox (badness 10000) detected at line 383 [][][] [151] Underfull \hbox (badness 10000) detected at line 409 [][][] Underfull \hbox (badness 10000) detected at line 412 [][][] Underfull \hbox (badness 10000) detected at line 415 [][][] Underfull \hbox (badness 10000) detected at line 443 [][][] Underfull \hbox (badness 10000) detected at line 446 [][][] Underfull \hbox (badness 10000) detected at line 449 [][][] Overfull \vbox (15.85518pt too high) has occurred while \output is active [152]) (./group___vatom.tex [153] Underfull \hbox (badness 10000) detected at line 97 [][][] [154] Underfull \hbox (badness 10000) detected at line 134 [][][] Underfull \hbox (badness 10000) detected at line 158 [][][] Underfull \hbox (badness 10000) detected at line 182 [][][] Underfull \hbox (badness 10000) detected at line 185 [][][] [155] Underfull \hbox (badness 10000) detected at line 202 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] Underfull \hbox (badness 10000) detected at line 227 [][][] Underfull \hbox (badness 10000) detected at line 249 [][][] Underfull \hbox (badness 10000) detected at line 271 [][][] [156] Underfull \hbox (badness 10000) detected at line 279 [][][] Underfull \hbox (badness 10000) detected at line 296 [][][] Underfull \hbox (badness 10000) detected at line 320 [][][] Underfull \hbox (badness 10000) detected at line 328 [][][] [157] Underfull \hbox (badness 10000) detected at line 345 [][][] Underfull \hbox (badness 10000) detected at line 353 [][][] Underfull \hbox (badness 10000) detected at line 370 [][][] Underfull \hbox (badness 10000) detected at line 378 [][][] Underfull \hbox (badness 10000) detected at line 395 [][][] Underfull \hbox (badness 10000) detected at line 403 [][][] [158] Underfull \hbox (badness 10000) detected at line 420 [][][] Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 445 [][][] Underfull \hbox (badness 10000) detected at line 469 [][][] [159] Underfull \hbox (badness 10000) detected at line 477 [][][] Underfull \hbox (badness 10000) detected at line 494 [][][] Underfull \hbox (badness 10000) detected at line 518 [][][] [160] Underfull \hbox (badness 10000) detected at line 542 [][][] Underfull \hbox (badness 10000) detected at line 566 [][][] Underfull \hbox (badness 10000) detected at line 590 [][][] [161] Underfull \hbox (badness 10000) detected at line 614 [][][] Underfull \hbox (badness 10000) detected at line 638 [][][] Underfull \hbox (badness 10000) detected at line 662 [][][] ) (./group___vcap.tex [162] Underfull \hbox (badness 10000) detected at line 36 [][][] [163] Underfull \hbox (badness 10000) detected at line 86 [][][] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 92 [][][] Underfull \hbox (badness 10000) detected at line 119 [][][] Underfull \hbox (badness 10000) detected at line 122 [][][] Underfull \hbox (badness 10000) detected at line 125 [][][] [164] Underfull \hbox (badness 10000) detected at line 152 [][][] Underfull \hbox (badness 10000) detected at line 155 [][][] Underfull \hbox (badness 10000) detected at line 158 [][][] ) (./group___vclist.tex [165] [166] Underfull \hbox (badness 10000) detected at line 110 [][][] Underfull \hbox (badness 10000) detected at line 140 [][][] Underfull \hbox (badness 10000) detected at line 143 [][][] [167] Underfull \hbox (badness 10000) detected at line 175 [][][] Underfull \hbox (badness 10000) detected at line 178 [][][] Underfull \hbox (badness 10000) detected at line 212 [][][] [168] Underfull \hbox (badness 10000) detected at line 234 [][][] Underfull \hbox (badness 10000) detected at line 256 [][][] Underfull \hbox (badness 10000) detected at line 259 [][][] Underfull \hbox (badness 10000) detected at line 283 [][][] Underfull \hbox (badness 10000) detected at line 286 [][][] [169] Underfull \hbox (badness 10000) detected at line 308 [][][] Underfull \hbox (badness 10000) detected at line 311 [][][] Underfull \hbox (badness 10000) detected at line 333 [][][] Underfull \hbox (badness 10000) detected at line 336 [][][] Underfull \hbox (badness 10000) detected at line 358 [][][] Underfull \hbox (badness 10000) detected at line 361 [][][] [170] Underfull \hbox (badness 10000) detected at line 385 [][][] Underfull \hbox (badness 10000) detected at line 407 [][][] ) (./group___vgreen.tex [171] Underfull \hbox (badness 10000) detected at line 57 [][][] Underfull \hbox (badness 10000) detected at line 60 [][][] [172] [173] Underfull \hbox (badness 10000) detected at line 141 [][][] Underfull \hbox (badness 10000) detected at line 159 [][][] Underfull \hbox (badness 10000) detected at line 178 [][][] [174] Underfull \hbox (badness 10000) detected at line 196 [][][] Underfull \hbox (badness 10000) detected at line 215 [][][] [175] Underfull \hbox (badness 10000) detected at line 239 [][][] Underfull \hbox (badness 10000) detected at line 258 [][][] Underfull \hbox (badness 10000) detected at line 282 [][][] [176] Underfull \hbox (badness 10000) detected at line 299 [][][] Underfull \hbox (badness 10000) detected at line 307 [][][] Underfull \hbox (badness 10000) detected at line 324 [][][] Underfull \hbox (badness 10000) detected at line 334 [][][] Underfull \hbox (badness 10000) detected at line 351 [][][] [177] Underfull \hbox (badness 10000) detected at line 373 [][][] Underfull \hbox (badness 10000) detected at line 395 [][][] Underfull \hbox (badness 10000) detected at line 403 [][][] Underfull \hbox (badness 10000) detected at line 424 [][][] [178] Underfull \hbox (badness 10000) detected at line 429 [][][] Underfull \hbox (badness 10000) detected at line 449 [][][] Underfull \hbox (badness 10000) detected at line 471 [][][] Underfull \hbox (badness 10000) detected at line 476 [][][] [179] Underfull \hbox (badness 10000) detected at line 500 [][][] Underfull \hbox (badness 10000) detected at line 517 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] ) (./group___vhal.tex [180] [181] [182] [183] Underfull \hbox (badness 10000) detected at line 380 [][][] Underfull \hbox (badness 10000) detected at line 411 [][][] [184] Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 445 [][][] Underfull \hbox (badness 10000) detected at line 476 [][][] Underfull \hbox (badness 10000) detected at line 493 [][][] Underfull \hbox (badness 10000) detected at line 516 [][][] [185] Underfull \hbox (badness 10000) detected at line 547 [][][] [186] Underfull \hbox (badness 10000) detected at line 682 [][][] Underfull \hbox (badness 10000) detected at line 729 [][][] [187] Underfull \hbox (badness 10000) detected at line 760 [][][] Underfull \hbox (badness 10000) detected at line 795 [][][] Underfull \hbox (badness 10000) detected at line 842 [][][] Missing character: There is no Å in font cmr10! Missing character: There is no Å in font cmr10! LaTeX Warning: Command \r invalid in math mode on input line 58. Missing character: There is no Å in font cmr10! [188] [189] Underfull \hbox (badness 10000) detected at line 1019 [][][] Underfull \hbox (badness 10000) detected at line 1022 [][][] Underfull \hbox (badness 10000) detected at line 1050 [][][] Underfull \hbox (badness 10000) detected at line 1053 [][][] Underfull \hbox (badness 10000) detected at line 1070 [][][] [190]) (./group___vmatrix.tex) (./group___vparam.tex [191] [192] Underfull \hbox (badness 10000) detected at line 120 [][][] Underfull \hbox (badness 10000) detected at line 130 [][][] [193] Underfull \hbox (badness 10000) detected at line 147 [][][] Underfull \hbox (badness 10000) detected at line 157 [][][] Underfull \hbox (badness 10000) detected at line 174 [][][] Underfull \hbox (badness 10000) detected at line 198 [][][] [194] Underfull \hbox (badness 10000) detected at line 222 [][][] Underfull \hbox (badness 10000) detected at line 225 [][][] Underfull \hbox (badness 10000) detected at line 242 [][][] Underfull \hbox (badness 10000) detected at line 250 [][][] Underfull \hbox (badness 10000) detected at line 267 [][][] [195] Underfull \hbox (badness 10000) detected at line 289 [][][] Underfull \hbox (badness 10000) detected at line 311 [][][] Underfull \hbox (badness 10000) detected at line 314 [][][] Underfull \hbox (badness 10000) detected at line 331 [][][] Underfull \hbox (badness 10000) detected at line 339 [][][] Underfull \hbox (badness 10000) detected at line 356 [][][] [196] Underfull \hbox (badness 10000) detected at line 378 [][][] Underfull \hbox (badness 10000) detected at line 400 [][][] Underfull \hbox (badness 10000) detected at line 412 [][][] Underfull \hbox (badness 10000) detected at line 415 [][][] Underfull \hbox (badness 10000) detected at line 418 [][][] [197] Underfull \hbox (badness 10000) detected at line 435 [][][] Underfull \hbox (badness 10000) detected at line 445 [][][] Underfull \hbox (badness 10000) detected at line 448 [][][] Underfull \hbox (badness 10000) detected at line 451 [][][] Underfull \hbox (badness 10000) detected at line 468 [][][] Underfull \hbox (badness 10000) detected at line 476 [][][] [198] Underfull \hbox (badness 10000) detected at line 493 [][][] Underfull \hbox (badness 10000) detected at line 509 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Underfull \hbox (badness 10000) detected at line 537 [][][] [199] Underfull \hbox (badness 10000) detected at line 553 [][][] Underfull \hbox (badness 10000) detected at line 570 [][][] Underfull \hbox (badness 10000) detected at line 594 [][][] Underfull \hbox (badness 10000) detected at line 602 [][][] [200] Underfull \hbox (badness 10000) detected at line 619 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] Underfull \hbox (badness 10000) detected at line 646 [][][] Underfull \hbox (badness 10000) detected at line 668 [][][] [201]) (./group___vpbe.tex [202] [203] Underfull \hbox (badness 10000) detected at line 128 [][][] Underfull \hbox (badness 10000) detected at line 131 [][][] LaTeX Warning: Command \r invalid in math mode on input line 133. Missing character: There is no Å in font cmr10! LaTeX Warning: Command \r invalid in math mode on input line 133. Missing character: There is no Å in font cmr10! [204] Underfull \hbox (badness 10000) detected at line 136 [][][] [205] Underfull \hbox (badness 10000) detected at line 186 [][][] Underfull \hbox (badness 10000) detected at line 189 [][][] LaTeX Warning: Command \r invalid in math mode on input line 190. Missing character: There is no Å in font cmr10! LaTeX Warning: Command \r invalid in math mode on input line 190. Missing character: There is no Å in font cmr10! Underfull \hbox (badness 10000) detected at line 195 [][][] Overfull \vbox (21.60152pt too high) has occurred while \output is active [206] Underfull \hbox (badness 10000) detected at line 247 [][][] Underfull \hbox (badness 10000) detected at line 269 [][][] Underfull \hbox (badness 10000) detected at line 291 [][][] Underfull \hbox (badness 10000) detected at line 299 [][][] [207] Overfull \hbox (151.96916pt too wide) in paragraph at lines 318--318 [] \T1/p cr/m/n/8 permittivity equal to the protein interior) and zero ionic[] Underfull \hbox (badness 10000) detected at line 325 [][][] Underfull \hbox (badness 10000) detected at line 333 [][][] Underfull \hbox (badness 10000) detected at line 350 [][][] Underfull \hbox (badness 10000) detected at line 358 [][][] [208] Underfull \hbox (badness 10000) detected at line 375 [][][] Underfull \hbox (badness 10000) detected at line 383 [][][] Underfull \hbox (badness 10000) detected at line 396 [][][] Underfull \hbox (badness 10000) detected at line 412 [][][] [209] Underfull \hbox (badness 10000) detected at line 436 [][][] Underfull \hbox (badness 10000) detected at line 453 [][][] Underfull \hbox (badness 10000) detected at line 461 [][][] Underfull \hbox (badness 10000) detected at line 478 [][][] Underfull \hbox (badness 10000) detected at line 486 [][][] Underfull \hbox (badness 10000) detected at line 503 [][][] [210] Underfull \hbox (badness 10000) detected at line 525 [][][] Underfull \hbox (badness 10000) detected at line 533 [][][] Underfull \hbox (badness 10000) detected at line 550 [][][] Underfull \hbox (badness 10000) detected at line 558 [][][] Underfull \hbox (badness 10000) detected at line 575 [][][] [211] Underfull \hbox (badness 10000) detected at line 583 [][][] Underfull \hbox (badness 10000) detected at line 600 [][][] Underfull \hbox (badness 10000) detected at line 608 [][][] Underfull \hbox (badness 10000) detected at line 625 [][][] Underfull \hbox (badness 10000) detected at line 633 [][][] [212] Underfull \hbox (badness 10000) detected at line 650 [][][] Underfull \hbox (badness 10000) detected at line 658 [][][] Underfull \hbox (badness 10000) detected at line 675 [][][] Underfull \hbox (badness 10000) detected at line 683 [][][] Underfull \hbox (badness 10000) detected at line 700 [][][] Underfull \hbox (badness 10000) detected at line 708 [][][] [213] Underfull \hbox (badness 10000) detected at line 725 [][][] Underfull \hbox (badness 10000) detected at line 733 [][][] Underfull \hbox (badness 10000) detected at line 750 [][][] Underfull \hbox (badness 10000) detected at line 758 [][][] Underfull \hbox (badness 10000) detected at line 775 [][][] [214] Underfull \hbox (badness 10000) detected at line 783 [][][] Underfull \hbox (badness 10000) detected at line 800 [][][] Underfull \hbox (badness 10000) detected at line 808 [][][] Underfull \hbox (badness 10000) detected at line 825 [][][] Underfull \hbox (badness 10000) detected at line 833 [][][] [215] Underfull \hbox (badness 10000) detected at line 850 [][][] Underfull \hbox (badness 10000) detected at line 858 [][][] LaTeX Warning: Command \r invalid in math mode on input line 859. Missing character: There is no Å in font cmr10! Underfull \hbox (badness 10000) detected at line 875 [][][] Underfull \hbox (badness 10000) detected at line 883 [][][] Underfull \hbox (badness 10000) detected at line 900 [][][] Underfull \hbox (badness 10000) detected at line 908 [][][] [216] Underfull \hbox (badness 10000) detected at line 925 [][][] Underfull \hbox (badness 10000) detected at line 933 [][][] ) (./group___vstring.tex [217] Underfull \hbox (badness 10000) detected at line 42 [][][] Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 67 [][][] Underfull \hbox (badness 10000) detected at line 70 [][][] Underfull \hbox (badness 10000) detected at line 80 [][][] Underfull \hbox (badness 10000) detected at line 93 [][][] [218] Underfull \hbox (badness 10000) detected at line 96 [][][] Underfull \hbox (badness 10000) detected at line 99 [][][] Underfull \hbox (badness 10000) detected at line 102 [][][] Underfull \hbox (badness 10000) detected at line 105 [][][] ) (./group___vunit.tex [219] LaTeX Warning: Command \r invalid in math mode on input line 39. Missing character: There is no Å in font cmr9! [220] LaTeX Warning: Command \r invalid in math mode on input line 142. Missing character: There is no Å in font cmr10! ) (./group___vgrid.tex [221] [222] [223] Underfull \hbox (badness 10000) detected at line 125 [][][] Underfull \hbox (badness 10000) detected at line 151 [][][] Underfull \hbox (badness 10000) detected at line 168 [][][] [224] Underfull \hbox (badness 10000) detected at line 196 [][][] Underfull \hbox (badness 10000) detected at line 213 [][][] Underfull \hbox (badness 10000) detected at line 229 [][][] [225] Underfull \hbox (badness 10000) detected at line 246 [][][] Underfull \hbox (badness 10000) detected at line 268 [][][] Underfull \hbox (badness 10000) detected at line 290 [][][] Underfull \hbox (badness 10000) detected at line 302 [][][] [226] Underfull \hbox (badness 10000) detected at line 319 [][][] Underfull \hbox (badness 10000) detected at line 327 [][][] Underfull \hbox (badness 10000) detected at line 344 [][][] Underfull \hbox (badness 10000) detected at line 352 [][][] Underfull \hbox (badness 10000) detected at line 369 [][][] Underfull \hbox (badness 10000) detected at line 377 [][][] [227] Underfull \hbox (badness 10000) detected at line 395 [][][] Underfull \hbox (badness 10000) detected at line 403 [][][] Underfull \hbox (badness 10000) detected at line 420 [][][] Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 445 [][][] [228] Underfull \hbox (badness 10000) detected at line 453 [][][] Underfull \hbox (badness 10000) detected at line 470 [][][] Underfull \hbox (badness 10000) detected at line 473 [][][] Underfull \hbox (badness 10000) detected at line 489 [][][] Underfull \hbox (badness 10000) detected at line 492 [][][] [229] Underfull \hbox (badness 10000) detected at line 509 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Underfull \hbox (badness 10000) detected at line 528 [][][] Underfull \hbox (badness 10000) detected at line 531 [][][] Underfull \hbox (badness 10000) detected at line 548 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] [230] Underfull \hbox (badness 10000) detected at line 575 [][][] Underfull \hbox (badness 10000) detected at line 583 [][][] Underfull \hbox (badness 10000) detected at line 600 [][][] Underfull \hbox (badness 10000) detected at line 612 [][][] [231] Underfull \hbox (badness 10000) detected at line 629 [][][] Underfull \hbox (badness 10000) detected at line 663 [][][] [232] Underfull \hbox (badness 10000) detected at line 697 [][][] Underfull \hbox (badness 10000) detected at line 702 [][][] ) (./group___vmgrid.tex [233] [234] Underfull \hbox (badness 10000) detected at line 105 [][][] Underfull \hbox (badness 10000) detected at line 115 [][][] Underfull \hbox (badness 10000) detected at line 132 [][][] Underfull \hbox (badness 10000) detected at line 135 [][][] Underfull \hbox (badness 10000) detected at line 152 [][][] [235] Underfull \hbox (badness 10000) detected at line 160 [][][] Underfull \hbox (badness 10000) detected at line 177 [][][] Underfull \hbox (badness 10000) detected at line 193 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] [236] Underfull \hbox (badness 10000) detected at line 232 [][][] Underfull \hbox (badness 10000) detected at line 254 [][][] Underfull \hbox (badness 10000) detected at line 264 [][][] Underfull \hbox (badness 10000) detected at line 277 [][][] [237] Underfull \hbox (badness 10000) detected at line 287 [][][] Underfull \hbox (badness 10000) detected at line 300 [][][] Underfull \hbox (badness 10000) detected at line 312 [][][] Underfull \hbox (badness 10000) detected at line 329 [][][] Underfull \hbox (badness 10000) detected at line 341 [][][] ) (./group___vopot.tex [238] [239] Underfull \hbox (badness 10000) detected at line 77 [][][] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 106 [][][] [240] Underfull \hbox (badness 10000) detected at line 120 [][][] Underfull \hbox (badness 10000) detected at line 137 [][][] Underfull \hbox (badness 10000) detected at line 153 [][][] Underfull \hbox (badness 10000) detected at line 170 [][][] [241] Underfull \hbox (badness 10000) detected at line 192 [][][] Underfull \hbox (badness 10000) detected at line 214 [][][] Underfull \hbox (badness 10000) detected at line 226 [][][] Underfull \hbox (badness 10000) detected at line 243 [][][] Overfull \vbox (28.1848pt too high) has occurred while \output is active [242] Underfull \hbox (badness 10000) detected at line 255 [][][] ) (./group___vpmg.tex [243] [244] [245] Underfull \hbox (badness 10000) detected at line 117 [][][] Underfull \hbox (badness 10000) detected at line 150 [][][] [246] Underfull \hbox (badness 10000) detected at line 186 [][][] [247] Underfull \hbox (badness 10000) detected at line 234 [][][] Underfull \hbox (badness 10000) detected at line 276 [][][] [248] Underfull \hbox (badness 10000) detected at line 324 [][][] [249] Underfull \hbox (badness 10000) detected at line 362 [][][] Underfull \hbox (badness 10000) detected at line 381 [][][] Underfull \hbox (badness 10000) detected at line 384 [][][] [250] Underfull \hbox (badness 10000) detected at line 416 [][][] Underfull \hbox (badness 10000) detected at line 419 [][][] Underfull \hbox (badness 10000) detected at line 422 [][][] [251] Underfull \hbox (badness 10000) detected at line 458 [][][] Underfull \hbox (badness 10000) detected at line 484 [][][] Underfull \hbox (badness 10000) detected at line 487 [][][] Underfull \hbox (badness 10000) detected at line 492 [][][] Overfull \vbox (1.11014pt too high) has occurred while \output is active [252] Underfull \hbox (badness 10000) detected at line 520 [][][] Underfull \hbox (badness 10000) detected at line 546 [][][] [253] Underfull \hbox (badness 10000) detected at line 572 [][][] Underfull \hbox (badness 10000) detected at line 604 [][][] Underfull \hbox (badness 10000) detected at line 607 [][][] Underfull \hbox (badness 10000) detected at line 610 [][][] [254] Underfull \hbox (badness 10000) detected at line 643 [][][] Underfull \hbox (badness 10000) detected at line 646 [][][] Underfull \hbox (badness 10000) detected at line 668 [][][] Underfull \hbox (badness 10000) detected at line 690 [][][] [255] Underfull \hbox (badness 10000) detected at line 712 [][][] Underfull \hbox (badness 10000) detected at line 715 [][][] Underfull \hbox (badness 10000) detected at line 718 [][][] Underfull \hbox (badness 10000) detected at line 742 [][][] [256] Underfull \hbox (badness 10000) detected at line 764 [][][] Underfull \hbox (badness 10000) detected at line 767 [][][] Underfull \hbox (badness 10000) detected at line 799 [][][] [257] Underfull \hbox (badness 10000) detected at line 802 [][][] Underfull \hbox (badness 10000) detected at line 856 [][][] Underfull \hbox (badness 10000) detected at line 859 [][][] Underfull \hbox (badness 10000) detected at line 864 [][][] [258] Underfull \hbox (badness 10000) detected at line 894 [][][] Underfull \hbox (badness 10000) detected at line 920 [][][] Underfull \hbox (badness 10000) detected at line 923 [][][] [259] Underfull \hbox (badness 10000) detected at line 928 [][][] Underfull \hbox (badness 10000) detected at line 956 [][][] Underfull \hbox (badness 10000) detected at line 982 [][][] [260] Underfull \hbox (badness 10000) detected at line 1008 [][][] Underfull \hbox (badness 10000) detected at line 1030 [][][] Underfull \hbox (badness 10000) detected at line 1033 [][][] [261] Underfull \hbox (badness 10000) detected at line 1055 [][][] Underfull \hbox (badness 10000) detected at line 1093 [][][] Underfull \hbox (badness 10000) detected at line 1096 [][][] [262] Underfull \hbox (badness 10000) detected at line 1099 [][][] Underfull \hbox (badness 10000) detected at line 1123 [][][] Underfull \hbox (badness 10000) detected at line 1160 [][][] [263] Underfull \hbox (badness 10000) detected at line 1163 [][][] Underfull \hbox (badness 10000) detected at line 1166 [][][] Underfull \hbox (badness 10000) detected at line 1190 [][][] Underfull \hbox (badness 10000) detected at line 1193 [][][] Underfull \hbox (badness 10000) detected at line 1198 [][][] [264] Underfull \hbox (badness 10000) detected at line 1226 [][][] Underfull \hbox (badness 10000) detected at line 1252 [][][] [265] Underfull \hbox (badness 10000) detected at line 1280 [][][] Underfull \hbox (badness 10000) detected at line 1283 [][][] Underfull \hbox (badness 10000) detected at line 1303 [][][] [266] Underfull \hbox (badness 10000) detected at line 1343 [][][] Underfull \hbox (badness 10000) detected at line 1346 [][][] Underfull \hbox (badness 10000) detected at line 1349 [][][] Underfull \hbox (badness 10000) detected at line 1373 [][][] [267] Underfull \hbox (badness 10000) detected at line 1401 [][][] Underfull \hbox (badness 10000) detected at line 1404 [][][] Underfull \hbox (badness 10000) detected at line 1426 [][][] Underfull \hbox (badness 10000) detected at line 1429 [][][] Underfull \hbox (badness 10000) detected at line 1432 [][][] Underfull \hbox (badness 10000) detected at line 1454 [][][] ) (./group___vpmgp.tex [268] Underfull \hbox (badness 10000) detected at line 45 [][][] [269] Underfull \hbox (badness 10000) detected at line 78 [][][] Underfull \hbox (badness 10000) detected at line 86 [][][] Underfull \hbox (badness 10000) detected at line 103 [][][] Underfull \hbox (badness 10000) detected at line 113 [][][] Underfull \hbox (badness 10000) detected at line 130 [][][] [270] Underfull \hbox (badness 10000) detected at line 152 [][][] Underfull \hbox (badness 10000) detected at line 174 [][][] [271] Underfull \hbox (badness 10000) detected at line 208 [][][] ) (./group___p_m_g_c.tex [272] [273] [274] [275] Underfull \hbox (badness 10000) detected at line 150 [][][] Underfull \hbox (badness 10000) detected at line 153 [][][] Underfull \hbox (badness 10000) detected at line 156 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 165--165 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [276] Underfull \hbox (badness 10000) detected at line 212 [][][] Underfull \hbox (badness 10000) detected at line 215 [][][] Underfull \hbox (badness 10000) detected at line 218 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 227--227 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [277] Underfull \hbox (badness 10000) detected at line 277 [][][] Underfull \hbox (badness 10000) detected at line 280 [][][] [278] Underfull \hbox (badness 10000) detected at line 308 [][][] Underfull \hbox (badness 10000) detected at line 311 [][][] Underfull \hbox (badness 10000) detected at line 339 [][][] Underfull \hbox (badness 10000) detected at line 342 [][][] Underfull \hbox (badness 10000) detected at line 345 [][][] [279] Overfull \hbox (304.08286pt too wide) in paragraph at lines 355--355 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 392 [][][] Underfull \hbox (badness 10000) detected at line 395 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 404--404 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [280] Underfull \hbox (badness 10000) detected at line 439 [][][] [281] Underfull \hbox (badness 10000) detected at line 503 [][][] Underfull \hbox (badness 10000) detected at line 506 [][][] Underfull \hbox (badness 10000) detected at line 509 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 518--518 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [282] Underfull \hbox (badness 10000) detected at line 556 [][][] Underfull \hbox (badness 10000) detected at line 559 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 568--568 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 603 [][][] Underfull \hbox (badness 10000) detected at line 606 [][][] [283] Underfull \hbox (badness 10000) detected at line 646 [][][] Underfull \hbox (badness 10000) detected at line 649 [][][] [284] [285] Underfull \hbox (badness 10000) detected at line 719 [][][] Underfull \hbox (badness 10000) detected at line 722 [][][] Underfull \hbox (badness 10000) detected at line 772 [][][] Underfull \hbox (badness 10000) detected at line 775 [][][] Underfull \hbox (badness 10000) detected at line 778 [][][] [286] Overfull \hbox (304.08286pt too wide) in paragraph at lines 788--788 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 825 [][][] Underfull \hbox (badness 10000) detected at line 828 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 837--837 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [287] [288] Underfull \hbox (badness 10000) detected at line 907 [][][] Underfull \hbox (badness 10000) detected at line 910 [][][] [289] [290] [291] Underfull \hbox (badness 10000) detected at line 1050 [][][] Underfull \hbox (badness 10000) detected at line 1053 [][][] [292] [293] [294] Underfull \hbox (badness 10000) detected at line 1229 [][][] Underfull \hbox (badness 10000) detected at line 1232 [][][] [295] [296] Underfull \hbox (badness 10000) detected at line 1382 [][][] Underfull \hbox (badness 10000) detected at line 1385 [][][] Underfull \hbox (badness 10000) detected at line 1388 [][][] [297] [298] Underfull \hbox (badness 10000) detected at line 1446 [][][] Underfull \hbox (badness 10000) detected at line 1449 [][][] Underfull \hbox (badness 10000) detected at line 1452 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 1462--1462 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 1501 [][][] Underfull \hbox (badness 10000) detected at line 1504 [][][] [299] [300] Underfull \hbox (badness 10000) detected at line 1584 [][][] Underfull \hbox (badness 10000) detected at line 1587 [][][] Underfull \hbox (badness 10000) detected at line 1590 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 1600--1600 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 1637 [][][] Underfull \hbox (badness 10000) detected at line 1640 [][][] [301] Underfull \hbox (badness 10000) detected at line 1643 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 1652--1652 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Overfull \vbox (9.44278pt too high) has occurred while \output is active [302] Underfull \hbox (badness 10000) detected at line 1730 [][][] Underfull \hbox (badness 10000) detected at line 1735 [][][] Underfull \hbox (badness 10000) detected at line 1738 [][][] Underfull \hbox (badness 10000) detected at line 1768 [][][] Underfull \hbox (badness 10000) detected at line 1771 [][][] [303] Underfull \hbox (badness 10000) detected at line 1805 [][][] Underfull \hbox (badness 10000) detected at line 1808 [][][] [304] Underfull \hbox (badness 10000) detected at line 1842 [][][] Underfull \hbox (badness 10000) detected at line 1845 [][][] Underfull \hbox (badness 10000) detected at line 1879 [][][] Underfull \hbox (badness 10000) detected at line 1882 [][][] [305] Underfull \hbox (badness 10000) detected at line 1885 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 1895--1895 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 1932 [][][] Underfull \hbox (badness 10000) detected at line 1935 [][][] Underfull \hbox (badness 10000) detected at line 1938 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 1947--1947 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [306] [307] Underfull \hbox (badness 10000) detected at line 2033 [][][] Underfull \hbox (badness 10000) detected at line 2036 [][][] Underfull \hbox (badness 10000) detected at line 2070 [][][] Underfull \hbox (badness 10000) detected at line 2073 [][][] Underfull \hbox (badness 10000) detected at line 2076 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 2086--2086 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [308] Underfull \hbox (badness 10000) detected at line 2123 [][][] Underfull \hbox (badness 10000) detected at line 2126 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2135--2135 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [309] Underfull \hbox (badness 10000) detected at line 2170 [][][] Underfull \hbox (badness 10000) detected at line 2173 [][][] Underfull \hbox (badness 10000) detected at line 2205 [][][] [310] Underfull \hbox (badness 10000) detected at line 2208 [][][] Underfull \hbox (badness 10000) detected at line 2244 [][][] Underfull \hbox (badness 10000) detected at line 2247 [][][] [311] Underfull \hbox (badness 10000) detected at line 2283 [][][] Underfull \hbox (badness 10000) detected at line 2286 [][][] [312] Underfull \hbox (badness 10000) detected at line 2314 [][][] Underfull \hbox (badness 10000) detected at line 2317 [][][] Underfull \hbox (badness 10000) detected at line 2320 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 2330--2330 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [313] Underfull \hbox (badness 10000) detected at line 2367 [][][] Underfull \hbox (badness 10000) detected at line 2370 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2379--2379 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 2414 [][][] Underfull \hbox (badness 10000) detected at line 2417 [][][] [314] [315] Underfull \hbox (badness 10000) detected at line 2503 [][][] Underfull \hbox (badness 10000) detected at line 2506 [][][] Underfull \hbox (badness 10000) detected at line 2509 [][][] [316] Underfull \hbox (badness 10000) detected at line 2557 [][][] Underfull \hbox (badness 10000) detected at line 2560 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2569--2569 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [317] Underfull \hbox (badness 10000) detected at line 2604 [][][] Underfull \hbox (badness 10000) detected at line 2607 [][][] [318] Underfull \hbox (badness 10000) detected at line 2697 [][][] Underfull \hbox (badness 10000) detected at line 2700 [][][] [319] Underfull \hbox (badness 10000) detected at line 2746 [][][] Underfull \hbox (badness 10000) detected at line 2749 [][][] Underfull \hbox (badness 10000) detected at line 2752 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 2762--2762 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [320] Underfull \hbox (badness 10000) detected at line 2799 [][][] Underfull \hbox (badness 10000) detected at line 2802 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2811--2811 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 2846 [][][] Underfull \hbox (badness 10000) detected at line 2849 [][][] [321] Underfull \hbox (badness 10000) detected at line 2905 [][][] Underfull \hbox (badness 10000) detected at line 2908 [][][] Overfull \vbox (18.98318pt too high) has occurred while \output is active [322] Underfull \hbox (badness 10000) detected at line 2946 [][][] Underfull \hbox (badness 10000) detected at line 2957 [][][] [323] Underfull \hbox (badness 10000) detected at line 2960 [][][] [324] Underfull \hbox (badness 10000) detected at line 3046 [][][] Underfull \hbox (badness 10000) detected at line 3049 [][][] Underfull \hbox (badness 10000) detected at line 3052 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3062--3062 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 3099 [][][] Underfull \hbox (badness 10000) detected at line 3102 [][][] [325] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 3111--3111 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 3146 [][][] Underfull \hbox (badness 10000) detected at line 3149 [][][] [326] Underfull \hbox (badness 10000) detected at line 3187 [][][] Underfull \hbox (badness 10000) detected at line 3190 [][][] Underfull \hbox (badness 10000) detected at line 3193 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3203--3203 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [327] Underfull \hbox (badness 10000) detected at line 3240 [][][] Underfull \hbox (badness 10000) detected at line 3243 [][][] Underfull \hbox (badness 10000) detected at line 3246 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 3255--3255 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [328] Underfull \hbox (badness 10000) detected at line 3288 [][][] [329] Underfull \hbox (badness 10000) detected at line 3342 [][][] [330] [331] Underfull \hbox (badness 10000) detected at line 3484 [][][] [332] Underfull \hbox (badness 10000) detected at line 3542 [][][] Underfull \hbox (badness 10000) detected at line 3545 [][][] [333] Underfull \hbox (badness 10000) detected at line 3585 [][][] Underfull \hbox (badness 10000) detected at line 3588 [][][] Underfull \hbox (badness 10000) detected at line 3591 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3601--3601 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [334] Underfull \hbox (badness 10000) detected at line 3638 [][][] Underfull \hbox (badness 10000) detected at line 3641 [][][] Underfull \hbox (badness 10000) detected at line 3644 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 3653--3653 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [335] Underfull \hbox (badness 10000) detected at line 3702 [][][] Underfull \hbox (badness 10000) detected at line 3705 [][][] [336] [337] Underfull \hbox (badness 10000) detected at line 3789 [][][] Underfull \hbox (badness 10000) detected at line 3792 [][][] [338] Underfull \hbox (badness 10000) detected at line 3890 [][][] Underfull \hbox (badness 10000) detected at line 3893 [][][] Underfull \hbox (badness 10000) detected at line 3896 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3906--3906 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [339] Underfull \hbox (badness 10000) detected at line 3943 [][][] Underfull \hbox (badness 10000) detected at line 3946 [][][] Underfull \hbox (badness 10000) detected at line 3972 [][][] Underfull \hbox (badness 10000) detected at line 3975 [][][] [340] Underfull \hbox (badness 10000) detected at line 4001 [][][] Underfull \hbox (badness 10000) detected at line 4004 [][][] [341] Underfull \hbox (badness 10000) detected at line 4034 [][][] Underfull \hbox (badness 10000) detected at line 4037 [][][] Underfull \hbox (badness 10000) detected at line 4040 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 4050--4050 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 4087 [][][] [342] Underfull \hbox (badness 10000) detected at line 4090 [][][] Underfull \hbox (badness 10000) detected at line 4093 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 4102--4102 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 4137 [][][] Underfull \hbox (badness 10000) detected at line 4140 [][][] [343] Underfull \hbox (badness 10000) detected at line 4194 [][][] [344] Underfull \hbox (badness 10000) detected at line 4216 [][][] Overfull \vbox (38.14133pt too high) has occurred while \output is active [345] Underfull \hbox (badness 10000) detected at line 4290 [][][] Underfull \hbox (badness 10000) detected at line 4293 [][][] [346] [347] Underfull \hbox (badness 10000) detected at line 4383 [][][] Underfull \hbox (badness 10000) detected at line 4386 [][][] Underfull \hbox (badness 10000) detected at line 4426 [][][] Underfull \hbox (badness 10000) detected at line 4429 [][][] [348] Underfull \hbox (badness 10000) detected at line 4471 [][][] Underfull \hbox (badness 10000) detected at line 4474 [][][] [349] Underfull \hbox (badness 10000) detected at line 4532 [][][] Underfull \hbox (badness 10000) detected at line 4535 [][][] Underfull \hbox (badness 10000) detected at line 4538 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 4548--4548 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [350] Underfull \hbox (badness 10000) detected at line 4585 [][][] Underfull \hbox (badness 10000) detected at line 4588 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 4597--4597 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [351] Underfull \hbox (badness 10000) detected at line 4630 [][][] Underfull \hbox (badness 10000) detected at line 4633 [][][] Underfull \hbox (badness 10000) detected at line 4636 [][][] [352] Underfull \hbox (badness 10000) detected at line 4692 [][][] Underfull \hbox (badness 10000) detected at line 4695 [][][] Underfull \hbox (badness 10000) detected at line 4727 [][][] Underfull \hbox (badness 10000) detected at line 4730 [][][] [353] Underfull \hbox (badness 10000) detected at line 4768 [][][] Underfull \hbox (badness 10000) detected at line 4771 [][][] Underfull \hbox (badness 10000) detected at line 4774 [][][] Overfull \hbox (20.88268pt too wide) in paragraph at lines 4784--4784 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute,[] [354] Underfull \hbox (badness 10000) detected at line 4822 [][][] Underfull \hbox (badness 10000) detected at line 4825 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 4834--4834 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [355] Underfull \hbox (badness 10000) detected at line 4869 [][][] Underfull \hbox (badness 10000) detected at line 4872 [][][] [356] Underfull \hbox (badness 10000) detected at line 4930 [][][] Underfull \hbox (badness 10000) detected at line 4933 [][][] Underfull \hbox (badness 10000) detected at line 4965 [][][] Underfull \hbox (badness 10000) detected at line 4968 [][][] Underfull \hbox (badness 10000) detected at line 4971 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 4981--4981 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [357] Underfull \hbox (badness 10000) detected at line 5018 [][][] Underfull \hbox (badness 10000) detected at line 5021 [][][] Underfull \hbox (badness 10000) detected at line 5024 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 5033--5033 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [358] Underfull \hbox (badness 10000) detected at line 5068 [][][] Underfull \hbox (badness 10000) detected at line 5071 [][][] Underfull \hbox (badness 10000) detected at line 5101 [][][] Underfull \hbox (badness 10000) detected at line 5104 [][][] Underfull \hbox (badness 10000) detected at line 5107 [][][] [359] Underfull \hbox (badness 10000) detected at line 5137 [][][] Underfull \hbox (badness 10000) detected at line 5140 [][][] Underfull \hbox (badness 10000) detected at line 5170 [][][] [360] Underfull \hbox (badness 10000) detected at line 5173 [][][] Underfull \hbox (badness 10000) detected at line 5203 [][][] Underfull \hbox (badness 10000) detected at line 5206 [][][] Underfull \hbox (badness 10000) detected at line 5234 [][][] [361] Underfull \hbox (badness 10000) detected at line 5237 [][][] Underfull \hbox (badness 10000) detected at line 5265 [][][] Underfull \hbox (badness 10000) detected at line 5268 [][][] ) (./group___frontend.tex [362] Underfull \hbox (badness 2495) in paragraph at lines 32--33 []\T1/phv/m/n/10 VPUBLIC Vrc[]_[][]Codes [] (int icalc, [] $\OMS/cmsy/m/n/10 ^^ C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 feparm, [] $\OMS /cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbeparm, [] Overfull \hbox (16.65858pt too wide) in paragraph at lines 40--41 []\T1/phv/m/n/10 VEXTERNC int [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], Overfull \hbox (16.91972pt too wide) in paragraph at lines 42--43 []\T1/phv/m/n/10 VEXTERNC void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh , [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/1 0 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], Underfull \hbox (badness 1910) in paragraph at lines 60--61 [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1 /phv/m/n/10 alist[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][] [], [] Underfull \hbox (badness 1237) in paragraph at lines 60--61 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 charge[]Map[][][], [] $\OMS/cmsy/m/n/10 ^^C $\T1/phv/m/n/10 pmgp[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pmg[][][], [] [363] Underfull \hbox (badness 5817) in paragraph at lines 78--79 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], Underfull \hbox (badness 5817) in paragraph at lines 80--81 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], [364] [365] Underfull \hbox (badness 10000) detected at line 178 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 211 [][][] [366] Underfull \hbox (badness 10000) detected at line 235 [][][] [367] Underfull \hbox (badness 10000) detected at line 275 [][][] Underfull \hbox (badness 10000) detected at line 297 [][][] Underfull \hbox (badness 10000) detected at line 314 [][][] Underfull \hbox (badness 10000) detected at line 317 [][][] [368] Underfull \hbox (badness 10000) detected at line 351 [][][] Underfull \hbox (badness 10000) detected at line 373 [][][] Underfull \hbox (badness 10000) detected at line 390 [][][] Underfull \hbox (badness 10000) detected at line 393 [][][] [369] [370] Underfull \hbox (badness 10000) detected at line 495 [][][] Underfull \hbox (badness 10000) detected at line 502 [][][] [371] Underfull \hbox (badness 10000) detected at line 572 [][][] Underfull \hbox (badness 10000) detected at line 575 [][][] [372] Underfull \hbox (badness 10000) detected at line 625 [][][] Underfull \hbox (badness 10000) detected at line 649 [][][] Underfull \hbox (badness 10000) detected at line 677 [][][] [373] Underfull \hbox (badness 10000) detected at line 694 [][][] Underfull \hbox (badness 10000) detected at line 720 [][][] Underfull \hbox (badness 10000) detected at line 748 [][][] [374] Underfull \hbox (badness 10000) detected at line 772 [][][] Underfull \hbox (badness 10000) detected at line 792 [][][] Underfull \hbox (badness 10000) detected at line 818 [][][] [375] Underfull \hbox (badness 10000) detected at line 842 [][][] Underfull \hbox (badness 10000) detected at line 866 [][][] Underfull \hbox (badness 10000) detected at line 876 [][][] Underfull \hbox (badness 10000) detected at line 895 [][][] [376] Underfull \hbox (badness 10000) detected at line 909 [][][] Underfull \hbox (badness 10000) detected at line 912 [][][] Underfull \hbox (badness 10000) detected at line 929 [][][] Underfull \hbox (badness 10000) detected at line 939 [][][] Underfull \hbox (badness 10000) detected at line 958 [][][] Underfull \hbox (badness 10000) detected at line 961 [][][] [377] Underfull \hbox (badness 10000) detected at line 981 [][][] Underfull \hbox (badness 10000) detected at line 984 [][][] Underfull \hbox (badness 10000) detected at line 1010 [][][] Underfull \hbox (badness 10000) detected at line 1013 [][][] [378] Underfull \hbox (badness 10000) detected at line 1035 [][][] Underfull \hbox (badness 10000) detected at line 1045 [][][] Underfull \hbox (badness 10000) detected at line 1064 [][][] Underfull \hbox (badness 10000) detected at line 1067 [][][] Underfull \hbox (badness 10000) detected at line 1091 [][][] [379] Underfull \hbox (badness 10000) detected at line 1105 [][][] Underfull \hbox (badness 10000) detected at line 1122 [][][] Underfull \hbox (badness 10000) detected at line 1134 [][][] Underfull \hbox (badness 10000) in paragraph at lines 1135--1136 Underfull \hbox (badness 10000) detected at line 1138 [][][] [380] Underfull \hbox (badness 10000) detected at line 1166 [][][] Underfull \hbox (badness 10000) detected at line 1180 [][][] Underfull \hbox (badness 10000) detected at line 1201 [][][] Underfull \hbox (badness 10000) detected at line 1204 [][][] [381] Underfull \hbox (badness 10000) detected at line 1228 [][][] Underfull \hbox (badness 10000) detected at line 1231 [][][] Underfull \hbox (badness 10000) detected at line 1259 [][][] Underfull \hbox (badness 10000) detected at line 1262 [][][] [382] Underfull \hbox (badness 10000) detected at line 1288 [][][] Underfull \hbox (badness 10000) detected at line 1291 [][][] Underfull \hbox (badness 10000) detected at line 1319 [][][] Underfull \hbox (badness 10000) detected at line 1322 [][][] [383] Underfull \hbox (badness 10000) detected at line 1348 [][][] Underfull \hbox (badness 10000) detected at line 1377 [][][] Underfull \hbox (badness 10000) detected at line 1380 [][][] Underfull \hbox (badness 10000) detected at line 1408 [][][] [384] Underfull \hbox (badness 10000) detected at line 1432 [][][] Underfull \hbox (badness 10000) detected at line 1454 [][][] Underfull \hbox (badness 10000) detected at line 1468 [][][] [385] Underfull \hbox (badness 10000) detected at line 1485 [][][] Underfull \hbox (badness 10000) detected at line 1497 [][][] Underfull \hbox (badness 10000) detected at line 1514 [][][] Underfull \hbox (badness 10000) detected at line 1528 [][][] [386] Underfull \hbox (badness 10000) detected at line 1562 [][][] Underfull \hbox (badness 10000) detected at line 1574 [][][] Underfull \hbox (badness 10000) detected at line 1591 [][][] Underfull \hbox (badness 10000) detected at line 1608 [][][] [387] Underfull \hbox (badness 10000) detected at line 1636 [][][] Underfull \hbox (badness 10000) detected at line 1650 [][][] [388] Underfull \hbox (badness 10000) detected at line 1688 [][][] Underfull \hbox (badness 10000) detected at line 1716 [][][] Underfull \hbox (badness 10000) detected at line 1733 [][][] [389] Underfull \hbox (badness 10000) detected at line 1747 [][][] Underfull \hbox (badness 10000) detected at line 1764 [][][] Underfull \hbox (badness 10000) detected at line 1792 [][][] [390] Underfull \hbox (badness 10000) detected at line 1809 [][][] Underfull \hbox (badness 10000) detected at line 1823 [][][] ) [391] [392] Chapter 8. (./struct_atom_force.tex Underfull \hbox (badness 10000) detected at line 32 [][][] [393]) (./structs_a_p_o_lparm.tex [394] Underfull \hbox (badness 10000) detected at line 88 [][][] [395] Underfull \hbox (badness 10000) detected at line 224 [][][] [396] Underfull \hbox (badness 10000) detected at line 237 [][][] Underfull \hbox (badness 10000) detected at line 250 [][][] Underfull \hbox (badness 10000) detected at line 263 [][][] Underfull \hbox (badness 10000) detected at line 276 [][][] Underfull \hbox (badness 10000) detected at line 289 [][][] Underfull \hbox (badness 10000) detected at line 302 [][][] [397] Underfull \hbox (badness 10000) detected at line 315 [][][] Underfull \hbox (badness 10000) detected at line 328 [][][] Underfull \hbox (badness 10000) detected at line 341 [][][] Underfull \hbox (badness 10000) detected at line 354 [][][] Underfull \hbox (badness 10000) detected at line 367 [][][] Underfull \hbox (badness 10000) detected at line 380 [][][] [398]) (./structs_b_e_mparm.tex [399] Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 53 [][][] [400] Underfull \hbox (badness 10000) detected at line 129 [][][] Underfull \hbox (badness 10000) detected at line 142 [][][] Underfull \hbox (badness 10000) detected at line 155 [][][] [401] Underfull \hbox (badness 10000) detected at line 168 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 194 [][][] ) (./structs_f_e_mparm.tex [402] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) in paragraph at lines 84--85 [403] [404] [405]) (./structs_g_e_o_f_l_o_wparm.tex Underfull \hbox (badness 10000) detected at line 30 [][][] Underfull \hbox (badness 10000) detected at line 33 [][][] [406]) (./structs_m_gparm.tex [407] Underfull \hbox (badness 10000) detected at line 120 [][][] Underfull \hbox (badness 10000) detected at line 123 [][][] [408] Underfull \hbox (badness 10000) in paragraph at lines 149--150 Underfull \hbox (badness 10000) in paragraph at lines 180--181 [409] Underfull \hbox (badness 10000) in paragraph at lines 261--262 [410] [411] Underfull \hbox (badness 10000) detected at line 434 [][][] Underfull \hbox (badness 10000) detected at line 447 [][][] Underfull \hbox (badness 10000) detected at line 460 [][][] Underfull \hbox (badness 10000) detected at line 473 [][][] [412] Underfull \hbox (badness 10000) detected at line 486 [][][] Underfull \hbox (badness 10000) detected at line 499 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] Underfull \hbox (badness 10000) detected at line 538 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] [413] Underfull \hbox (badness 10000) detected at line 564 [][][] Underfull \hbox (badness 10000) detected at line 577 [][][] Underfull \hbox (badness 10000) detected at line 590 [][][] Underfull \hbox (badness 10000) detected at line 603 [][][] Underfull \hbox (badness 10000) detected at line 616 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] [414] Underfull \hbox (badness 10000) detected at line 642 [][][] Underfull \hbox (badness 10000) detected at line 655 [][][] Underfull \hbox (badness 10000) detected at line 668 [][][] ) (./structs_n_osh.tex [415] Underfull \hbox (badness 10000) detected at line 108 [][][] [416] [417] [418] [419] [420]) (./structs_n_osh__calc.tex [421] Underfull \hbox (badness 10000) detected at line 38 [][][] [422]) (./structs_p_b_a_mparm.tex [423] Underfull \hbox (badness 10000) detected at line 106 [][][] Underfull \hbox (badness 10000) detected at line 109 [][][] [424] [425] [426] [427]) (./structs_p_b_eparm.tex [428] [429] Underfull \hbox (badness 10000) detected at line 142 [][][] Underfull \hbox (badness 10000) detected at line 145 [][][] [430] [431] [432] Underfull \hbox (badness 10000) detected at line 391 [][][] Underfull \hbox (badness 10000) detected at line 404 [][][] Underfull \hbox (badness 10000) detected at line 417 [][][] Underfull \hbox (badness 10000) detected at line 430 [][][] [433] Underfull \hbox (badness 10000) detected at line 473 [][][] Underfull \hbox (badness 10000) detected at line 486 [][][] Underfull \hbox (badness 10000) detected at line 499 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] [434] Underfull \hbox (badness 10000) detected at line 538 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] Underfull \hbox (badness 10000) detected at line 564 [][][] Underfull \hbox (badness 10000) detected at line 577 [][][] Underfull \hbox (badness 10000) detected at line 590 [][][] Underfull \hbox (badness 10000) detected at line 603 [][][] [435] Underfull \hbox (badness 10000) detected at line 616 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] [436] [437]) (./structs_p_b_s_a_mparm.tex [438] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] [439]) (./structs_vacc.tex [440] Underfull \hbox (badness 10000) detected at line 36 [][][] [441]) (./structs_vacc_surf.tex Underfull \hbox (badness 10000) detected at line 36 [][][] [442]) (./structs_valist.tex [443] Underfull \hbox (badness 10000) detected at line 36 [][][] [444]) (./structs_vatom.tex Underfull \hbox (badness 10000) detected at line 36 [][][] Underfull \hbox (badness 10000) in paragraph at lines 62--63 [445] Underfull \hbox (badness 10000) in paragraph at lines 93--94 Underfull \hbox (badness 10000) in paragraph at lines 114--115 ) (./structs_vclist.tex [446] Underfull \hbox (badness 10000) detected at line 40 [][][] [447]) (./structs_vclist_cell.tex Underfull \hbox (badness 10000) detected at line 24 [][][] ) (./structs_vcsm.tex [448] Underfull \hbox (badness 10000) detected at line 42 [][][] [449]) (./structs_vfetk.tex [450] Underfull \hbox (badness 10000) detected at line 60 [][][] [451] Underfull \hbox (badness 10000) in paragraph at lines 116--117 [452]) (./structs_vfetk___local_var.tex [453] Underfull \hbox (badness 10000) detected at line 86 [][][] [454] [455] [456] [457]) (./structs_vgreen.tex Underfull \hbox (badness 10000) detected at line 34 [][][] [458]) (./structs_vgrid.tex [459] Underfull \hbox (badness 10000) detected at line 52 [][][] [460] [461]) (./structs_vmgrid.tex Underfull \hbox (badness 10000) detected at line 24 [][][] ) (./structs_vopot.tex [462] Underfull \hbox (badness 10000) detected at line 26 [][][] ) (./structs_vparam___atom_data.tex [463] Underfull \hbox (badness 10000) detected at line 30 [][][] Underfull \hbox (badness 10000) detected at line 33 [][][] ) (./structs_vpbe.tex [464] Underfull \hbox (badness 10000) detected at line 86 [][][] [465] [466] [467] [468]) (./structs_vpee.tex [469] Underfull \hbox (badness 10000) detected at line 34 [][][] ) (./structs_vpmg.tex [470] [471] Underfull \hbox (badness 10000) detected at line 116 [][][] [472] [473] [474] [475] [476]) (./structs_vpmgp.tex [477] Underfull \hbox (badness 10000) detected at line 126 [][][] [478] Underfull \hbox (badness 10000) in paragraph at lines 164--165 Underfull \hbox (badness 10000) in paragraph at lines 175--176 Underfull \hbox (badness 10000) in paragraph at lines 186--187 [479] Underfull \hbox (badness 10000) in paragraph at lines 234--235 [480] [481] [482] [483] Underfull \hbox (badness 10000) in paragraph at lines 506--507 Underfull \hbox (badness 10000) in paragraph at lines 527--528 [484] Underfull \hbox (badness 10000) in paragraph at lines 548--549 Underfull \hbox (badness 10000) in paragraph at lines 589--590 [485] Underfull \hbox (badness 10000) in paragraph at lines 630--631 Underfull \hbox (badness 10000) in paragraph at lines 671--672 ) (./struct_vparam.tex [486] Underfull \hbox (badness 10000) detected at line 26 [][][] ) (./struct_vparam___res_data.tex [487] Underfull \hbox (badness 10000) detected at line 28 [][][] ) [488] Chapter 9. (./mainpage_8h_source.tex) (./apbs_8h.tex <./apbs_8h__incl.pdf> <./apbs_8h__dep __incl.pdf> [489] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] Underfull \hbox (badness 10000) detected at line 58 [][][] [490]) (./apbs_8h_source.tex) (./vcsm_8c.tex [491] <./vcsm_8c__incl.pdf> [492] Underfull \hbox (badness 10000) detected at line 53 [][][] Underfull \hbox (badness 10000) detected at line 56 [][][] Underfull \hbox (badness 10000) detected at line 59 [][][] [493]) (./vcsm_8c_source.tex [494] [495] [496] [497] [498] [499]) (./vcsm_8h.tex <./vcsm_8h__incl.pdf> <./vcsm_8h__dep__incl.pdf> [500] [501] Underfull \hbox (badness 10000) detected at line 77 [][][] Underfull \hbox (badness 10000) detected at line 80 [][][] Underfull \hbox (badness 10000) detected at line 83 [][][] [502]) (./vcsm_8h_source.tex [503]) (./vfetk_8c.tex [504] <./vfetk_8c__incl.pdf > [505] [506] Underfull \hbox (badness 10000) detected at line 163 [][][] Underfull \hbox (badness 10000) detected at line 166 [][][] [507] Underfull \hbox (badness 10000) detected at line 169 [][][] [508] [509] [510] [511]) (./vfetk_8c_source.tex [512] [513] [514] [515] [516] [517] [518] [519] [520] [521] [522] [523] [524] [525] [526] [527] [528] [529] [530] [531] [532] [533] [534] [535] [536] [537] [538] [539] [540] [541]) (./vfetk_8h.tex [542] <./vfetk_8h__incl.pdf> <./vfetk_8h__dep__inc l.pdf> [543] [544] [545] Underfull \hbox (badness 10000) detected at line 189 [][][] [546] Underfull \hbox (badness 10000) detected at line 192 [][][] Underfull \hbox (badness 10000) detected at line 195 [][][] ) (./vfetk_8h_source.tex [547] [548] [549] [550] [551] [552]) (./vpee_8c.tex <. /vpee_8c__incl.pdf> [553] Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 53 [][][] Underfull \hbox (badness 10000) detected at line 56 [][][] [554]) (./vpee_8c_source.tex [555] [556] [557] [558] [559] [560]) (./vpee_8h.tex [561] <./vpee_8h__incl.pdf> <./vpee_8h__dep__incl.pdf> [562] Underfull \hbox (badness 10000) detected at line 57 [][][] Underfull \hbox (badness 10000) detected at line 60 [][][] Underfull \hbox (badness 10000) detected at line 63 [][][] [563]) (./vpee_8h_source.tex [564]) (./apolparm_8c.tex <./apolparm_8c__incl.pdf > [565] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) detected at line 71 [][][] [566] [567]) (./apolparm_8c_source.tex [568] [569] [570] [571] [572] [573] [574] [575]) (./apolparm_8h_source.tex [576]) (./bemparm_8c.tex <./bemparm_8c__ incl.pdf> [577] [578] Underfull \hbox (badness 10000) detected at line 49 [][][] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] [579] Underfull \hbox (badness 10000) detected at line 121 [][][] ) (./bemparm_8c_source.tex [580] [581] [582] [583]) (./bemparm_8h_source.tex [584]) (./femparm_8c.tex <./femparm_8c__incl.pdf> [585] [586] Underfull \hbox (badness 10000) detected at line 59 [][][] Underfull \hbox (badness 10000) detected at line 62 [][][] Underfull \hbox (badness 10000) detected at line 65 [][][] [587] [588]) (./femparm_8c_source.tex [589] [590] [591] [592] [593]) (./femparm_8h.tex <./femparm_8h__incl.pdf> [594] <./femparm_8h__dep__incl.pdf> [595] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 92 [][][] Underfull \hbox (badness 10000) detected at line 95 [][][] [596]) (./femparm_8h_source.tex [597]) (./geoflowparm_8c.tex [598] <./geoflowpa rm_8c__incl.pdf> [599] Underfull \hbox (badness 10000) detected at line 47 [][][] Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 53 [][][] [600]) (./geoflowparm_8c_source.tex [601] [602]) (./geoflowparm_8h.tex [603] <. /geoflowparm_8h__incl.pdf> <./geoflowparm_8h__dep__incl.pdf> [604] [605] Underfull \hbox (badness 10000) detected at line 71 [][][] Underfull \hbox (badness 10000) detected at line 74 [][][] Underfull \hbox (badness 10000) detected at line 77 [][][] [606]) (./geoflowparm_8h_source.tex [607]) (./mgparm_8c.tex <./mgparm_8c__incl. pdf> [608] [609] Underfull \hbox (badness 10000) detected at line 95 [][][] Underfull \hbox (badness 10000) detected at line 98 [][][] Underfull \hbox (badness 10000) detected at line 101 [][][] [610] [611]) (./mgparm_8c_source.tex [612] [613] [614] [615] [616] [617] [618] [619] [620] [621] [622] [623]) (./mgparm_8h.tex <./mgparm_8h__incl.pdf> [624] <./mgparm_8h__dep__incl.pdf> [625] [626] Underfull \hbox (badness 10000) detected at line 104 [][][] Underfull \hbox (badness 10000) detected at line 107 [][][] Underfull \hbox (badness 10000) detected at line 110 [][][] [627]) (./mgparm_8h_source.tex [628]) (./nosh_8c.tex <./nosh_8c__incl.pdf> [629] [630] [631] Underfull \hbox (badness 10000) detected at line 151 [][][] Underfull \hbox (badness 10000) detected at line 154 [][][] Underfull \hbox (badness 10000) detected at line 157 [][][] [632] [633] [634] [635] [636]) (./nosh_8c_source.tex [637] [638] [639] [640] [641] [642] [643] [644] [645] [646] [647] [648] [649] [650] [651] [652] [653] [654] [655] [656] [657] [658] [659] [660] [661] [662] [663] [664] [665] [666] [667] [668] [669] [670] [671] [672] [673] [674] [675] [676]) (./nosh_8h.tex <./nosh_8h__incl.pdf> [677] <./nosh_8h__dep__incl.pdf> [678] [679] [680] Underfull \hbox (badness 10000) detected at line 171 [][][] Underfull \hbox (badness 10000) detected at line 174 [][][] Underfull \hbox (badness 10000) detected at line 177 [][][] ) (./nosh_8h_source.tex [681] [682] [683]) (./pbamparm_8c.tex <./pbamparm_8c__i ncl.pdf> [684] [685] Underfull \hbox (badness 10000) detected at line 69 [][][] Underfull \hbox (badness 10000) detected at line 72 [][][] Underfull \hbox (badness 10000) detected at line 75 [][][] [686]) (./pbamparm_8c_source.tex [687] [688] [689] [690] [691] [692] [693] [694] [695]) (./pbamparm_8h.tex <./pbamparm_8h__incl.pdf> <./pbamparm_8h__dep__ incl.pdf> [696] [697] Underfull \hbox (badness 10000) detected at line 102 [][][] [698] Underfull \hbox (badness 10000) detected at line 105 [][][] Underfull \hbox (badness 10000) detected at line 108 [][][] [699]) (./pbamparm_8h_source.tex [700]) (./pbeparm_8c.tex [701] <./pbeparm_8c__ incl.pdf> [702] Underfull \hbox (badness 10000) detected at line 101 [][][] Underfull \hbox (badness 10000) detected at line 104 [][][] Underfull \hbox (badness 10000) detected at line 107 [][][] [703] [704] [705] [706] [707]) (./pbeparm_8c_source.tex [708] [709] [710] [711] [712] [713] [714] [715] [716] [717] [718] [719] [720] [721] [722]) (./pbeparm_8h.tex <./pbeparm_8h__incl.pdf> [723] <./pbeparm_8h__dep__incl.pdf> [724] Underfull \hbox (badness 10000) detected at line 88 [][][] Underfull \hbox (badness 10000) detected at line 91 [][][] Underfull \hbox (badness 10000) detected at line 94 [][][] [725]) (./pbeparm_8h_source.tex [726] [727]) (./pbsamparm_8c.tex <./pbsamparm_8 c__incl.pdf> [728] [729] Underfull \hbox (badness 10000) detected at line 49 [][][] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] [730]) (./pbsamparm_8c_source.tex [731] [732]) (./pbsamparm_8h.tex [733] <./pbs amparm_8h__incl.pdf> <./pbsamparm_8h__dep__incl.pdf> [734] [735] Underfull \hbox (badness 10000) detected at line 86 [][][] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 92 [][][] [736]) (./pbsamparm_8h_source.tex [737]) (./vacc_8c.tex <./vacc_8c__incl.pdf> [738] [739] [740] Underfull \hbox (badness 10000) detected at line 107 [][][] Underfull \hbox (badness 10000) detected at line 110 [][][] Underfull \hbox (badness 10000) detected at line 113 [][][] [741] Underfull \hbox (badness 10000) detected at line 179 [][][] Underfull \hbox (badness 10000) detected at line 182 [][][] Underfull \hbox (badness 10000) detected at line 208 [][][] Underfull \hbox (badness 10000) detected at line 211 [][][] [742] [743]) (./vacc_8c_source.tex [744] [745] [746] [747] [748] [749] [750] [751] [752] [753] [754] [755] [756] [757] [758] [759] [760] [761] [762] [763] [764] [765] [766]) (./vacc_8h.tex <./vacc_8h__incl.pdf> <./vacc_8h__dep__ incl.pdf> [767] [768] [769] Underfull \hbox (badness 10000) detected at line 123 [][][] Underfull \hbox (badness 10000) detected at line 126 [][][] Underfull \hbox (badness 10000) detected at line 129 [][][] [770]) (./vacc_8h_source.tex [771] [772] [773]) (./valist_8c.tex <./valist_8c__ incl.pdf> [774] [775] Underfull \hbox (badness 2293) in paragraph at lines 54--56 []\T1/phv/m/n/10 VPRIVATE Vrc[]_[][]Codes [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/ m/n/10 thee, Vio $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 sock, int $\OMS/cmsy/m/n/ 10 ^^C$\T1/phv/m/n/10 serial, char atom[] Underfull \hbox (badness 10000) detected at line 82 [][][] Underfull \hbox (badness 10000) detected at line 85 [][][] Underfull \hbox (badness 10000) detected at line 88 [][][] [776] [777] [778]) (./valist_8c_source.tex [779] [780] [781] [782] [783] [784] [785] [786] [787] [788]) (./valist_8h.tex [789] <./valist_8h__incl.pdf> < ./valist_8h__dep__incl.pdf> [790] Underfull \hbox (badness 10000) detected at line 77 [][][] Underfull \hbox (badness 10000) detected at line 80 [][][] Underfull \hbox (badness 10000) detected at line 83 [][][] [791]) (./valist_8h_source.tex [792] [793]) (./vatom_8c.tex <./vatom_8c__incl.p df> [794] Underfull \hbox (badness 10000) detected at line 71 [][][] Underfull \hbox (badness 10000) detected at line 74 [][][] Underfull \hbox (badness 10000) detected at line 77 [][][] [795]) (./vatom_8c_source.tex [796] [797] [798]) (./vatom_8h.tex <./vatom_8h__i ncl.pdf> [799] <./vatom_8h__dep__incl.pdf> [800] [801] Underfull \hbox (badness 10000) detected at line 96 [][][] Underfull \hbox (badness 10000) detected at line 99 [][][] Underfull \hbox (badness 10000) detected at line 102 [][][] ) (./vatom_8h_source.tex [802] [803]) (./vcap_8c.tex <./vcap_8c__incl.pdf> [804] Underfull \hbox (badness 10000) detected at line 31 [][][] Underfull \hbox (badness 10000) detected at line 34 [][][] Underfull \hbox (badness 10000) detected at line 37 [][][] [805]) (./vcap_8c_source.tex [806]) (./vcap_8h.tex <./vcap_8h__incl.pdf> <./vca p_8h__dep__incl.pdf> [807] Underfull \hbox (badness 10000) detected at line 47 [][][] Underfull \hbox (badness 10000) detected at line 50 [][][] [808] Underfull \hbox (badness 10000) detected at line 53 [][][] ) (./vcap_8h_source.tex [809]) (./vclist_8c.tex <./vclist_8c__incl.pdf> Underfull \hbox (badness 4060) in paragraph at lines 32--34 []\T1/phv/m/n/10 VPRIVATE void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 thee , dou-ble lower[]_[]corner[][][], dou-ble upper[]_[] [810] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) detected at line 71 [][][] [811] [812]) (./vclist_8c_source.tex [813] [814] [815] [816] [817]) (./vclist_8h.tex [818] <./vclist_8h__incl.pdf> <./vclist_8h__dep__incl.pdf> [819] [820] Underfull \hbox (badness 10000) detected at line 84 [][][] Underfull \hbox (badness 10000) detected at line 87 [][][] Underfull \hbox (badness 10000) detected at line 90 [][][] [821]) (./vclist_8h_source.tex [822]) (./vgreen_8c.tex [823] <./vgreen_8c__incl .pdf> [824] Underfull \hbox (badness 10000) detected at line 55 [][][] Underfull \hbox (badness 10000) detected at line 58 [][][] Underfull \hbox (badness 10000) detected at line 61 [][][] [825]) (./vgreen_8c_source.tex [826] [827] [828] [829] [830] [831]) (./vgreen_8h.tex <./vgreen_8h__incl.pdf> [832] <./vgreen_8h__dep__incl.pdf> [833] Underfull \hbox (badness 10000) detected at line 72 [][][] Underfull \hbox (badness 10000) detected at line 75 [][][] ) (./vgreen_8h_source.tex [834]) (./vhal_8h.tex [835] <./vhal_8h__incl.pdf> <./ vhal_8h__dep__incl.pdf> [836] [837] [838] [839] Underfull \hbox (badness 10000) detected at line 303 [][][] Underfull \hbox (badness 10000) detected at line 306 [][][] Underfull \hbox (badness 10000) detected at line 309 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 318--318 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [840] [841] [842] [843] [844] [845] [846]) (./vhal_8h_source.tex [847] [848] [849] [850] [851] [852] [853] [854]) (./vmatrix_8h.tex [855] <./vmatrix_8h__dep __incl.pdf> Underfull \hbox (badness 10000) detected at line 36 [][][] Underfull \hbox (badness 10000) detected at line 39 [][][] Underfull \hbox (badness 10000) detected at line 42 [][][] [856] [857]) (./vmatrix_8h_source.tex [858]) (./vparam_8c.tex <./vparam_8c__inc l.pdf> [859] Underfull \hbox (badness 10000) detected at line 78 [][][] Underfull \hbox (badness 10000) detected at line 81 [][][] [860] Underfull \hbox (badness 10000) detected at line 84 [][][] ) (./vparam_8c_source.tex [861] [862] [863] [864] [865] [866] [867] [868]) (./vparam_8h.tex [869] <./vparam_8h__incl.pdf> <./vparam_8h__dep__incl.pdf> [870] [871] Underfull \hbox (badness 10000) detected at line 96 [][][] Underfull \hbox (badness 10000) detected at line 99 [][][] Underfull \hbox (badness 10000) detected at line 102 [][][] [872]) (./vparam_8h_source.tex [873]) (./vpbe_8c.tex <./vpbe_8c__incl.pdf> [874] [875] Underfull \hbox (badness 10000) detected at line 90 [][][] Underfull \hbox (badness 10000) detected at line 93 [][][] [876] Underfull \hbox (badness 10000) detected at line 96 [][][] ) (./vpbe_8c_source.tex [877] [878] [879] [880] [881] [882] [883]) (./vpbe_8h.tex <./vpbe_8h__incl.pdf> <./vpbe_8h__dep__incl.pdf> [884] [885] Underfull \hbox (badness 10000) detected at line 111 [][][] Underfull \hbox (badness 10000) detected at line 114 [][][] Underfull \hbox (badness 10000) detected at line 117 [][][] [886]) (./vpbe_8h_source.tex [887] [888] [889]) (./vstring_8c.tex <./vstring_8c __incl.pdf> [890] Underfull \hbox (badness 10000) detected at line 31 [][][] Underfull \hbox (badness 10000) detected at line 34 [][][] Underfull \hbox (badness 10000) detected at line 37 [][][] ) (./vstring_8c_source.tex [891] [892] [893]) (./vstring_8h.tex <./vstring_8h__ incl.pdf> <./vstring_8h__dep__incl.pdf> [894] Underfull \hbox (badness 10000) detected at line 41 [][][] Underfull \hbox (badness 10000) detected at line 44 [][][] Underfull \hbox (badness 10000) detected at line 47 [][][] [895]) (./vstring_8h_source.tex) (./vunit_8h.tex <./vunit_8h__dep__incl.pdf> [896] LaTeX Warning: Command \r invalid in math mode on input line 42. Missing character: There is no Å in font cmr9! Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] Underfull \hbox (badness 10000) detected at line 58 [][][] [897]) (./vunit_8h_source.tex) (./main_8c.tex [898] <./main_8c__incl.pdf> Underfull \hbox (badness 10000) detected at line 28 [][][] Underfull \hbox (badness 10000) detected at line 41 [][][] Underfull \hbox (badness 10000) detected at line 44 [][][] [899]) (./main_8c_source.tex [900] [901] [902] [903] [904] [905] [906] [907] [908] [909] [910]) (./vgrid_8c.tex <./vgrid_8c__incl.pdf> [911] [912] Underfull \hbox (badness 10000) detected at line 84 [][][] Underfull \hbox (badness 10000) detected at line 87 [][][] Underfull \hbox (badness 10000) detected at line 90 [][][] [913] Underfull \hbox (badness 10000) detected at line 169 [][][] [914]) (./vgrid_8c_source.tex [915] [916] [917] [918] [919] [920] [921] [922] [923] [924] [925] [926] [927] [928] [929] [930] [931] [932] [933] [934] [935] [936] [937]) (./vgrid_8h.tex [938] <./vgrid_8h__incl.pdf> <./vgrid_ 8h__dep__incl.pdf> [939] [940] Underfull \hbox (badness 10000) detected at line 93 [][][] [941] Underfull \hbox (badness 10000) detected at line 96 [][][] Underfull \hbox (badness 10000) detected at line 99 [][][] [942] Underfull \hbox (badness 10000) detected at line 165 [][][] ) (./vgrid_8h_source.tex [943]) (./vmgrid_8c.tex [944] <./vmgrid_8c__incl.pdf> [945] Underfull \hbox (badness 10000) detected at line 41 [][][] Underfull \hbox (badness 10000) detected at line 44 [][][] Underfull \hbox (badness 10000) detected at line 47 [][][] Underfull \hbox (badness 10000) detected at line 50 [][][] Overfull \hbox (1024.08331pt too wide) in paragraph at lines 59--59 []\T1/pcr/m/n/8 * Copyright (c) 2010, Pacific Northwest National Laboratory. Portions Copyright (c) 2002-2020, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2020, T he Regents of the University of California. Portions Copyright (c) 1995, Michae l Holst.[] ) (./vmgrid_8c_source.tex [946] [947] [948]) (./vmgrid_8h.tex <./vmgrid_8h__inc l.pdf> <./vmgrid_8h__dep__incl.pdf> [949] [950] Underfull \hbox (badness 10000) detected at line 71 [][][] Underfull \hbox (badness 10000) detected at line 74 [][][] Underfull \hbox (badness 10000) detected at line 77 [][][] [951]) (./vmgrid_8h_source.tex) (./vopot_8c.tex [952] <./vopot_8c__incl.pdf> Underfull \hbox (badness 10000) detected at line 44 [][][] Underfull \hbox (badness 10000) detected at line 47 [][][] Underfull \hbox (badness 10000) detected at line 50 [][][] [953]) (./vopot_8c_source.tex [954] [955] [956] [957] [958]) (./vopot_8h.tex <. /vopot_8h__incl.pdf> <./vopot_8h__dep__incl.pdf> [959] [960] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) detected at line 71 [][][] ) (./vopot_8h_source.tex [961]) (./vpmg_8c.tex <./vpmg_8c__incl.pdf> [962] [963] [964] [965] Underfull \hbox (badness 10000) detected at line 173 [][][] Underfull \hbox (badness 10000) detected at line 176 [][][] Underfull \hbox (badness 10000) detected at line 179 [][][] [966] Underfull \hbox (badness 10000) detected at line 261 [][][] [967] Underfull \hbox (badness 10000) detected at line 288 [][][] [968] Underfull \hbox (badness 10000) detected at line 384 [][][] Underfull \hbox (badness 10000) detected at line 387 [][][] Underfull \hbox (badness 10000) detected at line 409 [][][] Underfull \hbox (badness 10000) detected at line 412 [][][] [969] Underfull \hbox (badness 10000) detected at line 434 [][][] Underfull \hbox (badness 10000) detected at line 437 [][][] Underfull \hbox (badness 10000) detected at line 459 [][][] Underfull \hbox (badness 10000) detected at line 462 [][][] Underfull \hbox (badness 10000) detected at line 484 [][][] Underfull \hbox (badness 10000) detected at line 487 [][][] [970] Underfull \hbox (badness 10000) detected at line 509 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Underfull \hbox (badness 10000) detected at line 534 [][][] Underfull \hbox (badness 10000) detected at line 537 [][][] Underfull \hbox (badness 10000) detected at line 554 [][][] Underfull \hbox (badness 10000) detected at line 557 [][][] [971] Underfull \hbox (badness 10000) detected at line 574 [][][] Underfull \hbox (badness 10000) detected at line 591 [][][] Underfull \hbox (badness 10000) detected at line 608 [][][] Underfull \hbox (badness 10000) detected at line 625 [][][] Underfull \hbox (badness 10000) detected at line 642 [][][] [972] Underfull \hbox (badness 10000) detected at line 659 [][][] Underfull \hbox (badness 10000) detected at line 676 [][][] Underfull \hbox (badness 10000) detected at line 697 [][][] Underfull \hbox (badness 10000) detected at line 700 [][][] Underfull \hbox (badness 10000) detected at line 717 [][][] [973] Underfull \hbox (badness 10000) detected at line 734 [][][] Underfull \hbox (badness 10000) detected at line 751 [][][] Underfull \hbox (badness 10000) detected at line 768 [][][] Underfull \hbox (badness 10000) detected at line 795 [][][] [974] Underfull \hbox (badness 10000) detected at line 832 [][][] [975] Underfull \hbox (badness 10000) detected at line 876 [][][] [976] Underfull \hbox (badness 10000) detected at line 926 [][][] Underfull \hbox (badness 10000) detected at line 948 [][][] [977] Underfull \hbox (badness 10000) detected at line 970 [][][] Underfull \hbox (badness 10000) detected at line 992 [][][] Underfull \hbox (badness 10000) detected at line 995 [][][] Underfull \hbox (badness 10000) detected at line 1012 [][][] Underfull \hbox (badness 10000) detected at line 1015 [][][] [978] Underfull \hbox (badness 10000) detected at line 1037 [][][] Underfull \hbox (badness 10000) detected at line 1040 [][][] Underfull \hbox (badness 10000) detected at line 1062 [][][] Underfull \hbox (badness 10000) detected at line 1065 [][][] Underfull \hbox (badness 10000) detected at line 1097 [][][] [979] Underfull \hbox (badness 10000) detected at line 1114 [][][] Underfull \hbox (badness 10000) detected at line 1146 [][][] Underfull \hbox (badness 10000) detected at line 1149 [][][] ) (./vpmg_8c_source.tex [980] [981] [982] [983] [984] [985] [986] [987] [988] [989] [990] [991] [992] [993] [994] [995] [996] [997] [998] [999] [1000] [1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008] [1009] [1010] [1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] [1021] [1022] [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] [1033] [1034] [1035] [1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] [1090] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112] [1113] [1114] [1115] [1116]) (./vpmg_8h.tex <./vpmg_8h__in cl.pdf> <./vpmg_8h__dep__incl.pdf> [1117] [1118] [1119] [1120] [1121] [1122] Underfull \hbox (badness 10000) detected at line 235 [][][] Underfull \hbox (badness 10000) detected at line 238 [][][] Underfull \hbox (badness 10000) detected at line 241 [][][] [1123] [1124] Underfull \hbox (badness 10000) detected at line 406 [][][] Underfull \hbox (badness 10000) detected at line 423 [][][] [1125] Underfull \hbox (badness 10000) detected at line 469 [][][] Underfull \hbox (badness 10000) detected at line 472 [][][] Underfull \hbox (badness 10000) detected at line 494 [][][] Underfull \hbox (badness 10000) detected at line 497 [][][] [1126] Underfull \hbox (badness 10000) detected at line 519 [][][] Underfull \hbox (badness 10000) detected at line 522 [][][] Underfull \hbox (badness 10000) detected at line 544 [][][] Underfull \hbox (badness 10000) detected at line 547 [][][] Underfull \hbox (badness 10000) detected at line 569 [][][] Underfull \hbox (badness 10000) detected at line 572 [][][] [1127] Underfull \hbox (badness 10000) detected at line 594 [][][] Underfull \hbox (badness 10000) detected at line 597 [][][] Underfull \hbox (badness 10000) detected at line 619 [][][] Underfull \hbox (badness 10000) detected at line 622 [][][] Underfull \hbox (badness 10000) detected at line 639 [][][] Underfull \hbox (badness 10000) detected at line 642 [][][] [1128] Underfull \hbox (badness 10000) detected at line 659 [][][] Underfull \hbox (badness 10000) detected at line 676 [][][] Underfull \hbox (badness 10000) detected at line 693 [][][] Underfull \hbox (badness 10000) detected at line 710 [][][] Underfull \hbox (badness 10000) detected at line 727 [][][] [1129] Underfull \hbox (badness 10000) detected at line 744 [][][] Underfull \hbox (badness 10000) detected at line 761 [][][] Underfull \hbox (badness 10000) detected at line 782 [][][] Underfull \hbox (badness 10000) detected at line 785 [][][] Underfull \hbox (badness 10000) detected at line 802 [][][] [1130] Underfull \hbox (badness 10000) detected at line 819 [][][] Underfull \hbox (badness 10000) detected at line 836 [][][] Underfull \hbox (badness 10000) detected at line 853 [][][] Underfull \hbox (badness 10000) detected at line 870 [][][] Underfull \hbox (badness 10000) detected at line 883 [][][] [1131] Underfull \hbox (badness 10000) detected at line 896 [][][] Underfull \hbox (badness 10000) detected at line 913 [][][] [1132] Underfull \hbox (badness 10000) detected at line 957 [][][] Underfull \hbox (badness 10000) detected at line 987 [][][] [1133] Underfull \hbox (badness 10000) detected at line 1009 [][][] Underfull \hbox (badness 10000) detected at line 1031 [][][] Underfull \hbox (badness 10000) detected at line 1053 [][][] Underfull \hbox (badness 10000) detected at line 1056 [][][] Underfull \hbox (badness 10000) detected at line 1073 [][][] [1134] Underfull \hbox (badness 10000) detected at line 1076 [][][] Underfull \hbox (badness 10000) detected at line 1098 [][][] Underfull \hbox (badness 10000) detected at line 1101 [][][] Underfull \hbox (badness 10000) detected at line 1123 [][][] Underfull \hbox (badness 10000) detected at line 1126 [][][] [1135] Underfull \hbox (badness 10000) detected at line 1158 [][][] Underfull \hbox (badness 10000) detected at line 1175 [][][] [1136] Underfull \hbox (badness 10000) detected at line 1207 [][][] Underfull \hbox (badness 10000) detected at line 1210 [][][] ) (./vpmg_8h_source.tex [1137] [1138] [1139] [1140] [1141] [1142] [1143] [1144]) (./vpmgp_8c.tex <./vpmgp_8c__incl.pdf> [1145] [1146] Underfull \hbox (badness 10000) detected at line 39 [][][] Underfull \hbox (badness 10000) detected at line 42 [][][] Underfull \hbox (badness 10000) detected at line 45 [][][] [1147]) (./vpmgp_8c_source.tex [1148] [1149] [1150]) (./vpmgp_8h.tex <./vpmgp_8 h__incl.pdf> [1151] <./vpmgp_8h__dep__incl.pdf> [1152] [1153] Underfull \hbox (badness 10000) detected at line 58 [][][] Underfull \hbox (badness 10000) detected at line 61 [][][] Underfull \hbox (badness 10000) detected at line 64 [][][] Underfull \hbox (badness 10000) detected at line 67 [][][] [1154]) (./vpmgp_8h_source.tex [1155]) (./build_ad_8c_source.tex [1156] [1157] [1158]) (./build_ad_8h_source.tex [1159]) (./build_bd_8c_source.tex [1160] [1161] [1162] [1163]) (./build_bd_8h_source.tex [1164]) (./build_gd_8c_source.tex [1165] [1166] [1167] [1168] [1169] [1170] [1171] [1172] [1173] [1174] [1175] [1176] [1177] [1178] [1179] [1180] [1181] [1182] [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] [1191] [1192] [1193] [1194] [1195] [1196] [1197] [1198] [1199] [1200] [1201] [1202]) (./build_gd_8h_source.tex [1203] [1204]) (./build_pd_8c_source.tex [1205] [1206] [1207] [1208] [1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216] [1217] [1218] [1219] [1220] [1221] [1222] [1223]) (./build_pd_8h_source.tex [1224] [1225] [1226]) (./cgd_8c_source.tex) (./cgd_8h_source.tex [1227]) (./gsd_8c_source.tex [1228] [1229] [1230] [1231]) (./gsd_8h_source.tex [1232]) (./matvecd_8c_source.tex [1233] [1234] [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242] [1243] [1244] [1245]) (./matvecd_8h_source.tex [1246] [1247] [1248] [1249] [1250] [1251]) (./mgcsd_8c_source.tex [1252] [1253] [1254] [1255] [1256] [1257]) (./mgcsd_8h_source.tex [1258]) (./mgdrvd_8c_source.tex [1259] [1260] [1261] [1262] [1263] [1264] [1265]) (./mgdrvd_8h_source.tex [1266] [1267]) (./mgfasd_8c_source.tex [1268] [1269] [1270] [1271] [1272] [1273]) (./mgfasd_8h_source.tex [1274] [1275]) (./mgsubd_8c_source.tex [1276] [1277] [1278] [1279] [1280] [1281] [1282] [1283] [1284] [1285] [1286]) (./mgsubd_8h_source.tex [1287] [1288] [1289] [1290]) (./mikpckd_8c_source.tex [1291] [1292] [1293] [1294]) (./mikpckd_8h_source.tex [1295] [1296] [1297]) (./mlinpckd_8c_source.tex [1298] [1299]) (./mlinpckd_8h_source.tex) (./mypdec_8c_source.tex [1300] [1301] [1302] [1303] [1304] [1305] [1306]) (./mypdec_8h_source.tex [1307]) (./newdrvd_8c_source.tex [1308] [1309] [1310] [1311]) (./newdrvd_8h_source.tex [1312]) (./newtond_8c_source.tex [1313] [1314] [1315] [1316] [1317] [1318] [1319]) (./newtond_8h_source.tex [1320]) (./powerd_8c_source.tex [1321] [1322] [1323] [1324] [1325]) (./powerd_8h_source.tex [1326]) (./smoothd_8c_source.tex [1327]) (./smoothd_8h_source.tex [1328]) (./routines_8c.tex <./routines_8c__incl.pdf> [1329] Underfull \hbox (badness 776) in paragraph at lines 48--49 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv /m/n/10 alist[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[] Underfull \hbox (badness 2856) in paragraph at lines 48--49 \T1/phv/m/n/10 YMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]ZMap[] [][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 kappa[]Map[][][], [] Underfull \hbox (badness 1237) in paragraph at lines 48--49 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 charge[]Map[][][], [] $\OMS/cmsy/m/n/10 ^^C $\T1/phv/m/n/10 pmgp[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pmg[][][], [] Underfull \hbox (badness 905) in paragraph at lines 62--63 []\T1/phv/m/n/10 VPUBLIC void [] (Vmem $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 mem , [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, int nforce[][][], [] $\OMS/cmsy /m/n/10 ^^C$\T1/phv/m/n/10 atom[] Underfull \hbox (badness 5817) in paragraph at lines 68--69 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], Underfull \hbox (badness 5817) in paragraph at lines 70--71 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], [1330] Underfull \hbox (badness 1442) in paragraph at lines 82--83 []\T1/phv/m/n/10 VPUBLIC int [] (Vcom $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 com, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, int nforce[][][], [] $\OMS/cmsy/ m/n/10 ^^C$\T1/phv/m/n/10 atom[] Underfull \hbox (badness 931) in paragraph at lines 88--89 []\T1/phv/m/n/10 VPUBLIC void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T 1/phv/m/n/10 fetk[][][], Gem Underfull \hbox (badness 2495) in paragraph at lines 90--91 []\T1/phv/m/n/10 VPUBLIC Vrc[]_[][]Codes [] (int icalc, [] $\OMS/cmsy/m/n/10 ^^ C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 feparm, [] $\OMS /cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbeparm, [] [1331] Underfull \hbox (badness 10000) detected at line 117 [][][] Underfull \hbox (badness 10000) detected at line 120 [][][] Underfull \hbox (badness 10000) detected at line 123 [][][] ) (./routines_8c_source.tex [1332] [1333] [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341] [1342] [1343] [1344] [1345] [1346] [1347] [1348] [1349] [1350] [1351] [1352] [1353] [1354] [1355] [1356] [1357] [1358] [1359] [1360] [1361] [1362] [1363] [1364] [1365] [1366] [1367] [1368] [1369] [1370] [1371] [1372] [1373] [1374] [1375] [1376] [1377] [1378] [1379] [1380] [1381] [1382] [1383] [1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] [1392] [1393] [1394] [1395] [1396] [1397] [1398] [1399] [1400]) (./routines_8h.tex <./routine s_8h__incl.pdf> <./routines_8h__dep__incl.pdf> [1401] Overfull \hbox (16.65858pt too wide) in paragraph at lines 52--53 []\T1/phv/m/n/10 VEXTERNC int [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], Overfull \hbox (16.91972pt too wide) in paragraph at lines 54--55 []\T1/phv/m/n/10 VEXTERNC void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh , [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/1 0 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], Underfull \hbox (badness 1910) in paragraph at lines 72--73 [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1 /phv/m/n/10 alist[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][] [], [] Underfull \hbox (badness 1237) in paragraph at lines 72--73 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 charge[]Map[][][], [] $\OMS/cmsy/m/n/10 ^^C $\T1/phv/m/n/10 pmgp[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pmg[][][], [] [1402] Underfull \hbox (badness 5817) in paragraph at lines 90--91 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], Underfull \hbox (badness 5817) in paragraph at lines 92--93 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], [1403] Underfull \hbox (badness 2495) in paragraph at lines 124--125 []\T1/phv/m/n/10 VPUBLIC Vrc[]_[][]Codes [] (int icalc, [] $\OMS/cmsy/m/n/10 ^^ C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 feparm, [] $\OMS /cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbeparm, [] Underfull \hbox (badness 10000) detected at line 147 [][][] Underfull \hbox (badness 10000) detected at line 150 [][][] Underfull \hbox (badness 10000) detected at line 153 [][][] [1404]) (./routines_8h_source.tex [1405] [1406] [1407] [1408] [1409]) [1410] (./refman.ind [1411] [1412] [1413] [1414] [1415] [1416] [1417] [1418] [1419] [1420] [1421] [1422] [1423] [1424] [1425] [1426] [1427] [1428] [1429] [1430] [1431] [1432] [1433] [1434] [1435] [1436] [1437] [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] [1449] [1450] [1451] [1452] [1453] [1454] [1455] [1456] [1457] [1458] [1459]) (./refman.aux) ) (see the transcript file for additional information)< /usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrro8a.pfb> Output written on refman.pdf (1517 pages, 6288270 bytes). Transcript written on refman.log. This is makeindex, version 2.17 [TeX Live 2023] (kpathsea + Thai support). Scanning input file refman.idx.......done (3687 entries accepted, 0 rejected). Sorting entries...................................done (46845 comparisons). Generating output file refman.ind.......done (5317 lines written, 0 warnings). Output written in refman.ind. Transcript written in refman.ilg. 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(/usr/share/texlive/texmf-dist/tex/latex/wasysym/uwasy.fd) [1{/var/lib/texmf/fo nts/map/pdftex/updmap/pdftex.map}{/usr/share/texlive/texmf-dist/fonts/enc/dvips /base/8r.enc}] [2] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] (./index.tex Chapter 1. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1phv.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [1] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [2]) (./bug.tex [3] [4] Chapter 2. [5] [6]) (./deprecated.tex [7] [8] Chapter 3. ) [9] [10] Chapter 4. (./modules.tex) [11] [12] Chapter 5. (./annotated.tex [13]) [14] Chapter 6. (./files.tex [15] [16] [17]) [18] Chapter 7. (./group___header.tex) (./group___vcsm.tex [19] Underfull \hbox (badness 10000) detected at line 93 [][][] [20] Underfull \hbox (badness 10000) detected at line 113 [][][] Underfull \hbox (badness 10000) detected at line 116 [][][] Underfull \hbox (badness 10000) detected at line 121 [][][] Underfull \hbox (badness 10000) detected at line 145 [][][] Underfull \hbox (badness 10000) detected at line 148 [][][] Underfull \hbox (badness 10000) detected at line 153 [][][] [21] Underfull \hbox (badness 10000) detected at line 179 [][][] Underfull \hbox (badness 10000) detected at line 201 [][][] Underfull \hbox (badness 10000) detected at line 223 [][][] Underfull \hbox (badness 10000) detected at line 226 [][][] Overfull \vbox (4.57304pt too high) has occurred while \output is active [22] Underfull \hbox (badness 10000) detected at line 252 [][][] Underfull \hbox (badness 10000) detected at line 255 [][][] Underfull \hbox (badness 10000) detected at line 281 [][][] Underfull \hbox (badness 10000) detected at line 284 [][][] [23] Underfull \hbox (badness 10000) detected at line 308 [][][] Underfull \hbox (badness 10000) detected at line 311 [][][] Underfull \hbox (badness 10000) detected at line 335 [][][] Underfull \hbox (badness 10000) detected at line 338 [][][] Underfull \hbox (badness 10000) detected at line 364 [][][] Underfull \hbox (badness 10000) detected at line 367 [][][] [24] Underfull \hbox (badness 10000) detected at line 393 [][][] Underfull \hbox (badness 10000) detected at line 396 [][][] Underfull \hbox (badness 10000) detected at line 418 [][][] Underfull \hbox (badness 10000) detected at line 421 [][][] [25] Underfull \hbox (badness 10000) detected at line 443 [][][] Underfull \hbox (badness 10000) detected at line 446 [][][] Underfull \hbox (badness 10000) detected at line 468 [][][] Underfull \hbox (badness 10000) detected at line 471 [][][] ) (./group___vfetk.tex [26] [27] [28] [29] [30] Underfull \hbox (badness 10000) detected at line 304 [][][] Underfull \hbox (badness 10000) detected at line 335 [][][] [31] Underfull \hbox (badness 10000) detected at line 398 [][][] Underfull \hbox (badness 10000) detected at line 429 [][][] Underfull \hbox (badness 10000) detected at line 463 [][][] Underfull \hbox (badness 10000) detected at line 466 [][][] [32] Underfull \hbox (badness 10000) detected at line 492 [][][] Underfull \hbox (badness 10000) detected at line 495 [][][] Underfull \hbox (badness 10000) detected at line 498 [][][] Underfull \hbox (badness 10000) detected at line 522 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] Underfull \hbox (badness 10000) detected at line 528 [][][] [33] Underfull \hbox (badness 10000) detected at line 559 [][][] Underfull \hbox (badness 10000) detected at line 569 [][][] [34] Underfull \hbox (badness 10000) detected at line 593 [][][] Underfull \hbox (badness 10000) detected at line 615 [][][] Underfull \hbox (badness 10000) detected at line 637 [][][] [35] Underfull \hbox (badness 10000) detected at line 658 [][][] Underfull \hbox (badness 10000) detected at line 661 [][][] Underfull \hbox (badness 10000) detected at line 668 [][][] Underfull \hbox (badness 10000) detected at line 671 [][][] Underfull \hbox (badness 10000) detected at line 701 [][][] [36] Underfull \hbox (badness 10000) detected at line 727 [][][] Underfull \hbox (badness 10000) detected at line 730 [][][] Underfull \hbox (badness 10000) detected at line 735 [][][] Underfull \hbox (badness 10000) detected at line 761 [][][] [37] Underfull \hbox (badness 10000) detected at line 789 [][][] Underfull \hbox (badness 10000) detected at line 792 [][][] Underfull \hbox (badness 10000) detected at line 814 [][][] Underfull \hbox (badness 10000) detected at line 817 [][][] Underfull \hbox (badness 10000) detected at line 820 [][][] [38] Underfull \hbox (badness 10000) detected at line 844 [][][] Underfull \hbox (badness 10000) detected at line 847 [][][] Underfull \hbox (badness 10000) detected at line 869 [][][] Underfull \hbox (badness 10000) detected at line 872 [][][] Underfull \hbox (badness 10000) detected at line 875 [][][] Underfull \hbox (badness 10000) detected at line 899 [][][] Underfull \hbox (badness 10000) detected at line 902 [][][] [39] Underfull \hbox (badness 10000) detected at line 924 [][][] Underfull \hbox (badness 10000) detected at line 927 [][][] Underfull \hbox (badness 10000) detected at line 949 [][][] [40] Underfull \hbox (badness 10000) detected at line 969 [][][] Underfull \hbox (badness 10000) detected at line 999 [][][] Underfull \hbox (badness 10000) detected at line 1002 [][][] Underfull \hbox (badness 10000) detected at line 1024 [][][] Underfull \hbox (badness 10000) detected at line 1027 [][][] [41] Underfull \hbox (badness 10000) detected at line 1053 [][][] Underfull \hbox (badness 10000) detected at line 1056 [][][] Underfull \hbox (badness 10000) detected at line 1080 [][][] Underfull \hbox (badness 10000) detected at line 1083 [][][] [42] Underfull \hbox (badness 10000) detected at line 1109 [][][] Underfull \hbox (badness 10000) detected at line 1146 [][][] Underfull \hbox (badness 10000) detected at line 1149 [][][] [43] Underfull \hbox (badness 10000) detected at line 1179 [][][] Underfull \hbox (badness 10000) detected at line 1182 [][][] Underfull \hbox (badness 10000) detected at line 1204 [][][] Underfull \hbox (badness 10000) detected at line 1207 [][][] [44] Underfull \hbox (badness 10000) detected at line 1232 [][][] Underfull \hbox (badness 10000) detected at line 1265 [][][] Underfull \hbox (badness 10000) detected at line 1268 [][][] [45] Underfull \hbox (badness 10000) detected at line 1298 [][][] Underfull \hbox (badness 10000) detected at line 1301 [][][] Underfull \hbox (badness 10000) detected at line 1327 [][][] [46] Underfull \hbox (badness 10000) detected at line 1355 [][][] Underfull \hbox (badness 10000) detected at line 1385 [][][] [47] Underfull \hbox (badness 10000) detected at line 1419 [][][] Underfull \hbox (badness 10000) detected at line 1422 [][][] Underfull \hbox (badness 10000) detected at line 1448 [][][] Underfull \hbox (badness 10000) detected at line 1451 [][][] [48] Underfull \hbox (badness 10000) detected at line 1477 [][][] Underfull \hbox (badness 10000) detected at line 1480 [][][] [49] Underfull \hbox (badness 10000) detected at line 1514 [][][] Underfull \hbox (badness 10000) detected at line 1517 [][][] Underfull \hbox (badness 10000) detected at line 1545 [][][] [50] Underfull \hbox (badness 10000) detected at line 1579 [][][] Underfull \hbox (badness 10000) detected at line 1582 [][][] [51] [52] Underfull \hbox (badness 10000) detected at line 1665 [][][] Underfull \hbox (badness 10000) detected at line 1699 [][][] Underfull \hbox (badness 10000) detected at line 1702 [][][] [53] Underfull \hbox (badness 10000) detected at line 1745 [][][] Underfull \hbox (badness 10000) detected at line 1755 [][][] Underfull \hbox (badness 10000) detected at line 1779 [][][] Underfull \hbox (badness 10000) detected at line 1782 [][][] Underfull \hbox (badness 10000) detected at line 1785 [][][] [54] Underfull \hbox (badness 10000) detected at line 1807 [][][] Underfull \hbox (badness 10000) detected at line 1810 [][][] Underfull \hbox (badness 10000) detected at line 1813 [][][] Underfull \hbox (badness 10000) detected at line 1835 [][][] [55] Underfull \hbox (badness 10000) detected at line 1861 [][][] Underfull \hbox (badness 10000) detected at line 1881 [][][] Underfull \hbox (badness 10000) detected at line 1886 [][][] ) (./group___vpee.tex [56] Underfull \hbox (badness 849) in paragraph at lines 45--46 \T1/phv/m/n/10 Holst par-al-lel re-fine-ment rou-tine es-sen-tially re-duces th e er-ror out-side the \T1/pcr/m/n/10 local^^D partition to zero. Underfull \hbox (badness 10000) in paragraph at lines 45--46 \T1/pcr/m/n/10 However, this leads to the need for a few final overlapping Schw arz solves to Underfull \hbox (badness 10000) in paragraph at lines 45--46 \T1/pcr/m/n/10 smooth out the errors near partition boundaries. Supposedly, if the region in Underfull \hbox (badness 10000) in paragraph at lines 45--46 \T1/pcr/m/n/10 which we allow error-based refinement includes the$\OML/cmm/m/it /10 <$\T1/pcr/m/n/10 /tt$\OML/cmm/m/it/10 >$\T1/pcr/m/n/10 local^^D partition a nd an Underfull \hbox (badness 10000) in paragraph at lines 45--46 \T1/pcr/m/n/10 external buffer zone approximately equal in size to the local re gion, then the Underfull \hbox (badness 10000) in paragraph at lines 45--46 \T1/pcr/m/n/10 solution will asymptotically approach the solution obtained via more typical Underfull \hbox (badness 10000) in paragraph at lines 45--46 \T1/pcr/m/n/10 methods. This is essentially a more flexible parallel implementa tion of MC\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 s [57] Underfull \hbox (badness 10000) detected at line 75 [][][] Underfull \hbox (badness 10000) detected at line 78 [][][] Underfull \hbox (badness 10000) detected at line 94 [][][] Underfull \hbox (badness 10000) detected at line 111 [][][] [58] Underfull \hbox (badness 10000) detected at line 114 [][][] Underfull \hbox (badness 10000) detected at line 132 [][][] Underfull \hbox (badness 10000) detected at line 149 [][][] Underfull \hbox (badness 10000) detected at line 171 [][][] [59] Underfull \hbox (badness 10000) detected at line 195 [][][] Underfull \hbox (badness 10000) detected at line 198 [][][] Underfull \hbox (badness 10000) detected at line 201 [][][] Overfull \vbox (42.60027pt too high) has occurred while \output is active [60] Underfull \hbox (badness 10000) detected at line 241 [][][] Underfull \hbox (badness 10000) detected at line 244 [][][] ) (./group___a_p_o_lparm.tex [61] Overfull \vbox (22.62613pt too high) has occurred while \output is active [62] Underfull \hbox (badness 10000) detected at line 212 [][][] Underfull \hbox (badness 10000) detected at line 220 [][][] [63] Underfull \hbox (badness 10000) detected at line 237 [][][] Underfull \hbox (badness 10000) detected at line 261 [][][] Underfull \hbox (badness 10000) detected at line 264 [][][] Underfull \hbox (badness 10000) detected at line 281 [][][] Underfull \hbox (badness 10000) detected at line 289 [][][] [64] Underfull \hbox (badness 10000) detected at line 306 [][][] Underfull \hbox (badness 10000) detected at line 328 [][][] ) (./group___b_e_mparm.tex [65] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] [66] Underfull \hbox (badness 10000) detected at line 125 [][][] Underfull \hbox (badness 10000) detected at line 133 [][][] Underfull \hbox (badness 10000) detected at line 150 [][][] Underfull \hbox (badness 10000) detected at line 158 [][][] Underfull \hbox (badness 10000) detected at line 175 [][][] [67] Underfull \hbox (badness 10000) detected at line 185 [][][] Underfull \hbox (badness 10000) detected at line 202 [][][] Underfull \hbox (badness 10000) detected at line 224 [][][] Underfull \hbox (badness 10000) detected at line 246 [][][] [68] Underfull \hbox (badness 10000) detected at line 258 [][][] ) (./group___f_e_mparm.tex [69] Underfull \hbox (badness 10000) detected at line 111 [][][] [70] Underfull \hbox (badness 10000) detected at line 155 [][][] Underfull \hbox (badness 10000) detected at line 158 [][][] Underfull \hbox (badness 10000) detected at line 197 [][][] Underfull \hbox (badness 10000) detected at line 231 [][][] [71] Underfull \hbox (badness 10000) detected at line 239 [][][] Underfull \hbox (badness 10000) detected at line 256 [][][] Underfull \hbox (badness 10000) detected at line 280 [][][] Underfull \hbox (badness 10000) detected at line 288 [][][] [72] Underfull \hbox (badness 10000) detected at line 305 [][][] Underfull \hbox (badness 10000) detected at line 315 [][][] Underfull \hbox (badness 10000) detected at line 332 [][][] Underfull \hbox (badness 10000) detected at line 354 [][][] ) (./group___g_e_o_f_l_o_wparm.tex [73] Underfull \hbox (badness 10000) detected at line 68 [][][] [74] Underfull \hbox (badness 10000) detected at line 71 [][][] Underfull \hbox (badness 10000) detected at line 124 [][][] Underfull \hbox (badness 10000) detected at line 132 [][][] [75] Underfull \hbox (badness 10000) detected at line 149 [][][] Underfull \hbox (badness 10000) detected at line 173 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 198 [][][] Underfull \hbox (badness 10000) detected at line 208 [][][] [76] Underfull \hbox (badness 10000) detected at line 225 [][][] Underfull \hbox (badness 10000) detected at line 247 [][][] Underfull \hbox (badness 10000) detected at line 269 [][][] [77] Underfull \hbox (badness 10000) detected at line 281 [][][] ) (./group___m_gparm.tex [78] [79] Underfull \hbox (badness 10000) detected at line 205 [][][] [80] Underfull \hbox (badness 10000) detected at line 217 [][][] Underfull \hbox (badness 10000) detected at line 234 [][][] Underfull \hbox (badness 10000) detected at line 246 [][][] Underfull \hbox (badness 10000) detected at line 263 [][][] Underfull \hbox (badness 10000) detected at line 271 [][][] [81] Underfull \hbox (badness 10000) detected at line 288 [][][] Underfull \hbox (badness 10000) detected at line 312 [][][] Underfull \hbox (badness 10000) detected at line 320 [][][] Underfull \hbox (badness 10000) detected at line 337 [][][] Underfull \hbox (badness 10000) detected at line 347 [][][] [82] Underfull \hbox (badness 10000) detected at line 364 [][][] Underfull \hbox (badness 10000) detected at line 386 [][][] Underfull \hbox (badness 10000) detected at line 408 [][][] Underfull \hbox (badness 10000) detected at line 416 [][][] [83] Underfull \hbox (badness 10000) detected at line 433 [][][] Underfull \hbox (badness 10000) detected at line 441 [][][] Underfull \hbox (badness 10000) detected at line 458 [][][] Underfull \hbox (badness 10000) detected at line 466 [][][] Underfull \hbox (badness 10000) detected at line 483 [][][] Underfull \hbox (badness 10000) detected at line 491 [][][] [84] Underfull \hbox (badness 10000) detected at line 508 [][][] Underfull \hbox (badness 10000) detected at line 516 [][][] Underfull \hbox (badness 10000) detected at line 533 [][][] Underfull \hbox (badness 10000) detected at line 541 [][][] Underfull \hbox (badness 10000) detected at line 558 [][][] [85] Underfull \hbox (badness 10000) detected at line 566 [][][] Underfull \hbox (badness 10000) detected at line 583 [][][] Underfull \hbox (badness 10000) detected at line 591 [][][] Underfull \hbox (badness 10000) detected at line 608 [][][] Underfull \hbox (badness 10000) detected at line 616 [][][] Underfull \hbox (badness 10000) detected at line 633 [][][] [86] Underfull \hbox (badness 10000) detected at line 645 [][][] Underfull \hbox (badness 10000) detected at line 662 [][][] Underfull \hbox (badness 10000) detected at line 686 [][][] [87] Underfull \hbox (badness 10000) detected at line 710 [][][] ) (./group___n_osh.tex [88] [89] [90] [91] [92] Underfull \hbox (badness 10000) detected at line 431 [][][] Underfull \hbox (badness 10000) detected at line 441 [][][] Underfull \hbox (badness 10000) detected at line 458 [][][] Underfull \hbox (badness 10000) detected at line 482 [][][] [93] Underfull \hbox (badness 10000) detected at line 490 [][][] Underfull \hbox (badness 10000) detected at line 507 [][][] Underfull \hbox (badness 10000) detected at line 529 [][][] Underfull \hbox (badness 10000) detected at line 539 [][][] Underfull \hbox (badness 10000) detected at line 556 [][][] [94] Underfull \hbox (badness 10000) detected at line 568 [][][] Underfull \hbox (badness 10000) detected at line 585 [][][] Underfull \hbox (badness 10000) detected at line 607 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] [95] Underfull \hbox (badness 10000) detected at line 639 [][][] Underfull \hbox (badness 10000) detected at line 656 [][][] Underfull \hbox (badness 10000) detected at line 659 [][][] Underfull \hbox (badness 10000) detected at line 669 [][][] Underfull \hbox (badness 10000) detected at line 672 [][][] Underfull \hbox (badness 10000) detected at line 689 [][][] Overfull \vbox (15.28305pt too high) has occurred while \output is active [96] Underfull \hbox (badness 10000) detected at line 699 [][][] Underfull \hbox (badness 10000) detected at line 716 [][][] Underfull \hbox (badness 10000) detected at line 726 [][][] Underfull \hbox (badness 10000) detected at line 743 [][][] Underfull \hbox (badness 10000) detected at line 753 [][][] [97] Underfull \hbox (badness 10000) detected at line 770 [][][] Underfull \hbox (badness 10000) detected at line 780 [][][] Underfull \hbox (badness 10000) detected at line 797 [][][] Underfull \hbox (badness 10000) detected at line 807 [][][] Underfull \hbox (badness 10000) detected at line 824 [][][] [98] Underfull \hbox (badness 10000) detected at line 834 [][][] Underfull \hbox (badness 10000) detected at line 851 [][][] Underfull \hbox (badness 10000) detected at line 861 [][][] Underfull \hbox (badness 10000) detected at line 878 [][][] Underfull \hbox (badness 10000) detected at line 888 [][][] [99] Underfull \hbox (badness 10000) detected at line 905 [][][] Underfull \hbox (badness 10000) detected at line 915 [][][] Underfull \hbox (badness 10000) detected at line 932 [][][] Underfull \hbox (badness 10000) detected at line 942 [][][] Underfull \hbox (badness 10000) detected at line 959 [][][] [100] Underfull \hbox (badness 10000) detected at line 969 [][][] Underfull \hbox (badness 10000) detected at line 986 [][][] Underfull \hbox (badness 10000) detected at line 996 [][][] Underfull \hbox (badness 10000) detected at line 1013 [][][] Underfull \hbox (badness 10000) detected at line 1016 [][][] Underfull \hbox (badness 10000) detected at line 1026 [][][] [101] Underfull \hbox (badness 10000) detected at line 1043 [][][] Underfull \hbox (badness 10000) detected at line 1048 [][][] Underfull \hbox (badness 10000) detected at line 1058 [][][] Underfull \hbox (badness 10000) detected at line 1075 [][][] Underfull \hbox (badness 10000) detected at line 1078 [][][] [102] Underfull \hbox (badness 10000) detected at line 1090 [][][] Underfull \hbox (badness 10000) detected at line 1093 [][][] Underfull \hbox (badness 10000) detected at line 1110 [][][] Underfull \hbox (badness 10000) detected at line 1113 [][][] Underfull \hbox (badness 10000) detected at line 1123 [][][] Underfull \hbox (badness 10000) detected at line 1126 [][][] Underfull \hbox (badness 10000) detected at line 1143 [][][] Underfull \hbox (badness 10000) detected at line 1146 [][][] [103] Underfull \hbox (badness 10000) detected at line 1158 [][][] Underfull \hbox (badness 10000) detected at line 1161 [][][] Underfull \hbox (badness 10000) detected at line 1178 [][][] Underfull \hbox (badness 10000) detected at line 1181 [][][] Underfull \hbox (badness 10000) detected at line 1191 [][][] Underfull \hbox (badness 10000) detected at line 1194 [][][] Underfull \hbox (badness 10000) detected at line 1211 [][][] [104] Underfull \hbox (badness 10000) detected at line 1214 [][][] Underfull \hbox (badness 10000) detected at line 1224 [][][] Underfull \hbox (badness 10000) detected at line 1248 [][][] Underfull \hbox (badness 10000) detected at line 1251 [][][] Underfull \hbox (badness 10000) detected at line 1261 [][][] Overfull \vbox (3.94589pt too high) has occurred while \output is active [105]) (./group___p_b_a_mparm.tex [106] Underfull \hbox (badness 10000) detected at line 116 [][][] Underfull \hbox (badness 10000) detected at line 119 [][][] [107] Underfull \hbox (badness 10000) detected at line 172 [][][] Underfull \hbox (badness 10000) detected at line 180 [][][] Underfull \hbox (badness 10000) detected at line 197 [][][] [108] Underfull \hbox (badness 10000) detected at line 221 [][][] Underfull \hbox (badness 10000) detected at line 229 [][][] Underfull \hbox (badness 10000) detected at line 246 [][][] Underfull \hbox (badness 10000) detected at line 256 [][][] [109] Underfull \hbox (badness 10000) detected at line 273 [][][] Underfull \hbox (badness 10000) detected at line 295 [][][] Underfull \hbox (badness 10000) detected at line 317 [][][] Underfull \hbox (badness 10000) detected at line 341 [][][] [110] Underfull \hbox (badness 10000) detected at line 365 [][][] Underfull \hbox (badness 10000) detected at line 389 [][][] Underfull \hbox (badness 10000) detected at line 413 [][][] [111] Underfull \hbox (badness 10000) detected at line 437 [][][] Underfull \hbox (badness 10000) detected at line 461 [][][] Underfull \hbox (badness 10000) detected at line 485 [][][] [112] Underfull \hbox (badness 10000) detected at line 509 [][][] Underfull \hbox (badness 10000) detected at line 533 [][][] Underfull \hbox (badness 10000) detected at line 557 [][][] [113] Underfull \hbox (badness 10000) detected at line 581 [][][] Underfull \hbox (badness 10000) detected at line 593 [][][] Underfull \hbox (badness 10000) detected at line 610 [][][] [114] Underfull \hbox (badness 10000) detected at line 634 [][][] ) (./group___p_b_eparm.tex [115] [116] Underfull \hbox (badness 10000) detected at line 209 [][][] Underfull \hbox (badness 10000) detected at line 212 [][][] [117] Underfull \hbox (badness 10000) detected at line 234 [][][] Underfull \hbox (badness 10000) detected at line 258 [][][] Underfull \hbox (badness 10000) detected at line 261 [][][] Underfull \hbox (badness 10000) detected at line 278 [][][] Underfull \hbox (badness 10000) detected at line 281 [][][] [118] Underfull \hbox (badness 10000) detected at line 303 [][][] Underfull \hbox (badness 10000) detected at line 325 [][][] Underfull \hbox (badness 10000) detected at line 347 [][][] Underfull \hbox (badness 10000) detected at line 350 [][][] [119] Underfull \hbox (badness 10000) detected at line 374 [][][] Underfull \hbox (badness 10000) detected at line 377 [][][] Underfull \hbox (badness 10000) detected at line 401 [][][] Underfull \hbox (badness 10000) detected at line 404 [][][] Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 431 [][][] [120]) (./group___p_b_s_a_mparm.tex [121] Underfull \hbox (badness 10000) detected at line 100 [][][] Underfull \hbox (badness 10000) detected at line 103 [][][] [122] Underfull \hbox (badness 10000) detected at line 156 [][][] Underfull \hbox (badness 10000) detected at line 164 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] [123] Underfull \hbox (badness 10000) detected at line 205 [][][] Underfull \hbox (badness 10000) detected at line 213 [][][] Underfull \hbox (badness 10000) detected at line 230 [][][] Underfull \hbox (badness 10000) detected at line 240 [][][] Underfull \hbox (badness 10000) detected at line 257 [][][] Overfull \vbox (0.37224pt too high) has occurred while \output is active [124] Underfull \hbox (badness 10000) detected at line 279 [][][] Underfull \hbox (badness 10000) detected at line 301 [][][] Underfull \hbox (badness 10000) detected at line 325 [][][] [125] Underfull \hbox (badness 10000) detected at line 349 [][][] Underfull \hbox (badness 10000) detected at line 373 [][][] Underfull \hbox (badness 10000) detected at line 397 [][][] [126] Underfull \hbox (badness 10000) detected at line 409 [][][] Underfull \hbox (badness 10000) detected at line 426 [][][] ) (./group___vacc.tex [127] [128] [129] Underfull \hbox (badness 10000) detected at line 149 [][][] Underfull \hbox (badness 10000) detected at line 179 [][][] [130] Underfull \hbox (badness 10000) detected at line 207 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] Underfull \hbox (badness 10000) detected at line 213 [][][] Underfull \hbox (badness 10000) detected at line 239 [][][] Underfull \hbox (badness 10000) detected at line 242 [][][] [131] Underfull \hbox (badness 10000) detected at line 268 [][][] Underfull \hbox (badness 10000) detected at line 271 [][][] Underfull \hbox (badness 10000) detected at line 283 [][][] Underfull \hbox (badness 10000) detected at line 305 [][][] Underfull \hbox (badness 10000) detected at line 308 [][][] [132] Underfull \hbox (badness 10000) detected at line 334 [][][] Underfull \hbox (badness 10000) detected at line 337 [][][] Underfull \hbox (badness 10000) detected at line 365 [][][] Underfull \hbox (badness 10000) detected at line 387 [][][] [133] Underfull \hbox (badness 10000) detected at line 411 [][][] Underfull \hbox (badness 10000) detected at line 414 [][][] Underfull \hbox (badness 10000) detected at line 417 [][][] Underfull \hbox (badness 10000) detected at line 447 [][][] Underfull \hbox (badness 10000) detected at line 450 [][][] [134] Underfull \hbox (badness 10000) detected at line 472 [][][] Underfull \hbox (badness 10000) detected at line 475 [][][] Underfull \hbox (badness 10000) detected at line 499 [][][] Underfull \hbox (badness 10000) detected at line 502 [][][] [135] Underfull \hbox (badness 10000) detected at line 530 [][][] Underfull \hbox (badness 10000) detected at line 533 [][][] Underfull \hbox (badness 10000) detected at line 536 [][][] Underfull \hbox (badness 10000) detected at line 562 [][][] Underfull \hbox (badness 10000) detected at line 565 [][][] [136] Underfull \hbox (badness 10000) detected at line 595 [][][] Underfull \hbox (badness 10000) detected at line 598 [][][] Underfull \hbox (badness 10000) detected at line 628 [][][] [137] Underfull \hbox (badness 10000) detected at line 660 [][][] Underfull \hbox (badness 10000) detected at line 692 [][][] [138] Underfull \hbox (badness 10000) detected at line 724 [][][] Underfull \hbox (badness 10000) detected at line 758 [][][] [139] Underfull \hbox (badness 10000) detected at line 790 [][][] Underfull \hbox (badness 10000) detected at line 820 [][][] [140] Underfull \hbox (badness 10000) detected at line 852 [][][] Underfull \hbox (badness 10000) detected at line 855 [][][] Underfull \hbox (badness 10000) detected at line 858 [][][] Underfull \hbox (badness 10000) detected at line 882 [][][] Underfull \hbox (badness 10000) detected at line 885 [][][] Underfull \hbox (badness 10000) detected at line 888 [][][] [141] Underfull \hbox (badness 10000) detected at line 918 [][][] Underfull \hbox (badness 10000) detected at line 921 [][][] Underfull \hbox (badness 10000) detected at line 941 [][][] Underfull \hbox (badness 10000) detected at line 944 [][][] Overfull \vbox (21.5778pt too high) has occurred while \output is active [142] Underfull \hbox (badness 10000) detected at line 972 [][][] Underfull \hbox (badness 10000) detected at line 975 [][][] Underfull \hbox (badness 10000) detected at line 1007 [][][] Underfull \hbox (badness 10000) detected at line 1010 [][][] [143] Underfull \hbox (badness 10000) detected at line 1040 [][][] Underfull \hbox (badness 10000) detected at line 1043 [][][] Underfull \hbox (badness 10000) detected at line 1069 [][][] Underfull \hbox (badness 10000) detected at line 1072 [][][] Overfull \vbox (18.93095pt too high) has occurred while \output is active [144] Underfull \hbox (badness 10000) detected at line 1100 [][][] Underfull \hbox (badness 10000) detected at line 1122 [][][] Underfull \hbox (badness 10000) detected at line 1146 [][][] Underfull \hbox (badness 10000) detected at line 1149 [][][] Underfull \hbox (badness 10000) detected at line 1152 [][][] [145]) (./group___valist.tex [146] Underfull \hbox (badness 10000) detected at line 91 [][][] Underfull \hbox (badness 10000) detected at line 94 [][][] Underfull \hbox (badness 10000) detected at line 111 [][][] Underfull \hbox (badness 10000) detected at line 114 [][][] Overfull \vbox (3.49948pt too high) has occurred while \output is active [147] Underfull \hbox (badness 10000) detected at line 136 [][][] Underfull \hbox (badness 10000) detected at line 158 [][][] Underfull \hbox (badness 10000) detected at line 180 [][][] Underfull \hbox (badness 10000) detected at line 183 [][][] [148] Underfull \hbox (badness 10000) detected at line 207 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] Underfull \hbox (badness 10000) detected at line 232 [][][] Underfull \hbox (badness 10000) detected at line 235 [][][] Underfull \hbox (badness 10000) detected at line 257 [][][] Underfull \hbox (badness 10000) detected at line 260 [][][] [149] Underfull \hbox (badness 10000) detected at line 282 [][][] Underfull \hbox (badness 10000) detected at line 285 [][][] Underfull \hbox (badness 10000) detected at line 307 [][][] Underfull \hbox (badness 10000) detected at line 310 [][][] Underfull \hbox (badness 10000) detected at line 332 [][][] [150] Underfull \hbox (badness 10000) detected at line 335 [][][] Underfull \hbox (badness 10000) detected at line 352 [][][] Underfull \hbox (badness 10000) detected at line 355 [][][] Underfull \hbox (badness 10000) detected at line 377 [][][] Underfull \hbox (badness 10000) detected at line 380 [][][] Underfull \hbox (badness 10000) detected at line 383 [][][] [151] Underfull \hbox (badness 10000) detected at line 409 [][][] Underfull \hbox (badness 10000) detected at line 412 [][][] Underfull \hbox (badness 10000) detected at line 415 [][][] Underfull \hbox (badness 10000) detected at line 443 [][][] Underfull \hbox (badness 10000) detected at line 446 [][][] Underfull \hbox (badness 10000) detected at line 449 [][][] Overfull \vbox (15.85518pt too high) has occurred while \output is active [152]) (./group___vatom.tex [153] Underfull \hbox (badness 10000) detected at line 97 [][][] [154] Underfull \hbox (badness 10000) detected at line 134 [][][] Underfull \hbox (badness 10000) detected at line 158 [][][] Underfull \hbox (badness 10000) detected at line 182 [][][] Underfull \hbox (badness 10000) detected at line 185 [][][] [155] Underfull \hbox (badness 10000) detected at line 202 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] Underfull \hbox (badness 10000) detected at line 227 [][][] Underfull \hbox (badness 10000) detected at line 249 [][][] Underfull \hbox (badness 10000) detected at line 271 [][][] [156] Underfull \hbox (badness 10000) detected at line 279 [][][] Underfull \hbox (badness 10000) detected at line 296 [][][] Underfull \hbox (badness 10000) detected at line 320 [][][] Underfull \hbox (badness 10000) detected at line 328 [][][] [157] Underfull \hbox (badness 10000) detected at line 345 [][][] Underfull \hbox (badness 10000) detected at line 353 [][][] Underfull \hbox (badness 10000) detected at line 370 [][][] Underfull \hbox (badness 10000) detected at line 378 [][][] Underfull \hbox (badness 10000) detected at line 395 [][][] Underfull \hbox (badness 10000) detected at line 403 [][][] [158] Underfull \hbox (badness 10000) detected at line 420 [][][] Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 445 [][][] Underfull \hbox (badness 10000) detected at line 469 [][][] [159] Underfull \hbox (badness 10000) detected at line 477 [][][] Underfull \hbox (badness 10000) detected at line 494 [][][] Underfull \hbox (badness 10000) detected at line 518 [][][] [160] Underfull \hbox (badness 10000) detected at line 542 [][][] Underfull \hbox (badness 10000) detected at line 566 [][][] Underfull \hbox (badness 10000) detected at line 590 [][][] [161] Underfull \hbox (badness 10000) detected at line 614 [][][] Underfull \hbox (badness 10000) detected at line 638 [][][] Underfull \hbox (badness 10000) detected at line 662 [][][] ) (./group___vcap.tex [162] Underfull \hbox (badness 10000) detected at line 36 [][][] [163] Underfull \hbox (badness 10000) detected at line 86 [][][] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 92 [][][] Underfull \hbox (badness 10000) detected at line 119 [][][] Underfull \hbox (badness 10000) detected at line 122 [][][] Underfull \hbox (badness 10000) detected at line 125 [][][] [164] Underfull \hbox (badness 10000) detected at line 152 [][][] Underfull \hbox (badness 10000) detected at line 155 [][][] Underfull \hbox (badness 10000) detected at line 158 [][][] ) (./group___vclist.tex [165] [166] Underfull \hbox (badness 10000) detected at line 110 [][][] Underfull \hbox (badness 10000) detected at line 140 [][][] Underfull \hbox (badness 10000) detected at line 143 [][][] [167] Underfull \hbox (badness 10000) detected at line 175 [][][] Underfull \hbox (badness 10000) detected at line 178 [][][] Underfull \hbox (badness 10000) detected at line 212 [][][] [168] Underfull \hbox (badness 10000) detected at line 234 [][][] Underfull \hbox (badness 10000) detected at line 256 [][][] Underfull \hbox (badness 10000) detected at line 259 [][][] Underfull \hbox (badness 10000) detected at line 283 [][][] Underfull \hbox (badness 10000) detected at line 286 [][][] [169] Underfull \hbox (badness 10000) detected at line 308 [][][] Underfull \hbox (badness 10000) detected at line 311 [][][] Underfull \hbox (badness 10000) detected at line 333 [][][] Underfull \hbox (badness 10000) detected at line 336 [][][] Underfull \hbox (badness 10000) detected at line 358 [][][] Underfull \hbox (badness 10000) detected at line 361 [][][] [170] Underfull \hbox (badness 10000) detected at line 385 [][][] Underfull \hbox (badness 10000) detected at line 407 [][][] ) (./group___vgreen.tex [171] Underfull \hbox (badness 10000) detected at line 57 [][][] Underfull \hbox (badness 10000) detected at line 60 [][][] [172] [173] Underfull \hbox (badness 10000) detected at line 141 [][][] Underfull \hbox (badness 10000) detected at line 159 [][][] Underfull \hbox (badness 10000) detected at line 178 [][][] [174] Underfull \hbox (badness 10000) detected at line 196 [][][] Underfull \hbox (badness 10000) detected at line 215 [][][] [175] Underfull \hbox (badness 10000) detected at line 239 [][][] Underfull \hbox (badness 10000) detected at line 258 [][][] Underfull \hbox (badness 10000) detected at line 282 [][][] [176] Underfull \hbox (badness 10000) detected at line 299 [][][] Underfull \hbox (badness 10000) detected at line 307 [][][] Underfull \hbox (badness 10000) detected at line 324 [][][] Underfull \hbox (badness 10000) detected at line 334 [][][] Underfull \hbox (badness 10000) detected at line 351 [][][] [177] Underfull \hbox (badness 10000) detected at line 373 [][][] Underfull \hbox (badness 10000) detected at line 395 [][][] Underfull \hbox (badness 10000) detected at line 403 [][][] Underfull \hbox (badness 10000) detected at line 424 [][][] [178] Underfull \hbox (badness 10000) detected at line 429 [][][] Underfull \hbox (badness 10000) detected at line 449 [][][] Underfull \hbox (badness 10000) detected at line 471 [][][] Underfull \hbox (badness 10000) detected at line 476 [][][] [179] Underfull \hbox (badness 10000) detected at line 500 [][][] Underfull \hbox (badness 10000) detected at line 517 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] ) (./group___vhal.tex [180] [181] [182] [183] Underfull \hbox (badness 10000) detected at line 380 [][][] Underfull \hbox (badness 10000) detected at line 411 [][][] [184] Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 445 [][][] Underfull \hbox (badness 10000) detected at line 476 [][][] Underfull \hbox (badness 10000) detected at line 493 [][][] Underfull \hbox (badness 10000) detected at line 516 [][][] [185] Underfull \hbox (badness 10000) detected at line 547 [][][] [186] Underfull \hbox (badness 10000) detected at line 682 [][][] Underfull \hbox (badness 10000) detected at line 729 [][][] [187] Underfull \hbox (badness 10000) detected at line 760 [][][] Underfull \hbox (badness 10000) detected at line 795 [][][] Underfull \hbox (badness 10000) detected at line 842 [][][] Missing character: There is no Å in font cmr10! Missing character: There is no Å in font cmr10! LaTeX Warning: Command \r invalid in math mode on input line 58. Missing character: There is no Å in font cmr10! [188] [189] Underfull \hbox (badness 10000) detected at line 1019 [][][] Underfull \hbox (badness 10000) detected at line 1022 [][][] Underfull \hbox (badness 10000) detected at line 1050 [][][] Underfull \hbox (badness 10000) detected at line 1053 [][][] Underfull \hbox (badness 10000) detected at line 1070 [][][] [190]) (./group___vmatrix.tex) (./group___vparam.tex [191] [192] Underfull \hbox (badness 10000) detected at line 120 [][][] Underfull \hbox (badness 10000) detected at line 130 [][][] [193] Underfull \hbox (badness 10000) detected at line 147 [][][] Underfull \hbox (badness 10000) detected at line 157 [][][] Underfull \hbox (badness 10000) detected at line 174 [][][] Underfull \hbox (badness 10000) detected at line 198 [][][] [194] Underfull \hbox (badness 10000) detected at line 222 [][][] Underfull \hbox (badness 10000) detected at line 225 [][][] Underfull \hbox (badness 10000) detected at line 242 [][][] Underfull \hbox (badness 10000) detected at line 250 [][][] Underfull \hbox (badness 10000) detected at line 267 [][][] [195] Underfull \hbox (badness 10000) detected at line 289 [][][] Underfull \hbox (badness 10000) detected at line 311 [][][] Underfull \hbox (badness 10000) detected at line 314 [][][] Underfull \hbox (badness 10000) detected at line 331 [][][] Underfull \hbox (badness 10000) detected at line 339 [][][] Underfull \hbox (badness 10000) detected at line 356 [][][] [196] Underfull \hbox (badness 10000) detected at line 378 [][][] Underfull \hbox (badness 10000) detected at line 400 [][][] Underfull \hbox (badness 10000) detected at line 412 [][][] Underfull \hbox (badness 10000) detected at line 415 [][][] Underfull \hbox (badness 10000) detected at line 418 [][][] [197] Underfull \hbox (badness 10000) detected at line 435 [][][] Underfull \hbox (badness 10000) detected at line 445 [][][] Underfull \hbox (badness 10000) detected at line 448 [][][] Underfull \hbox (badness 10000) detected at line 451 [][][] Underfull \hbox (badness 10000) detected at line 468 [][][] Underfull \hbox (badness 10000) detected at line 476 [][][] [198] Underfull \hbox (badness 10000) detected at line 493 [][][] Underfull \hbox (badness 10000) detected at line 509 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Underfull \hbox (badness 10000) detected at line 537 [][][] [199] Underfull \hbox (badness 10000) detected at line 553 [][][] Underfull \hbox (badness 10000) detected at line 570 [][][] Underfull \hbox (badness 10000) detected at line 594 [][][] Underfull \hbox (badness 10000) detected at line 602 [][][] [200] Underfull \hbox (badness 10000) detected at line 619 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] Underfull \hbox (badness 10000) detected at line 646 [][][] Underfull \hbox (badness 10000) detected at line 668 [][][] [201]) (./group___vpbe.tex [202] [203] Underfull \hbox (badness 10000) detected at line 128 [][][] Underfull \hbox (badness 10000) detected at line 131 [][][] LaTeX Warning: Command \r invalid in math mode on input line 133. Missing character: There is no Å in font cmr10! LaTeX Warning: Command \r invalid in math mode on input line 133. Missing character: There is no Å in font cmr10! [204] Underfull \hbox (badness 10000) detected at line 136 [][][] [205] Underfull \hbox (badness 10000) detected at line 186 [][][] Underfull \hbox (badness 10000) detected at line 189 [][][] LaTeX Warning: Command \r invalid in math mode on input line 190. Missing character: There is no Å in font cmr10! LaTeX Warning: Command \r invalid in math mode on input line 190. Missing character: There is no Å in font cmr10! Underfull \hbox (badness 10000) detected at line 195 [][][] Overfull \vbox (21.60152pt too high) has occurred while \output is active [206] Underfull \hbox (badness 10000) detected at line 247 [][][] Underfull \hbox (badness 10000) detected at line 269 [][][] Underfull \hbox (badness 10000) detected at line 291 [][][] Underfull \hbox (badness 10000) detected at line 299 [][][] [207] Overfull \hbox (151.96916pt too wide) in paragraph at lines 318--318 [] \T1/p cr/m/n/8 permittivity equal to the protein interior) and zero ionic[] Underfull \hbox (badness 10000) detected at line 325 [][][] Underfull \hbox (badness 10000) detected at line 333 [][][] Underfull \hbox (badness 10000) detected at line 350 [][][] Underfull \hbox (badness 10000) detected at line 358 [][][] [208] Underfull \hbox (badness 10000) detected at line 375 [][][] Underfull \hbox (badness 10000) detected at line 383 [][][] Underfull \hbox (badness 10000) detected at line 396 [][][] Underfull \hbox (badness 10000) detected at line 412 [][][] [209] Underfull \hbox (badness 10000) detected at line 436 [][][] Underfull \hbox (badness 10000) detected at line 453 [][][] Underfull \hbox (badness 10000) detected at line 461 [][][] Underfull \hbox (badness 10000) detected at line 478 [][][] Underfull \hbox (badness 10000) detected at line 486 [][][] Underfull \hbox (badness 10000) detected at line 503 [][][] [210] Underfull \hbox (badness 10000) detected at line 525 [][][] Underfull \hbox (badness 10000) detected at line 533 [][][] Underfull \hbox (badness 10000) detected at line 550 [][][] Underfull \hbox (badness 10000) detected at line 558 [][][] Underfull \hbox (badness 10000) detected at line 575 [][][] [211] Underfull \hbox (badness 10000) detected at line 583 [][][] Underfull \hbox (badness 10000) detected at line 600 [][][] Underfull \hbox (badness 10000) detected at line 608 [][][] Underfull \hbox (badness 10000) detected at line 625 [][][] Underfull \hbox (badness 10000) detected at line 633 [][][] [212] Underfull \hbox (badness 10000) detected at line 650 [][][] Underfull \hbox (badness 10000) detected at line 658 [][][] Underfull \hbox (badness 10000) detected at line 675 [][][] Underfull \hbox (badness 10000) detected at line 683 [][][] Underfull \hbox (badness 10000) detected at line 700 [][][] Underfull \hbox (badness 10000) detected at line 708 [][][] [213] Underfull \hbox (badness 10000) detected at line 725 [][][] Underfull \hbox (badness 10000) detected at line 733 [][][] Underfull \hbox (badness 10000) detected at line 750 [][][] Underfull \hbox (badness 10000) detected at line 758 [][][] Underfull \hbox (badness 10000) detected at line 775 [][][] [214] Underfull \hbox (badness 10000) detected at line 783 [][][] Underfull \hbox (badness 10000) detected at line 800 [][][] Underfull \hbox (badness 10000) detected at line 808 [][][] Underfull \hbox (badness 10000) detected at line 825 [][][] Underfull \hbox (badness 10000) detected at line 833 [][][] [215] Underfull \hbox (badness 10000) detected at line 850 [][][] Underfull \hbox (badness 10000) detected at line 858 [][][] LaTeX Warning: Command \r invalid in math mode on input line 859. Missing character: There is no Å in font cmr10! Underfull \hbox (badness 10000) detected at line 875 [][][] Underfull \hbox (badness 10000) detected at line 883 [][][] Underfull \hbox (badness 10000) detected at line 900 [][][] Underfull \hbox (badness 10000) detected at line 908 [][][] [216] Underfull \hbox (badness 10000) detected at line 925 [][][] Underfull \hbox (badness 10000) detected at line 933 [][][] ) (./group___vstring.tex [217] Underfull \hbox (badness 10000) detected at line 42 [][][] Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 67 [][][] Underfull \hbox (badness 10000) detected at line 70 [][][] Underfull \hbox (badness 10000) detected at line 80 [][][] Underfull \hbox (badness 10000) detected at line 93 [][][] [218] Underfull \hbox (badness 10000) detected at line 96 [][][] Underfull \hbox (badness 10000) detected at line 99 [][][] Underfull \hbox (badness 10000) detected at line 102 [][][] Underfull \hbox (badness 10000) detected at line 105 [][][] ) (./group___vunit.tex [219] LaTeX Warning: Command \r invalid in math mode on input line 39. Missing character: There is no Å in font cmr9! [220] LaTeX Warning: Command \r invalid in math mode on input line 142. Missing character: There is no Å in font cmr10! ) (./group___vgrid.tex [221] [222] [223] Underfull \hbox (badness 10000) detected at line 125 [][][] Underfull \hbox (badness 10000) detected at line 151 [][][] Underfull \hbox (badness 10000) detected at line 168 [][][] [224] Underfull \hbox (badness 10000) detected at line 196 [][][] Underfull \hbox (badness 10000) detected at line 213 [][][] Underfull \hbox (badness 10000) detected at line 229 [][][] [225] Underfull \hbox (badness 10000) detected at line 246 [][][] Underfull \hbox (badness 10000) detected at line 268 [][][] Underfull \hbox (badness 10000) detected at line 290 [][][] Underfull \hbox (badness 10000) detected at line 302 [][][] [226] Underfull \hbox (badness 10000) detected at line 319 [][][] Underfull \hbox (badness 10000) detected at line 327 [][][] Underfull \hbox (badness 10000) detected at line 344 [][][] Underfull \hbox (badness 10000) detected at line 352 [][][] Underfull \hbox (badness 10000) detected at line 369 [][][] Underfull \hbox (badness 10000) detected at line 377 [][][] [227] Underfull \hbox (badness 10000) detected at line 395 [][][] Underfull \hbox (badness 10000) detected at line 403 [][][] Underfull \hbox (badness 10000) detected at line 420 [][][] Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 445 [][][] [228] Underfull \hbox (badness 10000) detected at line 453 [][][] Underfull \hbox (badness 10000) detected at line 470 [][][] Underfull \hbox (badness 10000) detected at line 473 [][][] Underfull \hbox (badness 10000) detected at line 489 [][][] Underfull \hbox (badness 10000) detected at line 492 [][][] [229] Underfull \hbox (badness 10000) detected at line 509 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Underfull \hbox (badness 10000) detected at line 528 [][][] Underfull \hbox (badness 10000) detected at line 531 [][][] Underfull \hbox (badness 10000) detected at line 548 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] [230] Underfull \hbox (badness 10000) detected at line 575 [][][] Underfull \hbox (badness 10000) detected at line 583 [][][] Underfull \hbox (badness 10000) detected at line 600 [][][] Underfull \hbox (badness 10000) detected at line 612 [][][] [231] Underfull \hbox (badness 10000) detected at line 629 [][][] Underfull \hbox (badness 10000) detected at line 663 [][][] [232] Underfull \hbox (badness 10000) detected at line 697 [][][] Underfull \hbox (badness 10000) detected at line 702 [][][] ) (./group___vmgrid.tex [233] [234] Underfull \hbox (badness 10000) detected at line 105 [][][] Underfull \hbox (badness 10000) detected at line 115 [][][] Underfull \hbox (badness 10000) detected at line 132 [][][] Underfull \hbox (badness 10000) detected at line 135 [][][] Underfull \hbox (badness 10000) detected at line 152 [][][] [235] Underfull \hbox (badness 10000) detected at line 160 [][][] Underfull \hbox (badness 10000) detected at line 177 [][][] Underfull \hbox (badness 10000) detected at line 193 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] [236] Underfull \hbox (badness 10000) detected at line 232 [][][] Underfull \hbox (badness 10000) detected at line 254 [][][] Underfull \hbox (badness 10000) detected at line 264 [][][] Underfull \hbox (badness 10000) detected at line 277 [][][] [237] Underfull \hbox (badness 10000) detected at line 287 [][][] Underfull \hbox (badness 10000) detected at line 300 [][][] Underfull \hbox (badness 10000) detected at line 312 [][][] Underfull \hbox (badness 10000) detected at line 329 [][][] Underfull \hbox (badness 10000) detected at line 341 [][][] ) (./group___vopot.tex [238] [239] Underfull \hbox (badness 10000) detected at line 77 [][][] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 106 [][][] [240] Underfull \hbox (badness 10000) detected at line 120 [][][] Underfull \hbox (badness 10000) detected at line 137 [][][] Underfull \hbox (badness 10000) detected at line 153 [][][] Underfull \hbox (badness 10000) detected at line 170 [][][] [241] Underfull \hbox (badness 10000) detected at line 192 [][][] Underfull \hbox (badness 10000) detected at line 214 [][][] Underfull \hbox (badness 10000) detected at line 226 [][][] Underfull \hbox (badness 10000) detected at line 243 [][][] Overfull \vbox (28.1848pt too high) has occurred while \output is active [242] Underfull \hbox (badness 10000) detected at line 255 [][][] ) (./group___vpmg.tex [243] [244] [245] Underfull \hbox (badness 10000) detected at line 117 [][][] Underfull \hbox (badness 10000) detected at line 150 [][][] [246] Underfull \hbox (badness 10000) detected at line 186 [][][] [247] Underfull \hbox (badness 10000) detected at line 234 [][][] Underfull \hbox (badness 10000) detected at line 276 [][][] [248] Underfull \hbox (badness 10000) detected at line 324 [][][] [249] Underfull \hbox (badness 10000) detected at line 362 [][][] Underfull \hbox (badness 10000) detected at line 381 [][][] Underfull \hbox (badness 10000) detected at line 384 [][][] [250] Underfull \hbox (badness 10000) detected at line 416 [][][] Underfull \hbox (badness 10000) detected at line 419 [][][] Underfull \hbox (badness 10000) detected at line 422 [][][] [251] Underfull \hbox (badness 10000) detected at line 458 [][][] Underfull \hbox (badness 10000) detected at line 484 [][][] Underfull \hbox (badness 10000) detected at line 487 [][][] Underfull \hbox (badness 10000) detected at line 492 [][][] Overfull \vbox (1.11014pt too high) has occurred while \output is active [252] Underfull \hbox (badness 10000) detected at line 520 [][][] Underfull \hbox (badness 10000) detected at line 546 [][][] [253] Underfull \hbox (badness 10000) detected at line 572 [][][] Underfull \hbox (badness 10000) detected at line 604 [][][] Underfull \hbox (badness 10000) detected at line 607 [][][] Underfull \hbox (badness 10000) detected at line 610 [][][] [254] Underfull \hbox (badness 10000) detected at line 643 [][][] Underfull \hbox (badness 10000) detected at line 646 [][][] Underfull \hbox (badness 10000) detected at line 668 [][][] Underfull \hbox (badness 10000) detected at line 690 [][][] [255] Underfull \hbox (badness 10000) detected at line 712 [][][] Underfull \hbox (badness 10000) detected at line 715 [][][] Underfull \hbox (badness 10000) detected at line 718 [][][] Underfull \hbox (badness 10000) detected at line 742 [][][] [256] Underfull \hbox (badness 10000) detected at line 764 [][][] Underfull \hbox (badness 10000) detected at line 767 [][][] Underfull \hbox (badness 10000) detected at line 799 [][][] [257] Underfull \hbox (badness 10000) detected at line 802 [][][] Underfull \hbox (badness 10000) detected at line 856 [][][] Underfull \hbox (badness 10000) detected at line 859 [][][] Underfull \hbox (badness 10000) detected at line 864 [][][] [258] Underfull \hbox (badness 10000) detected at line 894 [][][] Underfull \hbox (badness 10000) detected at line 920 [][][] Underfull \hbox (badness 10000) detected at line 923 [][][] [259] Underfull \hbox (badness 10000) detected at line 928 [][][] Underfull \hbox (badness 10000) detected at line 956 [][][] Underfull \hbox (badness 10000) detected at line 982 [][][] [260] Underfull \hbox (badness 10000) detected at line 1008 [][][] Underfull \hbox (badness 10000) detected at line 1030 [][][] Underfull \hbox (badness 10000) detected at line 1033 [][][] [261] Underfull \hbox (badness 10000) detected at line 1055 [][][] Underfull \hbox (badness 10000) detected at line 1093 [][][] Underfull \hbox (badness 10000) detected at line 1096 [][][] [262] Underfull \hbox (badness 10000) detected at line 1099 [][][] Underfull \hbox (badness 10000) detected at line 1123 [][][] Underfull \hbox (badness 10000) detected at line 1160 [][][] [263] Underfull \hbox (badness 10000) detected at line 1163 [][][] Underfull \hbox (badness 10000) detected at line 1166 [][][] Underfull \hbox (badness 10000) detected at line 1190 [][][] Underfull \hbox (badness 10000) detected at line 1193 [][][] Underfull \hbox (badness 10000) detected at line 1198 [][][] [264] Underfull \hbox (badness 10000) detected at line 1226 [][][] Underfull \hbox (badness 10000) detected at line 1252 [][][] [265] Underfull \hbox (badness 10000) detected at line 1280 [][][] Underfull \hbox (badness 10000) detected at line 1283 [][][] Underfull \hbox (badness 10000) detected at line 1303 [][][] [266] Underfull \hbox (badness 10000) detected at line 1343 [][][] Underfull \hbox (badness 10000) detected at line 1346 [][][] Underfull \hbox (badness 10000) detected at line 1349 [][][] Underfull \hbox (badness 10000) detected at line 1373 [][][] [267] Underfull \hbox (badness 10000) detected at line 1401 [][][] Underfull \hbox (badness 10000) detected at line 1404 [][][] Underfull \hbox (badness 10000) detected at line 1426 [][][] Underfull \hbox (badness 10000) detected at line 1429 [][][] Underfull \hbox (badness 10000) detected at line 1432 [][][] Underfull \hbox (badness 10000) detected at line 1454 [][][] ) (./group___vpmgp.tex [268] Underfull \hbox (badness 10000) detected at line 45 [][][] [269] Underfull \hbox (badness 10000) detected at line 78 [][][] Underfull \hbox (badness 10000) detected at line 86 [][][] Underfull \hbox (badness 10000) detected at line 103 [][][] Underfull \hbox (badness 10000) detected at line 113 [][][] Underfull \hbox (badness 10000) detected at line 130 [][][] [270] Underfull \hbox (badness 10000) detected at line 152 [][][] Underfull \hbox (badness 10000) detected at line 174 [][][] [271] Underfull \hbox (badness 10000) detected at line 208 [][][] ) (./group___p_m_g_c.tex [272] [273] [274] [275] Underfull \hbox (badness 10000) detected at line 150 [][][] Underfull \hbox (badness 10000) detected at line 153 [][][] Underfull \hbox (badness 10000) detected at line 156 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 165--165 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [276] Underfull \hbox (badness 10000) detected at line 212 [][][] Underfull \hbox (badness 10000) detected at line 215 [][][] Underfull \hbox (badness 10000) detected at line 218 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 227--227 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [277] Underfull \hbox (badness 10000) detected at line 277 [][][] Underfull \hbox (badness 10000) detected at line 280 [][][] [278] Underfull \hbox (badness 10000) detected at line 308 [][][] Underfull \hbox (badness 10000) detected at line 311 [][][] Underfull \hbox (badness 10000) detected at line 339 [][][] Underfull \hbox (badness 10000) detected at line 342 [][][] Underfull \hbox (badness 10000) detected at line 345 [][][] [279] Overfull \hbox (304.08286pt too wide) in paragraph at lines 355--355 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 392 [][][] Underfull \hbox (badness 10000) detected at line 395 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 404--404 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [280] Underfull \hbox (badness 10000) detected at line 439 [][][] [281] Underfull \hbox (badness 10000) detected at line 503 [][][] Underfull \hbox (badness 10000) detected at line 506 [][][] Underfull \hbox (badness 10000) detected at line 509 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 518--518 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [282] Underfull \hbox (badness 10000) detected at line 556 [][][] Underfull \hbox (badness 10000) detected at line 559 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 568--568 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 603 [][][] Underfull \hbox (badness 10000) detected at line 606 [][][] [283] Underfull \hbox (badness 10000) detected at line 646 [][][] Underfull \hbox (badness 10000) detected at line 649 [][][] [284] [285] Underfull \hbox (badness 10000) detected at line 719 [][][] Underfull \hbox (badness 10000) detected at line 722 [][][] Underfull \hbox (badness 10000) detected at line 772 [][][] Underfull \hbox (badness 10000) detected at line 775 [][][] Underfull \hbox (badness 10000) detected at line 778 [][][] [286] Overfull \hbox (304.08286pt too wide) in paragraph at lines 788--788 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 825 [][][] Underfull \hbox (badness 10000) detected at line 828 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 837--837 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [287] [288] Underfull \hbox (badness 10000) detected at line 907 [][][] Underfull \hbox (badness 10000) detected at line 910 [][][] [289] [290] [291] Underfull \hbox (badness 10000) detected at line 1050 [][][] Underfull \hbox (badness 10000) detected at line 1053 [][][] [292] [293] [294] Underfull \hbox (badness 10000) detected at line 1229 [][][] Underfull \hbox (badness 10000) detected at line 1232 [][][] [295] [296] Underfull \hbox (badness 10000) detected at line 1382 [][][] Underfull \hbox (badness 10000) detected at line 1385 [][][] Underfull \hbox (badness 10000) detected at line 1388 [][][] [297] [298] Underfull \hbox (badness 10000) detected at line 1446 [][][] Underfull \hbox (badness 10000) detected at line 1449 [][][] Underfull \hbox (badness 10000) detected at line 1452 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 1462--1462 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 1501 [][][] Underfull \hbox (badness 10000) detected at line 1504 [][][] [299] [300] Underfull \hbox (badness 10000) detected at line 1584 [][][] Underfull \hbox (badness 10000) detected at line 1587 [][][] Underfull \hbox (badness 10000) detected at line 1590 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 1600--1600 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 1637 [][][] Underfull \hbox (badness 10000) detected at line 1640 [][][] [301] Underfull \hbox (badness 10000) detected at line 1643 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 1652--1652 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Overfull \vbox (9.44278pt too high) has occurred while \output is active [302] Underfull \hbox (badness 10000) detected at line 1730 [][][] Underfull \hbox (badness 10000) detected at line 1735 [][][] Underfull \hbox (badness 10000) detected at line 1738 [][][] Underfull \hbox (badness 10000) detected at line 1768 [][][] Underfull \hbox (badness 10000) detected at line 1771 [][][] [303] Underfull \hbox (badness 10000) detected at line 1805 [][][] Underfull \hbox (badness 10000) detected at line 1808 [][][] [304] Underfull \hbox (badness 10000) detected at line 1842 [][][] Underfull \hbox (badness 10000) detected at line 1845 [][][] Underfull \hbox (badness 10000) detected at line 1879 [][][] Underfull \hbox (badness 10000) detected at line 1882 [][][] [305] Underfull \hbox (badness 10000) detected at line 1885 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 1895--1895 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 1932 [][][] Underfull \hbox (badness 10000) detected at line 1935 [][][] Underfull \hbox (badness 10000) detected at line 1938 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 1947--1947 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [306] [307] Underfull \hbox (badness 10000) detected at line 2033 [][][] Underfull \hbox (badness 10000) detected at line 2036 [][][] Underfull \hbox (badness 10000) detected at line 2070 [][][] Underfull \hbox (badness 10000) detected at line 2073 [][][] Underfull \hbox (badness 10000) detected at line 2076 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 2086--2086 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [308] Underfull \hbox (badness 10000) detected at line 2123 [][][] Underfull \hbox (badness 10000) detected at line 2126 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2135--2135 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [309] Underfull \hbox (badness 10000) detected at line 2170 [][][] Underfull \hbox (badness 10000) detected at line 2173 [][][] Underfull \hbox (badness 10000) detected at line 2205 [][][] [310] Underfull \hbox (badness 10000) detected at line 2208 [][][] Underfull \hbox (badness 10000) detected at line 2244 [][][] Underfull \hbox (badness 10000) detected at line 2247 [][][] [311] Underfull \hbox (badness 10000) detected at line 2283 [][][] Underfull \hbox (badness 10000) detected at line 2286 [][][] [312] Underfull \hbox (badness 10000) detected at line 2314 [][][] Underfull \hbox (badness 10000) detected at line 2317 [][][] Underfull \hbox (badness 10000) detected at line 2320 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 2330--2330 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [313] Underfull \hbox (badness 10000) detected at line 2367 [][][] Underfull \hbox (badness 10000) detected at line 2370 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2379--2379 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 2414 [][][] Underfull \hbox (badness 10000) detected at line 2417 [][][] [314] [315] Underfull \hbox (badness 10000) detected at line 2503 [][][] Underfull \hbox (badness 10000) detected at line 2506 [][][] Underfull \hbox (badness 10000) detected at line 2509 [][][] [316] Underfull \hbox (badness 10000) detected at line 2557 [][][] Underfull \hbox (badness 10000) detected at line 2560 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2569--2569 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [317] Underfull \hbox (badness 10000) detected at line 2604 [][][] Underfull \hbox (badness 10000) detected at line 2607 [][][] [318] Underfull \hbox (badness 10000) detected at line 2697 [][][] Underfull \hbox (badness 10000) detected at line 2700 [][][] [319] Underfull \hbox (badness 10000) detected at line 2746 [][][] Underfull \hbox (badness 10000) detected at line 2749 [][][] Underfull \hbox (badness 10000) detected at line 2752 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 2762--2762 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [320] Underfull \hbox (badness 10000) detected at line 2799 [][][] Underfull \hbox (badness 10000) detected at line 2802 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2811--2811 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 2846 [][][] Underfull \hbox (badness 10000) detected at line 2849 [][][] [321] Underfull \hbox (badness 10000) detected at line 2905 [][][] Underfull \hbox (badness 10000) detected at line 2908 [][][] Overfull \vbox (18.98318pt too high) has occurred while \output is active [322] Underfull \hbox (badness 10000) detected at line 2946 [][][] Underfull \hbox (badness 10000) detected at line 2957 [][][] [323] Underfull \hbox (badness 10000) detected at line 2960 [][][] [324] Underfull \hbox (badness 10000) detected at line 3046 [][][] Underfull \hbox (badness 10000) detected at line 3049 [][][] Underfull \hbox (badness 10000) detected at line 3052 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3062--3062 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 3099 [][][] Underfull \hbox (badness 10000) detected at line 3102 [][][] [325] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 3111--3111 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 3146 [][][] Underfull \hbox (badness 10000) detected at line 3149 [][][] [326] Underfull \hbox (badness 10000) detected at line 3187 [][][] Underfull \hbox (badness 10000) detected at line 3190 [][][] Underfull \hbox (badness 10000) detected at line 3193 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3203--3203 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [327] Underfull \hbox (badness 10000) detected at line 3240 [][][] Underfull \hbox (badness 10000) detected at line 3243 [][][] Underfull \hbox (badness 10000) detected at line 3246 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 3255--3255 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [328] Underfull \hbox (badness 10000) detected at line 3288 [][][] [329] Underfull \hbox (badness 10000) detected at line 3342 [][][] [330] [331] Underfull \hbox (badness 10000) detected at line 3484 [][][] [332] Underfull \hbox (badness 10000) detected at line 3542 [][][] Underfull \hbox (badness 10000) detected at line 3545 [][][] [333] Underfull \hbox (badness 10000) detected at line 3585 [][][] Underfull \hbox (badness 10000) detected at line 3588 [][][] Underfull \hbox (badness 10000) detected at line 3591 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3601--3601 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [334] Underfull \hbox (badness 10000) detected at line 3638 [][][] Underfull \hbox (badness 10000) detected at line 3641 [][][] Underfull \hbox (badness 10000) detected at line 3644 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 3653--3653 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [335] Underfull \hbox (badness 10000) detected at line 3702 [][][] Underfull \hbox (badness 10000) detected at line 3705 [][][] [336] [337] Underfull \hbox (badness 10000) detected at line 3789 [][][] Underfull \hbox (badness 10000) detected at line 3792 [][][] [338] Underfull \hbox (badness 10000) detected at line 3890 [][][] Underfull \hbox (badness 10000) detected at line 3893 [][][] Underfull \hbox (badness 10000) detected at line 3896 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3906--3906 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [339] Underfull \hbox (badness 10000) detected at line 3943 [][][] Underfull \hbox (badness 10000) detected at line 3946 [][][] Underfull \hbox (badness 10000) detected at line 3972 [][][] Underfull \hbox (badness 10000) detected at line 3975 [][][] [340] Underfull \hbox (badness 10000) detected at line 4001 [][][] Underfull \hbox (badness 10000) detected at line 4004 [][][] [341] Underfull \hbox (badness 10000) detected at line 4034 [][][] Underfull \hbox (badness 10000) detected at line 4037 [][][] Underfull \hbox (badness 10000) detected at line 4040 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 4050--4050 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 4087 [][][] [342] Underfull \hbox (badness 10000) detected at line 4090 [][][] Underfull \hbox (badness 10000) detected at line 4093 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 4102--4102 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 4137 [][][] Underfull \hbox (badness 10000) detected at line 4140 [][][] [343] Underfull \hbox (badness 10000) detected at line 4194 [][][] [344] Underfull \hbox (badness 10000) detected at line 4216 [][][] Overfull \vbox (38.14133pt too high) has occurred while \output is active [345] Underfull \hbox (badness 10000) detected at line 4290 [][][] Underfull \hbox (badness 10000) detected at line 4293 [][][] [346] [347] Underfull \hbox (badness 10000) detected at line 4383 [][][] Underfull \hbox (badness 10000) detected at line 4386 [][][] Underfull \hbox (badness 10000) detected at line 4426 [][][] Underfull \hbox (badness 10000) detected at line 4429 [][][] [348] Underfull \hbox (badness 10000) detected at line 4471 [][][] Underfull \hbox (badness 10000) detected at line 4474 [][][] [349] Underfull \hbox (badness 10000) detected at line 4532 [][][] Underfull \hbox (badness 10000) detected at line 4535 [][][] Underfull \hbox (badness 10000) detected at line 4538 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 4548--4548 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [350] Underfull \hbox (badness 10000) detected at line 4585 [][][] Underfull \hbox (badness 10000) detected at line 4588 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 4597--4597 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [351] Underfull \hbox (badness 10000) detected at line 4630 [][][] Underfull \hbox (badness 10000) detected at line 4633 [][][] Underfull \hbox (badness 10000) detected at line 4636 [][][] [352] Underfull \hbox (badness 10000) detected at line 4692 [][][] Underfull \hbox (badness 10000) detected at line 4695 [][][] Underfull \hbox (badness 10000) detected at line 4727 [][][] Underfull \hbox (badness 10000) detected at line 4730 [][][] [353] Underfull \hbox (badness 10000) detected at line 4768 [][][] Underfull \hbox (badness 10000) detected at line 4771 [][][] Underfull \hbox (badness 10000) detected at line 4774 [][][] Overfull \hbox (20.88268pt too wide) in paragraph at lines 4784--4784 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute,[] [354] Underfull \hbox (badness 10000) detected at line 4822 [][][] Underfull \hbox (badness 10000) detected at line 4825 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 4834--4834 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [355] Underfull \hbox (badness 10000) detected at line 4869 [][][] Underfull \hbox (badness 10000) detected at line 4872 [][][] [356] Underfull \hbox (badness 10000) detected at line 4930 [][][] Underfull \hbox (badness 10000) detected at line 4933 [][][] Underfull \hbox (badness 10000) detected at line 4965 [][][] Underfull \hbox (badness 10000) detected at line 4968 [][][] Underfull \hbox (badness 10000) detected at line 4971 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 4981--4981 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [357] Underfull \hbox (badness 10000) detected at line 5018 [][][] Underfull \hbox (badness 10000) detected at line 5021 [][][] Underfull \hbox (badness 10000) detected at line 5024 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 5033--5033 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [358] Underfull \hbox (badness 10000) detected at line 5068 [][][] Underfull \hbox (badness 10000) detected at line 5071 [][][] Underfull \hbox (badness 10000) detected at line 5101 [][][] Underfull \hbox (badness 10000) detected at line 5104 [][][] Underfull \hbox (badness 10000) detected at line 5107 [][][] [359] Underfull \hbox (badness 10000) detected at line 5137 [][][] Underfull \hbox (badness 10000) detected at line 5140 [][][] Underfull \hbox (badness 10000) detected at line 5170 [][][] [360] Underfull \hbox (badness 10000) detected at line 5173 [][][] Underfull \hbox (badness 10000) detected at line 5203 [][][] Underfull \hbox (badness 10000) detected at line 5206 [][][] Underfull \hbox (badness 10000) detected at line 5234 [][][] [361] Underfull \hbox (badness 10000) detected at line 5237 [][][] Underfull \hbox (badness 10000) detected at line 5265 [][][] Underfull \hbox (badness 10000) detected at line 5268 [][][] ) (./group___frontend.tex [362] Underfull \hbox (badness 2495) in paragraph at lines 32--33 []\T1/phv/m/n/10 VPUBLIC Vrc[]_[][]Codes [] (int icalc, [] $\OMS/cmsy/m/n/10 ^^ C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 feparm, [] $\OMS /cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbeparm, [] Overfull \hbox (16.65858pt too wide) in paragraph at lines 40--41 []\T1/phv/m/n/10 VEXTERNC int [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], Overfull \hbox (16.91972pt too wide) in paragraph at lines 42--43 []\T1/phv/m/n/10 VEXTERNC void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh , [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/1 0 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], Underfull \hbox (badness 1910) in paragraph at lines 60--61 [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1 /phv/m/n/10 alist[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][] [], [] Underfull \hbox (badness 1237) in paragraph at lines 60--61 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 charge[]Map[][][], [] $\OMS/cmsy/m/n/10 ^^C $\T1/phv/m/n/10 pmgp[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pmg[][][], [] [363] Underfull \hbox (badness 5817) in paragraph at lines 78--79 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], Underfull \hbox (badness 5817) in paragraph at lines 80--81 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], [364] [365] Underfull \hbox (badness 10000) detected at line 178 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 211 [][][] [366] Underfull \hbox (badness 10000) detected at line 235 [][][] [367] Underfull \hbox (badness 10000) detected at line 275 [][][] Underfull \hbox (badness 10000) detected at line 297 [][][] Underfull \hbox (badness 10000) detected at line 314 [][][] Underfull \hbox (badness 10000) detected at line 317 [][][] [368] Underfull \hbox (badness 10000) detected at line 351 [][][] Underfull \hbox (badness 10000) detected at line 373 [][][] Underfull \hbox (badness 10000) detected at line 390 [][][] Underfull \hbox (badness 10000) detected at line 393 [][][] [369] [370] Underfull \hbox (badness 10000) detected at line 495 [][][] Underfull \hbox (badness 10000) detected at line 502 [][][] [371] Underfull \hbox (badness 10000) detected at line 572 [][][] Underfull \hbox (badness 10000) detected at line 575 [][][] [372] Underfull \hbox (badness 10000) detected at line 625 [][][] Underfull \hbox (badness 10000) detected at line 649 [][][] Underfull \hbox (badness 10000) detected at line 677 [][][] [373] Underfull \hbox (badness 10000) detected at line 694 [][][] Underfull \hbox (badness 10000) detected at line 720 [][][] Underfull \hbox (badness 10000) detected at line 748 [][][] [374] Underfull \hbox (badness 10000) detected at line 772 [][][] Underfull \hbox (badness 10000) detected at line 792 [][][] Underfull \hbox (badness 10000) detected at line 818 [][][] [375] Underfull \hbox (badness 10000) detected at line 842 [][][] Underfull \hbox (badness 10000) detected at line 866 [][][] Underfull \hbox (badness 10000) detected at line 876 [][][] Underfull \hbox (badness 10000) detected at line 895 [][][] [376] Underfull \hbox (badness 10000) detected at line 909 [][][] Underfull \hbox (badness 10000) detected at line 912 [][][] Underfull \hbox (badness 10000) detected at line 929 [][][] Underfull \hbox (badness 10000) detected at line 939 [][][] Underfull \hbox (badness 10000) detected at line 958 [][][] Underfull \hbox (badness 10000) detected at line 961 [][][] [377] Underfull \hbox (badness 10000) detected at line 981 [][][] Underfull \hbox (badness 10000) detected at line 984 [][][] Underfull \hbox (badness 10000) detected at line 1010 [][][] Underfull \hbox (badness 10000) detected at line 1013 [][][] [378] Underfull \hbox (badness 10000) detected at line 1035 [][][] Underfull \hbox (badness 10000) detected at line 1045 [][][] Underfull \hbox (badness 10000) detected at line 1064 [][][] Underfull \hbox (badness 10000) detected at line 1067 [][][] Underfull \hbox (badness 10000) detected at line 1091 [][][] [379] Underfull \hbox (badness 10000) detected at line 1105 [][][] Underfull \hbox (badness 10000) detected at line 1122 [][][] Underfull \hbox (badness 10000) detected at line 1134 [][][] Underfull \hbox (badness 10000) in paragraph at lines 1135--1136 Underfull \hbox (badness 10000) detected at line 1138 [][][] [380] Underfull \hbox (badness 10000) detected at line 1166 [][][] Underfull \hbox (badness 10000) detected at line 1180 [][][] Underfull \hbox (badness 10000) detected at line 1201 [][][] Underfull \hbox (badness 10000) detected at line 1204 [][][] [381] Underfull \hbox (badness 10000) detected at line 1228 [][][] Underfull \hbox (badness 10000) detected at line 1231 [][][] Underfull \hbox (badness 10000) detected at line 1259 [][][] Underfull \hbox (badness 10000) detected at line 1262 [][][] [382] Underfull \hbox (badness 10000) detected at line 1288 [][][] Underfull \hbox (badness 10000) detected at line 1291 [][][] Underfull \hbox (badness 10000) detected at line 1319 [][][] Underfull \hbox (badness 10000) detected at line 1322 [][][] [383] Underfull \hbox (badness 10000) detected at line 1348 [][][] Underfull \hbox (badness 10000) detected at line 1377 [][][] Underfull \hbox (badness 10000) detected at line 1380 [][][] Underfull \hbox (badness 10000) detected at line 1408 [][][] [384] Underfull \hbox (badness 10000) detected at line 1432 [][][] Underfull \hbox (badness 10000) detected at line 1454 [][][] Underfull \hbox (badness 10000) detected at line 1468 [][][] [385] Underfull \hbox (badness 10000) detected at line 1485 [][][] Underfull \hbox (badness 10000) detected at line 1497 [][][] Underfull \hbox (badness 10000) detected at line 1514 [][][] Underfull \hbox (badness 10000) detected at line 1528 [][][] [386] Underfull \hbox (badness 10000) detected at line 1562 [][][] Underfull \hbox (badness 10000) detected at line 1574 [][][] Underfull \hbox (badness 10000) detected at line 1591 [][][] Underfull \hbox (badness 10000) detected at line 1608 [][][] [387] Underfull \hbox (badness 10000) detected at line 1636 [][][] Underfull \hbox (badness 10000) detected at line 1650 [][][] [388] Underfull \hbox (badness 10000) detected at line 1688 [][][] Underfull \hbox (badness 10000) detected at line 1716 [][][] Underfull \hbox (badness 10000) detected at line 1733 [][][] [389] Underfull \hbox (badness 10000) detected at line 1747 [][][] Underfull \hbox (badness 10000) detected at line 1764 [][][] Underfull \hbox (badness 10000) detected at line 1792 [][][] [390] Underfull \hbox (badness 10000) detected at line 1809 [][][] Underfull \hbox (badness 10000) detected at line 1823 [][][] ) [391] [392] Chapter 8. (./struct_atom_force.tex Underfull \hbox (badness 10000) detected at line 32 [][][] [393]) (./structs_a_p_o_lparm.tex [394] Underfull \hbox (badness 10000) detected at line 88 [][][] [395] Underfull \hbox (badness 10000) detected at line 224 [][][] [396] Underfull \hbox (badness 10000) detected at line 237 [][][] Underfull \hbox (badness 10000) detected at line 250 [][][] Underfull \hbox (badness 10000) detected at line 263 [][][] Underfull \hbox (badness 10000) detected at line 276 [][][] Underfull \hbox (badness 10000) detected at line 289 [][][] Underfull \hbox (badness 10000) detected at line 302 [][][] [397] Underfull \hbox (badness 10000) detected at line 315 [][][] Underfull \hbox (badness 10000) detected at line 328 [][][] Underfull \hbox (badness 10000) detected at line 341 [][][] Underfull \hbox (badness 10000) detected at line 354 [][][] Underfull \hbox (badness 10000) detected at line 367 [][][] Underfull \hbox (badness 10000) detected at line 380 [][][] [398]) (./structs_b_e_mparm.tex [399] Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 53 [][][] [400] Underfull \hbox (badness 10000) detected at line 129 [][][] Underfull \hbox (badness 10000) detected at line 142 [][][] Underfull \hbox (badness 10000) detected at line 155 [][][] [401] Underfull \hbox (badness 10000) detected at line 168 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 194 [][][] ) (./structs_f_e_mparm.tex [402] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) in paragraph at lines 84--85 [403] [404] [405]) (./structs_g_e_o_f_l_o_wparm.tex Underfull \hbox (badness 10000) detected at line 30 [][][] Underfull \hbox (badness 10000) detected at line 33 [][][] [406]) (./structs_m_gparm.tex [407] Underfull \hbox (badness 10000) detected at line 120 [][][] Underfull \hbox (badness 10000) detected at line 123 [][][] [408] Underfull \hbox (badness 10000) in paragraph at lines 149--150 Underfull \hbox (badness 10000) in paragraph at lines 180--181 [409] Underfull \hbox (badness 10000) in paragraph at lines 261--262 [410] [411] Underfull \hbox (badness 10000) detected at line 434 [][][] Underfull \hbox (badness 10000) detected at line 447 [][][] Underfull \hbox (badness 10000) detected at line 460 [][][] Underfull \hbox (badness 10000) detected at line 473 [][][] [412] Underfull \hbox (badness 10000) detected at line 486 [][][] Underfull \hbox (badness 10000) detected at line 499 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] Underfull \hbox (badness 10000) detected at line 538 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] [413] Underfull \hbox (badness 10000) detected at line 564 [][][] Underfull \hbox (badness 10000) detected at line 577 [][][] Underfull \hbox (badness 10000) detected at line 590 [][][] Underfull \hbox (badness 10000) detected at line 603 [][][] Underfull \hbox (badness 10000) detected at line 616 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] [414] Underfull \hbox (badness 10000) detected at line 642 [][][] Underfull \hbox (badness 10000) detected at line 655 [][][] Underfull \hbox (badness 10000) detected at line 668 [][][] ) (./structs_n_osh.tex [415] Underfull \hbox (badness 10000) detected at line 108 [][][] [416] [417] [418] [419] [420]) (./structs_n_osh__calc.tex [421] Underfull \hbox (badness 10000) detected at line 38 [][][] [422]) (./structs_p_b_a_mparm.tex [423] Underfull \hbox (badness 10000) detected at line 106 [][][] Underfull \hbox (badness 10000) detected at line 109 [][][] [424] [425] [426] [427]) (./structs_p_b_eparm.tex [428] [429] Underfull \hbox (badness 10000) detected at line 142 [][][] Underfull \hbox (badness 10000) detected at line 145 [][][] [430] [431] [432] Underfull \hbox (badness 10000) detected at line 391 [][][] Underfull \hbox (badness 10000) detected at line 404 [][][] Underfull \hbox (badness 10000) detected at line 417 [][][] Underfull \hbox (badness 10000) detected at line 430 [][][] [433] Underfull \hbox (badness 10000) detected at line 473 [][][] Underfull \hbox (badness 10000) detected at line 486 [][][] Underfull \hbox (badness 10000) detected at line 499 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] [434] Underfull \hbox (badness 10000) detected at line 538 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] Underfull \hbox (badness 10000) detected at line 564 [][][] Underfull \hbox (badness 10000) detected at line 577 [][][] Underfull \hbox (badness 10000) detected at line 590 [][][] Underfull \hbox (badness 10000) detected at line 603 [][][] [435] Underfull \hbox (badness 10000) detected at line 616 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] [436] [437]) (./structs_p_b_s_a_mparm.tex [438] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] [439]) (./structs_vacc.tex [440] Underfull \hbox (badness 10000) detected at line 36 [][][] [441]) (./structs_vacc_surf.tex Underfull \hbox (badness 10000) detected at line 36 [][][] [442]) (./structs_valist.tex [443] Underfull \hbox (badness 10000) detected at line 36 [][][] [444]) (./structs_vatom.tex Underfull \hbox (badness 10000) detected at line 36 [][][] Underfull \hbox (badness 10000) in paragraph at lines 62--63 [445] Underfull \hbox (badness 10000) in paragraph at lines 93--94 Underfull \hbox (badness 10000) in paragraph at lines 114--115 ) (./structs_vclist.tex [446] Underfull \hbox (badness 10000) detected at line 40 [][][] [447]) (./structs_vclist_cell.tex Underfull \hbox (badness 10000) detected at line 24 [][][] ) (./structs_vcsm.tex [448] Underfull \hbox (badness 10000) detected at line 42 [][][] [449]) (./structs_vfetk.tex [450] Underfull \hbox (badness 10000) detected at line 60 [][][] [451] Underfull \hbox (badness 10000) in paragraph at lines 116--117 [452]) (./structs_vfetk___local_var.tex [453] Underfull \hbox (badness 10000) detected at line 86 [][][] [454] [455] [456] [457]) (./structs_vgreen.tex Underfull \hbox (badness 10000) detected at line 34 [][][] [458]) (./structs_vgrid.tex [459] Underfull \hbox (badness 10000) detected at line 52 [][][] [460] [461]) (./structs_vmgrid.tex Underfull \hbox (badness 10000) detected at line 24 [][][] ) (./structs_vopot.tex [462] Underfull \hbox (badness 10000) detected at line 26 [][][] ) (./structs_vparam___atom_data.tex [463] Underfull \hbox (badness 10000) detected at line 30 [][][] Underfull \hbox (badness 10000) detected at line 33 [][][] ) (./structs_vpbe.tex [464] Underfull \hbox (badness 10000) detected at line 86 [][][] [465] [466] [467] [468]) (./structs_vpee.tex [469] Underfull \hbox (badness 10000) detected at line 34 [][][] ) (./structs_vpmg.tex [470] [471] Underfull \hbox (badness 10000) detected at line 116 [][][] [472] [473] [474] [475] [476]) (./structs_vpmgp.tex [477] Underfull \hbox (badness 10000) detected at line 126 [][][] [478] Underfull \hbox (badness 10000) in paragraph at lines 164--165 Underfull \hbox (badness 10000) in paragraph at lines 175--176 Underfull \hbox (badness 10000) in paragraph at lines 186--187 [479] Underfull \hbox (badness 10000) in paragraph at lines 234--235 [480] [481] [482] [483] Underfull \hbox (badness 10000) in paragraph at lines 506--507 Underfull \hbox (badness 10000) in paragraph at lines 527--528 [484] Underfull \hbox (badness 10000) in paragraph at lines 548--549 Underfull \hbox (badness 10000) in paragraph at lines 589--590 [485] Underfull \hbox (badness 10000) in paragraph at lines 630--631 Underfull \hbox (badness 10000) in paragraph at lines 671--672 ) (./struct_vparam.tex [486] Underfull \hbox (badness 10000) detected at line 26 [][][] ) (./struct_vparam___res_data.tex [487] Underfull \hbox (badness 10000) detected at line 28 [][][] ) [488] Chapter 9. (./mainpage_8h_source.tex) (./apbs_8h.tex <./apbs_8h__incl.pdf> <./apbs_8h__dep __incl.pdf> [489] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] Underfull \hbox (badness 10000) detected at line 58 [][][] [490]) (./apbs_8h_source.tex) (./vcsm_8c.tex [491] <./vcsm_8c__incl.pdf> [492] Underfull \hbox (badness 10000) detected at line 53 [][][] Underfull \hbox (badness 10000) detected at line 56 [][][] Underfull \hbox (badness 10000) detected at line 59 [][][] [493]) (./vcsm_8c_source.tex [494] [495] [496] [497] [498] [499]) (./vcsm_8h.tex <./vcsm_8h__incl.pdf> <./vcsm_8h__dep__incl.pdf> [500] [501] Underfull \hbox (badness 10000) detected at line 77 [][][] Underfull \hbox (badness 10000) detected at line 80 [][][] Underfull \hbox (badness 10000) detected at line 83 [][][] [502]) (./vcsm_8h_source.tex [503]) (./vfetk_8c.tex [504] <./vfetk_8c__incl.pdf > [505] [506] Underfull \hbox (badness 10000) detected at line 163 [][][] Underfull \hbox (badness 10000) detected at line 166 [][][] [507] Underfull \hbox (badness 10000) detected at line 169 [][][] [508] [509] [510] [511]) (./vfetk_8c_source.tex [512] [513] [514] [515] [516] [517] [518] [519] [520] [521] [522] [523] [524] [525] [526] [527] [528] [529] [530] [531] [532] [533] [534] [535] [536] [537] [538] [539] [540] [541]) (./vfetk_8h.tex [542] <./vfetk_8h__incl.pdf> <./vfetk_8h__dep__inc l.pdf> [543] [544] [545] Underfull \hbox (badness 10000) detected at line 189 [][][] [546] Underfull \hbox (badness 10000) detected at line 192 [][][] Underfull \hbox (badness 10000) detected at line 195 [][][] ) (./vfetk_8h_source.tex [547] [548] [549] [550] [551] [552]) (./vpee_8c.tex <. /vpee_8c__incl.pdf> [553] Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 53 [][][] Underfull \hbox (badness 10000) detected at line 56 [][][] [554]) (./vpee_8c_source.tex [555] [556] [557] [558] [559] [560]) (./vpee_8h.tex [561] <./vpee_8h__incl.pdf> <./vpee_8h__dep__incl.pdf> [562] Underfull \hbox (badness 10000) detected at line 57 [][][] Underfull \hbox (badness 10000) detected at line 60 [][][] Underfull \hbox (badness 10000) detected at line 63 [][][] [563]) (./vpee_8h_source.tex [564]) (./apolparm_8c.tex <./apolparm_8c__incl.pdf > [565] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) detected at line 71 [][][] [566] [567]) (./apolparm_8c_source.tex [568] [569] [570] [571] [572] [573] [574] [575]) (./apolparm_8h_source.tex [576]) (./bemparm_8c.tex <./bemparm_8c__ incl.pdf> [577] [578] Underfull \hbox (badness 10000) detected at line 49 [][][] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] [579] Underfull \hbox (badness 10000) detected at line 121 [][][] ) (./bemparm_8c_source.tex [580] [581] [582] [583]) (./bemparm_8h_source.tex [584]) (./femparm_8c.tex <./femparm_8c__incl.pdf> [585] [586] Underfull \hbox (badness 10000) detected at line 59 [][][] Underfull \hbox (badness 10000) detected at line 62 [][][] Underfull \hbox (badness 10000) detected at line 65 [][][] [587] [588]) (./femparm_8c_source.tex [589] [590] [591] [592] [593]) (./femparm_8h.tex <./femparm_8h__incl.pdf> [594] <./femparm_8h__dep__incl.pdf> [595] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 92 [][][] Underfull \hbox (badness 10000) detected at line 95 [][][] [596]) (./femparm_8h_source.tex [597]) (./geoflowparm_8c.tex [598] <./geoflowpa rm_8c__incl.pdf> [599] Underfull \hbox (badness 10000) detected at line 47 [][][] Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 53 [][][] [600]) (./geoflowparm_8c_source.tex [601] [602]) (./geoflowparm_8h.tex [603] <. /geoflowparm_8h__incl.pdf> <./geoflowparm_8h__dep__incl.pdf> [604] [605] Underfull \hbox (badness 10000) detected at line 71 [][][] Underfull \hbox (badness 10000) detected at line 74 [][][] Underfull \hbox (badness 10000) detected at line 77 [][][] [606]) (./geoflowparm_8h_source.tex [607]) (./mgparm_8c.tex <./mgparm_8c__incl. pdf> [608] [609] Underfull \hbox (badness 10000) detected at line 95 [][][] Underfull \hbox (badness 10000) detected at line 98 [][][] Underfull \hbox (badness 10000) detected at line 101 [][][] [610] [611]) (./mgparm_8c_source.tex [612] [613] [614] [615] [616] [617] [618] [619] [620] [621] [622] [623]) (./mgparm_8h.tex <./mgparm_8h__incl.pdf> [624] <./mgparm_8h__dep__incl.pdf> [625] [626] Underfull \hbox (badness 10000) detected at line 104 [][][] Underfull \hbox (badness 10000) detected at line 107 [][][] Underfull \hbox (badness 10000) detected at line 110 [][][] [627]) (./mgparm_8h_source.tex [628]) (./nosh_8c.tex <./nosh_8c__incl.pdf> [629] [630] [631] Underfull \hbox (badness 10000) detected at line 151 [][][] Underfull \hbox (badness 10000) detected at line 154 [][][] Underfull \hbox (badness 10000) detected at line 157 [][][] [632] [633] [634] [635] [636]) (./nosh_8c_source.tex [637] [638] [639] [640] [641] [642] [643] [644] [645] [646] [647] [648] [649] [650] [651] [652] [653] [654] [655] [656] [657] [658] [659] [660] [661] [662] [663] [664] [665] [666] [667] [668] [669] [670] [671] [672] [673] [674] [675] [676]) (./nosh_8h.tex <./nosh_8h__incl.pdf> [677] <./nosh_8h__dep__incl.pdf> [678] [679] [680] Underfull \hbox (badness 10000) detected at line 171 [][][] Underfull \hbox (badness 10000) detected at line 174 [][][] Underfull \hbox (badness 10000) detected at line 177 [][][] ) (./nosh_8h_source.tex [681] [682] [683]) (./pbamparm_8c.tex <./pbamparm_8c__i ncl.pdf> [684] [685] Underfull \hbox (badness 10000) detected at line 69 [][][] Underfull \hbox (badness 10000) detected at line 72 [][][] Underfull \hbox (badness 10000) detected at line 75 [][][] [686]) (./pbamparm_8c_source.tex [687] [688] [689] [690] [691] [692] [693] [694] [695]) (./pbamparm_8h.tex <./pbamparm_8h__incl.pdf> <./pbamparm_8h__dep__ incl.pdf> [696] [697] Underfull \hbox (badness 10000) detected at line 102 [][][] [698] Underfull \hbox (badness 10000) detected at line 105 [][][] Underfull \hbox (badness 10000) detected at line 108 [][][] [699]) (./pbamparm_8h_source.tex [700]) (./pbeparm_8c.tex [701] <./pbeparm_8c__ incl.pdf> [702] Underfull \hbox (badness 10000) detected at line 101 [][][] Underfull \hbox (badness 10000) detected at line 104 [][][] Underfull \hbox (badness 10000) detected at line 107 [][][] [703] [704] [705] [706] [707]) (./pbeparm_8c_source.tex [708] [709] [710] [711] [712] [713] [714] [715] [716] [717] [718] [719] [720] [721] [722]) (./pbeparm_8h.tex <./pbeparm_8h__incl.pdf> [723] <./pbeparm_8h__dep__incl.pdf> [724] Underfull \hbox (badness 10000) detected at line 88 [][][] Underfull \hbox (badness 10000) detected at line 91 [][][] Underfull \hbox (badness 10000) detected at line 94 [][][] [725]) (./pbeparm_8h_source.tex [726] [727]) (./pbsamparm_8c.tex <./pbsamparm_8 c__incl.pdf> [728] [729] Underfull \hbox (badness 10000) detected at line 49 [][][] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] [730]) (./pbsamparm_8c_source.tex [731] [732]) (./pbsamparm_8h.tex [733] <./pbs amparm_8h__incl.pdf> <./pbsamparm_8h__dep__incl.pdf> [734] [735] Underfull \hbox (badness 10000) detected at line 86 [][][] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 92 [][][] [736]) (./pbsamparm_8h_source.tex [737]) (./vacc_8c.tex <./vacc_8c__incl.pdf> [738] [739] [740] Underfull \hbox (badness 10000) detected at line 107 [][][] Underfull \hbox (badness 10000) detected at line 110 [][][] Underfull \hbox (badness 10000) detected at line 113 [][][] [741] Underfull \hbox (badness 10000) detected at line 179 [][][] Underfull \hbox (badness 10000) detected at line 182 [][][] Underfull \hbox (badness 10000) detected at line 208 [][][] Underfull \hbox (badness 10000) detected at line 211 [][][] [742] [743]) (./vacc_8c_source.tex [744] [745] [746] [747] [748] [749] [750] [751] [752] [753] [754] [755] [756] [757] [758] [759] [760] [761] [762] [763] [764] [765] [766]) (./vacc_8h.tex <./vacc_8h__incl.pdf> <./vacc_8h__dep__ incl.pdf> [767] [768] [769] Underfull \hbox (badness 10000) detected at line 123 [][][] Underfull \hbox (badness 10000) detected at line 126 [][][] Underfull \hbox (badness 10000) detected at line 129 [][][] [770]) (./vacc_8h_source.tex [771] [772] [773]) (./valist_8c.tex <./valist_8c__ incl.pdf> [774] [775] Underfull \hbox (badness 2293) in paragraph at lines 54--56 []\T1/phv/m/n/10 VPRIVATE Vrc[]_[][]Codes [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/ m/n/10 thee, Vio $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 sock, int $\OMS/cmsy/m/n/ 10 ^^C$\T1/phv/m/n/10 serial, char atom[] Underfull \hbox (badness 10000) detected at line 82 [][][] Underfull \hbox (badness 10000) detected at line 85 [][][] Underfull \hbox (badness 10000) detected at line 88 [][][] [776] [777] [778]) (./valist_8c_source.tex [779] [780] [781] [782] [783] [784] [785] [786] [787] [788]) (./valist_8h.tex [789] <./valist_8h__incl.pdf> < ./valist_8h__dep__incl.pdf> [790] Underfull \hbox (badness 10000) detected at line 77 [][][] Underfull \hbox (badness 10000) detected at line 80 [][][] Underfull \hbox (badness 10000) detected at line 83 [][][] [791]) (./valist_8h_source.tex [792] [793]) (./vatom_8c.tex <./vatom_8c__incl.p df> [794] Underfull \hbox (badness 10000) detected at line 71 [][][] Underfull \hbox (badness 10000) detected at line 74 [][][] Underfull \hbox (badness 10000) detected at line 77 [][][] [795]) (./vatom_8c_source.tex [796] [797] [798]) (./vatom_8h.tex <./vatom_8h__i ncl.pdf> [799] <./vatom_8h__dep__incl.pdf> [800] [801] Underfull \hbox (badness 10000) detected at line 96 [][][] Underfull \hbox (badness 10000) detected at line 99 [][][] Underfull \hbox (badness 10000) detected at line 102 [][][] ) (./vatom_8h_source.tex [802] [803]) (./vcap_8c.tex <./vcap_8c__incl.pdf> [804] Underfull \hbox (badness 10000) detected at line 31 [][][] Underfull \hbox (badness 10000) detected at line 34 [][][] Underfull \hbox (badness 10000) detected at line 37 [][][] [805]) (./vcap_8c_source.tex [806]) (./vcap_8h.tex <./vcap_8h__incl.pdf> <./vca p_8h__dep__incl.pdf> [807] Underfull \hbox (badness 10000) detected at line 47 [][][] Underfull \hbox (badness 10000) detected at line 50 [][][] [808] Underfull \hbox (badness 10000) detected at line 53 [][][] ) (./vcap_8h_source.tex [809]) (./vclist_8c.tex <./vclist_8c__incl.pdf> Underfull \hbox (badness 4060) in paragraph at lines 32--34 []\T1/phv/m/n/10 VPRIVATE void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 thee , dou-ble lower[]_[]corner[][][], dou-ble upper[]_[] [810] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) detected at line 71 [][][] [811] [812]) (./vclist_8c_source.tex [813] [814] [815] [816] [817]) (./vclist_8h.tex [818] <./vclist_8h__incl.pdf> <./vclist_8h__dep__incl.pdf> [819] [820] Underfull \hbox (badness 10000) detected at line 84 [][][] Underfull \hbox (badness 10000) detected at line 87 [][][] Underfull \hbox (badness 10000) detected at line 90 [][][] [821]) (./vclist_8h_source.tex [822]) (./vgreen_8c.tex [823] <./vgreen_8c__incl .pdf> [824] Underfull \hbox (badness 10000) detected at line 55 [][][] Underfull \hbox (badness 10000) detected at line 58 [][][] Underfull \hbox (badness 10000) detected at line 61 [][][] [825]) (./vgreen_8c_source.tex [826] [827] [828] [829] [830] [831]) (./vgreen_8h.tex <./vgreen_8h__incl.pdf> [832] <./vgreen_8h__dep__incl.pdf> [833] Underfull \hbox (badness 10000) detected at line 72 [][][] Underfull \hbox (badness 10000) detected at line 75 [][][] ) (./vgreen_8h_source.tex [834]) (./vhal_8h.tex [835] <./vhal_8h__incl.pdf> <./ vhal_8h__dep__incl.pdf> [836] [837] [838] [839] Underfull \hbox (badness 10000) detected at line 303 [][][] Underfull \hbox (badness 10000) detected at line 306 [][][] Underfull \hbox (badness 10000) detected at line 309 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 318--318 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [840] [841] [842] [843] [844] [845] [846]) (./vhal_8h_source.tex [847] [848] [849] [850] [851] [852] [853] [854]) (./vmatrix_8h.tex [855] <./vmatrix_8h__dep __incl.pdf> Underfull \hbox (badness 10000) detected at line 36 [][][] Underfull \hbox (badness 10000) detected at line 39 [][][] Underfull \hbox (badness 10000) detected at line 42 [][][] [856] [857]) (./vmatrix_8h_source.tex [858]) (./vparam_8c.tex <./vparam_8c__inc l.pdf> [859] Underfull \hbox (badness 10000) detected at line 78 [][][] Underfull \hbox (badness 10000) detected at line 81 [][][] [860] Underfull \hbox (badness 10000) detected at line 84 [][][] ) (./vparam_8c_source.tex [861] [862] [863] [864] [865] [866] [867] [868]) (./vparam_8h.tex [869] <./vparam_8h__incl.pdf> <./vparam_8h__dep__incl.pdf> [870] [871] Underfull \hbox (badness 10000) detected at line 96 [][][] Underfull \hbox (badness 10000) detected at line 99 [][][] Underfull \hbox (badness 10000) detected at line 102 [][][] [872]) (./vparam_8h_source.tex [873]) (./vpbe_8c.tex <./vpbe_8c__incl.pdf> [874] [875] Underfull \hbox (badness 10000) detected at line 90 [][][] Underfull \hbox (badness 10000) detected at line 93 [][][] [876] Underfull \hbox (badness 10000) detected at line 96 [][][] ) (./vpbe_8c_source.tex [877] [878] [879] [880] [881] [882] [883]) (./vpbe_8h.tex <./vpbe_8h__incl.pdf> <./vpbe_8h__dep__incl.pdf> [884] [885] Underfull \hbox (badness 10000) detected at line 111 [][][] Underfull \hbox (badness 10000) detected at line 114 [][][] Underfull \hbox (badness 10000) detected at line 117 [][][] [886]) (./vpbe_8h_source.tex [887] [888] [889]) (./vstring_8c.tex <./vstring_8c __incl.pdf> [890] Underfull \hbox (badness 10000) detected at line 31 [][][] Underfull \hbox (badness 10000) detected at line 34 [][][] Underfull \hbox (badness 10000) detected at line 37 [][][] ) (./vstring_8c_source.tex [891] [892] [893]) (./vstring_8h.tex <./vstring_8h__ incl.pdf> <./vstring_8h__dep__incl.pdf> [894] Underfull \hbox (badness 10000) detected at line 41 [][][] Underfull \hbox (badness 10000) detected at line 44 [][][] Underfull \hbox (badness 10000) detected at line 47 [][][] [895]) (./vstring_8h_source.tex) (./vunit_8h.tex <./vunit_8h__dep__incl.pdf> [896] LaTeX Warning: Command \r invalid in math mode on input line 42. Missing character: There is no Å in font cmr9! Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] Underfull \hbox (badness 10000) detected at line 58 [][][] [897]) (./vunit_8h_source.tex) (./main_8c.tex [898] <./main_8c__incl.pdf> Underfull \hbox (badness 10000) detected at line 28 [][][] Underfull \hbox (badness 10000) detected at line 41 [][][] Underfull \hbox (badness 10000) detected at line 44 [][][] [899]) (./main_8c_source.tex [900] [901] [902] [903] [904] [905] [906] [907] [908] [909] [910]) (./vgrid_8c.tex <./vgrid_8c__incl.pdf> [911] [912] Underfull \hbox (badness 10000) detected at line 84 [][][] Underfull \hbox (badness 10000) detected at line 87 [][][] Underfull \hbox (badness 10000) detected at line 90 [][][] [913] Underfull \hbox (badness 10000) detected at line 169 [][][] [914]) (./vgrid_8c_source.tex [915] [916] [917] [918] [919] [920] [921] [922] [923] [924] [925] [926] [927] [928] [929] [930] [931] [932] [933] [934] [935] [936] [937]) (./vgrid_8h.tex [938] <./vgrid_8h__incl.pdf> <./vgrid_ 8h__dep__incl.pdf> [939] [940] Underfull \hbox (badness 10000) detected at line 93 [][][] [941] Underfull \hbox (badness 10000) detected at line 96 [][][] Underfull \hbox (badness 10000) detected at line 99 [][][] [942] Underfull \hbox (badness 10000) detected at line 165 [][][] ) (./vgrid_8h_source.tex [943]) (./vmgrid_8c.tex [944] <./vmgrid_8c__incl.pdf> [945] Underfull \hbox (badness 10000) detected at line 41 [][][] Underfull \hbox (badness 10000) detected at line 44 [][][] Underfull \hbox (badness 10000) detected at line 47 [][][] Underfull \hbox (badness 10000) detected at line 50 [][][] Overfull \hbox (1024.08331pt too wide) in paragraph at lines 59--59 []\T1/pcr/m/n/8 * Copyright (c) 2010, Pacific Northwest National Laboratory. Portions Copyright (c) 2002-2020, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2020, T he Regents of the University of California. Portions Copyright (c) 1995, Michae l Holst.[] ) (./vmgrid_8c_source.tex [946] [947] [948]) (./vmgrid_8h.tex <./vmgrid_8h__inc l.pdf> <./vmgrid_8h__dep__incl.pdf> [949] [950] Underfull \hbox (badness 10000) detected at line 71 [][][] Underfull \hbox (badness 10000) detected at line 74 [][][] Underfull \hbox (badness 10000) detected at line 77 [][][] [951]) (./vmgrid_8h_source.tex) (./vopot_8c.tex [952] <./vopot_8c__incl.pdf> Underfull \hbox (badness 10000) detected at line 44 [][][] Underfull \hbox (badness 10000) detected at line 47 [][][] Underfull \hbox (badness 10000) detected at line 50 [][][] [953]) (./vopot_8c_source.tex [954] [955] [956] [957] [958]) (./vopot_8h.tex <. /vopot_8h__incl.pdf> <./vopot_8h__dep__incl.pdf> [959] [960] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) detected at line 71 [][][] ) (./vopot_8h_source.tex [961]) (./vpmg_8c.tex <./vpmg_8c__incl.pdf> [962] [963] [964] [965] Underfull \hbox (badness 10000) detected at line 173 [][][] Underfull \hbox (badness 10000) detected at line 176 [][][] Underfull \hbox (badness 10000) detected at line 179 [][][] [966] Underfull \hbox (badness 10000) detected at line 261 [][][] [967] Underfull \hbox (badness 10000) detected at line 288 [][][] [968] Underfull \hbox (badness 10000) detected at line 384 [][][] Underfull \hbox (badness 10000) detected at line 387 [][][] Underfull \hbox (badness 10000) detected at line 409 [][][] Underfull \hbox (badness 10000) detected at line 412 [][][] [969] Underfull \hbox (badness 10000) detected at line 434 [][][] Underfull \hbox (badness 10000) detected at line 437 [][][] Underfull \hbox (badness 10000) detected at line 459 [][][] Underfull \hbox (badness 10000) detected at line 462 [][][] Underfull \hbox (badness 10000) detected at line 484 [][][] Underfull \hbox (badness 10000) detected at line 487 [][][] [970] Underfull \hbox (badness 10000) detected at line 509 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Underfull \hbox (badness 10000) detected at line 534 [][][] Underfull \hbox (badness 10000) detected at line 537 [][][] Underfull \hbox (badness 10000) detected at line 554 [][][] Underfull \hbox (badness 10000) detected at line 557 [][][] [971] Underfull \hbox (badness 10000) detected at line 574 [][][] Underfull \hbox (badness 10000) detected at line 591 [][][] Underfull \hbox (badness 10000) detected at line 608 [][][] Underfull \hbox (badness 10000) detected at line 625 [][][] Underfull \hbox (badness 10000) detected at line 642 [][][] [972] Underfull \hbox (badness 10000) detected at line 659 [][][] Underfull \hbox (badness 10000) detected at line 676 [][][] Underfull \hbox (badness 10000) detected at line 697 [][][] Underfull \hbox (badness 10000) detected at line 700 [][][] Underfull \hbox (badness 10000) detected at line 717 [][][] [973] Underfull \hbox (badness 10000) detected at line 734 [][][] Underfull \hbox (badness 10000) detected at line 751 [][][] Underfull \hbox (badness 10000) detected at line 768 [][][] Underfull \hbox (badness 10000) detected at line 795 [][][] [974] Underfull \hbox (badness 10000) detected at line 832 [][][] [975] Underfull \hbox (badness 10000) detected at line 876 [][][] [976] Underfull \hbox (badness 10000) detected at line 926 [][][] Underfull \hbox (badness 10000) detected at line 948 [][][] [977] Underfull \hbox (badness 10000) detected at line 970 [][][] Underfull \hbox (badness 10000) detected at line 992 [][][] Underfull \hbox (badness 10000) detected at line 995 [][][] Underfull \hbox (badness 10000) detected at line 1012 [][][] Underfull \hbox (badness 10000) detected at line 1015 [][][] [978] Underfull \hbox (badness 10000) detected at line 1037 [][][] Underfull \hbox (badness 10000) detected at line 1040 [][][] Underfull \hbox (badness 10000) detected at line 1062 [][][] Underfull \hbox (badness 10000) detected at line 1065 [][][] Underfull \hbox (badness 10000) detected at line 1097 [][][] [979] Underfull \hbox (badness 10000) detected at line 1114 [][][] Underfull \hbox (badness 10000) detected at line 1146 [][][] Underfull \hbox (badness 10000) detected at line 1149 [][][] ) (./vpmg_8c_source.tex [980] [981] [982] [983] [984] [985] [986] [987] [988] [989] [990] [991] [992] [993] [994] [995] [996] [997] [998] [999] [1000] [1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008] [1009] [1010] [1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] [1021] [1022] [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] [1033] [1034] [1035] [1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] [1090] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112] [1113] [1114] [1115] [1116]) (./vpmg_8h.tex <./vpmg_8h__in cl.pdf> <./vpmg_8h__dep__incl.pdf> [1117] [1118] [1119] [1120] [1121] [1122] Underfull \hbox (badness 10000) detected at line 235 [][][] Underfull \hbox (badness 10000) detected at line 238 [][][] Underfull \hbox (badness 10000) detected at line 241 [][][] [1123] [1124] Underfull \hbox (badness 10000) detected at line 406 [][][] Underfull \hbox (badness 10000) detected at line 423 [][][] [1125] Underfull \hbox (badness 10000) detected at line 469 [][][] Underfull \hbox (badness 10000) detected at line 472 [][][] Underfull \hbox (badness 10000) detected at line 494 [][][] Underfull \hbox (badness 10000) detected at line 497 [][][] [1126] Underfull \hbox (badness 10000) detected at line 519 [][][] Underfull \hbox (badness 10000) detected at line 522 [][][] Underfull \hbox (badness 10000) detected at line 544 [][][] Underfull \hbox (badness 10000) detected at line 547 [][][] Underfull \hbox (badness 10000) detected at line 569 [][][] Underfull \hbox (badness 10000) detected at line 572 [][][] [1127] Underfull \hbox (badness 10000) detected at line 594 [][][] Underfull \hbox (badness 10000) detected at line 597 [][][] Underfull \hbox (badness 10000) detected at line 619 [][][] Underfull \hbox (badness 10000) detected at line 622 [][][] Underfull \hbox (badness 10000) detected at line 639 [][][] Underfull \hbox (badness 10000) detected at line 642 [][][] [1128] Underfull \hbox (badness 10000) detected at line 659 [][][] Underfull \hbox (badness 10000) detected at line 676 [][][] Underfull \hbox (badness 10000) detected at line 693 [][][] Underfull \hbox (badness 10000) detected at line 710 [][][] Underfull \hbox (badness 10000) detected at line 727 [][][] [1129] Underfull \hbox (badness 10000) detected at line 744 [][][] Underfull \hbox (badness 10000) detected at line 761 [][][] Underfull \hbox (badness 10000) detected at line 782 [][][] Underfull \hbox (badness 10000) detected at line 785 [][][] Underfull \hbox (badness 10000) detected at line 802 [][][] [1130] Underfull \hbox (badness 10000) detected at line 819 [][][] Underfull \hbox (badness 10000) detected at line 836 [][][] Underfull \hbox (badness 10000) detected at line 853 [][][] Underfull \hbox (badness 10000) detected at line 870 [][][] Underfull \hbox (badness 10000) detected at line 883 [][][] [1131] Underfull \hbox (badness 10000) detected at line 896 [][][] Underfull \hbox (badness 10000) detected at line 913 [][][] [1132] Underfull \hbox (badness 10000) detected at line 957 [][][] Underfull \hbox (badness 10000) detected at line 987 [][][] [1133] Underfull \hbox (badness 10000) detected at line 1009 [][][] Underfull \hbox (badness 10000) detected at line 1031 [][][] Underfull \hbox (badness 10000) detected at line 1053 [][][] Underfull \hbox (badness 10000) detected at line 1056 [][][] Underfull \hbox (badness 10000) detected at line 1073 [][][] [1134] Underfull \hbox (badness 10000) detected at line 1076 [][][] Underfull \hbox (badness 10000) detected at line 1098 [][][] Underfull \hbox (badness 10000) detected at line 1101 [][][] Underfull \hbox (badness 10000) detected at line 1123 [][][] Underfull \hbox (badness 10000) detected at line 1126 [][][] [1135] Underfull \hbox (badness 10000) detected at line 1158 [][][] Underfull \hbox (badness 10000) detected at line 1175 [][][] [1136] Underfull \hbox (badness 10000) detected at line 1207 [][][] Underfull \hbox (badness 10000) detected at line 1210 [][][] ) (./vpmg_8h_source.tex [1137] [1138] [1139] [1140] [1141] [1142] [1143] [1144]) (./vpmgp_8c.tex <./vpmgp_8c__incl.pdf> [1145] [1146] Underfull \hbox (badness 10000) detected at line 39 [][][] Underfull \hbox (badness 10000) detected at line 42 [][][] Underfull \hbox (badness 10000) detected at line 45 [][][] [1147]) (./vpmgp_8c_source.tex [1148] [1149] [1150]) (./vpmgp_8h.tex <./vpmgp_8 h__incl.pdf> [1151] <./vpmgp_8h__dep__incl.pdf> [1152] [1153] Underfull \hbox (badness 10000) detected at line 58 [][][] Underfull \hbox (badness 10000) detected at line 61 [][][] Underfull \hbox (badness 10000) detected at line 64 [][][] Underfull \hbox (badness 10000) detected at line 67 [][][] [1154]) (./vpmgp_8h_source.tex [1155]) (./build_ad_8c_source.tex [1156] [1157] [1158]) (./build_ad_8h_source.tex [1159]) (./build_bd_8c_source.tex [1160] [1161] [1162] [1163]) (./build_bd_8h_source.tex [1164]) (./build_gd_8c_source.tex [1165] [1166] [1167] [1168] [1169] [1170] [1171] [1172] [1173] [1174] [1175] [1176] [1177] [1178] [1179] [1180] [1181] [1182] [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] [1191] [1192] [1193] [1194] [1195] [1196] [1197] [1198] [1199] [1200] [1201] [1202]) (./build_gd_8h_source.tex [1203] [1204]) (./build_pd_8c_source.tex [1205] [1206] [1207] [1208] [1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216] [1217] [1218] [1219] [1220] [1221] [1222] [1223]) (./build_pd_8h_source.tex [1224] [1225] [1226]) (./cgd_8c_source.tex) (./cgd_8h_source.tex [1227]) (./gsd_8c_source.tex [1228] [1229] [1230] [1231]) (./gsd_8h_source.tex [1232]) (./matvecd_8c_source.tex [1233] [1234] [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242] [1243] [1244] [1245]) (./matvecd_8h_source.tex [1246] [1247] [1248] [1249] [1250] [1251]) (./mgcsd_8c_source.tex [1252] [1253] [1254] [1255] [1256] [1257]) (./mgcsd_8h_source.tex [1258]) (./mgdrvd_8c_source.tex [1259] [1260] [1261] [1262] [1263] [1264] [1265]) (./mgdrvd_8h_source.tex [1266] [1267]) (./mgfasd_8c_source.tex [1268] [1269] [1270] [1271] [1272] [1273]) (./mgfasd_8h_source.tex [1274] [1275]) (./mgsubd_8c_source.tex [1276] [1277] [1278] [1279] [1280] [1281] [1282] [1283] [1284] [1285] [1286]) (./mgsubd_8h_source.tex [1287] [1288] [1289] [1290]) (./mikpckd_8c_source.tex [1291] [1292] [1293] [1294]) (./mikpckd_8h_source.tex [1295] [1296] [1297]) (./mlinpckd_8c_source.tex [1298] [1299]) (./mlinpckd_8h_source.tex) (./mypdec_8c_source.tex [1300] [1301] [1302] [1303] [1304] [1305] [1306]) (./mypdec_8h_source.tex [1307]) (./newdrvd_8c_source.tex [1308] [1309] [1310] [1311]) (./newdrvd_8h_source.tex [1312]) (./newtond_8c_source.tex [1313] [1314] [1315] [1316] [1317] [1318] [1319]) (./newtond_8h_source.tex [1320]) (./powerd_8c_source.tex [1321] [1322] [1323] [1324] [1325]) (./powerd_8h_source.tex [1326]) (./smoothd_8c_source.tex [1327]) (./smoothd_8h_source.tex [1328]) (./routines_8c.tex <./routines_8c__incl.pdf> [1329] Underfull \hbox (badness 776) in paragraph at lines 48--49 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv /m/n/10 alist[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[] Underfull \hbox (badness 2856) in paragraph at lines 48--49 \T1/phv/m/n/10 YMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]ZMap[] [][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 kappa[]Map[][][], [] Underfull \hbox (badness 1237) in paragraph at lines 48--49 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 charge[]Map[][][], [] $\OMS/cmsy/m/n/10 ^^C $\T1/phv/m/n/10 pmgp[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pmg[][][], [] Underfull \hbox (badness 905) in paragraph at lines 62--63 []\T1/phv/m/n/10 VPUBLIC void [] (Vmem $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 mem , [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, int nforce[][][], [] $\OMS/cmsy /m/n/10 ^^C$\T1/phv/m/n/10 atom[] Underfull \hbox (badness 5817) in paragraph at lines 68--69 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], Underfull \hbox (badness 5817) in paragraph at lines 70--71 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], [1330] Underfull \hbox (badness 1442) in paragraph at lines 82--83 []\T1/phv/m/n/10 VPUBLIC int [] (Vcom $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 com, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, int nforce[][][], [] $\OMS/cmsy/ m/n/10 ^^C$\T1/phv/m/n/10 atom[] Underfull \hbox (badness 931) in paragraph at lines 88--89 []\T1/phv/m/n/10 VPUBLIC void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T 1/phv/m/n/10 fetk[][][], Gem Underfull \hbox (badness 2495) in paragraph at lines 90--91 []\T1/phv/m/n/10 VPUBLIC Vrc[]_[][]Codes [] (int icalc, [] $\OMS/cmsy/m/n/10 ^^ C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 feparm, [] $\OMS /cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbeparm, [] [1331] Underfull \hbox (badness 10000) detected at line 117 [][][] Underfull \hbox (badness 10000) detected at line 120 [][][] Underfull \hbox (badness 10000) detected at line 123 [][][] ) (./routines_8c_source.tex [1332] [1333] [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341] [1342] [1343] [1344] [1345] [1346] [1347] [1348] [1349] [1350] [1351] [1352] [1353] [1354] [1355] [1356] [1357] [1358] [1359] [1360] [1361] [1362] [1363] [1364] [1365] [1366] [1367] [1368] [1369] [1370] [1371] [1372] [1373] [1374] [1375] [1376] [1377] [1378] [1379] [1380] [1381] [1382] [1383] [1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] [1392] [1393] [1394] [1395] [1396] [1397] [1398] [1399] [1400]) (./routines_8h.tex <./routine s_8h__incl.pdf> <./routines_8h__dep__incl.pdf> [1401] Overfull \hbox (16.65858pt too wide) in paragraph at lines 52--53 []\T1/phv/m/n/10 VEXTERNC int [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], Overfull \hbox (16.91972pt too wide) in paragraph at lines 54--55 []\T1/phv/m/n/10 VEXTERNC void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh , [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/1 0 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], Underfull \hbox (badness 1910) in paragraph at lines 72--73 [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1 /phv/m/n/10 alist[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][] [], [] Underfull \hbox (badness 1237) in paragraph at lines 72--73 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 charge[]Map[][][], [] $\OMS/cmsy/m/n/10 ^^C $\T1/phv/m/n/10 pmgp[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pmg[][][], [] [1402] Underfull \hbox (badness 5817) in paragraph at lines 90--91 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], Underfull \hbox (badness 5817) in paragraph at lines 92--93 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], [1403] Underfull \hbox (badness 2495) in paragraph at lines 124--125 []\T1/phv/m/n/10 VPUBLIC Vrc[]_[][]Codes [] (int icalc, [] $\OMS/cmsy/m/n/10 ^^ C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 feparm, [] $\OMS /cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbeparm, [] Underfull \hbox (badness 10000) detected at line 147 [][][] Underfull \hbox (badness 10000) detected at line 150 [][][] Underfull \hbox (badness 10000) detected at line 153 [][][] [1404]) (./routines_8h_source.tex [1405] [1406] [1407] [1408] [1409]) [1410] (./refman.ind [1411] [1412] [1413] [1414] [1415] [1416] [1417] [1418] [1419] [1420] [1421] [1422] [1423] [1424] [1425] [1426] [1427] [1428] [1429] [1430] [1431] [1432] [1433] [1434] [1435] [1436] [1437] [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] [1449] [1450] [1451] [1452] [1453] [1454] [1455] [1456] [1457] [1458] [1459]) (./refman.aux) ) (see the transcript file for additional information)< /usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrro8a.pfb> Output written on refman.pdf (1517 pages, 6288270 bytes). Transcript written on refman.log. [ 55%] Built target doc-pdf [ 56%] Building C object tools/mesh/CMakeFiles/mgmesh.dir/mgmesh.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/mgmesh.c:10: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: ‘GEOFLOWparm_parseVDW’ declared ‘static’ but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: ‘GEOFLOWparm_parseETOL’ declared ‘static’ but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: ‘PBAMparm_parseSalt’ declared ‘static’ but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: ‘PBAMparm_parseRunType’ declared ‘static’ but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: ‘PBAMparm_parseRunName’ declared ‘static’ but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: ‘PBAMparm_parseRandorient’ declared ‘static’ but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: ‘PBAMparm_parsePBCS’ declared ‘static’ but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: ‘PBAMparm_parseUnits’ declared ‘static’ but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: ‘PBAMparm_parse3Dmap’ declared ‘static’ but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: ‘PBAMparm_parseGrid2D’ declared ‘static’ but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: ‘PBAMparm_parseDX’ declared ‘static’ but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: ‘PBAMparm_parseGridPts’ declared ‘static’ but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: ‘PBAMparm_parseTermcombine’ declared ‘static’ but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: ‘PBAMparm_parseDiff’ declared ‘static’ but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: ‘PBAMparm_parseXYZ’ declared ‘static’ but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: ‘PBSAMparm_parseTolsp’ declared ‘static’ but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: ‘PBSAMparm_parseSurf’ declared ‘static’ but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: ‘PBSAMparm_parseImat’ declared ‘static’ but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: ‘PBSAMparm_parseExp’ declared ‘static’ but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: ‘PBSAMparm_parseMSMS’ declared ‘static’ but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: ‘bcolcomp’ declared ‘static’ but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: ‘bcolcomp2’ declared ‘static’ but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: ‘bcolcomp3’ declared ‘static’ but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: ‘bcolcomp4’ declared ‘static’ but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: ‘pcolcomp’ declared ‘static’ but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: ‘bspline2’ declared ‘static’ but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: ‘dbspline2’ declared ‘static’ but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: ‘VFCHI4’ declared ‘static’ but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: ‘bspline4’ declared ‘static’ but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: ‘dbspline4’ declared ‘static’ but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: ‘d2bspline4’ declared ‘static’ but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: ‘d3bspline4’ declared ‘static’ but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: ‘Vpmg_polarizEnergy’ declared ‘static’ but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: ‘Vpmg_qfEnergyPoint’ declared ‘static’ but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: ‘Vpmg_qfEnergyVolume’ declared ‘static’ but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: ‘Vpmg_splineSelect’ declared ‘static’ but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: ‘focusFillBound’ declared ‘static’ but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: ‘bcfl1’ declared ‘static’ but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: ‘bcfl2’ declared ‘static’ but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: ‘multipolebc’ declared ‘static’ but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: ‘bcfl1sp’ declared ‘static’ but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: ‘bcCalc’ declared ‘static’ but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: ‘fillcoCoef’ declared ‘static’ but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: ‘fillcoCoefMap’ declared ‘static’ but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: ‘fillcoCoefMol’ declared ‘static’ but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: ‘fillcoCoefMolIon’ declared ‘static’ but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: ‘fillcoCoefMolDiel’ declared ‘static’ but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: ‘fillcoCoefMolDielNoSmooth’ declared ‘static’ but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: ‘fillcoCoefMolDielSmooth’ declared ‘static’ but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: ‘fillcoCoefSpline’ declared ‘static’ but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: ‘fillcoCoefSpline3’ declared ‘static’ but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: ‘fillcoCoefSpline4’ declared ‘static’ but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: ‘fillcoCharge’ declared ‘static’ but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: ‘fillcoChargeMap’ declared ‘static’ but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: ‘fillcoChargeSpline1’ declared ‘static’ but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: ‘fillcoChargeSpline2’ declared ‘static’ but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: ‘fillcoPermanentMultipole’ declared ‘static’ but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: ‘fillcoInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: ‘fillcoNLInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: ‘extEnergy’ declared ‘static’ but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: ‘qfForceSpline1’ declared ‘static’ but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: ‘qfForceSpline2’ declared ‘static’ but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: ‘qfForceSpline4’ declared ‘static’ but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: ‘zlapSolve’ declared ‘static’ but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: ‘markSphere’ declared ‘static’ but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: ‘Vpmg_qmEnergySMPBE’ declared ‘static’ but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: ‘Vpmg_qmEnergyNONLIN’ declared ‘static’ but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ [ 57%] Linking C executable ../bin/mgmesh [ 57%] Built target mgmesh [ 58%] Building C object tools/mesh/CMakeFiles/smooth.dir/smooth.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/smooth.c:13: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: ‘GEOFLOWparm_parseVDW’ declared ‘static’ but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: ‘GEOFLOWparm_parseETOL’ declared ‘static’ but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: ‘PBAMparm_parseSalt’ declared ‘static’ but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: ‘PBAMparm_parseRunType’ declared ‘static’ but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: ‘PBAMparm_parseRunName’ declared ‘static’ but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: ‘PBAMparm_parseRandorient’ declared ‘static’ but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: ‘PBAMparm_parsePBCS’ declared ‘static’ but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: ‘PBAMparm_parseUnits’ declared ‘static’ but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: ‘PBAMparm_parse3Dmap’ declared ‘static’ but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: ‘PBAMparm_parseGrid2D’ declared ‘static’ but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: ‘PBAMparm_parseDX’ declared ‘static’ but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: ‘PBAMparm_parseGridPts’ declared ‘static’ but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: ‘PBAMparm_parseTermcombine’ declared ‘static’ but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: ‘PBAMparm_parseDiff’ declared ‘static’ but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: ‘PBAMparm_parseXYZ’ declared ‘static’ but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: ‘PBSAMparm_parseTolsp’ declared ‘static’ but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: ‘PBSAMparm_parseSurf’ declared ‘static’ but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: ‘PBSAMparm_parseImat’ declared ‘static’ but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: ‘PBSAMparm_parseExp’ declared ‘static’ but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: ‘PBSAMparm_parseMSMS’ declared ‘static’ but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: ‘bcolcomp’ declared ‘static’ but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: ‘bcolcomp2’ declared ‘static’ but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: ‘bcolcomp3’ declared ‘static’ but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: ‘bcolcomp4’ declared ‘static’ but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: ‘pcolcomp’ declared ‘static’ but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: ‘bspline2’ declared ‘static’ but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: ‘dbspline2’ declared ‘static’ but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: ‘VFCHI4’ declared ‘static’ but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: ‘bspline4’ declared ‘static’ but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: ‘dbspline4’ declared ‘static’ but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: ‘d2bspline4’ declared ‘static’ but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: ‘d3bspline4’ declared ‘static’ but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: ‘Vpmg_polarizEnergy’ declared ‘static’ but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: ‘Vpmg_qfEnergyPoint’ declared ‘static’ but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: ‘Vpmg_qfEnergyVolume’ declared ‘static’ but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: ‘Vpmg_splineSelect’ declared ‘static’ but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: ‘focusFillBound’ declared ‘static’ but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: ‘bcfl1’ declared ‘static’ but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: ‘bcfl2’ declared ‘static’ but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: ‘multipolebc’ declared ‘static’ but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: ‘bcfl1sp’ declared ‘static’ but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: ‘bcCalc’ declared ‘static’ but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: ‘fillcoCoef’ declared ‘static’ but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: ‘fillcoCoefMap’ declared ‘static’ but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: ‘fillcoCoefMol’ declared ‘static’ but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: ‘fillcoCoefMolIon’ declared ‘static’ but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: ‘fillcoCoefMolDiel’ declared ‘static’ but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: ‘fillcoCoefMolDielNoSmooth’ declared ‘static’ but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: ‘fillcoCoefMolDielSmooth’ declared ‘static’ but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: ‘fillcoCoefSpline’ declared ‘static’ but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: ‘fillcoCoefSpline3’ declared ‘static’ but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: ‘fillcoCoefSpline4’ declared ‘static’ but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: ‘fillcoCharge’ declared ‘static’ but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: ‘fillcoChargeMap’ declared ‘static’ but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: ‘fillcoChargeSpline1’ declared ‘static’ but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: ‘fillcoChargeSpline2’ declared ‘static’ but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: ‘fillcoPermanentMultipole’ declared ‘static’ but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: ‘fillcoInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: ‘fillcoNLInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: ‘extEnergy’ declared ‘static’ but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: ‘qfForceSpline1’ declared ‘static’ but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: ‘qfForceSpline2’ declared ‘static’ but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: ‘qfForceSpline4’ declared ‘static’ but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: ‘zlapSolve’ declared ‘static’ but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: ‘markSphere’ declared ‘static’ but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: ‘Vpmg_qmEnergySMPBE’ declared ‘static’ but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: ‘Vpmg_qmEnergyNONLIN’ declared ‘static’ but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/smooth.c: In function ‘main’: /builddir/build/BUILD/apbs-3.0.0/tools/mesh/smooth.c:169:15: warning: ‘format’ may be used uninitialized [-Wmaybe-uninitialized] 169 | } else if (format == VDF_DXBIN) { | ^ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/smooth.c:66:18: note: ‘format’ was declared here 66 | Vdata_Format format; int gotFormat = 0; | ^~~~~~ [ 59%] Linking C executable ../bin/smooth [ 59%] Built target smooth [ 60%] Building C object tools/mesh/CMakeFiles/dxmath.dir/dxmath.c.o /builddir/build/BUILD/apbs-3.0.0/tools/mesh/dxmath.c: In function ‘main’: /builddir/build/BUILD/apbs-3.0.0/tools/mesh/dxmath.c:41:10: warning: unused variable ‘format’ [-Wunused-variable] 41 | char format[VMAX_BUFSIZE]; | ^~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/dxmath.c:13: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h: At top level: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: ‘GEOFLOWparm_parseVDW’ declared ‘static’ but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: ‘GEOFLOWparm_parseETOL’ declared ‘static’ but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: ‘PBAMparm_parseSalt’ declared ‘static’ but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: ‘PBAMparm_parseRunType’ declared ‘static’ but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: ‘PBAMparm_parseRunName’ declared ‘static’ but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: ‘PBAMparm_parseRandorient’ declared ‘static’ but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: ‘PBAMparm_parsePBCS’ declared ‘static’ but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: ‘PBAMparm_parseUnits’ declared ‘static’ but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: ‘PBAMparm_parse3Dmap’ declared ‘static’ but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: ‘PBAMparm_parseGrid2D’ declared ‘static’ but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: ‘PBAMparm_parseDX’ declared ‘static’ but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: ‘PBAMparm_parseGridPts’ declared ‘static’ but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: ‘PBAMparm_parseTermcombine’ declared ‘static’ but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: ‘PBAMparm_parseDiff’ declared ‘static’ but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: ‘PBAMparm_parseXYZ’ declared ‘static’ but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: ‘PBSAMparm_parseTolsp’ declared ‘static’ but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: ‘PBSAMparm_parseSurf’ declared ‘static’ but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: ‘PBSAMparm_parseImat’ declared ‘static’ but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: ‘PBSAMparm_parseExp’ declared ‘static’ but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: ‘PBSAMparm_parseMSMS’ declared ‘static’ but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: ‘bcolcomp’ declared ‘static’ but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: ‘bcolcomp2’ declared ‘static’ but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: ‘bcolcomp3’ declared ‘static’ but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: ‘bcolcomp4’ declared ‘static’ but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: ‘pcolcomp’ declared ‘static’ but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: ‘bspline2’ declared ‘static’ but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: ‘dbspline2’ declared ‘static’ but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: ‘VFCHI4’ declared ‘static’ but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: ‘bspline4’ declared ‘static’ but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: ‘dbspline4’ declared ‘static’ but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: ‘d2bspline4’ declared ‘static’ but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: ‘d3bspline4’ declared ‘static’ but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: ‘Vpmg_polarizEnergy’ declared ‘static’ but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: ‘Vpmg_qfEnergyPoint’ declared ‘static’ but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: ‘Vpmg_qfEnergyVolume’ declared ‘static’ but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: ‘Vpmg_splineSelect’ declared ‘static’ but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: ‘focusFillBound’ declared ‘static’ but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: ‘bcfl1’ declared ‘static’ but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: ‘bcfl2’ declared ‘static’ but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: ‘multipolebc’ declared ‘static’ but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: ‘bcfl1sp’ declared ‘static’ but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: ‘bcCalc’ declared ‘static’ but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: ‘fillcoCoef’ declared ‘static’ but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: ‘fillcoCoefMap’ declared ‘static’ but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: ‘fillcoCoefMol’ declared ‘static’ but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: ‘fillcoCoefMolIon’ declared ‘static’ but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: ‘fillcoCoefMolDiel’ declared ‘static’ but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: ‘fillcoCoefMolDielNoSmooth’ declared ‘static’ but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: ‘fillcoCoefMolDielSmooth’ declared ‘static’ but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: ‘fillcoCoefSpline’ declared ‘static’ but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: ‘fillcoCoefSpline3’ declared ‘static’ but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: ‘fillcoCoefSpline4’ declared ‘static’ but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: ‘fillcoCharge’ declared ‘static’ but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: ‘fillcoChargeMap’ declared ‘static’ but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: ‘fillcoChargeSpline1’ declared ‘static’ but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: ‘fillcoChargeSpline2’ declared ‘static’ but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: ‘fillcoPermanentMultipole’ declared ‘static’ but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: ‘fillcoInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: ‘fillcoNLInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: ‘extEnergy’ declared ‘static’ but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: ‘qfForceSpline1’ declared ‘static’ but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: ‘qfForceSpline2’ declared ‘static’ but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: ‘qfForceSpline4’ declared ‘static’ but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: ‘zlapSolve’ declared ‘static’ but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: ‘markSphere’ declared ‘static’ but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: ‘Vpmg_qmEnergySMPBE’ declared ‘static’ but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: ‘Vpmg_qmEnergyNONLIN’ declared ‘static’ but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ [ 62%] Linking C executable ../bin/dxmath [ 62%] Built target dxmath [ 63%] Building C object tools/mesh/CMakeFiles/mergedx.dir/mergedx.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/mergedx.c:8: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: ‘GEOFLOWparm_parseVDW’ declared ‘static’ but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: ‘GEOFLOWparm_parseETOL’ declared ‘static’ but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: ‘PBAMparm_parseSalt’ declared ‘static’ but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: ‘PBAMparm_parseRunType’ declared ‘static’ but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: ‘PBAMparm_parseRunName’ declared ‘static’ but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: ‘PBAMparm_parseRandorient’ declared ‘static’ but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: ‘PBAMparm_parsePBCS’ declared ‘static’ but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: ‘PBAMparm_parseUnits’ declared ‘static’ but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: ‘PBAMparm_parse3Dmap’ declared ‘static’ but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: ‘PBAMparm_parseGrid2D’ declared ‘static’ but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: ‘PBAMparm_parseDX’ declared ‘static’ but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: ‘PBAMparm_parseGridPts’ declared ‘static’ but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: ‘PBAMparm_parseTermcombine’ declared ‘static’ but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: ‘PBAMparm_parseDiff’ declared ‘static’ but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: ‘PBAMparm_parseXYZ’ declared ‘static’ but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: ‘PBSAMparm_parseTolsp’ declared ‘static’ but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: ‘PBSAMparm_parseSurf’ declared ‘static’ but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: ‘PBSAMparm_parseImat’ declared ‘static’ but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: ‘PBSAMparm_parseExp’ declared ‘static’ but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: ‘PBSAMparm_parseMSMS’ declared ‘static’ but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: ‘bcolcomp’ declared ‘static’ but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: ‘bcolcomp2’ declared ‘static’ but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: ‘bcolcomp3’ declared ‘static’ but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: ‘bcolcomp4’ declared ‘static’ but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: ‘pcolcomp’ declared ‘static’ but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: ‘bspline2’ declared ‘static’ but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: ‘dbspline2’ declared ‘static’ but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: ‘VFCHI4’ declared ‘static’ but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: ‘bspline4’ declared ‘static’ but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: ‘dbspline4’ declared ‘static’ but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: ‘d2bspline4’ declared ‘static’ but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: ‘d3bspline4’ declared ‘static’ but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: ‘Vpmg_polarizEnergy’ declared ‘static’ but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: ‘Vpmg_qfEnergyPoint’ declared ‘static’ but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: ‘Vpmg_qfEnergyVolume’ declared ‘static’ but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: ‘Vpmg_splineSelect’ declared ‘static’ but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: ‘focusFillBound’ declared ‘static’ but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: ‘bcfl1’ declared ‘static’ but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: ‘bcfl2’ declared ‘static’ but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: ‘multipolebc’ declared ‘static’ but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: ‘bcfl1sp’ declared ‘static’ but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: ‘bcCalc’ declared ‘static’ but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: ‘fillcoCoef’ declared ‘static’ but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: ‘fillcoCoefMap’ declared ‘static’ but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: ‘fillcoCoefMol’ declared ‘static’ but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: ‘fillcoCoefMolIon’ declared ‘static’ but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: ‘fillcoCoefMolDiel’ declared ‘static’ but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: ‘fillcoCoefMolDielNoSmooth’ declared ‘static’ but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: ‘fillcoCoefMolDielSmooth’ declared ‘static’ but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: ‘fillcoCoefSpline’ declared ‘static’ but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: ‘fillcoCoefSpline3’ declared ‘static’ but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: ‘fillcoCoefSpline4’ declared ‘static’ but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: ‘fillcoCharge’ declared ‘static’ but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: ‘fillcoChargeMap’ declared ‘static’ but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: ‘fillcoChargeSpline1’ declared ‘static’ but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: ‘fillcoChargeSpline2’ declared ‘static’ but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: ‘fillcoPermanentMultipole’ declared ‘static’ but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: ‘fillcoInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: ‘fillcoNLInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: ‘extEnergy’ declared ‘static’ but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: ‘qfForceSpline1’ declared ‘static’ but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: ‘qfForceSpline2’ declared ‘static’ but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: ‘qfForceSpline4’ declared ‘static’ but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: ‘zlapSolve’ declared ‘static’ but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: ‘markSphere’ declared ‘static’ but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: ‘Vpmg_qmEnergySMPBE’ declared ‘static’ but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: ‘Vpmg_qmEnergyNONLIN’ declared ‘static’ but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/mergedx.c: In function ‘main’: /builddir/build/BUILD/apbs-3.0.0/tools/mesh/mergedx.c:81:13: warning: ‘nx’ may be used uninitialized [-Wmaybe-uninitialized] 81 | mgrid = Vgrid_ctor(nx, ny, nz, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, VNULL); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/mergedx.c:29:9: note: ‘nx’ was declared here 29 | int nx, ny, nz, count, numfnams; | ^~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/mergedx.c:81:13: warning: ‘ny’ may be used uninitialized [-Wmaybe-uninitialized] 81 | mgrid = Vgrid_ctor(nx, ny, nz, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, VNULL); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/mergedx.c:29:13: note: ‘ny’ was declared here 29 | int nx, ny, nz, count, numfnams; | ^~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/mergedx.c:81:13: warning: ‘nz’ may be used uninitialized [-Wmaybe-uninitialized] 81 | mgrid = Vgrid_ctor(nx, ny, nz, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, VNULL); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/mergedx.c:29:17: note: ‘nz’ was declared here 29 | int nx, ny, nz, count, numfnams; | ^~ [ 64%] Linking C executable ../bin/mergedx [ 64%] Built target mergedx [ 65%] Building C object tools/mesh/CMakeFiles/mergedx2.dir/mergedx2.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/mergedx2.c:8: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: ‘GEOFLOWparm_parseVDW’ declared ‘static’ but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: ‘GEOFLOWparm_parseETOL’ declared ‘static’ but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: ‘PBAMparm_parseSalt’ declared ‘static’ but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: ‘PBAMparm_parseRunType’ declared ‘static’ but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: ‘PBAMparm_parseRunName’ declared ‘static’ but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: ‘PBAMparm_parseRandorient’ declared ‘static’ but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: ‘PBAMparm_parsePBCS’ declared ‘static’ but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: ‘PBAMparm_parseUnits’ declared ‘static’ but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: ‘PBAMparm_parse3Dmap’ declared ‘static’ but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: ‘PBAMparm_parseGrid2D’ declared ‘static’ but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: ‘PBAMparm_parseDX’ declared ‘static’ but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: ‘PBAMparm_parseGridPts’ declared ‘static’ but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: ‘PBAMparm_parseTermcombine’ declared ‘static’ but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: ‘PBAMparm_parseDiff’ declared ‘static’ but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: ‘PBAMparm_parseXYZ’ declared ‘static’ but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: ‘PBSAMparm_parseTolsp’ declared ‘static’ but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: ‘PBSAMparm_parseSurf’ declared ‘static’ but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: ‘PBSAMparm_parseImat’ declared ‘static’ but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: ‘PBSAMparm_parseExp’ declared ‘static’ but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: ‘PBSAMparm_parseMSMS’ declared ‘static’ but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: ‘bcolcomp’ declared ‘static’ but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: ‘bcolcomp2’ declared ‘static’ but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: ‘bcolcomp3’ declared ‘static’ but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: ‘bcolcomp4’ declared ‘static’ but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: ‘pcolcomp’ declared ‘static’ but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: ‘bspline2’ declared ‘static’ but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: ‘dbspline2’ declared ‘static’ but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: ‘VFCHI4’ declared ‘static’ but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: ‘bspline4’ declared ‘static’ but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: ‘dbspline4’ declared ‘static’ but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: ‘d2bspline4’ declared ‘static’ but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: ‘d3bspline4’ declared ‘static’ but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: ‘Vpmg_polarizEnergy’ declared ‘static’ but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: ‘Vpmg_qfEnergyPoint’ declared ‘static’ but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: ‘Vpmg_qfEnergyVolume’ declared ‘static’ but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: ‘Vpmg_splineSelect’ declared ‘static’ but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: ‘focusFillBound’ declared ‘static’ but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: ‘bcfl1’ declared ‘static’ but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: ‘bcfl2’ declared ‘static’ but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: ‘multipolebc’ declared ‘static’ but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: ‘bcfl1sp’ declared ‘static’ but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: ‘bcCalc’ declared ‘static’ but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: ‘fillcoCoef’ declared ‘static’ but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: ‘fillcoCoefMap’ declared ‘static’ but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: ‘fillcoCoefMol’ declared ‘static’ but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: ‘fillcoCoefMolIon’ declared ‘static’ but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: ‘fillcoCoefMolDiel’ declared ‘static’ but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: ‘fillcoCoefMolDielNoSmooth’ declared ‘static’ but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: ‘fillcoCoefMolDielSmooth’ declared ‘static’ but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: ‘fillcoCoefSpline’ declared ‘static’ but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: ‘fillcoCoefSpline3’ declared ‘static’ but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: ‘fillcoCoefSpline4’ declared ‘static’ but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: ‘fillcoCharge’ declared ‘static’ but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: ‘fillcoChargeMap’ declared ‘static’ but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: ‘fillcoChargeSpline1’ declared ‘static’ but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: ‘fillcoChargeSpline2’ declared ‘static’ but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: ‘fillcoPermanentMultipole’ declared ‘static’ but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: ‘fillcoInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: ‘fillcoNLInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: ‘extEnergy’ declared ‘static’ but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: ‘qfForceSpline1’ declared ‘static’ but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: ‘qfForceSpline2’ declared ‘static’ but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: ‘qfForceSpline4’ declared ‘static’ but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: ‘zlapSolve’ declared ‘static’ but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: ‘markSphere’ declared ‘static’ but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: ‘Vpmg_qmEnergySMPBE’ declared ‘static’ but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: ‘Vpmg_qmEnergyNONLIN’ declared ‘static’ but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ [ 66%] Linking C executable ../bin/mergedx2 [ 66%] Built target mergedx2 [ 67%] Building C object tools/mesh/CMakeFiles/value.dir/value.c.o /builddir/build/BUILD/apbs-3.0.0/tools/mesh/value.c: In function ‘main’: /builddir/build/BUILD/apbs-3.0.0/tools/mesh/value.c:37:9: warning: unused variable ‘inorm’ [-Wunused-variable] 37 | int inorm; | ^~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/value.c:8: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h: At top level: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: ‘GEOFLOWparm_parseVDW’ declared ‘static’ but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: ‘GEOFLOWparm_parseETOL’ declared ‘static’ but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: ‘PBAMparm_parseSalt’ declared ‘static’ but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: ‘PBAMparm_parseRunType’ declared ‘static’ but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: ‘PBAMparm_parseRunName’ declared ‘static’ but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: ‘PBAMparm_parseRandorient’ declared ‘static’ but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: ‘PBAMparm_parsePBCS’ declared ‘static’ but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: ‘PBAMparm_parseUnits’ declared ‘static’ but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: ‘PBAMparm_parse3Dmap’ declared ‘static’ but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: ‘PBAMparm_parseGrid2D’ declared ‘static’ but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: ‘PBAMparm_parseDX’ declared ‘static’ but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: ‘PBAMparm_parseGridPts’ declared ‘static’ but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: ‘PBAMparm_parseTermcombine’ declared ‘static’ but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: ‘PBAMparm_parseDiff’ declared ‘static’ but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: ‘PBAMparm_parseXYZ’ declared ‘static’ but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: ‘PBSAMparm_parseTolsp’ declared ‘static’ but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: ‘PBSAMparm_parseSurf’ declared ‘static’ but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: ‘PBSAMparm_parseImat’ declared ‘static’ but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: ‘PBSAMparm_parseExp’ declared ‘static’ but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: ‘PBSAMparm_parseMSMS’ declared ‘static’ but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: ‘bcolcomp’ declared ‘static’ but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: ‘bcolcomp2’ declared ‘static’ but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: ‘bcolcomp3’ declared ‘static’ but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: ‘bcolcomp4’ declared ‘static’ but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: ‘pcolcomp’ declared ‘static’ but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: ‘bspline2’ declared ‘static’ but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: ‘dbspline2’ declared ‘static’ but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: ‘VFCHI4’ declared ‘static’ but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: ‘bspline4’ declared ‘static’ but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: ‘dbspline4’ declared ‘static’ but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: ‘d2bspline4’ declared ‘static’ but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: ‘d3bspline4’ declared ‘static’ but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: ‘Vpmg_polarizEnergy’ declared ‘static’ but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: ‘Vpmg_qfEnergyPoint’ declared ‘static’ but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: ‘Vpmg_qfEnergyVolume’ declared ‘static’ but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: ‘Vpmg_splineSelect’ declared ‘static’ but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: ‘focusFillBound’ declared ‘static’ but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: ‘bcfl1’ declared ‘static’ but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: ‘bcfl2’ declared ‘static’ but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: ‘multipolebc’ declared ‘static’ but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: ‘bcfl1sp’ declared ‘static’ but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: ‘bcCalc’ declared ‘static’ but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: ‘fillcoCoef’ declared ‘static’ but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: ‘fillcoCoefMap’ declared ‘static’ but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: ‘fillcoCoefMol’ declared ‘static’ but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: ‘fillcoCoefMolIon’ declared ‘static’ but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: ‘fillcoCoefMolDiel’ declared ‘static’ but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: ‘fillcoCoefMolDielNoSmooth’ declared ‘static’ but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: ‘fillcoCoefMolDielSmooth’ declared ‘static’ but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: ‘fillcoCoefSpline’ declared ‘static’ but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: ‘fillcoCoefSpline3’ declared ‘static’ but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: ‘fillcoCoefSpline4’ declared ‘static’ but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: ‘fillcoCharge’ declared ‘static’ but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: ‘fillcoChargeMap’ declared ‘static’ but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: ‘fillcoChargeSpline1’ declared ‘static’ but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: ‘fillcoChargeSpline2’ declared ‘static’ but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: ‘fillcoPermanentMultipole’ declared ‘static’ but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: ‘fillcoInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: ‘fillcoNLInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: ‘extEnergy’ declared ‘static’ but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: ‘qfForceSpline1’ declared ‘static’ but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: ‘qfForceSpline2’ declared ‘static’ but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: ‘qfForceSpline4’ declared ‘static’ but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: ‘zlapSolve’ declared ‘static’ but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: ‘markSphere’ declared ‘static’ but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: ‘Vpmg_qmEnergySMPBE’ declared ‘static’ but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: ‘Vpmg_qmEnergyNONLIN’ declared ‘static’ but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ [ 68%] Linking C executable ../bin/value [ 68%] Built target value [ 70%] Building C object tools/mesh/CMakeFiles/multivalue.dir/multivalue.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/multivalue.c:46: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: ‘GEOFLOWparm_parseVDW’ declared ‘static’ but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: ‘GEOFLOWparm_parseETOL’ declared ‘static’ but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: ‘PBAMparm_parseSalt’ declared ‘static’ but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: ‘PBAMparm_parseRunType’ declared ‘static’ but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: ‘PBAMparm_parseRunName’ declared ‘static’ but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: ‘PBAMparm_parseRandorient’ declared ‘static’ but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: ‘PBAMparm_parsePBCS’ declared ‘static’ but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: ‘PBAMparm_parseUnits’ declared ‘static’ but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: ‘PBAMparm_parse3Dmap’ declared ‘static’ but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: ‘PBAMparm_parseGrid2D’ declared ‘static’ but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: ‘PBAMparm_parseDX’ declared ‘static’ but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: ‘PBAMparm_parseGridPts’ declared ‘static’ but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: ‘PBAMparm_parseTermcombine’ declared ‘static’ but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: ‘PBAMparm_parseDiff’ declared ‘static’ but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: ‘PBAMparm_parseXYZ’ declared ‘static’ but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: ‘PBSAMparm_parseTolsp’ declared ‘static’ but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: ‘PBSAMparm_parseSurf’ declared ‘static’ but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: ‘PBSAMparm_parseImat’ declared ‘static’ but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: ‘PBSAMparm_parseExp’ declared ‘static’ but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: ‘PBSAMparm_parseMSMS’ declared ‘static’ but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: ‘bcolcomp’ declared ‘static’ but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: ‘bcolcomp2’ declared ‘static’ but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: ‘bcolcomp3’ declared ‘static’ but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: ‘bcolcomp4’ declared ‘static’ but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: ‘pcolcomp’ declared ‘static’ but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: ‘bspline2’ declared ‘static’ but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: ‘dbspline2’ declared ‘static’ but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: ‘VFCHI4’ declared ‘static’ but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: ‘bspline4’ declared ‘static’ but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: ‘dbspline4’ declared ‘static’ but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: ‘d2bspline4’ declared ‘static’ but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: ‘d3bspline4’ declared ‘static’ but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: ‘Vpmg_polarizEnergy’ declared ‘static’ but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: ‘Vpmg_qfEnergyPoint’ declared ‘static’ but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: ‘Vpmg_qfEnergyVolume’ declared ‘static’ but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: ‘Vpmg_splineSelect’ declared ‘static’ but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: ‘focusFillBound’ declared ‘static’ but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: ‘bcfl1’ declared ‘static’ but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: ‘bcfl2’ declared ‘static’ but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: ‘multipolebc’ declared ‘static’ but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: ‘bcfl1sp’ declared ‘static’ but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: ‘bcCalc’ declared ‘static’ but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: ‘fillcoCoef’ declared ‘static’ but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: ‘fillcoCoefMap’ declared ‘static’ but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: ‘fillcoCoefMol’ declared ‘static’ but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: ‘fillcoCoefMolIon’ declared ‘static’ but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: ‘fillcoCoefMolDiel’ declared ‘static’ but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: ‘fillcoCoefMolDielNoSmooth’ declared ‘static’ but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: ‘fillcoCoefMolDielSmooth’ declared ‘static’ but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: ‘fillcoCoefSpline’ declared ‘static’ but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: ‘fillcoCoefSpline3’ declared ‘static’ but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: ‘fillcoCoefSpline4’ declared ‘static’ but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: ‘fillcoCharge’ declared ‘static’ but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: ‘fillcoChargeMap’ declared ‘static’ but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: ‘fillcoChargeSpline1’ declared ‘static’ but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: ‘fillcoChargeSpline2’ declared ‘static’ but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: ‘fillcoPermanentMultipole’ declared ‘static’ but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: ‘fillcoInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: ‘fillcoNLInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: ‘extEnergy’ declared ‘static’ but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: ‘qfForceSpline1’ declared ‘static’ but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: ‘qfForceSpline2’ declared ‘static’ but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: ‘qfForceSpline4’ declared ‘static’ but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: ‘zlapSolve’ declared ‘static’ but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: ‘markSphere’ declared ‘static’ but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: ‘Vpmg_qmEnergySMPBE’ declared ‘static’ but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: ‘Vpmg_qmEnergyNONLIN’ declared ‘static’ but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ [ 71%] Linking C executable ../bin/multivalue [ 71%] Built target multivalue [ 72%] Building C object tools/mesh/CMakeFiles/benchmark.dir/benchmark.c.o /builddir/build/BUILD/apbs-3.0.0/tools/mesh/benchmark.c: In function ‘main’: /builddir/build/BUILD/apbs-3.0.0/tools/mesh/benchmark.c:28:12: warning: unused variable ‘grid’ [-Wunused-variable] 28 | Vgrid *grid; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/benchmark.c:18:58: warning: unused variable ‘sum’ [-Wunused-variable] 18 | double hy, hx, hzed, xmin, ymin, zmin, pt[3], value, sum, dtmp; | ^~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/benchmark.c:18:51: warning: unused variable ‘value’ [-Wunused-variable] 18 | double hy, hx, hzed, xmin, ymin, zmin, pt[3], value, sum, dtmp; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/benchmark.c:18:44: warning: unused variable ‘pt’ [-Wunused-variable] 18 | double hy, hx, hzed, xmin, ymin, zmin, pt[3], value, sum, dtmp; | ^~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/benchmark.c:18:38: warning: variable ‘zmin’ set but not used [-Wunused-but-set-variable] 18 | double hy, hx, hzed, xmin, ymin, zmin, pt[3], value, sum, dtmp; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/benchmark.c:18:32: warning: variable ‘ymin’ set but not used [-Wunused-but-set-variable] 18 | double hy, hx, hzed, xmin, ymin, zmin, pt[3], value, sum, dtmp; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/benchmark.c:18:26: warning: variable ‘xmin’ set but not used [-Wunused-but-set-variable] 18 | double hy, hx, hzed, xmin, ymin, zmin, pt[3], value, sum, dtmp; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/benchmark.c:18:20: warning: variable ‘hzed’ set but not used [-Wunused-but-set-variable] 18 | double hy, hx, hzed, xmin, ymin, zmin, pt[3], value, sum, dtmp; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/benchmark.c:18:16: warning: variable ‘hx’ set but not used [-Wunused-but-set-variable] 18 | double hy, hx, hzed, xmin, ymin, zmin, pt[3], value, sum, dtmp; | ^~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/benchmark.c:18:12: warning: variable ‘hy’ set but not used [-Wunused-but-set-variable] 18 | double hy, hx, hzed, xmin, ymin, zmin, pt[3], value, sum, dtmp; | ^~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/benchmark.c:17:27: warning: unused variable ‘k’ [-Wunused-variable] 17 | int nx, ny, nz, i, j, k, itmp; | ^ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/benchmark.c:17:24: warning: unused variable ‘j’ [-Wunused-variable] 17 | int nx, ny, nz, i, j, k, itmp; | ^ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/benchmark.c:17:21: warning: unused variable ‘i’ [-Wunused-variable] 17 | int nx, ny, nz, i, j, k, itmp; | ^ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/benchmark.c:8: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h: At top level: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: ‘GEOFLOWparm_parseVDW’ declared ‘static’ but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: ‘GEOFLOWparm_parseETOL’ declared ‘static’ but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: ‘PBAMparm_parseSalt’ declared ‘static’ but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: ‘PBAMparm_parseRunType’ declared ‘static’ but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: ‘PBAMparm_parseRunName’ declared ‘static’ but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: ‘PBAMparm_parseRandorient’ declared ‘static’ but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: ‘PBAMparm_parsePBCS’ declared ‘static’ but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: ‘PBAMparm_parseUnits’ declared ‘static’ but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: ‘PBAMparm_parse3Dmap’ declared ‘static’ but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: ‘PBAMparm_parseGrid2D’ declared ‘static’ but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: ‘PBAMparm_parseDX’ declared ‘static’ but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: ‘PBAMparm_parseGridPts’ declared ‘static’ but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: ‘PBAMparm_parseTermcombine’ declared ‘static’ but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: ‘PBAMparm_parseDiff’ declared ‘static’ but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: ‘PBAMparm_parseXYZ’ declared ‘static’ but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: ‘PBSAMparm_parseTolsp’ declared ‘static’ but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: ‘PBSAMparm_parseSurf’ declared ‘static’ but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: ‘PBSAMparm_parseImat’ declared ‘static’ but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: ‘PBSAMparm_parseExp’ declared ‘static’ but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: ‘PBSAMparm_parseMSMS’ declared ‘static’ but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: ‘bcolcomp’ declared ‘static’ but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: ‘bcolcomp2’ declared ‘static’ but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: ‘bcolcomp3’ declared ‘static’ but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: ‘bcolcomp4’ declared ‘static’ but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: ‘pcolcomp’ declared ‘static’ but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: ‘bspline2’ declared ‘static’ but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: ‘dbspline2’ declared ‘static’ but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: ‘VFCHI4’ declared ‘static’ but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: ‘bspline4’ declared ‘static’ but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: ‘dbspline4’ declared ‘static’ but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: ‘d2bspline4’ declared ‘static’ but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: ‘d3bspline4’ declared ‘static’ but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: ‘Vpmg_polarizEnergy’ declared ‘static’ but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: ‘Vpmg_qfEnergyPoint’ declared ‘static’ but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: ‘Vpmg_qfEnergyVolume’ declared ‘static’ but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: ‘Vpmg_splineSelect’ declared ‘static’ but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: ‘focusFillBound’ declared ‘static’ but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: ‘bcfl1’ declared ‘static’ but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: ‘bcfl2’ declared ‘static’ but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: ‘multipolebc’ declared ‘static’ but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: ‘bcfl1sp’ declared ‘static’ but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: ‘bcCalc’ declared ‘static’ but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: ‘fillcoCoef’ declared ‘static’ but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: ‘fillcoCoefMap’ declared ‘static’ but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: ‘fillcoCoefMol’ declared ‘static’ but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: ‘fillcoCoefMolIon’ declared ‘static’ but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: ‘fillcoCoefMolDiel’ declared ‘static’ but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: ‘fillcoCoefMolDielNoSmooth’ declared ‘static’ but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: ‘fillcoCoefMolDielSmooth’ declared ‘static’ but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: ‘fillcoCoefSpline’ declared ‘static’ but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: ‘fillcoCoefSpline3’ declared ‘static’ but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: ‘fillcoCoefSpline4’ declared ‘static’ but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: ‘fillcoCharge’ declared ‘static’ but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: ‘fillcoChargeMap’ declared ‘static’ but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: ‘fillcoChargeSpline1’ declared ‘static’ but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: ‘fillcoChargeSpline2’ declared ‘static’ but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: ‘fillcoPermanentMultipole’ declared ‘static’ but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: ‘fillcoInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: ‘fillcoNLInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: ‘extEnergy’ declared ‘static’ but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: ‘qfForceSpline1’ declared ‘static’ but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: ‘qfForceSpline2’ declared ‘static’ but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: ‘qfForceSpline4’ declared ‘static’ but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: ‘zlapSolve’ declared ‘static’ but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: ‘markSphere’ declared ‘static’ but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: ‘Vpmg_qmEnergySMPBE’ declared ‘static’ but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: ‘Vpmg_qmEnergyNONLIN’ declared ‘static’ but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ [ 73%] Linking C executable ../bin/benchmark [ 73%] Built target benchmark [ 74%] Building C object tools/mesh/CMakeFiles/similarity.dir/similarity.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/similarity.c:13: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: ‘GEOFLOWparm_parseVDW’ declared ‘static’ but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: ‘GEOFLOWparm_parseETOL’ declared ‘static’ but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: ‘PBAMparm_parseSalt’ declared ‘static’ but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: ‘PBAMparm_parseRunType’ declared ‘static’ but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: ‘PBAMparm_parseRunName’ declared ‘static’ but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: ‘PBAMparm_parseRandorient’ declared ‘static’ but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: ‘PBAMparm_parsePBCS’ declared ‘static’ but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: ‘PBAMparm_parseUnits’ declared ‘static’ but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: ‘PBAMparm_parse3Dmap’ declared ‘static’ but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: ‘PBAMparm_parseGrid2D’ declared ‘static’ but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: ‘PBAMparm_parseDX’ declared ‘static’ but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: ‘PBAMparm_parseGridPts’ declared ‘static’ but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: ‘PBAMparm_parseTermcombine’ declared ‘static’ but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: ‘PBAMparm_parseDiff’ declared ‘static’ but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: ‘PBAMparm_parseXYZ’ declared ‘static’ but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: ‘PBSAMparm_parseTolsp’ declared ‘static’ but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: ‘PBSAMparm_parseSurf’ declared ‘static’ but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: ‘PBSAMparm_parseImat’ declared ‘static’ but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: ‘PBSAMparm_parseExp’ declared ‘static’ but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: ‘PBSAMparm_parseMSMS’ declared ‘static’ but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: ‘bcolcomp’ declared ‘static’ but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: ‘bcolcomp2’ declared ‘static’ but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: ‘bcolcomp3’ declared ‘static’ but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: ‘bcolcomp4’ declared ‘static’ but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: ‘pcolcomp’ declared ‘static’ but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: ‘bspline2’ declared ‘static’ but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: ‘dbspline2’ declared ‘static’ but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: ‘VFCHI4’ declared ‘static’ but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: ‘bspline4’ declared ‘static’ but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: ‘dbspline4’ declared ‘static’ but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: ‘d2bspline4’ declared ‘static’ but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: ‘d3bspline4’ declared ‘static’ but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: ‘Vpmg_polarizEnergy’ declared ‘static’ but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: ‘Vpmg_qfEnergyPoint’ declared ‘static’ but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: ‘Vpmg_qfEnergyVolume’ declared ‘static’ but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: ‘Vpmg_splineSelect’ declared ‘static’ but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: ‘focusFillBound’ declared ‘static’ but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: ‘bcfl1’ declared ‘static’ but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: ‘bcfl2’ declared ‘static’ but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: ‘multipolebc’ declared ‘static’ but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: ‘bcfl1sp’ declared ‘static’ but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: ‘bcCalc’ declared ‘static’ but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: ‘fillcoCoef’ declared ‘static’ but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: ‘fillcoCoefMap’ declared ‘static’ but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: ‘fillcoCoefMol’ declared ‘static’ but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: ‘fillcoCoefMolIon’ declared ‘static’ but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: ‘fillcoCoefMolDiel’ declared ‘static’ but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: ‘fillcoCoefMolDielNoSmooth’ declared ‘static’ but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: ‘fillcoCoefMolDielSmooth’ declared ‘static’ but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: ‘fillcoCoefSpline’ declared ‘static’ but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: ‘fillcoCoefSpline3’ declared ‘static’ but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: ‘fillcoCoefSpline4’ declared ‘static’ but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: ‘fillcoCharge’ declared ‘static’ but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: ‘fillcoChargeMap’ declared ‘static’ but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: ‘fillcoChargeSpline1’ declared ‘static’ but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: ‘fillcoChargeSpline2’ declared ‘static’ but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: ‘fillcoPermanentMultipole’ declared ‘static’ but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: ‘fillcoInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: ‘fillcoNLInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: ‘extEnergy’ declared ‘static’ but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: ‘qfForceSpline1’ declared ‘static’ but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: ‘qfForceSpline2’ declared ‘static’ but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: ‘qfForceSpline4’ declared ‘static’ but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: ‘zlapSolve’ declared ‘static’ but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: ‘markSphere’ declared ‘static’ but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: ‘Vpmg_qmEnergySMPBE’ declared ‘static’ but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: ‘Vpmg_qmEnergyNONLIN’ declared ‘static’ but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/similarity.c: In function ‘main’: /builddir/build/BUILD/apbs-3.0.0/tools/mesh/similarity.c:298:13: warning: ‘strncpy’ specified bound 1024 equals destination size [-Wstringop-truncation] 298 | strncpy(scalar1Path, tstr, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/similarity.c:305:13: warning: ‘strncpy’ specified bound 1024 equals destination size [-Wstringop-truncation] 305 | strncpy(scalar2Path, tstr, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/similarity.c:312:13: warning: ‘strncpy’ specified bound 1024 equals destination size [-Wstringop-truncation] 312 | strncpy(transformPath, tstr, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/similarity.c:322:13: warning: ‘strncpy’ specified bound 1024 equals destination size [-Wstringop-truncation] 322 | strncpy(mask1Path, tstr, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/similarity.c:329:13: warning: ‘strncpy’ specified bound 1024 equals destination size [-Wstringop-truncation] 329 | strncpy(mask2Path, tstr, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/similarity.c:338:9: warning: ‘format’ may be used uninitialized [-Wmaybe-uninitialized] 338 | switch (format) { | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/similarity.c:270:18: note: ‘format’ was declared here 270 | Vdata_Format format; | ^~~~~~ [ 75%] Linking C executable ../bin/similarity [ 75%] Built target similarity [ 77%] Building C object tools/mesh/CMakeFiles/analysis.dir/analysis.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:14: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: ‘GEOFLOWparm_parseVDW’ declared ‘static’ but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: ‘GEOFLOWparm_parseETOL’ declared ‘static’ but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: ‘PBAMparm_parseSalt’ declared ‘static’ but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: ‘PBAMparm_parseRunType’ declared ‘static’ but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: ‘PBAMparm_parseRunName’ declared ‘static’ but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: ‘PBAMparm_parseRandorient’ declared ‘static’ but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: ‘PBAMparm_parsePBCS’ declared ‘static’ but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: ‘PBAMparm_parseUnits’ declared ‘static’ but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: ‘PBAMparm_parse3Dmap’ declared ‘static’ but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: ‘PBAMparm_parseGrid2D’ declared ‘static’ but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: ‘PBAMparm_parseDX’ declared ‘static’ but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: ‘PBAMparm_parseGridPts’ declared ‘static’ but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: ‘PBAMparm_parseTermcombine’ declared ‘static’ but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: ‘PBAMparm_parseDiff’ declared ‘static’ but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: ‘PBAMparm_parseXYZ’ declared ‘static’ but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: ‘PBSAMparm_parseTolsp’ declared ‘static’ but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: ‘PBSAMparm_parseSurf’ declared ‘static’ but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: ‘PBSAMparm_parseImat’ declared ‘static’ but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: ‘PBSAMparm_parseExp’ declared ‘static’ but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: ‘PBSAMparm_parseMSMS’ declared ‘static’ but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: ‘bcolcomp’ declared ‘static’ but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: ‘bcolcomp2’ declared ‘static’ but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: ‘bcolcomp3’ declared ‘static’ but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: ‘bcolcomp4’ declared ‘static’ but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: ‘pcolcomp’ declared ‘static’ but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: ‘bspline2’ declared ‘static’ but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: ‘dbspline2’ declared ‘static’ but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: ‘VFCHI4’ declared ‘static’ but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: ‘bspline4’ declared ‘static’ but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: ‘dbspline4’ declared ‘static’ but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: ‘d2bspline4’ declared ‘static’ but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: ‘d3bspline4’ declared ‘static’ but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: ‘Vpmg_polarizEnergy’ declared ‘static’ but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: ‘Vpmg_qfEnergyPoint’ declared ‘static’ but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: ‘Vpmg_qfEnergyVolume’ declared ‘static’ but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: ‘Vpmg_splineSelect’ declared ‘static’ but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: ‘focusFillBound’ declared ‘static’ but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: ‘bcfl1’ declared ‘static’ but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: ‘bcfl2’ declared ‘static’ but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: ‘multipolebc’ declared ‘static’ but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: ‘bcfl1sp’ declared ‘static’ but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: ‘bcCalc’ declared ‘static’ but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: ‘fillcoCoef’ declared ‘static’ but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: ‘fillcoCoefMap’ declared ‘static’ but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: ‘fillcoCoefMol’ declared ‘static’ but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: ‘fillcoCoefMolIon’ declared ‘static’ but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: ‘fillcoCoefMolDiel’ declared ‘static’ but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: ‘fillcoCoefMolDielNoSmooth’ declared ‘static’ but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: ‘fillcoCoefMolDielSmooth’ declared ‘static’ but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: ‘fillcoCoefSpline’ declared ‘static’ but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: ‘fillcoCoefSpline3’ declared ‘static’ but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: ‘fillcoCoefSpline4’ declared ‘static’ but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: ‘fillcoCharge’ declared ‘static’ but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: ‘fillcoChargeMap’ declared ‘static’ but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: ‘fillcoChargeSpline1’ declared ‘static’ but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: ‘fillcoChargeSpline2’ declared ‘static’ but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: ‘fillcoPermanentMultipole’ declared ‘static’ but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: ‘fillcoInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: ‘fillcoNLInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: ‘extEnergy’ declared ‘static’ but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: ‘qfForceSpline1’ declared ‘static’ but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: ‘qfForceSpline2’ declared ‘static’ but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: ‘qfForceSpline4’ declared ‘static’ but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: ‘zlapSolve’ declared ‘static’ but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: ‘markSphere’ declared ‘static’ but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: ‘Vpmg_qmEnergySMPBE’ declared ‘static’ but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: ‘Vpmg_qmEnergyNONLIN’ declared ‘static’ but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c: In function ‘main’: /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:123:13: warning: ‘strncpy’ specified bound 1024 equals destination size [-Wstringop-truncation] 123 | strncpy(scalarPath, tstr, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:133:13: warning: ‘strncpy’ specified bound 1024 equals destination size [-Wstringop-truncation] 133 | strncpy(maskPath, tstr, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:142:9: warning: ‘format’ may be used uninitialized [-Wmaybe-uninitialized] 142 | switch (format) { | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:95:18: note: ‘format’ was declared here 95 | Vdata_Format format; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:286:5: warning: ‘maxG2’ may be used uninitialized [-Wmaybe-uninitialized] 286 | Vnm_print(1, "Max gradient-squared value = %1.12E\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 287 | maxG2); | ~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:85:29: note: ‘maxG2’ was declared here 85 | double maxS, maxSpt[3], maxG2, maxG2pt[3]; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:290:5: warning: ‘minG2’ may be used uninitialized [-Wmaybe-uninitialized] 290 | Vnm_print(1, "Min gradient-squared value = %1.12E\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 291 | minG2); | ~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:86:29: note: ‘minG2’ was declared here 86 | double minS, minSpt[3], minG2, minG2pt[3]; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:280:5: warning: ‘maxSpt[1]’ may be used uninitialized [-Wmaybe-uninitialized] 280 | Vnm_print(1, "Max scalar value location = (%4.3f, %4.3f, %4.3f)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 281 | maxSpt[0], maxSpt[1], maxSpt[2]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:85:18: note: ‘maxSpt[1]’ was declared here 85 | double maxS, maxSpt[3], maxG2, maxG2pt[3]; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:280:5: warning: ‘maxSpt[2]’ may be used uninitialized [-Wmaybe-uninitialized] 280 | Vnm_print(1, "Max scalar value location = (%4.3f, %4.3f, %4.3f)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 281 | maxSpt[0], maxSpt[1], maxSpt[2]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:85:18: note: ‘maxSpt[2]’ was declared here 85 | double maxS, maxSpt[3], maxG2, maxG2pt[3]; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:288:5: warning: ‘maxG2pt[0]’ may be used uninitialized [-Wmaybe-uninitialized] 288 | Vnm_print(1, "Max gradient-squared value location = (%4.3f, %4.3f, %4.3f)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 289 | maxG2pt[0], maxG2pt[1], maxG2pt[2]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:85:36: note: ‘maxG2pt[0]’ was declared here 85 | double maxS, maxSpt[3], maxG2, maxG2pt[3]; | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:288:5: warning: ‘maxG2pt[1]’ may be used uninitialized [-Wmaybe-uninitialized] 288 | Vnm_print(1, "Max gradient-squared value location = (%4.3f, %4.3f, %4.3f)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 289 | maxG2pt[0], maxG2pt[1], maxG2pt[2]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:85:36: note: ‘maxG2pt[1]’ was declared here 85 | double maxS, maxSpt[3], maxG2, maxG2pt[3]; | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:280:5: warning: ‘maxSpt[0]’ may be used uninitialized [-Wmaybe-uninitialized] 280 | Vnm_print(1, "Max scalar value location = (%4.3f, %4.3f, %4.3f)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 281 | maxSpt[0], maxSpt[1], maxSpt[2]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:85:18: note: ‘maxSpt[0]’ was declared here 85 | double maxS, maxSpt[3], maxG2, maxG2pt[3]; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:288:5: warning: ‘maxG2pt[2]’ may be used uninitialized [-Wmaybe-uninitialized] 288 | Vnm_print(1, "Max gradient-squared value location = (%4.3f, %4.3f, %4.3f)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 289 | maxG2pt[0], maxG2pt[1], maxG2pt[2]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:85:36: note: ‘maxG2pt[2]’ was declared here 85 | double maxS, maxSpt[3], maxG2, maxG2pt[3]; | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:284:5: warning: ‘minSpt[0]’ may be used uninitialized [-Wmaybe-uninitialized] 284 | Vnm_print(1, "Min scalar value location = (%4.3f, %4.3f, %4.3f)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 285 | minSpt[0], minSpt[1], minSpt[2]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:86:18: note: ‘minSpt[0]’ was declared here 86 | double minS, minSpt[3], minG2, minG2pt[3]; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:284:5: warning: ‘minSpt[1]’ may be used uninitialized [-Wmaybe-uninitialized] 284 | Vnm_print(1, "Min scalar value location = (%4.3f, %4.3f, %4.3f)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 285 | minSpt[0], minSpt[1], minSpt[2]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:86:18: note: ‘minSpt[1]’ was declared here 86 | double minS, minSpt[3], minG2, minG2pt[3]; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:284:5: warning: ‘minSpt[2]’ may be used uninitialized [-Wmaybe-uninitialized] 284 | Vnm_print(1, "Min scalar value location = (%4.3f, %4.3f, %4.3f)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 285 | minSpt[0], minSpt[1], minSpt[2]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:86:18: note: ‘minSpt[2]’ was declared here 86 | double minS, minSpt[3], minG2, minG2pt[3]; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:292:5: warning: ‘minG2pt[0]’ may be used uninitialized [-Wmaybe-uninitialized] 292 | Vnm_print(1, "Min gradient-squared value location = (%4.3f, %4.3f, %4.3f)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 293 | minG2pt[0], minG2pt[1], minG2pt[2]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:86:36: note: ‘minG2pt[0]’ was declared here 86 | double minS, minSpt[3], minG2, minG2pt[3]; | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:292:5: warning: ‘minG2pt[1]’ may be used uninitialized [-Wmaybe-uninitialized] 292 | Vnm_print(1, "Min gradient-squared value location = (%4.3f, %4.3f, %4.3f)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 293 | minG2pt[0], minG2pt[1], minG2pt[2]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:86:36: note: ‘minG2pt[1]’ was declared here 86 | double minS, minSpt[3], minG2, minG2pt[3]; | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:292:5: warning: ‘minG2pt[2]’ may be used uninitialized [-Wmaybe-uninitialized] 292 | Vnm_print(1, "Min gradient-squared value location = (%4.3f, %4.3f, %4.3f)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 293 | minG2pt[0], minG2pt[1], minG2pt[2]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:86:36: note: ‘minG2pt[2]’ was declared here 86 | double minS, minSpt[3], minG2, minG2pt[3]; | ^~~~~~~ [ 78%] Linking C executable ../bin/analysis [ 78%] Built target analysis [ 79%] Building C object tools/mesh/CMakeFiles/dx2mol.dir/dx2mol.c.o /builddir/build/BUILD/apbs-3.0.0/tools/mesh/dx2mol.c: In function ‘main’: /builddir/build/BUILD/apbs-3.0.0/tools/mesh/dx2mol.c:28:12: warning: unused variable ‘avg’ [-Wunused-variable] 28 | double avg; | ^~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/dx2mol.c:19: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h: At top level: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: ‘GEOFLOWparm_parseVDW’ declared ‘static’ but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: ‘GEOFLOWparm_parseETOL’ declared ‘static’ but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: ‘PBAMparm_parseSalt’ declared ‘static’ but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: ‘PBAMparm_parseRunType’ declared ‘static’ but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: ‘PBAMparm_parseRunName’ declared ‘static’ but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: ‘PBAMparm_parseRandorient’ declared ‘static’ but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: ‘PBAMparm_parsePBCS’ declared ‘static’ but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: ‘PBAMparm_parseUnits’ declared ‘static’ but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: ‘PBAMparm_parse3Dmap’ declared ‘static’ but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: ‘PBAMparm_parseGrid2D’ declared ‘static’ but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: ‘PBAMparm_parseDX’ declared ‘static’ but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: ‘PBAMparm_parseGridPts’ declared ‘static’ but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: ‘PBAMparm_parseTermcombine’ declared ‘static’ but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: ‘PBAMparm_parseDiff’ declared ‘static’ but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: ‘PBAMparm_parseXYZ’ declared ‘static’ but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: ‘PBSAMparm_parseTolsp’ declared ‘static’ but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: ‘PBSAMparm_parseSurf’ declared ‘static’ but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: ‘PBSAMparm_parseImat’ declared ‘static’ but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: ‘PBSAMparm_parseExp’ declared ‘static’ but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: ‘PBSAMparm_parseMSMS’ declared ‘static’ but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: ‘bcolcomp’ declared ‘static’ but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: ‘bcolcomp2’ declared ‘static’ but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: ‘bcolcomp3’ declared ‘static’ but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: ‘bcolcomp4’ declared ‘static’ but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: ‘pcolcomp’ declared ‘static’ but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: ‘bspline2’ declared ‘static’ but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: ‘dbspline2’ declared ‘static’ but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: ‘VFCHI4’ declared ‘static’ but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: ‘bspline4’ declared ‘static’ but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: ‘dbspline4’ declared ‘static’ but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: ‘d2bspline4’ declared ‘static’ but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: ‘d3bspline4’ declared ‘static’ but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: ‘Vpmg_polarizEnergy’ declared ‘static’ but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: ‘Vpmg_qfEnergyPoint’ declared ‘static’ but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: ‘Vpmg_qfEnergyVolume’ declared ‘static’ but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: ‘Vpmg_splineSelect’ declared ‘static’ but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: ‘focusFillBound’ declared ‘static’ but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: ‘bcfl1’ declared ‘static’ but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: ‘bcfl2’ declared ‘static’ but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: ‘multipolebc’ declared ‘static’ but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: ‘bcfl1sp’ declared ‘static’ but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: ‘bcCalc’ declared ‘static’ but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: ‘fillcoCoef’ declared ‘static’ but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: ‘fillcoCoefMap’ declared ‘static’ but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: ‘fillcoCoefMol’ declared ‘static’ but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: ‘fillcoCoefMolIon’ declared ‘static’ but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: ‘fillcoCoefMolDiel’ declared ‘static’ but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: ‘fillcoCoefMolDielNoSmooth’ declared ‘static’ but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: ‘fillcoCoefMolDielSmooth’ declared ‘static’ but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: ‘fillcoCoefSpline’ declared ‘static’ but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: ‘fillcoCoefSpline3’ declared ‘static’ but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: ‘fillcoCoefSpline4’ declared ‘static’ but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: ‘fillcoCharge’ declared ‘static’ but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: ‘fillcoChargeMap’ declared ‘static’ but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: ‘fillcoChargeSpline1’ declared ‘static’ but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: ‘fillcoChargeSpline2’ declared ‘static’ but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: ‘fillcoPermanentMultipole’ declared ‘static’ but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: ‘fillcoInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: ‘fillcoNLInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: ‘extEnergy’ declared ‘static’ but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: ‘qfForceSpline1’ declared ‘static’ but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: ‘qfForceSpline2’ declared ‘static’ but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: ‘qfForceSpline4’ declared ‘static’ but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: ‘zlapSolve’ declared ‘static’ but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: ‘markSphere’ declared ‘static’ but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: ‘Vpmg_qmEnergySMPBE’ declared ‘static’ but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: ‘Vpmg_qmEnergyNONLIN’ declared ‘static’ but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ [ 80%] Linking C executable ../bin/dx2mol [ 80%] Built target dx2mol [ 81%] Building C object tools/mesh/CMakeFiles/dx2uhbd.dir/dx2uhbd.c.o /builddir/build/BUILD/apbs-3.0.0/tools/mesh/dx2uhbd.c: In function ‘main’: /builddir/build/BUILD/apbs-3.0.0/tools/mesh/dx2uhbd.c:25:10: warning: unused variable ‘avg’ [-Wunused-variable] 25 | double avg; | ^~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/dx2uhbd.c:24:19: warning: unused variable ‘k’ [-Wunused-variable] 24 | size_t u, i, j, k, nx, ny, nz; | ^ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/dx2uhbd.c:24:16: warning: unused variable ‘j’ [-Wunused-variable] 24 | size_t u, i, j, k, nx, ny, nz; | ^ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/dx2uhbd.c:24:13: warning: unused variable ‘i’ [-Wunused-variable] 24 | size_t u, i, j, k, nx, ny, nz; | ^ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/dx2uhbd.c:24:10: warning: unused variable ‘u’ [-Wunused-variable] 24 | size_t u, i, j, k, nx, ny, nz; | ^ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/dx2uhbd.c:17: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h: At top level: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: ‘GEOFLOWparm_parseVDW’ declared ‘static’ but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: ‘GEOFLOWparm_parseETOL’ declared ‘static’ but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: ‘PBAMparm_parseSalt’ declared ‘static’ but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: ‘PBAMparm_parseRunType’ declared ‘static’ but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: ‘PBAMparm_parseRunName’ declared ‘static’ but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: ‘PBAMparm_parseRandorient’ declared ‘static’ but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: ‘PBAMparm_parsePBCS’ declared ‘static’ but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: ‘PBAMparm_parseUnits’ declared ‘static’ but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: ‘PBAMparm_parse3Dmap’ declared ‘static’ but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: ‘PBAMparm_parseGrid2D’ declared ‘static’ but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: ‘PBAMparm_parseDX’ declared ‘static’ but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: ‘PBAMparm_parseGridPts’ declared ‘static’ but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: ‘PBAMparm_parseTermcombine’ declared ‘static’ but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: ‘PBAMparm_parseDiff’ declared ‘static’ but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: ‘PBAMparm_parseXYZ’ declared ‘static’ but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: ‘PBSAMparm_parseTolsp’ declared ‘static’ but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: ‘PBSAMparm_parseSurf’ declared ‘static’ but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: ‘PBSAMparm_parseImat’ declared ‘static’ but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: ‘PBSAMparm_parseExp’ declared ‘static’ but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: ‘PBSAMparm_parseMSMS’ declared ‘static’ but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: ‘bcolcomp’ declared ‘static’ but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: ‘bcolcomp2’ declared ‘static’ but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: ‘bcolcomp3’ declared ‘static’ but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: ‘bcolcomp4’ declared ‘static’ but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: ‘pcolcomp’ declared ‘static’ but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: ‘bspline2’ declared ‘static’ but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: ‘dbspline2’ declared ‘static’ but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: ‘VFCHI4’ declared ‘static’ but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: ‘bspline4’ declared ‘static’ but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: ‘dbspline4’ declared ‘static’ but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: ‘d2bspline4’ declared ‘static’ but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: ‘d3bspline4’ declared ‘static’ but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: ‘Vpmg_polarizEnergy’ declared ‘static’ but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: ‘Vpmg_qfEnergyPoint’ declared ‘static’ but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: ‘Vpmg_qfEnergyVolume’ declared ‘static’ but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: ‘Vpmg_splineSelect’ declared ‘static’ but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: ‘focusFillBound’ declared ‘static’ but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: ‘bcfl1’ declared ‘static’ but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: ‘bcfl2’ declared ‘static’ but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: ‘multipolebc’ declared ‘static’ but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: ‘bcfl1sp’ declared ‘static’ but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: ‘bcCalc’ declared ‘static’ but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: ‘fillcoCoef’ declared ‘static’ but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: ‘fillcoCoefMap’ declared ‘static’ but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: ‘fillcoCoefMol’ declared ‘static’ but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: ‘fillcoCoefMolIon’ declared ‘static’ but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: ‘fillcoCoefMolDiel’ declared ‘static’ but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: ‘fillcoCoefMolDielNoSmooth’ declared ‘static’ but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: ‘fillcoCoefMolDielSmooth’ declared ‘static’ but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: ‘fillcoCoefSpline’ declared ‘static’ but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: ‘fillcoCoefSpline3’ declared ‘static’ but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: ‘fillcoCoefSpline4’ declared ‘static’ but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: ‘fillcoCharge’ declared ‘static’ but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: ‘fillcoChargeMap’ declared ‘static’ but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: ‘fillcoChargeSpline1’ declared ‘static’ but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: ‘fillcoChargeSpline2’ declared ‘static’ but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: ‘fillcoPermanentMultipole’ declared ‘static’ but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: ‘fillcoInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: ‘fillcoNLInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: ‘extEnergy’ declared ‘static’ but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: ‘qfForceSpline1’ declared ‘static’ but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: ‘qfForceSpline2’ declared ‘static’ but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: ‘qfForceSpline4’ declared ‘static’ but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: ‘zlapSolve’ declared ‘static’ but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: ‘markSphere’ declared ‘static’ but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: ‘Vpmg_qmEnergySMPBE’ declared ‘static’ but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: ‘Vpmg_qmEnergyNONLIN’ declared ‘static’ but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ [ 82%] Linking C executable ../bin/dx2uhbd [ 82%] Built target dx2uhbd [ 83%] Building C object tools/mesh/CMakeFiles/del2dx.dir/del2dx.c.o /builddir/build/BUILD/apbs-3.0.0/tools/mesh/del2dx.c: In function ‘main’: /builddir/build/BUILD/apbs-3.0.0/tools/mesh/del2dx.c:45:64: warning: variable ‘extent’ set but not used [-Wunused-but-set-variable] 45 | float val, xmax, scale, oldmid[3], temp, xdata, range, extent, origin[3], delta[3]; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/del2dx.c:45:50: warning: unused variable ‘xdata’ [-Wunused-variable] 45 | float val, xmax, scale, oldmid[3], temp, xdata, range, extent, origin[3], delta[3]; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/del2dx.c:45:15: warning: unused variable ‘val’ [-Wunused-variable] 45 | float val, xmax, scale, oldmid[3], temp, xdata, range, extent, origin[3], delta[3]; | ^~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/del2dx.c:16: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h: At top level: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: ‘GEOFLOWparm_parseVDW’ declared ‘static’ but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: ‘GEOFLOWparm_parseETOL’ declared ‘static’ but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: ‘PBAMparm_parseSalt’ declared ‘static’ but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: ‘PBAMparm_parseRunType’ declared ‘static’ but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: ‘PBAMparm_parseRunName’ declared ‘static’ but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: ‘PBAMparm_parseRandorient’ declared ‘static’ but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: ‘PBAMparm_parsePBCS’ declared ‘static’ but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: ‘PBAMparm_parseUnits’ declared ‘static’ but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: ‘PBAMparm_parse3Dmap’ declared ‘static’ but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: ‘PBAMparm_parseGrid2D’ declared ‘static’ but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: ‘PBAMparm_parseDX’ declared ‘static’ but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: ‘PBAMparm_parseGridPts’ declared ‘static’ but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: ‘PBAMparm_parseTermcombine’ declared ‘static’ but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: ‘PBAMparm_parseDiff’ declared ‘static’ but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: ‘PBAMparm_parseXYZ’ declared ‘static’ but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: ‘PBSAMparm_parseTolsp’ declared ‘static’ but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: ‘PBSAMparm_parseSurf’ declared ‘static’ but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: ‘PBSAMparm_parseImat’ declared ‘static’ but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: ‘PBSAMparm_parseExp’ declared ‘static’ but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: ‘PBSAMparm_parseMSMS’ declared ‘static’ but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: ‘bcolcomp’ declared ‘static’ but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: ‘bcolcomp2’ declared ‘static’ but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: ‘bcolcomp3’ declared ‘static’ but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: ‘bcolcomp4’ declared ‘static’ but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: ‘pcolcomp’ declared ‘static’ but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: ‘bspline2’ declared ‘static’ but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: ‘dbspline2’ declared ‘static’ but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: ‘VFCHI4’ declared ‘static’ but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: ‘bspline4’ declared ‘static’ but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: ‘dbspline4’ declared ‘static’ but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: ‘d2bspline4’ declared ‘static’ but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: ‘d3bspline4’ declared ‘static’ but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: ‘Vpmg_polarizEnergy’ declared ‘static’ but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: ‘Vpmg_qfEnergyPoint’ declared ‘static’ but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: ‘Vpmg_qfEnergyVolume’ declared ‘static’ but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: ‘Vpmg_splineSelect’ declared ‘static’ but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: ‘focusFillBound’ declared ‘static’ but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: ‘bcfl1’ declared ‘static’ but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: ‘bcfl2’ declared ‘static’ but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: ‘multipolebc’ declared ‘static’ but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: ‘bcfl1sp’ declared ‘static’ but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: ‘bcCalc’ declared ‘static’ but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: ‘fillcoCoef’ declared ‘static’ but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: ‘fillcoCoefMap’ declared ‘static’ but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: ‘fillcoCoefMol’ declared ‘static’ but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: ‘fillcoCoefMolIon’ declared ‘static’ but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: ‘fillcoCoefMolDiel’ declared ‘static’ but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: ‘fillcoCoefMolDielNoSmooth’ declared ‘static’ but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: ‘fillcoCoefMolDielSmooth’ declared ‘static’ but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: ‘fillcoCoefSpline’ declared ‘static’ but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: ‘fillcoCoefSpline3’ declared ‘static’ but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: ‘fillcoCoefSpline4’ declared ‘static’ but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: ‘fillcoCharge’ declared ‘static’ but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: ‘fillcoChargeMap’ declared ‘static’ but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: ‘fillcoChargeSpline1’ declared ‘static’ but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: ‘fillcoChargeSpline2’ declared ‘static’ but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: ‘fillcoPermanentMultipole’ declared ‘static’ but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: ‘fillcoInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: ‘fillcoNLInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: ‘extEnergy’ declared ‘static’ but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: ‘qfForceSpline1’ declared ‘static’ but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: ‘qfForceSpline2’ declared ‘static’ but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: ‘qfForceSpline4’ declared ‘static’ but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: ‘zlapSolve’ declared ‘static’ but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: ‘markSphere’ declared ‘static’ but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: ‘Vpmg_qmEnergySMPBE’ declared ‘static’ but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: ‘Vpmg_qmEnergyNONLIN’ declared ‘static’ but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/del2dx.c: In function ‘main’: /builddir/build/BUILD/apbs-3.0.0/tools/mesh/del2dx.c:76:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 76 | fread(&igrid, 1, sizeof(int), pfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/del2dx.c:89:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 89 | fread(buffer, 1, sizeof(char) * 10, pfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/del2dx.c:97:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 97 | fread(data, tot_grid, sizeof(float), pfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/del2dx.c:103:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 103 | fread(&scale, 1, sizeof(float), pfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/del2dx.c:106:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 106 | fread(oldmid, 3, sizeof(float), pfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 85%] Linking C executable ../bin/del2dx [ 85%] Built target del2dx [ 86%] Building C object tools/mesh/CMakeFiles/tensor2dx.dir/tensor2dx.c.o /builddir/build/BUILD/apbs-3.0.0/tools/mesh/tensor2dx.c: In function ‘main’: /builddir/build/BUILD/apbs-3.0.0/tools/mesh/tensor2dx.c:42:19: warning: unused variable ‘index’ [-Wunused-variable] 42 | int i,j,k,index,icol; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/tensor2dx.c:42:17: warning: unused variable ‘k’ [-Wunused-variable] 42 | int i,j,k,index,icol; | ^ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/tensor2dx.c:42:15: warning: unused variable ‘j’ [-Wunused-variable] 42 | int i,j,k,index,icol; | ^ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/tensor2dx.c:14: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h: At top level: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: ‘GEOFLOWparm_parseVDW’ declared ‘static’ but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: ‘GEOFLOWparm_parseETOL’ declared ‘static’ but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: ‘PBAMparm_parseSalt’ declared ‘static’ but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: ‘PBAMparm_parseRunType’ declared ‘static’ but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: ‘PBAMparm_parseRunName’ declared ‘static’ but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: ‘PBAMparm_parseRandorient’ declared ‘static’ but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: ‘PBAMparm_parsePBCS’ declared ‘static’ but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: ‘PBAMparm_parseUnits’ declared ‘static’ but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: ‘PBAMparm_parse3Dmap’ declared ‘static’ but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: ‘PBAMparm_parseGrid2D’ declared ‘static’ but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: ‘PBAMparm_parseDX’ declared ‘static’ but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: ‘PBAMparm_parseGridPts’ declared ‘static’ but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: ‘PBAMparm_parseTermcombine’ declared ‘static’ but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: ‘PBAMparm_parseDiff’ declared ‘static’ but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: ‘PBAMparm_parseXYZ’ declared ‘static’ but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: ‘PBSAMparm_parseTolsp’ declared ‘static’ but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: ‘PBSAMparm_parseSurf’ declared ‘static’ but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: ‘PBSAMparm_parseImat’ declared ‘static’ but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: ‘PBSAMparm_parseExp’ declared ‘static’ but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: ‘PBSAMparm_parseMSMS’ declared ‘static’ but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: ‘bcolcomp’ declared ‘static’ but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: ‘bcolcomp2’ declared ‘static’ but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: ‘bcolcomp3’ declared ‘static’ but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: ‘bcolcomp4’ declared ‘static’ but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: ‘pcolcomp’ declared ‘static’ but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: ‘bspline2’ declared ‘static’ but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: ‘dbspline2’ declared ‘static’ but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: ‘VFCHI4’ declared ‘static’ but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: ‘bspline4’ declared ‘static’ but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: ‘dbspline4’ declared ‘static’ but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: ‘d2bspline4’ declared ‘static’ but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: ‘d3bspline4’ declared ‘static’ but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: ‘Vpmg_polarizEnergy’ declared ‘static’ but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: ‘Vpmg_qfEnergyPoint’ declared ‘static’ but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: ‘Vpmg_qfEnergyVolume’ declared ‘static’ but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: ‘Vpmg_splineSelect’ declared ‘static’ but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: ‘focusFillBound’ declared ‘static’ but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: ‘bcfl1’ declared ‘static’ but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: ‘bcfl2’ declared ‘static’ but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: ‘multipolebc’ declared ‘static’ but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: ‘bcfl1sp’ declared ‘static’ but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: ‘bcCalc’ declared ‘static’ but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: ‘fillcoCoef’ declared ‘static’ but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: ‘fillcoCoefMap’ declared ‘static’ but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: ‘fillcoCoefMol’ declared ‘static’ but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: ‘fillcoCoefMolIon’ declared ‘static’ but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: ‘fillcoCoefMolDiel’ declared ‘static’ but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: ‘fillcoCoefMolDielNoSmooth’ declared ‘static’ but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: ‘fillcoCoefMolDielSmooth’ declared ‘static’ but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: ‘fillcoCoefSpline’ declared ‘static’ but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: ‘fillcoCoefSpline3’ declared ‘static’ but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: ‘fillcoCoefSpline4’ declared ‘static’ but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: ‘fillcoCharge’ declared ‘static’ but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: ‘fillcoChargeMap’ declared ‘static’ but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: ‘fillcoChargeSpline1’ declared ‘static’ but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: ‘fillcoChargeSpline2’ declared ‘static’ but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: ‘fillcoPermanentMultipole’ declared ‘static’ but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: ‘fillcoInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: ‘fillcoNLInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: ‘extEnergy’ declared ‘static’ but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: ‘qfForceSpline1’ declared ‘static’ but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: ‘qfForceSpline2’ declared ‘static’ but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: ‘qfForceSpline4’ declared ‘static’ but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: ‘zlapSolve’ declared ‘static’ but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: ‘markSphere’ declared ‘static’ but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: ‘Vpmg_qmEnergySMPBE’ declared ‘static’ but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: ‘Vpmg_qmEnergyNONLIN’ declared ‘static’ but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/tensor2dx.c: In function ‘main’: /builddir/build/BUILD/apbs-3.0.0/tools/mesh/tensor2dx.c:97:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 97 | fscanf(pfile1,"%lf %lf %lf",&origin_xyz[0],&origin_xyz[1],&origin_xyz[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/tensor2dx.c:98:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 98 | fscanf(pfile1,"%lf %lf %lf",&gspace[0],&gspace[1],&gspace[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/tensor2dx.c:137:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 137 | fscanf(pfile2,"%i %i %i",&itmp[0],&itmp[1],&itmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/tensor2dx.c:138:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 138 | fscanf(pfile2,"%lf %lf %lf",&datapt[0],&tmp[1],&tmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/tensor2dx.c:139:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 139 | fscanf(pfile2,"%lf %lf %lf",&tmp[0],&datapt[1],&tmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/tensor2dx.c:140:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 140 | fscanf(pfile2,"%lf %lf %lf",&tmp[0],&tmp[1],&datapt[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/tensor2dx.c:155:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 155 | fscanf(pfile2,"%i %i %i",&itmp[0],&itmp[1],&itmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/tensor2dx.c:156:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 156 | fscanf(pfile2,"%lf %lf %lf",&datapt[0],&tmp[1],&tmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/tensor2dx.c:157:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 157 | fscanf(pfile2,"%lf %lf %lf",&tmp[0],&datapt[1],&tmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/tensor2dx.c:158:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 158 | fscanf(pfile2,"%lf %lf %lf",&tmp[0],&tmp[1],&datapt[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 87%] Linking C executable ../bin/tensor2dx [ 87%] Built target tensor2dx [ 88%] Building C object tools/mesh/CMakeFiles/uhbd_asc2bin.dir/uhbd_asc2bin.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:93, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:3: /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c: In function ‘main’: /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_grid’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:24:5: note: in expansion of macro ‘MAT3’ 24 | MAT3(grid, MXGRD, MXGRD, MXGRD); | ^~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h: At top level: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: ‘GEOFLOWparm_parseVDW’ declared ‘static’ but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: ‘GEOFLOWparm_parseETOL’ declared ‘static’ but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: ‘PBAMparm_parseSalt’ declared ‘static’ but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: ‘PBAMparm_parseRunType’ declared ‘static’ but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: ‘PBAMparm_parseRunName’ declared ‘static’ but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: ‘PBAMparm_parseRandorient’ declared ‘static’ but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: ‘PBAMparm_parsePBCS’ declared ‘static’ but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: ‘PBAMparm_parseUnits’ declared ‘static’ but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: ‘PBAMparm_parse3Dmap’ declared ‘static’ but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: ‘PBAMparm_parseGrid2D’ declared ‘static’ but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: ‘PBAMparm_parseDX’ declared ‘static’ but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: ‘PBAMparm_parseGridPts’ declared ‘static’ but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: ‘PBAMparm_parseTermcombine’ declared ‘static’ but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: ‘PBAMparm_parseDiff’ declared ‘static’ but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: ‘PBAMparm_parseXYZ’ declared ‘static’ but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: ‘PBSAMparm_parseTolsp’ declared ‘static’ but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: ‘PBSAMparm_parseSurf’ declared ‘static’ but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: ‘PBSAMparm_parseImat’ declared ‘static’ but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: ‘PBSAMparm_parseExp’ declared ‘static’ but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: ‘PBSAMparm_parseMSMS’ declared ‘static’ but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: ‘bcolcomp’ declared ‘static’ but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: ‘bcolcomp2’ declared ‘static’ but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: ‘bcolcomp3’ declared ‘static’ but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: ‘bcolcomp4’ declared ‘static’ but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: ‘pcolcomp’ declared ‘static’ but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: ‘bspline2’ declared ‘static’ but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: ‘dbspline2’ declared ‘static’ but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: ‘VFCHI4’ declared ‘static’ but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: ‘bspline4’ declared ‘static’ but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: ‘dbspline4’ declared ‘static’ but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: ‘d2bspline4’ declared ‘static’ but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: ‘d3bspline4’ declared ‘static’ but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: ‘Vpmg_polarizEnergy’ declared ‘static’ but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: ‘Vpmg_qfEnergyPoint’ declared ‘static’ but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: ‘Vpmg_qfEnergyVolume’ declared ‘static’ but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: ‘Vpmg_splineSelect’ declared ‘static’ but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: ‘focusFillBound’ declared ‘static’ but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: ‘bcfl1’ declared ‘static’ but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: ‘bcfl2’ declared ‘static’ but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: ‘multipolebc’ declared ‘static’ but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: ‘bcfl1sp’ declared ‘static’ but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: ‘bcCalc’ declared ‘static’ but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: ‘fillcoCoef’ declared ‘static’ but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: ‘fillcoCoefMap’ declared ‘static’ but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: ‘fillcoCoefMol’ declared ‘static’ but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: ‘fillcoCoefMolIon’ declared ‘static’ but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: ‘fillcoCoefMolDiel’ declared ‘static’ but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: ‘fillcoCoefMolDielNoSmooth’ declared ‘static’ but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: ‘fillcoCoefMolDielSmooth’ declared ‘static’ but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: ‘fillcoCoefSpline’ declared ‘static’ but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: ‘fillcoCoefSpline3’ declared ‘static’ but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: ‘fillcoCoefSpline4’ declared ‘static’ but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: ‘fillcoCharge’ declared ‘static’ but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: ‘fillcoChargeMap’ declared ‘static’ but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: ‘fillcoChargeSpline1’ declared ‘static’ but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: ‘fillcoChargeSpline2’ declared ‘static’ but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: ‘fillcoPermanentMultipole’ declared ‘static’ but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: ‘fillcoInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: ‘fillcoNLInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: ‘extEnergy’ declared ‘static’ but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: ‘qfForceSpline1’ declared ‘static’ but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: ‘qfForceSpline2’ declared ‘static’ but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: ‘qfForceSpline4’ declared ‘static’ but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: ‘zlapSolve’ declared ‘static’ but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: ‘markSphere’ declared ‘static’ but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: ‘Vpmg_qmEnergySMPBE’ declared ‘static’ but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: ‘Vpmg_qmEnergyNONLIN’ declared ‘static’ but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c: In function ‘main’: /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:30:5: warning: ignoring return value of ‘scanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 30 | scanf("%s", flnm); | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:42:5: warning: ignoring return value of ‘scanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 42 | scanf("%s", newfile); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:54:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 54 | fscanf(inFile, "%s", title); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:57:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 57 | fscanf(inFile, "%lf", &scale); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:60:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | fscanf(inFile, "%lf", &dum2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:63:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 63 | fscanf(inFile, "%d", &grdflg); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:66:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | fscanf(inFile, "%d", &idum2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:69:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 69 | fscanf(inFile, "%d", &km); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:72:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 72 | fscanf(inFile, "%d", &one); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:75:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 75 | fscanf(inFile, "%d", &km); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:78:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 78 | fscanf(inFile, "%d", &im); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:81:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 81 | fscanf(inFile, "%d", &jm); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:84:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 84 | fscanf(inFile, "%d", &km); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:87:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 87 | fscanf(inFile, "%lf", &h); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:90:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 90 | fscanf(inFile, "%lf", &ox); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:93:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 93 | fscanf(inFile, "%lf", &oy); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:96:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 96 | fscanf(inFile, "%lf", &oz); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:99:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 99 | fscanf(inFile, "%lf", &dum3); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:102:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 102 | fscanf(inFile, "%lf", &dum4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:105:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 105 | fscanf(inFile, "%lf", &dum5); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:108:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 108 | fscanf(inFile, "%lf", &dum6); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:111:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 111 | fscanf(inFile, "%lf", &dum7); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:114:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 114 | fscanf(inFile, "%lf", &dum8); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:117:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 117 | fscanf(inFile, "%d", &idum3); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:120:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 120 | fscanf(inFile, "%d", &idum4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:125:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 125 | fscanf(inFile, "%d", &kk); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:128:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 128 | fscanf(inFile, "%d", &im); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:131:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 131 | fscanf(inFile, "%d", &jm); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:138:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 138 | fscanf(inFile, "%lf", RAT3(grid, i, j, k)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 89%] Linking C executable ../bin/uhbd_asc2bin [ 89%] Built target uhbd_asc2bin [ 90%] Building C object tools/manip/CMakeFiles/coulomb.dir/coulomb.c.o /builddir/build/BUILD/apbs-3.0.0/tools/manip/coulomb.c: In function ‘main’: /builddir/build/BUILD/apbs-3.0.0/tools/manip/coulomb.c:20:12: warning: unused variable ‘j’ [-Wunused-variable] 20 | int i, j; | ^ /builddir/build/BUILD/apbs-3.0.0/tools/manip/coulomb.c:18:34: warning: unused variable ‘disp’ [-Wunused-variable] 18 | double *pos, energy, zmagic, disp[3], force[3]; | ^~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/manip/coulomb.c:8: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h: At top level: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: ‘GEOFLOWparm_parseVDW’ declared ‘static’ but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: ‘GEOFLOWparm_parseETOL’ declared ‘static’ but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: ‘PBAMparm_parseSalt’ declared ‘static’ but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: ‘PBAMparm_parseRunType’ declared ‘static’ but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: ‘PBAMparm_parseRunName’ declared ‘static’ but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: ‘PBAMparm_parseRandorient’ declared ‘static’ but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: ‘PBAMparm_parsePBCS’ declared ‘static’ but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: ‘PBAMparm_parseUnits’ declared ‘static’ but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: ‘PBAMparm_parse3Dmap’ declared ‘static’ but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: ‘PBAMparm_parseGrid2D’ declared ‘static’ but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: ‘PBAMparm_parseDX’ declared ‘static’ but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: ‘PBAMparm_parseGridPts’ declared ‘static’ but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: ‘PBAMparm_parseTermcombine’ declared ‘static’ but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: ‘PBAMparm_parseDiff’ declared ‘static’ but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: ‘PBAMparm_parseXYZ’ declared ‘static’ but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: ‘PBSAMparm_parseTolsp’ declared ‘static’ but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: ‘PBSAMparm_parseSurf’ declared ‘static’ but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: ‘PBSAMparm_parseImat’ declared ‘static’ but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: ‘PBSAMparm_parseExp’ declared ‘static’ but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: ‘PBSAMparm_parseMSMS’ declared ‘static’ but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: ‘bcolcomp’ declared ‘static’ but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: ‘bcolcomp2’ declared ‘static’ but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: ‘bcolcomp3’ declared ‘static’ but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: ‘bcolcomp4’ declared ‘static’ but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: ‘pcolcomp’ declared ‘static’ but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: ‘bspline2’ declared ‘static’ but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: ‘dbspline2’ declared ‘static’ but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: ‘VFCHI4’ declared ‘static’ but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: ‘bspline4’ declared ‘static’ but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: ‘dbspline4’ declared ‘static’ but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: ‘d2bspline4’ declared ‘static’ but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: ‘d3bspline4’ declared ‘static’ but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: ‘Vpmg_polarizEnergy’ declared ‘static’ but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: ‘Vpmg_qfEnergyPoint’ declared ‘static’ but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: ‘Vpmg_qfEnergyVolume’ declared ‘static’ but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: ‘Vpmg_splineSelect’ declared ‘static’ but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: ‘focusFillBound’ declared ‘static’ but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: ‘bcfl1’ declared ‘static’ but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: ‘bcfl2’ declared ‘static’ but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: ‘multipolebc’ declared ‘static’ but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: ‘bcfl1sp’ declared ‘static’ but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: ‘bcCalc’ declared ‘static’ but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: ‘fillcoCoef’ declared ‘static’ but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: ‘fillcoCoefMap’ declared ‘static’ but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: ‘fillcoCoefMol’ declared ‘static’ but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: ‘fillcoCoefMolIon’ declared ‘static’ but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: ‘fillcoCoefMolDiel’ declared ‘static’ but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: ‘fillcoCoefMolDielNoSmooth’ declared ‘static’ but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: ‘fillcoCoefMolDielSmooth’ declared ‘static’ but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: ‘fillcoCoefSpline’ declared ‘static’ but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: ‘fillcoCoefSpline3’ declared ‘static’ but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: ‘fillcoCoefSpline4’ declared ‘static’ but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: ‘fillcoCharge’ declared ‘static’ but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: ‘fillcoChargeMap’ declared ‘static’ but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: ‘fillcoChargeSpline1’ declared ‘static’ but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: ‘fillcoChargeSpline2’ declared ‘static’ but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: ‘fillcoPermanentMultipole’ declared ‘static’ but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: ‘fillcoInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: ‘fillcoNLInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: ‘extEnergy’ declared ‘static’ but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: ‘qfForceSpline1’ declared ‘static’ but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: ‘qfForceSpline2’ declared ‘static’ but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: ‘qfForceSpline4’ declared ‘static’ but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: ‘zlapSolve’ declared ‘static’ but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: ‘markSphere’ declared ‘static’ but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: ‘Vpmg_qmEnergySMPBE’ declared ‘static’ but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: ‘Vpmg_qmEnergyNONLIN’ declared ‘static’ but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ [ 91%] Linking C executable ../bin/coulomb [ 91%] Built target coulomb [ 93%] Building C object tools/manip/CMakeFiles/born.dir/born.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/manip/born.c:8: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: ‘GEOFLOWparm_parseVDW’ declared ‘static’ but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: ‘GEOFLOWparm_parseETOL’ declared ‘static’ but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: ‘PBAMparm_parseSalt’ declared ‘static’ but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: ‘PBAMparm_parseRunType’ declared ‘static’ but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: ‘PBAMparm_parseRunName’ declared ‘static’ but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: ‘PBAMparm_parseRandorient’ declared ‘static’ but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: ‘PBAMparm_parsePBCS’ declared ‘static’ but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: ‘PBAMparm_parseUnits’ declared ‘static’ but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: ‘PBAMparm_parse3Dmap’ declared ‘static’ but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: ‘PBAMparm_parseGrid2D’ declared ‘static’ but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: ‘PBAMparm_parseDX’ declared ‘static’ but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: ‘PBAMparm_parseGridPts’ declared ‘static’ but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: ‘PBAMparm_parseTermcombine’ declared ‘static’ but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: ‘PBAMparm_parseDiff’ declared ‘static’ but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: ‘PBAMparm_parseXYZ’ declared ‘static’ but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: ‘PBSAMparm_parseTolsp’ declared ‘static’ but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: ‘PBSAMparm_parseSurf’ declared ‘static’ but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: ‘PBSAMparm_parseImat’ declared ‘static’ but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: ‘PBSAMparm_parseExp’ declared ‘static’ but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: ‘PBSAMparm_parseMSMS’ declared ‘static’ but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: ‘bcolcomp’ declared ‘static’ but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: ‘bcolcomp2’ declared ‘static’ but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: ‘bcolcomp3’ declared ‘static’ but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: ‘bcolcomp4’ declared ‘static’ but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: ‘pcolcomp’ declared ‘static’ but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: ‘bspline2’ declared ‘static’ but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: ‘dbspline2’ declared ‘static’ but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: ‘VFCHI4’ declared ‘static’ but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: ‘bspline4’ declared ‘static’ but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: ‘dbspline4’ declared ‘static’ but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: ‘d2bspline4’ declared ‘static’ but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: ‘d3bspline4’ declared ‘static’ but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: ‘Vpmg_polarizEnergy’ declared ‘static’ but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: ‘Vpmg_qfEnergyPoint’ declared ‘static’ but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: ‘Vpmg_qfEnergyVolume’ declared ‘static’ but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: ‘Vpmg_splineSelect’ declared ‘static’ but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: ‘focusFillBound’ declared ‘static’ but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: ‘bcfl1’ declared ‘static’ but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: ‘bcfl2’ declared ‘static’ but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: ‘multipolebc’ declared ‘static’ but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: ‘bcfl1sp’ declared ‘static’ but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: ‘bcCalc’ declared ‘static’ but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: ‘fillcoCoef’ declared ‘static’ but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: ‘fillcoCoefMap’ declared ‘static’ but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: ‘fillcoCoefMol’ declared ‘static’ but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: ‘fillcoCoefMolIon’ declared ‘static’ but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: ‘fillcoCoefMolDiel’ declared ‘static’ but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: ‘fillcoCoefMolDielNoSmooth’ declared ‘static’ but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: ‘fillcoCoefMolDielSmooth’ declared ‘static’ but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: ‘fillcoCoefSpline’ declared ‘static’ but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: ‘fillcoCoefSpline3’ declared ‘static’ but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: ‘fillcoCoefSpline4’ declared ‘static’ but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: ‘fillcoCharge’ declared ‘static’ but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: ‘fillcoChargeMap’ declared ‘static’ but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: ‘fillcoChargeSpline1’ declared ‘static’ but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: ‘fillcoChargeSpline2’ declared ‘static’ but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: ‘fillcoPermanentMultipole’ declared ‘static’ but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: ‘fillcoInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: ‘fillcoNLInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: ‘extEnergy’ declared ‘static’ but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: ‘qfForceSpline1’ declared ‘static’ but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: ‘qfForceSpline2’ declared ‘static’ but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: ‘qfForceSpline4’ declared ‘static’ but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: ‘zlapSolve’ declared ‘static’ but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: ‘markSphere’ declared ‘static’ but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: ‘Vpmg_qmEnergySMPBE’ declared ‘static’ but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: ‘Vpmg_qmEnergyNONLIN’ declared ‘static’ but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ [ 94%] Linking C executable ../bin/born [ 94%] Built target born [ 95%] Swig compile apbslib.i for python [ 95%] Built target apbslib_swig_compilation [ 96%] Building C object tools/python/CMakeFiles/_apbslib.dir/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c.o /builddir/build/BUILD/apbs-3.0.0/build/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c: In function ‘getPotentials’: /builddir/build/BUILD/apbs-3.0.0/build/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c:3573:12: warning: unused variable ‘rc’ [-Wunused-variable] 3573 | int i, rc, nx, ny, nz; | ^~ /builddir/build/BUILD/apbs-3.0.0/build/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c: In function ‘getForces’: /builddir/build/BUILD/apbs-3.0.0/build/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c:3627:31: warning: unused variable ‘npholder’ [-Wunused-variable] 3627 | PyObject *npvalues, *np, *npholder; | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/build/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c:3627:26: warning: unused variable ‘np’ [-Wunused-variable] 3627 | PyObject *npvalues, *np, *npholder; | ^~ /builddir/build/BUILD/apbs-3.0.0/build/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c:3627:15: warning: unused variable ‘npvalues’ [-Wunused-variable] 3627 | PyObject *npvalues, *np, *npholder; | ^~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/src/routines.h:64, from /builddir/build/BUILD/apbs-3.0.0/build/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c:3036: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h: At top level: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: ‘GEOFLOWparm_parseVDW’ declared ‘static’ but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: ‘GEOFLOWparm_parseETOL’ declared ‘static’ but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: ‘PBAMparm_parseSalt’ declared ‘static’ but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: ‘PBAMparm_parseRunType’ declared ‘static’ but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: ‘PBAMparm_parseRunName’ declared ‘static’ but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: ‘PBAMparm_parseRandorient’ declared ‘static’ but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: ‘PBAMparm_parsePBCS’ declared ‘static’ but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: ‘PBAMparm_parseUnits’ declared ‘static’ but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: ‘PBAMparm_parse3Dmap’ declared ‘static’ but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: ‘PBAMparm_parseGrid2D’ declared ‘static’ but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: ‘PBAMparm_parseDX’ declared ‘static’ but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: ‘PBAMparm_parseGridPts’ declared ‘static’ but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: ‘PBAMparm_parseTermcombine’ declared ‘static’ but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: ‘PBAMparm_parseDiff’ declared ‘static’ but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: ‘PBAMparm_parseXYZ’ declared ‘static’ but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: ‘PBSAMparm_parseTolsp’ declared ‘static’ but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: ‘PBSAMparm_parseSurf’ declared ‘static’ but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: ‘PBSAMparm_parseImat’ declared ‘static’ but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: ‘PBSAMparm_parseExp’ declared ‘static’ but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: ‘PBSAMparm_parseMSMS’ declared ‘static’ but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: ‘bcolcomp’ declared ‘static’ but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: ‘bcolcomp2’ declared ‘static’ but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: ‘bcolcomp3’ declared ‘static’ but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: ‘bcolcomp4’ declared ‘static’ but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: ‘pcolcomp’ declared ‘static’ but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: ‘bspline2’ declared ‘static’ but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: ‘dbspline2’ declared ‘static’ but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: ‘VFCHI4’ declared ‘static’ but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: ‘bspline4’ declared ‘static’ but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: ‘dbspline4’ declared ‘static’ but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: ‘d2bspline4’ declared ‘static’ but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: ‘d3bspline4’ declared ‘static’ but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: ‘Vpmg_polarizEnergy’ declared ‘static’ but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: ‘Vpmg_qfEnergyPoint’ declared ‘static’ but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: ‘Vpmg_qfEnergyVolume’ declared ‘static’ but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: ‘Vpmg_splineSelect’ declared ‘static’ but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: ‘focusFillBound’ declared ‘static’ but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: ‘bcfl1’ declared ‘static’ but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: ‘bcfl2’ declared ‘static’ but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: ‘multipolebc’ declared ‘static’ but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: ‘bcfl1sp’ declared ‘static’ but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: ‘bcCalc’ declared ‘static’ but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: ‘fillcoCoef’ declared ‘static’ but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: ‘fillcoCoefMap’ declared ‘static’ but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: ‘fillcoCoefMol’ declared ‘static’ but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: ‘fillcoCoefMolIon’ declared ‘static’ but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: ‘fillcoCoefMolDiel’ declared ‘static’ but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: ‘fillcoCoefMolDielNoSmooth’ declared ‘static’ but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: ‘fillcoCoefMolDielSmooth’ declared ‘static’ but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: ‘fillcoCoefSpline’ declared ‘static’ but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: ‘fillcoCoefSpline3’ declared ‘static’ but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: ‘fillcoCoefSpline4’ declared ‘static’ but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: ‘fillcoCharge’ declared ‘static’ but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: ‘fillcoChargeMap’ declared ‘static’ but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: ‘fillcoChargeSpline1’ declared ‘static’ but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: ‘fillcoChargeSpline2’ declared ‘static’ but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: ‘fillcoPermanentMultipole’ declared ‘static’ but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: ‘fillcoInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: ‘fillcoNLInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: ‘extEnergy’ declared ‘static’ but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: ‘qfForceSpline1’ declared ‘static’ but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: ‘qfForceSpline2’ declared ‘static’ but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: ‘qfForceSpline4’ declared ‘static’ but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: ‘zlapSolve’ declared ‘static’ but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: ‘markSphere’ declared ‘static’ but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: ‘Vpmg_qmEnergySMPBE’ declared ‘static’ but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: ‘Vpmg_qmEnergyNONLIN’ declared ‘static’ but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ [ 97%] Linking C shared library ../../lib/_apbslib.so [ 97%] Built target _apbslib [ 98%] Building C object contrib/iapbs/src/CMakeFiles/iapbs.dir/apbs_driver.c.o /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:62:21: warning: argument 23 of type ‘double[1]’ with mismatched bound [-Warray-parameter=] 62 | double esenergy[1], | ~~~~~~~^~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:19: /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.h:173:30: note: previously declared as ‘double[20]’ 173 | double esEnergy[NOSH_MAXCALC], | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:63:21: warning: argument 24 of type ‘double[1]’ with mismatched bound [-Warray-parameter=] 63 | double npenergy[1], | ~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.h:174:30: note: previously declared as ‘double[20]’ 174 | double npEnergy[NOSH_MAXCALC], | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c: In function ‘apbsdrv_’: /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:283:5: warning: multi-line comment [-Wcomment] 283 | // Vnm_print(1,"\nError you must provide a parameter file if you\n" \ | ^ /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:115:21: warning: unused variable ‘isolve’ [-Wunused-variable] 115 | int rank, size, isolve, debug, natom; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:103:11: warning: unused variable ‘gm’ [-Wunused-variable] 103 | void *gm[NOSH_MAXMOL]; | ^~ /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:102:11: warning: variable ‘fetk’ set but not used [-Wunused-but-set-variable] 102 | void *fetk[NOSH_MAXCALC]; | ^~~~ /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:90:14: warning: unused variable ‘feparm’ [-Wunused-variable] 90 | FEMparm *feparm = VNULL; | ^~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:11: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h: At top level: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: ‘GEOFLOWparm_parseVDW’ declared ‘static’ but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: ‘GEOFLOWparm_parseETOL’ declared ‘static’ but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: ‘PBAMparm_parseSalt’ declared ‘static’ but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: ‘PBAMparm_parseRunType’ declared ‘static’ but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: ‘PBAMparm_parseRunName’ declared ‘static’ but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: ‘PBAMparm_parseRandorient’ declared ‘static’ but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: ‘PBAMparm_parsePBCS’ declared ‘static’ but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: ‘PBAMparm_parseUnits’ declared ‘static’ but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: ‘PBAMparm_parse3Dmap’ declared ‘static’ but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: ‘PBAMparm_parseGrid2D’ declared ‘static’ but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: ‘PBAMparm_parseDX’ declared ‘static’ but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: ‘PBAMparm_parseGridPts’ declared ‘static’ but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: ‘PBAMparm_parseTermcombine’ declared ‘static’ but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: ‘PBAMparm_parseDiff’ declared ‘static’ but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: ‘PBAMparm_parseXYZ’ declared ‘static’ but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: ‘PBSAMparm_parseTolsp’ declared ‘static’ but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: ‘PBSAMparm_parseSurf’ declared ‘static’ but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: ‘PBSAMparm_parseImat’ declared ‘static’ but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: ‘PBSAMparm_parseExp’ declared ‘static’ but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: ‘PBSAMparm_parseMSMS’ declared ‘static’ but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: ‘bcolcomp’ declared ‘static’ but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: ‘bcolcomp2’ declared ‘static’ but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: ‘bcolcomp3’ declared ‘static’ but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: ‘bcolcomp4’ declared ‘static’ but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: ‘pcolcomp’ declared ‘static’ but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: ‘bspline2’ declared ‘static’ but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: ‘dbspline2’ declared ‘static’ but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: ‘VFCHI4’ declared ‘static’ but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: ‘bspline4’ declared ‘static’ but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: ‘dbspline4’ declared ‘static’ but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: ‘d2bspline4’ declared ‘static’ but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: ‘d3bspline4’ declared ‘static’ but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: ‘Vpmg_polarizEnergy’ declared ‘static’ but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: ‘Vpmg_qfEnergyPoint’ declared ‘static’ but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: ‘Vpmg_qfEnergyVolume’ declared ‘static’ but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: ‘Vpmg_splineSelect’ declared ‘static’ but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: ‘focusFillBound’ declared ‘static’ but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: ‘bcfl1’ declared ‘static’ but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: ‘bcfl2’ declared ‘static’ but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: ‘multipolebc’ declared ‘static’ but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: ‘bcfl1sp’ declared ‘static’ but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: ‘bcCalc’ declared ‘static’ but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: ‘fillcoCoef’ declared ‘static’ but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: ‘fillcoCoefMap’ declared ‘static’ but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: ‘fillcoCoefMol’ declared ‘static’ but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: ‘fillcoCoefMolIon’ declared ‘static’ but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: ‘fillcoCoefMolDiel’ declared ‘static’ but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: ‘fillcoCoefMolDielNoSmooth’ declared ‘static’ but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: ‘fillcoCoefMolDielSmooth’ declared ‘static’ but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: ‘fillcoCoefSpline’ declared ‘static’ but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: ‘fillcoCoefSpline3’ declared ‘static’ but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: ‘fillcoCoefSpline4’ declared ‘static’ but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: ‘fillcoCharge’ declared ‘static’ but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: ‘fillcoChargeMap’ declared ‘static’ but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: ‘fillcoChargeSpline1’ declared ‘static’ but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: ‘fillcoChargeSpline2’ declared ‘static’ but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: ‘fillcoPermanentMultipole’ declared ‘static’ but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: ‘fillcoInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: ‘fillcoNLInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: ‘extEnergy’ declared ‘static’ but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: ‘qfForceSpline1’ declared ‘static’ but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: ‘qfForceSpline2’ declared ‘static’ but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: ‘qfForceSpline4’ declared ‘static’ but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: ‘zlapSolve’ declared ‘static’ but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: ‘markSphere’ declared ‘static’ but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: ‘Vpmg_qmEnergySMPBE’ declared ‘static’ but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: ‘Vpmg_qmEnergyNONLIN’ declared ‘static’ but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c: In function ‘setupString’: /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:943:26: warning: ‘write pot dx iapbs-pot-’ directive writing 23 bytes into a region of size between 1 and 4096 [-Wformat-overflow=] 943 | sprintf(string, "%swrite pot dx iapbs-pot-%d\n", string, getpid()); | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:964, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:67: In function ‘sprintf’, inlined from ‘setupString’ at /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:943:7: /usr/include/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 26 and 4131 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /usr/include/bits/stdio2.h:30:10: warning: ‘__sprintf_chk’ argument 5 overlaps destination object ‘string.1’ [-Wrestrict] /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c: In function ‘setupString’: /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:803:17: note: destination object referenced by ‘restrict’-qualified argument 1 was declared here 803 | static char string[MAX_BUF_SIZE]; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c: In function ‘getElecEnergy’: /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:1060:29: warning: ‘scalar’ may be used uninitialized [-Wmaybe-uninitialized] 1060 | ltenergy += (scalar * Vunit_kb * (1e-3) * Vunit_Na * /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:1043:32: note: ‘scalar’ was declared here 1043 | double ltenergy, gtenergy, scalar; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c: In function ‘apbsdrv_’: /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:554:56: warning: ‘outputformat’ may be used uninitialized [-Wmaybe-uninitialized] 554 | if ((pbeparm->calcenergy == PCE_COMPS) && (outputformat != OUTPUT_NULL)){ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:118:20: note: ‘outputformat’ was declared here 118 | Voutput_Format outputformat; | ^~~~~~~~~~~~ [100%] Linking C static library ../../../lib/libiapbs.a [100%] Built target iapbs make: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.6JFV7u + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64 ++ dirname /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd apbs-3.0.0 + /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64 'INSTALL=/usr/bin/install -p' -C build make: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 5%] Built target apbs_mg [ 26%] Built target apbs_generic [ 47%] Built target apbs_pmgc [ 48%] Built target apbs [ 49%] Built target apbs_routines [ 52%] Built target apbs-bin [ 54%] Generating documentation with Doxygen warning: Tag 'TCL_SUBST' at line 213 of file '/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'COLS_IN_ALPHA_INDEX' at line 857 of file '/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'HTML_TIMESTAMP' at line 953 of file '/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'FORMULA_TRANSPARENT' at line 1175 of file '/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'LATEX_SOURCE_CODE' at line 1313 of file '/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'PERL_PATH' at line 1565 of file '/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'CLASS_DIAGRAMS' at line 1577 of file '/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'MSCGEN_PATH' at line 1586 of file '/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'DOT_FONTNAME' at line 1616 of file '/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'DOT_FONTSIZE' at line 1621 of file '/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'DOT_TRANSPARENT' at line 1770 of file '/builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: tag INPUT: input source '/builddir/build/BUILD/apbs-3.0.0/doc/license/LICENSE.txt' does not exist warning: source '/builddir/build/BUILD/apbs-3.0.0/doc/license/LICENSE.txt' is not a readable file or directory... skipping. Doxygen version used: 1.9.7 Searching for include files... Searching for example files... Searching for images... Searching for dot files... Searching for msc files... Searching for dia files... Searching for files to exclude Searching INPUT for files to process... Searching for files in directory /builddir/build/BUILD/apbs-3.0.0/src Searching for files in directory /builddir/build/BUILD/apbs-3.0.0/src/pmgc Searching for files in directory /builddir/build/BUILD/apbs-3.0.0/src/mg Searching for files in directory /builddir/build/BUILD/apbs-3.0.0/src/generic Searching for files in directory /builddir/build/BUILD/apbs-3.0.0/src/fem Reading formula repository... Reading and parsing tag files Parsing files Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/apbs.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/apbs.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/fem/vcsm.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/fem/vcsm.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/fem/vcsm.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/fem/vcsm.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c... 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Parsing file /builddir/build/BUILD/apbs-3.0.0/src/mg/vopot.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmgp.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmgp.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmgp.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmgp.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/cgd.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/cgd.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/cgd.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/cgd.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgcsd.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgcsd.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgcsd.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgcsd.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgfasd.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgfasd.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgfasd.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgfasd.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mlinpckd.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mlinpckd.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mlinpckd.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mlinpckd.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.h... Parsing file /builddir/build/builddir/build/BUILD/apbs-3.0.0/src/generic/bemparm.h:7: warning: the name 'beparm.h' supplied as the argument in the \file statement is not an input file /BUILD/apbs-3.0.0/src/pmgc/mypdec.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newtond.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newtond.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newtond.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newtond.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/powerd.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/powerd.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/powerd.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/powerd.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/smoothd.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/smoothd.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/pmgc/smoothd.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/pmgc/smoothd.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/routines.c... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/routines.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0/src/routines.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/src/routines.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/mainpage.h... Parsing file /builddir/build/BUILD/apbs-3.0.0/build/doc/programmer/mainpage.h... Building macro definition list... Building group list... Building directory list... Building namespace list... Building file list... Building class list... Building concept list... Computing nesting relations for classes... Associating documentation with classes... Associating documentation with concepts... Building example list... Searching for enumerations... Searching for documented typedefs... Searching for members imported via using declarations... Searching for included using directives... Searching for documented variables... Building interface member list... Building member list... Searching for friends... Searching for documented defines... Computing class inheritance relations... Computing class usage relations... Flushing cached template relations that have become invalid... Computing class relations... Add enum values to enums... Searching for member function documentation... Creating members for template instances... Building page list... Search for main page... Computing page relations... Determining the scope of groups... Sorting lists... Determining which enums are documented Computing member relations... Building full member lists recursively... Adding members to member groups. Computing member references... Inheriting documentation... Generating disk names... Adding source references... Adding xrefitems... Sorting member lists... Setting anonymous enum type... Computing dependencies between directories... Generating citations page... Counting members... Counting data structures... Resolving user defined references... Finding anchors and sections in the documentation... Transferring function references... Combining using relations... Adding members to index pages... Correcting members for VHDL... Computing tooltip texts... Generating style sheet... Generating search indices... Generating images for formulas in HTML... Generating example documentation... Generating file sources... Generating code for file doc/programmer/mainpage.h... Generating code for file src/apbs.h... Generating code for file src/fem/vcsm.c... Generating code for file src/fem/vcsm.h... Generating code for file src/fem/vfetk.c... Generating code for file src/fem/vfetk.h... Generating code for file src/fem/vpee.c... Generating code for file src/fem/vpee.h... Generating code for file src/generic/apolparm.c... Generating code for file src/generic/apolparm.h... Generating code for file src/generic/bemparm.c... Generating code for file src/generic/bemparm.h... Generating code for file src/generic/femparm.c... Generatin/builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:2095: warning: Member polyEval(int numP, double p[], double c[][VMAXP], double xv[]) (function) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:1528: warning: Member Vfetk_PDE_initElement(PDE *thee, int elementType, int chart, double tvx[][3], void *data) (function) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:1571: warning: Member Vfetk_PDE_initPoint(PDE *thee, int pointType, int chart, double txq[], double tU[], double tdU[][3]) (function) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:1741: warning: Member Vfetk_PDE_DFu_wv(PDE *thee, int key, double W[], double dW[][VAPBS_DIM], double V[], double dV[][3]) (function) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:1902: warning: Member Vfetk_PDE_bisectEdge(int dim, int dimII, int edgeType, int chart[], double vx[][3]) (function) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:1912: warning: Member Vfetk_PDE_mapBoundary(int dim, int dimII, int vertexType, int chart, double vx[3]) (function) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:1917: warning: Member Vfetk_PDE_markSimplex(int dim, int dimII, int simplexType, int faceType[VAPBS_NVS], int vertexType[VAPBS_NVS], int chart[], double vx[][3], void *simplex) (function) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:1998: warning: Member Vfetk_PDE_oneChart(int dim, int dimII, int objType, int chart[], double vx[][3], int dimV) (function) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:86: warning: Member var (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:93: warning: Member diriCubeString (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:130: warning: Member neumCubeString (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:366: warning: Member dim_2DP1 (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:386: warning: Member lgr_2DP1[3][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:395: warning: Member lgr_2DP1x[3][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:402: warning: Member lgr_2DP1y[3][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:409: warning: Member lgr_2DP1z[3][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:437: warning: Member dim_3DP1 (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:438: warning: Member lgr_3DP1[VAPBS_NVS][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:446: warning: Member lgr_3DP1x[VAPBS_NVS][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:454: warning: Member lgr_3DP1y[VAPBS_NVS][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:462: warning: Member lgr_3DP1z[VAPBS_NVS][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:476: warning: Member P_DEG (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:482: warning: Member numP (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:483: warning: Member c[VMAXP][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:484: warning: Member cx[VMAXP][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:485: warning: Member cy[VMAXP][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.c:486: warning: Member cz[VMAXP][VMAXP] (variable) of file vfetk.c is not documented. g code for file src/generic/femparm.h... Generating code for file src/generic/geoflowparm.c... Generating code for file src/generic/geoflowparm.h... Generating code for file src/generic/mgparm.c... Generating code for file src/generic/mgparm.h... Generating code for file src/generic/nosh.c... Generating code for file src/generic/nosh.h... Generating code for file src/generic/pbamparm.c... Generating code for file src/generic/pbamparm.h... Generating code for file src/generic/pbeparm.c... Generating code for file src/generic/pbeparm.h... Generating code for file src/generic/pbsamparm.c... Generating code for file src/generic/pbsamparm.h... Generating code for file src/generic/vacc.c... Generating code for file src/generic/vacc.h... Generating code for file src/generic/valist.c... Generating code for file src/generic/valist.h... Generating code for file src/generic/vatom.c... Generating code for file src/generic/vatom.h... Generating code for file src/generic/vcap.c... Generating code for file src/generic/vcap.h... Generating code for file src/generic/vclist.c... Generating code for file src/generic/vclist.h... Generating code for file src/generic/vgreen.c... Generating code for file src/generic/vgreen.h... Generating code for file src/generic/vhal.h... Generating code for file src/generic/vmatrix.h... Generating code for file src/generic/vparam.c... Generating code for file src/generic/vparam.h... Generating code for file src/generic/vpbe.c... Generating code for file src/generic/vpbe.h... Generating code for file src/generic/vstring.c... Generating code for file src/generic/vstring.h... Generating code for file src/generic/vunit.h... Generating code for file src/main.c... Generating code for file src/mg/vgrid.c... Generating code for file src/mg/vgrid.h... Generating code for file src/mg/vmgrid.c... Generating code for file src/mg/vmgrid.h... Generating code for file src/mg/vopot.c... Generating code for file src/mg/vopot.h... Generating code for file src/mg/vpmg.c... Generating code for file src/mg/vpmg.h... Generating code for file src/mg/vpmgp.c... Generating code for file src/mg/vpmgp.h... Generating code for file src/pmgc/buildAd.c... Generating code for file src/pmgc/buildAd.h... Generating code for file src/pmgc/buildBd.c... Generating code for file src/pmgc/buildBd.h... Generating code for file src/pmgc/buildGd.c... Generating code for file src/pmgc/buildGd.h... Generating code for file src/pmgc/buildPd.c... Generating code for file src/pmgc/buildPd.h... Generating code for file src/pmgc/cgd.c... Generating code for file src/pmgc/cgd.h... Generating code for file src/pmgc/gsd.c... Generating code for file src/pmgc/gsd.h... Generating code for file src/pmgc/matvecd.c... Generating code for file src/pmgc/matvecd.h... Generating code for file src/pmgc/mgcsd.c... Generating code for file src/pmgc/mgcsd.h... Generating code for file src/pmgc/mgdrvd.c... Generating code for file src/pmgc/mgdrvd.h... Generating code for file src/pmgc/mgfasd.c... Generating code for file src/pmgc/mgfasd.h... Generating code for file src/pmgc/mgsubd.c... Generating code for file src/pmgc/mgsubd.h... Generating code for file src/pmgc/mikpckd.c... Generating code for file src/pmgc/mikpckd.h... Generating code for file src/pmgc/mlinpckd.c... Generating code for file src/pmgc/mlinpckd.h... Generating code for file src/pmgc/mypdec.c... Generating code for file src/pmgc/mypdec.h... Generating code for file src/pmgc/newdrvd.c... Generating code for file src/pmgc/newdrvd.h... Generating code for file src/pmgc/newtond.c... Generating code for file src/pmgc/newtond.h... Generating code for file src/pmgc/powerd.c... Generating code for file src/pmgc/powerd.h... Generating code for file src/pmgc/smoothd.c... Generating code for file src/pmgc/smoothd.h... Generating code for file src/routines.c... Generating code for file src/routines.h... Generating file documentation... Generating docs for file src/apbs.h... Generating docs for file src/fem/vcsm.c... Generating docs for file src/fem/vcsm.h... Generating docs for file src/fem/vfetk.c... Generating do/builddir/build/BUILD/apbs-3.0.0/src/fem/vfetk.h:207: warning: Member Vfetk (typedef) of file vfetk.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vpee.c:498: warning: Member Vpee_userDefined(Vpee *thee, SS *sm) (function) of file vpee.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vpee.c:532: warning: Member Vpee_ourSimp(Vpee *thee, SS *sm, int rcol) (function) of file vpee.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vpee.c:66: warning: Member Aprx_estNonlinResid(Aprx *thee, SS *sm, Bvec *u, Bvec *ud, Bvec *f) (function) of file vpee.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vpee.c:72: warning: Member Aprx_estLocalProblem(Aprx *thee, SS *sm, Bvec *u, Bvec *ud, Bvec *f) (function) of file vpee.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vpee.c:77: warning: Member Aprx_estDualProblem(Aprx *thee, SS *sm, Bvec *u, Bvec *ud, Bvec *f) (function) of file vpee.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/apolparm.c:237: warning: Member APOLparm_parseGRID(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/apolparm.c:268: warning: Member APOLparm_parseMOL(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/apolparm.c:287: warning: Member APOLparm_parseSRFM(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/apolparm.c:309: warning: Member APOLparm_parseSRAD(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/apolparm.c:328: warning: Member APOLparm_parseSWIN(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/apolparm.c:347: warning: Member APOLparm_parseTEMP(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/apolparm.c:366: warning: Member APOLparm_parseGAMMA(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/apolparm.c:385: warning: Member APOLparm_parseCALCENERGY(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/apolparm.c:438: warning: Member APOLparm_parseCALCFORCE(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/apolparm.c:491: warning: Member APOLparm_parseBCONC(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/apolparm.c:510: warning: Member APOLparm_parseSDENS(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/apolparm.c:529: warning: Member APOLparm_parseDPOS(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/apolparm.c:558: warning: Member APOLparm_parsePRESS(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/bemparm.c:210: warning: Member BEMparm_parseTREE_ORDER(BEMparm *thee, Vio *sock) (function) of file bemparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/bemparm.c:233: warning: Member BEMparm_parseTREE_N0(BEMparm *thee, Vio *sock) (function) of file bemparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/bemparm.c:256: warning: Member BEMparm_parseMAC(BEMparm *thee, Vio *sock) (function) of file bemparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/bemparm.c:279: warning: Member BEMparm_parseMESH(BEMparm *thee, Vio *sock) (function) of file bemparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/bemparm.c:308: warning: Member BEMparm_parseOUTDATA(BEMparm *thee, Vio *sock) (function) of file bemparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/femparm.c:196: warning: Member FEMparm_parseDOMAINLENGTH(FEMparm *thee, Vio *sock) (function) of file femparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/femparm.c:221: warning: Member FEMparm_parseETOL(FEMparm *thee, Vio *sock) (function) of file femparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/femparm.c:244: warning: Member FEMparm_parseEKEY(FEMparm *thee, Vio *sock) (function) of file femparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/femparm.c:276: warning: Member FEMparm_parseAKEYPRE(FEMparm *thee, Vio *sock) (function) of file femparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/femparm.c:303: warning: Member FEMparm_parseAKEYSOLVE(FEMparm *thee, Vio *sock) (function) of file femparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/femparm.c:333: warning: Member FEMparm_parseTARGETNUM(FEMparm *thee, Vio *sock) (function) of file femparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/femparm.c:352: warning: Member FEMparm_parseTARGETRES(FEMparm *thee, Vio *sock) (function) of file femparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/femparm.c:372: warning: Member FEMparm_parseMAXSOLVE(FEMparm *thee, Vio *sock) (function) of file femparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/femparm.c:391: warning: Member FEMparm_parseMAXVERT(FEMparm *thee, Vio *sock) (function) of file femparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/femparm.c:411: warning: Member FEMparm_parseUSEMESH(FEMparm *thee, Vio *sock) (function) of file femparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/femparm.h:182: warning: Member FEMparm (typedef) of file femparm.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.c:138: warning: Member FUBAR(const char *name) (function) of file geoflowparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.c:143: warning: Member parseNonNeg(double *tf, double def, int *set, char *name, Vio *sock) (function) of file geoflowparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.c:164: warning: Member GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock) (function) of file geoflowparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.c:186: warning: Member GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock) (function) of file geoflowparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169: warning: Member GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock) (function) of file geoflowparm.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171: warning: Member GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock) (function) of file geoflowparm.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:415: warning: Member MGparm_parseDIME(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:446: warning: Member MGparm_parseCHGM(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:497: warning: Member MGparm_parseNLEV(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:516: warning: Member MGparm_parseETOL(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:539: warning: Member MGparm_parseGRID(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:570: warning: Member MGparm_parseGLEN(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:601: warning: Member MGparm_parseGAMMA(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:616: warning: Member MGparm_parseGCENT(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:668: warning: Member MGparm_parseCGLEN(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:699: warning: Member MGparm_parseFGLEN(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:730: warning: Member MGparm_parseCGCENT(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:782: warning: Member MGparm_parseFGCENT(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:834: warning: Member MGparm_parsePDIME(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:872: warning: Member MGparm_parseOFRAC(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:892: warning: Member MGparm_parseASYNC(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.c:912: warning: Member MGparm_parseUSEAQUA(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/mgparm.h:203: warning: Member MGparm (typedef) of file mgparm.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:970: warning: Member NOsh_parseREAD(NOsh *thee, Vio *sock) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:1021: warning: Member NOsh_parsePRINT(NOsh *thee, Vio *sock) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:1187: warning: Member NOsh_parseELEC(NOsh *thee, Vio *sock) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:1313: warning: Member NOsh_parseAPOLAR(NOsh *thee, Vio *sock) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:2385: warning: Member NOsh_parseFEM(NOsh *thee, Vio *sock, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:1510: warning: Member NOsh_parseMG(NOsh *thee, Vio *sock, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:2845: warning: Member NOsh_parseBEM(NOsh *thee, Vio *sock, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:2934: warning: Member NOsh_parseGEOFLOW(NOsh *thee, Vio *sock, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:3048: warning: Member NOsh_parsePBAM(NOsh *thee, Vio *sock, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:3166: warning: Member NOsh_parsePBSAM(NOsh *thee, Vio *sock, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:2508: warning: Member NOsh_parseAPOL(NOsh *thee, Vio *sock, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:1603: warning: Member NOsh_setupCalcMG(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:1815: warning: Member NOsh_setupCalcMGAUTO(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:1747: warning: Member NOsh_setupCalcMGMANUAL(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:2090: warning: Member NOsh_setupCalcMGPARA(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:1722: warning: Member NOsh_setupCalcFEM(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:2471: warning: Member NOsh_setupCalcFEMANUAL(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:1638: warning: Member NOsh_setupCalcBEM(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:1666: warning: Member NOsh_setupCalcGEOFLOW(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:1686: warning: Member NOsh_setupCalcPBAM(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:1704: warning: Member NOsh_setupCalcPBSAM(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:2612: warning: Member NOsh_setupCalcBEMMANUAL(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:2677: warning: Member NOsh_setupCalcGEOFLOWMANUAL(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:2735: warning: Member NOsh_setupCalcPBAMAUTO(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:2786: warning: Member NOsh_setupCalcPBSAMAUTO(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:2581: warning: Member NOsh_setupCalcAPOL(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:598: warning: Member NOsh_parseREAD_MOL(NOsh *thee, Vio *sock) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:675: warning: Member NOsh_parseREAD_PARM(NOsh *thee, Vio *sock) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:739: warning: Member NOsh_parseREAD_DIEL(NOsh *thee, Vio *sock) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:793: warning: Member NOsh_parseREAD_KAPPA(NOsh *thee, Vio *sock) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:839: warning: Member NOsh_parseREAD_POTENTIAL(NOsh *thee, Vio *sock) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:884: warning: Member NOsh_parseREAD_CHARGE(NOsh *thee, Vio *sock) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:930: warning: Member NOsh_parseREAD_MESH(NOsh *thee, Vio *sock) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:188: warning: Member NOsh_calc (typedef) of file nosh.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c:458: warning: Member PBAMparm_parseNtraj(PBAMparm *thee, Vio *sock) (function) of file pbamparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c:549: warning: Member PBAMparm_parseTerm(PBAMparm *thee, Vio *sock) (function) of file pbamparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:77: warning: Member PBAMPARM_MAXWRITE (macro definition) of file pbamparm.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:78: warning: Member PBAMPARM_MAXMOL (macro definition) of file pbamparm.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:87: warning: Member PBEparm_getzmem(PBEparm *thee) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:91: warning: Member PBEparm_getLmem(PBEparm *thee) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:95: warning: Member PBEparm_getmembraneDiel(PBEparm *thee) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:99: warning: Member PBEparm_getmemv(PBEparm *thee) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:368: warning: Member PBEparm_parseLPBE(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:375: warning: Member PBEparm_parseNPBE(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:382: warning: Member PBEparm_parseMOL(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:401: warning: Member PBEparm_parseLRPBE(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:408: warning: Member PBEparm_parseNRPBE(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:415: warning: Member PBEparm_parseSMPBE(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:474: warning: Member PBEparm_parseBCFL(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:555: warning: Member PBEparm_parseION(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:652: warning: Member PBEparm_parsePDIE(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:671: warning: Member PBEparm_parseSDENS(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:690: warning: Member PBEparm_parseSDIE(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:709: warning: Member PBEparm_parseSRFM(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:780: warning: Member PBEparm_parseSRAD(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:799: warning: Member PBEparm_parseSWIN(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:818: warning: Member PBEparm_parseTEMP(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:837: warning: Member PBEparm_parseUSEMAP(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:895: warning: Member PBEparm_parseCALCENERGY(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:948: warning: Member PBEparm_parseCALCFORCE(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:1005: warning: Member PBEparm_parseZMEM(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:1025: warning: Member PBEparm_parseLMEM(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:1044: warning: Member PBEparm_parseMDIE(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:1063: warning: Member PBEparm_parseMEMV(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:1084: warning: Member PBEparm_parseWRITE(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.c:1178: warning: Member PBEparm_parseWRITEMAT(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:77: warning: Member PBSAMPARM_MAXWRITE (macro definition) of file pbsamparm.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:78: warning: Member PBSAMPARM_MAXMOL (macro definition) of file pbsamparm.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:277: warning: Member Vacc_vdwAcc(Vacc *thee, double center[3]) (function) of file vacc.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:307: warning: Member Vacc_ivdwAcc(Vacc *thee, double center[3], double radius) (function) of file vacc.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:679: warning: Member Vacc_writeGMV(Vacc *thee, double radius, int meth, Gem *gm, char *iodev, char *iofmt, char *iohost, char *iofile) (function) of file vacc.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:1252: warning: Member Vacc_SASAPos(Vacc *thee, double radius) (function) of file vacc.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:1277: warning: Member Vacc_atomSASAPos(Vacc *thee, double radius, Vatom *atom, int mode) (function) of file vacc.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:76: warning: The following parameter of ivdwAccExclus(Vacc *thee, double center[3], double radius, int atomID) is not documented: parameter 'thee' /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:490: warning: The following parameter of splineAcc(Vacc *thee, double center[VAPBS_DIM], double win, double infrad, VclistCell *cell) is not documented: parameter 'thee' /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:186: warning: Member Valist_readPDBSerial(Valist *thee, Vio *sock, int *serial) (function) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:206: warning: Member Valist_readPDBAtomName(Valist *thee, Vio *sock, char atomName[VMAX_ARGLEN]) (function) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:224: warning: Member Valist_readPDBResidueName(Valist *thee, Vio *sock, char resName[VMAX_ARGLEN]) (function) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:242: warning: Member Valist_readPDBResidueNumber(Valist *thee, Vio *sock, int *resSeq) (function) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:298: warning: Member Valist_readPDBAtomCoord(Valist *thee, Vio *sock, double *coord) (function) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:316: warning: Member Valist_readPDBChargeRadius(Valist *thee, Vio *sock, double *charge, double *radius) (function) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:344: warning: Member Valist_readPDB_throughXYZ(Valist *thee, Vio *sock, int *serial, char atomName[VMAX_ARGLEN], char resName[VMAX_ARGLEN], int *resSeq, double *x, double *y, double *z) (function) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:424: warning: Member Valist_getAtomStorage(Valist *thee, Vatom **plist, int *pnlist, int *pnatoms) (function) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:480: warning: Member Valist_setAtomArray(Valist *thee, Vatom **plist, int nlist, int natoms) (function) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:60: warning: Member Valist_whiteChars (variable) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:61: warning: Member Valist_commChars (variable) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:62: warning: Member Valist_xmlwhiteChars (variable) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vclist.c:128: warning: Member VCLIST_INFLATE (macro definition) of file vclist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vclist.c:90: warning: Member Vclist_getMolDims(Vclist *thee, double lower_corner[VAPBS_DIM], double upper_corner[VAPBS_DIM], double *r_max) (function) of file vclist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vclist.c:125: warning: Member Vclist_setupGrid(Vclist *thee) (function) of file vclist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vclist.c:174: warning: Member Vclist_storeParms(Vclist *thee, Valist *alist, double max_radius, int npts[VAPBS_DIM], Vclist_DomainMode mode, double lower_corner[VAPBS_DIM], double upper_corner[VAPBS_DIM]) (function) of file vclist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vclist.c:231: warning: Member Vclist_gridSpan(Vclist *thee, Vatom *atom, int imin[VAPBS_DIM], int imax[VAPBS_DIM]) (function) of file vclist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vclist.c:262: warning: Member Vclist_arrayIndex(Vclist *thee, int i, int j, int k) (function) of file vclist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vclist.c:270: warning: Member Vclist_assignAtoms(Vclist *thee) (function) of file vclist.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vclist.h:94: warning: Member Vclist_DomainMode (typedef) of file vclist.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:425: warning: Member treesetup(Vgreen *thee) (function) of file vgreen.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:505: warning: Member treecleanup(Vgreen *thee) (function) of file vgreen.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:525: warning: Member treecalc(Vgreen *thee, double *xtar, double *ytar, double *ztar, double *qtar, int numtars, double *tpengtar, double *x, double *y, double *z, double *q, int numpars, double *fx, double *fy, double *fz, int iflag, int farrdim, int arrdim) (function) of file vgreen.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:458: warning: Member MAX_HASH_DIM (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:572: warning: Member OS_SEP_STR (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:573: warning: Member OS_SEP_CHAR (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:600: warning: Member ANNOUNCE_FUNCTION (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:601: warning: Member WARN_UNTESTED (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:602: warning: Member WARN_PARTTESTED (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:653: warning: Member VCHANNELEDMESSAGE0(channel, msg) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:658: warning: Member VCHANNELEDMESSAGE1(channel, msg, arg0) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:665: warning: Member VCHANNELEDMESSAGE2(channel, msg, arg0, arg1) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:672: warning: Member VCHANNELEDMESSAGE3(channel, msg, arg0, arg1, arg2) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:679: warning: Member VMESSAGE0(msg) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:680: warning: Member VMESSAGE1(msg, arg0) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:681: warning: Member VMESSAGE2(msg, arg0, arg1) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:682: warning: Member VMESSAGE3(msg, arg0, arg1, arg2) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:684: warning: Member VERRMSG0(msg) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:685: warning: Member VERRMSG1(msg, arg0) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:686: warning: Member VERRMSG2(msg, arg0, arg1) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:687: warning: Member VERRMSG3(msg, arg0, arg1, arg2) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:731: warning: Member VASSERT_MSG0(cnd, msg) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:741: warning: Member VASSERT_MSG1(cnd, msg, arg) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:753: warning: Member VASSERT_MSG2(cnd, msg, arg0, arg1) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:825: warning: Member VWARN_MSG0(cnd, msg) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:838: warning: Member VWARN_MSG1(cnd, msg, arg0) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:853: warning: Member VWARN_MSG2(cnd, msg, arg0, arg1) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:899: warning: Member VABORT_MSG0(msg) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:907: warning: Member VABORT_MSG1(msg, arg) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:917: warning: Member VABORT_MSG2(msg, arg0, arg1) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:944: warning: Member PRINT_INT(expr) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:945: warning: Member PRINT_DBL(expr) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:948: warning: Member VMALLOC(vmem, n, type) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:950: warning: Member VFREE(vmem, n, type, ptr) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:952: warning: Member VFILL(vec, n, val) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:959: warning: Member VCOPY(srcvec, dstvec, i, n) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:968: warning: Member VAT(array, i) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:969: warning: Member RAT(array, i) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:73: warning: Member Vrc_Codes (typedef) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:95: warning: Member Vsol_Meth (typedef) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:133: warning: Member Vsurf_Meth (typedef) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:244: warning: Member Vchrg_Meth (typedef) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:262: warning: Member Vchrg_Src (typedef) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:302: warning: Member Vdata_Type (typedef) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:323: warning: Member Vdata_Format (typedef) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vhal.h:966: warning: Member wrap_text(char *str, int right_margin, int left_padding) (function) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:64: warning: Member MAT2(mat, dx, dy) (macro definition) of file vmatrix.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:68: warning: Member RAT2(mat, x, y) (macro definition) of file vmatrix.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:71: warning: Member VAT2(mat, x, y) (macro definition) of file vmatrix.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:76: warning: Member MAT3(mat, dx, dy, dz) (macro definition) of file vmatrix.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:81: warning: Member RAT3(mat, x, y, z) (macro definition) of file vmatrix.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:84: warning: Member VAT3(mat, x, y, z) (macro definition) of file vmatrix.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vparam.h:127: warning: Member Vparam_ResData (typedef) of file vparam.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vparam.h:147: warning: Member Vparam (typedef) of file vparam.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/vpbe.c:62: warning: Member MAX_SPLINE_WINDOW (macro definition) of file vpbe.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vgrid.c:67: warning: Member IJK(i, j, k) (macro definition) of file vgrid.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vgrid.c:77: warning: Member MCwhiteChars (variable) of file vgrid.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vgrid.c:78: warning: Member MCcommChars (variable) of file vgrid.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vgrid.c:79: warning: Member Vcompare (variable) of file vgrid.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vgrid.c:80: warning: Member Vprecision[26] (variable) of file vgrid.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vopot.c:113: warning: Member IJK(i, j, k) (macro definition) of file vopot.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:1401: warning: Member Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:2828: warning: Member bcCalcOrig(Vpmg *thee) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3130: warning: Member gridPointIsValid(int i, int j, int k, int nx, int ny, int nz) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3313: warning: Member packAtoms(double *ax, double *ay, double *az, double *charge, double *size, Vpmg *thee) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3338: warning: Member packUnpack(int nx, int ny, int nz, int ngrid, double *gx, double *gy, double *gz, double *value, Vpmg *thee, int pack) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3407: warning: Member bcflnew(Vpmg *thee) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3597: warning: Member bcfl_sdh(Vpmg *thee) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3868: warning: Member bcfl_mdh(Vpmg *thee) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3995: warning: Member bcfl_mem(double zmem, double L, double eps_m, double eps_w, double V, double xkappa, double *gxcf, double *gycf, double *gzcf, double *xf, double *yf, double *zf, int nx, int ny, int nz) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:4174: warning: Member bcfl_map(Vpmg *thee) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:6684: warning: Member markFrac(double rtot, double *tpos, int nx, int ny, int nz, double hx, double hy, double hzed, double xmin, double ymin, double zmin, double *xarray, double *yarray, double *zarray) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10260: warning: Member fillcoPermanentInduced(Vpmg *thee) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1056: warning: The following parameter of bcfl1(double size, double *apos, double charge, double xkappa, double pre1, double *gxcf, double *gycf, double *gzcf, double *xf, double *yf, double *zf, int nx, int ny, int nz) is not documented: parameter 'size' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1362: warning: argument 'hz' of command @param is not found in the argument list of markSphere(double rtot, double *tpos, int nx, int ny, int nz, double hx, double hy, double hzed, double xmin, double ymin, double zmin, double *array, double markVal) /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1362: warning: The following parameter of markSphere(double rtot, double *tpos, int nx, int ny, int nz, double hx, double hy, double hzed, double xmin, double ymin, double zmin, double *array, double markVal) is not documented: parameter 'rtot' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1105: warning: The following parameter of multipolebc(double r, double kappa, double eps_p, double eps_w, double rad, double tsr[3]) is not documented: parameter 'r' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1315: warning: The following parameters of qfForceSpline1(Vpmg *thee, double *force, int atomID) are not documented: parameter 'thee' parameter 'force' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1325: warning: The following parameters of qfForceSpline2(Vpmg *thee, double *force, int atomID) are not documented: parameter 'thee' parameter 'force' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1335: warning: The following parameters of qfForceSpline4(Vpmg *thee, double *force, int atomID) are not documented: parameter 'thee' parameter 'force' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:995: warning: The following parameter of Vpmg_polarizEnergy(Vpmg *thee, int extFlag) is not documented: parameter 'thee' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1006: warning: The following parameter of Vpmg_qfEnergyPoint(Vpmg *thee, int extFlag) is not documented: parameter 'thee' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1017: warning: The following parameter of Vpmg_qfEnergyVolume(Vpmg *thee, int extFlag) is not documented: parameter 'thee' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1029: warning: The following parameter of Vpmg_splineSelect(int srfm, Vacc *acc, double *gpos, double win, double infrad, Vatom *atom, double *force) is not documented: parameter 'srfm' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1348: warning: The following parameters of zlapSolve(Vpmg *thee, double **solution, double **source, double **work1) are not documented: parameter 'thee' parameter 'solution' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:105: warning: Member VPMGMAXPART (macro definition) of file vpmg.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1392: warning: Member VCUB(x) (macro definition) of file vpmg.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1393: warning: Member VLOG(x) (macro definition) of file vpmg.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1395: warning: Member IJK(i, j, k) (macro definition) of file vpmg.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1396: warning: Member IJKx(j, k, i) (macro definition) of file vpmg.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1397: warning: Member IJKy(i, k, j) (macro definition) of file vpmg.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1398: warning: Member IJKz(i, j, k) (macro definition) of file vpmg.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1399: warning: Member VFCHI(iint, iflt) (macro definition) of file vpmg.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385: warning: Member Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag) (function) of file vpmg.h is not documented. /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1056: warning: The following parameter of bcfl1(double size, double *apos, double charge, double xkappa, double pre1, double *gxcf, double *gycf, double *gzcf, double *xf, double *yf, double *zf, int nx, int ny, int nz) is not documented: parameter 'size' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1362: warning: The following parameter of markSphere(double rtot, double *tpos, int nx, int ny, int nz, double hx, double hy, double hzed, double xmin, double ymin, double zmin, double *array, double markVal) is not documented: parameter 'rtot' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1105: warning: The following parameter of multipolebc(double r, double kappa, double eps_p, double eps_w, double rad, double tsr[3]) is not documented: parameter 'r' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1315: warning: The following parameters of qfForceSpline1(Vpmg *thee, double *force, int atomID) are not documented: parameter 'thee' parameter 'force' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1325: warning: The following parameters of qfForceSpline2(Vpmg *thee, double *force, int atomID) are not documented: parameter 'thee' parameter 'force' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1335: warning: The following parameters of qfForceSpline4(Vpmg *thee, double *force, int atomID) are not documented: parameter 'thee' parameter 'force' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:995: warning: The following parameter of Vpmg_polarizEnergy(Vpmg *thee, int extFlag) is not documented: parameter 'thee' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1006: warning: The following parameter of Vpmg_qfEnergyPoint(Vpmg *thee, int extFlag) is not documented: parameter 'thee' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1017: warning: The following parameter of Vpmg_qfEnergyVolume(Vpmg *thee, int extFlag) is not documented: parameter 'thee' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1029: warning: The following parameter of Vpmg_splineSelect(int srfm, Vacc *acc, double *gpos, double win, double infrad, Vatom *atom, double *force) is not documented: parameter 'srfm' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1348: warning: The following parameters of zlapSolve(Vpmg *thee, double **solution, double **source, double **work1) are not documented: parameter 'thee' parameter 'solution' /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmgp.c:294: warning: Member coarsenThis(int nOld) (function) of file vpmgp.c is not documented. /builddir/build/BUILD/apbs-3.0.0/src/fem/vpee.h:17: warning: end of comment block while expecting command /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:247: warning: argument 'parm' of command @param is not found in the argument list of PBAMparm_parseSalt(PBAMparm *thee, Vio *sock) /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:247: warning: The following parameter of PBAMparm_parseSalt(PBAMparm *thee, Vio *sock) is not documented: parameter 'sock' /builddir/build/BUILD/apbs-3.0.0/src/routines.h:513: warning: The following parameter of energyAPOL(APOLparm *apolparm, double sasa, double sav, double atomsasa[], double atomwcaEnergy[], int numatoms) is not documented: parameter 'apolparm' /builddir/build/BUILD/apbs-3.0.0/src/routines.h:610: warning: The following parameter of killFE(NOsh *nosh, Vpbe *pbe[NOSH_MAXCALC], Vfetk *fetk[NOSH_MAXCALC], Gem *gem[NOSH_MAXMOL]) is not documented: parameter 'nosh' /builddir/build/BUILD/apbs-3.0.0/src/routines.h:262: warning: The following parameter of killMG(NOsh *nosh, Vpbe *pbe[NOSH_MAXCALC], Vpmgp *pmgp[NOSH_MAXCALC], Vpmg *pmg[NOSH_MAXCALC]) is not documented: parameter 'nosh' /builddir/build/BUILD/apbs-3.0.0/src/routines.c:882: warning: argument 'charge' of command @param is not found in the argument list of loadChargeMaps(NOsh *nosh, Vgrid *map[NOSH_MAXMOL]) /builddir/build/BUILD/apbs-3.0.0/src/routines.c:882: warning: The following parameter of loadChargeMaps(NOsh *nosh, Vgrid *map[NOSH_MAXMOL]) is not documented: parameter 'map' /builddir/build/BUILD/apbs-3.0.0/src/routines.c:662: warning: argument 'kappa' of command @param is not found in the argument list of loadKappaMaps(NOsh *nosh, Vgrid *map[NOSH_MAXMOL]) /builddir/build/BUILD/apbs-3.0.0/src/routines.c:662: warning: The following parameter of loadKappaMaps(NOsh *nosh, Vgrid *map[NOSH_MAXMOL]) is not documented: parameter 'map' /builddir/build/BUILD/apbs-3.0.0/src/routines.c:791: warning: argument 'pot' of command @param is not found in the argument list of loadPotMaps(NOsh *nosh, Vgrid *map[NOSH_MAXMOL]) /builddir/build/BUILD/apbs-3.0.0/src/routines.c:791: warning: The following parameter of loadPotMaps(NOsh *nosh, Vgrid *map[NOSH_MAXMOL]) is not documented: parameter 'map' /builddir/build/BUILD/apbs-3.0.0/src/routines.h:622: warning: argument 'nosh' of command @param is not found in the argument list of preRefineFE(int i, FEMparm *feparm, Vfetk *fetk[NOSH_MAXCALC]) /builddir/build/BUILD/apbs-3.0.0/src/routines.h:494: warning: The following parameter of printApolForce(Vcom *com, NOsh *nosh, int nforce[NOSH_MAXCALC], AtomForce *atomForce[NOSH_MAXCALC], int i) is not documented: parameter 'com' /builddir/build/BUILD/apbs-3.0.0/src/routines.h:445: warning: The following parameter of printElecEnergy(Vcom *com, NOsh *nosh, double totEnergy[NOSH_MAXCALC], int iprint) is not documented: parameter 'com' /builddir/build/BUILD/apbs-3.0.0/src/routines.h:481: warning: The following parameter of printElecForce(Vcom *com, NOsh *nosh, int nforce[NOSH_MAXCALC], AtomForce *atomForce[NOSH_MAXCALC], int i) is not documented: parameter 'com' /builddir/build/BUILD/apbs-3.0.0/src/routines.h:432: warning: The following parameter of printEnergy(Vcom *com, NOsh *nosh, double totEnergy[NOSH_MAXCALC], int iprint) is not documented: parameter 'com' /builddir/build/BUILD/apbs-3.0.0/src/routines.h:468: warning: The following parameter of printForce(Vcom *com, NOsh *nosh, int nforce[NOSH_MAXCALC], AtomForce *atomForce[NOSH_MAXCALC], int i) is not documented: parameter 'com' /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4125: warning: argument 'i' of command @param is not found in the argument list of solveFE(int icalc, PBEparm *pbeparm, FEMparm *feparm, Vfetk *fetk[NOSH_MAXCALC]) /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:104: warning: Member vdw (variable) of struct sGEOFLOWparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:105: warning: Member setvdw (variable) of struct sGEOFLOWparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:111: warning: Member salt (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:112: warning: Member setsalt (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:115: warning: Member runtype[CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:116: warning: Member setruntype (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:119: warning: Member runname[CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:120: warning: Member setrunname (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:123: warning: Member setrandorient (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:126: warning: Member pbcboxlen (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:127: warning: Member setpbcs (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:130: warning: Member units[CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:131: warning: Member setunits (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:137: warning: Member gridpt (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:138: warning: Member setgridpt (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:141: warning: Member map3dname[CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:142: warning: Member set3dmap (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:145: warning: Member grid2Dname[PBAMPARM_MAXWRITE][CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:146: warning: Member grid2Dax[PBAMPARM_MAXWRITE][CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:147: warning: Member grid2Dloc[PBAMPARM_MAXWRITE] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:148: warning: Member grid2Dct (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:149: warning: Member setgrid2Dname (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:152: warning: Member dxname[CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:153: warning: Member setdxname (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:158: warning: Member ntraj (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:159: warning: Member setntraj (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:161: warning: Member termcombine[CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:162: warning: Member settermcombine (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:164: warning: Member diffct (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:165: warning: Member moveType[PBAMPARM_MAXMOL][CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:166: warning: Member transDiff[PBAMPARM_MAXMOL] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:167: warning: Member rotDiff[PBAMPARM_MAXMOL] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:169: warning: Member termct (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:170: warning: Member setterm (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:172: warning: Member termnam[PBAMPARM_MAXWRITE][CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:173: warning: Member termnu[PBAMPARM_MAXWRITE][1] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:174: warning: Member termVal[PBAMPARM_MAXWRITE] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:175: warning: Member confil[PBAMPARM_MAXWRITE][CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:176: warning: Member conpad[PBAMPARM_MAXWRITE] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:177: warning: Member confilct (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:179: warning: Member setxyz (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:180: warning: Member xyzct[PBAMPARM_MAXMOL] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:181: warning: Member xyzfil[PBAMPARM_MAXMOL][PBAMPARM_MAXWRITE][CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.h:202: warning: Member pbam_3dmapstem[VMAX_ARGLEN] (variable) of struct sPBEparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbeparm.h:203: warning: Member pbam_3dmapflag (variable) of struct sPBEparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:112: warning: Member settolsp (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:113: warning: Member tolsp (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:115: warning: Member setmsms (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:116: warning: Member probe_radius (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:117: warning: Member density (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:119: warning: Member setsurf (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:120: warning: Member surfct (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:121: warning: Member surffil[PBSAMPARM_MAXMOL][CHR_MAXLEN] (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:123: warning: Member setimat (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:124: warning: Member imatct (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:125: warning: Member imatfil[PBSAMPARM_MAXMOL][CHR_MAXLEN] (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:127: warning: Member setexp (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:128: warning: Member expct (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:129: warning: Member expfil[PBSAMPARM_MAXMOL][CHR_MAXLEN] (variable) of struct sPBSAMparm is not documented. cs for file src/fem/vfetk.h... Generating docs for file src/fem/vpee.c... Generating docs for file src/fem/vpee.h... Generating docs for file src/generic/apolparm.c... Generating docs for file src/generic/bemparm.c... Generating docs for file src/generic/femparm.c... Generating docs for file src/generic/femparm.h... Generating docs for file src/generic/geoflowparm.c... Generating docs for file src/generic/geoflowparm.h... Generating docs for file src/generic/mgparm.c... Generating docs for file src/generic/mgparm.h... Generating docs for file src/generic/nosh.c... Generating docs for file src/generic/nosh.h... Generating docs for file src/generic/pbamparm.c... Generating docs for file src/generic/pbamparm.h... Generating docs for file src/generic/pbeparm.c... Generating docs for file src/generic/pbeparm.h... Generating docs for file src/generic/pbsamparm.c... Generating docs for file src/generic/pbsamparm.h... Generating docs for file src/generic/vacc.c... Generating docs for file src/generic/vacc.h... Generating docs for file src/generic/valist.c... Generating docs for file src/generic/valist.h... Generating docs for file src/generic/vatom.c... Generating docs for file src/generic/vatom.h... Generating docs for file src/generic/vcap.c... Generating docs for file src/generic/vcap.h... Generating docs for file src/generic/vclist.c... Generating docs for file src/generic/vclist.h... Generating docs for file src/generic/vgreen.c... Generating docs for file src/generic/vgreen.h... Generating docs for file src/generic/vhal.h... Generating docs for file src/generic/vmatrix.h... Generating docs for file src/generic/vparam.c... Generating docs for file src/generic/vparam.h... Generating docs for file src/generic/vpbe.c... Generating docs for file src/generic/vpbe.h... Generating docs for file src/generic/vstring.c... Generating docs for file src/generic/vstring.h... Generating docs for file src/generic/vunit.h... Generating docs for file src/main.c... Generating docs for file src/mg/vgrid.c... Generating docs for file src/mg/vgrid.h... Generating docs for file src/mg/vmgrid.c... Generating docs for file src/mg/vmgrid.h... Generating docs for file src/mg/vopot.c... Generating docs for file src/mg/vopot.h... Generating docs for file src/mg/vpmg.c... Generating docs for file src/mg/vpmg.h... Generating docs for file src/mg/vpmgp.c... Generating docs for file src/mg/vpmgp.h... Generating docs for file src/routines.c... Generating docs for file src/routines.h... Generating page documentation... Generating docs for page bug... Generating docs for page deprecated... Generating group documentation... Generating class documentation... Generating docs for compound AtomForce... Generating docs for compound sAPOLparm... Generating docs for compound sBEMparm... Generating docs for compound sFEMparm... Generating docs for compound sGEOFLOWparm... Generating docs for compound sMGparm... Generating docs for compound sNOsh... Generating docs for compound sNOsh_calc... Generating docs for compound sPBAMparm... Generating docs for compound sPBEparm... Generating docs for compound sPBSAMparm... Generating docs for compound sVacc... Generating docs for compound sVaccSurf... Generating docs for compound sValist... Generating docs for compound sVatom... Generating docs for compound sVclist... Generating docs for compound sVclistCell... Generating docs for compound sVcsm... Generating docs for compound sVfetk... Generating docs for compound sVfetk_LocalVar... Generating docs for compound sVgreen... Generating docs for compound sVgrid... Generating docs for compound sVmgrid... Generating docs for compound sVopot... Generating docs for compound sVparam_AtomData... Generating docs for compound sVpbe... Generating docs for compound sVpee... Generating docs for compound sVpmg... Generating docs for compound sVpmgp... Generating docs for compound Vparam... Generating docs for compound Vparam_ResData... Generating concept documentation... Generating namespace documentation... Generating graph info page... Generating directory documentation... Generating dependency graph for directory src/fem Generating dependency graph for directory src/generic Generating dependency graph for directory src/mg Generating dependency graph for directory src/pmgc Generating dependency graph for directory doc/programmer Generating dependency graph for directory src Generating index page... Generating main page... Generating page index... Generating module index... Generating namespace index... Generating namespace member index... Generating concept index... Generating annotated compound index... Generating alphabetical compound index... Generating hierarchical class index... Generating graphical class hierarchy... Generating member index... Generating file index... Generating file member index... Generating example index... finalizing index lists... writing tag file... Running plantuml with JAVA... Running dot... type lookup cache used 2284/65536 hits=42785 misses=2418 symbol lookup cache used 5514/65536 hits=45117 misses=5514 finished... 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[31] Underfull \hbox (badness 10000) detected at line 398 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.19 on input line 414. Underfull \hbox (badness 10000) detected at line 429 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.20 on input line 445. Underfull \hbox (badness 10000) detected at line 463 [][][] Underfull \hbox (badness 10000) detected at line 466 [][][] [32] Package longtable Warning: Column widths have changed (longtable) in table 7.21 on input line 477. Underfull \hbox (badness 10000) detected at line 492 [][][] Underfull \hbox (badness 10000) detected at line 495 [][][] Underfull \hbox (badness 10000) detected at line 498 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.22 on input line 507. Underfull \hbox (badness 10000) detected at line 522 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] Underfull \hbox (badness 10000) detected at line 528 [][][] [33] Package longtable Warning: Column widths have changed (longtable) in table 7.23 on input line 539. Underfull \hbox (badness 10000) detected at line 559 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.24 on input line 568. Underfull \hbox (badness 10000) detected at line 569 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.25 on input line 578. [34] Underfull \hbox (badness 10000) detected at line 593 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.26 on input line 600. Underfull \hbox (badness 10000) detected at line 615 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.27 on input line 622. Underfull \hbox (badness 10000) detected at line 637 [][][] [35] Underfull \hbox (badness 10000) detected at line 658 [][][] Underfull \hbox (badness 10000) detected at line 661 [][][] Underfull \hbox (badness 10000) detected at line 668 [][][] Underfull \hbox (badness 10000) detected at line 671 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.28 on input line 686. Underfull \hbox (badness 10000) detected at line 701 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.29 on input line 712. [36] Underfull \hbox (badness 10000) detected at line 727 [][][] Underfull \hbox (badness 10000) detected at line 730 [][][] Underfull \hbox (badness 10000) detected at line 735 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.30 on input line 746. Underfull \hbox (badness 10000) detected at line 761 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.31 on input line 774. [37] Underfull \hbox (badness 10000) detected at line 789 [][][] Underfull \hbox (badness 10000) detected at line 792 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.32 on input line 799. Underfull \hbox (badness 10000) detected at line 814 [][][] Underfull \hbox (badness 10000) detected at line 817 [][][] Underfull \hbox (badness 10000) detected at line 820 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.33 on input line 829. [38] Underfull \hbox (badness 10000) detected at line 844 [][][] Underfull \hbox (badness 10000) detected at line 847 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.34 on input line 854. Underfull \hbox (badness 10000) detected at line 869 [][][] Underfull \hbox (badness 10000) detected at line 872 [][][] Underfull \hbox (badness 10000) detected at line 875 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.35 on input line 884. Underfull \hbox (badness 10000) detected at line 899 [][][] Underfull \hbox (badness 10000) detected at line 902 [][][] [39] Package longtable Warning: Column widths have changed (longtable) in table 7.36 on input line 909. Underfull \hbox (badness 10000) detected at line 924 [][][] Underfull \hbox (badness 10000) detected at line 927 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.37 on input line 934. Underfull \hbox (badness 10000) detected at line 949 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.38 on input line 958. [40] Underfull \hbox (badness 10000) detected at line 969 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.39 on input line 984. Underfull \hbox (badness 10000) detected at line 999 [][][] Underfull \hbox (badness 10000) detected at line 1002 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.40 on input line 1009. Underfull \hbox (badness 10000) detected at line 1024 [][][] Underfull \hbox (badness 10000) detected at line 1027 [][][] [41] Package longtable Warning: Column widths have changed (longtable) in table 7.41 on input line 1042. Underfull \hbox (badness 10000) detected at line 1053 [][][] Underfull \hbox (badness 10000) detected at line 1056 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.42 on input line 1065. Underfull \hbox (badness 10000) detected at line 1080 [][][] Underfull \hbox (badness 10000) detected at line 1083 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.43 on input line 1094. [42] Underfull \hbox (badness 10000) detected at line 1109 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.44 on input line 1128. Underfull \hbox (badness 10000) detected at line 1146 [][][] Underfull \hbox (badness 10000) detected at line 1149 [][][] [43] Package longtable Warning: Column widths have changed (longtable) in table 7.45 on input line 1168. Underfull \hbox (badness 10000) detected at line 1179 [][][] Underfull \hbox (badness 10000) detected at line 1182 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.46 on input line 1189. Underfull \hbox (badness 10000) detected at line 1204 [][][] Underfull \hbox (badness 10000) detected at line 1207 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.47 on input line 1214. [44] Underfull \hbox (badness 10000) detected at line 1232 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.48 on input line 1247. Underfull \hbox (badness 10000) detected at line 1265 [][][] Underfull \hbox (badness 10000) detected at line 1268 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.49 on input line 1283. [45] Underfull \hbox (badness 10000) detected at line 1298 [][][] Underfull \hbox (badness 10000) detected at line 1301 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.50 on input line 1312. Underfull \hbox (badness 10000) detected at line 1327 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.51 on input line 1344. [46] Underfull \hbox (badness 10000) detected at line 1355 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.52 on input line 1370. Underfull \hbox (badness 10000) detected at line 1385 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.53 on input line 1406. [47] Underfull \hbox (badness 10000) detected at line 1419 [][][] Underfull \hbox (badness 10000) detected at line 1422 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.54 on input line 1433. Underfull \hbox (badness 10000) detected at line 1448 [][][] Underfull \hbox (badness 10000) detected at line 1451 [][][] [48] Package longtable Warning: Column widths have changed (longtable) in table 7.55 on input line 1466. Underfull \hbox (badness 10000) detected at line 1477 [][][] Underfull \hbox (badness 10000) detected at line 1480 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.56 on input line 1503. [49] Underfull \hbox (badness 10000) detected at line 1514 [][][] Underfull \hbox (badness 10000) detected at line 1517 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.57 on input line 1534. Underfull \hbox (badness 10000) detected at line 1545 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.58 on input line 1564. [50] Underfull \hbox (badness 10000) detected at line 1579 [][][] Underfull \hbox (badness 10000) detected at line 1582 [][][] [51] Package longtable Warning: Column widths have changed (longtable) in table 7.59 on input line 1650. [52] Underfull \hbox (badness 10000) detected at line 1665 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.60 on input line 1684. Underfull \hbox (badness 10000) detected at line 1699 [][][] Underfull \hbox (badness 10000) detected at line 1702 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.61 on input line 1721. [53] Underfull \hbox (badness 10000) detected at line 1745 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.62 on input line 1754. Underfull \hbox (badness 10000) detected at line 1755 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.63 on input line 1764. Underfull \hbox (badness 10000) detected at line 1779 [][][] Underfull \hbox (badness 10000) detected at line 1782 [][][] Underfull \hbox (badness 10000) detected at line 1785 [][][] [54] Package longtable Warning: Column widths have changed (longtable) in table 7.64 on input line 1796. Underfull \hbox (badness 10000) detected at line 1807 [][][] Underfull \hbox (badness 10000) detected at line 1810 [][][] Underfull \hbox (badness 10000) detected at line 1813 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.65 on input line 1820. Underfull \hbox (badness 10000) detected at line 1835 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.66 on input line 1846. [55] Underfull \hbox (badness 10000) detected at line 1861 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.67 on input line 1880. Underfull \hbox (badness 10000) detected at line 1881 [][][] Underfull \hbox (badness 10000) detected at line 1886 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.68 on input line 1905. ) (./group___vpee.tex [56] Underfull \hbox (badness 849) in paragraph at lines 45--46 \T1/phv/m/n/10 Holst par-al-lel re-fine-ment rou-tine es-sen-tially re-duces th e er-ror out-side the \T1/pcr/m/n/10 local^^D partition to zero. Underfull \hbox (badness 10000) in paragraph at lines 45--46 \T1/pcr/m/n/10 However, this leads to the need for a few final overlapping Schw arz solves to Underfull \hbox (badness 10000) in paragraph at lines 45--46 \T1/pcr/m/n/10 smooth out the errors near partition boundaries. Supposedly, if the region in Underfull \hbox (badness 10000) in paragraph at lines 45--46 \T1/pcr/m/n/10 which we allow error-based refinement includes the$\OML/cmm/m/it /10 <$\T1/pcr/m/n/10 /tt$\OML/cmm/m/it/10 >$\T1/pcr/m/n/10 local^^D partition a nd an Underfull \hbox (badness 10000) in paragraph at lines 45--46 \T1/pcr/m/n/10 external buffer zone approximately equal in size to the local re gion, then the Underfull \hbox (badness 10000) in paragraph at lines 45--46 \T1/pcr/m/n/10 solution will asymptotically approach the solution obtained via more typical Underfull \hbox (badness 10000) in paragraph at lines 45--46 \T1/pcr/m/n/10 methods. This is essentially a more flexible parallel implementa tion of MC\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 s [57] Underfull \hbox (badness 10000) detected at line 75 [][][] Underfull \hbox (badness 10000) detected at line 78 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.69 on input line 93. Underfull \hbox (badness 10000) detected at line 94 [][][] Underfull \hbox (badness 10000) detected at line 111 [][][] [58] Underfull \hbox (badness 10000) detected at line 114 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.70 on input line 131. Underfull \hbox (badness 10000) detected at line 132 [][][] Underfull \hbox (badness 10000) detected at line 149 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.71 on input line 156. Underfull \hbox (badness 10000) detected at line 171 [][][] [59] Package longtable Warning: Column widths have changed (longtable) in table 7.72 on input line 178. Underfull \hbox (badness 10000) detected at line 195 [][][] Underfull \hbox (badness 10000) detected at line 198 [][][] Underfull \hbox (badness 10000) detected at line 201 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.73 on input line 226. Overfull \vbox (42.60027pt too high) has occurred while \output is active [60] Underfull \hbox (badness 10000) detected at line 241 [][][] Underfull \hbox (badness 10000) detected at line 244 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.74 on input line 251. ) (./group___a_p_o_lparm.tex [61] Package longtable Warning: Column widths have changed (longtable) in table 7.75 on input line 138. Overfull \vbox (22.62613pt too high) has occurred while \output is active [62] Package longtable Warning: Column widths have changed (longtable) in table 7.76 on input line 166. Package longtable Warning: Column widths have changed (longtable) in table 7.77 on input line 194. Underfull \hbox (badness 10000) detected at line 212 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.78 on input line 219. Underfull \hbox (badness 10000) detected at line 220 [][][] [63] Underfull \hbox (badness 10000) detected at line 237 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.79 on input line 246. Underfull \hbox (badness 10000) detected at line 261 [][][] Underfull \hbox (badness 10000) detected at line 264 [][][] Underfull \hbox (badness 10000) detected at line 281 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.80 on input line 288. Underfull \hbox (badness 10000) detected at line 289 [][][] [64] Underfull \hbox (badness 10000) detected at line 306 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.81 on input line 313. Underfull \hbox (badness 10000) detected at line 328 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.82 on input line 335. ) (./group___b_e_mparm.tex [65] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.83 on input line 107. [66] Underfull \hbox (badness 10000) detected at line 125 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.84 on input line 132. Underfull \hbox (badness 10000) detected at line 133 [][][] Underfull \hbox (badness 10000) detected at line 150 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.85 on input line 157. Underfull \hbox (badness 10000) detected at line 158 [][][] Underfull \hbox (badness 10000) detected at line 175 [][][] [67] Package longtable Warning: Column widths have changed (longtable) in table 7.86 on input line 184. Underfull \hbox (badness 10000) detected at line 185 [][][] Underfull \hbox (badness 10000) detected at line 202 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.87 on input line 209. Underfull \hbox (badness 10000) detected at line 224 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.88 on input line 231. Underfull \hbox (badness 10000) detected at line 246 [][][] [68] Package longtable Warning: Column widths have changed (longtable) in table 7.89 on input line 257. Underfull \hbox (badness 10000) detected at line 258 [][][] ) (./group___f_e_mparm.tex [69] Underfull \hbox (badness 10000) detected at line 111 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.90 on input line 140. [70] Underfull \hbox (badness 10000) detected at line 155 [][][] Underfull \hbox (badness 10000) detected at line 158 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.91 on input line 182. Underfull \hbox (badness 10000) detected at line 197 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.92 on input line 213. Underfull \hbox (badness 10000) detected at line 231 [][][] [71] Package longtable Warning: Column widths have changed (longtable) in table 7.93 on input line 238. Underfull \hbox (badness 10000) detected at line 239 [][][] Underfull \hbox (badness 10000) detected at line 256 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.94 on input line 265. Underfull \hbox (badness 10000) detected at line 280 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.95 on input line 287. Underfull \hbox (badness 10000) detected at line 288 [][][] [72] Underfull \hbox (badness 10000) detected at line 305 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.96 on input line 314. Underfull \hbox (badness 10000) detected at line 315 [][][] Underfull \hbox (badness 10000) detected at line 332 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.97 on input line 339. Underfull \hbox (badness 10000) detected at line 354 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.98 on input line 361. ) (./group___g_e_o_f_l_o_wparm.tex [73] Underfull \hbox (badness 10000) detected at line 68 [][][] [74] Underfull \hbox (badness 10000) detected at line 71 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.99 on input line 106. Underfull \hbox (badness 10000) detected at line 124 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.100 on input line 131. Underfull \hbox (badness 10000) detected at line 132 [][][] [75] Underfull \hbox (badness 10000) detected at line 149 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.101 on input line 158. Underfull \hbox (badness 10000) detected at line 173 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.102 on input line 180. Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 198 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.103 on input line 207. Underfull \hbox (badness 10000) detected at line 208 [][][] [76] Underfull \hbox (badness 10000) detected at line 225 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.104 on input line 232. Underfull \hbox (badness 10000) detected at line 247 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.105 on input line 254. Underfull \hbox (badness 10000) detected at line 269 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.106 on input line 280. [77] Underfull \hbox (badness 10000) detected at line 281 [][][] ) (./group___m_gparm.tex [78] [79] Package longtable Warning: Column widths have changed (longtable) in table 7.107 on input line 159. Package longtable Warning: Column widths have changed (longtable) in table 7.108 on input line 187. Underfull \hbox (badness 10000) detected at line 205 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.109 on input line 216. [80] Underfull \hbox (badness 10000) detected at line 217 [][][] Underfull \hbox (badness 10000) detected at line 234 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.110 on input line 245. Underfull \hbox (badness 10000) detected at line 246 [][][] Underfull \hbox (badness 10000) detected at line 263 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.111 on input line 270. Underfull \hbox (badness 10000) detected at line 271 [][][] [81] Underfull \hbox (badness 10000) detected at line 288 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.112 on input line 297. Underfull \hbox (badness 10000) detected at line 312 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.113 on input line 319. Underfull \hbox (badness 10000) detected at line 320 [][][] Underfull \hbox (badness 10000) detected at line 337 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.114 on input line 346. Underfull \hbox (badness 10000) detected at line 347 [][][] [82] Underfull \hbox (badness 10000) detected at line 364 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.115 on input line 371. Underfull \hbox (badness 10000) detected at line 386 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.116 on input line 393. Underfull \hbox (badness 10000) detected at line 408 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.117 on input line 415. Underfull \hbox (badness 10000) detected at line 416 [][][] [83] Underfull \hbox (badness 10000) detected at line 433 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.118 on input line 440. Underfull \hbox (badness 10000) detected at line 441 [][][] Underfull \hbox (badness 10000) detected at line 458 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.119 on input line 465. Underfull \hbox (badness 10000) detected at line 466 [][][] Underfull \hbox (badness 10000) detected at line 483 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.120 on input line 490. Underfull \hbox (badness 10000) detected at line 491 [][][] [84] Underfull \hbox (badness 10000) detected at line 508 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.121 on input line 515. Underfull \hbox (badness 10000) detected at line 516 [][][] Underfull \hbox (badness 10000) detected at line 533 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.122 on input line 540. Underfull \hbox (badness 10000) detected at line 541 [][][] Underfull \hbox (badness 10000) detected at line 558 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.123 on input line 565. [85] Underfull \hbox (badness 10000) detected at line 566 [][][] Underfull \hbox (badness 10000) detected at line 583 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.124 on input line 590. Underfull \hbox (badness 10000) detected at line 591 [][][] Underfull \hbox (badness 10000) detected at line 608 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.125 on input line 615. Underfull \hbox (badness 10000) detected at line 616 [][][] Underfull \hbox (badness 10000) detected at line 633 [][][] [86] Package longtable Warning: Column widths have changed (longtable) in table 7.126 on input line 644. Underfull \hbox (badness 10000) detected at line 645 [][][] Underfull \hbox (badness 10000) detected at line 662 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.127 on input line 671. Underfull \hbox (badness 10000) detected at line 686 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.128 on input line 695. [87] Underfull \hbox (badness 10000) detected at line 710 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.129 on input line 719. ) (./group___n_osh.tex [88] [89] [90] Package longtable Warning: Column widths have changed (longtable) in table 7.130 on input line 321. [91] Package longtable Warning: Column widths have changed (longtable) in table 7.131 on input line 349. Package longtable Warning: Column widths have changed (longtable) in table 7.132 on input line 373. Package longtable Warning: Column widths have changed (longtable) in table 7.133 on input line 413. [92] Underfull \hbox (badness 10000) detected at line 431 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.134 on input line 440. Underfull \hbox (badness 10000) detected at line 441 [][][] Underfull \hbox (badness 10000) detected at line 458 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.135 on input line 467. Underfull \hbox (badness 10000) detected at line 482 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.136 on input line 489. [93] Underfull \hbox (badness 10000) detected at line 490 [][][] Underfull \hbox (badness 10000) detected at line 507 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.137 on input line 514. Underfull \hbox (badness 10000) detected at line 529 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.138 on input line 538. Underfull \hbox (badness 10000) detected at line 539 [][][] Underfull \hbox (badness 10000) detected at line 556 [][][] [94] Package longtable Warning: Column widths have changed (longtable) in table 7.139 on input line 567. Underfull \hbox (badness 10000) detected at line 568 [][][] Underfull \hbox (badness 10000) detected at line 585 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.140 on input line 592. Underfull \hbox (badness 10000) detected at line 607 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.141 on input line 614. Underfull \hbox (badness 10000) detected at line 629 [][][] [95] Package longtable Warning: Column widths have changed (longtable) in table 7.142 on input line 638. Underfull \hbox (badness 10000) detected at line 639 [][][] Underfull \hbox (badness 10000) detected at line 656 [][][] Underfull \hbox (badness 10000) detected at line 659 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.143 on input line 668. Underfull \hbox (badness 10000) detected at line 669 [][][] Underfull \hbox (badness 10000) detected at line 672 [][][] Underfull \hbox (badness 10000) detected at line 689 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.144 on input line 698. Overfull \vbox (15.28305pt too high) has occurred while \output is active [96] Underfull \hbox (badness 10000) detected at line 699 [][][] Underfull \hbox (badness 10000) detected at line 716 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.145 on input line 725. Underfull \hbox (badness 10000) detected at line 726 [][][] Underfull \hbox (badness 10000) detected at line 743 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.146 on input line 752. Underfull \hbox (badness 10000) detected at line 753 [][][] [97] Underfull \hbox (badness 10000) detected at line 770 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.147 on input line 779. Underfull \hbox (badness 10000) detected at line 780 [][][] Underfull \hbox (badness 10000) detected at line 797 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.148 on input line 806. Underfull \hbox (badness 10000) detected at line 807 [][][] Underfull \hbox (badness 10000) detected at line 824 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.149 on input line 833. [98] Underfull \hbox (badness 10000) detected at line 834 [][][] Underfull \hbox (badness 10000) detected at line 851 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.150 on input line 860. Underfull \hbox (badness 10000) detected at line 861 [][][] Underfull \hbox (badness 10000) detected at line 878 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.151 on input line 887. Underfull \hbox (badness 10000) detected at line 888 [][][] [99] Underfull \hbox (badness 10000) detected at line 905 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.152 on input line 914. Underfull \hbox (badness 10000) detected at line 915 [][][] Underfull \hbox (badness 10000) detected at line 932 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.153 on input line 941. Underfull \hbox (badness 10000) detected at line 942 [][][] Underfull \hbox (badness 10000) detected at line 959 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.154 on input line 968. [100] Underfull \hbox (badness 10000) detected at line 969 [][][] Underfull \hbox (badness 10000) detected at line 986 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.155 on input line 995. Underfull \hbox (badness 10000) detected at line 996 [][][] Underfull \hbox (badness 10000) detected at line 1013 [][][] Underfull \hbox (badness 10000) detected at line 1016 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.156 on input line 1025. Underfull \hbox (badness 10000) detected at line 1026 [][][] [101] Underfull \hbox (badness 10000) detected at line 1043 [][][] Underfull \hbox (badness 10000) detected at line 1048 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.157 on input line 1057. Underfull \hbox (badness 10000) detected at line 1058 [][][] Underfull \hbox (badness 10000) detected at line 1075 [][][] Underfull \hbox (badness 10000) detected at line 1078 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.158 on input line 1089. [102] Underfull \hbox (badness 10000) detected at line 1090 [][][] Underfull \hbox (badness 10000) detected at line 1093 [][][] Underfull \hbox (badness 10000) detected at line 1110 [][][] Underfull \hbox (badness 10000) detected at line 1113 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.159 on input line 1122. Underfull \hbox (badness 10000) detected at line 1123 [][][] Underfull \hbox (badness 10000) detected at line 1126 [][][] Underfull \hbox (badness 10000) detected at line 1143 [][][] Underfull \hbox (badness 10000) detected at line 1146 [][][] [103] Package longtable Warning: Column widths have changed (longtable) in table 7.160 on input line 1157. Underfull \hbox (badness 10000) detected at line 1158 [][][] Underfull \hbox (badness 10000) detected at line 1161 [][][] Underfull \hbox (badness 10000) detected at line 1178 [][][] Underfull \hbox (badness 10000) detected at line 1181 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.161 on input line 1190. Underfull \hbox (badness 10000) detected at line 1191 [][][] Underfull \hbox (badness 10000) detected at line 1194 [][][] Underfull \hbox (badness 10000) detected at line 1211 [][][] [104] Underfull \hbox (badness 10000) detected at line 1214 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.162 on input line 1223. Underfull \hbox (badness 10000) detected at line 1224 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.163 on input line 1233. Underfull \hbox (badness 10000) detected at line 1248 [][][] Underfull \hbox (badness 10000) detected at line 1251 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.164 on input line 1260. Underfull \hbox (badness 10000) detected at line 1261 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.165 on input line 1270. Overfull \vbox (3.94589pt too high) has occurred while \output is active [105]) (./group___p_b_a_mparm.tex [106] Underfull \hbox (badness 10000) detected at line 116 [][][] Underfull \hbox (badness 10000) detected at line 119 [][][] [107] Package longtable Warning: Column widths have changed (longtable) in table 7.166 on input line 154. Underfull \hbox (badness 10000) detected at line 172 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.167 on input line 179. Underfull \hbox (badness 10000) detected at line 180 [][][] Underfull \hbox (badness 10000) detected at line 197 [][][] [108] Package longtable Warning: Column widths have changed (longtable) in table 7.168 on input line 206. Underfull \hbox (badness 10000) detected at line 221 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.169 on input line 228. Underfull \hbox (badness 10000) detected at line 229 [][][] Underfull \hbox (badness 10000) detected at line 246 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.170 on input line 255. Underfull \hbox (badness 10000) detected at line 256 [][][] [109] Underfull \hbox (badness 10000) detected at line 273 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.171 on input line 280. Underfull \hbox (badness 10000) detected at line 295 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.172 on input line 302. Underfull \hbox (badness 10000) detected at line 317 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.173 on input line 326. Underfull \hbox (badness 10000) detected at line 341 [][][] [110] Package longtable Warning: Column widths have changed (longtable) in table 7.174 on input line 350. Underfull \hbox (badness 10000) detected at line 365 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.175 on input line 374. Underfull \hbox (badness 10000) detected at line 389 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.176 on input line 398. Underfull \hbox (badness 10000) detected at line 413 [][][] [111] Package longtable Warning: Column widths have changed (longtable) in table 7.177 on input line 422. Underfull \hbox (badness 10000) detected at line 437 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.178 on input line 446. Underfull \hbox (badness 10000) detected at line 461 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.179 on input line 470. Underfull \hbox (badness 10000) detected at line 485 [][][] [112] Package longtable Warning: Column widths have changed (longtable) in table 7.180 on input line 494. Underfull \hbox (badness 10000) detected at line 509 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.181 on input line 518. Underfull \hbox (badness 10000) detected at line 533 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.182 on input line 542. Underfull \hbox (badness 10000) detected at line 557 [][][] [113] Package longtable Warning: Column widths have changed (longtable) in table 7.183 on input line 566. Underfull \hbox (badness 10000) detected at line 581 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.184 on input line 592. Underfull \hbox (badness 10000) detected at line 593 [][][] Underfull \hbox (badness 10000) detected at line 610 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.185 on input line 619. [114] Underfull \hbox (badness 10000) detected at line 634 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.186 on input line 643. ) (./group___p_b_eparm.tex [115] [116] Package longtable Warning: Column widths have changed (longtable) in table 7.187 on input line 163. Package longtable Warning: Column widths have changed (longtable) in table 7.188 on input line 191. Underfull \hbox (badness 10000) detected at line 209 [][][] Underfull \hbox (badness 10000) detected at line 212 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.189 on input line 219. [117] Underfull \hbox (badness 10000) detected at line 234 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.190 on input line 243. Underfull \hbox (badness 10000) detected at line 258 [][][] Underfull \hbox (badness 10000) detected at line 261 [][][] Underfull \hbox (badness 10000) detected at line 278 [][][] Underfull \hbox (badness 10000) detected at line 281 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.191 on input line 288. [118] Underfull \hbox (badness 10000) detected at line 303 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.192 on input line 310. Underfull \hbox (badness 10000) detected at line 325 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.193 on input line 332. Underfull \hbox (badness 10000) detected at line 347 [][][] Underfull \hbox (badness 10000) detected at line 350 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.194 on input line 359. [119] Underfull \hbox (badness 10000) detected at line 374 [][][] Underfull \hbox (badness 10000) detected at line 377 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.195 on input line 386. Underfull \hbox (badness 10000) detected at line 401 [][][] Underfull \hbox (badness 10000) detected at line 404 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.196 on input line 413. Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 431 [][][] [120] Package longtable Warning: Column widths have changed (longtable) in table 7.197 on input line 442. ) (./group___p_b_s_a_mparm.tex [121] Underfull \hbox (badness 10000) detected at line 100 [][][] Underfull \hbox (badness 10000) detected at line 103 [][][] [122] Package longtable Warning: Column widths have changed (longtable) in table 7.198 on input line 138. Underfull \hbox (badness 10000) detected at line 156 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.199 on input line 163. Underfull \hbox (badness 10000) detected at line 164 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.200 on input line 190. [123] Underfull \hbox (badness 10000) detected at line 205 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.201 on input line 212. Underfull \hbox (badness 10000) detected at line 213 [][][] Underfull \hbox (badness 10000) detected at line 230 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.202 on input line 239. Underfull \hbox (badness 10000) detected at line 240 [][][] Underfull \hbox (badness 10000) detected at line 257 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.203 on input line 264. Overfull \vbox (0.37224pt too high) has occurred while \output is active [124] Underfull \hbox (badness 10000) detected at line 279 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.204 on input line 286. Underfull \hbox (badness 10000) detected at line 301 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.205 on input line 310. Underfull \hbox (badness 10000) detected at line 325 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.206 on input line 334. [125] Underfull \hbox (badness 10000) detected at line 349 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.207 on input line 358. Underfull \hbox (badness 10000) detected at line 373 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.208 on input line 382. Underfull \hbox (badness 10000) detected at line 397 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.209 on input line 408. [126] Underfull \hbox (badness 10000) detected at line 409 [][][] Underfull \hbox (badness 10000) detected at line 426 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.210 on input line 435. ) (./group___vacc.tex [127] [128] [129] Underfull \hbox (badness 10000) detected at line 149 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.211 on input line 164. Underfull \hbox (badness 10000) detected at line 179 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.212 on input line 192. [130] Underfull \hbox (badness 10000) detected at line 207 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] Underfull \hbox (badness 10000) detected at line 213 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.213 on input line 224. Underfull \hbox (badness 10000) detected at line 239 [][][] Underfull \hbox (badness 10000) detected at line 242 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.214 on input line 253. [131] Underfull \hbox (badness 10000) detected at line 268 [][][] Underfull \hbox (badness 10000) detected at line 271 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.215 on input line 282. Underfull \hbox (badness 10000) detected at line 283 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.216 on input line 290. Underfull \hbox (badness 10000) detected at line 305 [][][] Underfull \hbox (badness 10000) detected at line 308 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.217 on input line 319. [132] Underfull \hbox (badness 10000) detected at line 334 [][][] Underfull \hbox (badness 10000) detected at line 337 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.218 on input line 350. Underfull \hbox (badness 10000) detected at line 365 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.219 on input line 372. Underfull \hbox (badness 10000) detected at line 387 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.220 on input line 394. [133] Underfull \hbox (badness 10000) detected at line 411 [][][] Underfull \hbox (badness 10000) detected at line 414 [][][] Underfull \hbox (badness 10000) detected at line 417 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.221 on input line 430. Underfull \hbox (badness 10000) detected at line 447 [][][] Underfull \hbox (badness 10000) detected at line 450 [][][] [134] Package longtable Warning: Column widths have changed (longtable) in table 7.222 on input line 461. Underfull \hbox (badness 10000) detected at line 472 [][][] Underfull \hbox (badness 10000) detected at line 475 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.223 on input line 482. Underfull \hbox (badness 10000) detected at line 499 [][][] Underfull \hbox (badness 10000) detected at line 502 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.224 on input line 515. [135] Underfull \hbox (badness 10000) detected at line 530 [][][] Underfull \hbox (badness 10000) detected at line 533 [][][] Underfull \hbox (badness 10000) detected at line 536 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.225 on input line 545. Underfull \hbox (badness 10000) detected at line 562 [][][] Underfull \hbox (badness 10000) detected at line 565 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.226 on input line 578. [136] Underfull \hbox (badness 10000) detected at line 595 [][][] Underfull \hbox (badness 10000) detected at line 598 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.227 on input line 613. Underfull \hbox (badness 10000) detected at line 628 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.228 on input line 643. [137] Underfull \hbox (badness 10000) detected at line 660 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.229 on input line 677. Underfull \hbox (badness 10000) detected at line 692 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.230 on input line 709. [138] Underfull \hbox (badness 10000) detected at line 724 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.231 on input line 741. Underfull \hbox (badness 10000) detected at line 758 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.232 on input line 775. [139] Underfull \hbox (badness 10000) detected at line 790 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.233 on input line 805. Underfull \hbox (badness 10000) detected at line 820 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.234 on input line 837. [140] Underfull \hbox (badness 10000) detected at line 852 [][][] Underfull \hbox (badness 10000) detected at line 855 [][][] Underfull \hbox (badness 10000) detected at line 858 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.235 on input line 867. Underfull \hbox (badness 10000) detected at line 882 [][][] Underfull \hbox (badness 10000) detected at line 885 [][][] Underfull \hbox (badness 10000) detected at line 888 [][][] [141] Package longtable Warning: Column widths have changed (longtable) in table 7.236 on input line 901. Underfull \hbox (badness 10000) detected at line 918 [][][] Underfull \hbox (badness 10000) detected at line 921 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.237 on input line 930. Underfull \hbox (badness 10000) detected at line 941 [][][] Underfull \hbox (badness 10000) detected at line 944 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.238 on input line 957. Overfull \vbox (21.5778pt too high) has occurred while \output is active [142] Underfull \hbox (badness 10000) detected at line 972 [][][] Underfull \hbox (badness 10000) detected at line 975 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.239 on input line 992. Underfull \hbox (badness 10000) detected at line 1007 [][][] Underfull \hbox (badness 10000) detected at line 1010 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.240 on input line 1025. [143] Underfull \hbox (badness 10000) detected at line 1040 [][][] Underfull \hbox (badness 10000) detected at line 1043 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.241 on input line 1054. Underfull \hbox (badness 10000) detected at line 1069 [][][] Underfull \hbox (badness 10000) detected at line 1072 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.242 on input line 1085. Overfull \vbox (18.93095pt too high) has occurred while \output is active [144] Underfull \hbox (badness 10000) detected at line 1100 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.243 on input line 1107. Underfull \hbox (badness 10000) detected at line 1122 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.244 on input line 1129. Underfull \hbox (badness 10000) detected at line 1146 [][][] Underfull \hbox (badness 10000) detected at line 1149 [][][] Underfull \hbox (badness 10000) detected at line 1152 [][][] [145] Package longtable Warning: Column widths have changed (longtable) in table 7.245 on input line 1161. ) (./group___valist.tex [146] Underfull \hbox (badness 10000) detected at line 91 [][][] Underfull \hbox (badness 10000) detected at line 94 [][][] Underfull \hbox (badness 10000) detected at line 111 [][][] Underfull \hbox (badness 10000) detected at line 114 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.246 on input line 121. Overfull \vbox (3.49948pt too high) has occurred while \output is active [147] Underfull \hbox (badness 10000) detected at line 136 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.247 on input line 143. Underfull \hbox (badness 10000) detected at line 158 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.248 on input line 165. Underfull \hbox (badness 10000) detected at line 180 [][][] Underfull \hbox (badness 10000) detected at line 183 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.249 on input line 192. [148] Underfull \hbox (badness 10000) detected at line 207 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.250 on input line 217. Underfull \hbox (badness 10000) detected at line 232 [][][] Underfull \hbox (badness 10000) detected at line 235 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.251 on input line 242. Underfull \hbox (badness 10000) detected at line 257 [][][] Underfull \hbox (badness 10000) detected at line 260 [][][] [149] Package longtable Warning: Column widths have changed (longtable) in table 7.252 on input line 267. Underfull \hbox (badness 10000) detected at line 282 [][][] Underfull \hbox (badness 10000) detected at line 285 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.253 on input line 292. Underfull \hbox (badness 10000) detected at line 307 [][][] Underfull \hbox (badness 10000) detected at line 310 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.254 on input line 317. Underfull \hbox (badness 10000) detected at line 332 [][][] [150] Underfull \hbox (badness 10000) detected at line 335 [][][] Underfull \hbox (badness 10000) detected at line 352 [][][] Underfull \hbox (badness 10000) detected at line 355 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.255 on input line 362. Underfull \hbox (badness 10000) detected at line 377 [][][] Underfull \hbox (badness 10000) detected at line 380 [][][] Underfull \hbox (badness 10000) detected at line 383 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.256 on input line 394. [151] Underfull \hbox (badness 10000) detected at line 409 [][][] Underfull \hbox (badness 10000) detected at line 412 [][][] Underfull \hbox (badness 10000) detected at line 415 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.257 on input line 428. Underfull \hbox (badness 10000) detected at line 443 [][][] Underfull \hbox (badness 10000) detected at line 446 [][][] Underfull \hbox (badness 10000) detected at line 449 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.258 on input line 462. Overfull \vbox (15.85518pt too high) has occurred while \output is active [152]) (./group___vatom.tex [153] Underfull \hbox (badness 10000) detected at line 97 [][][] [154] Underfull \hbox (badness 10000) detected at line 134 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.259 on input line 143. Underfull \hbox (badness 10000) detected at line 158 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.260 on input line 167. Underfull \hbox (badness 10000) detected at line 182 [][][] Underfull \hbox (badness 10000) detected at line 185 [][][] [155] Underfull \hbox (badness 10000) detected at line 202 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.261 on input line 209. Underfull \hbox (badness 10000) detected at line 210 [][][] Underfull \hbox (badness 10000) detected at line 227 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.262 on input line 234. Underfull \hbox (badness 10000) detected at line 249 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.263 on input line 256. Underfull \hbox (badness 10000) detected at line 271 [][][] [156] Package longtable Warning: Column widths have changed (longtable) in table 7.264 on input line 278. Underfull \hbox (badness 10000) detected at line 279 [][][] Underfull \hbox (badness 10000) detected at line 296 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.265 on input line 305. Underfull \hbox (badness 10000) detected at line 320 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.266 on input line 327. Underfull \hbox (badness 10000) detected at line 328 [][][] [157] Underfull \hbox (badness 10000) detected at line 345 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.267 on input line 352. Underfull \hbox (badness 10000) detected at line 353 [][][] Underfull \hbox (badness 10000) detected at line 370 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.268 on input line 377. Underfull \hbox (badness 10000) detected at line 378 [][][] Underfull \hbox (badness 10000) detected at line 395 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.269 on input line 402. Underfull \hbox (badness 10000) detected at line 403 [][][] [158] Underfull \hbox (badness 10000) detected at line 420 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.270 on input line 427. Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 445 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.271 on input line 454. Underfull \hbox (badness 10000) detected at line 469 [][][] [159] Package longtable Warning: Column widths have changed (longtable) in table 7.272 on input line 476. Underfull \hbox (badness 10000) detected at line 477 [][][] Underfull \hbox (badness 10000) detected at line 494 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.273 on input line 503. Underfull \hbox (badness 10000) detected at line 518 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.274 on input line 527. [160] Underfull \hbox (badness 10000) detected at line 542 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.275 on input line 551. Underfull \hbox (badness 10000) detected at line 566 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.276 on input line 575. Underfull \hbox (badness 10000) detected at line 590 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.277 on input line 599. [161] Underfull \hbox (badness 10000) detected at line 614 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.278 on input line 623. Underfull \hbox (badness 10000) detected at line 638 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.279 on input line 647. Underfull \hbox (badness 10000) detected at line 662 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.280 on input line 671. ) (./group___vcap.tex [162] Underfull \hbox (badness 10000) detected at line 36 [][][] [163] Underfull \hbox (badness 10000) detected at line 86 [][][] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 92 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.281 on input line 101. Underfull \hbox (badness 10000) detected at line 119 [][][] Underfull \hbox (badness 10000) detected at line 122 [][][] Underfull \hbox (badness 10000) detected at line 125 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.282 on input line 134. [164] Underfull \hbox (badness 10000) detected at line 152 [][][] Underfull \hbox (badness 10000) detected at line 155 [][][] Underfull \hbox (badness 10000) detected at line 158 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.283 on input line 167. ) (./group___vclist.tex [165] [166] Underfull \hbox (badness 10000) detected at line 110 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.284 on input line 122. Underfull \hbox (badness 10000) detected at line 140 [][][] Underfull \hbox (badness 10000) detected at line 143 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.285 on input line 160. [167] Underfull \hbox (badness 10000) detected at line 175 [][][] Underfull \hbox (badness 10000) detected at line 178 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.286 on input line 197. Underfull \hbox (badness 10000) detected at line 212 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.287 on input line 219. [168] Underfull \hbox (badness 10000) detected at line 234 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.288 on input line 241. Underfull \hbox (badness 10000) detected at line 256 [][][] Underfull \hbox (badness 10000) detected at line 259 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.289 on input line 268. Underfull \hbox (badness 10000) detected at line 283 [][][] Underfull \hbox (badness 10000) detected at line 286 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.290 on input line 293. [169] Underfull \hbox (badness 10000) detected at line 308 [][][] Underfull \hbox (badness 10000) detected at line 311 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.291 on input line 318. Underfull \hbox (badness 10000) detected at line 333 [][][] Underfull \hbox (badness 10000) detected at line 336 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.292 on input line 343. Underfull \hbox (badness 10000) detected at line 358 [][][] Underfull \hbox (badness 10000) detected at line 361 [][][] [170] Package longtable Warning: Column widths have changed (longtable) in table 7.293 on input line 370. Underfull \hbox (badness 10000) detected at line 385 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.294 on input line 392. Underfull \hbox (badness 10000) detected at line 407 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.295 on input line 414. ) (./group___vgreen.tex [171] Underfull \hbox (badness 10000) detected at line 57 [][][] Underfull \hbox (badness 10000) detected at line 60 [][][] [172] [173] Underfull \hbox (badness 10000) detected at line 141 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.296 on input line 158. Underfull \hbox (badness 10000) detected at line 159 [][][] Underfull \hbox (badness 10000) detected at line 178 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.297 on input line 195. [174] Underfull \hbox (badness 10000) detected at line 196 [][][] Underfull \hbox (badness 10000) detected at line 215 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.298 on input line 238. [175] Underfull \hbox (badness 10000) detected at line 239 [][][] Underfull \hbox (badness 10000) detected at line 258 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.299 on input line 281. Underfull \hbox (badness 10000) detected at line 282 [][][] [176] Underfull \hbox (badness 10000) detected at line 299 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.300 on input line 306. Underfull \hbox (badness 10000) detected at line 307 [][][] Underfull \hbox (badness 10000) detected at line 324 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.301 on input line 333. Underfull \hbox (badness 10000) detected at line 334 [][][] Underfull \hbox (badness 10000) detected at line 351 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.302 on input line 358. [177] Underfull \hbox (badness 10000) detected at line 373 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.303 on input line 380. Underfull \hbox (badness 10000) detected at line 395 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.304 on input line 402. Underfull \hbox (badness 10000) detected at line 403 [][][] Underfull \hbox (badness 10000) detected at line 424 [][][] [178] Underfull \hbox (badness 10000) detected at line 429 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.305 on input line 448. Underfull \hbox (badness 10000) detected at line 449 [][][] Underfull \hbox (badness 10000) detected at line 471 [][][] Underfull \hbox (badness 10000) detected at line 476 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.306 on input line 499. [179] Underfull \hbox (badness 10000) detected at line 500 [][][] Underfull \hbox (badness 10000) detected at line 517 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.307 on input line 524. Underfull \hbox (badness 10000) detected at line 525 [][][] ) (./group___vhal.tex [180] [181] [182] [183] Underfull \hbox (badness 10000) detected at line 380 [][][] Underfull \hbox (badness 10000) detected at line 411 [][][] [184] Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 445 [][][] Underfull \hbox (badness 10000) detected at line 476 [][][] Underfull \hbox (badness 10000) detected at line 493 [][][] Underfull \hbox (badness 10000) detected at line 516 [][][] [185] Underfull \hbox (badness 10000) detected at line 547 [][][] [186] Underfull \hbox (badness 10000) detected at line 682 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.308 on input line 714. Underfull \hbox (badness 10000) detected at line 729 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.309 on input line 745. [187] Underfull \hbox (badness 10000) detected at line 760 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.310 on input line 780. Underfull \hbox (badness 10000) detected at line 795 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.311 on input line 827. Underfull \hbox (badness 10000) detected at line 842 [][][] Missing character: There is no Å in font cmr10! Missing character: There is no Å in font cmr10! LaTeX Warning: Command \r invalid in math mode on input line 58. Missing character: There is no Å in font cmr10! Package longtable Warning: Column widths have changed (longtable) in table 7.312 on input line 906. [188] Package longtable Warning: Column widths have changed (longtable) in table 7.313 on input line 934. Package longtable Warning: Column widths have changed (longtable) in table 7.314 on input line 980. [189] Package longtable Warning: Column widths have changed (longtable) in table 7.315 on input line 1004. Underfull \hbox (badness 10000) detected at line 1019 [][][] Underfull \hbox (badness 10000) detected at line 1022 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.316 on input line 1035. Underfull \hbox (badness 10000) detected at line 1050 [][][] Underfull \hbox (badness 10000) detected at line 1053 [][][] Underfull \hbox (badness 10000) detected at line 1070 [][][] [190] Package longtable Warning: Column widths have changed (longtable) in table 7.317 on input line 1095. ) (./group___vmatrix.tex) (./group___vparam.tex [191] [192] Underfull \hbox (badness 10000) detected at line 120 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.318 on input line 129. Underfull \hbox (badness 10000) detected at line 130 [][][] [193] Underfull \hbox (badness 10000) detected at line 147 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.319 on input line 156. Underfull \hbox (badness 10000) detected at line 157 [][][] Underfull \hbox (badness 10000) detected at line 174 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.320 on input line 183. Underfull \hbox (badness 10000) detected at line 198 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.321 on input line 207. [194] Underfull \hbox (badness 10000) detected at line 222 [][][] Underfull \hbox (badness 10000) detected at line 225 [][][] Underfull \hbox (badness 10000) detected at line 242 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.322 on input line 249. Underfull \hbox (badness 10000) detected at line 250 [][][] Underfull \hbox (badness 10000) detected at line 267 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.323 on input line 274. [195] Underfull \hbox (badness 10000) detected at line 289 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.324 on input line 296. Underfull \hbox (badness 10000) detected at line 311 [][][] Underfull \hbox (badness 10000) detected at line 314 [][][] Underfull \hbox (badness 10000) detected at line 331 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.325 on input line 338. Underfull \hbox (badness 10000) detected at line 339 [][][] Underfull \hbox (badness 10000) detected at line 356 [][][] [196] Package longtable Warning: Column widths have changed (longtable) in table 7.326 on input line 363. Underfull \hbox (badness 10000) detected at line 378 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.327 on input line 385. Underfull \hbox (badness 10000) detected at line 400 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.328 on input line 411. Underfull \hbox (badness 10000) detected at line 412 [][][] Underfull \hbox (badness 10000) detected at line 415 [][][] Underfull \hbox (badness 10000) detected at line 418 [][][] [197] Underfull \hbox (badness 10000) detected at line 435 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.329 on input line 444. Underfull \hbox (badness 10000) detected at line 445 [][][] Underfull \hbox (badness 10000) detected at line 448 [][][] Underfull \hbox (badness 10000) detected at line 451 [][][] Underfull \hbox (badness 10000) detected at line 468 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.330 on input line 475. Underfull \hbox (badness 10000) detected at line 476 [][][] [198] Underfull \hbox (badness 10000) detected at line 493 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.331 on input line 508. Underfull \hbox (badness 10000) detected at line 509 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Underfull \hbox (badness 10000) detected at line 537 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.332 on input line 552. [199] Underfull \hbox (badness 10000) detected at line 553 [][][] Underfull \hbox (badness 10000) detected at line 570 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.333 on input line 579. Underfull \hbox (badness 10000) detected at line 594 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.334 on input line 601. Underfull \hbox (badness 10000) detected at line 602 [][][] [200] Underfull \hbox (badness 10000) detected at line 619 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.335 on input line 628. Underfull \hbox (badness 10000) detected at line 629 [][][] Underfull \hbox (badness 10000) detected at line 646 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.336 on input line 653. Underfull \hbox (badness 10000) detected at line 668 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.337 on input line 675. [201]) (./group___vpbe.tex [202] [203] Underfull \hbox (badness 10000) detected at line 128 [][][] Underfull \hbox (badness 10000) detected at line 131 [][][] LaTeX Warning: Command \r invalid in math mode on input line 133. Missing character: There is no Å in font cmr10! LaTeX Warning: Command \r invalid in math mode on input line 133. Missing character: There is no Å in font cmr10! [204] Underfull \hbox (badness 10000) detected at line 136 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.338 on input line 171. [205] Underfull \hbox (badness 10000) detected at line 186 [][][] Underfull \hbox (badness 10000) detected at line 189 [][][] LaTeX Warning: Command \r invalid in math mode on input line 190. Missing character: There is no Å in font cmr10! LaTeX Warning: Command \r invalid in math mode on input line 190. Missing character: There is no Å in font cmr10! Underfull \hbox (badness 10000) detected at line 195 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.339 on input line 232. Overfull \vbox (21.60152pt too high) has occurred while \output is active [206] Underfull \hbox (badness 10000) detected at line 247 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.340 on input line 254. Underfull \hbox (badness 10000) detected at line 269 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.341 on input line 276. Underfull \hbox (badness 10000) detected at line 291 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.342 on input line 298. Underfull \hbox (badness 10000) detected at line 299 [][][] [207] Overfull \hbox (151.96916pt too wide) in paragraph at lines 318--318 [] \T1/p cr/m/n/8 permittivity equal to the protein interior) and zero ionic[] Underfull \hbox (badness 10000) detected at line 325 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.343 on input line 332. Underfull \hbox (badness 10000) detected at line 333 [][][] Underfull \hbox (badness 10000) detected at line 350 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.344 on input line 357. Underfull \hbox (badness 10000) detected at line 358 [][][] [208] Underfull \hbox (badness 10000) detected at line 375 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.345 on input line 382. Underfull \hbox (badness 10000) detected at line 383 [][][] Underfull \hbox (badness 10000) detected at line 396 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.346 on input line 411. Underfull \hbox (badness 10000) detected at line 412 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.347 on input line 435. [209] Underfull \hbox (badness 10000) detected at line 436 [][][] Underfull \hbox (badness 10000) detected at line 453 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.348 on input line 460. Underfull \hbox (badness 10000) detected at line 461 [][][] Underfull \hbox (badness 10000) detected at line 478 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.349 on input line 485. Underfull \hbox (badness 10000) detected at line 486 [][][] Underfull \hbox (badness 10000) detected at line 503 [][][] [210] Package longtable Warning: Column widths have changed (longtable) in table 7.350 on input line 510. Underfull \hbox (badness 10000) detected at line 525 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.351 on input line 532. Underfull \hbox (badness 10000) detected at line 533 [][][] Underfull \hbox (badness 10000) detected at line 550 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.352 on input line 557. Underfull \hbox (badness 10000) detected at line 558 [][][] Underfull \hbox (badness 10000) detected at line 575 [][][] [211] Package longtable Warning: Column widths have changed (longtable) in table 7.353 on input line 582. Underfull \hbox (badness 10000) detected at line 583 [][][] Underfull \hbox (badness 10000) detected at line 600 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.354 on input line 607. Underfull \hbox (badness 10000) detected at line 608 [][][] Underfull \hbox (badness 10000) detected at line 625 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.355 on input line 632. Underfull \hbox (badness 10000) detected at line 633 [][][] [212] Underfull \hbox (badness 10000) detected at line 650 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.356 on input line 657. Underfull \hbox (badness 10000) detected at line 658 [][][] Underfull \hbox (badness 10000) detected at line 675 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.357 on input line 682. Underfull \hbox (badness 10000) detected at line 683 [][][] Underfull \hbox (badness 10000) detected at line 700 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.358 on input line 707. Underfull \hbox (badness 10000) detected at line 708 [][][] [213] Underfull \hbox (badness 10000) detected at line 725 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.359 on input line 732. Underfull \hbox (badness 10000) detected at line 733 [][][] Underfull \hbox (badness 10000) detected at line 750 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.360 on input line 757. Underfull \hbox (badness 10000) detected at line 758 [][][] Underfull \hbox (badness 10000) detected at line 775 [][][] [214] Package longtable Warning: Column widths have changed (longtable) in table 7.361 on input line 782. Underfull \hbox (badness 10000) detected at line 783 [][][] Underfull \hbox (badness 10000) detected at line 800 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.362 on input line 807. Underfull \hbox (badness 10000) detected at line 808 [][][] Underfull \hbox (badness 10000) detected at line 825 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.363 on input line 832. Underfull \hbox (badness 10000) detected at line 833 [][][] [215] Underfull \hbox (badness 10000) detected at line 850 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.364 on input line 857. Underfull \hbox (badness 10000) detected at line 858 [][][] LaTeX Warning: Command \r invalid in math mode on input line 859. Missing character: There is no Å in font cmr10! Underfull \hbox (badness 10000) detected at line 875 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.365 on input line 882. Underfull \hbox (badness 10000) detected at line 883 [][][] Underfull \hbox (badness 10000) detected at line 900 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.366 on input line 907. Underfull \hbox (badness 10000) detected at line 908 [][][] [216] Underfull \hbox (badness 10000) detected at line 925 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.367 on input line 932. Underfull \hbox (badness 10000) detected at line 933 [][][] ) (./group___vstring.tex [217] Underfull \hbox (badness 10000) detected at line 42 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.368 on input line 49. Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 67 [][][] Underfull \hbox (badness 10000) detected at line 70 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.369 on input line 79. Underfull \hbox (badness 10000) detected at line 80 [][][] Underfull \hbox (badness 10000) detected at line 93 [][][] [218] Underfull \hbox (badness 10000) detected at line 96 [][][] Underfull \hbox (badness 10000) detected at line 99 [][][] Underfull \hbox (badness 10000) detected at line 102 [][][] Underfull \hbox (badness 10000) detected at line 105 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.370 on input line 116. ) (./group___vunit.tex [219] LaTeX Warning: Command \r invalid in math mode on input line 39. Missing character: There is no Å in font cmr9! [220] LaTeX Warning: Command \r invalid in math mode on input line 142. Missing character: There is no Å in font cmr10! ) (./group___vgrid.tex [221] [222] [223] Underfull \hbox (badness 10000) detected at line 125 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.371 on input line 150. Underfull \hbox (badness 10000) detected at line 151 [][][] Underfull \hbox (badness 10000) detected at line 168 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.372 on input line 195. [224] Underfull \hbox (badness 10000) detected at line 196 [][][] Underfull \hbox (badness 10000) detected at line 213 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.373 on input line 228. Underfull \hbox (badness 10000) detected at line 229 [][][] [225] Underfull \hbox (badness 10000) detected at line 246 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.374 on input line 253. Underfull \hbox (badness 10000) detected at line 268 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.375 on input line 275. Underfull \hbox (badness 10000) detected at line 290 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.376 on input line 301. Underfull \hbox (badness 10000) detected at line 302 [][][] [226] Underfull \hbox (badness 10000) detected at line 319 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.377 on input line 326. Underfull \hbox (badness 10000) detected at line 327 [][][] Underfull \hbox (badness 10000) detected at line 344 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.378 on input line 351. Underfull \hbox (badness 10000) detected at line 352 [][][] Underfull \hbox (badness 10000) detected at line 369 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.379 on input line 376. Underfull \hbox (badness 10000) detected at line 377 [][][] [227] Underfull \hbox (badness 10000) detected at line 395 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.380 on input line 402. Underfull \hbox (badness 10000) detected at line 403 [][][] Underfull \hbox (badness 10000) detected at line 420 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.381 on input line 427. Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 445 [][][] [228] Package longtable Warning: Column widths have changed (longtable) in table 7.382 on input line 452. Underfull \hbox (badness 10000) detected at line 453 [][][] Underfull \hbox (badness 10000) detected at line 470 [][][] Underfull \hbox (badness 10000) detected at line 473 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.383 on input line 488. Underfull \hbox (badness 10000) detected at line 489 [][][] Underfull \hbox (badness 10000) detected at line 492 [][][] [229] Underfull \hbox (badness 10000) detected at line 509 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.384 on input line 527. Underfull \hbox (badness 10000) detected at line 528 [][][] Underfull \hbox (badness 10000) detected at line 531 [][][] Underfull \hbox (badness 10000) detected at line 548 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.385 on input line 560. [230] Underfull \hbox (badness 10000) detected at line 575 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.386 on input line 582. Underfull \hbox (badness 10000) detected at line 583 [][][] Underfull \hbox (badness 10000) detected at line 600 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.387 on input line 611. Underfull \hbox (badness 10000) detected at line 612 [][][] [231] Underfull \hbox (badness 10000) detected at line 629 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.388 on input line 648. Underfull \hbox (badness 10000) detected at line 663 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.389 on input line 682. [232] Underfull \hbox (badness 10000) detected at line 697 [][][] Underfull \hbox (badness 10000) detected at line 702 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.390 on input line 721. ) (./group___vmgrid.tex [233] [234] Underfull \hbox (badness 10000) detected at line 105 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.391 on input line 114. Underfull \hbox (badness 10000) detected at line 115 [][][] Underfull \hbox (badness 10000) detected at line 132 [][][] Underfull \hbox (badness 10000) detected at line 135 [][][] Underfull \hbox (badness 10000) detected at line 152 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.392 on input line 159. [235] Underfull \hbox (badness 10000) detected at line 160 [][][] Underfull \hbox (badness 10000) detected at line 177 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.393 on input line 192. Underfull \hbox (badness 10000) detected at line 193 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.394 on input line 217. [236] Underfull \hbox (badness 10000) detected at line 232 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.395 on input line 239. Underfull \hbox (badness 10000) detected at line 254 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.396 on input line 263. Underfull \hbox (badness 10000) detected at line 264 [][][] Underfull \hbox (badness 10000) detected at line 277 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.397 on input line 286. [237] Underfull \hbox (badness 10000) detected at line 287 [][][] Underfull \hbox (badness 10000) detected at line 300 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.398 on input line 311. Underfull \hbox (badness 10000) detected at line 312 [][][] Underfull \hbox (badness 10000) detected at line 329 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.399 on input line 340. Underfull \hbox (badness 10000) detected at line 341 [][][] ) (./group___vopot.tex [238] [239] Underfull \hbox (badness 10000) detected at line 77 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.400 on input line 88. Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 106 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.401 on input line 119. [240] Underfull \hbox (badness 10000) detected at line 120 [][][] Underfull \hbox (badness 10000) detected at line 137 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.402 on input line 152. Underfull \hbox (badness 10000) detected at line 153 [][][] Underfull \hbox (badness 10000) detected at line 170 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.403 on input line 177. [241] Underfull \hbox (badness 10000) detected at line 192 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.404 on input line 199. Underfull \hbox (badness 10000) detected at line 214 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.405 on input line 225. Underfull \hbox (badness 10000) detected at line 226 [][][] Underfull \hbox (badness 10000) detected at line 243 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.406 on input line 254. Overfull \vbox (28.1848pt too high) has occurred while \output is active [242] Underfull \hbox (badness 10000) detected at line 255 [][][] ) (./group___vpmg.tex [243] [244] [245] Underfull \hbox (badness 10000) detected at line 117 [][][] Underfull \hbox (badness 10000) detected at line 150 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.407 on input line 171. [246] Underfull \hbox (badness 10000) detected at line 186 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.408 on input line 219. [247] Underfull \hbox (badness 10000) detected at line 234 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.409 on input line 261. Underfull \hbox (badness 10000) detected at line 276 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.410 on input line 309. [248] Underfull \hbox (badness 10000) detected at line 324 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.411 on input line 347. [249] Underfull \hbox (badness 10000) detected at line 362 [][][] Underfull \hbox (badness 10000) detected at line 381 [][][] Underfull \hbox (badness 10000) detected at line 384 [][][] [250] Package longtable Warning: Column widths have changed (longtable) in table 7.412 on input line 401. Underfull \hbox (badness 10000) detected at line 416 [][][] Underfull \hbox (badness 10000) detected at line 419 [][][] Underfull \hbox (badness 10000) detected at line 422 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.413 on input line 443. [251] Underfull \hbox (badness 10000) detected at line 458 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.414 on input line 473. Underfull \hbox (badness 10000) detected at line 484 [][][] Underfull \hbox (badness 10000) detected at line 487 [][][] Underfull \hbox (badness 10000) detected at line 492 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.415 on input line 505. Overfull \vbox (1.11014pt too high) has occurred while \output is active [252] Underfull \hbox (badness 10000) detected at line 520 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.416 on input line 535. Underfull \hbox (badness 10000) detected at line 546 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.417 on input line 561. [253] Underfull \hbox (badness 10000) detected at line 572 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.418 on input line 583. Underfull \hbox (badness 10000) detected at line 604 [][][] Underfull \hbox (badness 10000) detected at line 607 [][][] Underfull \hbox (badness 10000) detected at line 610 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.419 on input line 619. [254] Underfull \hbox (badness 10000) detected at line 643 [][][] Underfull \hbox (badness 10000) detected at line 646 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.420 on input line 653. Underfull \hbox (badness 10000) detected at line 668 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.421 on input line 675. Underfull \hbox (badness 10000) detected at line 690 [][][] [255] Package longtable Warning: Column widths have changed (longtable) in table 7.422 on input line 697. Underfull \hbox (badness 10000) detected at line 712 [][][] Underfull \hbox (badness 10000) detected at line 715 [][][] Underfull \hbox (badness 10000) detected at line 718 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.423 on input line 727. Underfull \hbox (badness 10000) detected at line 742 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.424 on input line 753. [256] Underfull \hbox (badness 10000) detected at line 764 [][][] Underfull \hbox (badness 10000) detected at line 767 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.425 on input line 784. Underfull \hbox (badness 10000) detected at line 799 [][][] [257] Underfull \hbox (badness 10000) detected at line 802 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.426 on input line 841. Underfull \hbox (badness 10000) detected at line 856 [][][] Underfull \hbox (badness 10000) detected at line 859 [][][] Underfull \hbox (badness 10000) detected at line 864 [][][] [258] Package longtable Warning: Column widths have changed (longtable) in table 7.427 on input line 879. Underfull \hbox (badness 10000) detected at line 894 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.428 on input line 909. Underfull \hbox (badness 10000) detected at line 920 [][][] Underfull \hbox (badness 10000) detected at line 923 [][][] [259] Underfull \hbox (badness 10000) detected at line 928 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.429 on input line 941. Underfull \hbox (badness 10000) detected at line 956 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.430 on input line 971. Underfull \hbox (badness 10000) detected at line 982 [][][] [260] Package longtable Warning: Column widths have changed (longtable) in table 7.431 on input line 997. Underfull \hbox (badness 10000) detected at line 1008 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.432 on input line 1019. Underfull \hbox (badness 10000) detected at line 1030 [][][] Underfull \hbox (badness 10000) detected at line 1033 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.433 on input line 1040. [261] Underfull \hbox (badness 10000) detected at line 1055 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.434 on input line 1076. Underfull \hbox (badness 10000) detected at line 1093 [][][] Underfull \hbox (badness 10000) detected at line 1096 [][][] [262] Underfull \hbox (badness 10000) detected at line 1099 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.435 on input line 1108. Underfull \hbox (badness 10000) detected at line 1123 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.436 on input line 1140. Underfull \hbox (badness 10000) detected at line 1160 [][][] [263] Underfull \hbox (badness 10000) detected at line 1163 [][][] Underfull \hbox (badness 10000) detected at line 1166 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.437 on input line 1175. Underfull \hbox (badness 10000) detected at line 1190 [][][] Underfull \hbox (badness 10000) detected at line 1193 [][][] Underfull \hbox (badness 10000) detected at line 1198 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.438 on input line 1211. [264] Underfull \hbox (badness 10000) detected at line 1226 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.439 on input line 1241. Underfull \hbox (badness 10000) detected at line 1252 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.440 on input line 1269. [265] Underfull \hbox (badness 10000) detected at line 1280 [][][] Underfull \hbox (badness 10000) detected at line 1283 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.441 on input line 1292. Underfull \hbox (badness 10000) detected at line 1303 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.442 on input line 1316. [266] Underfull \hbox (badness 10000) detected at line 1343 [][][] Underfull \hbox (badness 10000) detected at line 1346 [][][] Underfull \hbox (badness 10000) detected at line 1349 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.443 on input line 1358. Underfull \hbox (badness 10000) detected at line 1373 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.444 on input line 1386. [267] Underfull \hbox (badness 10000) detected at line 1401 [][][] Underfull \hbox (badness 10000) detected at line 1404 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.445 on input line 1411. Underfull \hbox (badness 10000) detected at line 1426 [][][] Underfull \hbox (badness 10000) detected at line 1429 [][][] Underfull \hbox (badness 10000) detected at line 1432 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.446 on input line 1439. Underfull \hbox (badness 10000) detected at line 1454 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.447 on input line 1461. ) (./group___vpmgp.tex [268] Underfull \hbox (badness 10000) detected at line 45 [][][] [269] Underfull \hbox (badness 10000) detected at line 78 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.448 on input line 85. Underfull \hbox (badness 10000) detected at line 86 [][][] Underfull \hbox (badness 10000) detected at line 103 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.449 on input line 112. Underfull \hbox (badness 10000) detected at line 113 [][][] Underfull \hbox (badness 10000) detected at line 130 [][][] [270] Package longtable Warning: Column widths have changed (longtable) in table 7.450 on input line 137. Underfull \hbox (badness 10000) detected at line 152 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.451 on input line 159. Underfull \hbox (badness 10000) detected at line 174 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.452 on input line 193. [271] Underfull \hbox (badness 10000) detected at line 208 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.453 on input line 215. ) (./group___p_m_g_c.tex [272] [273] [274] [275] Underfull \hbox (badness 10000) detected at line 150 [][][] Underfull \hbox (badness 10000) detected at line 153 [][][] Underfull \hbox (badness 10000) detected at line 156 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 165--165 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [276] Underfull \hbox (badness 10000) detected at line 212 [][][] Underfull \hbox (badness 10000) detected at line 215 [][][] Underfull \hbox (badness 10000) detected at line 218 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 227--227 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [277] Underfull \hbox (badness 10000) detected at line 277 [][][] Underfull \hbox (badness 10000) detected at line 280 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.454 on input line 293. [278] Underfull \hbox (badness 10000) detected at line 308 [][][] Underfull \hbox (badness 10000) detected at line 311 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.455 on input line 324. Underfull \hbox (badness 10000) detected at line 339 [][][] Underfull \hbox (badness 10000) detected at line 342 [][][] Underfull \hbox (badness 10000) detected at line 345 [][][] [279] Overfull \hbox (304.08286pt too wide) in paragraph at lines 355--355 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 392 [][][] Underfull \hbox (badness 10000) detected at line 395 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 404--404 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [280] Underfull \hbox (badness 10000) detected at line 439 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.456 on input line 488. [281] Underfull \hbox (badness 10000) detected at line 503 [][][] Underfull \hbox (badness 10000) detected at line 506 [][][] Underfull \hbox (badness 10000) detected at line 509 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 518--518 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [282] Underfull \hbox (badness 10000) detected at line 556 [][][] Underfull \hbox (badness 10000) detected at line 559 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 568--568 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 603 [][][] Underfull \hbox (badness 10000) detected at line 606 [][][] [283] Package longtable Warning: Column widths have changed (longtable) in table 7.457 on input line 631. Underfull \hbox (badness 10000) detected at line 646 [][][] Underfull \hbox (badness 10000) detected at line 649 [][][] [284] Package longtable Warning: Column widths have changed (longtable) in table 7.458 on input line 704. [285] Underfull \hbox (badness 10000) detected at line 719 [][][] Underfull \hbox (badness 10000) detected at line 722 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.459 on input line 757. Underfull \hbox (badness 10000) detected at line 772 [][][] Underfull \hbox (badness 10000) detected at line 775 [][][] Underfull \hbox (badness 10000) detected at line 778 [][][] [286] Overfull \hbox (304.08286pt too wide) in paragraph at lines 788--788 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 825 [][][] Underfull \hbox (badness 10000) detected at line 828 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 837--837 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [287] Package longtable Warning: Column widths have changed (longtable) in table 7.460 on input line 892. [288] Underfull \hbox (badness 10000) detected at line 907 [][][] Underfull \hbox (badness 10000) detected at line 910 [][][] [289] Package longtable Warning: Column widths have changed (longtable) in table 7.461 on input line 1035. [290] [291] Underfull \hbox (badness 10000) detected at line 1050 [][][] Underfull \hbox (badness 10000) detected at line 1053 [][][] [292] Package longtable Warning: Column widths have changed (longtable) in table 7.462 on input line 1214. [293] [294] Underfull \hbox (badness 10000) detected at line 1229 [][][] Underfull \hbox (badness 10000) detected at line 1232 [][][] [295] Package longtable Warning: Column widths have changed (longtable) in table 7.463 on input line 1367. [296] Underfull \hbox (badness 10000) detected at line 1382 [][][] Underfull \hbox (badness 10000) detected at line 1385 [][][] Underfull \hbox (badness 10000) detected at line 1388 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.464 on input line 1431. [297] [298] Underfull \hbox (badness 10000) detected at line 1446 [][][] Underfull \hbox (badness 10000) detected at line 1449 [][][] Underfull \hbox (badness 10000) detected at line 1452 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 1462--1462 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 1501 [][][] Underfull \hbox (badness 10000) detected at line 1504 [][][] [299] Package longtable Warning: Column widths have changed (longtable) in table 7.465 on input line 1569. [300] Underfull \hbox (badness 10000) detected at line 1584 [][][] Underfull \hbox (badness 10000) detected at line 1587 [][][] Underfull \hbox (badness 10000) detected at line 1590 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 1600--1600 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 1637 [][][] Underfull \hbox (badness 10000) detected at line 1640 [][][] [301] Underfull \hbox (badness 10000) detected at line 1643 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 1652--1652 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Package longtable Warning: Column widths have changed (longtable) in table 7.466 on input line 1715. Overfull \vbox (9.44278pt too high) has occurred while \output is active [302] Underfull \hbox (badness 10000) detected at line 1730 [][][] Underfull \hbox (badness 10000) detected at line 1735 [][][] Underfull \hbox (badness 10000) detected at line 1738 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.467 on input line 1753. Underfull \hbox (badness 10000) detected at line 1768 [][][] Underfull \hbox (badness 10000) detected at line 1771 [][][] [303] Package longtable Warning: Column widths have changed (longtable) in table 7.468 on input line 1790. Underfull \hbox (badness 10000) detected at line 1805 [][][] Underfull \hbox (badness 10000) detected at line 1808 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.469 on input line 1827. [304] Underfull \hbox (badness 10000) detected at line 1842 [][][] Underfull \hbox (badness 10000) detected at line 1845 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.470 on input line 1864. Underfull \hbox (badness 10000) detected at line 1879 [][][] Underfull \hbox (badness 10000) detected at line 1882 [][][] [305] Underfull \hbox (badness 10000) detected at line 1885 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 1895--1895 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 1932 [][][] Underfull \hbox (badness 10000) detected at line 1935 [][][] Underfull \hbox (badness 10000) detected at line 1938 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 1947--1947 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [306] Package longtable Warning: Column widths have changed (longtable) in table 7.471 on input line 2018. [307] Underfull \hbox (badness 10000) detected at line 2033 [][][] Underfull \hbox (badness 10000) detected at line 2036 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.472 on input line 2055. Underfull \hbox (badness 10000) detected at line 2070 [][][] Underfull \hbox (badness 10000) detected at line 2073 [][][] Underfull \hbox (badness 10000) detected at line 2076 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 2086--2086 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [308] Underfull \hbox (badness 10000) detected at line 2123 [][][] Underfull \hbox (badness 10000) detected at line 2126 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2135--2135 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [309] Underfull \hbox (badness 10000) detected at line 2170 [][][] Underfull \hbox (badness 10000) detected at line 2173 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.473 on input line 2190. Underfull \hbox (badness 10000) detected at line 2205 [][][] [310] Underfull \hbox (badness 10000) detected at line 2208 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.474 on input line 2229. Underfull \hbox (badness 10000) detected at line 2244 [][][] Underfull \hbox (badness 10000) detected at line 2247 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.475 on input line 2268. [311] Underfull \hbox (badness 10000) detected at line 2283 [][][] Underfull \hbox (badness 10000) detected at line 2286 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.476 on input line 2299. [312] Underfull \hbox (badness 10000) detected at line 2314 [][][] Underfull \hbox (badness 10000) detected at line 2317 [][][] Underfull \hbox (badness 10000) detected at line 2320 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 2330--2330 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [313] Underfull \hbox (badness 10000) detected at line 2367 [][][] Underfull \hbox (badness 10000) detected at line 2370 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2379--2379 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 2414 [][][] Underfull \hbox (badness 10000) detected at line 2417 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.477 on input line 2488. [314] [315] Underfull \hbox (badness 10000) detected at line 2503 [][][] Underfull \hbox (badness 10000) detected at line 2506 [][][] Underfull \hbox (badness 10000) detected at line 2509 [][][] [316] Underfull \hbox (badness 10000) detected at line 2557 [][][] Underfull \hbox (badness 10000) detected at line 2560 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2569--2569 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [317] Underfull \hbox (badness 10000) detected at line 2604 [][][] Underfull \hbox (badness 10000) detected at line 2607 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.478 on input line 2682. [318] Underfull \hbox (badness 10000) detected at line 2697 [][][] Underfull \hbox (badness 10000) detected at line 2700 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.479 on input line 2731. [319] Underfull \hbox (badness 10000) detected at line 2746 [][][] Underfull \hbox (badness 10000) detected at line 2749 [][][] Underfull \hbox (badness 10000) detected at line 2752 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 2762--2762 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [320] Underfull \hbox (badness 10000) detected at line 2799 [][][] Underfull \hbox (badness 10000) detected at line 2802 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2811--2811 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 2846 [][][] Underfull \hbox (badness 10000) detected at line 2849 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.480 on input line 2890. [321] Underfull \hbox (badness 10000) detected at line 2905 [][][] Underfull \hbox (badness 10000) detected at line 2908 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.481 on input line 2931. Overfull \vbox (18.98318pt too high) has occurred while \output is active [322] Underfull \hbox (badness 10000) detected at line 2946 [][][] Underfull \hbox (badness 10000) detected at line 2957 [][][] [323] Underfull \hbox (badness 10000) detected at line 2960 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.482 on input line 3031. [324] Underfull \hbox (badness 10000) detected at line 3046 [][][] Underfull \hbox (badness 10000) detected at line 3049 [][][] Underfull \hbox (badness 10000) detected at line 3052 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3062--3062 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 3099 [][][] Underfull \hbox (badness 10000) detected at line 3102 [][][] [325] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 3111--3111 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 3146 [][][] Underfull \hbox (badness 10000) detected at line 3149 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.483 on input line 3172. [326] Underfull \hbox (badness 10000) detected at line 3187 [][][] Underfull \hbox (badness 10000) detected at line 3190 [][][] Underfull \hbox (badness 10000) detected at line 3193 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3203--3203 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [327] Underfull \hbox (badness 10000) detected at line 3240 [][][] Underfull \hbox (badness 10000) detected at line 3243 [][][] Underfull \hbox (badness 10000) detected at line 3246 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 3255--3255 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [328] Underfull \hbox (badness 10000) detected at line 3288 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.484 on input line 3327. [329] Underfull \hbox (badness 10000) detected at line 3342 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.485 on input line 3418. [330] [331] Underfull \hbox (badness 10000) detected at line 3484 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.486 on input line 3527. [332] Underfull \hbox (badness 10000) detected at line 3542 [][][] Underfull \hbox (badness 10000) detected at line 3545 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.487 on input line 3570. [333] Underfull \hbox (badness 10000) detected at line 3585 [][][] Underfull \hbox (badness 10000) detected at line 3588 [][][] Underfull \hbox (badness 10000) detected at line 3591 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3601--3601 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [334] Underfull \hbox (badness 10000) detected at line 3638 [][][] Underfull \hbox (badness 10000) detected at line 3641 [][][] Underfull \hbox (badness 10000) detected at line 3644 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 3653--3653 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [335] Underfull \hbox (badness 10000) detected at line 3702 [][][] Underfull \hbox (badness 10000) detected at line 3705 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.488 on input line 3774. [336] [337] Underfull \hbox (badness 10000) detected at line 3789 [][][] Underfull \hbox (badness 10000) detected at line 3792 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.489 on input line 3875. [338] Underfull \hbox (badness 10000) detected at line 3890 [][][] Underfull \hbox (badness 10000) detected at line 3893 [][][] Underfull \hbox (badness 10000) detected at line 3896 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3906--3906 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [339] Underfull \hbox (badness 10000) detected at line 3943 [][][] Underfull \hbox (badness 10000) detected at line 3946 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.490 on input line 3957. Underfull \hbox (badness 10000) detected at line 3972 [][][] Underfull \hbox (badness 10000) detected at line 3975 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.491 on input line 3986. [340] Underfull \hbox (badness 10000) detected at line 4001 [][][] Underfull \hbox (badness 10000) detected at line 4004 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.492 on input line 4019. [341] Underfull \hbox (badness 10000) detected at line 4034 [][][] Underfull \hbox (badness 10000) detected at line 4037 [][][] Underfull \hbox (badness 10000) detected at line 4040 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 4050--4050 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 4087 [][][] [342] Underfull \hbox (badness 10000) detected at line 4090 [][][] Underfull \hbox (badness 10000) detected at line 4093 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 4102--4102 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 4137 [][][] Underfull \hbox (badness 10000) detected at line 4140 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.493 on input line 4179. [343] Underfull \hbox (badness 10000) detected at line 4194 [][][] [344] Underfull \hbox (badness 10000) detected at line 4216 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.494 on input line 4275. Overfull \vbox (38.14133pt too high) has occurred while \output is active [345] Underfull \hbox (badness 10000) detected at line 4290 [][][] Underfull \hbox (badness 10000) detected at line 4293 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.495 on input line 4368. [346] [347] Underfull \hbox (badness 10000) detected at line 4383 [][][] Underfull \hbox (badness 10000) detected at line 4386 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.496 on input line 4411. Underfull \hbox (badness 10000) detected at line 4426 [][][] Underfull \hbox (badness 10000) detected at line 4429 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.497 on input line 4456. [348] Underfull \hbox (badness 10000) detected at line 4471 [][][] Underfull \hbox (badness 10000) detected at line 4474 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.498 on input line 4517. [349] Underfull \hbox (badness 10000) detected at line 4532 [][][] Underfull \hbox (badness 10000) detected at line 4535 [][][] Underfull \hbox (badness 10000) detected at line 4538 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 4548--4548 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [350] Underfull \hbox (badness 10000) detected at line 4585 [][][] Underfull \hbox (badness 10000) detected at line 4588 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 4597--4597 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [351] Underfull \hbox (badness 10000) detected at line 4630 [][][] Underfull \hbox (badness 10000) detected at line 4633 [][][] Underfull \hbox (badness 10000) detected at line 4636 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.499 on input line 4681. [352] Underfull \hbox (badness 10000) detected at line 4692 [][][] Underfull \hbox (badness 10000) detected at line 4695 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.500 on input line 4712. Underfull \hbox (badness 10000) detected at line 4727 [][][] Underfull \hbox (badness 10000) detected at line 4730 [][][] [353] Package longtable Warning: Column widths have changed (longtable) in table 7.501 on input line 4753. Underfull \hbox (badness 10000) detected at line 4768 [][][] Underfull \hbox (badness 10000) detected at line 4771 [][][] Underfull \hbox (badness 10000) detected at line 4774 [][][] Overfull \hbox (20.88268pt too wide) in paragraph at lines 4784--4784 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute,[] [354] Underfull \hbox (badness 10000) detected at line 4822 [][][] Underfull \hbox (badness 10000) detected at line 4825 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 4834--4834 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [355] Underfull \hbox (badness 10000) detected at line 4869 [][][] Underfull \hbox (badness 10000) detected at line 4872 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.502 on input line 4915. [356] Underfull \hbox (badness 10000) detected at line 4930 [][][] Underfull \hbox (badness 10000) detected at line 4933 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.503 on input line 4950. Underfull \hbox (badness 10000) detected at line 4965 [][][] Underfull \hbox (badness 10000) detected at line 4968 [][][] Underfull \hbox (badness 10000) detected at line 4971 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 4981--4981 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [357] Underfull \hbox (badness 10000) detected at line 5018 [][][] Underfull \hbox (badness 10000) detected at line 5021 [][][] Underfull \hbox (badness 10000) detected at line 5024 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 5033--5033 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [358] Underfull \hbox (badness 10000) detected at line 5068 [][][] Underfull \hbox (badness 10000) detected at line 5071 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.504 on input line 5086. Underfull \hbox (badness 10000) detected at line 5101 [][][] Underfull \hbox (badness 10000) detected at line 5104 [][][] Underfull \hbox (badness 10000) detected at line 5107 [][][] [359] Package longtable Warning: Column widths have changed (longtable) in table 7.505 on input line 5122. Underfull \hbox (badness 10000) detected at line 5137 [][][] Underfull \hbox (badness 10000) detected at line 5140 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.506 on input line 5155. Underfull \hbox (badness 10000) detected at line 5170 [][][] [360] Underfull \hbox (badness 10000) detected at line 5173 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.507 on input line 5188. Underfull \hbox (badness 10000) detected at line 5203 [][][] Underfull \hbox (badness 10000) detected at line 5206 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.508 on input line 5219. Underfull \hbox (badness 10000) detected at line 5234 [][][] [361] Underfull \hbox (badness 10000) detected at line 5237 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.509 on input line 5250. Underfull \hbox (badness 10000) detected at line 5265 [][][] Underfull \hbox (badness 10000) detected at line 5268 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.510 on input line 5283. ) (./group___frontend.tex [362] Underfull \hbox (badness 2495) in paragraph at lines 32--33 []\T1/phv/m/n/10 VPUBLIC Vrc[]_[][]Codes [] (int icalc, [] $\OMS/cmsy/m/n/10 ^^ C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 feparm, [] $\OMS /cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbeparm, [] Overfull \hbox (16.65858pt too wide) in paragraph at lines 40--41 []\T1/phv/m/n/10 VEXTERNC int [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], Overfull \hbox (16.91972pt too wide) in paragraph at lines 42--43 []\T1/phv/m/n/10 VEXTERNC void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh , [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/1 0 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], Underfull \hbox (badness 1910) in paragraph at lines 60--61 [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1 /phv/m/n/10 alist[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][] [], [] Underfull \hbox (badness 1237) in paragraph at lines 60--61 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 charge[]Map[][][], [] $\OMS/cmsy/m/n/10 ^^C $\T1/phv/m/n/10 pmgp[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pmg[][][], [] [363] Underfull \hbox (badness 5817) in paragraph at lines 78--79 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], Underfull \hbox (badness 5817) in paragraph at lines 80--81 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], [364] [365] Underfull \hbox (badness 10000) detected at line 178 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.511 on input line 196. Underfull \hbox (badness 10000) detected at line 211 [][][] [366] Package longtable Warning: Column widths have changed (longtable) in table 7.512 on input line 232. Underfull \hbox (badness 10000) detected at line 235 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.513 on input line 260. [367] Underfull \hbox (badness 10000) detected at line 275 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.514 on input line 296. Underfull \hbox (badness 10000) detected at line 297 [][][] Underfull \hbox (badness 10000) detected at line 314 [][][] Underfull \hbox (badness 10000) detected at line 317 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.515 on input line 336. [368] Underfull \hbox (badness 10000) detected at line 351 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.516 on input line 372. Underfull \hbox (badness 10000) detected at line 373 [][][] Underfull \hbox (badness 10000) detected at line 390 [][][] Underfull \hbox (badness 10000) detected at line 393 [][][] [369] Package longtable Warning: Column widths have changed (longtable) in table 7.517 on input line 480. [370] Underfull \hbox (badness 10000) detected at line 495 [][][] Underfull \hbox (badness 10000) detected at line 502 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.518 on input line 557. [371] Underfull \hbox (badness 10000) detected at line 572 [][][] Underfull \hbox (badness 10000) detected at line 575 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.519 on input line 610. [372] Underfull \hbox (badness 10000) detected at line 625 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.520 on input line 634. Underfull \hbox (badness 10000) detected at line 649 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.521 on input line 662. Underfull \hbox (badness 10000) detected at line 677 [][][] [373] Underfull \hbox (badness 10000) detected at line 694 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.522 on input line 705. Underfull \hbox (badness 10000) detected at line 720 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.523 on input line 733. Underfull \hbox (badness 10000) detected at line 748 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.524 on input line 757. [374] Underfull \hbox (badness 10000) detected at line 772 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.525 on input line 781. Underfull \hbox (badness 10000) detected at line 792 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.526 on input line 803. Underfull \hbox (badness 10000) detected at line 818 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.527 on input line 827. [375] Underfull \hbox (badness 10000) detected at line 842 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.528 on input line 851. Underfull \hbox (badness 10000) detected at line 866 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.529 on input line 875. Underfull \hbox (badness 10000) detected at line 876 [][][] Underfull \hbox (badness 10000) detected at line 895 [][][] [376] Package longtable Warning: Column widths have changed (longtable) in table 7.530 on input line 908. Underfull \hbox (badness 10000) detected at line 909 [][][] Underfull \hbox (badness 10000) detected at line 912 [][][] Underfull \hbox (badness 10000) detected at line 929 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.531 on input line 938. Underfull \hbox (badness 10000) detected at line 939 [][][] Underfull \hbox (badness 10000) detected at line 958 [][][] Underfull \hbox (badness 10000) detected at line 961 [][][] [377] Package longtable Warning: Column widths have changed (longtable) in table 7.532 on input line 970. Underfull \hbox (badness 10000) detected at line 981 [][][] Underfull \hbox (badness 10000) detected at line 984 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.533 on input line 995. Underfull \hbox (badness 10000) detected at line 1010 [][][] Underfull \hbox (badness 10000) detected at line 1013 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.534 on input line 1020. [378] Underfull \hbox (badness 10000) detected at line 1035 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.535 on input line 1044. Underfull \hbox (badness 10000) detected at line 1045 [][][] Underfull \hbox (badness 10000) detected at line 1064 [][][] Underfull \hbox (badness 10000) detected at line 1067 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.536 on input line 1076. Underfull \hbox (badness 10000) detected at line 1091 [][][] [379] Package longtable Warning: Column widths have changed (longtable) in table 7.537 on input line 1104. Underfull \hbox (badness 10000) detected at line 1105 [][][] Underfull \hbox (badness 10000) detected at line 1122 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.538 on input line 1133. Underfull \hbox (badness 10000) detected at line 1134 [][][] Underfull \hbox (badness 10000) in paragraph at lines 1135--1136 Underfull \hbox (badness 10000) detected at line 1138 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.539 on input line 1151. [380] Underfull \hbox (badness 10000) detected at line 1166 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.540 on input line 1179. Underfull \hbox (badness 10000) detected at line 1180 [][][] Underfull \hbox (badness 10000) detected at line 1201 [][][] Underfull \hbox (badness 10000) detected at line 1204 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.541 on input line 1213. [381] Underfull \hbox (badness 10000) detected at line 1228 [][][] Underfull \hbox (badness 10000) detected at line 1231 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.542 on input line 1244. Underfull \hbox (badness 10000) detected at line 1259 [][][] Underfull \hbox (badness 10000) detected at line 1262 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.543 on input line 1273. [382] Underfull \hbox (badness 10000) detected at line 1288 [][][] Underfull \hbox (badness 10000) detected at line 1291 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.544 on input line 1304. Underfull \hbox (badness 10000) detected at line 1319 [][][] Underfull \hbox (badness 10000) detected at line 1322 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.545 on input line 1333. [383] Underfull \hbox (badness 10000) detected at line 1348 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.546 on input line 1362. Underfull \hbox (badness 10000) detected at line 1377 [][][] Underfull \hbox (badness 10000) detected at line 1380 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.547 on input line 1393. Underfull \hbox (badness 10000) detected at line 1408 [][][] [384] Package longtable Warning: Column widths have changed (longtable) in table 7.548 on input line 1417. Underfull \hbox (badness 10000) detected at line 1432 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.549 on input line 1439. Underfull \hbox (badness 10000) detected at line 1454 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.550 on input line 1467. Underfull \hbox (badness 10000) detected at line 1468 [][][] [385] Underfull \hbox (badness 10000) detected at line 1485 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.551 on input line 1496. Underfull \hbox (badness 10000) detected at line 1497 [][][] Underfull \hbox (badness 10000) detected at line 1514 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.552 on input line 1527. Underfull \hbox (badness 10000) detected at line 1528 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.553 on input line 1547. [386] Underfull \hbox (badness 10000) detected at line 1562 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.554 on input line 1573. Underfull \hbox (badness 10000) detected at line 1574 [][][] Underfull \hbox (badness 10000) detected at line 1591 [][][] Underfull \hbox (badness 10000) detected at line 1608 [][][] [387] Package longtable Warning: Column widths have changed (longtable) in table 7.555 on input line 1621. Underfull \hbox (badness 10000) detected at line 1636 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.556 on input line 1649. Underfull \hbox (badness 10000) detected at line 1650 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.557 on input line 1673. [388] Underfull \hbox (badness 10000) detected at line 1688 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.558 on input line 1715. Underfull \hbox (badness 10000) detected at line 1716 [][][] Underfull \hbox (badness 10000) detected at line 1733 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.559 on input line 1746. [389] Underfull \hbox (badness 10000) detected at line 1747 [][][] Underfull \hbox (badness 10000) detected at line 1764 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.560 on input line 1791. Underfull \hbox (badness 10000) detected at line 1792 [][][] [390] Underfull \hbox (badness 10000) detected at line 1809 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.561 on input line 1822. Underfull \hbox (badness 10000) detected at line 1823 [][][] ) [391] [392] Chapter 8. (./struct_atom_force.tex Underfull \hbox (badness 10000) detected at line 32 [][][] [393]) (./structs_a_p_o_lparm.tex [394] Underfull \hbox (badness 10000) detected at line 88 [][][] [395] Underfull \hbox (badness 10000) detected at line 224 [][][] [396] Underfull \hbox (badness 10000) detected at line 237 [][][] Underfull \hbox (badness 10000) detected at line 250 [][][] Underfull \hbox (badness 10000) detected at line 263 [][][] Underfull \hbox (badness 10000) detected at line 276 [][][] Underfull \hbox (badness 10000) detected at line 289 [][][] Underfull \hbox (badness 10000) detected at line 302 [][][] [397] Underfull \hbox (badness 10000) detected at line 315 [][][] Underfull \hbox (badness 10000) detected at line 328 [][][] Underfull \hbox (badness 10000) detected at line 341 [][][] Underfull \hbox (badness 10000) detected at line 354 [][][] Underfull \hbox (badness 10000) detected at line 367 [][][] Underfull \hbox (badness 10000) detected at line 380 [][][] [398]) (./structs_b_e_mparm.tex [399] Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 53 [][][] [400] Underfull \hbox (badness 10000) detected at line 129 [][][] Underfull \hbox (badness 10000) detected at line 142 [][][] Underfull \hbox (badness 10000) detected at line 155 [][][] [401] Underfull \hbox (badness 10000) detected at line 168 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 194 [][][] ) (./structs_f_e_mparm.tex [402] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) in paragraph at lines 84--85 [403] [404] [405]) (./structs_g_e_o_f_l_o_wparm.tex Underfull \hbox (badness 10000) detected at line 30 [][][] Underfull \hbox (badness 10000) detected at line 33 [][][] [406]) (./structs_m_gparm.tex [407] Underfull \hbox (badness 10000) detected at line 120 [][][] Underfull \hbox (badness 10000) detected at line 123 [][][] [408] Underfull \hbox (badness 10000) in paragraph at lines 149--150 Underfull \hbox (badness 10000) in paragraph at lines 180--181 [409] Underfull \hbox (badness 10000) in paragraph at lines 261--262 [410] [411] Underfull \hbox (badness 10000) detected at line 434 [][][] Underfull \hbox (badness 10000) detected at line 447 [][][] Underfull \hbox (badness 10000) detected at line 460 [][][] Underfull \hbox (badness 10000) detected at line 473 [][][] [412] Underfull \hbox (badness 10000) detected at line 486 [][][] Underfull \hbox (badness 10000) detected at line 499 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] Underfull \hbox (badness 10000) detected at line 538 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] [413] Underfull \hbox (badness 10000) detected at line 564 [][][] Underfull \hbox (badness 10000) detected at line 577 [][][] Underfull \hbox (badness 10000) detected at line 590 [][][] Underfull \hbox (badness 10000) detected at line 603 [][][] Underfull \hbox (badness 10000) detected at line 616 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] [414] Underfull \hbox (badness 10000) detected at line 642 [][][] Underfull \hbox (badness 10000) detected at line 655 [][][] Underfull \hbox (badness 10000) detected at line 668 [][][] ) (./structs_n_osh.tex [415] Underfull \hbox (badness 10000) detected at line 108 [][][] [416] [417] [418] [419] [420]) (./structs_n_osh__calc.tex [421] Underfull \hbox (badness 10000) detected at line 38 [][][] [422]) (./structs_p_b_a_mparm.tex [423] Underfull \hbox (badness 10000) detected at line 106 [][][] Underfull \hbox (badness 10000) detected at line 109 [][][] [424] [425] [426] [427]) (./structs_p_b_eparm.tex [428] [429] Underfull \hbox (badness 10000) detected at line 142 [][][] Underfull \hbox (badness 10000) detected at line 145 [][][] [430] [431] [432] Underfull \hbox (badness 10000) detected at line 391 [][][] Underfull \hbox (badness 10000) detected at line 404 [][][] Underfull \hbox (badness 10000) detected at line 417 [][][] Underfull \hbox (badness 10000) detected at line 430 [][][] [433] Underfull \hbox (badness 10000) detected at line 473 [][][] Underfull \hbox (badness 10000) detected at line 486 [][][] Underfull \hbox (badness 10000) detected at line 499 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] [434] Underfull \hbox (badness 10000) detected at line 538 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] Underfull \hbox (badness 10000) detected at line 564 [][][] Underfull \hbox (badness 10000) detected at line 577 [][][] Underfull \hbox (badness 10000) detected at line 590 [][][] Underfull \hbox (badness 10000) detected at line 603 [][][] [435] Underfull \hbox (badness 10000) detected at line 616 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] [436] [437]) (./structs_p_b_s_a_mparm.tex [438] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] [439]) (./structs_vacc.tex [440] Underfull \hbox (badness 10000) detected at line 36 [][][] [441]) (./structs_vacc_surf.tex Underfull \hbox (badness 10000) detected at line 36 [][][] [442]) (./structs_valist.tex [443] Underfull \hbox (badness 10000) detected at line 36 [][][] [444]) (./structs_vatom.tex Underfull \hbox (badness 10000) detected at line 36 [][][] Underfull \hbox (badness 10000) in paragraph at lines 62--63 [445] Underfull \hbox (badness 10000) in paragraph at lines 93--94 Underfull \hbox (badness 10000) in paragraph at lines 114--115 ) (./structs_vclist.tex [446] Underfull \hbox (badness 10000) detected at line 40 [][][] [447]) (./structs_vclist_cell.tex Underfull \hbox (badness 10000) detected at line 24 [][][] ) (./structs_vcsm.tex [448] Underfull \hbox (badness 10000) detected at line 42 [][][] [449]) (./structs_vfetk.tex [450] Underfull \hbox (badness 10000) detected at line 60 [][][] [451] Underfull \hbox (badness 10000) in paragraph at lines 116--117 [452]) (./structs_vfetk___local_var.tex [453] Underfull \hbox (badness 10000) detected at line 86 [][][] [454] [455] [456] [457]) (./structs_vgreen.tex Underfull \hbox (badness 10000) detected at line 34 [][][] [458]) (./structs_vgrid.tex [459] Underfull \hbox (badness 10000) detected at line 52 [][][] [460] [461]) (./structs_vmgrid.tex Underfull \hbox (badness 10000) detected at line 24 [][][] ) (./structs_vopot.tex [462] Underfull \hbox (badness 10000) detected at line 26 [][][] ) (./structs_vparam___atom_data.tex [463] Underfull \hbox (badness 10000) detected at line 30 [][][] Underfull \hbox (badness 10000) detected at line 33 [][][] ) (./structs_vpbe.tex [464] Underfull \hbox (badness 10000) detected at line 86 [][][] [465] [466] [467] [468]) (./structs_vpee.tex [469] Underfull \hbox (badness 10000) detected at line 34 [][][] ) (./structs_vpmg.tex [470] [471] Underfull \hbox (badness 10000) detected at line 116 [][][] [472] [473] [474] [475] [476]) (./structs_vpmgp.tex [477] Underfull \hbox (badness 10000) detected at line 126 [][][] [478] Underfull \hbox (badness 10000) in paragraph at lines 164--165 Underfull \hbox (badness 10000) in paragraph at lines 175--176 Underfull \hbox (badness 10000) in paragraph at lines 186--187 [479] Underfull \hbox (badness 10000) in paragraph at lines 234--235 [480] [481] [482] [483] Underfull \hbox (badness 10000) in paragraph at lines 506--507 Underfull \hbox (badness 10000) in paragraph at lines 527--528 [484] Underfull \hbox (badness 10000) in paragraph at lines 548--549 Underfull \hbox (badness 10000) in paragraph at lines 589--590 [485] Underfull \hbox (badness 10000) in paragraph at lines 630--631 Underfull \hbox (badness 10000) in paragraph at lines 671--672 ) (./struct_vparam.tex [486] Underfull \hbox (badness 10000) detected at line 26 [][][] ) (./struct_vparam___res_data.tex [487] Underfull \hbox (badness 10000) detected at line 28 [][][] ) [488] Chapter 9. (./mainpage_8h_source.tex) (./apbs_8h.tex <./apbs_8h__incl.pdf> <./apbs_8h__dep __incl.pdf> [489] Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 53 [][][] Underfull \hbox (badness 10000) detected at line 56 [][][] [490]) (./apbs_8h_source.tex) (./vcsm_8c.tex [491] <./vcsm_8c__incl.pdf> [492] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] Underfull \hbox (badness 10000) detected at line 58 [][][] [493]) (./vcsm_8c_source.tex [494] [495] [496] [497] [498] [499]) (./vcsm_8h.tex <./vcsm_8h__incl.pdf> <./vcsm_8h__dep__incl.pdf> [500] [501] Underfull \hbox (badness 10000) detected at line 75 [][][] Underfull \hbox (badness 10000) detected at line 78 [][][] Underfull \hbox (badness 10000) detected at line 81 [][][] [502]) (./vcsm_8h_source.tex [503]) (./vfetk_8c.tex [504] <./vfetk_8c__incl.pdf > [505] [506] Underfull \hbox (badness 10000) detected at line 162 [][][] Underfull \hbox (badness 10000) detected at line 165 [][][] [507] Underfull \hbox (badness 10000) detected at line 168 [][][] [508] [509] [510] [511]) (./vfetk_8c_source.tex [512] [513] [514] [515] [516] [517] [518] [519] [520] [521] [522] [523] [524] [525] [526] [527] [528] [529] [530] [531] [532] [533] [534] [535] [536] [537] [538] [539] [540] [541]) (./vfetk_8h.tex [542] <./vfetk_8h__incl.pdf> <./vfetk_8h__dep__inc l.pdf> [543] [544] [545] Underfull \hbox (badness 10000) detected at line 187 [][][] [546] Underfull \hbox (badness 10000) detected at line 190 [][][] Underfull \hbox (badness 10000) detected at line 193 [][][] ) (./vfetk_8h_source.tex [547] [548] [549] [550] [551] [552]) (./vpee_8c.tex <. /vpee_8c__incl.pdf> [553] Underfull \hbox (badness 10000) detected at line 49 [][][] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] [554]) (./vpee_8c_source.tex [555] [556] [557] [558] [559] [560]) (./vpee_8h.tex [561] <./vpee_8h__incl.pdf> <./vpee_8h__dep__incl.pdf> [562] Underfull \hbox (badness 10000) detected at line 55 [][][] Underfull \hbox (badness 10000) detected at line 58 [][][] Underfull \hbox (badness 10000) detected at line 61 [][][] [563]) (./vpee_8h_source.tex [564]) (./apolparm_8c.tex <./apolparm_8c__incl.pdf > [565] Underfull \hbox (badness 10000) detected at line 64 [][][] Underfull \hbox (badness 10000) detected at line 67 [][][] Underfull \hbox (badness 10000) detected at line 70 [][][] [566] [567]) (./apolparm_8c_source.tex [568] [569] [570] [571] [572] [573] [574] [575]) (./apolparm_8h_source.tex [576]) (./bemparm_8c.tex <./bemparm_8c__ incl.pdf> [577] [578] Underfull \hbox (badness 10000) detected at line 48 [][][] Underfull \hbox (badness 10000) detected at line 51 [][][] Underfull \hbox (badness 10000) detected at line 54 [][][] [579] Underfull \hbox (badness 10000) detected at line 120 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.1 on input line 129. ) (./bemparm_8c_source.tex [580] [581] [582] [583]) (./bemparm_8h_source.tex [584]) (./femparm_8c.tex <./femparm_8c__incl.pdf> [585] [586] Underfull \hbox (badness 10000) detected at line 58 [][][] Underfull \hbox (badness 10000) detected at line 61 [][][] Underfull \hbox (badness 10000) detected at line 64 [][][] [587] [588]) (./femparm_8c_source.tex [589] [590] [591] [592] [593]) (./femparm_8h.tex <./femparm_8h__incl.pdf> [594] <./femparm_8h__dep__incl.pdf> [595] Underfull \hbox (badness 10000) detected at line 87 [][][] Underfull \hbox (badness 10000) detected at line 90 [][][] Underfull \hbox (badness 10000) detected at line 93 [][][] [596]) (./femparm_8h_source.tex [597]) (./geoflowparm_8c.tex [598] <./geoflowpa rm_8c__incl.pdf> [599] Underfull \hbox (badness 10000) detected at line 46 [][][] Underfull \hbox (badness 10000) detected at line 49 [][][] Underfull \hbox (badness 10000) detected at line 52 [][][] [600]) (./geoflowparm_8c_source.tex [601] [602]) (./geoflowparm_8h.tex [603] <. /geoflowparm_8h__incl.pdf> <./geoflowparm_8h__dep__incl.pdf> [604] [605] Underfull \hbox (badness 10000) detected at line 69 [][][] Underfull \hbox (badness 10000) detected at line 72 [][][] Underfull \hbox (badness 10000) detected at line 75 [][][] [606]) (./geoflowparm_8h_source.tex [607]) (./mgparm_8c.tex <./mgparm_8c__incl. pdf> [608] [609] Underfull \hbox (badness 10000) detected at line 94 [][][] Underfull \hbox (badness 10000) detected at line 97 [][][] Underfull \hbox (badness 10000) detected at line 100 [][][] [610] [611]) (./mgparm_8c_source.tex [612] [613] [614] [615] [616] [617] [618] [619] [620] [621] [622] [623]) (./mgparm_8h.tex <./mgparm_8h__incl.pdf> [624] <./mgparm_8h__dep__incl.pdf> [625] [626] Underfull \hbox (badness 10000) detected at line 102 [][][] Underfull \hbox (badness 10000) detected at line 105 [][][] Underfull \hbox (badness 10000) detected at line 108 [][][] [627]) (./mgparm_8h_source.tex [628]) (./nosh_8c.tex <./nosh_8c__incl.pdf> [629] [630] [631] Underfull \hbox (badness 10000) detected at line 150 [][][] Underfull \hbox (badness 10000) detected at line 153 [][][] Underfull \hbox (badness 10000) detected at line 156 [][][] [632] [633] [634] [635] [636]) (./nosh_8c_source.tex [637] [638] [639] [640] [641] [642] [643] [644] [645] [646] [647] [648] [649] [650] [651] [652] [653] [654] [655] [656] [657] [658] [659] [660] [661] [662] [663] [664] [665] [666] [667] [668] [669] [670] [671] [672] [673] [674] [675] [676]) (./nosh_8h.tex <./nosh_8h__incl.pdf> [677] <./nosh_8h__dep__incl.pdf> [678] [679] [680] Underfull \hbox (badness 10000) detected at line 169 [][][] Underfull \hbox (badness 10000) detected at line 172 [][][] Underfull \hbox (badness 10000) detected at line 175 [][][] ) (./nosh_8h_source.tex [681] [682] [683]) (./pbamparm_8c.tex <./pbamparm_8c__i ncl.pdf> [684] [685] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) detected at line 71 [][][] Underfull \hbox (badness 10000) detected at line 74 [][][] [686]) (./pbamparm_8c_source.tex [687] [688] [689] [690] [691] [692] [693] [694] [695]) (./pbamparm_8h.tex <./pbamparm_8h__incl.pdf> <./pbamparm_8h__dep__ incl.pdf> [696] [697] Underfull \hbox (badness 10000) detected at line 100 [][][] [698] Underfull \hbox (badness 10000) detected at line 103 [][][] Underfull \hbox (badness 10000) detected at line 106 [][][] [699]) (./pbamparm_8h_source.tex [700]) (./pbeparm_8c.tex [701] <./pbeparm_8c__ incl.pdf> [702] Underfull \hbox (badness 10000) detected at line 100 [][][] Underfull \hbox (badness 10000) detected at line 103 [][][] Underfull \hbox (badness 10000) detected at line 106 [][][] [703] [704] [705] [706] [707]) (./pbeparm_8c_source.tex [708] [709] [710] [711] [712] [713] [714] [715] [716] [717] [718] [719] [720] [721] [722]) (./pbeparm_8h.tex <./pbeparm_8h__incl.pdf> [723] <./pbeparm_8h__dep__incl.pdf> [724] Underfull \hbox (badness 10000) detected at line 86 [][][] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 92 [][][] [725]) (./pbeparm_8h_source.tex [726] [727]) (./pbsamparm_8c.tex <./pbsamparm_8 c__incl.pdf> [728] [729] Underfull \hbox (badness 10000) detected at line 48 [][][] Underfull \hbox (badness 10000) detected at line 51 [][][] Underfull \hbox (badness 10000) detected at line 54 [][][] [730]) (./pbsamparm_8c_source.tex [731] [732]) (./pbsamparm_8h.tex [733] <./pbs amparm_8h__incl.pdf> <./pbsamparm_8h__dep__incl.pdf> [734] [735] Underfull \hbox (badness 10000) detected at line 84 [][][] Underfull \hbox (badness 10000) detected at line 87 [][][] Underfull \hbox (badness 10000) detected at line 90 [][][] [736]) (./pbsamparm_8h_source.tex [737]) (./vacc_8c.tex <./vacc_8c__incl.pdf> [738] [739] [740] Underfull \hbox (badness 10000) detected at line 106 [][][] Underfull \hbox (badness 10000) detected at line 109 [][][] Underfull \hbox (badness 10000) detected at line 112 [][][] [741] Underfull \hbox (badness 10000) detected at line 178 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.2 on input line 192. Underfull \hbox (badness 10000) detected at line 207 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] [742] Package longtable Warning: Column widths have changed (longtable) in table 9.3 on input line 223. [743]) (./vacc_8c_source.tex [744] [745] [746] [747] [748] [749] [750] [751] [752] [753] [754] [755] [756] [757] [758] [759] [760] [761] [762] [763] [764] [765] [766]) (./vacc_8h.tex <./vacc_8h__incl.pdf> <./vacc_8h__dep__incl.p df> [767] [768] [769] Underfull \hbox (badness 10000) detected at line 121 [][][] Underfull \hbox (badness 10000) detected at line 124 [][][] Underfull \hbox (badness 10000) detected at line 127 [][][] [770]) (./vacc_8h_source.tex [771] [772] [773]) (./valist_8c.tex <./valist_8c__ incl.pdf> [774] [775] Underfull \hbox (badness 2293) in paragraph at lines 53--55 []\T1/phv/m/n/10 VPRIVATE Vrc[]_[][]Codes [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/ m/n/10 thee, Vio $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 sock, int $\OMS/cmsy/m/n/ 10 ^^C$\T1/phv/m/n/10 serial, char atom[] Underfull \hbox (badness 10000) detected at line 81 [][][] Underfull \hbox (badness 10000) detected at line 84 [][][] Underfull \hbox (badness 10000) detected at line 87 [][][] [776] [777] [778]) (./valist_8c_source.tex [779] [780] [781] [782] [783] [784] [785] [786] [787] [788]) (./valist_8h.tex [789] <./valist_8h__incl.pdf> < ./valist_8h__dep__incl.pdf> [790] Underfull \hbox (badness 10000) detected at line 75 [][][] Underfull \hbox (badness 10000) detected at line 78 [][][] Underfull \hbox (badness 10000) detected at line 81 [][][] [791]) (./valist_8h_source.tex [792] [793]) (./vatom_8c.tex <./vatom_8c__incl.p df> [794] Underfull \hbox (badness 10000) detected at line 70 [][][] Underfull \hbox (badness 10000) detected at line 73 [][][] Underfull \hbox (badness 10000) detected at line 76 [][][] [795]) (./vatom_8c_source.tex [796] [797] [798]) (./vatom_8h.tex <./vatom_8h__i ncl.pdf> [799] <./vatom_8h__dep__incl.pdf> [800] [801] Underfull \hbox (badness 10000) detected at line 94 [][][] Underfull \hbox (badness 10000) detected at line 97 [][][] Underfull \hbox (badness 10000) detected at line 100 [][][] ) (./vatom_8h_source.tex [802] [803]) (./vcap_8c.tex <./vcap_8c__incl.pdf> [804] Underfull \hbox (badness 10000) detected at line 30 [][][] Underfull \hbox (badness 10000) detected at line 33 [][][] Underfull \hbox (badness 10000) detected at line 36 [][][] [805]) (./vcap_8c_source.tex [806]) (./vcap_8h.tex <./vcap_8h__incl.pdf> <./vca p_8h__dep__incl.pdf> [807] Underfull \hbox (badness 10000) detected at line 45 [][][] Underfull \hbox (badness 10000) detected at line 48 [][][] [808] Underfull \hbox (badness 10000) detected at line 51 [][][] ) (./vcap_8h_source.tex [809]) (./vclist_8c.tex <./vclist_8c__incl.pdf> Underfull \hbox (badness 4060) in paragraph at lines 31--33 []\T1/phv/m/n/10 VPRIVATE void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 thee , dou-ble lower[]_[]corner[][][], dou-ble upper[]_[] [810] Underfull \hbox (badness 10000) detected at line 64 [][][] Underfull \hbox (badness 10000) detected at line 67 [][][] Underfull \hbox (badness 10000) detected at line 70 [][][] [811] [812]) (./vclist_8c_source.tex [813] [814] [815] [816] [817]) (./vclist_8h.tex [818] <./vclist_8h__incl.pdf> <./vclist_8h__dep__incl.pdf> [819] [820] Underfull \hbox (badness 10000) detected at line 82 [][][] Underfull \hbox (badness 10000) detected at line 85 [][][] Underfull \hbox (badness 10000) detected at line 88 [][][] [821]) (./vclist_8h_source.tex [822]) (./vgreen_8c.tex [823] <./vgreen_8c__incl .pdf> [824] Underfull \hbox (badness 10000) detected at line 54 [][][] Underfull \hbox (badness 10000) detected at line 57 [][][] Underfull \hbox (badness 10000) detected at line 60 [][][] [825]) (./vgreen_8c_source.tex [826] [827] [828] [829] [830] [831]) (./vgreen_8h.tex <./vgreen_8h__incl.pdf> [832] <./vgreen_8h__dep__incl.pdf> [833] Underfull \hbox (badness 10000) detected at line 70 [][][] Underfull \hbox (badness 10000) detected at line 73 [][][] ) (./vgreen_8h_source.tex [834]) (./vhal_8h.tex [835] <./vhal_8h__incl.pdf> <./ vhal_8h__dep__incl.pdf> [836] [837] [838] [839] Underfull \hbox (badness 10000) detected at line 301 [][][] Underfull \hbox (badness 10000) detected at line 304 [][][] Underfull \hbox (badness 10000) detected at line 307 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 316--316 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [840] [841] [842] [843] [844] [845] [846]) (./vhal_8h_source.tex [847] [848] [849] [850] [851] [852] [853] [854]) (./vmatrix_8h.tex [855] <./vmatrix_8h__dep __incl.pdf> Underfull \hbox (badness 10000) detected at line 35 [][][] Underfull \hbox (badness 10000) detected at line 38 [][][] Underfull \hbox (badness 10000) detected at line 41 [][][] [856] [857]) (./vmatrix_8h_source.tex [858]) (./vparam_8c.tex <./vparam_8c__inc l.pdf> [859] Underfull \hbox (badness 10000) detected at line 77 [][][] Underfull \hbox (badness 10000) detected at line 80 [][][] [860] Underfull \hbox (badness 10000) detected at line 83 [][][] ) (./vparam_8c_source.tex [861] [862] [863] [864] [865] [866] [867] [868]) (./vparam_8h.tex [869] <./vparam_8h__incl.pdf> <./vparam_8h__dep__incl.pdf> [870] [871] Underfull \hbox (badness 10000) detected at line 94 [][][] Underfull \hbox (badness 10000) detected at line 97 [][][] Underfull \hbox (badness 10000) detected at line 100 [][][] [872]) (./vparam_8h_source.tex [873]) (./vpbe_8c.tex <./vpbe_8c__incl.pdf> [874] [875] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 92 [][][] [876] Underfull \hbox (badness 10000) detected at line 95 [][][] ) (./vpbe_8c_source.tex [877] [878] [879] [880] [881] [882] [883]) (./vpbe_8h.tex <./vpbe_8h__incl.pdf> <./vpbe_8h__dep__incl.pdf> [884] [885] Underfull \hbox (badness 10000) detected at line 109 [][][] Underfull \hbox (badness 10000) detected at line 112 [][][] Underfull \hbox (badness 10000) detected at line 115 [][][] [886]) (./vpbe_8h_source.tex [887] [888] [889]) (./vstring_8c.tex <./vstring_8c __incl.pdf> [890] Underfull \hbox (badness 10000) detected at line 30 [][][] Underfull \hbox (badness 10000) detected at line 33 [][][] Underfull \hbox (badness 10000) detected at line 36 [][][] ) (./vstring_8c_source.tex [891] [892] [893]) (./vstring_8h.tex <./vstring_8h__ incl.pdf> <./vstring_8h__dep__incl.pdf> [894] Underfull \hbox (badness 10000) detected at line 39 [][][] Underfull \hbox (badness 10000) detected at line 42 [][][] Underfull \hbox (badness 10000) detected at line 45 [][][] [895]) (./vstring_8h_source.tex) (./vunit_8h.tex <./vunit_8h__dep__incl.pdf> [896] LaTeX Warning: Command \r invalid in math mode on input line 41. Missing character: There is no Å in font cmr9! Underfull \hbox (badness 10000) detected at line 49 [][][] Underfull \hbox (badness 10000) detected at line 54 [][][] Underfull \hbox (badness 10000) detected at line 57 [][][] [897]) (./vunit_8h_source.tex) (./main_8c.tex [898] <./main_8c__incl.pdf> Underfull \hbox (badness 10000) detected at line 27 [][][] Underfull \hbox (badness 10000) detected at line 40 [][][] Underfull \hbox (badness 10000) detected at line 43 [][][] [899]) (./main_8c_source.tex [900] [901] [902] [903] [904] [905] [906] [907] [908] [909] [910]) (./vgrid_8c.tex <./vgrid_8c__incl.pdf> [911] [912] Underfull \hbox (badness 10000) detected at line 83 [][][] Underfull \hbox (badness 10000) detected at line 86 [][][] Underfull \hbox (badness 10000) detected at line 89 [][][] [913] Underfull \hbox (badness 10000) detected at line 168 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.4 on input line 187. [914]) (./vgrid_8c_source.tex [915] [916] [917] [918] [919] [920] [921] [922] [923] [924] [925] [926] [927] [928] [929] [930] [931] [932] [933] [934] [935] [936] [937]) (./vgrid_8h.tex [938] <./vgrid_8h__incl.pdf> <./vgrid_ 8h__dep__incl.pdf> [939] [940] Underfull \hbox (badness 10000) detected at line 91 [][][] [941] Underfull \hbox (badness 10000) detected at line 94 [][][] Underfull \hbox (badness 10000) detected at line 97 [][][] [942] Underfull \hbox (badness 10000) detected at line 163 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.5 on input line 182. ) (./vgrid_8h_source.tex [943]) (./vmgrid_8c.tex [944] <./vmgrid_8c__incl.pdf> [945] Underfull \hbox (badness 10000) detected at line 40 [][][] Underfull \hbox (badness 10000) detected at line 43 [][][] Underfull \hbox (badness 10000) detected at line 46 [][][] Underfull \hbox (badness 10000) detected at line 49 [][][] Overfull \hbox (1024.08331pt too wide) in paragraph at lines 58--58 []\T1/pcr/m/n/8 * Copyright (c) 2010, Pacific Northwest National Laboratory. Portions Copyright (c) 2002-2020, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2020, T he Regents of the University of California. Portions Copyright (c) 1995, Michae l Holst.[] ) (./vmgrid_8c_source.tex [946] [947] [948]) (./vmgrid_8h.tex <./vmgrid_8h__inc l.pdf> <./vmgrid_8h__dep__incl.pdf> [949] [950] Underfull \hbox (badness 10000) detected at line 69 [][][] Underfull \hbox (badness 10000) detected at line 72 [][][] Underfull \hbox (badness 10000) detected at line 75 [][][] [951]) (./vmgrid_8h_source.tex) (./vopot_8c.tex [952] <./vopot_8c__incl.pdf> Underfull \hbox (badness 10000) detected at line 43 [][][] Underfull \hbox (badness 10000) detected at line 46 [][][] Underfull \hbox (badness 10000) detected at line 49 [][][] [953]) (./vopot_8c_source.tex [954] [955] [956] [957] [958]) (./vopot_8h.tex <. /vopot_8h__incl.pdf> <./vopot_8h__dep__incl.pdf> [959] [960] Underfull \hbox (badness 10000) detected at line 63 [][][] Underfull \hbox (badness 10000) detected at line 66 [][][] Underfull \hbox (badness 10000) detected at line 69 [][][] ) (./vopot_8h_source.tex [961]) (./vpmg_8c.tex <./vpmg_8c__incl.pdf> [962] [963] [964] [965] Underfull \hbox (badness 10000) detected at line 172 [][][] Underfull \hbox (badness 10000) detected at line 175 [][][] Underfull \hbox (badness 10000) detected at line 178 [][][] [966] Underfull \hbox (badness 10000) detected at line 260 [][][] [967] Underfull \hbox (badness 10000) detected at line 287 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.6 on input line 318. [968] Underfull \hbox (badness 10000) detected at line 383 [][][] Underfull \hbox (badness 10000) detected at line 386 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.7 on input line 393. Underfull \hbox (badness 10000) detected at line 408 [][][] Underfull \hbox (badness 10000) detected at line 411 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.8 on input line 418. [969] Underfull \hbox (badness 10000) detected at line 433 [][][] Underfull \hbox (badness 10000) detected at line 436 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.9 on input line 443. Underfull \hbox (badness 10000) detected at line 458 [][][] Underfull \hbox (badness 10000) detected at line 461 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.10 on input line 468. Underfull \hbox (badness 10000) detected at line 483 [][][] Underfull \hbox (badness 10000) detected at line 486 [][][] [970] Package longtable Warning: Column widths have changed (longtable) in table 9.11 on input line 493. Underfull \hbox (badness 10000) detected at line 508 [][][] Underfull \hbox (badness 10000) detected at line 511 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.12 on input line 518. Underfull \hbox (badness 10000) detected at line 533 [][][] Underfull \hbox (badness 10000) detected at line 536 [][][] Underfull \hbox (badness 10000) detected at line 553 [][][] Underfull \hbox (badness 10000) detected at line 556 [][][] [971] Underfull \hbox (badness 10000) detected at line 573 [][][] Underfull \hbox (badness 10000) detected at line 590 [][][] Underfull \hbox (badness 10000) detected at line 607 [][][] Underfull \hbox (badness 10000) detected at line 624 [][][] Underfull \hbox (badness 10000) detected at line 641 [][][] [972] Underfull \hbox (badness 10000) detected at line 658 [][][] Underfull \hbox (badness 10000) detected at line 675 [][][] Underfull \hbox (badness 10000) detected at line 696 [][][] Underfull \hbox (badness 10000) detected at line 699 [][][] Underfull \hbox (badness 10000) detected at line 716 [][][] [973] Underfull \hbox (badness 10000) detected at line 733 [][][] Underfull \hbox (badness 10000) detected at line 750 [][][] Underfull \hbox (badness 10000) detected at line 767 [][][] Underfull \hbox (badness 10000) detected at line 794 [][][] [974] Underfull \hbox (badness 10000) detected at line 831 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.13 on input line 860. [975] Underfull \hbox (badness 10000) detected at line 875 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.14 on input line 890. [976] Underfull \hbox (badness 10000) detected at line 925 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.15 on input line 932. Underfull \hbox (badness 10000) detected at line 947 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.16 on input line 954. [977] Underfull \hbox (badness 10000) detected at line 969 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.17 on input line 976. Underfull \hbox (badness 10000) detected at line 991 [][][] Underfull \hbox (badness 10000) detected at line 994 [][][] Underfull \hbox (badness 10000) detected at line 1011 [][][] Underfull \hbox (badness 10000) detected at line 1014 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.18 on input line 1021. [978] Underfull \hbox (badness 10000) detected at line 1036 [][][] Underfull \hbox (badness 10000) detected at line 1039 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.19 on input line 1046. Underfull \hbox (badness 10000) detected at line 1061 [][][] Underfull \hbox (badness 10000) detected at line 1064 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.20 on input line 1071. Underfull \hbox (badness 10000) detected at line 1096 [][][] [979] Underfull \hbox (badness 10000) detected at line 1113 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.21 on input line 1130. Underfull \hbox (badness 10000) detected at line 1145 [][][] Underfull \hbox (badness 10000) detected at line 1148 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.22 on input line 1157. ) (./vpmg_8c_source.tex [980] [981] [982] [983] [984] [985] [986] [987] [988] [989] [990] [991] [992] [993] [994] [995] [996] [997] [998] [999] [1000] [1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008] [1009] [1010] [1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] [1021] [1022] [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] [1033] [1034] [1035] [1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] [1090] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112] [1113] [1114] [1115] [1116]) (./vpmg_8h.tex <./vpmg_8h__in cl.pdf> <./vpmg_8h__dep__incl.pdf> [1117] [1118] [1119] [1120] [1121] [1122] Underfull \hbox (badness 10000) detected at line 233 [][][] Underfull \hbox (badness 10000) detected at line 236 [][][] Underfull \hbox (badness 10000) detected at line 239 [][][] [1123] [1124] Underfull \hbox (badness 10000) detected at line 404 [][][] Underfull \hbox (badness 10000) detected at line 421 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.23 on input line 452. [1125] Underfull \hbox (badness 10000) detected at line 467 [][][] Underfull \hbox (badness 10000) detected at line 470 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.24 on input line 477. Underfull \hbox (badness 10000) detected at line 492 [][][] Underfull \hbox (badness 10000) detected at line 495 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.25 on input line 502. [1126] Underfull \hbox (badness 10000) detected at line 517 [][][] Underfull \hbox (badness 10000) detected at line 520 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.26 on input line 527. Underfull \hbox (badness 10000) detected at line 542 [][][] Underfull \hbox (badness 10000) detected at line 545 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.27 on input line 552. Underfull \hbox (badness 10000) detected at line 567 [][][] Underfull \hbox (badness 10000) detected at line 570 [][][] [1127] Package longtable Warning: Column widths have changed (longtable) in table 9.28 on input line 577. Underfull \hbox (badness 10000) detected at line 592 [][][] Underfull \hbox (badness 10000) detected at line 595 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.29 on input line 602. Underfull \hbox (badness 10000) detected at line 617 [][][] Underfull \hbox (badness 10000) detected at line 620 [][][] Underfull \hbox (badness 10000) detected at line 637 [][][] Underfull \hbox (badness 10000) detected at line 640 [][][] [1128] Underfull \hbox (badness 10000) detected at line 657 [][][] Underfull \hbox (badness 10000) detected at line 674 [][][] Underfull \hbox (badness 10000) detected at line 691 [][][] Underfull \hbox (badness 10000) detected at line 708 [][][] Underfull \hbox (badness 10000) detected at line 725 [][][] [1129] Underfull \hbox (badness 10000) detected at line 742 [][][] Underfull \hbox (badness 10000) detected at line 759 [][][] Underfull \hbox (badness 10000) detected at line 780 [][][] Underfull \hbox (badness 10000) detected at line 783 [][][] Underfull \hbox (badness 10000) detected at line 800 [][][] [1130] Underfull \hbox (badness 10000) detected at line 817 [][][] Underfull \hbox (badness 10000) detected at line 834 [][][] Underfull \hbox (badness 10000) detected at line 851 [][][] Underfull \hbox (badness 10000) detected at line 868 [][][] Underfull \hbox (badness 10000) detected at line 881 [][][] [1131] Underfull \hbox (badness 10000) detected at line 894 [][][] Underfull \hbox (badness 10000) detected at line 911 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.30 on input line 940. [1132] Underfull \hbox (badness 10000) detected at line 955 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.31 on input line 970. Underfull \hbox (badness 10000) detected at line 985 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.32 on input line 992. [1133] Underfull \hbox (badness 10000) detected at line 1007 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.33 on input line 1014. Underfull \hbox (badness 10000) detected at line 1029 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.34 on input line 1036. Underfull \hbox (badness 10000) detected at line 1051 [][][] Underfull \hbox (badness 10000) detected at line 1054 [][][] Underfull \hbox (badness 10000) detected at line 1071 [][][] [1134] Underfull \hbox (badness 10000) detected at line 1074 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.35 on input line 1081. Underfull \hbox (badness 10000) detected at line 1096 [][][] Underfull \hbox (badness 10000) detected at line 1099 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.36 on input line 1106. Underfull \hbox (badness 10000) detected at line 1121 [][][] Underfull \hbox (badness 10000) detected at line 1124 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.37 on input line 1131. [1135] Underfull \hbox (badness 10000) detected at line 1156 [][][] Underfull \hbox (badness 10000) detected at line 1173 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.38 on input line 1190. [1136] Underfull \hbox (badness 10000) detected at line 1205 [][][] Underfull \hbox (badness 10000) detected at line 1208 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.39 on input line 1217. ) (./vpmg_8h_source.tex [1137] [1138] [1139] [1140] [1141] [1142] [1143] [1144]) (./vpmgp_8c.tex <./vpmgp_8c__incl.pdf> [1145] [1146] Underfull \hbox (badness 10000) detected at line 38 [][][] Underfull \hbox (badness 10000) detected at line 41 [][][] Underfull \hbox (badness 10000) detected at line 44 [][][] [1147]) (./vpmgp_8c_source.tex [1148] [1149] [1150]) (./vpmgp_8h.tex <./vpmgp_8 h__incl.pdf> [1151] <./vpmgp_8h__dep__incl.pdf> [1152] [1153] Underfull \hbox (badness 10000) detected at line 56 [][][] Underfull \hbox (badness 10000) detected at line 59 [][][] Underfull \hbox (badness 10000) detected at line 62 [][][] Underfull \hbox (badness 10000) detected at line 65 [][][] [1154]) (./vpmgp_8h_source.tex [1155]) (./build_ad_8c_source.tex [1156] [1157] [1158]) (./build_ad_8h_source.tex [1159]) (./build_bd_8c_source.tex [1160] [1161] [1162] [1163]) (./build_bd_8h_source.tex [1164]) (./build_gd_8c_source.tex [1165] [1166] [1167] [1168] [1169] [1170] [1171] [1172] [1173] [1174] [1175] [1176] [1177] [1178] [1179] [1180] [1181] [1182] [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] [1191] [1192] [1193] [1194] [1195] [1196] [1197] [1198] [1199] [1200] [1201] [1202]) (./build_gd_8h_source.tex [1203] [1204]) (./build_pd_8c_source.tex [1205] [1206] [1207] [1208] [1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216] [1217] [1218] [1219] [1220] [1221] [1222] [1223]) (./build_pd_8h_source.tex [1224] [1225] [1226]) (./cgd_8c_source.tex) (./cgd_8h_source.tex [1227]) (./gsd_8c_source.tex [1228] [1229] [1230] [1231]) (./gsd_8h_source.tex [1232]) (./matvecd_8c_source.tex [1233] [1234] [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242] [1243] [1244] [1245]) (./matvecd_8h_source.tex [1246] [1247] [1248] [1249] [1250] [1251]) 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(./powerd_8h_source.tex [1326]) (./smoothd_8c_source.tex [1327]) (./smoothd_8h_source.tex [1328]) (./routines_8c.tex <./routines_8c__incl.pdf> [1329] Underfull \hbox (badness 776) in paragraph at lines 47--48 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv /m/n/10 alist[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[] Underfull \hbox (badness 2856) in paragraph at lines 47--48 \T1/phv/m/n/10 YMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]ZMap[] [][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 kappa[]Map[][][], [] Underfull \hbox (badness 1237) in paragraph at lines 47--48 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 charge[]Map[][][], [] $\OMS/cmsy/m/n/10 ^^C $\T1/phv/m/n/10 pmgp[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pmg[][][], [] Underfull \hbox (badness 905) in paragraph at lines 61--62 []\T1/phv/m/n/10 VPUBLIC void [] (Vmem $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 mem , [] 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<./routines_8h__dep__incl.pdf> [1401] Overfull \hbox (16.65858pt too wide) in paragraph at lines 50--51 []\T1/phv/m/n/10 VEXTERNC int [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], Overfull \hbox (16.91972pt too wide) in paragraph at lines 52--53 []\T1/phv/m/n/10 VEXTERNC void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh , [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/1 0 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], Underfull \hbox (badness 1910) in paragraph at lines 70--71 [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1 /phv/m/n/10 alist[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][] [], [] Underfull \hbox (badness 1237) in paragraph at lines 70--71 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 charge[]Map[][][], [] $\OMS/cmsy/m/n/10 ^^C $\T1/phv/m/n/10 pmgp[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pmg[][][], [] [1402] Underfull \hbox (badness 5817) in paragraph at lines 88--89 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], Underfull \hbox (badness 5817) in paragraph at lines 90--91 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], [1403] Underfull \hbox (badness 2495) in paragraph at lines 122--123 []\T1/phv/m/n/10 VPUBLIC Vrc[]_[][]Codes [] (int icalc, [] $\OMS/cmsy/m/n/10 ^^ C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 feparm, [] $\OMS /cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbeparm, [] Underfull \hbox (badness 10000) detected at line 145 [][][] Underfull \hbox (badness 10000) detected at line 148 [][][] Underfull \hbox (badness 10000) detected at line 151 [][][] [1404]) (./routines_8h_source.tex [1405] [1406] [1407] [1408] [1409]) [1410] No file refman.ind. 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(./group___header.tex) (./group___vcsm.tex [19] Underfull \hbox (badness 10000) detected at line 93 [][][] [20] Underfull \hbox (badness 10000) detected at line 113 [][][] Underfull \hbox (badness 10000) detected at line 116 [][][] Underfull \hbox (badness 10000) detected at line 121 [][][] Underfull \hbox (badness 10000) detected at line 145 [][][] Underfull \hbox (badness 10000) detected at line 148 [][][] Underfull \hbox (badness 10000) detected at line 153 [][][] [21] Underfull \hbox (badness 10000) detected at line 179 [][][] Underfull \hbox (badness 10000) detected at line 201 [][][] Underfull \hbox (badness 10000) detected at line 223 [][][] Underfull \hbox (badness 10000) detected at line 226 [][][] Overfull \vbox (4.57304pt too high) has occurred while \output is active [22] Underfull \hbox (badness 10000) detected at line 252 [][][] Underfull \hbox (badness 10000) detected at line 255 [][][] Underfull \hbox (badness 10000) detected at line 281 [][][] Underfull \hbox (badness 10000) detected at line 284 [][][] [23] Underfull \hbox (badness 10000) detected at line 308 [][][] Underfull \hbox (badness 10000) detected at line 311 [][][] Underfull \hbox (badness 10000) detected at line 335 [][][] Underfull \hbox (badness 10000) detected at line 338 [][][] Underfull \hbox (badness 10000) detected at line 364 [][][] Underfull \hbox (badness 10000) detected at line 367 [][][] [24] Underfull \hbox (badness 10000) detected at line 393 [][][] Underfull \hbox (badness 10000) detected at line 396 [][][] Underfull \hbox (badness 10000) detected at line 418 [][][] Underfull \hbox (badness 10000) detected at line 421 [][][] [25] Underfull \hbox (badness 10000) detected at line 443 [][][] Underfull \hbox (badness 10000) detected at line 446 [][][] Underfull \hbox (badness 10000) detected at line 468 [][][] Underfull \hbox (badness 10000) detected at line 471 [][][] ) (./group___vfetk.tex [26] [27] [28] [29] [30] Underfull \hbox (badness 10000) detected at line 304 [][][] Underfull \hbox (badness 10000) detected at line 335 [][][] [31] Underfull \hbox (badness 10000) detected at line 398 [][][] Underfull \hbox (badness 10000) detected at line 429 [][][] Underfull \hbox (badness 10000) detected at line 463 [][][] Underfull \hbox (badness 10000) detected at line 466 [][][] [32] Underfull \hbox (badness 10000) detected at line 492 [][][] Underfull \hbox (badness 10000) detected at line 495 [][][] Underfull \hbox (badness 10000) detected at line 498 [][][] Underfull \hbox (badness 10000) detected at line 522 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] Underfull \hbox (badness 10000) detected at line 528 [][][] [33] Underfull \hbox (badness 10000) detected at line 559 [][][] Underfull \hbox (badness 10000) detected at line 569 [][][] [34] Underfull \hbox (badness 10000) detected at line 593 [][][] Underfull \hbox (badness 10000) detected at line 615 [][][] Underfull \hbox (badness 10000) detected at line 637 [][][] [35] Underfull \hbox (badness 10000) detected at line 658 [][][] Underfull \hbox (badness 10000) detected at line 661 [][][] Underfull \hbox (badness 10000) detected at line 668 [][][] Underfull \hbox (badness 10000) detected at line 671 [][][] Underfull \hbox (badness 10000) detected at line 701 [][][] [36] Underfull \hbox (badness 10000) detected at line 727 [][][] Underfull \hbox (badness 10000) detected at line 730 [][][] Underfull \hbox (badness 10000) detected at line 735 [][][] Underfull \hbox (badness 10000) detected at line 761 [][][] [37] Underfull \hbox (badness 10000) detected at line 789 [][][] Underfull \hbox (badness 10000) detected at line 792 [][][] Underfull \hbox (badness 10000) detected at line 814 [][][] Underfull \hbox (badness 10000) detected at line 817 [][][] Underfull \hbox (badness 10000) detected at line 820 [][][] [38] Underfull \hbox (badness 10000) detected at line 844 [][][] Underfull \hbox (badness 10000) detected at line 847 [][][] Underfull \hbox (badness 10000) detected at line 869 [][][] Underfull \hbox (badness 10000) detected at line 872 [][][] Underfull \hbox (badness 10000) detected at line 875 [][][] Underfull \hbox (badness 10000) detected at line 899 [][][] Underfull \hbox (badness 10000) detected at line 902 [][][] [39] Underfull \hbox (badness 10000) detected at line 924 [][][] Underfull \hbox (badness 10000) detected at line 927 [][][] Underfull \hbox (badness 10000) detected at line 949 [][][] [40] Underfull \hbox (badness 10000) detected at line 969 [][][] Underfull \hbox (badness 10000) detected at line 999 [][][] Underfull \hbox (badness 10000) detected at line 1002 [][][] Underfull \hbox (badness 10000) detected at line 1024 [][][] Underfull \hbox (badness 10000) detected at line 1027 [][][] [41] Underfull \hbox (badness 10000) detected at line 1053 [][][] Underfull \hbox (badness 10000) detected at line 1056 [][][] Underfull \hbox (badness 10000) detected at line 1080 [][][] Underfull \hbox (badness 10000) detected at line 1083 [][][] [42] Underfull \hbox (badness 10000) detected at line 1109 [][][] Underfull \hbox (badness 10000) detected at line 1146 [][][] Underfull \hbox (badness 10000) detected at line 1149 [][][] [43] Underfull \hbox (badness 10000) detected at line 1179 [][][] Underfull \hbox (badness 10000) detected at line 1182 [][][] Underfull \hbox (badness 10000) detected at line 1204 [][][] Underfull \hbox (badness 10000) detected at line 1207 [][][] [44] Underfull \hbox (badness 10000) detected at line 1232 [][][] Underfull \hbox (badness 10000) detected at line 1265 [][][] Underfull \hbox (badness 10000) detected at line 1268 [][][] [45] Underfull \hbox (badness 10000) detected at line 1298 [][][] Underfull \hbox (badness 10000) detected at line 1301 [][][] Underfull \hbox (badness 10000) detected at line 1327 [][][] [46] Underfull \hbox (badness 10000) detected at line 1355 [][][] Underfull \hbox (badness 10000) detected at line 1385 [][][] [47] Underfull \hbox (badness 10000) detected at line 1419 [][][] Underfull \hbox (badness 10000) detected at line 1422 [][][] Underfull \hbox (badness 10000) detected at line 1448 [][][] Underfull \hbox (badness 10000) detected at line 1451 [][][] [48] Underfull \hbox (badness 10000) detected at line 1477 [][][] Underfull \hbox (badness 10000) detected at line 1480 [][][] [49] Underfull \hbox (badness 10000) detected at line 1514 [][][] Underfull \hbox (badness 10000) detected at line 1517 [][][] Underfull \hbox (badness 10000) detected at line 1545 [][][] [50] Underfull \hbox (badness 10000) detected at line 1579 [][][] Underfull \hbox (badness 10000) detected at line 1582 [][][] [51] [52] Underfull \hbox (badness 10000) detected at line 1665 [][][] Underfull \hbox (badness 10000) detected at line 1699 [][][] Underfull \hbox (badness 10000) detected at line 1702 [][][] [53] Underfull \hbox (badness 10000) detected at line 1745 [][][] Underfull \hbox (badness 10000) detected at line 1755 [][][] Underfull \hbox (badness 10000) detected at line 1779 [][][] Underfull \hbox (badness 10000) detected at line 1782 [][][] Underfull \hbox (badness 10000) detected at line 1785 [][][] [54] Underfull \hbox (badness 10000) detected at line 1807 [][][] Underfull \hbox (badness 10000) detected at line 1810 [][][] Underfull \hbox (badness 10000) detected at line 1813 [][][] Underfull \hbox (badness 10000) detected at line 1835 [][][] [55] Underfull \hbox (badness 10000) detected at line 1861 [][][] Underfull \hbox (badness 10000) detected at line 1881 [][][] Underfull \hbox (badness 10000) detected at line 1886 [][][] ) (./group___vpee.tex [56] Underfull \hbox (badness 849) in paragraph at lines 45--46 \T1/phv/m/n/10 Holst par-al-lel re-fine-ment rou-tine es-sen-tially re-duces th e er-ror out-side the \T1/pcr/m/n/10 local^^D partition to zero. Underfull \hbox (badness 10000) in paragraph at lines 45--46 \T1/pcr/m/n/10 However, this leads to the need for a few final overlapping Schw arz solves to Underfull \hbox (badness 10000) in paragraph at lines 45--46 \T1/pcr/m/n/10 smooth out the errors near partition boundaries. Supposedly, if the region in Underfull \hbox (badness 10000) in paragraph at lines 45--46 \T1/pcr/m/n/10 which we allow error-based refinement includes the$\OML/cmm/m/it /10 <$\T1/pcr/m/n/10 /tt$\OML/cmm/m/it/10 >$\T1/pcr/m/n/10 local^^D partition a nd an Underfull \hbox (badness 10000) in paragraph at lines 45--46 \T1/pcr/m/n/10 external buffer zone approximately equal in size to the local re gion, then the Underfull \hbox (badness 10000) in paragraph at lines 45--46 \T1/pcr/m/n/10 solution will asymptotically approach the solution obtained via more typical Underfull \hbox (badness 10000) in paragraph at lines 45--46 \T1/pcr/m/n/10 methods. This is essentially a more flexible parallel implementa tion of MC\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 s [57] Underfull \hbox (badness 10000) detected at line 75 [][][] Underfull \hbox (badness 10000) detected at line 78 [][][] Underfull \hbox (badness 10000) detected at line 94 [][][] Underfull \hbox (badness 10000) detected at line 111 [][][] [58] Underfull \hbox (badness 10000) detected at line 114 [][][] Underfull \hbox (badness 10000) detected at line 132 [][][] Underfull \hbox (badness 10000) detected at line 149 [][][] Underfull \hbox (badness 10000) detected at line 171 [][][] [59] Underfull \hbox (badness 10000) detected at line 195 [][][] Underfull \hbox (badness 10000) detected at line 198 [][][] Underfull \hbox (badness 10000) detected at line 201 [][][] Overfull \vbox (42.60027pt too high) has occurred while \output is active [60] Underfull \hbox (badness 10000) detected at line 241 [][][] Underfull \hbox (badness 10000) detected at line 244 [][][] ) (./group___a_p_o_lparm.tex [61] Overfull \vbox (22.62613pt too high) has occurred while \output is active [62] Underfull \hbox (badness 10000) detected at line 212 [][][] Underfull \hbox (badness 10000) detected at line 220 [][][] [63] Underfull \hbox (badness 10000) detected at line 237 [][][] Underfull \hbox (badness 10000) detected at line 261 [][][] Underfull \hbox (badness 10000) detected at line 264 [][][] Underfull \hbox (badness 10000) detected at line 281 [][][] Underfull \hbox (badness 10000) detected at line 289 [][][] [64] Underfull \hbox (badness 10000) detected at line 306 [][][] Underfull \hbox (badness 10000) detected at line 328 [][][] ) (./group___b_e_mparm.tex [65] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] [66] Underfull \hbox (badness 10000) detected at line 125 [][][] Underfull \hbox (badness 10000) detected at line 133 [][][] Underfull \hbox (badness 10000) detected at line 150 [][][] Underfull \hbox (badness 10000) detected at line 158 [][][] Underfull \hbox (badness 10000) detected at line 175 [][][] [67] Underfull \hbox (badness 10000) detected at line 185 [][][] Underfull \hbox (badness 10000) detected at line 202 [][][] Underfull \hbox (badness 10000) detected at line 224 [][][] Underfull \hbox (badness 10000) detected at line 246 [][][] [68] Underfull \hbox (badness 10000) detected at line 258 [][][] ) (./group___f_e_mparm.tex [69] Underfull \hbox (badness 10000) detected at line 111 [][][] [70] Underfull \hbox (badness 10000) detected at line 155 [][][] Underfull \hbox (badness 10000) detected at line 158 [][][] Underfull \hbox (badness 10000) detected at line 197 [][][] Underfull \hbox (badness 10000) detected at line 231 [][][] [71] Underfull \hbox (badness 10000) detected at line 239 [][][] Underfull \hbox (badness 10000) detected at line 256 [][][] Underfull \hbox (badness 10000) detected at line 280 [][][] Underfull \hbox (badness 10000) detected at line 288 [][][] [72] Underfull \hbox (badness 10000) detected at line 305 [][][] Underfull \hbox (badness 10000) detected at line 315 [][][] Underfull \hbox (badness 10000) detected at line 332 [][][] Underfull \hbox (badness 10000) detected at line 354 [][][] ) (./group___g_e_o_f_l_o_wparm.tex [73] Underfull \hbox (badness 10000) detected at line 68 [][][] [74] Underfull \hbox (badness 10000) detected at line 71 [][][] Underfull \hbox (badness 10000) detected at line 124 [][][] Underfull \hbox (badness 10000) detected at line 132 [][][] [75] Underfull \hbox (badness 10000) detected at line 149 [][][] Underfull \hbox (badness 10000) detected at line 173 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 198 [][][] Underfull \hbox (badness 10000) detected at line 208 [][][] [76] Underfull \hbox (badness 10000) detected at line 225 [][][] Underfull \hbox (badness 10000) detected at line 247 [][][] Underfull \hbox (badness 10000) detected at line 269 [][][] [77] Underfull \hbox (badness 10000) detected at line 281 [][][] ) (./group___m_gparm.tex [78] [79] Underfull \hbox (badness 10000) detected at line 205 [][][] [80] Underfull \hbox (badness 10000) detected at line 217 [][][] Underfull \hbox (badness 10000) detected at line 234 [][][] Underfull \hbox (badness 10000) detected at line 246 [][][] Underfull \hbox (badness 10000) detected at line 263 [][][] Underfull \hbox (badness 10000) detected at line 271 [][][] [81] Underfull \hbox (badness 10000) detected at line 288 [][][] Underfull \hbox (badness 10000) detected at line 312 [][][] Underfull \hbox (badness 10000) detected at line 320 [][][] Underfull \hbox (badness 10000) detected at line 337 [][][] Underfull \hbox (badness 10000) detected at line 347 [][][] [82] Underfull \hbox (badness 10000) detected at line 364 [][][] Underfull \hbox (badness 10000) detected at line 386 [][][] Underfull \hbox (badness 10000) detected at line 408 [][][] Underfull \hbox (badness 10000) detected at line 416 [][][] [83] Underfull \hbox (badness 10000) detected at line 433 [][][] Underfull \hbox (badness 10000) detected at line 441 [][][] Underfull \hbox (badness 10000) detected at line 458 [][][] Underfull \hbox (badness 10000) detected at line 466 [][][] Underfull \hbox (badness 10000) detected at line 483 [][][] Underfull \hbox (badness 10000) detected at line 491 [][][] [84] Underfull \hbox (badness 10000) detected at line 508 [][][] Underfull \hbox (badness 10000) detected at line 516 [][][] Underfull \hbox (badness 10000) detected at line 533 [][][] Underfull \hbox (badness 10000) detected at line 541 [][][] Underfull \hbox (badness 10000) detected at line 558 [][][] [85] Underfull \hbox (badness 10000) detected at line 566 [][][] Underfull \hbox (badness 10000) detected at line 583 [][][] Underfull \hbox (badness 10000) detected at line 591 [][][] Underfull \hbox (badness 10000) detected at line 608 [][][] Underfull \hbox (badness 10000) detected at line 616 [][][] Underfull \hbox (badness 10000) detected at line 633 [][][] [86] Underfull \hbox (badness 10000) detected at line 645 [][][] Underfull \hbox (badness 10000) detected at line 662 [][][] Underfull \hbox (badness 10000) detected at line 686 [][][] [87] Underfull \hbox (badness 10000) detected at line 710 [][][] ) (./group___n_osh.tex [88] [89] [90] [91] [92] Underfull \hbox (badness 10000) detected at line 431 [][][] Underfull \hbox (badness 10000) detected at line 441 [][][] Underfull \hbox (badness 10000) detected at line 458 [][][] Underfull \hbox (badness 10000) detected at line 482 [][][] [93] Underfull \hbox (badness 10000) detected at line 490 [][][] Underfull \hbox (badness 10000) detected at line 507 [][][] Underfull \hbox (badness 10000) detected at line 529 [][][] Underfull \hbox (badness 10000) detected at line 539 [][][] Underfull \hbox (badness 10000) detected at line 556 [][][] [94] Underfull \hbox (badness 10000) detected at line 568 [][][] Underfull \hbox (badness 10000) detected at line 585 [][][] Underfull \hbox (badness 10000) detected at line 607 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] [95] Underfull \hbox (badness 10000) detected at line 639 [][][] Underfull \hbox (badness 10000) detected at line 656 [][][] Underfull \hbox (badness 10000) detected at line 659 [][][] Underfull \hbox (badness 10000) detected at line 669 [][][] Underfull \hbox (badness 10000) detected at line 672 [][][] Underfull \hbox (badness 10000) detected at line 689 [][][] Overfull \vbox (15.28305pt too high) has occurred while \output is active [96] Underfull \hbox (badness 10000) detected at line 699 [][][] Underfull \hbox (badness 10000) detected at line 716 [][][] Underfull \hbox (badness 10000) detected at line 726 [][][] Underfull \hbox (badness 10000) detected at line 743 [][][] Underfull \hbox (badness 10000) detected at line 753 [][][] [97] Underfull \hbox (badness 10000) detected at line 770 [][][] Underfull \hbox (badness 10000) detected at line 780 [][][] Underfull \hbox (badness 10000) detected at line 797 [][][] Underfull \hbox (badness 10000) detected at line 807 [][][] Underfull \hbox (badness 10000) detected at line 824 [][][] [98] Underfull \hbox (badness 10000) detected at line 834 [][][] Underfull \hbox (badness 10000) detected at line 851 [][][] Underfull \hbox (badness 10000) detected at line 861 [][][] Underfull \hbox (badness 10000) detected at line 878 [][][] Underfull \hbox (badness 10000) detected at line 888 [][][] [99] Underfull \hbox (badness 10000) detected at line 905 [][][] Underfull \hbox (badness 10000) detected at line 915 [][][] Underfull \hbox (badness 10000) detected at line 932 [][][] Underfull \hbox (badness 10000) detected at line 942 [][][] Underfull \hbox (badness 10000) detected at line 959 [][][] [100] Underfull \hbox (badness 10000) detected at line 969 [][][] Underfull \hbox (badness 10000) detected at line 986 [][][] Underfull \hbox (badness 10000) detected at line 996 [][][] Underfull \hbox (badness 10000) detected at line 1013 [][][] Underfull \hbox (badness 10000) detected at line 1016 [][][] Underfull \hbox (badness 10000) detected at line 1026 [][][] [101] Underfull \hbox (badness 10000) detected at line 1043 [][][] Underfull \hbox (badness 10000) detected at line 1048 [][][] Underfull \hbox (badness 10000) detected at line 1058 [][][] Underfull \hbox (badness 10000) detected at line 1075 [][][] Underfull \hbox (badness 10000) detected at line 1078 [][][] [102] Underfull \hbox (badness 10000) detected at line 1090 [][][] Underfull \hbox (badness 10000) detected at line 1093 [][][] Underfull \hbox (badness 10000) detected at line 1110 [][][] Underfull \hbox (badness 10000) detected at line 1113 [][][] Underfull \hbox (badness 10000) detected at line 1123 [][][] Underfull \hbox (badness 10000) detected at line 1126 [][][] Underfull \hbox (badness 10000) detected at line 1143 [][][] Underfull \hbox (badness 10000) detected at line 1146 [][][] [103] Underfull \hbox (badness 10000) detected at line 1158 [][][] Underfull \hbox (badness 10000) detected at line 1161 [][][] Underfull \hbox (badness 10000) detected at line 1178 [][][] Underfull \hbox (badness 10000) detected at line 1181 [][][] Underfull \hbox (badness 10000) detected at line 1191 [][][] Underfull \hbox (badness 10000) detected at line 1194 [][][] Underfull \hbox (badness 10000) detected at line 1211 [][][] [104] Underfull \hbox (badness 10000) detected at line 1214 [][][] Underfull \hbox (badness 10000) detected at line 1224 [][][] Underfull \hbox (badness 10000) detected at line 1248 [][][] Underfull \hbox (badness 10000) detected at line 1251 [][][] Underfull \hbox (badness 10000) detected at line 1261 [][][] Overfull \vbox (3.94589pt too high) has occurred while \output is active [105]) (./group___p_b_a_mparm.tex [106] Underfull \hbox (badness 10000) detected at line 116 [][][] Underfull \hbox (badness 10000) detected at line 119 [][][] [107] Underfull \hbox (badness 10000) detected at line 172 [][][] Underfull \hbox (badness 10000) detected at line 180 [][][] Underfull \hbox (badness 10000) detected at line 197 [][][] [108] Underfull \hbox (badness 10000) detected at line 221 [][][] Underfull \hbox (badness 10000) detected at line 229 [][][] Underfull \hbox (badness 10000) detected at line 246 [][][] Underfull \hbox (badness 10000) detected at line 256 [][][] [109] Underfull \hbox (badness 10000) detected at line 273 [][][] Underfull \hbox (badness 10000) detected at line 295 [][][] Underfull \hbox (badness 10000) detected at line 317 [][][] Underfull \hbox (badness 10000) detected at line 341 [][][] [110] Underfull \hbox (badness 10000) detected at line 365 [][][] Underfull \hbox (badness 10000) detected at line 389 [][][] Underfull \hbox (badness 10000) detected at line 413 [][][] [111] Underfull \hbox (badness 10000) detected at line 437 [][][] Underfull \hbox (badness 10000) detected at line 461 [][][] Underfull \hbox (badness 10000) detected at line 485 [][][] [112] Underfull \hbox (badness 10000) detected at line 509 [][][] Underfull \hbox (badness 10000) detected at line 533 [][][] Underfull \hbox (badness 10000) detected at line 557 [][][] [113] Underfull \hbox (badness 10000) detected at line 581 [][][] Underfull \hbox (badness 10000) detected at line 593 [][][] Underfull \hbox (badness 10000) detected at line 610 [][][] [114] Underfull \hbox (badness 10000) detected at line 634 [][][] ) (./group___p_b_eparm.tex [115] [116] Underfull \hbox (badness 10000) detected at line 209 [][][] Underfull \hbox (badness 10000) detected at line 212 [][][] [117] Underfull \hbox (badness 10000) detected at line 234 [][][] Underfull \hbox (badness 10000) detected at line 258 [][][] Underfull \hbox (badness 10000) detected at line 261 [][][] Underfull \hbox (badness 10000) detected at line 278 [][][] Underfull \hbox (badness 10000) detected at line 281 [][][] [118] Underfull \hbox (badness 10000) detected at line 303 [][][] Underfull \hbox (badness 10000) detected at line 325 [][][] Underfull \hbox (badness 10000) detected at line 347 [][][] Underfull \hbox (badness 10000) detected at line 350 [][][] [119] Underfull \hbox (badness 10000) detected at line 374 [][][] Underfull \hbox (badness 10000) detected at line 377 [][][] Underfull \hbox (badness 10000) detected at line 401 [][][] Underfull \hbox (badness 10000) detected at line 404 [][][] Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 431 [][][] [120]) (./group___p_b_s_a_mparm.tex [121] Underfull \hbox (badness 10000) detected at line 100 [][][] Underfull \hbox (badness 10000) detected at line 103 [][][] [122] Underfull \hbox (badness 10000) detected at line 156 [][][] Underfull \hbox (badness 10000) detected at line 164 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] [123] Underfull \hbox (badness 10000) detected at line 205 [][][] Underfull \hbox (badness 10000) detected at line 213 [][][] Underfull \hbox (badness 10000) detected at line 230 [][][] Underfull \hbox (badness 10000) detected at line 240 [][][] Underfull \hbox (badness 10000) detected at line 257 [][][] Overfull \vbox (0.37224pt too high) has occurred while \output is active [124] Underfull \hbox (badness 10000) detected at line 279 [][][] Underfull \hbox (badness 10000) detected at line 301 [][][] Underfull \hbox (badness 10000) detected at line 325 [][][] [125] Underfull \hbox (badness 10000) detected at line 349 [][][] Underfull \hbox (badness 10000) detected at line 373 [][][] Underfull \hbox (badness 10000) detected at line 397 [][][] [126] Underfull \hbox (badness 10000) detected at line 409 [][][] Underfull \hbox (badness 10000) detected at line 426 [][][] ) (./group___vacc.tex [127] [128] [129] Underfull \hbox (badness 10000) detected at line 149 [][][] Underfull \hbox (badness 10000) detected at line 179 [][][] [130] Underfull \hbox (badness 10000) detected at line 207 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] Underfull \hbox (badness 10000) detected at line 213 [][][] Underfull \hbox (badness 10000) detected at line 239 [][][] Underfull \hbox (badness 10000) detected at line 242 [][][] [131] Underfull \hbox (badness 10000) detected at line 268 [][][] Underfull \hbox (badness 10000) detected at line 271 [][][] Underfull \hbox (badness 10000) detected at line 283 [][][] Underfull \hbox (badness 10000) detected at line 305 [][][] Underfull \hbox (badness 10000) detected at line 308 [][][] [132] Underfull \hbox (badness 10000) detected at line 334 [][][] Underfull \hbox (badness 10000) detected at line 337 [][][] Underfull \hbox (badness 10000) detected at line 365 [][][] Underfull \hbox (badness 10000) detected at line 387 [][][] [133] Underfull \hbox (badness 10000) detected at line 411 [][][] Underfull \hbox (badness 10000) detected at line 414 [][][] Underfull \hbox (badness 10000) detected at line 417 [][][] Underfull \hbox (badness 10000) detected at line 447 [][][] Underfull \hbox (badness 10000) detected at line 450 [][][] [134] Underfull \hbox (badness 10000) detected at line 472 [][][] Underfull \hbox (badness 10000) detected at line 475 [][][] Underfull \hbox (badness 10000) detected at line 499 [][][] Underfull \hbox (badness 10000) detected at line 502 [][][] [135] Underfull \hbox (badness 10000) detected at line 530 [][][] Underfull \hbox (badness 10000) detected at line 533 [][][] Underfull \hbox (badness 10000) detected at line 536 [][][] Underfull \hbox (badness 10000) detected at line 562 [][][] Underfull \hbox (badness 10000) detected at line 565 [][][] [136] Underfull \hbox (badness 10000) detected at line 595 [][][] Underfull \hbox (badness 10000) detected at line 598 [][][] Underfull \hbox (badness 10000) detected at line 628 [][][] [137] Underfull \hbox (badness 10000) detected at line 660 [][][] Underfull \hbox (badness 10000) detected at line 692 [][][] [138] Underfull \hbox (badness 10000) detected at line 724 [][][] Underfull \hbox (badness 10000) detected at line 758 [][][] [139] Underfull \hbox (badness 10000) detected at line 790 [][][] Underfull \hbox (badness 10000) detected at line 820 [][][] [140] Underfull \hbox (badness 10000) detected at line 852 [][][] Underfull \hbox (badness 10000) detected at line 855 [][][] Underfull \hbox (badness 10000) detected at line 858 [][][] Underfull \hbox (badness 10000) detected at line 882 [][][] Underfull \hbox (badness 10000) detected at line 885 [][][] Underfull \hbox (badness 10000) detected at line 888 [][][] [141] Underfull \hbox (badness 10000) detected at line 918 [][][] Underfull \hbox (badness 10000) detected at line 921 [][][] Underfull \hbox (badness 10000) detected at line 941 [][][] Underfull \hbox (badness 10000) detected at line 944 [][][] Overfull \vbox (21.5778pt too high) has occurred while \output is active [142] Underfull \hbox (badness 10000) detected at line 972 [][][] Underfull \hbox (badness 10000) detected at line 975 [][][] Underfull \hbox (badness 10000) detected at line 1007 [][][] Underfull \hbox (badness 10000) detected at line 1010 [][][] [143] Underfull \hbox (badness 10000) detected at line 1040 [][][] Underfull \hbox (badness 10000) detected at line 1043 [][][] Underfull \hbox (badness 10000) detected at line 1069 [][][] Underfull \hbox (badness 10000) detected at line 1072 [][][] Overfull \vbox (18.93095pt too high) has occurred while \output is active [144] Underfull \hbox (badness 10000) detected at line 1100 [][][] Underfull \hbox (badness 10000) detected at line 1122 [][][] Underfull \hbox (badness 10000) detected at line 1146 [][][] Underfull \hbox (badness 10000) detected at line 1149 [][][] Underfull \hbox (badness 10000) detected at line 1152 [][][] [145]) (./group___valist.tex [146] Underfull \hbox (badness 10000) detected at line 91 [][][] Underfull \hbox (badness 10000) detected at line 94 [][][] Underfull \hbox (badness 10000) detected at line 111 [][][] Underfull \hbox (badness 10000) detected at line 114 [][][] Overfull \vbox (3.49948pt too high) has occurred while \output is active [147] Underfull \hbox (badness 10000) detected at line 136 [][][] Underfull \hbox (badness 10000) detected at line 158 [][][] Underfull \hbox (badness 10000) detected at line 180 [][][] Underfull \hbox (badness 10000) detected at line 183 [][][] [148] Underfull \hbox (badness 10000) detected at line 207 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] Underfull \hbox (badness 10000) detected at line 232 [][][] Underfull \hbox (badness 10000) detected at line 235 [][][] Underfull \hbox (badness 10000) detected at line 257 [][][] Underfull \hbox (badness 10000) detected at line 260 [][][] [149] Underfull \hbox (badness 10000) detected at line 282 [][][] Underfull \hbox (badness 10000) detected at line 285 [][][] Underfull \hbox (badness 10000) detected at line 307 [][][] Underfull \hbox (badness 10000) detected at line 310 [][][] Underfull \hbox (badness 10000) detected at line 332 [][][] [150] Underfull \hbox (badness 10000) detected at line 335 [][][] Underfull \hbox (badness 10000) detected at line 352 [][][] Underfull \hbox (badness 10000) detected at line 355 [][][] Underfull \hbox (badness 10000) detected at line 377 [][][] Underfull \hbox (badness 10000) detected at line 380 [][][] Underfull \hbox (badness 10000) detected at line 383 [][][] [151] Underfull \hbox (badness 10000) detected at line 409 [][][] Underfull \hbox (badness 10000) detected at line 412 [][][] Underfull \hbox (badness 10000) detected at line 415 [][][] Underfull \hbox (badness 10000) detected at line 443 [][][] Underfull \hbox (badness 10000) detected at line 446 [][][] Underfull \hbox (badness 10000) detected at line 449 [][][] Overfull \vbox (15.85518pt too high) has occurred while \output is active [152]) (./group___vatom.tex [153] Underfull \hbox (badness 10000) detected at line 97 [][][] [154] Underfull \hbox (badness 10000) detected at line 134 [][][] Underfull \hbox (badness 10000) detected at line 158 [][][] Underfull \hbox (badness 10000) detected at line 182 [][][] Underfull \hbox (badness 10000) detected at line 185 [][][] [155] Underfull \hbox (badness 10000) detected at line 202 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] Underfull \hbox (badness 10000) detected at line 227 [][][] Underfull \hbox (badness 10000) detected at line 249 [][][] Underfull \hbox (badness 10000) detected at line 271 [][][] [156] Underfull \hbox (badness 10000) detected at line 279 [][][] Underfull \hbox (badness 10000) detected at line 296 [][][] Underfull \hbox (badness 10000) detected at line 320 [][][] Underfull \hbox (badness 10000) detected at line 328 [][][] [157] Underfull \hbox (badness 10000) detected at line 345 [][][] Underfull \hbox (badness 10000) detected at line 353 [][][] Underfull \hbox (badness 10000) detected at line 370 [][][] Underfull \hbox (badness 10000) detected at line 378 [][][] Underfull \hbox (badness 10000) detected at line 395 [][][] Underfull \hbox (badness 10000) detected at line 403 [][][] [158] Underfull \hbox (badness 10000) detected at line 420 [][][] Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 445 [][][] Underfull \hbox (badness 10000) detected at line 469 [][][] [159] Underfull \hbox (badness 10000) detected at line 477 [][][] Underfull \hbox (badness 10000) detected at line 494 [][][] Underfull \hbox (badness 10000) detected at line 518 [][][] [160] Underfull \hbox (badness 10000) detected at line 542 [][][] Underfull \hbox (badness 10000) detected at line 566 [][][] Underfull \hbox (badness 10000) detected at line 590 [][][] [161] Underfull \hbox (badness 10000) detected at line 614 [][][] Underfull \hbox (badness 10000) detected at line 638 [][][] Underfull \hbox (badness 10000) detected at line 662 [][][] ) (./group___vcap.tex [162] Underfull \hbox (badness 10000) detected at line 36 [][][] [163] Underfull \hbox (badness 10000) detected at line 86 [][][] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 92 [][][] Underfull \hbox (badness 10000) detected at line 119 [][][] Underfull \hbox (badness 10000) detected at line 122 [][][] Underfull \hbox (badness 10000) detected at line 125 [][][] [164] Underfull \hbox (badness 10000) detected at line 152 [][][] Underfull \hbox (badness 10000) detected at line 155 [][][] Underfull \hbox (badness 10000) detected at line 158 [][][] ) (./group___vclist.tex [165] [166] Underfull \hbox (badness 10000) detected at line 110 [][][] Underfull \hbox (badness 10000) detected at line 140 [][][] Underfull \hbox (badness 10000) detected at line 143 [][][] [167] Underfull \hbox (badness 10000) detected at line 175 [][][] Underfull \hbox (badness 10000) detected at line 178 [][][] Underfull \hbox (badness 10000) detected at line 212 [][][] [168] Underfull \hbox (badness 10000) detected at line 234 [][][] Underfull \hbox (badness 10000) detected at line 256 [][][] Underfull \hbox (badness 10000) detected at line 259 [][][] Underfull \hbox (badness 10000) detected at line 283 [][][] Underfull \hbox (badness 10000) detected at line 286 [][][] [169] Underfull \hbox (badness 10000) detected at line 308 [][][] Underfull \hbox (badness 10000) detected at line 311 [][][] Underfull \hbox (badness 10000) detected at line 333 [][][] Underfull \hbox (badness 10000) detected at line 336 [][][] Underfull \hbox (badness 10000) detected at line 358 [][][] Underfull \hbox (badness 10000) detected at line 361 [][][] [170] Underfull \hbox (badness 10000) detected at line 385 [][][] Underfull \hbox (badness 10000) detected at line 407 [][][] ) (./group___vgreen.tex [171] Underfull \hbox (badness 10000) detected at line 57 [][][] Underfull \hbox (badness 10000) detected at line 60 [][][] [172] [173] Underfull \hbox (badness 10000) detected at line 141 [][][] Underfull \hbox (badness 10000) detected at line 159 [][][] Underfull \hbox (badness 10000) detected at line 178 [][][] [174] Underfull \hbox (badness 10000) detected at line 196 [][][] Underfull \hbox (badness 10000) detected at line 215 [][][] [175] Underfull \hbox (badness 10000) detected at line 239 [][][] Underfull \hbox (badness 10000) detected at line 258 [][][] Underfull \hbox (badness 10000) detected at line 282 [][][] [176] Underfull \hbox (badness 10000) detected at line 299 [][][] Underfull \hbox (badness 10000) detected at line 307 [][][] Underfull \hbox (badness 10000) detected at line 324 [][][] Underfull \hbox (badness 10000) detected at line 334 [][][] Underfull \hbox (badness 10000) detected at line 351 [][][] [177] Underfull \hbox (badness 10000) detected at line 373 [][][] Underfull \hbox (badness 10000) detected at line 395 [][][] Underfull \hbox (badness 10000) detected at line 403 [][][] Underfull \hbox (badness 10000) detected at line 424 [][][] [178] Underfull \hbox (badness 10000) detected at line 429 [][][] Underfull \hbox (badness 10000) detected at line 449 [][][] Underfull \hbox (badness 10000) detected at line 471 [][][] Underfull \hbox (badness 10000) detected at line 476 [][][] [179] Underfull \hbox (badness 10000) detected at line 500 [][][] Underfull \hbox (badness 10000) detected at line 517 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] ) (./group___vhal.tex [180] [181] [182] [183] Underfull \hbox (badness 10000) detected at line 380 [][][] Underfull \hbox (badness 10000) detected at line 411 [][][] [184] Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 445 [][][] Underfull \hbox (badness 10000) detected at line 476 [][][] Underfull \hbox (badness 10000) detected at line 493 [][][] Underfull \hbox (badness 10000) detected at line 516 [][][] [185] Underfull \hbox (badness 10000) detected at line 547 [][][] [186] Underfull \hbox (badness 10000) detected at line 682 [][][] Underfull \hbox (badness 10000) detected at line 729 [][][] [187] Underfull \hbox (badness 10000) detected at line 760 [][][] Underfull \hbox (badness 10000) detected at line 795 [][][] Underfull \hbox (badness 10000) detected at line 842 [][][] Missing character: There is no Å in font cmr10! Missing character: There is no Å in font cmr10! LaTeX Warning: Command \r invalid in math mode on input line 58. Missing character: There is no Å in font cmr10! [188] [189] Underfull \hbox (badness 10000) detected at line 1019 [][][] Underfull \hbox (badness 10000) detected at line 1022 [][][] Underfull \hbox (badness 10000) detected at line 1050 [][][] Underfull \hbox (badness 10000) detected at line 1053 [][][] Underfull \hbox (badness 10000) detected at line 1070 [][][] [190]) (./group___vmatrix.tex) (./group___vparam.tex [191] [192] Underfull \hbox (badness 10000) detected at line 120 [][][] Underfull \hbox (badness 10000) detected at line 130 [][][] [193] Underfull \hbox (badness 10000) detected at line 147 [][][] Underfull \hbox (badness 10000) detected at line 157 [][][] Underfull \hbox (badness 10000) detected at line 174 [][][] Underfull \hbox (badness 10000) detected at line 198 [][][] [194] Underfull \hbox (badness 10000) detected at line 222 [][][] Underfull \hbox (badness 10000) detected at line 225 [][][] Underfull \hbox (badness 10000) detected at line 242 [][][] Underfull \hbox (badness 10000) detected at line 250 [][][] Underfull \hbox (badness 10000) detected at line 267 [][][] [195] Underfull \hbox (badness 10000) detected at line 289 [][][] Underfull \hbox (badness 10000) detected at line 311 [][][] Underfull \hbox (badness 10000) detected at line 314 [][][] Underfull \hbox (badness 10000) detected at line 331 [][][] Underfull \hbox (badness 10000) detected at line 339 [][][] Underfull \hbox (badness 10000) detected at line 356 [][][] [196] Underfull \hbox (badness 10000) detected at line 378 [][][] Underfull \hbox (badness 10000) detected at line 400 [][][] Underfull \hbox (badness 10000) detected at line 412 [][][] Underfull \hbox (badness 10000) detected at line 415 [][][] Underfull \hbox (badness 10000) detected at line 418 [][][] [197] Underfull \hbox (badness 10000) detected at line 435 [][][] Underfull \hbox (badness 10000) detected at line 445 [][][] Underfull \hbox (badness 10000) detected at line 448 [][][] Underfull \hbox (badness 10000) detected at line 451 [][][] Underfull \hbox (badness 10000) detected at line 468 [][][] Underfull \hbox (badness 10000) detected at line 476 [][][] [198] Underfull \hbox (badness 10000) detected at line 493 [][][] Underfull \hbox (badness 10000) detected at line 509 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Underfull \hbox (badness 10000) detected at line 537 [][][] [199] Underfull \hbox (badness 10000) detected at line 553 [][][] Underfull \hbox (badness 10000) detected at line 570 [][][] Underfull \hbox (badness 10000) detected at line 594 [][][] Underfull \hbox (badness 10000) detected at line 602 [][][] [200] Underfull \hbox (badness 10000) detected at line 619 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] Underfull \hbox (badness 10000) detected at line 646 [][][] Underfull \hbox (badness 10000) detected at line 668 [][][] [201]) (./group___vpbe.tex [202] [203] Underfull \hbox (badness 10000) detected at line 128 [][][] Underfull \hbox (badness 10000) detected at line 131 [][][] LaTeX Warning: Command \r invalid in math mode on input line 133. Missing character: There is no Å in font cmr10! LaTeX Warning: Command \r invalid in math mode on input line 133. Missing character: There is no Å in font cmr10! [204] Underfull \hbox (badness 10000) detected at line 136 [][][] [205] Underfull \hbox (badness 10000) detected at line 186 [][][] Underfull \hbox (badness 10000) detected at line 189 [][][] LaTeX Warning: Command \r invalid in math mode on input line 190. Missing character: There is no Å in font cmr10! LaTeX Warning: Command \r invalid in math mode on input line 190. Missing character: There is no Å in font cmr10! Underfull \hbox (badness 10000) detected at line 195 [][][] Overfull \vbox (21.60152pt too high) has occurred while \output is active [206] Underfull \hbox (badness 10000) detected at line 247 [][][] Underfull \hbox (badness 10000) detected at line 269 [][][] Underfull \hbox (badness 10000) detected at line 291 [][][] Underfull \hbox (badness 10000) detected at line 299 [][][] [207] Overfull \hbox (151.96916pt too wide) in paragraph at lines 318--318 [] \T1/p cr/m/n/8 permittivity equal to the protein interior) and zero ionic[] Underfull \hbox (badness 10000) detected at line 325 [][][] Underfull \hbox (badness 10000) detected at line 333 [][][] Underfull \hbox (badness 10000) detected at line 350 [][][] Underfull \hbox (badness 10000) detected at line 358 [][][] [208] Underfull \hbox (badness 10000) detected at line 375 [][][] Underfull \hbox (badness 10000) detected at line 383 [][][] Underfull \hbox (badness 10000) detected at line 396 [][][] Underfull \hbox (badness 10000) detected at line 412 [][][] [209] Underfull \hbox (badness 10000) detected at line 436 [][][] Underfull \hbox (badness 10000) detected at line 453 [][][] Underfull \hbox (badness 10000) detected at line 461 [][][] Underfull \hbox (badness 10000) detected at line 478 [][][] Underfull \hbox (badness 10000) detected at line 486 [][][] Underfull \hbox (badness 10000) detected at line 503 [][][] [210] Underfull \hbox (badness 10000) detected at line 525 [][][] Underfull \hbox (badness 10000) detected at line 533 [][][] Underfull \hbox (badness 10000) detected at line 550 [][][] Underfull \hbox (badness 10000) detected at line 558 [][][] Underfull \hbox (badness 10000) detected at line 575 [][][] [211] Underfull \hbox (badness 10000) detected at line 583 [][][] Underfull \hbox (badness 10000) detected at line 600 [][][] Underfull \hbox (badness 10000) detected at line 608 [][][] Underfull \hbox (badness 10000) detected at line 625 [][][] Underfull \hbox (badness 10000) detected at line 633 [][][] [212] Underfull \hbox (badness 10000) detected at line 650 [][][] Underfull \hbox (badness 10000) detected at line 658 [][][] Underfull \hbox (badness 10000) detected at line 675 [][][] Underfull \hbox (badness 10000) detected at line 683 [][][] Underfull \hbox (badness 10000) detected at line 700 [][][] Underfull \hbox (badness 10000) detected at line 708 [][][] [213] Underfull \hbox (badness 10000) detected at line 725 [][][] Underfull \hbox (badness 10000) detected at line 733 [][][] Underfull \hbox (badness 10000) detected at line 750 [][][] Underfull \hbox (badness 10000) detected at line 758 [][][] Underfull \hbox (badness 10000) detected at line 775 [][][] [214] Underfull \hbox (badness 10000) detected at line 783 [][][] Underfull \hbox (badness 10000) detected at line 800 [][][] Underfull \hbox (badness 10000) detected at line 808 [][][] Underfull \hbox (badness 10000) detected at line 825 [][][] Underfull \hbox (badness 10000) detected at line 833 [][][] [215] Underfull \hbox (badness 10000) detected at line 850 [][][] Underfull \hbox (badness 10000) detected at line 858 [][][] LaTeX Warning: Command \r invalid in math mode on input line 859. Missing character: There is no Å in font cmr10! Underfull \hbox (badness 10000) detected at line 875 [][][] Underfull \hbox (badness 10000) detected at line 883 [][][] Underfull \hbox (badness 10000) detected at line 900 [][][] Underfull \hbox (badness 10000) detected at line 908 [][][] [216] Underfull \hbox (badness 10000) detected at line 925 [][][] Underfull \hbox (badness 10000) detected at line 933 [][][] ) (./group___vstring.tex [217] Underfull \hbox (badness 10000) detected at line 42 [][][] Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 67 [][][] Underfull \hbox (badness 10000) detected at line 70 [][][] Underfull \hbox (badness 10000) detected at line 80 [][][] Underfull \hbox (badness 10000) detected at line 93 [][][] [218] Underfull \hbox (badness 10000) detected at line 96 [][][] Underfull \hbox (badness 10000) detected at line 99 [][][] Underfull \hbox (badness 10000) detected at line 102 [][][] Underfull \hbox (badness 10000) detected at line 105 [][][] ) (./group___vunit.tex [219] LaTeX Warning: Command \r invalid in math mode on input line 39. Missing character: There is no Å in font cmr9! [220] LaTeX Warning: Command \r invalid in math mode on input line 142. Missing character: There is no Å in font cmr10! ) (./group___vgrid.tex [221] [222] [223] Underfull \hbox (badness 10000) detected at line 125 [][][] Underfull \hbox (badness 10000) detected at line 151 [][][] Underfull \hbox (badness 10000) detected at line 168 [][][] [224] Underfull \hbox (badness 10000) detected at line 196 [][][] Underfull \hbox (badness 10000) detected at line 213 [][][] Underfull \hbox (badness 10000) detected at line 229 [][][] [225] Underfull \hbox (badness 10000) detected at line 246 [][][] Underfull \hbox (badness 10000) detected at line 268 [][][] Underfull \hbox (badness 10000) detected at line 290 [][][] Underfull \hbox (badness 10000) detected at line 302 [][][] [226] Underfull \hbox (badness 10000) detected at line 319 [][][] Underfull \hbox (badness 10000) detected at line 327 [][][] Underfull \hbox (badness 10000) detected at line 344 [][][] Underfull \hbox (badness 10000) detected at line 352 [][][] Underfull \hbox (badness 10000) detected at line 369 [][][] Underfull \hbox (badness 10000) detected at line 377 [][][] [227] Underfull \hbox (badness 10000) detected at line 395 [][][] Underfull \hbox (badness 10000) detected at line 403 [][][] Underfull \hbox (badness 10000) detected at line 420 [][][] Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 445 [][][] [228] Underfull \hbox (badness 10000) detected at line 453 [][][] Underfull \hbox (badness 10000) detected at line 470 [][][] Underfull \hbox (badness 10000) detected at line 473 [][][] Underfull \hbox (badness 10000) detected at line 489 [][][] Underfull \hbox (badness 10000) detected at line 492 [][][] [229] Underfull \hbox (badness 10000) detected at line 509 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Underfull \hbox (badness 10000) detected at line 528 [][][] Underfull \hbox (badness 10000) detected at line 531 [][][] Underfull \hbox (badness 10000) detected at line 548 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] [230] Underfull \hbox (badness 10000) detected at line 575 [][][] Underfull \hbox (badness 10000) detected at line 583 [][][] Underfull \hbox (badness 10000) detected at line 600 [][][] Underfull \hbox (badness 10000) detected at line 612 [][][] [231] Underfull \hbox (badness 10000) detected at line 629 [][][] Underfull \hbox (badness 10000) detected at line 663 [][][] [232] Underfull \hbox (badness 10000) detected at line 697 [][][] Underfull \hbox (badness 10000) detected at line 702 [][][] ) (./group___vmgrid.tex [233] [234] Underfull \hbox (badness 10000) detected at line 105 [][][] Underfull \hbox (badness 10000) detected at line 115 [][][] Underfull \hbox (badness 10000) detected at line 132 [][][] Underfull \hbox (badness 10000) detected at line 135 [][][] Underfull \hbox (badness 10000) detected at line 152 [][][] [235] Underfull \hbox (badness 10000) detected at line 160 [][][] Underfull \hbox (badness 10000) detected at line 177 [][][] Underfull \hbox (badness 10000) detected at line 193 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] [236] Underfull \hbox (badness 10000) detected at line 232 [][][] Underfull \hbox (badness 10000) detected at line 254 [][][] Underfull \hbox (badness 10000) detected at line 264 [][][] Underfull \hbox (badness 10000) detected at line 277 [][][] [237] Underfull \hbox (badness 10000) detected at line 287 [][][] Underfull \hbox (badness 10000) detected at line 300 [][][] Underfull \hbox (badness 10000) detected at line 312 [][][] Underfull \hbox (badness 10000) detected at line 329 [][][] Underfull \hbox (badness 10000) detected at line 341 [][][] ) (./group___vopot.tex [238] [239] Underfull \hbox (badness 10000) detected at line 77 [][][] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 106 [][][] [240] Underfull \hbox (badness 10000) detected at line 120 [][][] Underfull \hbox (badness 10000) detected at line 137 [][][] Underfull \hbox (badness 10000) detected at line 153 [][][] Underfull \hbox (badness 10000) detected at line 170 [][][] [241] Underfull \hbox (badness 10000) detected at line 192 [][][] Underfull \hbox (badness 10000) detected at line 214 [][][] Underfull \hbox (badness 10000) detected at line 226 [][][] Underfull \hbox (badness 10000) detected at line 243 [][][] Overfull \vbox (28.1848pt too high) has occurred while \output is active [242] Underfull \hbox (badness 10000) detected at line 255 [][][] ) (./group___vpmg.tex [243] [244] [245] Underfull \hbox (badness 10000) detected at line 117 [][][] Underfull \hbox (badness 10000) detected at line 150 [][][] [246] Underfull \hbox (badness 10000) detected at line 186 [][][] [247] Underfull \hbox (badness 10000) detected at line 234 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.409 on input line 261. Underfull \hbox (badness 10000) detected at line 276 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.410 on input line 309. [248] Underfull \hbox (badness 10000) detected at line 324 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.411 on input line 347. [249] Underfull \hbox (badness 10000) detected at line 362 [][][] Underfull \hbox (badness 10000) detected at line 381 [][][] Underfull \hbox (badness 10000) detected at line 384 [][][] [250] Underfull \hbox (badness 10000) detected at line 416 [][][] Underfull \hbox (badness 10000) detected at line 419 [][][] Underfull \hbox (badness 10000) detected at line 422 [][][] [251] Underfull \hbox (badness 10000) detected at line 458 [][][] Underfull \hbox (badness 10000) detected at line 484 [][][] Underfull \hbox (badness 10000) detected at line 487 [][][] Underfull \hbox (badness 10000) detected at line 492 [][][] Overfull \vbox (1.11014pt too high) has occurred while \output is active [252] Underfull \hbox (badness 10000) detected at line 520 [][][] Underfull \hbox (badness 10000) detected at line 546 [][][] [253] Underfull \hbox (badness 10000) detected at line 572 [][][] Underfull \hbox (badness 10000) detected at line 604 [][][] Underfull \hbox (badness 10000) detected at line 607 [][][] Underfull \hbox (badness 10000) detected at line 610 [][][] [254] Underfull \hbox (badness 10000) detected at line 643 [][][] Underfull \hbox (badness 10000) detected at line 646 [][][] Underfull \hbox (badness 10000) detected at line 668 [][][] Underfull \hbox (badness 10000) detected at line 690 [][][] [255] Underfull \hbox (badness 10000) detected at line 712 [][][] Underfull \hbox (badness 10000) detected at line 715 [][][] Underfull \hbox (badness 10000) detected at line 718 [][][] Underfull \hbox (badness 10000) detected at line 742 [][][] [256] Underfull \hbox (badness 10000) detected at line 764 [][][] Underfull \hbox (badness 10000) detected at line 767 [][][] Underfull \hbox (badness 10000) detected at line 799 [][][] [257] Underfull \hbox (badness 10000) detected at line 802 [][][] Underfull \hbox (badness 10000) detected at line 856 [][][] Underfull \hbox (badness 10000) detected at line 859 [][][] Underfull \hbox (badness 10000) detected at line 864 [][][] [258] Underfull \hbox (badness 10000) detected at line 894 [][][] Underfull \hbox (badness 10000) detected at line 920 [][][] Underfull \hbox (badness 10000) detected at line 923 [][][] [259] Underfull \hbox (badness 10000) detected at line 928 [][][] Underfull \hbox (badness 10000) detected at line 956 [][][] Underfull \hbox (badness 10000) detected at line 982 [][][] [260] Underfull \hbox (badness 10000) detected at line 1008 [][][] Underfull \hbox (badness 10000) detected at line 1030 [][][] Underfull \hbox (badness 10000) detected at line 1033 [][][] [261] Underfull \hbox (badness 10000) detected at line 1055 [][][] Underfull \hbox (badness 10000) detected at line 1093 [][][] Underfull \hbox (badness 10000) detected at line 1096 [][][] [262] Underfull \hbox (badness 10000) detected at line 1099 [][][] Underfull \hbox (badness 10000) detected at line 1123 [][][] Underfull \hbox (badness 10000) detected at line 1160 [][][] [263] Underfull \hbox (badness 10000) detected at line 1163 [][][] Underfull \hbox (badness 10000) detected at line 1166 [][][] Underfull \hbox (badness 10000) detected at line 1190 [][][] Underfull \hbox (badness 10000) detected at line 1193 [][][] Underfull \hbox (badness 10000) detected at line 1198 [][][] [264] Underfull \hbox (badness 10000) detected at line 1226 [][][] Underfull \hbox (badness 10000) detected at line 1252 [][][] [265] Underfull \hbox (badness 10000) detected at line 1280 [][][] Underfull \hbox (badness 10000) detected at line 1283 [][][] Underfull \hbox (badness 10000) detected at line 1303 [][][] [266] Underfull \hbox (badness 10000) detected at line 1343 [][][] Underfull \hbox (badness 10000) detected at line 1346 [][][] Underfull \hbox (badness 10000) detected at line 1349 [][][] Underfull \hbox (badness 10000) detected at line 1373 [][][] [267] Underfull \hbox (badness 10000) detected at line 1401 [][][] Underfull \hbox (badness 10000) detected at line 1404 [][][] Underfull \hbox (badness 10000) detected at line 1426 [][][] Underfull \hbox (badness 10000) detected at line 1429 [][][] Underfull \hbox (badness 10000) detected at line 1432 [][][] Underfull \hbox (badness 10000) detected at line 1454 [][][] ) (./group___vpmgp.tex [268] Underfull \hbox (badness 10000) detected at line 45 [][][] [269] Underfull \hbox (badness 10000) detected at line 78 [][][] Underfull \hbox (badness 10000) detected at line 86 [][][] Underfull \hbox (badness 10000) detected at line 103 [][][] Underfull \hbox (badness 10000) detected at line 113 [][][] Underfull \hbox (badness 10000) detected at line 130 [][][] [270] Underfull \hbox (badness 10000) detected at line 152 [][][] Underfull \hbox (badness 10000) detected at line 174 [][][] [271] Underfull \hbox (badness 10000) detected at line 208 [][][] ) (./group___p_m_g_c.tex [272] [273] [274] [275] Underfull \hbox (badness 10000) detected at line 150 [][][] Underfull \hbox (badness 10000) detected at line 153 [][][] Underfull \hbox (badness 10000) detected at line 156 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 165--165 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [276] Underfull \hbox (badness 10000) detected at line 212 [][][] Underfull \hbox (badness 10000) detected at line 215 [][][] Underfull \hbox (badness 10000) detected at line 218 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 227--227 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [277] Underfull \hbox (badness 10000) detected at line 277 [][][] Underfull \hbox (badness 10000) detected at line 280 [][][] [278] Underfull \hbox (badness 10000) detected at line 308 [][][] Underfull \hbox (badness 10000) detected at line 311 [][][] Underfull \hbox (badness 10000) detected at line 339 [][][] Underfull \hbox (badness 10000) detected at line 342 [][][] Underfull \hbox (badness 10000) detected at line 345 [][][] [279] Overfull \hbox (304.08286pt too wide) in paragraph at lines 355--355 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 392 [][][] Underfull \hbox (badness 10000) detected at line 395 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 404--404 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [280] Underfull \hbox (badness 10000) detected at line 439 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.456 on input line 488. [281] Underfull \hbox (badness 10000) detected at line 503 [][][] Underfull \hbox (badness 10000) detected at line 506 [][][] Underfull \hbox (badness 10000) detected at line 509 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 518--518 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [282] Underfull \hbox (badness 10000) detected at line 556 [][][] Underfull \hbox (badness 10000) detected at line 559 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 568--568 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 603 [][][] Underfull \hbox (badness 10000) detected at line 606 [][][] [283] Underfull \hbox (badness 10000) detected at line 646 [][][] Underfull \hbox (badness 10000) detected at line 649 [][][] [284] [285] Underfull \hbox (badness 10000) detected at line 719 [][][] Underfull \hbox (badness 10000) detected at line 722 [][][] Underfull \hbox (badness 10000) detected at line 772 [][][] Underfull \hbox (badness 10000) detected at line 775 [][][] Underfull \hbox (badness 10000) detected at line 778 [][][] [286] Overfull \hbox (304.08286pt too wide) in paragraph at lines 788--788 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 825 [][][] Underfull \hbox (badness 10000) detected at line 828 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 837--837 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [287] Package longtable Warning: Column widths have changed (longtable) in table 7.460 on input line 892. [288] Underfull \hbox (badness 10000) detected at line 907 [][][] Underfull \hbox (badness 10000) detected at line 910 [][][] [289] Package longtable Warning: Column widths have changed (longtable) in table 7.461 on input line 1035. [290] [291] Underfull \hbox (badness 10000) detected at line 1050 [][][] Underfull \hbox (badness 10000) detected at line 1053 [][][] [292] Package longtable Warning: Column widths have changed (longtable) in table 7.462 on input line 1214. [293] [294] Underfull \hbox (badness 10000) detected at line 1229 [][][] Underfull \hbox (badness 10000) detected at line 1232 [][][] [295] Package longtable Warning: Column widths have changed (longtable) in table 7.463 on input line 1367. [296] Underfull \hbox (badness 10000) detected at line 1382 [][][] Underfull \hbox (badness 10000) detected at line 1385 [][][] Underfull \hbox (badness 10000) detected at line 1388 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.464 on input line 1431. [297] [298] Underfull \hbox (badness 10000) detected at line 1446 [][][] Underfull \hbox (badness 10000) detected at line 1449 [][][] Underfull \hbox (badness 10000) detected at line 1452 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 1462--1462 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 1501 [][][] Underfull \hbox (badness 10000) detected at line 1504 [][][] [299] Package longtable Warning: Column widths have changed (longtable) in table 7.465 on input line 1569. [300] Underfull \hbox (badness 10000) detected at line 1584 [][][] Underfull \hbox (badness 10000) detected at line 1587 [][][] Underfull \hbox (badness 10000) detected at line 1590 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 1600--1600 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 1637 [][][] Underfull \hbox (badness 10000) detected at line 1640 [][][] [301] Underfull \hbox (badness 10000) detected at line 1643 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 1652--1652 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Package longtable Warning: Column widths have changed (longtable) in table 7.466 on input line 1715. Overfull \vbox (9.44278pt too high) has occurred while \output is active [302] Underfull \hbox (badness 10000) detected at line 1730 [][][] Underfull \hbox (badness 10000) detected at line 1735 [][][] Underfull \hbox (badness 10000) detected at line 1738 [][][] Underfull \hbox (badness 10000) detected at line 1768 [][][] Underfull \hbox (badness 10000) detected at line 1771 [][][] [303] Underfull \hbox (badness 10000) detected at line 1805 [][][] Underfull \hbox (badness 10000) detected at line 1808 [][][] [304] Underfull \hbox (badness 10000) detected at line 1842 [][][] Underfull \hbox (badness 10000) detected at line 1845 [][][] Underfull \hbox (badness 10000) detected at line 1879 [][][] Underfull \hbox (badness 10000) detected at line 1882 [][][] [305] Underfull \hbox (badness 10000) detected at line 1885 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 1895--1895 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 1932 [][][] Underfull \hbox (badness 10000) detected at line 1935 [][][] Underfull \hbox (badness 10000) detected at line 1938 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 1947--1947 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [306] Package longtable Warning: Column widths have changed (longtable) in table 7.471 on input line 2018. [307] Underfull \hbox (badness 10000) detected at line 2033 [][][] Underfull \hbox (badness 10000) detected at line 2036 [][][] Underfull \hbox (badness 10000) detected at line 2070 [][][] Underfull \hbox (badness 10000) detected at line 2073 [][][] Underfull \hbox (badness 10000) detected at line 2076 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 2086--2086 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [308] Underfull \hbox (badness 10000) detected at line 2123 [][][] Underfull \hbox (badness 10000) detected at line 2126 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2135--2135 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [309] Underfull \hbox (badness 10000) detected at line 2170 [][][] Underfull \hbox (badness 10000) detected at line 2173 [][][] Underfull \hbox (badness 10000) detected at line 2205 [][][] [310] Underfull \hbox (badness 10000) detected at line 2208 [][][] Underfull \hbox (badness 10000) detected at line 2244 [][][] Underfull \hbox (badness 10000) detected at line 2247 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.475 on input line 2268. [311] Underfull \hbox (badness 10000) detected at line 2283 [][][] Underfull \hbox (badness 10000) detected at line 2286 [][][] [312] Underfull \hbox (badness 10000) detected at line 2314 [][][] Underfull \hbox (badness 10000) detected at line 2317 [][][] Underfull \hbox (badness 10000) detected at line 2320 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 2330--2330 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [313] Underfull \hbox (badness 10000) detected at line 2367 [][][] Underfull \hbox (badness 10000) detected at line 2370 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2379--2379 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 2414 [][][] Underfull \hbox (badness 10000) detected at line 2417 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.477 on input line 2488. [314] [315] Underfull \hbox (badness 10000) detected at line 2503 [][][] Underfull \hbox (badness 10000) detected at line 2506 [][][] Underfull \hbox (badness 10000) detected at line 2509 [][][] [316] Underfull \hbox (badness 10000) detected at line 2557 [][][] Underfull \hbox (badness 10000) detected at line 2560 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2569--2569 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [317] Underfull \hbox (badness 10000) detected at line 2604 [][][] Underfull \hbox (badness 10000) detected at line 2607 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.478 on input line 2682. [318] Underfull \hbox (badness 10000) detected at line 2697 [][][] Underfull \hbox (badness 10000) detected at line 2700 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.479 on input line 2731. [319] Underfull \hbox (badness 10000) detected at line 2746 [][][] Underfull \hbox (badness 10000) detected at line 2749 [][][] Underfull \hbox (badness 10000) detected at line 2752 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 2762--2762 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [320] Underfull \hbox (badness 10000) detected at line 2799 [][][] Underfull \hbox (badness 10000) detected at line 2802 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2811--2811 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 2846 [][][] Underfull \hbox (badness 10000) detected at line 2849 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.480 on input line 2890. [321] Underfull \hbox (badness 10000) detected at line 2905 [][][] Underfull \hbox (badness 10000) detected at line 2908 [][][] Overfull \vbox (18.98318pt too high) has occurred while \output is active [322] Underfull \hbox (badness 10000) detected at line 2946 [][][] Underfull \hbox (badness 10000) detected at line 2957 [][][] [323] Underfull \hbox (badness 10000) detected at line 2960 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.482 on input line 3031. [324] Underfull \hbox (badness 10000) detected at line 3046 [][][] Underfull \hbox (badness 10000) detected at line 3049 [][][] Underfull \hbox (badness 10000) detected at line 3052 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3062--3062 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 3099 [][][] Underfull \hbox (badness 10000) detected at line 3102 [][][] [325] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 3111--3111 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 3146 [][][] Underfull \hbox (badness 10000) detected at line 3149 [][][] [326] Underfull \hbox (badness 10000) detected at line 3187 [][][] Underfull \hbox (badness 10000) detected at line 3190 [][][] Underfull \hbox (badness 10000) detected at line 3193 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3203--3203 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [327] Underfull \hbox (badness 10000) detected at line 3240 [][][] Underfull \hbox (badness 10000) detected at line 3243 [][][] Underfull \hbox (badness 10000) detected at line 3246 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 3255--3255 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [328] Underfull \hbox (badness 10000) detected at line 3288 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.484 on input line 3327. [329] Underfull \hbox (badness 10000) detected at line 3342 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.485 on input line 3418. [330] [331] Underfull \hbox (badness 10000) detected at line 3484 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.486 on input line 3527. [332] Underfull \hbox (badness 10000) detected at line 3542 [][][] Underfull \hbox (badness 10000) detected at line 3545 [][][] [333] Underfull \hbox (badness 10000) detected at line 3585 [][][] Underfull \hbox (badness 10000) detected at line 3588 [][][] Underfull \hbox (badness 10000) detected at line 3591 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3601--3601 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [334] Underfull \hbox (badness 10000) detected at line 3638 [][][] Underfull \hbox (badness 10000) detected at line 3641 [][][] Underfull \hbox (badness 10000) detected at line 3644 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 3653--3653 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [335] Underfull \hbox (badness 10000) detected at line 3702 [][][] Underfull \hbox (badness 10000) detected at line 3705 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.488 on input line 3774. [336] [337] Underfull \hbox (badness 10000) detected at line 3789 [][][] Underfull \hbox (badness 10000) detected at line 3792 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.489 on input line 3875. [338] Underfull \hbox (badness 10000) detected at line 3890 [][][] Underfull \hbox (badness 10000) detected at line 3893 [][][] Underfull \hbox (badness 10000) detected at line 3896 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3906--3906 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [339] Underfull \hbox (badness 10000) detected at line 3943 [][][] Underfull \hbox (badness 10000) detected at line 3946 [][][] Underfull \hbox (badness 10000) detected at line 3972 [][][] Underfull \hbox (badness 10000) detected at line 3975 [][][] [340] Underfull \hbox (badness 10000) detected at line 4001 [][][] Underfull \hbox (badness 10000) detected at line 4004 [][][] [341] Underfull \hbox (badness 10000) detected at line 4034 [][][] Underfull \hbox (badness 10000) detected at line 4037 [][][] Underfull \hbox (badness 10000) detected at line 4040 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 4050--4050 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 4087 [][][] [342] Underfull \hbox (badness 10000) detected at line 4090 [][][] Underfull \hbox (badness 10000) detected at line 4093 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 4102--4102 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 4137 [][][] Underfull \hbox (badness 10000) detected at line 4140 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.493 on input line 4179. [343] Underfull \hbox (badness 10000) detected at line 4194 [][][] [344] Underfull \hbox (badness 10000) detected at line 4216 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.494 on input line 4275. Overfull \vbox (38.14133pt too high) has occurred while \output is active [345] Underfull \hbox (badness 10000) detected at line 4290 [][][] Underfull \hbox (badness 10000) detected at line 4293 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.495 on input line 4368. [346] [347] Underfull \hbox (badness 10000) detected at line 4383 [][][] Underfull \hbox (badness 10000) detected at line 4386 [][][] Underfull \hbox (badness 10000) detected at line 4426 [][][] Underfull \hbox (badness 10000) detected at line 4429 [][][] [348] Underfull \hbox (badness 10000) detected at line 4471 [][][] Underfull \hbox (badness 10000) detected at line 4474 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.498 on input line 4517. [349] Underfull \hbox (badness 10000) detected at line 4532 [][][] Underfull \hbox (badness 10000) detected at line 4535 [][][] Underfull \hbox (badness 10000) detected at line 4538 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 4548--4548 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [350] Underfull \hbox (badness 10000) detected at line 4585 [][][] Underfull \hbox (badness 10000) detected at line 4588 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 4597--4597 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [351] Underfull \hbox (badness 10000) detected at line 4630 [][][] Underfull \hbox (badness 10000) detected at line 4633 [][][] Underfull \hbox (badness 10000) detected at line 4636 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.499 on input line 4681. [352] Underfull \hbox (badness 10000) detected at line 4692 [][][] Underfull \hbox (badness 10000) detected at line 4695 [][][] Underfull \hbox (badness 10000) detected at line 4727 [][][] Underfull \hbox (badness 10000) detected at line 4730 [][][] [353] Underfull \hbox (badness 10000) detected at line 4768 [][][] Underfull \hbox (badness 10000) detected at line 4771 [][][] Underfull \hbox (badness 10000) detected at line 4774 [][][] Overfull \hbox (20.88268pt too wide) in paragraph at lines 4784--4784 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute,[] [354] Underfull \hbox (badness 10000) detected at line 4822 [][][] Underfull \hbox (badness 10000) detected at line 4825 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 4834--4834 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [355] Underfull \hbox (badness 10000) detected at line 4869 [][][] Underfull \hbox (badness 10000) detected at line 4872 [][][] Package longtable Warning: Column widths have changed (longtable) in table 7.502 on input line 4915. [356] Underfull \hbox (badness 10000) detected at line 4930 [][][] Underfull \hbox (badness 10000) detected at line 4933 [][][] Underfull \hbox (badness 10000) detected at line 4965 [][][] Underfull \hbox (badness 10000) detected at line 4968 [][][] Underfull \hbox (badness 10000) detected at line 4971 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 4981--4981 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [357] Underfull \hbox (badness 10000) detected at line 5018 [][][] Underfull \hbox (badness 10000) detected at line 5021 [][][] Underfull \hbox (badness 10000) detected at line 5024 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 5033--5033 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [358] Underfull \hbox (badness 10000) detected at line 5068 [][][] Underfull \hbox (badness 10000) detected at line 5071 [][][] Underfull \hbox (badness 10000) detected at line 5101 [][][] Underfull \hbox (badness 10000) detected at line 5104 [][][] Underfull \hbox (badness 10000) detected at line 5107 [][][] [359] Underfull \hbox (badness 10000) detected at line 5137 [][][] Underfull \hbox (badness 10000) detected at line 5140 [][][] Underfull \hbox (badness 10000) detected at line 5170 [][][] [360] Underfull \hbox (badness 10000) detected at line 5173 [][][] Underfull \hbox (badness 10000) detected at line 5203 [][][] Underfull \hbox (badness 10000) detected at line 5206 [][][] Underfull \hbox (badness 10000) detected at line 5234 [][][] [361] Underfull \hbox (badness 10000) detected at line 5237 [][][] Underfull \hbox (badness 10000) detected at line 5265 [][][] Underfull \hbox (badness 10000) detected at line 5268 [][][] ) (./group___frontend.tex [362] Underfull \hbox (badness 2495) in paragraph at lines 32--33 []\T1/phv/m/n/10 VPUBLIC Vrc[]_[][]Codes [] (int icalc, [] $\OMS/cmsy/m/n/10 ^^ C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 feparm, [] $\OMS /cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbeparm, [] Overfull \hbox (16.65858pt too wide) in paragraph at lines 40--41 []\T1/phv/m/n/10 VEXTERNC int [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], Overfull \hbox (16.91972pt too wide) in paragraph at lines 42--43 []\T1/phv/m/n/10 VEXTERNC void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh , [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/1 0 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], Underfull \hbox (badness 1910) in paragraph at lines 60--61 [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1 /phv/m/n/10 alist[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][] [], [] Underfull \hbox (badness 1237) in paragraph at lines 60--61 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 charge[]Map[][][], [] $\OMS/cmsy/m/n/10 ^^C $\T1/phv/m/n/10 pmgp[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pmg[][][], [] [363] Underfull \hbox (badness 5817) in paragraph at lines 78--79 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], Underfull \hbox (badness 5817) in paragraph at lines 80--81 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], [364] [365] Underfull \hbox (badness 10000) detected at line 178 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 211 [][][] [366] Underfull \hbox (badness 10000) detected at line 235 [][][] [367] Underfull \hbox (badness 10000) detected at line 275 [][][] Underfull \hbox (badness 10000) detected at line 297 [][][] Underfull \hbox (badness 10000) detected at line 314 [][][] Underfull \hbox (badness 10000) detected at line 317 [][][] [368] Underfull \hbox (badness 10000) detected at line 351 [][][] Underfull \hbox (badness 10000) detected at line 373 [][][] Underfull \hbox (badness 10000) detected at line 390 [][][] Underfull \hbox (badness 10000) detected at line 393 [][][] [369] [370] Underfull \hbox (badness 10000) detected at line 495 [][][] Underfull \hbox (badness 10000) detected at line 502 [][][] [371] Underfull \hbox (badness 10000) detected at line 572 [][][] Underfull \hbox (badness 10000) detected at line 575 [][][] [372] Underfull \hbox (badness 10000) detected at line 625 [][][] Underfull \hbox (badness 10000) detected at line 649 [][][] Underfull \hbox (badness 10000) detected at line 677 [][][] [373] Underfull \hbox (badness 10000) detected at line 694 [][][] Underfull \hbox (badness 10000) detected at line 720 [][][] Underfull \hbox (badness 10000) detected at line 748 [][][] [374] Underfull \hbox (badness 10000) detected at line 772 [][][] Underfull \hbox (badness 10000) detected at line 792 [][][] Underfull \hbox (badness 10000) detected at line 818 [][][] [375] Underfull \hbox (badness 10000) detected at line 842 [][][] Underfull \hbox (badness 10000) detected at line 866 [][][] Underfull \hbox (badness 10000) detected at line 876 [][][] Underfull \hbox (badness 10000) detected at line 895 [][][] [376] Underfull \hbox (badness 10000) detected at line 909 [][][] Underfull \hbox (badness 10000) detected at line 912 [][][] Underfull \hbox (badness 10000) detected at line 929 [][][] Underfull \hbox (badness 10000) detected at line 939 [][][] Underfull \hbox (badness 10000) detected at line 958 [][][] Underfull \hbox (badness 10000) detected at line 961 [][][] [377] Underfull \hbox (badness 10000) detected at line 981 [][][] Underfull \hbox (badness 10000) detected at line 984 [][][] Underfull \hbox (badness 10000) detected at line 1010 [][][] Underfull \hbox (badness 10000) detected at line 1013 [][][] [378] Underfull \hbox (badness 10000) detected at line 1035 [][][] Underfull \hbox (badness 10000) detected at line 1045 [][][] Underfull \hbox (badness 10000) detected at line 1064 [][][] Underfull \hbox (badness 10000) detected at line 1067 [][][] Underfull \hbox (badness 10000) detected at line 1091 [][][] [379] Underfull \hbox (badness 10000) detected at line 1105 [][][] Underfull \hbox (badness 10000) detected at line 1122 [][][] Underfull \hbox (badness 10000) detected at line 1134 [][][] Underfull \hbox (badness 10000) in paragraph at lines 1135--1136 Underfull \hbox (badness 10000) detected at line 1138 [][][] [380] Underfull \hbox (badness 10000) detected at line 1166 [][][] Underfull \hbox (badness 10000) detected at line 1180 [][][] Underfull \hbox (badness 10000) detected at line 1201 [][][] Underfull \hbox (badness 10000) detected at line 1204 [][][] [381] Underfull \hbox (badness 10000) detected at line 1228 [][][] Underfull \hbox (badness 10000) detected at line 1231 [][][] Underfull \hbox (badness 10000) detected at line 1259 [][][] Underfull \hbox (badness 10000) detected at line 1262 [][][] [382] Underfull \hbox (badness 10000) detected at line 1288 [][][] Underfull \hbox (badness 10000) detected at line 1291 [][][] Underfull \hbox (badness 10000) detected at line 1319 [][][] Underfull \hbox (badness 10000) detected at line 1322 [][][] [383] Underfull \hbox (badness 10000) detected at line 1348 [][][] Underfull \hbox (badness 10000) detected at line 1377 [][][] Underfull \hbox (badness 10000) detected at line 1380 [][][] Underfull \hbox (badness 10000) detected at line 1408 [][][] [384] Underfull \hbox (badness 10000) detected at line 1432 [][][] Underfull \hbox (badness 10000) detected at line 1454 [][][] Underfull \hbox (badness 10000) detected at line 1468 [][][] [385] Underfull \hbox (badness 10000) detected at line 1485 [][][] Underfull \hbox (badness 10000) detected at line 1497 [][][] Underfull \hbox (badness 10000) detected at line 1514 [][][] Underfull \hbox (badness 10000) detected at line 1528 [][][] [386] Underfull \hbox (badness 10000) detected at line 1562 [][][] Underfull \hbox (badness 10000) detected at line 1574 [][][] Underfull \hbox (badness 10000) detected at line 1591 [][][] Underfull \hbox (badness 10000) detected at line 1608 [][][] [387] Underfull \hbox (badness 10000) detected at line 1636 [][][] Underfull \hbox (badness 10000) detected at line 1650 [][][] [388] Underfull \hbox (badness 10000) detected at line 1688 [][][] Underfull \hbox (badness 10000) detected at line 1716 [][][] Underfull \hbox (badness 10000) detected at line 1733 [][][] [389] Underfull \hbox (badness 10000) detected at line 1747 [][][] Underfull \hbox (badness 10000) detected at line 1764 [][][] Underfull \hbox (badness 10000) detected at line 1792 [][][] [390] Underfull \hbox (badness 10000) detected at line 1809 [][][] Underfull \hbox (badness 10000) detected at line 1823 [][][] ) [391] [392] Chapter 8. (./struct_atom_force.tex Underfull \hbox (badness 10000) detected at line 32 [][][] [393]) (./structs_a_p_o_lparm.tex [394] Underfull \hbox (badness 10000) detected at line 88 [][][] [395] Underfull \hbox (badness 10000) detected at line 224 [][][] [396] Underfull \hbox (badness 10000) detected at line 237 [][][] Underfull \hbox (badness 10000) detected at line 250 [][][] Underfull \hbox (badness 10000) detected at line 263 [][][] Underfull \hbox (badness 10000) detected at line 276 [][][] Underfull \hbox (badness 10000) detected at line 289 [][][] Underfull \hbox (badness 10000) detected at line 302 [][][] [397] Underfull \hbox (badness 10000) detected at line 315 [][][] Underfull \hbox (badness 10000) detected at line 328 [][][] Underfull \hbox (badness 10000) detected at line 341 [][][] Underfull \hbox (badness 10000) detected at line 354 [][][] Underfull \hbox (badness 10000) detected at line 367 [][][] Underfull \hbox (badness 10000) detected at line 380 [][][] [398]) (./structs_b_e_mparm.tex [399] Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 53 [][][] [400] Underfull \hbox (badness 10000) detected at line 129 [][][] Underfull \hbox (badness 10000) detected at line 142 [][][] Underfull \hbox (badness 10000) detected at line 155 [][][] [401] Underfull \hbox (badness 10000) detected at line 168 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 194 [][][] ) (./structs_f_e_mparm.tex [402] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) in paragraph at lines 84--85 [403] [404] [405]) (./structs_g_e_o_f_l_o_wparm.tex Underfull \hbox (badness 10000) detected at line 30 [][][] Underfull \hbox (badness 10000) detected at line 33 [][][] [406]) (./structs_m_gparm.tex [407] Underfull \hbox (badness 10000) detected at line 120 [][][] Underfull \hbox (badness 10000) detected at line 123 [][][] [408] Underfull \hbox (badness 10000) in paragraph at lines 149--150 Underfull \hbox (badness 10000) in paragraph at lines 180--181 [409] Underfull \hbox (badness 10000) in paragraph at lines 261--262 [410] [411] Underfull \hbox (badness 10000) detected at line 434 [][][] Underfull \hbox (badness 10000) detected at line 447 [][][] Underfull \hbox (badness 10000) detected at line 460 [][][] Underfull \hbox (badness 10000) detected at line 473 [][][] [412] Underfull \hbox (badness 10000) detected at line 486 [][][] Underfull \hbox (badness 10000) detected at line 499 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] Underfull \hbox (badness 10000) detected at line 538 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] [413] Underfull \hbox (badness 10000) detected at line 564 [][][] Underfull \hbox (badness 10000) detected at line 577 [][][] Underfull \hbox (badness 10000) detected at line 590 [][][] Underfull \hbox (badness 10000) detected at line 603 [][][] Underfull \hbox (badness 10000) detected at line 616 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] [414] Underfull \hbox (badness 10000) detected at line 642 [][][] Underfull \hbox (badness 10000) detected at line 655 [][][] Underfull \hbox (badness 10000) detected at line 668 [][][] ) (./structs_n_osh.tex [415] Underfull \hbox (badness 10000) detected at line 108 [][][] [416] [417] [418] [419] [420]) (./structs_n_osh__calc.tex [421] Underfull \hbox (badness 10000) detected at line 38 [][][] [422]) (./structs_p_b_a_mparm.tex [423] Underfull \hbox (badness 10000) detected at line 106 [][][] Underfull \hbox (badness 10000) detected at line 109 [][][] [424] [425] [426] [427]) (./structs_p_b_eparm.tex [428] [429] Underfull \hbox (badness 10000) detected at line 142 [][][] Underfull \hbox (badness 10000) detected at line 145 [][][] [430] [431] [432] Underfull \hbox (badness 10000) detected at line 391 [][][] Underfull \hbox (badness 10000) detected at line 404 [][][] Underfull \hbox (badness 10000) detected at line 417 [][][] Underfull \hbox (badness 10000) detected at line 430 [][][] [433] Underfull \hbox (badness 10000) detected at line 473 [][][] Underfull \hbox (badness 10000) detected at line 486 [][][] Underfull \hbox (badness 10000) detected at line 499 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] [434] Underfull \hbox (badness 10000) detected at line 538 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] Underfull \hbox (badness 10000) detected at line 564 [][][] Underfull \hbox (badness 10000) detected at line 577 [][][] Underfull \hbox (badness 10000) detected at line 590 [][][] Underfull \hbox (badness 10000) detected at line 603 [][][] [435] Underfull \hbox (badness 10000) detected at line 616 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] [436] [437]) (./structs_p_b_s_a_mparm.tex [438] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] [439]) (./structs_vacc.tex [440] Underfull \hbox (badness 10000) detected at line 36 [][][] [441]) (./structs_vacc_surf.tex Underfull \hbox (badness 10000) detected at line 36 [][][] [442]) (./structs_valist.tex [443] Underfull \hbox (badness 10000) detected at line 36 [][][] [444]) (./structs_vatom.tex Underfull \hbox (badness 10000) detected at line 36 [][][] Underfull \hbox (badness 10000) in paragraph at lines 62--63 [445] Underfull \hbox (badness 10000) in paragraph at lines 93--94 Underfull \hbox (badness 10000) in paragraph at lines 114--115 ) (./structs_vclist.tex [446] Underfull \hbox (badness 10000) detected at line 40 [][][] [447]) (./structs_vclist_cell.tex Underfull \hbox (badness 10000) detected at line 24 [][][] ) (./structs_vcsm.tex [448] Underfull \hbox (badness 10000) detected at line 42 [][][] [449]) (./structs_vfetk.tex [450] Underfull \hbox (badness 10000) detected at line 60 [][][] [451] Underfull \hbox (badness 10000) in paragraph at lines 116--117 [452]) (./structs_vfetk___local_var.tex [453] Underfull \hbox (badness 10000) detected at line 86 [][][] [454] [455] [456] [457]) (./structs_vgreen.tex Underfull \hbox (badness 10000) detected at line 34 [][][] [458]) (./structs_vgrid.tex [459] Underfull \hbox (badness 10000) detected at line 52 [][][] [460] [461]) (./structs_vmgrid.tex Underfull \hbox (badness 10000) detected at line 24 [][][] ) (./structs_vopot.tex [462] Underfull \hbox (badness 10000) detected at line 26 [][][] ) (./structs_vparam___atom_data.tex [463] Underfull \hbox (badness 10000) detected at line 30 [][][] Underfull \hbox (badness 10000) detected at line 33 [][][] ) (./structs_vpbe.tex [464] Underfull \hbox (badness 10000) detected at line 86 [][][] [465] [466] [467] [468]) (./structs_vpee.tex [469] Underfull \hbox (badness 10000) detected at line 34 [][][] ) (./structs_vpmg.tex [470] [471] Underfull \hbox (badness 10000) detected at line 116 [][][] [472] [473] [474] [475] [476]) (./structs_vpmgp.tex [477] Underfull \hbox (badness 10000) detected at line 126 [][][] [478] Underfull \hbox (badness 10000) in paragraph at lines 164--165 Underfull \hbox (badness 10000) in paragraph at lines 175--176 Underfull \hbox (badness 10000) in paragraph at lines 186--187 [479] Underfull \hbox (badness 10000) in paragraph at lines 234--235 [480] [481] [482] [483] Underfull \hbox (badness 10000) in paragraph at lines 506--507 Underfull \hbox (badness 10000) in paragraph at lines 527--528 [484] Underfull \hbox (badness 10000) in paragraph at lines 548--549 Underfull \hbox (badness 10000) in paragraph at lines 589--590 [485] Underfull \hbox (badness 10000) in paragraph at lines 630--631 Underfull \hbox (badness 10000) in paragraph at lines 671--672 ) (./struct_vparam.tex [486] Underfull \hbox (badness 10000) detected at line 26 [][][] ) (./struct_vparam___res_data.tex [487] Underfull \hbox (badness 10000) detected at line 28 [][][] ) [488] Chapter 9. (./mainpage_8h_source.tex) (./apbs_8h.tex <./apbs_8h__incl.pdf> <./apbs_8h__dep __incl.pdf> [489] Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 53 [][][] Underfull \hbox (badness 10000) detected at line 56 [][][] [490]) (./apbs_8h_source.tex) (./vcsm_8c.tex [491] <./vcsm_8c__incl.pdf> [492] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] Underfull \hbox (badness 10000) detected at line 58 [][][] [493]) (./vcsm_8c_source.tex [494] [495] [496] [497] [498] [499]) (./vcsm_8h.tex <./vcsm_8h__incl.pdf> <./vcsm_8h__dep__incl.pdf> [500] [501] Underfull \hbox (badness 10000) detected at line 75 [][][] Underfull \hbox (badness 10000) detected at line 78 [][][] Underfull \hbox (badness 10000) detected at line 81 [][][] [502]) (./vcsm_8h_source.tex [503]) (./vfetk_8c.tex [504] <./vfetk_8c__incl.pdf > [505] [506] Underfull \hbox (badness 10000) detected at line 162 [][][] Underfull \hbox (badness 10000) detected at line 165 [][][] [507] Underfull \hbox (badness 10000) detected at line 168 [][][] [508] [509] [510] [511]) (./vfetk_8c_source.tex [512] [513] [514] [515] [516] [517] [518] [519] [520] [521] [522] [523] [524] [525] [526] [527] [528] [529] [530] [531] [532] [533] [534] [535] [536] [537] [538] [539] [540] [541]) (./vfetk_8h.tex [542] <./vfetk_8h__incl.pdf> <./vfetk_8h__dep__inc l.pdf> [543] [544] [545] Underfull \hbox (badness 10000) detected at line 187 [][][] [546] Underfull \hbox (badness 10000) detected at line 190 [][][] Underfull \hbox (badness 10000) detected at line 193 [][][] ) (./vfetk_8h_source.tex [547] [548] [549] [550] [551] [552]) (./vpee_8c.tex <. /vpee_8c__incl.pdf> [553] Underfull \hbox (badness 10000) detected at line 49 [][][] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] [554]) (./vpee_8c_source.tex [555] [556] [557] [558] [559] [560]) (./vpee_8h.tex [561] <./vpee_8h__incl.pdf> <./vpee_8h__dep__incl.pdf> [562] Underfull \hbox (badness 10000) detected at line 55 [][][] Underfull \hbox (badness 10000) detected at line 58 [][][] Underfull \hbox (badness 10000) detected at line 61 [][][] [563]) (./vpee_8h_source.tex [564]) (./apolparm_8c.tex <./apolparm_8c__incl.pdf > [565] Underfull \hbox (badness 10000) detected at line 64 [][][] Underfull \hbox (badness 10000) detected at line 67 [][][] Underfull \hbox (badness 10000) detected at line 70 [][][] [566] [567]) (./apolparm_8c_source.tex [568] [569] [570] [571] [572] [573] [574] [575]) (./apolparm_8h_source.tex [576]) (./bemparm_8c.tex <./bemparm_8c__ incl.pdf> [577] [578] Underfull \hbox (badness 10000) detected at line 48 [][][] Underfull \hbox (badness 10000) detected at line 51 [][][] Underfull \hbox (badness 10000) detected at line 54 [][][] [579] Underfull \hbox (badness 10000) detected at line 120 [][][] ) (./bemparm_8c_source.tex [580] [581] [582] [583]) (./bemparm_8h_source.tex [584]) (./femparm_8c.tex <./femparm_8c__incl.pdf> [585] [586] Underfull \hbox (badness 10000) detected at line 58 [][][] Underfull \hbox (badness 10000) detected at line 61 [][][] Underfull \hbox (badness 10000) detected at line 64 [][][] [587] [588]) (./femparm_8c_source.tex [589] [590] [591] [592] [593]) (./femparm_8h.tex <./femparm_8h__incl.pdf> [594] <./femparm_8h__dep__incl.pdf> [595] Underfull \hbox (badness 10000) detected at line 87 [][][] Underfull \hbox (badness 10000) detected at line 90 [][][] Underfull \hbox (badness 10000) detected at line 93 [][][] [596]) (./femparm_8h_source.tex [597]) (./geoflowparm_8c.tex [598] <./geoflowpa rm_8c__incl.pdf> [599] Underfull \hbox (badness 10000) detected at line 46 [][][] Underfull \hbox (badness 10000) detected at line 49 [][][] Underfull \hbox (badness 10000) detected at line 52 [][][] [600]) (./geoflowparm_8c_source.tex [601] [602]) (./geoflowparm_8h.tex [603] <. /geoflowparm_8h__incl.pdf> <./geoflowparm_8h__dep__incl.pdf> [604] [605] Underfull \hbox (badness 10000) detected at line 69 [][][] Underfull \hbox (badness 10000) detected at line 72 [][][] Underfull \hbox (badness 10000) detected at line 75 [][][] [606]) (./geoflowparm_8h_source.tex [607]) (./mgparm_8c.tex <./mgparm_8c__incl. pdf> [608] [609] Underfull \hbox (badness 10000) detected at line 94 [][][] Underfull \hbox (badness 10000) detected at line 97 [][][] Underfull \hbox (badness 10000) detected at line 100 [][][] [610] [611]) (./mgparm_8c_source.tex [612] [613] [614] [615] [616] [617] [618] [619] [620] [621] [622] [623]) (./mgparm_8h.tex <./mgparm_8h__incl.pdf> [624] <./mgparm_8h__dep__incl.pdf> [625] [626] Underfull \hbox (badness 10000) detected at line 102 [][][] Underfull \hbox (badness 10000) detected at line 105 [][][] Underfull \hbox (badness 10000) detected at line 108 [][][] [627]) (./mgparm_8h_source.tex [628]) (./nosh_8c.tex <./nosh_8c__incl.pdf> [629] [630] [631] Underfull \hbox (badness 10000) detected at line 150 [][][] Underfull \hbox (badness 10000) detected at line 153 [][][] Underfull \hbox (badness 10000) detected at line 156 [][][] [632] [633] [634] [635] [636]) (./nosh_8c_source.tex [637] [638] [639] [640] [641] [642] [643] [644] [645] [646] [647] [648] [649] [650] [651] [652] [653] [654] [655] [656] [657] [658] [659] [660] [661] [662] [663] [664] [665] [666] [667] [668] [669] [670] [671] [672] [673] [674] [675] [676]) (./nosh_8h.tex <./nosh_8h__incl.pdf> [677] <./nosh_8h__dep__incl.pdf> [678] [679] [680] Underfull \hbox (badness 10000) detected at line 169 [][][] Underfull \hbox (badness 10000) detected at line 172 [][][] Underfull \hbox (badness 10000) detected at line 175 [][][] ) (./nosh_8h_source.tex [681] [682] [683]) (./pbamparm_8c.tex <./pbamparm_8c__i ncl.pdf> [684] [685] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) detected at line 71 [][][] Underfull \hbox (badness 10000) detected at line 74 [][][] [686]) (./pbamparm_8c_source.tex [687] [688] [689] [690] [691] [692] [693] [694] [695]) (./pbamparm_8h.tex <./pbamparm_8h__incl.pdf> <./pbamparm_8h__dep__ incl.pdf> [696] [697] Underfull \hbox (badness 10000) detected at line 100 [][][] [698] Underfull \hbox (badness 10000) detected at line 103 [][][] Underfull \hbox (badness 10000) detected at line 106 [][][] [699]) (./pbamparm_8h_source.tex [700]) (./pbeparm_8c.tex [701] <./pbeparm_8c__ incl.pdf> [702] Underfull \hbox (badness 10000) detected at line 100 [][][] Underfull \hbox (badness 10000) detected at line 103 [][][] Underfull \hbox (badness 10000) detected at line 106 [][][] [703] [704] [705] [706] [707]) (./pbeparm_8c_source.tex [708] [709] [710] [711] [712] [713] [714] [715] [716] [717] [718] [719] [720] [721] [722]) (./pbeparm_8h.tex <./pbeparm_8h__incl.pdf> [723] <./pbeparm_8h__dep__incl.pdf> [724] Underfull \hbox (badness 10000) detected at line 86 [][][] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 92 [][][] [725]) (./pbeparm_8h_source.tex [726] [727]) (./pbsamparm_8c.tex <./pbsamparm_8 c__incl.pdf> [728] [729] Underfull \hbox (badness 10000) detected at line 48 [][][] Underfull \hbox (badness 10000) detected at line 51 [][][] Underfull \hbox (badness 10000) detected at line 54 [][][] [730]) (./pbsamparm_8c_source.tex [731] [732]) (./pbsamparm_8h.tex [733] <./pbs amparm_8h__incl.pdf> <./pbsamparm_8h__dep__incl.pdf> [734] [735] Underfull \hbox (badness 10000) detected at line 84 [][][] Underfull \hbox (badness 10000) detected at line 87 [][][] Underfull \hbox (badness 10000) detected at line 90 [][][] [736]) (./pbsamparm_8h_source.tex [737]) (./vacc_8c.tex <./vacc_8c__incl.pdf> [738] [739] [740] Underfull \hbox (badness 10000) detected at line 106 [][][] Underfull \hbox (badness 10000) detected at line 109 [][][] Underfull \hbox (badness 10000) detected at line 112 [][][] [741] Underfull \hbox (badness 10000) detected at line 178 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 207 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] [742] [743]) (./vacc_8c_source.tex [744] [745] [746] [747] [748] [749] [750] [751] [752] [753] [754] [755] [756] [757] [758] [759] [760] [761] [762] [763] [764] [765] [766]) (./vacc_8h.tex <./vacc_8h__incl.pdf> <./vacc_8h__dep__ incl.pdf> [767] [768] [769] Underfull \hbox (badness 10000) detected at line 121 [][][] Underfull \hbox (badness 10000) detected at line 124 [][][] Underfull \hbox (badness 10000) detected at line 127 [][][] [770]) (./vacc_8h_source.tex [771] [772] [773]) (./valist_8c.tex <./valist_8c__ incl.pdf> [774] [775] Underfull \hbox (badness 2293) in paragraph at lines 53--55 []\T1/phv/m/n/10 VPRIVATE Vrc[]_[][]Codes [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/ m/n/10 thee, Vio $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 sock, int $\OMS/cmsy/m/n/ 10 ^^C$\T1/phv/m/n/10 serial, char atom[] Underfull \hbox (badness 10000) detected at line 81 [][][] Underfull \hbox (badness 10000) detected at line 84 [][][] Underfull \hbox (badness 10000) detected at line 87 [][][] [776] [777] [778]) (./valist_8c_source.tex [779] [780] [781] [782] [783] [784] [785] [786] [787] [788]) (./valist_8h.tex [789] <./valist_8h__incl.pdf> < ./valist_8h__dep__incl.pdf> [790] Underfull \hbox (badness 10000) detected at line 75 [][][] Underfull \hbox (badness 10000) detected at line 78 [][][] Underfull \hbox (badness 10000) detected at line 81 [][][] [791]) (./valist_8h_source.tex [792] [793]) (./vatom_8c.tex <./vatom_8c__incl.p df> [794] Underfull \hbox (badness 10000) detected at line 70 [][][] Underfull \hbox (badness 10000) detected at line 73 [][][] Underfull \hbox (badness 10000) detected at line 76 [][][] [795]) (./vatom_8c_source.tex [796] [797] [798]) (./vatom_8h.tex <./vatom_8h__i ncl.pdf> [799] <./vatom_8h__dep__incl.pdf> [800] [801] Underfull \hbox (badness 10000) detected at line 94 [][][] Underfull \hbox (badness 10000) detected at line 97 [][][] Underfull \hbox (badness 10000) detected at line 100 [][][] ) (./vatom_8h_source.tex [802] [803]) (./vcap_8c.tex <./vcap_8c__incl.pdf> [804] Underfull \hbox (badness 10000) detected at line 30 [][][] Underfull \hbox (badness 10000) detected at line 33 [][][] Underfull \hbox (badness 10000) detected at line 36 [][][] [805]) (./vcap_8c_source.tex [806]) (./vcap_8h.tex <./vcap_8h__incl.pdf> <./vca p_8h__dep__incl.pdf> [807] Underfull \hbox (badness 10000) detected at line 45 [][][] Underfull \hbox (badness 10000) detected at line 48 [][][] [808] Underfull \hbox (badness 10000) detected at line 51 [][][] ) (./vcap_8h_source.tex [809]) (./vclist_8c.tex <./vclist_8c__incl.pdf> Underfull \hbox (badness 4060) in paragraph at lines 31--33 []\T1/phv/m/n/10 VPRIVATE void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 thee , dou-ble lower[]_[]corner[][][], dou-ble upper[]_[] [810] Underfull \hbox (badness 10000) detected at line 64 [][][] Underfull \hbox (badness 10000) detected at line 67 [][][] Underfull \hbox (badness 10000) detected at line 70 [][][] [811] [812]) (./vclist_8c_source.tex [813] [814] [815] [816] [817]) (./vclist_8h.tex [818] <./vclist_8h__incl.pdf> <./vclist_8h__dep__incl.pdf> [819] [820] Underfull \hbox (badness 10000) detected at line 82 [][][] Underfull \hbox (badness 10000) detected at line 85 [][][] Underfull \hbox (badness 10000) detected at line 88 [][][] [821]) (./vclist_8h_source.tex [822]) (./vgreen_8c.tex [823] <./vgreen_8c__incl .pdf> [824] Underfull \hbox (badness 10000) detected at line 54 [][][] Underfull \hbox (badness 10000) detected at line 57 [][][] Underfull \hbox (badness 10000) detected at line 60 [][][] [825]) (./vgreen_8c_source.tex [826] [827] [828] [829] [830] [831]) (./vgreen_8h.tex <./vgreen_8h__incl.pdf> [832] <./vgreen_8h__dep__incl.pdf> [833] Underfull \hbox (badness 10000) detected at line 70 [][][] Underfull \hbox (badness 10000) detected at line 73 [][][] ) (./vgreen_8h_source.tex [834]) (./vhal_8h.tex [835] <./vhal_8h__incl.pdf> <./ vhal_8h__dep__incl.pdf> [836] [837] [838] [839] Underfull \hbox (badness 10000) detected at line 301 [][][] Underfull \hbox (badness 10000) detected at line 304 [][][] Underfull \hbox (badness 10000) detected at line 307 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 316--316 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [840] [841] [842] [843] [844] [845] [846]) (./vhal_8h_source.tex [847] [848] [849] [850] [851] [852] [853] [854]) (./vmatrix_8h.tex [855] <./vmatrix_8h__dep __incl.pdf> Underfull \hbox (badness 10000) detected at line 35 [][][] Underfull \hbox (badness 10000) detected at line 38 [][][] Underfull \hbox (badness 10000) detected at line 41 [][][] [856] [857]) (./vmatrix_8h_source.tex [858]) (./vparam_8c.tex <./vparam_8c__inc l.pdf> [859] Underfull \hbox (badness 10000) detected at line 77 [][][] Underfull \hbox (badness 10000) detected at line 80 [][][] [860] Underfull \hbox (badness 10000) detected at line 83 [][][] ) (./vparam_8c_source.tex [861] [862] [863] [864] [865] [866] [867] [868]) (./vparam_8h.tex [869] <./vparam_8h__incl.pdf> <./vparam_8h__dep__incl.pdf> [870] [871] Underfull \hbox (badness 10000) detected at line 94 [][][] Underfull \hbox (badness 10000) detected at line 97 [][][] Underfull \hbox (badness 10000) detected at line 100 [][][] [872]) (./vparam_8h_source.tex [873]) (./vpbe_8c.tex <./vpbe_8c__incl.pdf> [874] [875] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 92 [][][] [876] Underfull \hbox (badness 10000) detected at line 95 [][][] ) (./vpbe_8c_source.tex [877] [878] [879] [880] [881] [882] [883]) (./vpbe_8h.tex <./vpbe_8h__incl.pdf> <./vpbe_8h__dep__incl.pdf> [884] [885] Underfull \hbox (badness 10000) detected at line 109 [][][] Underfull \hbox (badness 10000) detected at line 112 [][][] Underfull \hbox (badness 10000) detected at line 115 [][][] [886]) (./vpbe_8h_source.tex [887] [888] [889]) (./vstring_8c.tex <./vstring_8c __incl.pdf> [890] Underfull \hbox (badness 10000) detected at line 30 [][][] Underfull \hbox (badness 10000) detected at line 33 [][][] Underfull \hbox (badness 10000) detected at line 36 [][][] ) (./vstring_8c_source.tex [891] [892] [893]) (./vstring_8h.tex <./vstring_8h__ incl.pdf> <./vstring_8h__dep__incl.pdf> [894] Underfull \hbox (badness 10000) detected at line 39 [][][] Underfull \hbox (badness 10000) detected at line 42 [][][] Underfull \hbox (badness 10000) detected at line 45 [][][] [895]) (./vstring_8h_source.tex) (./vunit_8h.tex <./vunit_8h__dep__incl.pdf> [896] LaTeX Warning: Command \r invalid in math mode on input line 41. Missing character: There is no Å in font cmr9! Underfull \hbox (badness 10000) detected at line 49 [][][] Underfull \hbox (badness 10000) detected at line 54 [][][] Underfull \hbox (badness 10000) detected at line 57 [][][] [897]) (./vunit_8h_source.tex) (./main_8c.tex [898] <./main_8c__incl.pdf> Underfull \hbox (badness 10000) detected at line 27 [][][] Underfull \hbox (badness 10000) detected at line 40 [][][] Underfull \hbox (badness 10000) detected at line 43 [][][] [899]) (./main_8c_source.tex [900] [901] [902] [903] [904] [905] [906] [907] [908] [909] [910]) (./vgrid_8c.tex <./vgrid_8c__incl.pdf> [911] [912] Underfull \hbox (badness 10000) detected at line 83 [][][] Underfull \hbox (badness 10000) detected at line 86 [][][] Underfull \hbox (badness 10000) detected at line 89 [][][] [913] Underfull \hbox (badness 10000) detected at line 168 [][][] [914]) (./vgrid_8c_source.tex [915] [916] [917] [918] [919] [920] [921] [922] [923] [924] [925] [926] [927] [928] [929] [930] [931] [932] [933] [934] [935] [936] [937]) (./vgrid_8h.tex [938] <./vgrid_8h__incl.pdf> <./vgrid_ 8h__dep__incl.pdf> [939] [940] Underfull \hbox (badness 10000) detected at line 91 [][][] [941] Underfull \hbox (badness 10000) detected at line 94 [][][] Underfull \hbox (badness 10000) detected at line 97 [][][] [942] Underfull \hbox (badness 10000) detected at line 163 [][][] ) (./vgrid_8h_source.tex [943]) (./vmgrid_8c.tex [944] <./vmgrid_8c__incl.pdf> [945] Underfull \hbox (badness 10000) detected at line 40 [][][] Underfull \hbox (badness 10000) detected at line 43 [][][] Underfull \hbox (badness 10000) detected at line 46 [][][] Underfull \hbox (badness 10000) detected at line 49 [][][] Overfull \hbox (1024.08331pt too wide) in paragraph at lines 58--58 []\T1/pcr/m/n/8 * Copyright (c) 2010, Pacific Northwest National Laboratory. Portions Copyright (c) 2002-2020, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2020, T he Regents of the University of California. Portions Copyright (c) 1995, Michae l Holst.[] ) (./vmgrid_8c_source.tex [946] [947] [948]) (./vmgrid_8h.tex <./vmgrid_8h__inc l.pdf> <./vmgrid_8h__dep__incl.pdf> [949] [950] Underfull \hbox (badness 10000) detected at line 69 [][][] Underfull \hbox (badness 10000) detected at line 72 [][][] Underfull \hbox (badness 10000) detected at line 75 [][][] [951]) (./vmgrid_8h_source.tex) (./vopot_8c.tex [952] <./vopot_8c__incl.pdf> Underfull \hbox (badness 10000) detected at line 43 [][][] Underfull \hbox (badness 10000) detected at line 46 [][][] Underfull \hbox (badness 10000) detected at line 49 [][][] [953]) (./vopot_8c_source.tex [954] [955] [956] [957] [958]) (./vopot_8h.tex <. /vopot_8h__incl.pdf> <./vopot_8h__dep__incl.pdf> [959] [960] Underfull \hbox (badness 10000) detected at line 63 [][][] Underfull \hbox (badness 10000) detected at line 66 [][][] Underfull \hbox (badness 10000) detected at line 69 [][][] ) (./vopot_8h_source.tex [961]) (./vpmg_8c.tex <./vpmg_8c__incl.pdf> [962] [963] [964] [965] Underfull \hbox (badness 10000) detected at line 172 [][][] Underfull \hbox (badness 10000) detected at line 175 [][][] Underfull \hbox (badness 10000) detected at line 178 [][][] [966] Underfull \hbox (badness 10000) detected at line 260 [][][] [967] Underfull \hbox (badness 10000) detected at line 287 [][][] [968] Underfull \hbox (badness 10000) detected at line 383 [][][] Underfull \hbox (badness 10000) detected at line 386 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.7 on input line 393. Underfull \hbox (badness 10000) detected at line 408 [][][] Underfull \hbox (badness 10000) detected at line 411 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.8 on input line 418. [969] Underfull \hbox (badness 10000) detected at line 433 [][][] Underfull \hbox (badness 10000) detected at line 436 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.9 on input line 443. Underfull \hbox (badness 10000) detected at line 458 [][][] Underfull \hbox (badness 10000) detected at line 461 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.10 on input line 468. Underfull \hbox (badness 10000) detected at line 483 [][][] Underfull \hbox (badness 10000) detected at line 486 [][][] [970] Package longtable Warning: Column widths have changed (longtable) in table 9.11 on input line 493. Underfull \hbox (badness 10000) detected at line 508 [][][] Underfull \hbox (badness 10000) detected at line 511 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.12 on input line 518. Underfull \hbox (badness 10000) detected at line 533 [][][] Underfull \hbox (badness 10000) detected at line 536 [][][] Underfull \hbox (badness 10000) detected at line 553 [][][] Underfull \hbox (badness 10000) detected at line 556 [][][] [971] Underfull \hbox (badness 10000) detected at line 573 [][][] Underfull \hbox (badness 10000) detected at line 590 [][][] Underfull \hbox (badness 10000) detected at line 607 [][][] Underfull \hbox (badness 10000) detected at line 624 [][][] Underfull \hbox (badness 10000) detected at line 641 [][][] [972] Underfull \hbox (badness 10000) detected at line 658 [][][] Underfull \hbox (badness 10000) detected at line 675 [][][] Underfull \hbox (badness 10000) detected at line 696 [][][] Underfull \hbox (badness 10000) detected at line 699 [][][] Underfull \hbox (badness 10000) detected at line 716 [][][] [973] Underfull \hbox (badness 10000) detected at line 733 [][][] Underfull \hbox (badness 10000) detected at line 750 [][][] Underfull \hbox (badness 10000) detected at line 767 [][][] Underfull \hbox (badness 10000) detected at line 794 [][][] [974] Underfull \hbox (badness 10000) detected at line 831 [][][] [975] Underfull \hbox (badness 10000) detected at line 875 [][][] [976] Underfull \hbox (badness 10000) detected at line 925 [][][] Underfull \hbox (badness 10000) detected at line 947 [][][] [977] Underfull \hbox (badness 10000) detected at line 969 [][][] Underfull \hbox (badness 10000) detected at line 991 [][][] Underfull \hbox (badness 10000) detected at line 994 [][][] Underfull \hbox (badness 10000) detected at line 1011 [][][] Underfull \hbox (badness 10000) detected at line 1014 [][][] [978] Underfull \hbox (badness 10000) detected at line 1036 [][][] Underfull \hbox (badness 10000) detected at line 1039 [][][] Underfull \hbox (badness 10000) detected at line 1061 [][][] Underfull \hbox (badness 10000) detected at line 1064 [][][] Underfull \hbox (badness 10000) detected at line 1096 [][][] [979] Underfull \hbox (badness 10000) detected at line 1113 [][][] Underfull \hbox (badness 10000) detected at line 1145 [][][] Underfull \hbox (badness 10000) detected at line 1148 [][][] ) (./vpmg_8c_source.tex [980] [981] [982] [983] [984] [985] [986] [987] [988] [989] [990] [991] [992] [993] [994] [995] [996] [997] [998] [999] [1000] [1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008] [1009] [1010] [1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] [1021] [1022] [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] [1033] [1034] [1035] [1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] [1090] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112] [1113] [1114] [1115] [1116]) (./vpmg_8h.tex <./vpmg_8h__in cl.pdf> <./vpmg_8h__dep__incl.pdf> [1117] [1118] [1119] [1120] [1121] [1122] Underfull \hbox (badness 10000) detected at line 233 [][][] Underfull \hbox (badness 10000) detected at line 236 [][][] Underfull \hbox (badness 10000) detected at line 239 [][][] [1123] [1124] Underfull \hbox (badness 10000) detected at line 404 [][][] Underfull \hbox (badness 10000) detected at line 421 [][][] [1125] Underfull \hbox (badness 10000) detected at line 467 [][][] Underfull \hbox (badness 10000) detected at line 470 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.24 on input line 477. Underfull \hbox (badness 10000) detected at line 492 [][][] Underfull \hbox (badness 10000) detected at line 495 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.25 on input line 502. [1126] Underfull \hbox (badness 10000) detected at line 517 [][][] Underfull \hbox (badness 10000) detected at line 520 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.26 on input line 527. Underfull \hbox (badness 10000) detected at line 542 [][][] Underfull \hbox (badness 10000) detected at line 545 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.27 on input line 552. Underfull \hbox (badness 10000) detected at line 567 [][][] Underfull \hbox (badness 10000) detected at line 570 [][][] [1127] Package longtable Warning: Column widths have changed (longtable) in table 9.28 on input line 577. Underfull \hbox (badness 10000) detected at line 592 [][][] Underfull \hbox (badness 10000) detected at line 595 [][][] Package longtable Warning: Column widths have changed (longtable) in table 9.29 on input line 602. Underfull \hbox (badness 10000) detected at line 617 [][][] Underfull \hbox (badness 10000) detected at line 620 [][][] Underfull \hbox (badness 10000) detected at line 637 [][][] Underfull \hbox (badness 10000) detected at line 640 [][][] [1128] Underfull \hbox (badness 10000) detected at line 657 [][][] Underfull \hbox (badness 10000) detected at line 674 [][][] Underfull \hbox (badness 10000) detected at line 691 [][][] Underfull \hbox (badness 10000) detected at line 708 [][][] Underfull \hbox (badness 10000) detected at line 725 [][][] [1129] Underfull \hbox (badness 10000) detected at line 742 [][][] Underfull \hbox (badness 10000) detected at line 759 [][][] Underfull \hbox (badness 10000) detected at line 780 [][][] Underfull \hbox (badness 10000) detected at line 783 [][][] Underfull \hbox (badness 10000) detected at line 800 [][][] [1130] Underfull \hbox (badness 10000) detected at line 817 [][][] Underfull \hbox (badness 10000) detected at line 834 [][][] Underfull \hbox (badness 10000) detected at line 851 [][][] Underfull \hbox (badness 10000) detected at line 868 [][][] Underfull \hbox (badness 10000) detected at line 881 [][][] [1131] Underfull \hbox (badness 10000) detected at line 894 [][][] Underfull \hbox (badness 10000) detected at line 911 [][][] [1132] Underfull \hbox (badness 10000) detected at line 955 [][][] Underfull \hbox (badness 10000) detected at line 985 [][][] [1133] Underfull \hbox (badness 10000) detected at line 1007 [][][] Underfull \hbox (badness 10000) detected at line 1029 [][][] Underfull \hbox (badness 10000) detected at line 1051 [][][] Underfull \hbox (badness 10000) detected at line 1054 [][][] Underfull \hbox (badness 10000) detected at line 1071 [][][] [1134] Underfull \hbox (badness 10000) detected at line 1074 [][][] Underfull \hbox (badness 10000) detected at line 1096 [][][] Underfull \hbox (badness 10000) detected at line 1099 [][][] Underfull \hbox (badness 10000) detected at line 1121 [][][] Underfull \hbox (badness 10000) detected at line 1124 [][][] [1135] Underfull \hbox (badness 10000) detected at line 1156 [][][] Underfull \hbox (badness 10000) detected at line 1173 [][][] [1136] Underfull \hbox (badness 10000) detected at line 1205 [][][] Underfull \hbox (badness 10000) detected at line 1208 [][][] ) (./vpmg_8h_source.tex [1137] [1138] [1139] [1140] [1141] [1142] [1143] [1144]) (./vpmgp_8c.tex <./vpmgp_8c__incl.pdf> [1145] [1146] Underfull \hbox (badness 10000) detected at line 38 [][][] Underfull \hbox (badness 10000) detected at line 41 [][][] Underfull \hbox (badness 10000) detected at line 44 [][][] [1147]) (./vpmgp_8c_source.tex [1148] [1149] [1150]) (./vpmgp_8h.tex <./vpmgp_8 h__incl.pdf> [1151] <./vpmgp_8h__dep__incl.pdf> [1152] [1153] Underfull \hbox (badness 10000) detected at line 56 [][][] Underfull \hbox (badness 10000) detected at line 59 [][][] Underfull \hbox (badness 10000) detected at line 62 [][][] Underfull \hbox (badness 10000) detected at line 65 [][][] [1154]) (./vpmgp_8h_source.tex [1155]) (./build_ad_8c_source.tex [1156] [1157] [1158]) (./build_ad_8h_source.tex [1159]) (./build_bd_8c_source.tex [1160] [1161] [1162] [1163]) (./build_bd_8h_source.tex [1164]) (./build_gd_8c_source.tex [1165] [1166] [1167] [1168] [1169] [1170] [1171] [1172] [1173] [1174] [1175] [1176] [1177] [1178] [1179] [1180] [1181] [1182] [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] [1191] [1192] [1193] [1194] [1195] [1196] [1197] [1198] [1199] [1200] [1201] [1202]) (./build_gd_8h_source.tex [1203] [1204]) (./build_pd_8c_source.tex [1205] [1206] [1207] [1208] [1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216] [1217] [1218] [1219] [1220] [1221] [1222] [1223]) (./build_pd_8h_source.tex [1224] [1225] [1226]) (./cgd_8c_source.tex) (./cgd_8h_source.tex [1227]) (./gsd_8c_source.tex [1228] [1229] [1230] [1231]) (./gsd_8h_source.tex [1232]) (./matvecd_8c_source.tex [1233] [1234] [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242] [1243] [1244] [1245]) (./matvecd_8h_source.tex [1246] [1247] [1248] [1249] [1250] [1251]) (./mgcsd_8c_source.tex [1252] [1253] [1254] [1255] [1256] [1257]) (./mgcsd_8h_source.tex [1258]) (./mgdrvd_8c_source.tex [1259] [1260] [1261] [1262] [1263] [1264] [1265]) (./mgdrvd_8h_source.tex [1266] [1267]) (./mgfasd_8c_source.tex [1268] [1269] [1270] [1271] [1272] [1273]) (./mgfasd_8h_source.tex [1274] [1275]) (./mgsubd_8c_source.tex [1276] [1277] [1278] [1279] [1280] [1281] [1282] [1283] [1284] [1285] [1286]) (./mgsubd_8h_source.tex [1287] [1288] [1289] [1290]) (./mikpckd_8c_source.tex [1291] [1292] [1293] [1294]) (./mikpckd_8h_source.tex [1295] [1296] [1297]) (./mlinpckd_8c_source.tex [1298] [1299]) (./mlinpckd_8h_source.tex) (./mypdec_8c_source.tex [1300] [1301] [1302] [1303] [1304] [1305] [1306]) (./mypdec_8h_source.tex [1307]) (./newdrvd_8c_source.tex [1308] [1309] [1310] [1311]) (./newdrvd_8h_source.tex [1312]) (./newtond_8c_source.tex [1313] [1314] [1315] [1316] [1317] [1318] [1319]) (./newtond_8h_source.tex [1320]) (./powerd_8c_source.tex [1321] [1322] [1323] [1324] [1325]) (./powerd_8h_source.tex [1326]) (./smoothd_8c_source.tex [1327]) (./smoothd_8h_source.tex [1328]) (./routines_8c.tex <./routines_8c__incl.pdf> [1329] Underfull \hbox (badness 776) in paragraph at lines 47--48 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv /m/n/10 alist[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[] Underfull \hbox (badness 2856) in paragraph at lines 47--48 \T1/phv/m/n/10 YMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]ZMap[] [][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 kappa[]Map[][][], [] Underfull \hbox (badness 1237) in paragraph at lines 47--48 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 charge[]Map[][][], [] $\OMS/cmsy/m/n/10 ^^C $\T1/phv/m/n/10 pmgp[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pmg[][][], [] Underfull \hbox (badness 905) in paragraph at lines 61--62 []\T1/phv/m/n/10 VPUBLIC void [] (Vmem $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 mem , [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, int nforce[][][], [] $\OMS/cmsy /m/n/10 ^^C$\T1/phv/m/n/10 atom[] Underfull \hbox (badness 5817) in paragraph at lines 67--68 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], Underfull \hbox (badness 5817) in paragraph at lines 69--70 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], [1330] Underfull \hbox (badness 1442) in paragraph at lines 81--82 []\T1/phv/m/n/10 VPUBLIC int [] (Vcom $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 com, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, int nforce[][][], [] $\OMS/cmsy/ m/n/10 ^^C$\T1/phv/m/n/10 atom[] Underfull \hbox (badness 931) in paragraph at lines 87--88 []\T1/phv/m/n/10 VPUBLIC void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T 1/phv/m/n/10 fetk[][][], Gem Underfull \hbox (badness 2495) in paragraph at lines 89--90 []\T1/phv/m/n/10 VPUBLIC Vrc[]_[][]Codes [] (int icalc, [] $\OMS/cmsy/m/n/10 ^^ C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 feparm, [] $\OMS /cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbeparm, [] [1331] Underfull \hbox (badness 10000) detected at line 116 [][][] Underfull \hbox (badness 10000) detected at line 119 [][][] Underfull \hbox (badness 10000) detected at line 122 [][][] ) (./routines_8c_source.tex [1332] [1333] [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341] [1342] [1343] [1344] [1345] [1346] [1347] [1348] [1349] [1350] [1351] [1352] [1353] [1354] [1355] [1356] [1357] [1358] [1359] [1360] [1361] [1362] [1363] [1364] [1365] [1366] [1367] [1368] [1369] [1370] [1371] [1372] [1373] [1374] [1375] [1376] [1377] [1378] [1379] [1380] [1381] [1382] [1383] [1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] [1392] [1393] [1394] [1395] [1396] [1397] [1398] [1399] [1400]) (./routines_8h.tex <./routine s_8h__incl.pdf> <./routines_8h__dep__incl.pdf> [1401] Overfull \hbox (16.65858pt too wide) in paragraph at lines 50--51 []\T1/phv/m/n/10 VEXTERNC int [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], Overfull \hbox (16.91972pt too wide) in paragraph at lines 52--53 []\T1/phv/m/n/10 VEXTERNC void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh , [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/1 0 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], Underfull \hbox (badness 1910) in paragraph at lines 70--71 [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1 /phv/m/n/10 alist[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][] [], [] Underfull \hbox (badness 1237) in paragraph at lines 70--71 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 charge[]Map[][][], [] $\OMS/cmsy/m/n/10 ^^C $\T1/phv/m/n/10 pmgp[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pmg[][][], [] [1402] Underfull \hbox (badness 5817) in paragraph at lines 88--89 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], Underfull \hbox (badness 5817) in paragraph at lines 90--91 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], [1403] Underfull \hbox (badness 2495) in paragraph at lines 122--123 []\T1/phv/m/n/10 VPUBLIC Vrc[]_[][]Codes [] (int icalc, [] $\OMS/cmsy/m/n/10 ^^ C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 feparm, [] $\OMS /cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbeparm, [] Underfull \hbox (badness 10000) detected at line 145 [][][] Underfull \hbox (badness 10000) detected at line 148 [][][] Underfull \hbox (badness 10000) detected at line 151 [][][] [1404]) (./routines_8h_source.tex [1405] [1406] [1407] [1408] [1409]) [1410] (./refman.ind [1411] [1412] [1413] [1414] [1415] [1416] [1417] [1418] [1419] [1420] [1421] [1422] [1423] [1424] [1425] [1426] [1427] [1428] [1429] [1430] [1431] [1432] [1433] [1434] [1435] [1436] [1437] [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] [1449] [1450] [1451] [1452] [1453] [1454] [1455] [1456] [1457] [1458] [1459]) Package longtable Warning: Table widths have changed. Rerun LaTeX. (./refman.aux) Package rerunfilecheck Warning: File `refman.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information)< /usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrro8a.pfb> Output written on refman.pdf (1517 pages, 6286495 bytes). Transcript written on refman.log. Package longtable Warning: Table widths have changed. Rerun LaTeX. Rerunning latex.... 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(/usr/share/texlive/texmf-dist/tex/latex/wasysym/uwasy.fd) [1{/var/lib/texmf/fo nts/map/pdftex/updmap/pdftex.map}{/usr/share/texlive/texmf-dist/fonts/enc/dvips /base/8r.enc}] [2] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] (./index.tex Chapter 1. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1phv.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [1] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [2]) (./bug.tex [3] [4] Chapter 2. [5] [6]) (./deprecated.tex [7] [8] Chapter 3. ) [9] [10] Chapter 4. (./modules.tex) [11] [12] Chapter 5. (./annotated.tex [13]) [14] Chapter 6. (./files.tex [15] [16] [17]) [18] Chapter 7. (./group___header.tex) (./group___vcsm.tex [19] Underfull \hbox (badness 10000) detected at line 93 [][][] [20] Underfull \hbox (badness 10000) detected at line 113 [][][] Underfull \hbox (badness 10000) detected at line 116 [][][] Underfull \hbox (badness 10000) detected at line 121 [][][] Underfull \hbox (badness 10000) detected at line 145 [][][] Underfull \hbox (badness 10000) detected at line 148 [][][] Underfull \hbox (badness 10000) detected at line 153 [][][] [21] Underfull \hbox (badness 10000) detected at line 179 [][][] Underfull \hbox (badness 10000) detected at line 201 [][][] Underfull \hbox (badness 10000) detected at line 223 [][][] Underfull \hbox (badness 10000) detected at line 226 [][][] Overfull \vbox (4.57304pt too high) has occurred while \output is active [22] Underfull \hbox (badness 10000) detected at line 252 [][][] Underfull \hbox (badness 10000) detected at line 255 [][][] Underfull \hbox (badness 10000) detected at line 281 [][][] Underfull \hbox (badness 10000) detected at line 284 [][][] [23] Underfull \hbox (badness 10000) detected at line 308 [][][] Underfull \hbox (badness 10000) detected at line 311 [][][] Underfull \hbox (badness 10000) detected at line 335 [][][] Underfull \hbox (badness 10000) detected at line 338 [][][] Underfull \hbox (badness 10000) detected at line 364 [][][] Underfull \hbox (badness 10000) detected at line 367 [][][] [24] Underfull \hbox (badness 10000) detected at line 393 [][][] Underfull \hbox (badness 10000) detected at line 396 [][][] Underfull \hbox (badness 10000) detected at line 418 [][][] Underfull \hbox (badness 10000) detected at line 421 [][][] [25] Underfull \hbox (badness 10000) detected at line 443 [][][] Underfull \hbox (badness 10000) detected at line 446 [][][] Underfull \hbox (badness 10000) detected at line 468 [][][] Underfull \hbox (badness 10000) detected at line 471 [][][] ) (./group___vfetk.tex [26] [27] [28] [29] [30] Underfull \hbox (badness 10000) detected at line 304 [][][] Underfull \hbox (badness 10000) detected at line 335 [][][] [31] Underfull \hbox (badness 10000) detected at line 398 [][][] Underfull \hbox (badness 10000) detected at line 429 [][][] Underfull \hbox (badness 10000) detected at line 463 [][][] Underfull \hbox (badness 10000) detected at line 466 [][][] [32] Underfull \hbox (badness 10000) detected at line 492 [][][] Underfull \hbox (badness 10000) detected at line 495 [][][] Underfull \hbox (badness 10000) detected at line 498 [][][] Underfull \hbox (badness 10000) detected at line 522 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] Underfull \hbox (badness 10000) detected at line 528 [][][] [33] Underfull \hbox (badness 10000) detected at line 559 [][][] Underfull \hbox (badness 10000) detected at line 569 [][][] [34] Underfull \hbox (badness 10000) detected at line 593 [][][] Underfull \hbox (badness 10000) detected at line 615 [][][] Underfull \hbox (badness 10000) detected at line 637 [][][] [35] Underfull \hbox (badness 10000) detected at line 658 [][][] Underfull \hbox (badness 10000) detected at line 661 [][][] Underfull \hbox (badness 10000) detected at line 668 [][][] Underfull \hbox (badness 10000) detected at line 671 [][][] Underfull \hbox (badness 10000) detected at line 701 [][][] [36] Underfull \hbox (badness 10000) detected at line 727 [][][] Underfull \hbox (badness 10000) detected at line 730 [][][] Underfull \hbox (badness 10000) detected at line 735 [][][] Underfull \hbox (badness 10000) detected at line 761 [][][] [37] Underfull \hbox (badness 10000) detected at line 789 [][][] Underfull \hbox (badness 10000) detected at line 792 [][][] Underfull \hbox (badness 10000) detected at line 814 [][][] Underfull \hbox (badness 10000) detected at line 817 [][][] Underfull \hbox (badness 10000) detected at line 820 [][][] [38] Underfull \hbox (badness 10000) detected at line 844 [][][] Underfull \hbox (badness 10000) detected at line 847 [][][] Underfull \hbox (badness 10000) detected at line 869 [][][] Underfull \hbox (badness 10000) detected at line 872 [][][] Underfull \hbox (badness 10000) detected at line 875 [][][] Underfull \hbox (badness 10000) detected at line 899 [][][] Underfull \hbox (badness 10000) detected at line 902 [][][] [39] Underfull \hbox (badness 10000) detected at line 924 [][][] Underfull \hbox (badness 10000) detected at line 927 [][][] Underfull \hbox (badness 10000) detected at line 949 [][][] [40] Underfull \hbox (badness 10000) detected at line 969 [][][] Underfull \hbox (badness 10000) detected at line 999 [][][] Underfull \hbox (badness 10000) detected at line 1002 [][][] Underfull \hbox (badness 10000) detected at line 1024 [][][] Underfull \hbox (badness 10000) detected at line 1027 [][][] [41] Underfull \hbox (badness 10000) detected at line 1053 [][][] Underfull \hbox (badness 10000) detected at line 1056 [][][] Underfull \hbox (badness 10000) detected at line 1080 [][][] Underfull \hbox (badness 10000) detected at line 1083 [][][] [42] Underfull \hbox (badness 10000) detected at line 1109 [][][] Underfull \hbox (badness 10000) detected at line 1146 [][][] Underfull \hbox (badness 10000) detected at line 1149 [][][] [43] Underfull \hbox (badness 10000) detected at line 1179 [][][] Underfull \hbox (badness 10000) detected at line 1182 [][][] Underfull \hbox (badness 10000) detected at line 1204 [][][] Underfull \hbox (badness 10000) detected at line 1207 [][][] [44] Underfull \hbox (badness 10000) detected at line 1232 [][][] Underfull \hbox (badness 10000) detected at line 1265 [][][] Underfull \hbox (badness 10000) detected at line 1268 [][][] [45] Underfull \hbox (badness 10000) detected at line 1298 [][][] Underfull \hbox (badness 10000) detected at line 1301 [][][] Underfull \hbox (badness 10000) detected at line 1327 [][][] [46] Underfull \hbox (badness 10000) detected at line 1355 [][][] Underfull \hbox (badness 10000) detected at line 1385 [][][] [47] Underfull \hbox (badness 10000) detected at line 1419 [][][] Underfull \hbox (badness 10000) detected at line 1422 [][][] Underfull \hbox (badness 10000) detected at line 1448 [][][] Underfull \hbox (badness 10000) detected at line 1451 [][][] [48] Underfull \hbox (badness 10000) detected at line 1477 [][][] Underfull \hbox (badness 10000) detected at line 1480 [][][] [49] Underfull \hbox (badness 10000) detected at line 1514 [][][] Underfull \hbox (badness 10000) detected at line 1517 [][][] Underfull \hbox (badness 10000) detected at line 1545 [][][] [50] Underfull \hbox (badness 10000) detected at line 1579 [][][] Underfull \hbox (badness 10000) detected at line 1582 [][][] [51] [52] Underfull \hbox (badness 10000) detected at line 1665 [][][] Underfull \hbox (badness 10000) detected at line 1699 [][][] Underfull \hbox (badness 10000) detected at line 1702 [][][] [53] Underfull \hbox (badness 10000) detected at line 1745 [][][] Underfull \hbox (badness 10000) detected at line 1755 [][][] Underfull \hbox (badness 10000) detected at line 1779 [][][] Underfull \hbox (badness 10000) detected at line 1782 [][][] Underfull \hbox (badness 10000) detected at line 1785 [][][] [54] Underfull \hbox (badness 10000) detected at line 1807 [][][] Underfull \hbox (badness 10000) detected at line 1810 [][][] Underfull \hbox (badness 10000) detected at line 1813 [][][] Underfull \hbox (badness 10000) detected at line 1835 [][][] [55] Underfull \hbox (badness 10000) detected at line 1861 [][][] Underfull \hbox (badness 10000) detected at line 1881 [][][] Underfull \hbox (badness 10000) detected at line 1886 [][][] ) (./group___vpee.tex [56] Underfull \hbox (badness 849) in paragraph at lines 45--46 \T1/phv/m/n/10 Holst par-al-lel re-fine-ment rou-tine es-sen-tially re-duces th e er-ror out-side the \T1/pcr/m/n/10 local^^D partition to zero. Underfull \hbox (badness 10000) in paragraph at lines 45--46 \T1/pcr/m/n/10 However, this leads to the need for a few final overlapping Schw arz solves to Underfull \hbox (badness 10000) in paragraph at lines 45--46 \T1/pcr/m/n/10 smooth out the errors near partition boundaries. Supposedly, if the region in Underfull \hbox (badness 10000) in paragraph at lines 45--46 \T1/pcr/m/n/10 which we allow error-based refinement includes the$\OML/cmm/m/it /10 <$\T1/pcr/m/n/10 /tt$\OML/cmm/m/it/10 >$\T1/pcr/m/n/10 local^^D partition a nd an Underfull \hbox (badness 10000) in paragraph at lines 45--46 \T1/pcr/m/n/10 external buffer zone approximately equal in size to the local re gion, then the Underfull \hbox (badness 10000) in paragraph at lines 45--46 \T1/pcr/m/n/10 solution will asymptotically approach the solution obtained via more typical Underfull \hbox (badness 10000) in paragraph at lines 45--46 \T1/pcr/m/n/10 methods. This is essentially a more flexible parallel implementa tion of MC\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 s [57] Underfull \hbox (badness 10000) detected at line 75 [][][] Underfull \hbox (badness 10000) detected at line 78 [][][] Underfull \hbox (badness 10000) detected at line 94 [][][] Underfull \hbox (badness 10000) detected at line 111 [][][] [58] Underfull \hbox (badness 10000) detected at line 114 [][][] Underfull \hbox (badness 10000) detected at line 132 [][][] Underfull \hbox (badness 10000) detected at line 149 [][][] Underfull \hbox (badness 10000) detected at line 171 [][][] [59] Underfull \hbox (badness 10000) detected at line 195 [][][] Underfull \hbox (badness 10000) detected at line 198 [][][] Underfull \hbox (badness 10000) detected at line 201 [][][] Overfull \vbox (42.60027pt too high) has occurred while \output is active [60] Underfull \hbox (badness 10000) detected at line 241 [][][] Underfull \hbox (badness 10000) detected at line 244 [][][] ) (./group___a_p_o_lparm.tex [61] Overfull \vbox (22.62613pt too high) has occurred while \output is active [62] Underfull \hbox (badness 10000) detected at line 212 [][][] Underfull \hbox (badness 10000) detected at line 220 [][][] [63] Underfull \hbox (badness 10000) detected at line 237 [][][] Underfull \hbox (badness 10000) detected at line 261 [][][] Underfull \hbox (badness 10000) detected at line 264 [][][] Underfull \hbox (badness 10000) detected at line 281 [][][] Underfull \hbox (badness 10000) detected at line 289 [][][] [64] Underfull \hbox (badness 10000) detected at line 306 [][][] Underfull \hbox (badness 10000) detected at line 328 [][][] ) (./group___b_e_mparm.tex [65] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] [66] Underfull \hbox (badness 10000) detected at line 125 [][][] Underfull \hbox (badness 10000) detected at line 133 [][][] Underfull \hbox (badness 10000) detected at line 150 [][][] Underfull \hbox (badness 10000) detected at line 158 [][][] Underfull \hbox (badness 10000) detected at line 175 [][][] [67] Underfull \hbox (badness 10000) detected at line 185 [][][] Underfull \hbox (badness 10000) detected at line 202 [][][] Underfull \hbox (badness 10000) detected at line 224 [][][] Underfull \hbox (badness 10000) detected at line 246 [][][] [68] Underfull \hbox (badness 10000) detected at line 258 [][][] ) (./group___f_e_mparm.tex [69] Underfull \hbox (badness 10000) detected at line 111 [][][] [70] Underfull \hbox (badness 10000) detected at line 155 [][][] Underfull \hbox (badness 10000) detected at line 158 [][][] Underfull \hbox (badness 10000) detected at line 197 [][][] Underfull \hbox (badness 10000) detected at line 231 [][][] [71] Underfull \hbox (badness 10000) detected at line 239 [][][] Underfull \hbox (badness 10000) detected at line 256 [][][] Underfull \hbox (badness 10000) detected at line 280 [][][] Underfull \hbox (badness 10000) detected at line 288 [][][] [72] Underfull \hbox (badness 10000) detected at line 305 [][][] Underfull \hbox (badness 10000) detected at line 315 [][][] Underfull \hbox (badness 10000) detected at line 332 [][][] Underfull \hbox (badness 10000) detected at line 354 [][][] ) (./group___g_e_o_f_l_o_wparm.tex [73] Underfull \hbox (badness 10000) detected at line 68 [][][] [74] Underfull \hbox (badness 10000) detected at line 71 [][][] Underfull \hbox (badness 10000) detected at line 124 [][][] Underfull \hbox (badness 10000) detected at line 132 [][][] [75] Underfull \hbox (badness 10000) detected at line 149 [][][] Underfull \hbox (badness 10000) detected at line 173 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 198 [][][] Underfull \hbox (badness 10000) detected at line 208 [][][] [76] Underfull \hbox (badness 10000) detected at line 225 [][][] Underfull \hbox (badness 10000) detected at line 247 [][][] Underfull \hbox (badness 10000) detected at line 269 [][][] [77] Underfull \hbox (badness 10000) detected at line 281 [][][] ) (./group___m_gparm.tex [78] [79] Underfull \hbox (badness 10000) detected at line 205 [][][] [80] Underfull \hbox (badness 10000) detected at line 217 [][][] Underfull \hbox (badness 10000) detected at line 234 [][][] Underfull \hbox (badness 10000) detected at line 246 [][][] Underfull \hbox (badness 10000) detected at line 263 [][][] Underfull \hbox (badness 10000) detected at line 271 [][][] [81] Underfull \hbox (badness 10000) detected at line 288 [][][] Underfull \hbox (badness 10000) detected at line 312 [][][] Underfull \hbox (badness 10000) detected at line 320 [][][] Underfull \hbox (badness 10000) detected at line 337 [][][] Underfull \hbox (badness 10000) detected at line 347 [][][] [82] Underfull \hbox (badness 10000) detected at line 364 [][][] Underfull \hbox (badness 10000) detected at line 386 [][][] Underfull \hbox (badness 10000) detected at line 408 [][][] Underfull \hbox (badness 10000) detected at line 416 [][][] [83] Underfull \hbox (badness 10000) detected at line 433 [][][] Underfull \hbox (badness 10000) detected at line 441 [][][] Underfull \hbox (badness 10000) detected at line 458 [][][] Underfull \hbox (badness 10000) detected at line 466 [][][] Underfull \hbox (badness 10000) detected at line 483 [][][] Underfull \hbox (badness 10000) detected at line 491 [][][] [84] Underfull \hbox (badness 10000) detected at line 508 [][][] Underfull \hbox (badness 10000) detected at line 516 [][][] Underfull \hbox (badness 10000) detected at line 533 [][][] Underfull \hbox (badness 10000) detected at line 541 [][][] Underfull \hbox (badness 10000) detected at line 558 [][][] [85] Underfull \hbox (badness 10000) detected at line 566 [][][] Underfull \hbox (badness 10000) detected at line 583 [][][] Underfull \hbox (badness 10000) detected at line 591 [][][] Underfull \hbox (badness 10000) detected at line 608 [][][] Underfull \hbox (badness 10000) detected at line 616 [][][] Underfull \hbox (badness 10000) detected at line 633 [][][] [86] Underfull \hbox (badness 10000) detected at line 645 [][][] Underfull \hbox (badness 10000) detected at line 662 [][][] Underfull \hbox (badness 10000) detected at line 686 [][][] [87] Underfull \hbox (badness 10000) detected at line 710 [][][] ) (./group___n_osh.tex [88] [89] [90] [91] [92] Underfull \hbox (badness 10000) detected at line 431 [][][] Underfull \hbox (badness 10000) detected at line 441 [][][] Underfull \hbox (badness 10000) detected at line 458 [][][] Underfull \hbox (badness 10000) detected at line 482 [][][] [93] Underfull \hbox (badness 10000) detected at line 490 [][][] Underfull \hbox (badness 10000) detected at line 507 [][][] Underfull \hbox (badness 10000) detected at line 529 [][][] Underfull \hbox (badness 10000) detected at line 539 [][][] Underfull \hbox (badness 10000) detected at line 556 [][][] [94] Underfull \hbox (badness 10000) detected at line 568 [][][] Underfull \hbox (badness 10000) detected at line 585 [][][] Underfull \hbox (badness 10000) detected at line 607 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] [95] Underfull \hbox (badness 10000) detected at line 639 [][][] Underfull \hbox (badness 10000) detected at line 656 [][][] Underfull \hbox (badness 10000) detected at line 659 [][][] Underfull \hbox (badness 10000) detected at line 669 [][][] Underfull \hbox (badness 10000) detected at line 672 [][][] Underfull \hbox (badness 10000) detected at line 689 [][][] Overfull \vbox (15.28305pt too high) has occurred while \output is active [96] Underfull \hbox (badness 10000) detected at line 699 [][][] Underfull \hbox (badness 10000) detected at line 716 [][][] Underfull \hbox (badness 10000) detected at line 726 [][][] Underfull \hbox (badness 10000) detected at line 743 [][][] Underfull \hbox (badness 10000) detected at line 753 [][][] [97] Underfull \hbox (badness 10000) detected at line 770 [][][] Underfull \hbox (badness 10000) detected at line 780 [][][] Underfull \hbox (badness 10000) detected at line 797 [][][] Underfull \hbox (badness 10000) detected at line 807 [][][] Underfull \hbox (badness 10000) detected at line 824 [][][] [98] Underfull \hbox (badness 10000) detected at line 834 [][][] Underfull \hbox (badness 10000) detected at line 851 [][][] Underfull \hbox (badness 10000) detected at line 861 [][][] Underfull \hbox (badness 10000) detected at line 878 [][][] Underfull \hbox (badness 10000) detected at line 888 [][][] [99] Underfull \hbox (badness 10000) detected at line 905 [][][] Underfull \hbox (badness 10000) detected at line 915 [][][] Underfull \hbox (badness 10000) detected at line 932 [][][] Underfull \hbox (badness 10000) detected at line 942 [][][] Underfull \hbox (badness 10000) detected at line 959 [][][] [100] Underfull \hbox (badness 10000) detected at line 969 [][][] Underfull \hbox (badness 10000) detected at line 986 [][][] Underfull \hbox (badness 10000) detected at line 996 [][][] Underfull \hbox (badness 10000) detected at line 1013 [][][] Underfull \hbox (badness 10000) detected at line 1016 [][][] Underfull \hbox (badness 10000) detected at line 1026 [][][] [101] Underfull \hbox (badness 10000) detected at line 1043 [][][] Underfull \hbox (badness 10000) detected at line 1048 [][][] Underfull \hbox (badness 10000) detected at line 1058 [][][] Underfull \hbox (badness 10000) detected at line 1075 [][][] Underfull \hbox (badness 10000) detected at line 1078 [][][] [102] Underfull \hbox (badness 10000) detected at line 1090 [][][] Underfull \hbox (badness 10000) detected at line 1093 [][][] Underfull \hbox (badness 10000) detected at line 1110 [][][] Underfull \hbox (badness 10000) detected at line 1113 [][][] Underfull \hbox (badness 10000) detected at line 1123 [][][] Underfull \hbox (badness 10000) detected at line 1126 [][][] Underfull \hbox (badness 10000) detected at line 1143 [][][] Underfull \hbox (badness 10000) detected at line 1146 [][][] [103] Underfull \hbox (badness 10000) detected at line 1158 [][][] Underfull \hbox (badness 10000) detected at line 1161 [][][] Underfull \hbox (badness 10000) detected at line 1178 [][][] Underfull \hbox (badness 10000) detected at line 1181 [][][] Underfull \hbox (badness 10000) detected at line 1191 [][][] Underfull \hbox (badness 10000) detected at line 1194 [][][] Underfull \hbox (badness 10000) detected at line 1211 [][][] [104] Underfull \hbox (badness 10000) detected at line 1214 [][][] Underfull \hbox (badness 10000) detected at line 1224 [][][] Underfull \hbox (badness 10000) detected at line 1248 [][][] Underfull \hbox (badness 10000) detected at line 1251 [][][] Underfull \hbox (badness 10000) detected at line 1261 [][][] Overfull \vbox (3.94589pt too high) has occurred while \output is active [105]) (./group___p_b_a_mparm.tex [106] Underfull \hbox (badness 10000) detected at line 116 [][][] Underfull \hbox (badness 10000) detected at line 119 [][][] [107] Underfull \hbox (badness 10000) detected at line 172 [][][] Underfull \hbox (badness 10000) detected at line 180 [][][] Underfull \hbox (badness 10000) detected at line 197 [][][] [108] Underfull \hbox (badness 10000) detected at line 221 [][][] Underfull \hbox (badness 10000) detected at line 229 [][][] Underfull \hbox (badness 10000) detected at line 246 [][][] Underfull \hbox (badness 10000) detected at line 256 [][][] [109] Underfull \hbox (badness 10000) detected at line 273 [][][] Underfull \hbox (badness 10000) detected at line 295 [][][] Underfull \hbox (badness 10000) detected at line 317 [][][] Underfull \hbox (badness 10000) detected at line 341 [][][] [110] Underfull \hbox (badness 10000) detected at line 365 [][][] Underfull \hbox (badness 10000) detected at line 389 [][][] Underfull \hbox (badness 10000) detected at line 413 [][][] [111] Underfull \hbox (badness 10000) detected at line 437 [][][] Underfull \hbox (badness 10000) detected at line 461 [][][] Underfull \hbox (badness 10000) detected at line 485 [][][] [112] Underfull \hbox (badness 10000) detected at line 509 [][][] Underfull \hbox (badness 10000) detected at line 533 [][][] Underfull \hbox (badness 10000) detected at line 557 [][][] [113] Underfull \hbox (badness 10000) detected at line 581 [][][] Underfull \hbox (badness 10000) detected at line 593 [][][] Underfull \hbox (badness 10000) detected at line 610 [][][] [114] Underfull \hbox (badness 10000) detected at line 634 [][][] ) (./group___p_b_eparm.tex [115] [116] Underfull \hbox (badness 10000) detected at line 209 [][][] Underfull \hbox (badness 10000) detected at line 212 [][][] [117] Underfull \hbox (badness 10000) detected at line 234 [][][] Underfull \hbox (badness 10000) detected at line 258 [][][] Underfull \hbox (badness 10000) detected at line 261 [][][] Underfull \hbox (badness 10000) detected at line 278 [][][] Underfull \hbox (badness 10000) detected at line 281 [][][] [118] Underfull \hbox (badness 10000) detected at line 303 [][][] Underfull \hbox (badness 10000) detected at line 325 [][][] Underfull \hbox (badness 10000) detected at line 347 [][][] Underfull \hbox (badness 10000) detected at line 350 [][][] [119] Underfull \hbox (badness 10000) detected at line 374 [][][] Underfull \hbox (badness 10000) detected at line 377 [][][] Underfull \hbox (badness 10000) detected at line 401 [][][] Underfull \hbox (badness 10000) detected at line 404 [][][] Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 431 [][][] [120]) (./group___p_b_s_a_mparm.tex [121] Underfull \hbox (badness 10000) detected at line 100 [][][] Underfull \hbox (badness 10000) detected at line 103 [][][] [122] Underfull \hbox (badness 10000) detected at line 156 [][][] Underfull \hbox (badness 10000) detected at line 164 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] [123] Underfull \hbox (badness 10000) detected at line 205 [][][] Underfull \hbox (badness 10000) detected at line 213 [][][] Underfull \hbox (badness 10000) detected at line 230 [][][] Underfull \hbox (badness 10000) detected at line 240 [][][] Underfull \hbox (badness 10000) detected at line 257 [][][] Overfull \vbox (0.37224pt too high) has occurred while \output is active [124] Underfull \hbox (badness 10000) detected at line 279 [][][] Underfull \hbox (badness 10000) detected at line 301 [][][] Underfull \hbox (badness 10000) detected at line 325 [][][] [125] Underfull \hbox (badness 10000) detected at line 349 [][][] Underfull \hbox (badness 10000) detected at line 373 [][][] Underfull \hbox (badness 10000) detected at line 397 [][][] [126] Underfull \hbox (badness 10000) detected at line 409 [][][] Underfull \hbox (badness 10000) detected at line 426 [][][] ) (./group___vacc.tex [127] [128] [129] Underfull \hbox (badness 10000) detected at line 149 [][][] Underfull \hbox (badness 10000) detected at line 179 [][][] [130] Underfull \hbox (badness 10000) detected at line 207 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] Underfull \hbox (badness 10000) detected at line 213 [][][] Underfull \hbox (badness 10000) detected at line 239 [][][] Underfull \hbox (badness 10000) detected at line 242 [][][] [131] Underfull \hbox (badness 10000) detected at line 268 [][][] Underfull \hbox (badness 10000) detected at line 271 [][][] Underfull \hbox (badness 10000) detected at line 283 [][][] Underfull \hbox (badness 10000) detected at line 305 [][][] Underfull \hbox (badness 10000) detected at line 308 [][][] [132] Underfull \hbox (badness 10000) detected at line 334 [][][] Underfull \hbox (badness 10000) detected at line 337 [][][] Underfull \hbox (badness 10000) detected at line 365 [][][] Underfull \hbox (badness 10000) detected at line 387 [][][] [133] Underfull \hbox (badness 10000) detected at line 411 [][][] Underfull \hbox (badness 10000) detected at line 414 [][][] Underfull \hbox (badness 10000) detected at line 417 [][][] Underfull \hbox (badness 10000) detected at line 447 [][][] Underfull \hbox (badness 10000) detected at line 450 [][][] [134] Underfull \hbox (badness 10000) detected at line 472 [][][] Underfull \hbox (badness 10000) detected at line 475 [][][] Underfull \hbox (badness 10000) detected at line 499 [][][] Underfull \hbox (badness 10000) detected at line 502 [][][] [135] Underfull \hbox (badness 10000) detected at line 530 [][][] Underfull \hbox (badness 10000) detected at line 533 [][][] Underfull \hbox (badness 10000) detected at line 536 [][][] Underfull \hbox (badness 10000) detected at line 562 [][][] Underfull \hbox (badness 10000) detected at line 565 [][][] [136] Underfull \hbox (badness 10000) detected at line 595 [][][] Underfull \hbox (badness 10000) detected at line 598 [][][] Underfull \hbox (badness 10000) detected at line 628 [][][] [137] Underfull \hbox (badness 10000) detected at line 660 [][][] Underfull \hbox (badness 10000) detected at line 692 [][][] [138] Underfull \hbox (badness 10000) detected at line 724 [][][] Underfull \hbox (badness 10000) detected at line 758 [][][] [139] Underfull \hbox (badness 10000) detected at line 790 [][][] Underfull \hbox (badness 10000) detected at line 820 [][][] [140] Underfull \hbox (badness 10000) detected at line 852 [][][] Underfull \hbox (badness 10000) detected at line 855 [][][] Underfull \hbox (badness 10000) detected at line 858 [][][] Underfull \hbox (badness 10000) detected at line 882 [][][] Underfull \hbox (badness 10000) detected at line 885 [][][] Underfull \hbox (badness 10000) detected at line 888 [][][] [141] Underfull \hbox (badness 10000) detected at line 918 [][][] Underfull \hbox (badness 10000) detected at line 921 [][][] Underfull \hbox (badness 10000) detected at line 941 [][][] Underfull \hbox (badness 10000) detected at line 944 [][][] Overfull \vbox (21.5778pt too high) has occurred while \output is active [142] Underfull \hbox (badness 10000) detected at line 972 [][][] Underfull \hbox (badness 10000) detected at line 975 [][][] Underfull \hbox (badness 10000) detected at line 1007 [][][] Underfull \hbox (badness 10000) detected at line 1010 [][][] [143] Underfull \hbox (badness 10000) detected at line 1040 [][][] Underfull \hbox (badness 10000) detected at line 1043 [][][] Underfull \hbox (badness 10000) detected at line 1069 [][][] Underfull \hbox (badness 10000) detected at line 1072 [][][] Overfull \vbox (18.93095pt too high) has occurred while \output is active [144] Underfull \hbox (badness 10000) detected at line 1100 [][][] Underfull \hbox (badness 10000) detected at line 1122 [][][] Underfull \hbox (badness 10000) detected at line 1146 [][][] Underfull \hbox (badness 10000) detected at line 1149 [][][] Underfull \hbox (badness 10000) detected at line 1152 [][][] [145]) (./group___valist.tex [146] Underfull \hbox (badness 10000) detected at line 91 [][][] Underfull \hbox (badness 10000) detected at line 94 [][][] Underfull \hbox (badness 10000) detected at line 111 [][][] Underfull \hbox (badness 10000) detected at line 114 [][][] Overfull \vbox (3.49948pt too high) has occurred while \output is active [147] Underfull \hbox (badness 10000) detected at line 136 [][][] Underfull \hbox (badness 10000) detected at line 158 [][][] Underfull \hbox (badness 10000) detected at line 180 [][][] Underfull \hbox (badness 10000) detected at line 183 [][][] [148] Underfull \hbox (badness 10000) detected at line 207 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] Underfull \hbox (badness 10000) detected at line 232 [][][] Underfull \hbox (badness 10000) detected at line 235 [][][] Underfull \hbox (badness 10000) detected at line 257 [][][] Underfull \hbox (badness 10000) detected at line 260 [][][] [149] Underfull \hbox (badness 10000) detected at line 282 [][][] Underfull \hbox (badness 10000) detected at line 285 [][][] Underfull \hbox (badness 10000) detected at line 307 [][][] Underfull \hbox (badness 10000) detected at line 310 [][][] Underfull \hbox (badness 10000) detected at line 332 [][][] [150] Underfull \hbox (badness 10000) detected at line 335 [][][] Underfull \hbox (badness 10000) detected at line 352 [][][] Underfull \hbox (badness 10000) detected at line 355 [][][] Underfull \hbox (badness 10000) detected at line 377 [][][] Underfull \hbox (badness 10000) detected at line 380 [][][] Underfull \hbox (badness 10000) detected at line 383 [][][] [151] Underfull \hbox (badness 10000) detected at line 409 [][][] Underfull \hbox (badness 10000) detected at line 412 [][][] Underfull \hbox (badness 10000) detected at line 415 [][][] Underfull \hbox (badness 10000) detected at line 443 [][][] Underfull \hbox (badness 10000) detected at line 446 [][][] Underfull \hbox (badness 10000) detected at line 449 [][][] Overfull \vbox (15.85518pt too high) has occurred while \output is active [152]) (./group___vatom.tex [153] Underfull \hbox (badness 10000) detected at line 97 [][][] [154] Underfull \hbox (badness 10000) detected at line 134 [][][] Underfull \hbox (badness 10000) detected at line 158 [][][] Underfull \hbox (badness 10000) detected at line 182 [][][] Underfull \hbox (badness 10000) detected at line 185 [][][] [155] Underfull \hbox (badness 10000) detected at line 202 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] Underfull \hbox (badness 10000) detected at line 227 [][][] Underfull \hbox (badness 10000) detected at line 249 [][][] Underfull \hbox (badness 10000) detected at line 271 [][][] [156] Underfull \hbox (badness 10000) detected at line 279 [][][] Underfull \hbox (badness 10000) detected at line 296 [][][] Underfull \hbox (badness 10000) detected at line 320 [][][] Underfull \hbox (badness 10000) detected at line 328 [][][] [157] Underfull \hbox (badness 10000) detected at line 345 [][][] Underfull \hbox (badness 10000) detected at line 353 [][][] Underfull \hbox (badness 10000) detected at line 370 [][][] Underfull \hbox (badness 10000) detected at line 378 [][][] Underfull \hbox (badness 10000) detected at line 395 [][][] Underfull \hbox (badness 10000) detected at line 403 [][][] [158] Underfull \hbox (badness 10000) detected at line 420 [][][] Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 445 [][][] Underfull \hbox (badness 10000) detected at line 469 [][][] [159] Underfull \hbox (badness 10000) detected at line 477 [][][] Underfull \hbox (badness 10000) detected at line 494 [][][] Underfull \hbox (badness 10000) detected at line 518 [][][] [160] Underfull \hbox (badness 10000) detected at line 542 [][][] Underfull \hbox (badness 10000) detected at line 566 [][][] Underfull \hbox (badness 10000) detected at line 590 [][][] [161] Underfull \hbox (badness 10000) detected at line 614 [][][] Underfull \hbox (badness 10000) detected at line 638 [][][] Underfull \hbox (badness 10000) detected at line 662 [][][] ) (./group___vcap.tex [162] Underfull \hbox (badness 10000) detected at line 36 [][][] [163] Underfull \hbox (badness 10000) detected at line 86 [][][] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 92 [][][] Underfull \hbox (badness 10000) detected at line 119 [][][] Underfull \hbox (badness 10000) detected at line 122 [][][] Underfull \hbox (badness 10000) detected at line 125 [][][] [164] Underfull \hbox (badness 10000) detected at line 152 [][][] Underfull \hbox (badness 10000) detected at line 155 [][][] Underfull \hbox (badness 10000) detected at line 158 [][][] ) (./group___vclist.tex [165] [166] Underfull \hbox (badness 10000) detected at line 110 [][][] Underfull \hbox (badness 10000) detected at line 140 [][][] Underfull \hbox (badness 10000) detected at line 143 [][][] [167] Underfull \hbox (badness 10000) detected at line 175 [][][] Underfull \hbox (badness 10000) detected at line 178 [][][] Underfull \hbox (badness 10000) detected at line 212 [][][] [168] Underfull \hbox (badness 10000) detected at line 234 [][][] Underfull \hbox (badness 10000) detected at line 256 [][][] Underfull \hbox (badness 10000) detected at line 259 [][][] Underfull \hbox (badness 10000) detected at line 283 [][][] Underfull \hbox (badness 10000) detected at line 286 [][][] [169] Underfull \hbox (badness 10000) detected at line 308 [][][] Underfull \hbox (badness 10000) detected at line 311 [][][] Underfull \hbox (badness 10000) detected at line 333 [][][] Underfull \hbox (badness 10000) detected at line 336 [][][] Underfull \hbox (badness 10000) detected at line 358 [][][] Underfull \hbox (badness 10000) detected at line 361 [][][] [170] Underfull \hbox (badness 10000) detected at line 385 [][][] Underfull \hbox (badness 10000) detected at line 407 [][][] ) (./group___vgreen.tex [171] Underfull \hbox (badness 10000) detected at line 57 [][][] Underfull \hbox (badness 10000) detected at line 60 [][][] [172] [173] Underfull \hbox (badness 10000) detected at line 141 [][][] Underfull \hbox (badness 10000) detected at line 159 [][][] Underfull \hbox (badness 10000) detected at line 178 [][][] [174] Underfull \hbox (badness 10000) detected at line 196 [][][] Underfull \hbox (badness 10000) detected at line 215 [][][] [175] Underfull \hbox (badness 10000) detected at line 239 [][][] Underfull \hbox (badness 10000) detected at line 258 [][][] Underfull \hbox (badness 10000) detected at line 282 [][][] [176] Underfull \hbox (badness 10000) detected at line 299 [][][] Underfull \hbox (badness 10000) detected at line 307 [][][] Underfull \hbox (badness 10000) detected at line 324 [][][] Underfull \hbox (badness 10000) detected at line 334 [][][] Underfull \hbox (badness 10000) detected at line 351 [][][] [177] Underfull \hbox (badness 10000) detected at line 373 [][][] Underfull \hbox (badness 10000) detected at line 395 [][][] Underfull \hbox (badness 10000) detected at line 403 [][][] Underfull \hbox (badness 10000) detected at line 424 [][][] [178] Underfull \hbox (badness 10000) detected at line 429 [][][] Underfull \hbox (badness 10000) detected at line 449 [][][] Underfull \hbox (badness 10000) detected at line 471 [][][] Underfull \hbox (badness 10000) detected at line 476 [][][] [179] Underfull \hbox (badness 10000) detected at line 500 [][][] Underfull \hbox (badness 10000) detected at line 517 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] ) (./group___vhal.tex [180] [181] [182] [183] Underfull \hbox (badness 10000) detected at line 380 [][][] Underfull \hbox (badness 10000) detected at line 411 [][][] [184] Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 445 [][][] Underfull \hbox (badness 10000) detected at line 476 [][][] Underfull \hbox (badness 10000) detected at line 493 [][][] Underfull \hbox (badness 10000) detected at line 516 [][][] [185] Underfull \hbox (badness 10000) detected at line 547 [][][] [186] Underfull \hbox (badness 10000) detected at line 682 [][][] Underfull \hbox (badness 10000) detected at line 729 [][][] [187] Underfull \hbox (badness 10000) detected at line 760 [][][] Underfull \hbox (badness 10000) detected at line 795 [][][] Underfull \hbox (badness 10000) detected at line 842 [][][] Missing character: There is no Å in font cmr10! Missing character: There is no Å in font cmr10! LaTeX Warning: Command \r invalid in math mode on input line 58. Missing character: There is no Å in font cmr10! [188] [189] Underfull \hbox (badness 10000) detected at line 1019 [][][] Underfull \hbox (badness 10000) detected at line 1022 [][][] Underfull \hbox (badness 10000) detected at line 1050 [][][] Underfull \hbox (badness 10000) detected at line 1053 [][][] Underfull \hbox (badness 10000) detected at line 1070 [][][] [190]) (./group___vmatrix.tex) (./group___vparam.tex [191] [192] Underfull \hbox (badness 10000) detected at line 120 [][][] Underfull \hbox (badness 10000) detected at line 130 [][][] [193] Underfull \hbox (badness 10000) detected at line 147 [][][] Underfull \hbox (badness 10000) detected at line 157 [][][] Underfull \hbox (badness 10000) detected at line 174 [][][] Underfull \hbox (badness 10000) detected at line 198 [][][] [194] Underfull \hbox (badness 10000) detected at line 222 [][][] Underfull \hbox (badness 10000) detected at line 225 [][][] Underfull \hbox (badness 10000) detected at line 242 [][][] Underfull \hbox (badness 10000) detected at line 250 [][][] Underfull \hbox (badness 10000) detected at line 267 [][][] [195] Underfull \hbox (badness 10000) detected at line 289 [][][] Underfull \hbox (badness 10000) detected at line 311 [][][] Underfull \hbox (badness 10000) detected at line 314 [][][] Underfull \hbox (badness 10000) detected at line 331 [][][] Underfull \hbox (badness 10000) detected at line 339 [][][] Underfull \hbox (badness 10000) detected at line 356 [][][] [196] Underfull \hbox (badness 10000) detected at line 378 [][][] Underfull \hbox (badness 10000) detected at line 400 [][][] Underfull \hbox (badness 10000) detected at line 412 [][][] Underfull \hbox (badness 10000) detected at line 415 [][][] Underfull \hbox (badness 10000) detected at line 418 [][][] [197] Underfull \hbox (badness 10000) detected at line 435 [][][] Underfull \hbox (badness 10000) detected at line 445 [][][] Underfull \hbox (badness 10000) detected at line 448 [][][] Underfull \hbox (badness 10000) detected at line 451 [][][] Underfull \hbox (badness 10000) detected at line 468 [][][] Underfull \hbox (badness 10000) detected at line 476 [][][] [198] Underfull \hbox (badness 10000) detected at line 493 [][][] Underfull \hbox (badness 10000) detected at line 509 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Underfull \hbox (badness 10000) detected at line 537 [][][] [199] Underfull \hbox (badness 10000) detected at line 553 [][][] Underfull \hbox (badness 10000) detected at line 570 [][][] Underfull \hbox (badness 10000) detected at line 594 [][][] Underfull \hbox (badness 10000) detected at line 602 [][][] [200] Underfull \hbox (badness 10000) detected at line 619 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] Underfull \hbox (badness 10000) detected at line 646 [][][] Underfull \hbox (badness 10000) detected at line 668 [][][] [201]) (./group___vpbe.tex [202] [203] Underfull \hbox (badness 10000) detected at line 128 [][][] Underfull \hbox (badness 10000) detected at line 131 [][][] LaTeX Warning: Command \r invalid in math mode on input line 133. Missing character: There is no Å in font cmr10! LaTeX Warning: Command \r invalid in math mode on input line 133. Missing character: There is no Å in font cmr10! [204] Underfull \hbox (badness 10000) detected at line 136 [][][] [205] Underfull \hbox (badness 10000) detected at line 186 [][][] Underfull \hbox (badness 10000) detected at line 189 [][][] LaTeX Warning: Command \r invalid in math mode on input line 190. Missing character: There is no Å in font cmr10! LaTeX Warning: Command \r invalid in math mode on input line 190. Missing character: There is no Å in font cmr10! Underfull \hbox (badness 10000) detected at line 195 [][][] Overfull \vbox (21.60152pt too high) has occurred while \output is active [206] Underfull \hbox (badness 10000) detected at line 247 [][][] Underfull \hbox (badness 10000) detected at line 269 [][][] Underfull \hbox (badness 10000) detected at line 291 [][][] Underfull \hbox (badness 10000) detected at line 299 [][][] [207] Overfull \hbox (151.96916pt too wide) in paragraph at lines 318--318 [] \T1/p cr/m/n/8 permittivity equal to the protein interior) and zero ionic[] Underfull \hbox (badness 10000) detected at line 325 [][][] Underfull \hbox (badness 10000) detected at line 333 [][][] Underfull \hbox (badness 10000) detected at line 350 [][][] Underfull \hbox (badness 10000) detected at line 358 [][][] [208] Underfull \hbox (badness 10000) detected at line 375 [][][] Underfull \hbox (badness 10000) detected at line 383 [][][] Underfull \hbox (badness 10000) detected at line 396 [][][] Underfull \hbox (badness 10000) detected at line 412 [][][] [209] Underfull \hbox (badness 10000) detected at line 436 [][][] Underfull \hbox (badness 10000) detected at line 453 [][][] Underfull \hbox (badness 10000) detected at line 461 [][][] Underfull \hbox (badness 10000) detected at line 478 [][][] Underfull \hbox (badness 10000) detected at line 486 [][][] Underfull \hbox (badness 10000) detected at line 503 [][][] [210] Underfull \hbox (badness 10000) detected at line 525 [][][] Underfull \hbox (badness 10000) detected at line 533 [][][] Underfull \hbox (badness 10000) detected at line 550 [][][] Underfull \hbox (badness 10000) detected at line 558 [][][] Underfull \hbox (badness 10000) detected at line 575 [][][] [211] Underfull \hbox (badness 10000) detected at line 583 [][][] Underfull \hbox (badness 10000) detected at line 600 [][][] Underfull \hbox (badness 10000) detected at line 608 [][][] Underfull \hbox (badness 10000) detected at line 625 [][][] Underfull \hbox (badness 10000) detected at line 633 [][][] [212] Underfull \hbox (badness 10000) detected at line 650 [][][] Underfull \hbox (badness 10000) detected at line 658 [][][] Underfull \hbox (badness 10000) detected at line 675 [][][] Underfull \hbox (badness 10000) detected at line 683 [][][] Underfull \hbox (badness 10000) detected at line 700 [][][] Underfull \hbox (badness 10000) detected at line 708 [][][] [213] Underfull \hbox (badness 10000) detected at line 725 [][][] Underfull \hbox (badness 10000) detected at line 733 [][][] Underfull \hbox (badness 10000) detected at line 750 [][][] Underfull \hbox (badness 10000) detected at line 758 [][][] Underfull \hbox (badness 10000) detected at line 775 [][][] [214] Underfull \hbox (badness 10000) detected at line 783 [][][] Underfull \hbox (badness 10000) detected at line 800 [][][] Underfull \hbox (badness 10000) detected at line 808 [][][] Underfull \hbox (badness 10000) detected at line 825 [][][] Underfull \hbox (badness 10000) detected at line 833 [][][] [215] Underfull \hbox (badness 10000) detected at line 850 [][][] Underfull \hbox (badness 10000) detected at line 858 [][][] LaTeX Warning: Command \r invalid in math mode on input line 859. Missing character: There is no Å in font cmr10! Underfull \hbox (badness 10000) detected at line 875 [][][] Underfull \hbox (badness 10000) detected at line 883 [][][] Underfull \hbox (badness 10000) detected at line 900 [][][] Underfull \hbox (badness 10000) detected at line 908 [][][] [216] Underfull \hbox (badness 10000) detected at line 925 [][][] Underfull \hbox (badness 10000) detected at line 933 [][][] ) (./group___vstring.tex [217] Underfull \hbox (badness 10000) detected at line 42 [][][] Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 67 [][][] Underfull \hbox (badness 10000) detected at line 70 [][][] Underfull \hbox (badness 10000) detected at line 80 [][][] Underfull \hbox (badness 10000) detected at line 93 [][][] [218] Underfull \hbox (badness 10000) detected at line 96 [][][] Underfull \hbox (badness 10000) detected at line 99 [][][] Underfull \hbox (badness 10000) detected at line 102 [][][] Underfull \hbox (badness 10000) detected at line 105 [][][] ) (./group___vunit.tex [219] LaTeX Warning: Command \r invalid in math mode on input line 39. Missing character: There is no Å in font cmr9! [220] LaTeX Warning: Command \r invalid in math mode on input line 142. Missing character: There is no Å in font cmr10! ) (./group___vgrid.tex [221] [222] [223] Underfull \hbox (badness 10000) detected at line 125 [][][] Underfull \hbox (badness 10000) detected at line 151 [][][] Underfull \hbox (badness 10000) detected at line 168 [][][] [224] Underfull \hbox (badness 10000) detected at line 196 [][][] Underfull \hbox (badness 10000) detected at line 213 [][][] Underfull \hbox (badness 10000) detected at line 229 [][][] [225] Underfull \hbox (badness 10000) detected at line 246 [][][] Underfull \hbox (badness 10000) detected at line 268 [][][] Underfull \hbox (badness 10000) detected at line 290 [][][] Underfull \hbox (badness 10000) detected at line 302 [][][] [226] Underfull \hbox (badness 10000) detected at line 319 [][][] Underfull \hbox (badness 10000) detected at line 327 [][][] Underfull \hbox (badness 10000) detected at line 344 [][][] Underfull \hbox (badness 10000) detected at line 352 [][][] Underfull \hbox (badness 10000) detected at line 369 [][][] Underfull \hbox (badness 10000) detected at line 377 [][][] [227] Underfull \hbox (badness 10000) detected at line 395 [][][] Underfull \hbox (badness 10000) detected at line 403 [][][] Underfull \hbox (badness 10000) detected at line 420 [][][] Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 445 [][][] [228] Underfull \hbox (badness 10000) detected at line 453 [][][] Underfull \hbox (badness 10000) detected at line 470 [][][] Underfull \hbox (badness 10000) detected at line 473 [][][] Underfull \hbox (badness 10000) detected at line 489 [][][] Underfull \hbox (badness 10000) detected at line 492 [][][] [229] Underfull \hbox (badness 10000) detected at line 509 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Underfull \hbox (badness 10000) detected at line 528 [][][] Underfull \hbox (badness 10000) detected at line 531 [][][] Underfull \hbox (badness 10000) detected at line 548 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] [230] Underfull \hbox (badness 10000) detected at line 575 [][][] Underfull \hbox (badness 10000) detected at line 583 [][][] Underfull \hbox (badness 10000) detected at line 600 [][][] Underfull \hbox (badness 10000) detected at line 612 [][][] [231] Underfull \hbox (badness 10000) detected at line 629 [][][] Underfull \hbox (badness 10000) detected at line 663 [][][] [232] Underfull \hbox (badness 10000) detected at line 697 [][][] Underfull \hbox (badness 10000) detected at line 702 [][][] ) (./group___vmgrid.tex [233] [234] Underfull \hbox (badness 10000) detected at line 105 [][][] Underfull \hbox (badness 10000) detected at line 115 [][][] Underfull \hbox (badness 10000) detected at line 132 [][][] Underfull \hbox (badness 10000) detected at line 135 [][][] Underfull \hbox (badness 10000) detected at line 152 [][][] [235] Underfull \hbox (badness 10000) detected at line 160 [][][] Underfull \hbox (badness 10000) detected at line 177 [][][] Underfull \hbox (badness 10000) detected at line 193 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] [236] Underfull \hbox (badness 10000) detected at line 232 [][][] Underfull \hbox (badness 10000) detected at line 254 [][][] Underfull \hbox (badness 10000) detected at line 264 [][][] Underfull \hbox (badness 10000) detected at line 277 [][][] [237] Underfull \hbox (badness 10000) detected at line 287 [][][] Underfull \hbox (badness 10000) detected at line 300 [][][] Underfull \hbox (badness 10000) detected at line 312 [][][] Underfull \hbox (badness 10000) detected at line 329 [][][] Underfull \hbox (badness 10000) detected at line 341 [][][] ) (./group___vopot.tex [238] [239] Underfull \hbox (badness 10000) detected at line 77 [][][] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 106 [][][] [240] Underfull \hbox (badness 10000) detected at line 120 [][][] Underfull \hbox (badness 10000) detected at line 137 [][][] Underfull \hbox (badness 10000) detected at line 153 [][][] Underfull \hbox (badness 10000) detected at line 170 [][][] [241] Underfull \hbox (badness 10000) detected at line 192 [][][] Underfull \hbox (badness 10000) detected at line 214 [][][] Underfull \hbox (badness 10000) detected at line 226 [][][] Underfull \hbox (badness 10000) detected at line 243 [][][] Overfull \vbox (28.1848pt too high) has occurred while \output is active [242] Underfull \hbox (badness 10000) detected at line 255 [][][] ) (./group___vpmg.tex [243] [244] [245] Underfull \hbox (badness 10000) detected at line 117 [][][] Underfull \hbox (badness 10000) detected at line 150 [][][] [246] Underfull \hbox (badness 10000) detected at line 186 [][][] [247] Underfull \hbox (badness 10000) detected at line 234 [][][] Underfull \hbox (badness 10000) detected at line 276 [][][] [248] Underfull \hbox (badness 10000) detected at line 324 [][][] [249] Underfull \hbox (badness 10000) detected at line 362 [][][] Underfull \hbox (badness 10000) detected at line 381 [][][] Underfull \hbox (badness 10000) detected at line 384 [][][] [250] Underfull \hbox (badness 10000) detected at line 416 [][][] Underfull \hbox (badness 10000) detected at line 419 [][][] Underfull \hbox (badness 10000) detected at line 422 [][][] [251] Underfull \hbox (badness 10000) detected at line 458 [][][] Underfull \hbox (badness 10000) detected at line 484 [][][] Underfull \hbox (badness 10000) detected at line 487 [][][] Underfull \hbox (badness 10000) detected at line 492 [][][] Overfull \vbox (1.11014pt too high) has occurred while \output is active [252] Underfull \hbox (badness 10000) detected at line 520 [][][] Underfull \hbox (badness 10000) detected at line 546 [][][] [253] Underfull \hbox (badness 10000) detected at line 572 [][][] Underfull \hbox (badness 10000) detected at line 604 [][][] Underfull \hbox (badness 10000) detected at line 607 [][][] Underfull \hbox (badness 10000) detected at line 610 [][][] [254] Underfull \hbox (badness 10000) detected at line 643 [][][] Underfull \hbox (badness 10000) detected at line 646 [][][] Underfull \hbox (badness 10000) detected at line 668 [][][] Underfull \hbox (badness 10000) detected at line 690 [][][] [255] Underfull \hbox (badness 10000) detected at line 712 [][][] Underfull \hbox (badness 10000) detected at line 715 [][][] Underfull \hbox (badness 10000) detected at line 718 [][][] Underfull \hbox (badness 10000) detected at line 742 [][][] [256] Underfull \hbox (badness 10000) detected at line 764 [][][] Underfull \hbox (badness 10000) detected at line 767 [][][] Underfull \hbox (badness 10000) detected at line 799 [][][] [257] Underfull \hbox (badness 10000) detected at line 802 [][][] Underfull \hbox (badness 10000) detected at line 856 [][][] Underfull \hbox (badness 10000) detected at line 859 [][][] Underfull \hbox (badness 10000) detected at line 864 [][][] [258] Underfull \hbox (badness 10000) detected at line 894 [][][] Underfull \hbox (badness 10000) detected at line 920 [][][] Underfull \hbox (badness 10000) detected at line 923 [][][] [259] Underfull \hbox (badness 10000) detected at line 928 [][][] Underfull \hbox (badness 10000) detected at line 956 [][][] Underfull \hbox (badness 10000) detected at line 982 [][][] [260] Underfull \hbox (badness 10000) detected at line 1008 [][][] Underfull \hbox (badness 10000) detected at line 1030 [][][] Underfull \hbox (badness 10000) detected at line 1033 [][][] [261] Underfull \hbox (badness 10000) detected at line 1055 [][][] Underfull \hbox (badness 10000) detected at line 1093 [][][] Underfull \hbox (badness 10000) detected at line 1096 [][][] [262] Underfull \hbox (badness 10000) detected at line 1099 [][][] Underfull \hbox (badness 10000) detected at line 1123 [][][] Underfull \hbox (badness 10000) detected at line 1160 [][][] [263] Underfull \hbox (badness 10000) detected at line 1163 [][][] Underfull \hbox (badness 10000) detected at line 1166 [][][] Underfull \hbox (badness 10000) detected at line 1190 [][][] Underfull \hbox (badness 10000) detected at line 1193 [][][] Underfull \hbox (badness 10000) detected at line 1198 [][][] [264] Underfull \hbox (badness 10000) detected at line 1226 [][][] Underfull \hbox (badness 10000) detected at line 1252 [][][] [265] Underfull \hbox (badness 10000) detected at line 1280 [][][] Underfull \hbox (badness 10000) detected at line 1283 [][][] Underfull \hbox (badness 10000) detected at line 1303 [][][] [266] Underfull \hbox (badness 10000) detected at line 1343 [][][] Underfull \hbox (badness 10000) detected at line 1346 [][][] Underfull \hbox (badness 10000) detected at line 1349 [][][] Underfull \hbox (badness 10000) detected at line 1373 [][][] [267] Underfull \hbox (badness 10000) detected at line 1401 [][][] Underfull \hbox (badness 10000) detected at line 1404 [][][] Underfull \hbox (badness 10000) detected at line 1426 [][][] Underfull \hbox (badness 10000) detected at line 1429 [][][] Underfull \hbox (badness 10000) detected at line 1432 [][][] Underfull \hbox (badness 10000) detected at line 1454 [][][] ) (./group___vpmgp.tex [268] Underfull \hbox (badness 10000) detected at line 45 [][][] [269] Underfull \hbox (badness 10000) detected at line 78 [][][] Underfull \hbox (badness 10000) detected at line 86 [][][] Underfull \hbox (badness 10000) detected at line 103 [][][] Underfull \hbox (badness 10000) detected at line 113 [][][] Underfull \hbox (badness 10000) detected at line 130 [][][] [270] Underfull \hbox (badness 10000) detected at line 152 [][][] Underfull \hbox (badness 10000) detected at line 174 [][][] [271] Underfull \hbox (badness 10000) detected at line 208 [][][] ) (./group___p_m_g_c.tex [272] [273] [274] [275] Underfull \hbox (badness 10000) detected at line 150 [][][] Underfull \hbox (badness 10000) detected at line 153 [][][] Underfull \hbox (badness 10000) detected at line 156 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 165--165 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [276] Underfull \hbox (badness 10000) detected at line 212 [][][] Underfull \hbox (badness 10000) detected at line 215 [][][] Underfull \hbox (badness 10000) detected at line 218 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 227--227 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [277] Underfull \hbox (badness 10000) detected at line 277 [][][] Underfull \hbox (badness 10000) detected at line 280 [][][] [278] Underfull \hbox (badness 10000) detected at line 308 [][][] Underfull \hbox (badness 10000) detected at line 311 [][][] Underfull \hbox (badness 10000) detected at line 339 [][][] Underfull \hbox (badness 10000) detected at line 342 [][][] Underfull \hbox (badness 10000) detected at line 345 [][][] [279] Overfull \hbox (304.08286pt too wide) in paragraph at lines 355--355 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 392 [][][] Underfull \hbox (badness 10000) detected at line 395 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 404--404 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [280] Underfull \hbox (badness 10000) detected at line 439 [][][] [281] Underfull \hbox (badness 10000) detected at line 503 [][][] Underfull \hbox (badness 10000) detected at line 506 [][][] Underfull \hbox (badness 10000) detected at line 509 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 518--518 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [282] Underfull \hbox (badness 10000) detected at line 556 [][][] Underfull \hbox (badness 10000) detected at line 559 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 568--568 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 603 [][][] Underfull \hbox (badness 10000) detected at line 606 [][][] [283] Underfull \hbox (badness 10000) detected at line 646 [][][] Underfull \hbox (badness 10000) detected at line 649 [][][] [284] [285] Underfull \hbox (badness 10000) detected at line 719 [][][] Underfull \hbox (badness 10000) detected at line 722 [][][] Underfull \hbox (badness 10000) detected at line 772 [][][] Underfull \hbox (badness 10000) detected at line 775 [][][] Underfull \hbox (badness 10000) detected at line 778 [][][] [286] Overfull \hbox (304.08286pt too wide) in paragraph at lines 788--788 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 825 [][][] Underfull \hbox (badness 10000) detected at line 828 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 837--837 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [287] [288] Underfull \hbox (badness 10000) detected at line 907 [][][] Underfull \hbox (badness 10000) detected at line 910 [][][] [289] [290] [291] Underfull \hbox (badness 10000) detected at line 1050 [][][] Underfull \hbox (badness 10000) detected at line 1053 [][][] [292] [293] [294] Underfull \hbox (badness 10000) detected at line 1229 [][][] Underfull \hbox (badness 10000) detected at line 1232 [][][] [295] [296] Underfull \hbox (badness 10000) detected at line 1382 [][][] Underfull \hbox (badness 10000) detected at line 1385 [][][] Underfull \hbox (badness 10000) detected at line 1388 [][][] [297] [298] Underfull \hbox (badness 10000) detected at line 1446 [][][] Underfull \hbox (badness 10000) detected at line 1449 [][][] Underfull \hbox (badness 10000) detected at line 1452 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 1462--1462 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 1501 [][][] Underfull \hbox (badness 10000) detected at line 1504 [][][] [299] [300] Underfull \hbox (badness 10000) detected at line 1584 [][][] Underfull \hbox (badness 10000) detected at line 1587 [][][] Underfull \hbox (badness 10000) detected at line 1590 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 1600--1600 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 1637 [][][] Underfull \hbox (badness 10000) detected at line 1640 [][][] [301] Underfull \hbox (badness 10000) detected at line 1643 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 1652--1652 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Overfull \vbox (9.44278pt too high) has occurred while \output is active [302] Underfull \hbox (badness 10000) detected at line 1730 [][][] Underfull \hbox (badness 10000) detected at line 1735 [][][] Underfull \hbox (badness 10000) detected at line 1738 [][][] Underfull \hbox (badness 10000) detected at line 1768 [][][] Underfull \hbox (badness 10000) detected at line 1771 [][][] [303] Underfull \hbox (badness 10000) detected at line 1805 [][][] Underfull \hbox (badness 10000) detected at line 1808 [][][] [304] Underfull \hbox (badness 10000) detected at line 1842 [][][] Underfull \hbox (badness 10000) detected at line 1845 [][][] Underfull \hbox (badness 10000) detected at line 1879 [][][] Underfull \hbox (badness 10000) detected at line 1882 [][][] [305] Underfull \hbox (badness 10000) detected at line 1885 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 1895--1895 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 1932 [][][] Underfull \hbox (badness 10000) detected at line 1935 [][][] Underfull \hbox (badness 10000) detected at line 1938 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 1947--1947 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [306] [307] Underfull \hbox (badness 10000) detected at line 2033 [][][] Underfull \hbox (badness 10000) detected at line 2036 [][][] Underfull \hbox (badness 10000) detected at line 2070 [][][] Underfull \hbox (badness 10000) detected at line 2073 [][][] Underfull \hbox (badness 10000) detected at line 2076 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 2086--2086 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [308] Underfull \hbox (badness 10000) detected at line 2123 [][][] Underfull \hbox (badness 10000) detected at line 2126 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2135--2135 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [309] Underfull \hbox (badness 10000) detected at line 2170 [][][] Underfull \hbox (badness 10000) detected at line 2173 [][][] Underfull \hbox (badness 10000) detected at line 2205 [][][] [310] Underfull \hbox (badness 10000) detected at line 2208 [][][] Underfull \hbox (badness 10000) detected at line 2244 [][][] Underfull \hbox (badness 10000) detected at line 2247 [][][] [311] Underfull \hbox (badness 10000) detected at line 2283 [][][] Underfull \hbox (badness 10000) detected at line 2286 [][][] [312] Underfull \hbox (badness 10000) detected at line 2314 [][][] Underfull \hbox (badness 10000) detected at line 2317 [][][] Underfull \hbox (badness 10000) detected at line 2320 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 2330--2330 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [313] Underfull \hbox (badness 10000) detected at line 2367 [][][] Underfull \hbox (badness 10000) detected at line 2370 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2379--2379 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 2414 [][][] Underfull \hbox (badness 10000) detected at line 2417 [][][] [314] [315] Underfull \hbox (badness 10000) detected at line 2503 [][][] Underfull \hbox (badness 10000) detected at line 2506 [][][] Underfull \hbox (badness 10000) detected at line 2509 [][][] [316] Underfull \hbox (badness 10000) detected at line 2557 [][][] Underfull \hbox (badness 10000) detected at line 2560 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2569--2569 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [317] Underfull \hbox (badness 10000) detected at line 2604 [][][] Underfull \hbox (badness 10000) detected at line 2607 [][][] [318] Underfull \hbox (badness 10000) detected at line 2697 [][][] Underfull \hbox (badness 10000) detected at line 2700 [][][] [319] Underfull \hbox (badness 10000) detected at line 2746 [][][] Underfull \hbox (badness 10000) detected at line 2749 [][][] Underfull \hbox (badness 10000) detected at line 2752 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 2762--2762 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [320] Underfull \hbox (badness 10000) detected at line 2799 [][][] Underfull \hbox (badness 10000) detected at line 2802 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2811--2811 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 2846 [][][] Underfull \hbox (badness 10000) detected at line 2849 [][][] [321] Underfull \hbox (badness 10000) detected at line 2905 [][][] Underfull \hbox (badness 10000) detected at line 2908 [][][] Overfull \vbox (18.98318pt too high) has occurred while \output is active [322] Underfull \hbox (badness 10000) detected at line 2946 [][][] Underfull \hbox (badness 10000) detected at line 2957 [][][] [323] Underfull \hbox (badness 10000) detected at line 2960 [][][] [324] Underfull \hbox (badness 10000) detected at line 3046 [][][] Underfull \hbox (badness 10000) detected at line 3049 [][][] Underfull \hbox (badness 10000) detected at line 3052 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3062--3062 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 3099 [][][] Underfull \hbox (badness 10000) detected at line 3102 [][][] [325] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 3111--3111 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 3146 [][][] Underfull \hbox (badness 10000) detected at line 3149 [][][] [326] Underfull \hbox (badness 10000) detected at line 3187 [][][] Underfull \hbox (badness 10000) detected at line 3190 [][][] Underfull \hbox (badness 10000) detected at line 3193 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3203--3203 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [327] Underfull \hbox (badness 10000) detected at line 3240 [][][] Underfull \hbox (badness 10000) detected at line 3243 [][][] Underfull \hbox (badness 10000) detected at line 3246 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 3255--3255 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [328] Underfull \hbox (badness 10000) detected at line 3288 [][][] [329] Underfull \hbox (badness 10000) detected at line 3342 [][][] [330] [331] Underfull \hbox (badness 10000) detected at line 3484 [][][] [332] Underfull \hbox (badness 10000) detected at line 3542 [][][] Underfull \hbox (badness 10000) detected at line 3545 [][][] [333] Underfull \hbox (badness 10000) detected at line 3585 [][][] Underfull \hbox (badness 10000) detected at line 3588 [][][] Underfull \hbox (badness 10000) detected at line 3591 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3601--3601 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [334] Underfull \hbox (badness 10000) detected at line 3638 [][][] Underfull \hbox (badness 10000) detected at line 3641 [][][] Underfull \hbox (badness 10000) detected at line 3644 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 3653--3653 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [335] Underfull \hbox (badness 10000) detected at line 3702 [][][] Underfull \hbox (badness 10000) detected at line 3705 [][][] [336] [337] Underfull \hbox (badness 10000) detected at line 3789 [][][] Underfull \hbox (badness 10000) detected at line 3792 [][][] [338] Underfull \hbox (badness 10000) detected at line 3890 [][][] Underfull \hbox (badness 10000) detected at line 3893 [][][] Underfull \hbox (badness 10000) detected at line 3896 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3906--3906 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [339] Underfull \hbox (badness 10000) detected at line 3943 [][][] Underfull \hbox (badness 10000) detected at line 3946 [][][] Underfull \hbox (badness 10000) detected at line 3972 [][][] Underfull \hbox (badness 10000) detected at line 3975 [][][] [340] Underfull \hbox (badness 10000) detected at line 4001 [][][] Underfull \hbox (badness 10000) detected at line 4004 [][][] [341] Underfull \hbox (badness 10000) detected at line 4034 [][][] Underfull \hbox (badness 10000) detected at line 4037 [][][] Underfull \hbox (badness 10000) detected at line 4040 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 4050--4050 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 4087 [][][] [342] Underfull \hbox (badness 10000) detected at line 4090 [][][] Underfull \hbox (badness 10000) detected at line 4093 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 4102--4102 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 4137 [][][] Underfull \hbox (badness 10000) detected at line 4140 [][][] [343] Underfull \hbox (badness 10000) detected at line 4194 [][][] [344] Underfull \hbox (badness 10000) detected at line 4216 [][][] Overfull \vbox (38.14133pt too high) has occurred while \output is active [345] Underfull \hbox (badness 10000) detected at line 4290 [][][] Underfull \hbox (badness 10000) detected at line 4293 [][][] [346] [347] Underfull \hbox (badness 10000) detected at line 4383 [][][] Underfull \hbox (badness 10000) detected at line 4386 [][][] Underfull \hbox (badness 10000) detected at line 4426 [][][] Underfull \hbox (badness 10000) detected at line 4429 [][][] [348] Underfull \hbox (badness 10000) detected at line 4471 [][][] Underfull \hbox (badness 10000) detected at line 4474 [][][] [349] Underfull \hbox (badness 10000) detected at line 4532 [][][] Underfull \hbox (badness 10000) detected at line 4535 [][][] Underfull \hbox (badness 10000) detected at line 4538 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 4548--4548 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [350] Underfull \hbox (badness 10000) detected at line 4585 [][][] Underfull \hbox (badness 10000) detected at line 4588 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 4597--4597 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [351] Underfull \hbox (badness 10000) detected at line 4630 [][][] Underfull \hbox (badness 10000) detected at line 4633 [][][] Underfull \hbox (badness 10000) detected at line 4636 [][][] [352] Underfull \hbox (badness 10000) detected at line 4692 [][][] Underfull \hbox (badness 10000) detected at line 4695 [][][] Underfull \hbox (badness 10000) detected at line 4727 [][][] Underfull \hbox (badness 10000) detected at line 4730 [][][] [353] Underfull \hbox (badness 10000) detected at line 4768 [][][] Underfull \hbox (badness 10000) detected at line 4771 [][][] Underfull \hbox (badness 10000) detected at line 4774 [][][] Overfull \hbox (20.88268pt too wide) in paragraph at lines 4784--4784 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute,[] [354] Underfull \hbox (badness 10000) detected at line 4822 [][][] Underfull \hbox (badness 10000) detected at line 4825 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 4834--4834 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [355] Underfull \hbox (badness 10000) detected at line 4869 [][][] Underfull \hbox (badness 10000) detected at line 4872 [][][] [356] Underfull \hbox (badness 10000) detected at line 4930 [][][] Underfull \hbox (badness 10000) detected at line 4933 [][][] Underfull \hbox (badness 10000) detected at line 4965 [][][] Underfull \hbox (badness 10000) detected at line 4968 [][][] Underfull \hbox (badness 10000) detected at line 4971 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 4981--4981 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [357] Underfull \hbox (badness 10000) detected at line 5018 [][][] Underfull \hbox (badness 10000) detected at line 5021 [][][] Underfull \hbox (badness 10000) detected at line 5024 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 5033--5033 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [358] Underfull \hbox (badness 10000) detected at line 5068 [][][] Underfull \hbox (badness 10000) detected at line 5071 [][][] Underfull \hbox (badness 10000) detected at line 5101 [][][] Underfull \hbox (badness 10000) detected at line 5104 [][][] Underfull \hbox (badness 10000) detected at line 5107 [][][] [359] Underfull \hbox (badness 10000) detected at line 5137 [][][] Underfull \hbox (badness 10000) detected at line 5140 [][][] Underfull \hbox (badness 10000) detected at line 5170 [][][] [360] Underfull \hbox (badness 10000) detected at line 5173 [][][] Underfull \hbox (badness 10000) detected at line 5203 [][][] Underfull \hbox (badness 10000) detected at line 5206 [][][] Underfull \hbox (badness 10000) detected at line 5234 [][][] [361] Underfull \hbox (badness 10000) detected at line 5237 [][][] Underfull \hbox (badness 10000) detected at line 5265 [][][] Underfull \hbox (badness 10000) detected at line 5268 [][][] ) (./group___frontend.tex [362] Underfull \hbox (badness 2495) in paragraph at lines 32--33 []\T1/phv/m/n/10 VPUBLIC Vrc[]_[][]Codes [] (int icalc, [] $\OMS/cmsy/m/n/10 ^^ C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 feparm, [] $\OMS /cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbeparm, [] Overfull \hbox (16.65858pt too wide) in paragraph at lines 40--41 []\T1/phv/m/n/10 VEXTERNC int [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], Overfull \hbox (16.91972pt too wide) in paragraph at lines 42--43 []\T1/phv/m/n/10 VEXTERNC void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh , [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/1 0 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], Underfull \hbox (badness 1910) in paragraph at lines 60--61 [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1 /phv/m/n/10 alist[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][] [], [] Underfull \hbox (badness 1237) in paragraph at lines 60--61 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 charge[]Map[][][], [] $\OMS/cmsy/m/n/10 ^^C $\T1/phv/m/n/10 pmgp[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pmg[][][], [] [363] Underfull \hbox (badness 5817) in paragraph at lines 78--79 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], Underfull \hbox (badness 5817) in paragraph at lines 80--81 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], [364] [365] Underfull \hbox (badness 10000) detected at line 178 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 211 [][][] [366] Underfull \hbox (badness 10000) detected at line 235 [][][] [367] Underfull \hbox (badness 10000) detected at line 275 [][][] Underfull \hbox (badness 10000) detected at line 297 [][][] Underfull \hbox (badness 10000) detected at line 314 [][][] Underfull \hbox (badness 10000) detected at line 317 [][][] [368] Underfull \hbox (badness 10000) detected at line 351 [][][] Underfull \hbox (badness 10000) detected at line 373 [][][] Underfull \hbox (badness 10000) detected at line 390 [][][] Underfull \hbox (badness 10000) detected at line 393 [][][] [369] [370] Underfull \hbox (badness 10000) detected at line 495 [][][] Underfull \hbox (badness 10000) detected at line 502 [][][] [371] Underfull \hbox (badness 10000) detected at line 572 [][][] Underfull \hbox (badness 10000) detected at line 575 [][][] [372] Underfull \hbox (badness 10000) detected at line 625 [][][] Underfull \hbox (badness 10000) detected at line 649 [][][] Underfull \hbox (badness 10000) detected at line 677 [][][] [373] Underfull \hbox (badness 10000) detected at line 694 [][][] Underfull \hbox (badness 10000) detected at line 720 [][][] Underfull \hbox (badness 10000) detected at line 748 [][][] [374] Underfull \hbox (badness 10000) detected at line 772 [][][] Underfull \hbox (badness 10000) detected at line 792 [][][] Underfull \hbox (badness 10000) detected at line 818 [][][] [375] Underfull \hbox (badness 10000) detected at line 842 [][][] Underfull \hbox (badness 10000) detected at line 866 [][][] Underfull \hbox (badness 10000) detected at line 876 [][][] Underfull \hbox (badness 10000) detected at line 895 [][][] [376] Underfull \hbox (badness 10000) detected at line 909 [][][] Underfull \hbox (badness 10000) detected at line 912 [][][] Underfull \hbox (badness 10000) detected at line 929 [][][] Underfull \hbox (badness 10000) detected at line 939 [][][] Underfull \hbox (badness 10000) detected at line 958 [][][] Underfull \hbox (badness 10000) detected at line 961 [][][] [377] Underfull \hbox (badness 10000) detected at line 981 [][][] Underfull \hbox (badness 10000) detected at line 984 [][][] Underfull \hbox (badness 10000) detected at line 1010 [][][] Underfull \hbox (badness 10000) detected at line 1013 [][][] [378] Underfull \hbox (badness 10000) detected at line 1035 [][][] Underfull \hbox (badness 10000) detected at line 1045 [][][] Underfull \hbox (badness 10000) detected at line 1064 [][][] Underfull \hbox (badness 10000) detected at line 1067 [][][] Underfull \hbox (badness 10000) detected at line 1091 [][][] [379] Underfull \hbox (badness 10000) detected at line 1105 [][][] Underfull \hbox (badness 10000) detected at line 1122 [][][] Underfull \hbox (badness 10000) detected at line 1134 [][][] Underfull \hbox (badness 10000) in paragraph at lines 1135--1136 Underfull \hbox (badness 10000) detected at line 1138 [][][] [380] Underfull \hbox (badness 10000) detected at line 1166 [][][] Underfull \hbox (badness 10000) detected at line 1180 [][][] Underfull \hbox (badness 10000) detected at line 1201 [][][] Underfull \hbox (badness 10000) detected at line 1204 [][][] [381] Underfull \hbox (badness 10000) detected at line 1228 [][][] Underfull \hbox (badness 10000) detected at line 1231 [][][] Underfull \hbox (badness 10000) detected at line 1259 [][][] Underfull \hbox (badness 10000) detected at line 1262 [][][] [382] Underfull \hbox (badness 10000) detected at line 1288 [][][] Underfull \hbox (badness 10000) detected at line 1291 [][][] Underfull \hbox (badness 10000) detected at line 1319 [][][] Underfull \hbox (badness 10000) detected at line 1322 [][][] [383] Underfull \hbox (badness 10000) detected at line 1348 [][][] Underfull \hbox (badness 10000) detected at line 1377 [][][] Underfull \hbox (badness 10000) detected at line 1380 [][][] Underfull \hbox (badness 10000) detected at line 1408 [][][] [384] Underfull \hbox (badness 10000) detected at line 1432 [][][] Underfull \hbox (badness 10000) detected at line 1454 [][][] Underfull \hbox (badness 10000) detected at line 1468 [][][] [385] Underfull \hbox (badness 10000) detected at line 1485 [][][] Underfull \hbox (badness 10000) detected at line 1497 [][][] Underfull \hbox (badness 10000) detected at line 1514 [][][] Underfull \hbox (badness 10000) detected at line 1528 [][][] [386] Underfull \hbox (badness 10000) detected at line 1562 [][][] Underfull \hbox (badness 10000) detected at line 1574 [][][] Underfull \hbox (badness 10000) detected at line 1591 [][][] Underfull \hbox (badness 10000) detected at line 1608 [][][] [387] Underfull \hbox (badness 10000) detected at line 1636 [][][] Underfull \hbox (badness 10000) detected at line 1650 [][][] [388] Underfull \hbox (badness 10000) detected at line 1688 [][][] Underfull \hbox (badness 10000) detected at line 1716 [][][] Underfull \hbox (badness 10000) detected at line 1733 [][][] [389] Underfull \hbox (badness 10000) detected at line 1747 [][][] Underfull \hbox (badness 10000) detected at line 1764 [][][] Underfull \hbox (badness 10000) detected at line 1792 [][][] [390] Underfull \hbox (badness 10000) detected at line 1809 [][][] Underfull \hbox (badness 10000) detected at line 1823 [][][] ) [391] [392] Chapter 8. (./struct_atom_force.tex Underfull \hbox (badness 10000) detected at line 32 [][][] [393]) (./structs_a_p_o_lparm.tex [394] Underfull \hbox (badness 10000) detected at line 88 [][][] [395] Underfull \hbox (badness 10000) detected at line 224 [][][] [396] Underfull \hbox (badness 10000) detected at line 237 [][][] Underfull \hbox (badness 10000) detected at line 250 [][][] Underfull \hbox (badness 10000) detected at line 263 [][][] Underfull \hbox (badness 10000) detected at line 276 [][][] Underfull \hbox (badness 10000) detected at line 289 [][][] Underfull \hbox (badness 10000) detected at line 302 [][][] [397] Underfull \hbox (badness 10000) detected at line 315 [][][] Underfull \hbox (badness 10000) detected at line 328 [][][] Underfull \hbox (badness 10000) detected at line 341 [][][] Underfull \hbox (badness 10000) detected at line 354 [][][] Underfull \hbox (badness 10000) detected at line 367 [][][] Underfull \hbox (badness 10000) detected at line 380 [][][] [398]) (./structs_b_e_mparm.tex [399] Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 53 [][][] [400] Underfull \hbox (badness 10000) detected at line 129 [][][] Underfull \hbox (badness 10000) detected at line 142 [][][] Underfull \hbox (badness 10000) detected at line 155 [][][] [401] Underfull \hbox (badness 10000) detected at line 168 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 194 [][][] ) (./structs_f_e_mparm.tex [402] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) in paragraph at lines 84--85 [403] [404] [405]) (./structs_g_e_o_f_l_o_wparm.tex Underfull \hbox (badness 10000) detected at line 30 [][][] Underfull \hbox (badness 10000) detected at line 33 [][][] [406]) (./structs_m_gparm.tex [407] Underfull \hbox (badness 10000) detected at line 120 [][][] Underfull \hbox (badness 10000) detected at line 123 [][][] [408] Underfull \hbox (badness 10000) in paragraph at lines 149--150 Underfull \hbox (badness 10000) in paragraph at lines 180--181 [409] Underfull \hbox (badness 10000) in paragraph at lines 261--262 [410] [411] Underfull \hbox (badness 10000) detected at line 434 [][][] Underfull \hbox (badness 10000) detected at line 447 [][][] Underfull \hbox (badness 10000) detected at line 460 [][][] Underfull \hbox (badness 10000) detected at line 473 [][][] [412] Underfull \hbox (badness 10000) detected at line 486 [][][] Underfull \hbox (badness 10000) detected at line 499 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] Underfull \hbox (badness 10000) detected at line 538 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] [413] Underfull \hbox (badness 10000) detected at line 564 [][][] Underfull \hbox (badness 10000) detected at line 577 [][][] Underfull \hbox (badness 10000) detected at line 590 [][][] Underfull \hbox (badness 10000) detected at line 603 [][][] Underfull \hbox (badness 10000) detected at line 616 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] [414] Underfull \hbox (badness 10000) detected at line 642 [][][] Underfull \hbox (badness 10000) detected at line 655 [][][] Underfull \hbox (badness 10000) detected at line 668 [][][] ) (./structs_n_osh.tex [415] Underfull \hbox (badness 10000) detected at line 108 [][][] [416] [417] [418] [419] [420]) (./structs_n_osh__calc.tex [421] Underfull \hbox (badness 10000) detected at line 38 [][][] [422]) (./structs_p_b_a_mparm.tex [423] Underfull \hbox (badness 10000) detected at line 106 [][][] Underfull \hbox (badness 10000) detected at line 109 [][][] [424] [425] [426] [427]) (./structs_p_b_eparm.tex [428] [429] Underfull \hbox (badness 10000) detected at line 142 [][][] Underfull \hbox (badness 10000) detected at line 145 [][][] [430] [431] [432] Underfull \hbox (badness 10000) detected at line 391 [][][] Underfull \hbox (badness 10000) detected at line 404 [][][] Underfull \hbox (badness 10000) detected at line 417 [][][] Underfull \hbox (badness 10000) detected at line 430 [][][] [433] Underfull \hbox (badness 10000) detected at line 473 [][][] Underfull \hbox (badness 10000) detected at line 486 [][][] Underfull \hbox (badness 10000) detected at line 499 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] [434] Underfull \hbox (badness 10000) detected at line 538 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] Underfull \hbox (badness 10000) detected at line 564 [][][] Underfull \hbox (badness 10000) detected at line 577 [][][] Underfull \hbox (badness 10000) detected at line 590 [][][] Underfull \hbox (badness 10000) detected at line 603 [][][] [435] Underfull \hbox (badness 10000) detected at line 616 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] [436] [437]) (./structs_p_b_s_a_mparm.tex [438] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] [439]) (./structs_vacc.tex [440] Underfull \hbox (badness 10000) detected at line 36 [][][] [441]) (./structs_vacc_surf.tex Underfull \hbox (badness 10000) detected at line 36 [][][] [442]) (./structs_valist.tex [443] Underfull \hbox (badness 10000) detected at line 36 [][][] [444]) (./structs_vatom.tex Underfull \hbox (badness 10000) detected at line 36 [][][] Underfull \hbox (badness 10000) in paragraph at lines 62--63 [445] Underfull \hbox (badness 10000) in paragraph at lines 93--94 Underfull \hbox (badness 10000) in paragraph at lines 114--115 ) (./structs_vclist.tex [446] Underfull \hbox (badness 10000) detected at line 40 [][][] [447]) (./structs_vclist_cell.tex Underfull \hbox (badness 10000) detected at line 24 [][][] ) (./structs_vcsm.tex [448] Underfull \hbox (badness 10000) detected at line 42 [][][] [449]) (./structs_vfetk.tex [450] Underfull \hbox (badness 10000) detected at line 60 [][][] [451] Underfull \hbox (badness 10000) in paragraph at lines 116--117 [452]) (./structs_vfetk___local_var.tex [453] Underfull \hbox (badness 10000) detected at line 86 [][][] [454] [455] [456] [457]) (./structs_vgreen.tex Underfull \hbox (badness 10000) detected at line 34 [][][] [458]) (./structs_vgrid.tex [459] Underfull \hbox (badness 10000) detected at line 52 [][][] [460] [461]) (./structs_vmgrid.tex Underfull \hbox (badness 10000) detected at line 24 [][][] ) (./structs_vopot.tex [462] Underfull \hbox (badness 10000) detected at line 26 [][][] ) (./structs_vparam___atom_data.tex [463] Underfull \hbox (badness 10000) detected at line 30 [][][] Underfull \hbox (badness 10000) detected at line 33 [][][] ) (./structs_vpbe.tex [464] Underfull \hbox (badness 10000) detected at line 86 [][][] [465] [466] [467] [468]) (./structs_vpee.tex [469] Underfull \hbox (badness 10000) detected at line 34 [][][] ) (./structs_vpmg.tex [470] [471] Underfull \hbox (badness 10000) detected at line 116 [][][] [472] [473] [474] [475] [476]) (./structs_vpmgp.tex [477] Underfull \hbox (badness 10000) detected at line 126 [][][] [478] Underfull \hbox (badness 10000) in paragraph at lines 164--165 Underfull \hbox (badness 10000) in paragraph at lines 175--176 Underfull \hbox (badness 10000) in paragraph at lines 186--187 [479] Underfull \hbox (badness 10000) in paragraph at lines 234--235 [480] [481] [482] [483] Underfull \hbox (badness 10000) in paragraph at lines 506--507 Underfull \hbox (badness 10000) in paragraph at lines 527--528 [484] Underfull \hbox (badness 10000) in paragraph at lines 548--549 Underfull \hbox (badness 10000) in paragraph at lines 589--590 [485] Underfull \hbox (badness 10000) in paragraph at lines 630--631 Underfull \hbox (badness 10000) in paragraph at lines 671--672 ) (./struct_vparam.tex [486] Underfull \hbox (badness 10000) detected at line 26 [][][] ) (./struct_vparam___res_data.tex [487] Underfull \hbox (badness 10000) detected at line 28 [][][] ) [488] Chapter 9. (./mainpage_8h_source.tex) (./apbs_8h.tex <./apbs_8h__incl.pdf> <./apbs_8h__dep __incl.pdf> [489] Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 53 [][][] Underfull \hbox (badness 10000) detected at line 56 [][][] [490]) (./apbs_8h_source.tex) (./vcsm_8c.tex [491] <./vcsm_8c__incl.pdf> [492] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] Underfull \hbox (badness 10000) detected at line 58 [][][] [493]) (./vcsm_8c_source.tex [494] [495] [496] [497] [498] [499]) (./vcsm_8h.tex <./vcsm_8h__incl.pdf> <./vcsm_8h__dep__incl.pdf> [500] [501] Underfull \hbox (badness 10000) detected at line 75 [][][] Underfull \hbox (badness 10000) detected at line 78 [][][] Underfull \hbox (badness 10000) detected at line 81 [][][] [502]) (./vcsm_8h_source.tex [503]) (./vfetk_8c.tex [504] <./vfetk_8c__incl.pdf > [505] [506] Underfull \hbox (badness 10000) detected at line 162 [][][] Underfull \hbox (badness 10000) detected at line 165 [][][] [507] Underfull \hbox (badness 10000) detected at line 168 [][][] [508] [509] [510] [511]) (./vfetk_8c_source.tex [512] [513] [514] [515] [516] [517] [518] [519] [520] [521] [522] [523] [524] [525] [526] [527] [528] [529] [530] [531] [532] [533] [534] [535] [536] [537] [538] [539] [540] [541]) (./vfetk_8h.tex [542] <./vfetk_8h__incl.pdf> <./vfetk_8h__dep__inc l.pdf> [543] [544] [545] Underfull \hbox (badness 10000) detected at line 187 [][][] [546] Underfull \hbox (badness 10000) detected at line 190 [][][] Underfull \hbox (badness 10000) detected at line 193 [][][] ) (./vfetk_8h_source.tex [547] [548] [549] [550] [551] [552]) (./vpee_8c.tex <. /vpee_8c__incl.pdf> [553] Underfull \hbox (badness 10000) detected at line 49 [][][] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] [554]) (./vpee_8c_source.tex [555] [556] [557] [558] [559] [560]) (./vpee_8h.tex [561] <./vpee_8h__incl.pdf> <./vpee_8h__dep__incl.pdf> [562] Underfull \hbox (badness 10000) detected at line 55 [][][] Underfull \hbox (badness 10000) detected at line 58 [][][] Underfull \hbox (badness 10000) detected at line 61 [][][] [563]) (./vpee_8h_source.tex [564]) (./apolparm_8c.tex <./apolparm_8c__incl.pdf > [565] Underfull \hbox (badness 10000) detected at line 64 [][][] Underfull \hbox (badness 10000) detected at line 67 [][][] Underfull \hbox (badness 10000) detected at line 70 [][][] [566] [567]) (./apolparm_8c_source.tex [568] [569] [570] [571] [572] [573] [574] [575]) (./apolparm_8h_source.tex [576]) (./bemparm_8c.tex <./bemparm_8c__ incl.pdf> [577] [578] Underfull \hbox (badness 10000) detected at line 48 [][][] Underfull \hbox (badness 10000) detected at line 51 [][][] Underfull \hbox (badness 10000) detected at line 54 [][][] [579] Underfull \hbox (badness 10000) detected at line 120 [][][] ) (./bemparm_8c_source.tex [580] [581] [582] [583]) (./bemparm_8h_source.tex [584]) (./femparm_8c.tex <./femparm_8c__incl.pdf> [585] [586] Underfull \hbox (badness 10000) detected at line 58 [][][] Underfull \hbox (badness 10000) detected at line 61 [][][] Underfull \hbox (badness 10000) detected at line 64 [][][] [587] [588]) (./femparm_8c_source.tex [589] [590] [591] [592] [593]) (./femparm_8h.tex <./femparm_8h__incl.pdf> [594] <./femparm_8h__dep__incl.pdf> [595] Underfull \hbox (badness 10000) detected at line 87 [][][] Underfull \hbox (badness 10000) detected at line 90 [][][] Underfull \hbox (badness 10000) detected at line 93 [][][] [596]) (./femparm_8h_source.tex [597]) (./geoflowparm_8c.tex [598] <./geoflowpa rm_8c__incl.pdf> [599] Underfull \hbox (badness 10000) detected at line 46 [][][] Underfull \hbox (badness 10000) detected at line 49 [][][] Underfull \hbox (badness 10000) detected at line 52 [][][] [600]) (./geoflowparm_8c_source.tex [601] [602]) (./geoflowparm_8h.tex [603] <. /geoflowparm_8h__incl.pdf> <./geoflowparm_8h__dep__incl.pdf> [604] [605] Underfull \hbox (badness 10000) detected at line 69 [][][] Underfull \hbox (badness 10000) detected at line 72 [][][] Underfull \hbox (badness 10000) detected at line 75 [][][] [606]) (./geoflowparm_8h_source.tex [607]) (./mgparm_8c.tex <./mgparm_8c__incl. pdf> [608] [609] Underfull \hbox (badness 10000) detected at line 94 [][][] Underfull \hbox (badness 10000) detected at line 97 [][][] Underfull \hbox (badness 10000) detected at line 100 [][][] [610] [611]) (./mgparm_8c_source.tex [612] [613] [614] [615] [616] [617] [618] [619] [620] [621] [622] [623]) (./mgparm_8h.tex <./mgparm_8h__incl.pdf> [624] <./mgparm_8h__dep__incl.pdf> [625] [626] Underfull \hbox (badness 10000) detected at line 102 [][][] Underfull \hbox (badness 10000) detected at line 105 [][][] Underfull \hbox (badness 10000) detected at line 108 [][][] [627]) (./mgparm_8h_source.tex [628]) (./nosh_8c.tex <./nosh_8c__incl.pdf> [629] [630] [631] Underfull \hbox (badness 10000) detected at line 150 [][][] Underfull \hbox (badness 10000) detected at line 153 [][][] Underfull \hbox (badness 10000) detected at line 156 [][][] [632] [633] [634] [635] [636]) (./nosh_8c_source.tex [637] [638] [639] [640] [641] [642] [643] [644] [645] [646] [647] [648] [649] [650] [651] [652] [653] [654] [655] [656] [657] [658] [659] [660] [661] [662] [663] [664] [665] [666] [667] [668] [669] [670] [671] [672] [673] [674] [675] [676]) (./nosh_8h.tex <./nosh_8h__incl.pdf> [677] <./nosh_8h__dep__incl.pdf> [678] [679] [680] Underfull \hbox (badness 10000) detected at line 169 [][][] Underfull \hbox (badness 10000) detected at line 172 [][][] Underfull \hbox (badness 10000) detected at line 175 [][][] ) (./nosh_8h_source.tex [681] [682] [683]) (./pbamparm_8c.tex <./pbamparm_8c__i ncl.pdf> [684] [685] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) detected at line 71 [][][] Underfull \hbox (badness 10000) detected at line 74 [][][] [686]) (./pbamparm_8c_source.tex [687] [688] [689] [690] [691] [692] [693] [694] [695]) (./pbamparm_8h.tex <./pbamparm_8h__incl.pdf> <./pbamparm_8h__dep__ incl.pdf> [696] [697] Underfull \hbox (badness 10000) detected at line 100 [][][] [698] Underfull \hbox (badness 10000) detected at line 103 [][][] Underfull \hbox (badness 10000) detected at line 106 [][][] [699]) (./pbamparm_8h_source.tex [700]) (./pbeparm_8c.tex [701] <./pbeparm_8c__ incl.pdf> [702] Underfull \hbox (badness 10000) detected at line 100 [][][] Underfull \hbox (badness 10000) detected at line 103 [][][] Underfull \hbox (badness 10000) detected at line 106 [][][] [703] [704] [705] [706] [707]) (./pbeparm_8c_source.tex [708] [709] [710] [711] [712] [713] [714] [715] [716] [717] [718] [719] [720] [721] [722]) (./pbeparm_8h.tex <./pbeparm_8h__incl.pdf> [723] <./pbeparm_8h__dep__incl.pdf> [724] Underfull \hbox (badness 10000) detected at line 86 [][][] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 92 [][][] [725]) (./pbeparm_8h_source.tex [726] [727]) (./pbsamparm_8c.tex <./pbsamparm_8 c__incl.pdf> [728] [729] Underfull \hbox (badness 10000) detected at line 48 [][][] Underfull \hbox (badness 10000) detected at line 51 [][][] Underfull \hbox (badness 10000) detected at line 54 [][][] [730]) (./pbsamparm_8c_source.tex [731] [732]) (./pbsamparm_8h.tex [733] <./pbs amparm_8h__incl.pdf> <./pbsamparm_8h__dep__incl.pdf> [734] [735] Underfull \hbox (badness 10000) detected at line 84 [][][] Underfull \hbox (badness 10000) detected at line 87 [][][] Underfull \hbox (badness 10000) detected at line 90 [][][] [736]) (./pbsamparm_8h_source.tex [737]) (./vacc_8c.tex <./vacc_8c__incl.pdf> [738] [739] [740] Underfull \hbox (badness 10000) detected at line 106 [][][] Underfull \hbox (badness 10000) detected at line 109 [][][] Underfull \hbox (badness 10000) detected at line 112 [][][] [741] Underfull \hbox (badness 10000) detected at line 178 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 207 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] [742] [743]) (./vacc_8c_source.tex [744] [745] [746] [747] [748] [749] [750] [751] [752] [753] [754] [755] [756] [757] [758] [759] [760] [761] [762] [763] [764] [765] [766]) (./vacc_8h.tex <./vacc_8h__incl.pdf> <./vacc_8h__dep__ incl.pdf> [767] [768] [769] Underfull \hbox (badness 10000) detected at line 121 [][][] Underfull \hbox (badness 10000) detected at line 124 [][][] Underfull \hbox (badness 10000) detected at line 127 [][][] [770]) (./vacc_8h_source.tex [771] [772] [773]) (./valist_8c.tex <./valist_8c__ incl.pdf> [774] [775] Underfull \hbox (badness 2293) in paragraph at lines 53--55 []\T1/phv/m/n/10 VPRIVATE Vrc[]_[][]Codes [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/ m/n/10 thee, Vio $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 sock, int $\OMS/cmsy/m/n/ 10 ^^C$\T1/phv/m/n/10 serial, char atom[] Underfull \hbox (badness 10000) detected at line 81 [][][] Underfull \hbox (badness 10000) detected at line 84 [][][] Underfull \hbox (badness 10000) detected at line 87 [][][] [776] [777] [778]) (./valist_8c_source.tex [779] [780] [781] [782] [783] [784] [785] [786] [787] [788]) (./valist_8h.tex [789] <./valist_8h__incl.pdf> < ./valist_8h__dep__incl.pdf> [790] Underfull \hbox (badness 10000) detected at line 75 [][][] Underfull \hbox (badness 10000) detected at line 78 [][][] Underfull \hbox (badness 10000) detected at line 81 [][][] [791]) (./valist_8h_source.tex [792] [793]) (./vatom_8c.tex <./vatom_8c__incl.p df> [794] Underfull \hbox (badness 10000) detected at line 70 [][][] Underfull \hbox (badness 10000) detected at line 73 [][][] Underfull \hbox (badness 10000) detected at line 76 [][][] [795]) (./vatom_8c_source.tex [796] [797] [798]) (./vatom_8h.tex <./vatom_8h__i ncl.pdf> [799] <./vatom_8h__dep__incl.pdf> [800] [801] Underfull \hbox (badness 10000) detected at line 94 [][][] Underfull \hbox (badness 10000) detected at line 97 [][][] Underfull \hbox (badness 10000) detected at line 100 [][][] ) (./vatom_8h_source.tex [802] [803]) (./vcap_8c.tex <./vcap_8c__incl.pdf> [804] Underfull \hbox (badness 10000) detected at line 30 [][][] Underfull \hbox (badness 10000) detected at line 33 [][][] Underfull \hbox (badness 10000) detected at line 36 [][][] [805]) (./vcap_8c_source.tex [806]) (./vcap_8h.tex <./vcap_8h__incl.pdf> <./vca p_8h__dep__incl.pdf> [807] Underfull \hbox (badness 10000) detected at line 45 [][][] Underfull \hbox (badness 10000) detected at line 48 [][][] [808] Underfull \hbox (badness 10000) detected at line 51 [][][] ) (./vcap_8h_source.tex [809]) (./vclist_8c.tex <./vclist_8c__incl.pdf> Underfull \hbox (badness 4060) in paragraph at lines 31--33 []\T1/phv/m/n/10 VPRIVATE void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 thee , dou-ble lower[]_[]corner[][][], dou-ble upper[]_[] [810] Underfull \hbox (badness 10000) detected at line 64 [][][] Underfull \hbox (badness 10000) detected at line 67 [][][] Underfull \hbox (badness 10000) detected at line 70 [][][] [811] [812]) (./vclist_8c_source.tex [813] [814] [815] [816] [817]) (./vclist_8h.tex [818] <./vclist_8h__incl.pdf> <./vclist_8h__dep__incl.pdf> [819] [820] Underfull \hbox (badness 10000) detected at line 82 [][][] Underfull \hbox (badness 10000) detected at line 85 [][][] Underfull \hbox (badness 10000) detected at line 88 [][][] [821]) (./vclist_8h_source.tex [822]) (./vgreen_8c.tex [823] <./vgreen_8c__incl .pdf> [824] Underfull \hbox (badness 10000) detected at line 54 [][][] Underfull \hbox (badness 10000) detected at line 57 [][][] Underfull \hbox (badness 10000) detected at line 60 [][][] [825]) (./vgreen_8c_source.tex [826] [827] [828] [829] [830] [831]) (./vgreen_8h.tex <./vgreen_8h__incl.pdf> [832] <./vgreen_8h__dep__incl.pdf> [833] Underfull \hbox (badness 10000) detected at line 70 [][][] Underfull \hbox (badness 10000) detected at line 73 [][][] ) (./vgreen_8h_source.tex [834]) (./vhal_8h.tex [835] <./vhal_8h__incl.pdf> <./ vhal_8h__dep__incl.pdf> [836] [837] [838] [839] Underfull \hbox (badness 10000) detected at line 301 [][][] Underfull \hbox (badness 10000) detected at line 304 [][][] Underfull \hbox (badness 10000) detected at line 307 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 316--316 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [840] [841] [842] [843] [844] [845] [846]) (./vhal_8h_source.tex [847] [848] [849] [850] [851] [852] [853] [854]) (./vmatrix_8h.tex [855] <./vmatrix_8h__dep __incl.pdf> Underfull \hbox (badness 10000) detected at line 35 [][][] Underfull \hbox (badness 10000) detected at line 38 [][][] Underfull \hbox (badness 10000) detected at line 41 [][][] [856] [857]) (./vmatrix_8h_source.tex [858]) (./vparam_8c.tex <./vparam_8c__inc l.pdf> [859] Underfull \hbox (badness 10000) detected at line 77 [][][] Underfull \hbox (badness 10000) detected at line 80 [][][] [860] Underfull \hbox (badness 10000) detected at line 83 [][][] ) (./vparam_8c_source.tex [861] [862] [863] [864] [865] [866] [867] [868]) (./vparam_8h.tex [869] <./vparam_8h__incl.pdf> <./vparam_8h__dep__incl.pdf> [870] [871] Underfull \hbox (badness 10000) detected at line 94 [][][] Underfull \hbox (badness 10000) detected at line 97 [][][] Underfull \hbox (badness 10000) detected at line 100 [][][] [872]) (./vparam_8h_source.tex [873]) (./vpbe_8c.tex <./vpbe_8c__incl.pdf> [874] [875] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 92 [][][] [876] Underfull \hbox (badness 10000) detected at line 95 [][][] ) (./vpbe_8c_source.tex [877] [878] [879] [880] [881] [882] [883]) (./vpbe_8h.tex <./vpbe_8h__incl.pdf> <./vpbe_8h__dep__incl.pdf> [884] [885] Underfull \hbox (badness 10000) detected at line 109 [][][] Underfull \hbox (badness 10000) detected at line 112 [][][] Underfull \hbox (badness 10000) detected at line 115 [][][] [886]) (./vpbe_8h_source.tex [887] [888] [889]) (./vstring_8c.tex <./vstring_8c __incl.pdf> [890] Underfull \hbox (badness 10000) detected at line 30 [][][] Underfull \hbox (badness 10000) detected at line 33 [][][] Underfull \hbox (badness 10000) detected at line 36 [][][] ) (./vstring_8c_source.tex [891] [892] [893]) (./vstring_8h.tex <./vstring_8h__ incl.pdf> <./vstring_8h__dep__incl.pdf> [894] Underfull \hbox (badness 10000) detected at line 39 [][][] Underfull \hbox (badness 10000) detected at line 42 [][][] Underfull \hbox (badness 10000) detected at line 45 [][][] [895]) (./vstring_8h_source.tex) (./vunit_8h.tex <./vunit_8h__dep__incl.pdf> [896] LaTeX Warning: Command \r invalid in math mode on input line 41. Missing character: There is no Å in font cmr9! Underfull \hbox (badness 10000) detected at line 49 [][][] Underfull \hbox (badness 10000) detected at line 54 [][][] Underfull \hbox (badness 10000) detected at line 57 [][][] [897]) (./vunit_8h_source.tex) (./main_8c.tex [898] <./main_8c__incl.pdf> Underfull \hbox (badness 10000) detected at line 27 [][][] Underfull \hbox (badness 10000) detected at line 40 [][][] Underfull \hbox (badness 10000) detected at line 43 [][][] [899]) (./main_8c_source.tex [900] [901] [902] [903] [904] [905] [906] [907] [908] [909] [910]) (./vgrid_8c.tex <./vgrid_8c__incl.pdf> [911] [912] Underfull \hbox (badness 10000) detected at line 83 [][][] Underfull \hbox (badness 10000) detected at line 86 [][][] Underfull \hbox (badness 10000) detected at line 89 [][][] [913] Underfull \hbox (badness 10000) detected at line 168 [][][] [914]) (./vgrid_8c_source.tex [915] [916] [917] [918] [919] [920] [921] [922] [923] [924] [925] [926] [927] [928] [929] [930] [931] [932] [933] [934] [935] [936] [937]) (./vgrid_8h.tex [938] <./vgrid_8h__incl.pdf> <./vgrid_ 8h__dep__incl.pdf> [939] [940] Underfull \hbox (badness 10000) detected at line 91 [][][] [941] Underfull \hbox (badness 10000) detected at line 94 [][][] Underfull \hbox (badness 10000) detected at line 97 [][][] [942] Underfull \hbox (badness 10000) detected at line 163 [][][] ) (./vgrid_8h_source.tex [943]) (./vmgrid_8c.tex [944] <./vmgrid_8c__incl.pdf> [945] Underfull \hbox (badness 10000) detected at line 40 [][][] Underfull \hbox (badness 10000) detected at line 43 [][][] Underfull \hbox (badness 10000) detected at line 46 [][][] Underfull \hbox (badness 10000) detected at line 49 [][][] Overfull \hbox (1024.08331pt too wide) in paragraph at lines 58--58 []\T1/pcr/m/n/8 * Copyright (c) 2010, Pacific Northwest National Laboratory. Portions Copyright (c) 2002-2020, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2020, T he Regents of the University of California. Portions Copyright (c) 1995, Michae l Holst.[] ) (./vmgrid_8c_source.tex [946] [947] [948]) (./vmgrid_8h.tex <./vmgrid_8h__inc l.pdf> <./vmgrid_8h__dep__incl.pdf> [949] [950] Underfull \hbox (badness 10000) detected at line 69 [][][] Underfull \hbox (badness 10000) detected at line 72 [][][] Underfull \hbox (badness 10000) detected at line 75 [][][] [951]) (./vmgrid_8h_source.tex) (./vopot_8c.tex [952] <./vopot_8c__incl.pdf> Underfull \hbox (badness 10000) detected at line 43 [][][] Underfull \hbox (badness 10000) detected at line 46 [][][] Underfull \hbox (badness 10000) detected at line 49 [][][] [953]) (./vopot_8c_source.tex [954] [955] [956] [957] [958]) (./vopot_8h.tex <. /vopot_8h__incl.pdf> <./vopot_8h__dep__incl.pdf> [959] [960] Underfull \hbox (badness 10000) detected at line 63 [][][] Underfull \hbox (badness 10000) detected at line 66 [][][] Underfull \hbox (badness 10000) detected at line 69 [][][] ) (./vopot_8h_source.tex [961]) (./vpmg_8c.tex <./vpmg_8c__incl.pdf> [962] [963] [964] [965] Underfull \hbox (badness 10000) detected at line 172 [][][] Underfull \hbox (badness 10000) detected at line 175 [][][] Underfull \hbox (badness 10000) detected at line 178 [][][] [966] Underfull \hbox (badness 10000) detected at line 260 [][][] [967] Underfull \hbox (badness 10000) detected at line 287 [][][] [968] Underfull \hbox (badness 10000) detected at line 383 [][][] Underfull \hbox (badness 10000) detected at line 386 [][][] Underfull \hbox (badness 10000) detected at line 408 [][][] Underfull \hbox (badness 10000) detected at line 411 [][][] [969] Underfull \hbox (badness 10000) detected at line 433 [][][] Underfull \hbox (badness 10000) detected at line 436 [][][] Underfull \hbox (badness 10000) detected at line 458 [][][] Underfull \hbox (badness 10000) detected at line 461 [][][] Underfull \hbox (badness 10000) detected at line 483 [][][] Underfull \hbox (badness 10000) detected at line 486 [][][] [970] Underfull \hbox (badness 10000) detected at line 508 [][][] Underfull \hbox (badness 10000) detected at line 511 [][][] Underfull \hbox (badness 10000) detected at line 533 [][][] Underfull \hbox (badness 10000) detected at line 536 [][][] Underfull \hbox (badness 10000) detected at line 553 [][][] Underfull \hbox (badness 10000) detected at line 556 [][][] [971] Underfull \hbox (badness 10000) detected at line 573 [][][] Underfull \hbox (badness 10000) detected at line 590 [][][] Underfull \hbox (badness 10000) detected at line 607 [][][] Underfull \hbox (badness 10000) detected at line 624 [][][] Underfull \hbox (badness 10000) detected at line 641 [][][] [972] Underfull \hbox (badness 10000) detected at line 658 [][][] Underfull \hbox (badness 10000) detected at line 675 [][][] Underfull \hbox (badness 10000) detected at line 696 [][][] Underfull \hbox (badness 10000) detected at line 699 [][][] Underfull \hbox (badness 10000) detected at line 716 [][][] [973] Underfull \hbox (badness 10000) detected at line 733 [][][] Underfull \hbox (badness 10000) detected at line 750 [][][] Underfull \hbox (badness 10000) detected at line 767 [][][] Underfull \hbox (badness 10000) detected at line 794 [][][] [974] Underfull \hbox (badness 10000) detected at line 831 [][][] [975] Underfull \hbox (badness 10000) detected at line 875 [][][] [976] Underfull \hbox (badness 10000) detected at line 925 [][][] Underfull \hbox (badness 10000) detected at line 947 [][][] [977] Underfull \hbox (badness 10000) detected at line 969 [][][] Underfull \hbox (badness 10000) detected at line 991 [][][] Underfull \hbox (badness 10000) detected at line 994 [][][] Underfull \hbox (badness 10000) detected at line 1011 [][][] Underfull \hbox (badness 10000) detected at line 1014 [][][] [978] Underfull \hbox (badness 10000) detected at line 1036 [][][] Underfull \hbox (badness 10000) detected at line 1039 [][][] Underfull \hbox (badness 10000) detected at line 1061 [][][] Underfull \hbox (badness 10000) detected at line 1064 [][][] Underfull \hbox (badness 10000) detected at line 1096 [][][] [979] Underfull \hbox (badness 10000) detected at line 1113 [][][] Underfull \hbox (badness 10000) detected at line 1145 [][][] Underfull \hbox (badness 10000) detected at line 1148 [][][] ) (./vpmg_8c_source.tex [980] [981] [982] [983] [984] [985] [986] [987] [988] [989] [990] [991] [992] [993] [994] [995] [996] [997] [998] [999] [1000] [1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008] [1009] [1010] [1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] [1021] [1022] [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] [1033] [1034] [1035] [1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] [1090] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112] [1113] [1114] [1115] [1116]) (./vpmg_8h.tex <./vpmg_8h__in cl.pdf> <./vpmg_8h__dep__incl.pdf> [1117] [1118] [1119] [1120] [1121] [1122] Underfull \hbox (badness 10000) detected at line 233 [][][] Underfull \hbox (badness 10000) detected at line 236 [][][] Underfull \hbox (badness 10000) detected at line 239 [][][] [1123] [1124] Underfull \hbox (badness 10000) detected at line 404 [][][] Underfull \hbox (badness 10000) detected at line 421 [][][] [1125] Underfull \hbox (badness 10000) detected at line 467 [][][] Underfull \hbox (badness 10000) detected at line 470 [][][] Underfull \hbox (badness 10000) detected at line 492 [][][] Underfull \hbox (badness 10000) detected at line 495 [][][] [1126] Underfull \hbox (badness 10000) detected at line 517 [][][] Underfull \hbox (badness 10000) detected at line 520 [][][] Underfull \hbox (badness 10000) detected at line 542 [][][] Underfull \hbox (badness 10000) detected at line 545 [][][] Underfull \hbox (badness 10000) detected at line 567 [][][] Underfull \hbox (badness 10000) detected at line 570 [][][] [1127] Underfull \hbox (badness 10000) detected at line 592 [][][] Underfull \hbox (badness 10000) detected at line 595 [][][] Underfull \hbox (badness 10000) detected at line 617 [][][] Underfull \hbox (badness 10000) detected at line 620 [][][] Underfull \hbox (badness 10000) detected at line 637 [][][] Underfull \hbox (badness 10000) detected at line 640 [][][] [1128] Underfull \hbox (badness 10000) detected at line 657 [][][] Underfull \hbox (badness 10000) detected at line 674 [][][] Underfull \hbox (badness 10000) detected at line 691 [][][] Underfull \hbox (badness 10000) detected at line 708 [][][] Underfull \hbox (badness 10000) detected at line 725 [][][] [1129] Underfull \hbox (badness 10000) detected at line 742 [][][] Underfull \hbox (badness 10000) detected at line 759 [][][] Underfull \hbox (badness 10000) detected at line 780 [][][] Underfull \hbox (badness 10000) detected at line 783 [][][] Underfull \hbox (badness 10000) detected at line 800 [][][] [1130] Underfull \hbox (badness 10000) detected at line 817 [][][] Underfull \hbox (badness 10000) detected at line 834 [][][] Underfull \hbox (badness 10000) detected at line 851 [][][] Underfull \hbox (badness 10000) detected at line 868 [][][] Underfull \hbox (badness 10000) detected at line 881 [][][] [1131] Underfull \hbox (badness 10000) detected at line 894 [][][] Underfull \hbox (badness 10000) detected at line 911 [][][] [1132] Underfull \hbox (badness 10000) detected at line 955 [][][] Underfull \hbox (badness 10000) detected at line 985 [][][] [1133] Underfull \hbox (badness 10000) detected at line 1007 [][][] Underfull \hbox (badness 10000) detected at line 1029 [][][] Underfull \hbox (badness 10000) detected at line 1051 [][][] Underfull \hbox (badness 10000) detected at line 1054 [][][] Underfull \hbox (badness 10000) detected at line 1071 [][][] [1134] Underfull \hbox (badness 10000) detected at line 1074 [][][] Underfull \hbox (badness 10000) detected at line 1096 [][][] Underfull \hbox (badness 10000) detected at line 1099 [][][] Underfull \hbox (badness 10000) detected at line 1121 [][][] Underfull \hbox (badness 10000) detected at line 1124 [][][] [1135] Underfull \hbox (badness 10000) detected at line 1156 [][][] Underfull \hbox (badness 10000) detected at line 1173 [][][] [1136] Underfull \hbox (badness 10000) detected at line 1205 [][][] Underfull \hbox (badness 10000) detected at line 1208 [][][] ) (./vpmg_8h_source.tex [1137] [1138] [1139] [1140] [1141] [1142] [1143] [1144]) (./vpmgp_8c.tex <./vpmgp_8c__incl.pdf> [1145] [1146] Underfull \hbox (badness 10000) detected at line 38 [][][] Underfull \hbox (badness 10000) detected at line 41 [][][] Underfull \hbox (badness 10000) detected at line 44 [][][] [1147]) (./vpmgp_8c_source.tex [1148] [1149] [1150]) (./vpmgp_8h.tex <./vpmgp_8 h__incl.pdf> [1151] <./vpmgp_8h__dep__incl.pdf> [1152] [1153] Underfull \hbox (badness 10000) detected at line 56 [][][] Underfull \hbox (badness 10000) detected at line 59 [][][] Underfull \hbox (badness 10000) detected at line 62 [][][] Underfull \hbox (badness 10000) detected at line 65 [][][] [1154]) (./vpmgp_8h_source.tex [1155]) (./build_ad_8c_source.tex [1156] [1157] [1158]) (./build_ad_8h_source.tex [1159]) (./build_bd_8c_source.tex [1160] [1161] [1162] [1163]) (./build_bd_8h_source.tex [1164]) (./build_gd_8c_source.tex [1165] [1166] [1167] [1168] [1169] [1170] [1171] [1172] [1173] [1174] [1175] [1176] [1177] [1178] [1179] [1180] [1181] [1182] [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] [1191] [1192] [1193] [1194] [1195] [1196] [1197] [1198] [1199] [1200] [1201] [1202]) (./build_gd_8h_source.tex [1203] [1204]) (./build_pd_8c_source.tex [1205] [1206] [1207] [1208] [1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216] [1217] [1218] [1219] [1220] [1221] [1222] [1223]) (./build_pd_8h_source.tex [1224] [1225] [1226]) (./cgd_8c_source.tex) (./cgd_8h_source.tex [1227]) (./gsd_8c_source.tex [1228] [1229] [1230] [1231]) (./gsd_8h_source.tex [1232]) (./matvecd_8c_source.tex [1233] [1234] [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242] [1243] [1244] [1245]) (./matvecd_8h_source.tex [1246] [1247] [1248] [1249] [1250] [1251]) (./mgcsd_8c_source.tex [1252] [1253] [1254] [1255] [1256] [1257]) (./mgcsd_8h_source.tex [1258]) (./mgdrvd_8c_source.tex [1259] [1260] [1261] [1262] [1263] [1264] [1265]) (./mgdrvd_8h_source.tex [1266] [1267]) (./mgfasd_8c_source.tex [1268] [1269] [1270] [1271] [1272] [1273]) (./mgfasd_8h_source.tex [1274] [1275]) (./mgsubd_8c_source.tex [1276] [1277] [1278] [1279] [1280] [1281] [1282] [1283] [1284] [1285] [1286]) (./mgsubd_8h_source.tex [1287] [1288] [1289] [1290]) (./mikpckd_8c_source.tex [1291] [1292] [1293] [1294]) (./mikpckd_8h_source.tex [1295] [1296] [1297]) (./mlinpckd_8c_source.tex [1298] [1299]) (./mlinpckd_8h_source.tex) (./mypdec_8c_source.tex [1300] [1301] [1302] [1303] [1304] [1305] [1306]) (./mypdec_8h_source.tex [1307]) (./newdrvd_8c_source.tex [1308] [1309] [1310] [1311]) (./newdrvd_8h_source.tex [1312]) (./newtond_8c_source.tex [1313] [1314] [1315] [1316] [1317] [1318] [1319]) (./newtond_8h_source.tex [1320]) (./powerd_8c_source.tex [1321] [1322] [1323] [1324] [1325]) (./powerd_8h_source.tex [1326]) (./smoothd_8c_source.tex [1327]) (./smoothd_8h_source.tex [1328]) (./routines_8c.tex <./routines_8c__incl.pdf> [1329] Underfull \hbox (badness 776) in paragraph at lines 47--48 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv /m/n/10 alist[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[] Underfull \hbox (badness 2856) in paragraph at lines 47--48 \T1/phv/m/n/10 YMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]ZMap[] [][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 kappa[]Map[][][], [] Underfull \hbox (badness 1237) in paragraph at lines 47--48 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 charge[]Map[][][], [] $\OMS/cmsy/m/n/10 ^^C $\T1/phv/m/n/10 pmgp[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pmg[][][], [] Underfull \hbox (badness 905) in paragraph at lines 61--62 []\T1/phv/m/n/10 VPUBLIC void [] (Vmem $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 mem , [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, int nforce[][][], [] $\OMS/cmsy /m/n/10 ^^C$\T1/phv/m/n/10 atom[] Underfull \hbox (badness 5817) in paragraph at lines 67--68 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], Underfull \hbox (badness 5817) in paragraph at lines 69--70 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], [1330] Underfull \hbox (badness 1442) in paragraph at lines 81--82 []\T1/phv/m/n/10 VPUBLIC int [] (Vcom $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 com, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, int nforce[][][], [] $\OMS/cmsy/ m/n/10 ^^C$\T1/phv/m/n/10 atom[] Underfull \hbox (badness 931) in paragraph at lines 87--88 []\T1/phv/m/n/10 VPUBLIC void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T 1/phv/m/n/10 fetk[][][], Gem Underfull \hbox (badness 2495) in paragraph at lines 89--90 []\T1/phv/m/n/10 VPUBLIC Vrc[]_[][]Codes [] (int icalc, [] $\OMS/cmsy/m/n/10 ^^ C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 feparm, [] $\OMS /cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbeparm, [] [1331] Underfull \hbox (badness 10000) detected at line 116 [][][] Underfull \hbox (badness 10000) detected at line 119 [][][] Underfull \hbox (badness 10000) detected at line 122 [][][] ) (./routines_8c_source.tex [1332] [1333] [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341] [1342] [1343] [1344] [1345] [1346] [1347] [1348] [1349] [1350] [1351] [1352] [1353] [1354] [1355] [1356] [1357] [1358] [1359] [1360] [1361] [1362] [1363] [1364] [1365] [1366] [1367] [1368] [1369] [1370] [1371] [1372] [1373] [1374] [1375] [1376] [1377] [1378] [1379] [1380] [1381] [1382] [1383] [1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] [1392] [1393] [1394] [1395] [1396] [1397] [1398] [1399] [1400]) (./routines_8h.tex <./routine s_8h__incl.pdf> <./routines_8h__dep__incl.pdf> [1401] Overfull \hbox (16.65858pt too wide) in paragraph at lines 50--51 []\T1/phv/m/n/10 VEXTERNC int [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], Overfull \hbox (16.91972pt too wide) in paragraph at lines 52--53 []\T1/phv/m/n/10 VEXTERNC void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh , [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/1 0 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], Underfull \hbox (badness 1910) in paragraph at lines 70--71 [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1 /phv/m/n/10 alist[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][] [], [] Underfull \hbox (badness 1237) in paragraph at lines 70--71 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 charge[]Map[][][], [] $\OMS/cmsy/m/n/10 ^^C $\T1/phv/m/n/10 pmgp[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pmg[][][], [] [1402] Underfull \hbox (badness 5817) in paragraph at lines 88--89 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], Underfull \hbox (badness 5817) in paragraph at lines 90--91 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], [1403] Underfull \hbox (badness 2495) in paragraph at lines 122--123 []\T1/phv/m/n/10 VPUBLIC Vrc[]_[][]Codes [] (int icalc, [] $\OMS/cmsy/m/n/10 ^^ C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 feparm, [] $\OMS /cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbeparm, [] Underfull \hbox (badness 10000) detected at line 145 [][][] Underfull \hbox (badness 10000) detected at line 148 [][][] Underfull \hbox (badness 10000) detected at line 151 [][][] [1404]) (./routines_8h_source.tex [1405] [1406] [1407] [1408] [1409]) [1410] (./refman.ind [1411] [1412] [1413] [1414] [1415] [1416] [1417] [1418] [1419] [1420] [1421] [1422] [1423] [1424] [1425] [1426] [1427] [1428] [1429] [1430] [1431] [1432] [1433] [1434] [1435] [1436] [1437] [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] [1449] [1450] [1451] [1452] [1453] [1454] [1455] [1456] [1457] [1458] [1459]) (./refman.aux) ) (see the transcript file for additional information)< /usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrro8a.pfb> Output written on refman.pdf (1517 pages, 6288270 bytes). Transcript written on refman.log. This is makeindex, version 2.17 [TeX Live 2023] (kpathsea + Thai support). Scanning input file refman.idx.......done (3687 entries accepted, 0 rejected). Sorting entries...................................done (46845 comparisons). Generating output file refman.ind.......done (5317 lines written, 0 warnings). Output written in refman.ind. Transcript written in refman.ilg. 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(/usr/share/texlive/texmf-dist/tex/latex/wasysym/uwasy.fd) [1{/var/lib/texmf/fo nts/map/pdftex/updmap/pdftex.map}{/usr/share/texlive/texmf-dist/fonts/enc/dvips /base/8r.enc}] [2] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] (./index.tex Chapter 1. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1phv.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [1] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [2]) (./bug.tex [3] [4] Chapter 2. [5] [6]) (./deprecated.tex [7] [8] Chapter 3. ) [9] [10] Chapter 4. (./modules.tex) [11] [12] Chapter 5. (./annotated.tex [13]) [14] Chapter 6. (./files.tex [15] [16] [17]) [18] Chapter 7. (./group___header.tex) (./group___vcsm.tex [19] Underfull \hbox (badness 10000) detected at line 93 [][][] [20] Underfull \hbox (badness 10000) detected at line 113 [][][] Underfull \hbox (badness 10000) detected at line 116 [][][] Underfull \hbox (badness 10000) detected at line 121 [][][] Underfull \hbox (badness 10000) detected at line 145 [][][] Underfull \hbox (badness 10000) detected at line 148 [][][] Underfull \hbox (badness 10000) detected at line 153 [][][] [21] Underfull \hbox (badness 10000) detected at line 179 [][][] Underfull \hbox (badness 10000) detected at line 201 [][][] Underfull \hbox (badness 10000) detected at line 223 [][][] Underfull \hbox (badness 10000) detected at line 226 [][][] Overfull \vbox (4.57304pt too high) has occurred while \output is active [22] Underfull \hbox (badness 10000) detected at line 252 [][][] Underfull \hbox (badness 10000) detected at line 255 [][][] Underfull \hbox (badness 10000) detected at line 281 [][][] Underfull \hbox (badness 10000) detected at line 284 [][][] [23] Underfull \hbox (badness 10000) detected at line 308 [][][] Underfull \hbox (badness 10000) detected at line 311 [][][] Underfull \hbox (badness 10000) detected at line 335 [][][] Underfull \hbox (badness 10000) detected at line 338 [][][] Underfull \hbox (badness 10000) detected at line 364 [][][] Underfull \hbox (badness 10000) detected at line 367 [][][] [24] Underfull \hbox (badness 10000) detected at line 393 [][][] Underfull \hbox (badness 10000) detected at line 396 [][][] Underfull \hbox (badness 10000) detected at line 418 [][][] Underfull \hbox (badness 10000) detected at line 421 [][][] [25] Underfull \hbox (badness 10000) detected at line 443 [][][] Underfull \hbox (badness 10000) detected at line 446 [][][] Underfull \hbox (badness 10000) detected at line 468 [][][] Underfull \hbox (badness 10000) detected at line 471 [][][] ) (./group___vfetk.tex [26] [27] [28] [29] [30] Underfull \hbox (badness 10000) detected at line 304 [][][] Underfull \hbox (badness 10000) detected at line 335 [][][] [31] Underfull \hbox (badness 10000) detected at line 398 [][][] Underfull \hbox (badness 10000) detected at line 429 [][][] Underfull \hbox (badness 10000) detected at line 463 [][][] Underfull \hbox (badness 10000) detected at line 466 [][][] [32] Underfull \hbox (badness 10000) detected at line 492 [][][] Underfull \hbox (badness 10000) detected at line 495 [][][] Underfull \hbox (badness 10000) detected at line 498 [][][] Underfull \hbox (badness 10000) detected at line 522 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] Underfull \hbox (badness 10000) detected at line 528 [][][] [33] Underfull \hbox (badness 10000) detected at line 559 [][][] Underfull \hbox (badness 10000) detected at line 569 [][][] [34] Underfull \hbox (badness 10000) detected at line 593 [][][] Underfull \hbox (badness 10000) detected at line 615 [][][] Underfull \hbox (badness 10000) detected at line 637 [][][] [35] Underfull \hbox (badness 10000) detected at line 658 [][][] Underfull \hbox (badness 10000) detected at line 661 [][][] Underfull \hbox (badness 10000) detected at line 668 [][][] Underfull \hbox (badness 10000) detected at line 671 [][][] Underfull \hbox (badness 10000) detected at line 701 [][][] [36] Underfull \hbox (badness 10000) detected at line 727 [][][] Underfull \hbox (badness 10000) detected at line 730 [][][] Underfull \hbox (badness 10000) detected at line 735 [][][] Underfull \hbox (badness 10000) detected at line 761 [][][] [37] Underfull \hbox (badness 10000) detected at line 789 [][][] Underfull \hbox (badness 10000) detected at line 792 [][][] Underfull \hbox (badness 10000) detected at line 814 [][][] Underfull \hbox (badness 10000) detected at line 817 [][][] Underfull \hbox (badness 10000) detected at line 820 [][][] [38] Underfull \hbox (badness 10000) detected at line 844 [][][] Underfull \hbox (badness 10000) detected at line 847 [][][] Underfull \hbox (badness 10000) detected at line 869 [][][] Underfull \hbox (badness 10000) detected at line 872 [][][] Underfull \hbox (badness 10000) detected at line 875 [][][] Underfull \hbox (badness 10000) detected at line 899 [][][] Underfull \hbox (badness 10000) detected at line 902 [][][] [39] Underfull \hbox (badness 10000) detected at line 924 [][][] Underfull \hbox (badness 10000) detected at line 927 [][][] Underfull \hbox (badness 10000) detected at line 949 [][][] [40] Underfull \hbox (badness 10000) detected at line 969 [][][] Underfull \hbox (badness 10000) detected at line 999 [][][] Underfull \hbox (badness 10000) detected at line 1002 [][][] Underfull \hbox (badness 10000) detected at line 1024 [][][] Underfull \hbox (badness 10000) detected at line 1027 [][][] [41] Underfull \hbox (badness 10000) detected at line 1053 [][][] Underfull \hbox (badness 10000) detected at line 1056 [][][] Underfull \hbox (badness 10000) detected at line 1080 [][][] Underfull \hbox (badness 10000) detected at line 1083 [][][] [42] Underfull \hbox (badness 10000) detected at line 1109 [][][] Underfull \hbox (badness 10000) detected at line 1146 [][][] Underfull \hbox (badness 10000) detected at line 1149 [][][] [43] Underfull \hbox (badness 10000) detected at line 1179 [][][] Underfull \hbox (badness 10000) detected at line 1182 [][][] Underfull \hbox (badness 10000) detected at line 1204 [][][] Underfull \hbox (badness 10000) detected at line 1207 [][][] [44] Underfull \hbox (badness 10000) detected at line 1232 [][][] Underfull \hbox (badness 10000) detected at line 1265 [][][] Underfull \hbox (badness 10000) detected at line 1268 [][][] [45] Underfull \hbox (badness 10000) detected at line 1298 [][][] Underfull \hbox (badness 10000) detected at line 1301 [][][] Underfull \hbox (badness 10000) detected at line 1327 [][][] [46] Underfull \hbox (badness 10000) detected at line 1355 [][][] Underfull \hbox (badness 10000) detected at line 1385 [][][] [47] Underfull \hbox (badness 10000) detected at line 1419 [][][] Underfull \hbox (badness 10000) detected at line 1422 [][][] Underfull \hbox (badness 10000) detected at line 1448 [][][] Underfull \hbox (badness 10000) detected at line 1451 [][][] [48] Underfull \hbox (badness 10000) detected at line 1477 [][][] Underfull \hbox (badness 10000) detected at line 1480 [][][] [49] Underfull \hbox (badness 10000) detected at line 1514 [][][] Underfull \hbox (badness 10000) detected at line 1517 [][][] Underfull \hbox (badness 10000) detected at line 1545 [][][] [50] Underfull \hbox (badness 10000) detected at line 1579 [][][] Underfull \hbox (badness 10000) detected at line 1582 [][][] [51] [52] Underfull \hbox (badness 10000) detected at line 1665 [][][] Underfull \hbox (badness 10000) detected at line 1699 [][][] Underfull \hbox (badness 10000) detected at line 1702 [][][] [53] Underfull \hbox (badness 10000) detected at line 1745 [][][] Underfull \hbox (badness 10000) detected at line 1755 [][][] Underfull \hbox (badness 10000) detected at line 1779 [][][] Underfull \hbox (badness 10000) detected at line 1782 [][][] Underfull \hbox (badness 10000) detected at line 1785 [][][] [54] Underfull \hbox (badness 10000) detected at line 1807 [][][] Underfull \hbox (badness 10000) detected at line 1810 [][][] Underfull \hbox (badness 10000) detected at line 1813 [][][] Underfull \hbox (badness 10000) detected at line 1835 [][][] [55] Underfull \hbox (badness 10000) detected at line 1861 [][][] Underfull \hbox (badness 10000) detected at line 1881 [][][] Underfull \hbox (badness 10000) detected at line 1886 [][][] ) (./group___vpee.tex [56] Underfull \hbox (badness 849) in paragraph at lines 45--46 \T1/phv/m/n/10 Holst par-al-lel re-fine-ment rou-tine es-sen-tially re-duces th e er-ror out-side the \T1/pcr/m/n/10 local^^D partition to zero. Underfull \hbox (badness 10000) in paragraph at lines 45--46 \T1/pcr/m/n/10 However, this leads to the need for a few final overlapping Schw arz solves to Underfull \hbox (badness 10000) in paragraph at lines 45--46 \T1/pcr/m/n/10 smooth out the errors near partition boundaries. Supposedly, if the region in Underfull \hbox (badness 10000) in paragraph at lines 45--46 \T1/pcr/m/n/10 which we allow error-based refinement includes the$\OML/cmm/m/it /10 <$\T1/pcr/m/n/10 /tt$\OML/cmm/m/it/10 >$\T1/pcr/m/n/10 local^^D partition a nd an Underfull \hbox (badness 10000) in paragraph at lines 45--46 \T1/pcr/m/n/10 external buffer zone approximately equal in size to the local re gion, then the Underfull \hbox (badness 10000) in paragraph at lines 45--46 \T1/pcr/m/n/10 solution will asymptotically approach the solution obtained via more typical Underfull \hbox (badness 10000) in paragraph at lines 45--46 \T1/pcr/m/n/10 methods. This is essentially a more flexible parallel implementa tion of MC\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 s [57] Underfull \hbox (badness 10000) detected at line 75 [][][] Underfull \hbox (badness 10000) detected at line 78 [][][] Underfull \hbox (badness 10000) detected at line 94 [][][] Underfull \hbox (badness 10000) detected at line 111 [][][] [58] Underfull \hbox (badness 10000) detected at line 114 [][][] Underfull \hbox (badness 10000) detected at line 132 [][][] Underfull \hbox (badness 10000) detected at line 149 [][][] Underfull \hbox (badness 10000) detected at line 171 [][][] [59] Underfull \hbox (badness 10000) detected at line 195 [][][] Underfull \hbox (badness 10000) detected at line 198 [][][] Underfull \hbox (badness 10000) detected at line 201 [][][] Overfull \vbox (42.60027pt too high) has occurred while \output is active [60] Underfull \hbox (badness 10000) detected at line 241 [][][] Underfull \hbox (badness 10000) detected at line 244 [][][] ) (./group___a_p_o_lparm.tex [61] Overfull \vbox (22.62613pt too high) has occurred while \output is active [62] Underfull \hbox (badness 10000) detected at line 212 [][][] Underfull \hbox (badness 10000) detected at line 220 [][][] [63] Underfull \hbox (badness 10000) detected at line 237 [][][] Underfull \hbox (badness 10000) detected at line 261 [][][] Underfull \hbox (badness 10000) detected at line 264 [][][] Underfull \hbox (badness 10000) detected at line 281 [][][] Underfull \hbox (badness 10000) detected at line 289 [][][] [64] Underfull \hbox (badness 10000) detected at line 306 [][][] Underfull \hbox (badness 10000) detected at line 328 [][][] ) (./group___b_e_mparm.tex [65] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] [66] Underfull \hbox (badness 10000) detected at line 125 [][][] Underfull \hbox (badness 10000) detected at line 133 [][][] Underfull \hbox (badness 10000) detected at line 150 [][][] Underfull \hbox (badness 10000) detected at line 158 [][][] Underfull \hbox (badness 10000) detected at line 175 [][][] [67] Underfull \hbox (badness 10000) detected at line 185 [][][] Underfull \hbox (badness 10000) detected at line 202 [][][] Underfull \hbox (badness 10000) detected at line 224 [][][] Underfull \hbox (badness 10000) detected at line 246 [][][] [68] Underfull \hbox (badness 10000) detected at line 258 [][][] ) (./group___f_e_mparm.tex [69] Underfull \hbox (badness 10000) detected at line 111 [][][] [70] Underfull \hbox (badness 10000) detected at line 155 [][][] Underfull \hbox (badness 10000) detected at line 158 [][][] Underfull \hbox (badness 10000) detected at line 197 [][][] Underfull \hbox (badness 10000) detected at line 231 [][][] [71] Underfull \hbox (badness 10000) detected at line 239 [][][] Underfull \hbox (badness 10000) detected at line 256 [][][] Underfull \hbox (badness 10000) detected at line 280 [][][] Underfull \hbox (badness 10000) detected at line 288 [][][] [72] Underfull \hbox (badness 10000) detected at line 305 [][][] Underfull \hbox (badness 10000) detected at line 315 [][][] Underfull \hbox (badness 10000) detected at line 332 [][][] Underfull \hbox (badness 10000) detected at line 354 [][][] ) (./group___g_e_o_f_l_o_wparm.tex [73] Underfull \hbox (badness 10000) detected at line 68 [][][] [74] Underfull \hbox (badness 10000) detected at line 71 [][][] Underfull \hbox (badness 10000) detected at line 124 [][][] Underfull \hbox (badness 10000) detected at line 132 [][][] [75] Underfull \hbox (badness 10000) detected at line 149 [][][] Underfull \hbox (badness 10000) detected at line 173 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 198 [][][] Underfull \hbox (badness 10000) detected at line 208 [][][] [76] Underfull \hbox (badness 10000) detected at line 225 [][][] Underfull \hbox (badness 10000) detected at line 247 [][][] Underfull \hbox (badness 10000) detected at line 269 [][][] [77] Underfull \hbox (badness 10000) detected at line 281 [][][] ) (./group___m_gparm.tex [78] [79] Underfull \hbox (badness 10000) detected at line 205 [][][] [80] Underfull \hbox (badness 10000) detected at line 217 [][][] Underfull \hbox (badness 10000) detected at line 234 [][][] Underfull \hbox (badness 10000) detected at line 246 [][][] Underfull \hbox (badness 10000) detected at line 263 [][][] Underfull \hbox (badness 10000) detected at line 271 [][][] [81] Underfull \hbox (badness 10000) detected at line 288 [][][] Underfull \hbox (badness 10000) detected at line 312 [][][] Underfull \hbox (badness 10000) detected at line 320 [][][] Underfull \hbox (badness 10000) detected at line 337 [][][] Underfull \hbox (badness 10000) detected at line 347 [][][] [82] Underfull \hbox (badness 10000) detected at line 364 [][][] Underfull \hbox (badness 10000) detected at line 386 [][][] Underfull \hbox (badness 10000) detected at line 408 [][][] Underfull \hbox (badness 10000) detected at line 416 [][][] [83] Underfull \hbox (badness 10000) detected at line 433 [][][] Underfull \hbox (badness 10000) detected at line 441 [][][] Underfull \hbox (badness 10000) detected at line 458 [][][] Underfull \hbox (badness 10000) detected at line 466 [][][] Underfull \hbox (badness 10000) detected at line 483 [][][] Underfull \hbox (badness 10000) detected at line 491 [][][] [84] Underfull \hbox (badness 10000) detected at line 508 [][][] Underfull \hbox (badness 10000) detected at line 516 [][][] Underfull \hbox (badness 10000) detected at line 533 [][][] Underfull \hbox (badness 10000) detected at line 541 [][][] Underfull \hbox (badness 10000) detected at line 558 [][][] [85] Underfull \hbox (badness 10000) detected at line 566 [][][] Underfull \hbox (badness 10000) detected at line 583 [][][] Underfull \hbox (badness 10000) detected at line 591 [][][] Underfull \hbox (badness 10000) detected at line 608 [][][] Underfull \hbox (badness 10000) detected at line 616 [][][] Underfull \hbox (badness 10000) detected at line 633 [][][] [86] Underfull \hbox (badness 10000) detected at line 645 [][][] Underfull \hbox (badness 10000) detected at line 662 [][][] Underfull \hbox (badness 10000) detected at line 686 [][][] [87] Underfull \hbox (badness 10000) detected at line 710 [][][] ) (./group___n_osh.tex [88] [89] [90] [91] [92] Underfull \hbox (badness 10000) detected at line 431 [][][] Underfull \hbox (badness 10000) detected at line 441 [][][] Underfull \hbox (badness 10000) detected at line 458 [][][] Underfull \hbox (badness 10000) detected at line 482 [][][] [93] Underfull \hbox (badness 10000) detected at line 490 [][][] Underfull \hbox (badness 10000) detected at line 507 [][][] Underfull \hbox (badness 10000) detected at line 529 [][][] Underfull \hbox (badness 10000) detected at line 539 [][][] Underfull \hbox (badness 10000) detected at line 556 [][][] [94] Underfull \hbox (badness 10000) detected at line 568 [][][] Underfull \hbox (badness 10000) detected at line 585 [][][] Underfull \hbox (badness 10000) detected at line 607 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] [95] Underfull \hbox (badness 10000) detected at line 639 [][][] Underfull \hbox (badness 10000) detected at line 656 [][][] Underfull \hbox (badness 10000) detected at line 659 [][][] Underfull \hbox (badness 10000) detected at line 669 [][][] Underfull \hbox (badness 10000) detected at line 672 [][][] Underfull \hbox (badness 10000) detected at line 689 [][][] Overfull \vbox (15.28305pt too high) has occurred while \output is active [96] Underfull \hbox (badness 10000) detected at line 699 [][][] Underfull \hbox (badness 10000) detected at line 716 [][][] Underfull \hbox (badness 10000) detected at line 726 [][][] Underfull \hbox (badness 10000) detected at line 743 [][][] Underfull \hbox (badness 10000) detected at line 753 [][][] [97] Underfull \hbox (badness 10000) detected at line 770 [][][] Underfull \hbox (badness 10000) detected at line 780 [][][] Underfull \hbox (badness 10000) detected at line 797 [][][] Underfull \hbox (badness 10000) detected at line 807 [][][] Underfull \hbox (badness 10000) detected at line 824 [][][] [98] Underfull \hbox (badness 10000) detected at line 834 [][][] Underfull \hbox (badness 10000) detected at line 851 [][][] Underfull \hbox (badness 10000) detected at line 861 [][][] Underfull \hbox (badness 10000) detected at line 878 [][][] Underfull \hbox (badness 10000) detected at line 888 [][][] [99] Underfull \hbox (badness 10000) detected at line 905 [][][] Underfull \hbox (badness 10000) detected at line 915 [][][] Underfull \hbox (badness 10000) detected at line 932 [][][] Underfull \hbox (badness 10000) detected at line 942 [][][] Underfull \hbox (badness 10000) detected at line 959 [][][] [100] Underfull \hbox (badness 10000) detected at line 969 [][][] Underfull \hbox (badness 10000) detected at line 986 [][][] Underfull \hbox (badness 10000) detected at line 996 [][][] Underfull \hbox (badness 10000) detected at line 1013 [][][] Underfull \hbox (badness 10000) detected at line 1016 [][][] Underfull \hbox (badness 10000) detected at line 1026 [][][] [101] Underfull \hbox (badness 10000) detected at line 1043 [][][] Underfull \hbox (badness 10000) detected at line 1048 [][][] Underfull \hbox (badness 10000) detected at line 1058 [][][] Underfull \hbox (badness 10000) detected at line 1075 [][][] Underfull \hbox (badness 10000) detected at line 1078 [][][] [102] Underfull \hbox (badness 10000) detected at line 1090 [][][] Underfull \hbox (badness 10000) detected at line 1093 [][][] Underfull \hbox (badness 10000) detected at line 1110 [][][] Underfull \hbox (badness 10000) detected at line 1113 [][][] Underfull \hbox (badness 10000) detected at line 1123 [][][] Underfull \hbox (badness 10000) detected at line 1126 [][][] Underfull \hbox (badness 10000) detected at line 1143 [][][] Underfull \hbox (badness 10000) detected at line 1146 [][][] [103] Underfull \hbox (badness 10000) detected at line 1158 [][][] Underfull \hbox (badness 10000) detected at line 1161 [][][] Underfull \hbox (badness 10000) detected at line 1178 [][][] Underfull \hbox (badness 10000) detected at line 1181 [][][] Underfull \hbox (badness 10000) detected at line 1191 [][][] Underfull \hbox (badness 10000) detected at line 1194 [][][] Underfull \hbox (badness 10000) detected at line 1211 [][][] [104] Underfull \hbox (badness 10000) detected at line 1214 [][][] Underfull \hbox (badness 10000) detected at line 1224 [][][] Underfull \hbox (badness 10000) detected at line 1248 [][][] Underfull \hbox (badness 10000) detected at line 1251 [][][] Underfull \hbox (badness 10000) detected at line 1261 [][][] Overfull \vbox (3.94589pt too high) has occurred while \output is active [105]) (./group___p_b_a_mparm.tex [106] Underfull \hbox (badness 10000) detected at line 116 [][][] Underfull \hbox (badness 10000) detected at line 119 [][][] [107] Underfull \hbox (badness 10000) detected at line 172 [][][] Underfull \hbox (badness 10000) detected at line 180 [][][] Underfull \hbox (badness 10000) detected at line 197 [][][] [108] Underfull \hbox (badness 10000) detected at line 221 [][][] Underfull \hbox (badness 10000) detected at line 229 [][][] Underfull \hbox (badness 10000) detected at line 246 [][][] Underfull \hbox (badness 10000) detected at line 256 [][][] [109] Underfull \hbox (badness 10000) detected at line 273 [][][] Underfull \hbox (badness 10000) detected at line 295 [][][] Underfull \hbox (badness 10000) detected at line 317 [][][] Underfull \hbox (badness 10000) detected at line 341 [][][] [110] Underfull \hbox (badness 10000) detected at line 365 [][][] Underfull \hbox (badness 10000) detected at line 389 [][][] Underfull \hbox (badness 10000) detected at line 413 [][][] [111] Underfull \hbox (badness 10000) detected at line 437 [][][] Underfull \hbox (badness 10000) detected at line 461 [][][] Underfull \hbox (badness 10000) detected at line 485 [][][] [112] Underfull \hbox (badness 10000) detected at line 509 [][][] Underfull \hbox (badness 10000) detected at line 533 [][][] Underfull \hbox (badness 10000) detected at line 557 [][][] [113] Underfull \hbox (badness 10000) detected at line 581 [][][] Underfull \hbox (badness 10000) detected at line 593 [][][] Underfull \hbox (badness 10000) detected at line 610 [][][] [114] Underfull \hbox (badness 10000) detected at line 634 [][][] ) (./group___p_b_eparm.tex [115] [116] Underfull \hbox (badness 10000) detected at line 209 [][][] Underfull \hbox (badness 10000) detected at line 212 [][][] [117] Underfull \hbox (badness 10000) detected at line 234 [][][] Underfull \hbox (badness 10000) detected at line 258 [][][] Underfull \hbox (badness 10000) detected at line 261 [][][] Underfull \hbox (badness 10000) detected at line 278 [][][] Underfull \hbox (badness 10000) detected at line 281 [][][] [118] Underfull \hbox (badness 10000) detected at line 303 [][][] Underfull \hbox (badness 10000) detected at line 325 [][][] Underfull \hbox (badness 10000) detected at line 347 [][][] Underfull \hbox (badness 10000) detected at line 350 [][][] [119] Underfull \hbox (badness 10000) detected at line 374 [][][] Underfull \hbox (badness 10000) detected at line 377 [][][] Underfull \hbox (badness 10000) detected at line 401 [][][] Underfull \hbox (badness 10000) detected at line 404 [][][] Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 431 [][][] [120]) (./group___p_b_s_a_mparm.tex [121] Underfull \hbox (badness 10000) detected at line 100 [][][] Underfull \hbox (badness 10000) detected at line 103 [][][] [122] Underfull \hbox (badness 10000) detected at line 156 [][][] Underfull \hbox (badness 10000) detected at line 164 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] [123] Underfull \hbox (badness 10000) detected at line 205 [][][] Underfull \hbox (badness 10000) detected at line 213 [][][] Underfull \hbox (badness 10000) detected at line 230 [][][] Underfull \hbox (badness 10000) detected at line 240 [][][] Underfull \hbox (badness 10000) detected at line 257 [][][] Overfull \vbox (0.37224pt too high) has occurred while \output is active [124] Underfull \hbox (badness 10000) detected at line 279 [][][] Underfull \hbox (badness 10000) detected at line 301 [][][] Underfull \hbox (badness 10000) detected at line 325 [][][] [125] Underfull \hbox (badness 10000) detected at line 349 [][][] Underfull \hbox (badness 10000) detected at line 373 [][][] Underfull \hbox (badness 10000) detected at line 397 [][][] [126] Underfull \hbox (badness 10000) detected at line 409 [][][] Underfull \hbox (badness 10000) detected at line 426 [][][] ) (./group___vacc.tex [127] [128] [129] Underfull \hbox (badness 10000) detected at line 149 [][][] Underfull \hbox (badness 10000) detected at line 179 [][][] [130] Underfull \hbox (badness 10000) detected at line 207 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] Underfull \hbox (badness 10000) detected at line 213 [][][] Underfull \hbox (badness 10000) detected at line 239 [][][] Underfull \hbox (badness 10000) detected at line 242 [][][] [131] Underfull \hbox (badness 10000) detected at line 268 [][][] Underfull \hbox (badness 10000) detected at line 271 [][][] Underfull \hbox (badness 10000) detected at line 283 [][][] Underfull \hbox (badness 10000) detected at line 305 [][][] Underfull \hbox (badness 10000) detected at line 308 [][][] [132] Underfull \hbox (badness 10000) detected at line 334 [][][] Underfull \hbox (badness 10000) detected at line 337 [][][] Underfull \hbox (badness 10000) detected at line 365 [][][] Underfull \hbox (badness 10000) detected at line 387 [][][] [133] Underfull \hbox (badness 10000) detected at line 411 [][][] Underfull \hbox (badness 10000) detected at line 414 [][][] Underfull \hbox (badness 10000) detected at line 417 [][][] Underfull \hbox (badness 10000) detected at line 447 [][][] Underfull \hbox (badness 10000) detected at line 450 [][][] [134] Underfull \hbox (badness 10000) detected at line 472 [][][] Underfull \hbox (badness 10000) detected at line 475 [][][] Underfull \hbox (badness 10000) detected at line 499 [][][] Underfull \hbox (badness 10000) detected at line 502 [][][] [135] Underfull \hbox (badness 10000) detected at line 530 [][][] Underfull \hbox (badness 10000) detected at line 533 [][][] Underfull \hbox (badness 10000) detected at line 536 [][][] Underfull \hbox (badness 10000) detected at line 562 [][][] Underfull \hbox (badness 10000) detected at line 565 [][][] [136] Underfull \hbox (badness 10000) detected at line 595 [][][] Underfull \hbox (badness 10000) detected at line 598 [][][] Underfull \hbox (badness 10000) detected at line 628 [][][] [137] Underfull \hbox (badness 10000) detected at line 660 [][][] Underfull \hbox (badness 10000) detected at line 692 [][][] [138] Underfull \hbox (badness 10000) detected at line 724 [][][] Underfull \hbox (badness 10000) detected at line 758 [][][] [139] Underfull \hbox (badness 10000) detected at line 790 [][][] Underfull \hbox (badness 10000) detected at line 820 [][][] [140] Underfull \hbox (badness 10000) detected at line 852 [][][] Underfull \hbox (badness 10000) detected at line 855 [][][] Underfull \hbox (badness 10000) detected at line 858 [][][] Underfull \hbox (badness 10000) detected at line 882 [][][] Underfull \hbox (badness 10000) detected at line 885 [][][] Underfull \hbox (badness 10000) detected at line 888 [][][] [141] Underfull \hbox (badness 10000) detected at line 918 [][][] Underfull \hbox (badness 10000) detected at line 921 [][][] Underfull \hbox (badness 10000) detected at line 941 [][][] Underfull \hbox (badness 10000) detected at line 944 [][][] Overfull \vbox (21.5778pt too high) has occurred while \output is active [142] Underfull \hbox (badness 10000) detected at line 972 [][][] Underfull \hbox (badness 10000) detected at line 975 [][][] Underfull \hbox (badness 10000) detected at line 1007 [][][] Underfull \hbox (badness 10000) detected at line 1010 [][][] [143] Underfull \hbox (badness 10000) detected at line 1040 [][][] Underfull \hbox (badness 10000) detected at line 1043 [][][] Underfull \hbox (badness 10000) detected at line 1069 [][][] Underfull \hbox (badness 10000) detected at line 1072 [][][] Overfull \vbox (18.93095pt too high) has occurred while \output is active [144] Underfull \hbox (badness 10000) detected at line 1100 [][][] Underfull \hbox (badness 10000) detected at line 1122 [][][] Underfull \hbox (badness 10000) detected at line 1146 [][][] Underfull \hbox (badness 10000) detected at line 1149 [][][] Underfull \hbox (badness 10000) detected at line 1152 [][][] [145]) (./group___valist.tex [146] Underfull \hbox (badness 10000) detected at line 91 [][][] Underfull \hbox (badness 10000) detected at line 94 [][][] Underfull \hbox (badness 10000) detected at line 111 [][][] Underfull \hbox (badness 10000) detected at line 114 [][][] Overfull \vbox (3.49948pt too high) has occurred while \output is active [147] Underfull \hbox (badness 10000) detected at line 136 [][][] Underfull \hbox (badness 10000) detected at line 158 [][][] Underfull \hbox (badness 10000) detected at line 180 [][][] Underfull \hbox (badness 10000) detected at line 183 [][][] [148] Underfull \hbox (badness 10000) detected at line 207 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] Underfull \hbox (badness 10000) detected at line 232 [][][] Underfull \hbox (badness 10000) detected at line 235 [][][] Underfull \hbox (badness 10000) detected at line 257 [][][] Underfull \hbox (badness 10000) detected at line 260 [][][] [149] Underfull \hbox (badness 10000) detected at line 282 [][][] Underfull \hbox (badness 10000) detected at line 285 [][][] Underfull \hbox (badness 10000) detected at line 307 [][][] Underfull \hbox (badness 10000) detected at line 310 [][][] Underfull \hbox (badness 10000) detected at line 332 [][][] [150] Underfull \hbox (badness 10000) detected at line 335 [][][] Underfull \hbox (badness 10000) detected at line 352 [][][] Underfull \hbox (badness 10000) detected at line 355 [][][] Underfull \hbox (badness 10000) detected at line 377 [][][] Underfull \hbox (badness 10000) detected at line 380 [][][] Underfull \hbox (badness 10000) detected at line 383 [][][] [151] Underfull \hbox (badness 10000) detected at line 409 [][][] Underfull \hbox (badness 10000) detected at line 412 [][][] Underfull \hbox (badness 10000) detected at line 415 [][][] Underfull \hbox (badness 10000) detected at line 443 [][][] Underfull \hbox (badness 10000) detected at line 446 [][][] Underfull \hbox (badness 10000) detected at line 449 [][][] Overfull \vbox (15.85518pt too high) has occurred while \output is active [152]) (./group___vatom.tex [153] Underfull \hbox (badness 10000) detected at line 97 [][][] [154] Underfull \hbox (badness 10000) detected at line 134 [][][] Underfull \hbox (badness 10000) detected at line 158 [][][] Underfull \hbox (badness 10000) detected at line 182 [][][] Underfull \hbox (badness 10000) detected at line 185 [][][] [155] Underfull \hbox (badness 10000) detected at line 202 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] Underfull \hbox (badness 10000) detected at line 227 [][][] Underfull \hbox (badness 10000) detected at line 249 [][][] Underfull \hbox (badness 10000) detected at line 271 [][][] [156] Underfull \hbox (badness 10000) detected at line 279 [][][] Underfull \hbox (badness 10000) detected at line 296 [][][] Underfull \hbox (badness 10000) detected at line 320 [][][] Underfull \hbox (badness 10000) detected at line 328 [][][] [157] Underfull \hbox (badness 10000) detected at line 345 [][][] Underfull \hbox (badness 10000) detected at line 353 [][][] Underfull \hbox (badness 10000) detected at line 370 [][][] Underfull \hbox (badness 10000) detected at line 378 [][][] Underfull \hbox (badness 10000) detected at line 395 [][][] Underfull \hbox (badness 10000) detected at line 403 [][][] [158] Underfull \hbox (badness 10000) detected at line 420 [][][] Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 445 [][][] Underfull \hbox (badness 10000) detected at line 469 [][][] [159] Underfull \hbox (badness 10000) detected at line 477 [][][] Underfull \hbox (badness 10000) detected at line 494 [][][] Underfull \hbox (badness 10000) detected at line 518 [][][] [160] Underfull \hbox (badness 10000) detected at line 542 [][][] Underfull \hbox (badness 10000) detected at line 566 [][][] Underfull \hbox (badness 10000) detected at line 590 [][][] [161] Underfull \hbox (badness 10000) detected at line 614 [][][] Underfull \hbox (badness 10000) detected at line 638 [][][] Underfull \hbox (badness 10000) detected at line 662 [][][] ) (./group___vcap.tex [162] Underfull \hbox (badness 10000) detected at line 36 [][][] [163] Underfull \hbox (badness 10000) detected at line 86 [][][] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 92 [][][] Underfull \hbox (badness 10000) detected at line 119 [][][] Underfull \hbox (badness 10000) detected at line 122 [][][] Underfull \hbox (badness 10000) detected at line 125 [][][] [164] Underfull \hbox (badness 10000) detected at line 152 [][][] Underfull \hbox (badness 10000) detected at line 155 [][][] Underfull \hbox (badness 10000) detected at line 158 [][][] ) (./group___vclist.tex [165] [166] Underfull \hbox (badness 10000) detected at line 110 [][][] Underfull \hbox (badness 10000) detected at line 140 [][][] Underfull \hbox (badness 10000) detected at line 143 [][][] [167] Underfull \hbox (badness 10000) detected at line 175 [][][] Underfull \hbox (badness 10000) detected at line 178 [][][] Underfull \hbox (badness 10000) detected at line 212 [][][] [168] Underfull \hbox (badness 10000) detected at line 234 [][][] Underfull \hbox (badness 10000) detected at line 256 [][][] Underfull \hbox (badness 10000) detected at line 259 [][][] Underfull \hbox (badness 10000) detected at line 283 [][][] Underfull \hbox (badness 10000) detected at line 286 [][][] [169] Underfull \hbox (badness 10000) detected at line 308 [][][] Underfull \hbox (badness 10000) detected at line 311 [][][] Underfull \hbox (badness 10000) detected at line 333 [][][] Underfull \hbox (badness 10000) detected at line 336 [][][] Underfull \hbox (badness 10000) detected at line 358 [][][] Underfull \hbox (badness 10000) detected at line 361 [][][] [170] Underfull \hbox (badness 10000) detected at line 385 [][][] Underfull \hbox (badness 10000) detected at line 407 [][][] ) (./group___vgreen.tex [171] Underfull \hbox (badness 10000) detected at line 57 [][][] Underfull \hbox (badness 10000) detected at line 60 [][][] [172] [173] Underfull \hbox (badness 10000) detected at line 141 [][][] Underfull \hbox (badness 10000) detected at line 159 [][][] Underfull \hbox (badness 10000) detected at line 178 [][][] [174] Underfull \hbox (badness 10000) detected at line 196 [][][] Underfull \hbox (badness 10000) detected at line 215 [][][] [175] Underfull \hbox (badness 10000) detected at line 239 [][][] Underfull \hbox (badness 10000) detected at line 258 [][][] Underfull \hbox (badness 10000) detected at line 282 [][][] [176] Underfull \hbox (badness 10000) detected at line 299 [][][] Underfull \hbox (badness 10000) detected at line 307 [][][] Underfull \hbox (badness 10000) detected at line 324 [][][] Underfull \hbox (badness 10000) detected at line 334 [][][] Underfull \hbox (badness 10000) detected at line 351 [][][] [177] Underfull \hbox (badness 10000) detected at line 373 [][][] Underfull \hbox (badness 10000) detected at line 395 [][][] Underfull \hbox (badness 10000) detected at line 403 [][][] Underfull \hbox (badness 10000) detected at line 424 [][][] [178] Underfull \hbox (badness 10000) detected at line 429 [][][] Underfull \hbox (badness 10000) detected at line 449 [][][] Underfull \hbox (badness 10000) detected at line 471 [][][] Underfull \hbox (badness 10000) detected at line 476 [][][] [179] Underfull \hbox (badness 10000) detected at line 500 [][][] Underfull \hbox (badness 10000) detected at line 517 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] ) (./group___vhal.tex [180] [181] [182] [183] Underfull \hbox (badness 10000) detected at line 380 [][][] Underfull \hbox (badness 10000) detected at line 411 [][][] [184] Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 445 [][][] Underfull \hbox (badness 10000) detected at line 476 [][][] Underfull \hbox (badness 10000) detected at line 493 [][][] Underfull \hbox (badness 10000) detected at line 516 [][][] [185] Underfull \hbox (badness 10000) detected at line 547 [][][] [186] Underfull \hbox (badness 10000) detected at line 682 [][][] Underfull \hbox (badness 10000) detected at line 729 [][][] [187] Underfull \hbox (badness 10000) detected at line 760 [][][] Underfull \hbox (badness 10000) detected at line 795 [][][] Underfull \hbox (badness 10000) detected at line 842 [][][] Missing character: There is no Å in font cmr10! Missing character: There is no Å in font cmr10! LaTeX Warning: Command \r invalid in math mode on input line 58. Missing character: There is no Å in font cmr10! [188] [189] Underfull \hbox (badness 10000) detected at line 1019 [][][] Underfull \hbox (badness 10000) detected at line 1022 [][][] Underfull \hbox (badness 10000) detected at line 1050 [][][] Underfull \hbox (badness 10000) detected at line 1053 [][][] Underfull \hbox (badness 10000) detected at line 1070 [][][] [190]) (./group___vmatrix.tex) (./group___vparam.tex [191] [192] Underfull \hbox (badness 10000) detected at line 120 [][][] Underfull \hbox (badness 10000) detected at line 130 [][][] [193] Underfull \hbox (badness 10000) detected at line 147 [][][] Underfull \hbox (badness 10000) detected at line 157 [][][] Underfull \hbox (badness 10000) detected at line 174 [][][] Underfull \hbox (badness 10000) detected at line 198 [][][] [194] Underfull \hbox (badness 10000) detected at line 222 [][][] Underfull \hbox (badness 10000) detected at line 225 [][][] Underfull \hbox (badness 10000) detected at line 242 [][][] Underfull \hbox (badness 10000) detected at line 250 [][][] Underfull \hbox (badness 10000) detected at line 267 [][][] [195] Underfull \hbox (badness 10000) detected at line 289 [][][] Underfull \hbox (badness 10000) detected at line 311 [][][] Underfull \hbox (badness 10000) detected at line 314 [][][] Underfull \hbox (badness 10000) detected at line 331 [][][] Underfull \hbox (badness 10000) detected at line 339 [][][] Underfull \hbox (badness 10000) detected at line 356 [][][] [196] Underfull \hbox (badness 10000) detected at line 378 [][][] Underfull \hbox (badness 10000) detected at line 400 [][][] Underfull \hbox (badness 10000) detected at line 412 [][][] Underfull \hbox (badness 10000) detected at line 415 [][][] Underfull \hbox (badness 10000) detected at line 418 [][][] [197] Underfull \hbox (badness 10000) detected at line 435 [][][] Underfull \hbox (badness 10000) detected at line 445 [][][] Underfull \hbox (badness 10000) detected at line 448 [][][] Underfull \hbox (badness 10000) detected at line 451 [][][] Underfull \hbox (badness 10000) detected at line 468 [][][] Underfull \hbox (badness 10000) detected at line 476 [][][] [198] Underfull \hbox (badness 10000) detected at line 493 [][][] Underfull \hbox (badness 10000) detected at line 509 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Underfull \hbox (badness 10000) detected at line 537 [][][] [199] Underfull \hbox (badness 10000) detected at line 553 [][][] Underfull \hbox (badness 10000) detected at line 570 [][][] Underfull \hbox (badness 10000) detected at line 594 [][][] Underfull \hbox (badness 10000) detected at line 602 [][][] [200] Underfull \hbox (badness 10000) detected at line 619 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] Underfull \hbox (badness 10000) detected at line 646 [][][] Underfull \hbox (badness 10000) detected at line 668 [][][] [201]) (./group___vpbe.tex [202] [203] Underfull \hbox (badness 10000) detected at line 128 [][][] Underfull \hbox (badness 10000) detected at line 131 [][][] LaTeX Warning: Command \r invalid in math mode on input line 133. Missing character: There is no Å in font cmr10! LaTeX Warning: Command \r invalid in math mode on input line 133. Missing character: There is no Å in font cmr10! [204] Underfull \hbox (badness 10000) detected at line 136 [][][] [205] Underfull \hbox (badness 10000) detected at line 186 [][][] Underfull \hbox (badness 10000) detected at line 189 [][][] LaTeX Warning: Command \r invalid in math mode on input line 190. Missing character: There is no Å in font cmr10! LaTeX Warning: Command \r invalid in math mode on input line 190. Missing character: There is no Å in font cmr10! Underfull \hbox (badness 10000) detected at line 195 [][][] Overfull \vbox (21.60152pt too high) has occurred while \output is active [206] Underfull \hbox (badness 10000) detected at line 247 [][][] Underfull \hbox (badness 10000) detected at line 269 [][][] Underfull \hbox (badness 10000) detected at line 291 [][][] Underfull \hbox (badness 10000) detected at line 299 [][][] [207] Overfull \hbox (151.96916pt too wide) in paragraph at lines 318--318 [] \T1/p cr/m/n/8 permittivity equal to the protein interior) and zero ionic[] Underfull \hbox (badness 10000) detected at line 325 [][][] Underfull \hbox (badness 10000) detected at line 333 [][][] Underfull \hbox (badness 10000) detected at line 350 [][][] Underfull \hbox (badness 10000) detected at line 358 [][][] [208] Underfull \hbox (badness 10000) detected at line 375 [][][] Underfull \hbox (badness 10000) detected at line 383 [][][] Underfull \hbox (badness 10000) detected at line 396 [][][] Underfull \hbox (badness 10000) detected at line 412 [][][] [209] Underfull \hbox (badness 10000) detected at line 436 [][][] Underfull \hbox (badness 10000) detected at line 453 [][][] Underfull \hbox (badness 10000) detected at line 461 [][][] Underfull \hbox (badness 10000) detected at line 478 [][][] Underfull \hbox (badness 10000) detected at line 486 [][][] Underfull \hbox (badness 10000) detected at line 503 [][][] [210] Underfull \hbox (badness 10000) detected at line 525 [][][] Underfull \hbox (badness 10000) detected at line 533 [][][] Underfull \hbox (badness 10000) detected at line 550 [][][] Underfull \hbox (badness 10000) detected at line 558 [][][] Underfull \hbox (badness 10000) detected at line 575 [][][] [211] Underfull \hbox (badness 10000) detected at line 583 [][][] Underfull \hbox (badness 10000) detected at line 600 [][][] Underfull \hbox (badness 10000) detected at line 608 [][][] Underfull \hbox (badness 10000) detected at line 625 [][][] Underfull \hbox (badness 10000) detected at line 633 [][][] [212] Underfull \hbox (badness 10000) detected at line 650 [][][] Underfull \hbox (badness 10000) detected at line 658 [][][] Underfull \hbox (badness 10000) detected at line 675 [][][] Underfull \hbox (badness 10000) detected at line 683 [][][] Underfull \hbox (badness 10000) detected at line 700 [][][] Underfull \hbox (badness 10000) detected at line 708 [][][] [213] Underfull \hbox (badness 10000) detected at line 725 [][][] Underfull \hbox (badness 10000) detected at line 733 [][][] Underfull \hbox (badness 10000) detected at line 750 [][][] Underfull \hbox (badness 10000) detected at line 758 [][][] Underfull \hbox (badness 10000) detected at line 775 [][][] [214] Underfull \hbox (badness 10000) detected at line 783 [][][] Underfull \hbox (badness 10000) detected at line 800 [][][] Underfull \hbox (badness 10000) detected at line 808 [][][] Underfull \hbox (badness 10000) detected at line 825 [][][] Underfull \hbox (badness 10000) detected at line 833 [][][] [215] Underfull \hbox (badness 10000) detected at line 850 [][][] Underfull \hbox (badness 10000) detected at line 858 [][][] LaTeX Warning: Command \r invalid in math mode on input line 859. Missing character: There is no Å in font cmr10! Underfull \hbox (badness 10000) detected at line 875 [][][] Underfull \hbox (badness 10000) detected at line 883 [][][] Underfull \hbox (badness 10000) detected at line 900 [][][] Underfull \hbox (badness 10000) detected at line 908 [][][] [216] Underfull \hbox (badness 10000) detected at line 925 [][][] Underfull \hbox (badness 10000) detected at line 933 [][][] ) (./group___vstring.tex [217] Underfull \hbox (badness 10000) detected at line 42 [][][] Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 67 [][][] Underfull \hbox (badness 10000) detected at line 70 [][][] Underfull \hbox (badness 10000) detected at line 80 [][][] Underfull \hbox (badness 10000) detected at line 93 [][][] [218] Underfull \hbox (badness 10000) detected at line 96 [][][] Underfull \hbox (badness 10000) detected at line 99 [][][] Underfull \hbox (badness 10000) detected at line 102 [][][] Underfull \hbox (badness 10000) detected at line 105 [][][] ) (./group___vunit.tex [219] LaTeX Warning: Command \r invalid in math mode on input line 39. Missing character: There is no Å in font cmr9! [220] LaTeX Warning: Command \r invalid in math mode on input line 142. Missing character: There is no Å in font cmr10! ) (./group___vgrid.tex [221] [222] [223] Underfull \hbox (badness 10000) detected at line 125 [][][] Underfull \hbox (badness 10000) detected at line 151 [][][] Underfull \hbox (badness 10000) detected at line 168 [][][] [224] Underfull \hbox (badness 10000) detected at line 196 [][][] Underfull \hbox (badness 10000) detected at line 213 [][][] Underfull \hbox (badness 10000) detected at line 229 [][][] [225] Underfull \hbox (badness 10000) detected at line 246 [][][] Underfull \hbox (badness 10000) detected at line 268 [][][] Underfull \hbox (badness 10000) detected at line 290 [][][] Underfull \hbox (badness 10000) detected at line 302 [][][] [226] Underfull \hbox (badness 10000) detected at line 319 [][][] Underfull \hbox (badness 10000) detected at line 327 [][][] Underfull \hbox (badness 10000) detected at line 344 [][][] Underfull \hbox (badness 10000) detected at line 352 [][][] Underfull \hbox (badness 10000) detected at line 369 [][][] Underfull \hbox (badness 10000) detected at line 377 [][][] [227] Underfull \hbox (badness 10000) detected at line 395 [][][] Underfull \hbox (badness 10000) detected at line 403 [][][] Underfull \hbox (badness 10000) detected at line 420 [][][] Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 445 [][][] [228] Underfull \hbox (badness 10000) detected at line 453 [][][] Underfull \hbox (badness 10000) detected at line 470 [][][] Underfull \hbox (badness 10000) detected at line 473 [][][] Underfull \hbox (badness 10000) detected at line 489 [][][] Underfull \hbox (badness 10000) detected at line 492 [][][] [229] Underfull \hbox (badness 10000) detected at line 509 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Underfull \hbox (badness 10000) detected at line 528 [][][] Underfull \hbox (badness 10000) detected at line 531 [][][] Underfull \hbox (badness 10000) detected at line 548 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] [230] Underfull \hbox (badness 10000) detected at line 575 [][][] Underfull \hbox (badness 10000) detected at line 583 [][][] Underfull \hbox (badness 10000) detected at line 600 [][][] Underfull \hbox (badness 10000) detected at line 612 [][][] [231] Underfull \hbox (badness 10000) detected at line 629 [][][] Underfull \hbox (badness 10000) detected at line 663 [][][] [232] Underfull \hbox (badness 10000) detected at line 697 [][][] Underfull \hbox (badness 10000) detected at line 702 [][][] ) (./group___vmgrid.tex [233] [234] Underfull \hbox (badness 10000) detected at line 105 [][][] Underfull \hbox (badness 10000) detected at line 115 [][][] Underfull \hbox (badness 10000) detected at line 132 [][][] Underfull \hbox (badness 10000) detected at line 135 [][][] Underfull \hbox (badness 10000) detected at line 152 [][][] [235] Underfull \hbox (badness 10000) detected at line 160 [][][] Underfull \hbox (badness 10000) detected at line 177 [][][] Underfull \hbox (badness 10000) detected at line 193 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] [236] Underfull \hbox (badness 10000) detected at line 232 [][][] Underfull \hbox (badness 10000) detected at line 254 [][][] Underfull \hbox (badness 10000) detected at line 264 [][][] Underfull \hbox (badness 10000) detected at line 277 [][][] [237] Underfull \hbox (badness 10000) detected at line 287 [][][] Underfull \hbox (badness 10000) detected at line 300 [][][] Underfull \hbox (badness 10000) detected at line 312 [][][] Underfull \hbox (badness 10000) detected at line 329 [][][] Underfull \hbox (badness 10000) detected at line 341 [][][] ) (./group___vopot.tex [238] [239] Underfull \hbox (badness 10000) detected at line 77 [][][] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 106 [][][] [240] Underfull \hbox (badness 10000) detected at line 120 [][][] Underfull \hbox (badness 10000) detected at line 137 [][][] Underfull \hbox (badness 10000) detected at line 153 [][][] Underfull \hbox (badness 10000) detected at line 170 [][][] [241] Underfull \hbox (badness 10000) detected at line 192 [][][] Underfull \hbox (badness 10000) detected at line 214 [][][] Underfull \hbox (badness 10000) detected at line 226 [][][] Underfull \hbox (badness 10000) detected at line 243 [][][] Overfull \vbox (28.1848pt too high) has occurred while \output is active [242] Underfull \hbox (badness 10000) detected at line 255 [][][] ) (./group___vpmg.tex [243] [244] [245] Underfull \hbox (badness 10000) detected at line 117 [][][] Underfull \hbox (badness 10000) detected at line 150 [][][] [246] Underfull \hbox (badness 10000) detected at line 186 [][][] [247] Underfull \hbox (badness 10000) detected at line 234 [][][] Underfull \hbox (badness 10000) detected at line 276 [][][] [248] Underfull \hbox (badness 10000) detected at line 324 [][][] [249] Underfull \hbox (badness 10000) detected at line 362 [][][] Underfull \hbox (badness 10000) detected at line 381 [][][] Underfull \hbox (badness 10000) detected at line 384 [][][] [250] Underfull \hbox (badness 10000) detected at line 416 [][][] Underfull \hbox (badness 10000) detected at line 419 [][][] Underfull \hbox (badness 10000) detected at line 422 [][][] [251] Underfull \hbox (badness 10000) detected at line 458 [][][] Underfull \hbox (badness 10000) detected at line 484 [][][] Underfull \hbox (badness 10000) detected at line 487 [][][] Underfull \hbox (badness 10000) detected at line 492 [][][] Overfull \vbox (1.11014pt too high) has occurred while \output is active [252] Underfull \hbox (badness 10000) detected at line 520 [][][] Underfull \hbox (badness 10000) detected at line 546 [][][] [253] Underfull \hbox (badness 10000) detected at line 572 [][][] Underfull \hbox (badness 10000) detected at line 604 [][][] Underfull \hbox (badness 10000) detected at line 607 [][][] Underfull \hbox (badness 10000) detected at line 610 [][][] [254] Underfull \hbox (badness 10000) detected at line 643 [][][] Underfull \hbox (badness 10000) detected at line 646 [][][] Underfull \hbox (badness 10000) detected at line 668 [][][] Underfull \hbox (badness 10000) detected at line 690 [][][] [255] Underfull \hbox (badness 10000) detected at line 712 [][][] Underfull \hbox (badness 10000) detected at line 715 [][][] Underfull \hbox (badness 10000) detected at line 718 [][][] Underfull \hbox (badness 10000) detected at line 742 [][][] [256] Underfull \hbox (badness 10000) detected at line 764 [][][] Underfull \hbox (badness 10000) detected at line 767 [][][] Underfull \hbox (badness 10000) detected at line 799 [][][] [257] Underfull \hbox (badness 10000) detected at line 802 [][][] Underfull \hbox (badness 10000) detected at line 856 [][][] Underfull \hbox (badness 10000) detected at line 859 [][][] Underfull \hbox (badness 10000) detected at line 864 [][][] [258] Underfull \hbox (badness 10000) detected at line 894 [][][] Underfull \hbox (badness 10000) detected at line 920 [][][] Underfull \hbox (badness 10000) detected at line 923 [][][] [259] Underfull \hbox (badness 10000) detected at line 928 [][][] Underfull \hbox (badness 10000) detected at line 956 [][][] Underfull \hbox (badness 10000) detected at line 982 [][][] [260] Underfull \hbox (badness 10000) detected at line 1008 [][][] Underfull \hbox (badness 10000) detected at line 1030 [][][] Underfull \hbox (badness 10000) detected at line 1033 [][][] [261] Underfull \hbox (badness 10000) detected at line 1055 [][][] Underfull \hbox (badness 10000) detected at line 1093 [][][] Underfull \hbox (badness 10000) detected at line 1096 [][][] [262] Underfull \hbox (badness 10000) detected at line 1099 [][][] Underfull \hbox (badness 10000) detected at line 1123 [][][] Underfull \hbox (badness 10000) detected at line 1160 [][][] [263] Underfull \hbox (badness 10000) detected at line 1163 [][][] Underfull \hbox (badness 10000) detected at line 1166 [][][] Underfull \hbox (badness 10000) detected at line 1190 [][][] Underfull \hbox (badness 10000) detected at line 1193 [][][] Underfull \hbox (badness 10000) detected at line 1198 [][][] [264] Underfull \hbox (badness 10000) detected at line 1226 [][][] Underfull \hbox (badness 10000) detected at line 1252 [][][] [265] Underfull \hbox (badness 10000) detected at line 1280 [][][] Underfull \hbox (badness 10000) detected at line 1283 [][][] Underfull \hbox (badness 10000) detected at line 1303 [][][] [266] Underfull \hbox (badness 10000) detected at line 1343 [][][] Underfull \hbox (badness 10000) detected at line 1346 [][][] Underfull \hbox (badness 10000) detected at line 1349 [][][] Underfull \hbox (badness 10000) detected at line 1373 [][][] [267] Underfull \hbox (badness 10000) detected at line 1401 [][][] Underfull \hbox (badness 10000) detected at line 1404 [][][] Underfull \hbox (badness 10000) detected at line 1426 [][][] Underfull \hbox (badness 10000) detected at line 1429 [][][] Underfull \hbox (badness 10000) detected at line 1432 [][][] Underfull \hbox (badness 10000) detected at line 1454 [][][] ) (./group___vpmgp.tex [268] Underfull \hbox (badness 10000) detected at line 45 [][][] [269] Underfull \hbox (badness 10000) detected at line 78 [][][] Underfull \hbox (badness 10000) detected at line 86 [][][] Underfull \hbox (badness 10000) detected at line 103 [][][] Underfull \hbox (badness 10000) detected at line 113 [][][] Underfull \hbox (badness 10000) detected at line 130 [][][] [270] Underfull \hbox (badness 10000) detected at line 152 [][][] Underfull \hbox (badness 10000) detected at line 174 [][][] [271] Underfull \hbox (badness 10000) detected at line 208 [][][] ) (./group___p_m_g_c.tex [272] [273] [274] [275] Underfull \hbox (badness 10000) detected at line 150 [][][] Underfull \hbox (badness 10000) detected at line 153 [][][] Underfull \hbox (badness 10000) detected at line 156 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 165--165 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [276] Underfull \hbox (badness 10000) detected at line 212 [][][] Underfull \hbox (badness 10000) detected at line 215 [][][] Underfull \hbox (badness 10000) detected at line 218 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 227--227 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [277] Underfull \hbox (badness 10000) detected at line 277 [][][] Underfull \hbox (badness 10000) detected at line 280 [][][] [278] Underfull \hbox (badness 10000) detected at line 308 [][][] Underfull \hbox (badness 10000) detected at line 311 [][][] Underfull \hbox (badness 10000) detected at line 339 [][][] Underfull \hbox (badness 10000) detected at line 342 [][][] Underfull \hbox (badness 10000) detected at line 345 [][][] [279] Overfull \hbox (304.08286pt too wide) in paragraph at lines 355--355 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 392 [][][] Underfull \hbox (badness 10000) detected at line 395 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 404--404 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [280] Underfull \hbox (badness 10000) detected at line 439 [][][] [281] Underfull \hbox (badness 10000) detected at line 503 [][][] Underfull \hbox (badness 10000) detected at line 506 [][][] Underfull \hbox (badness 10000) detected at line 509 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 518--518 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [282] Underfull \hbox (badness 10000) detected at line 556 [][][] Underfull \hbox (badness 10000) detected at line 559 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 568--568 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 603 [][][] Underfull \hbox (badness 10000) detected at line 606 [][][] [283] Underfull \hbox (badness 10000) detected at line 646 [][][] Underfull \hbox (badness 10000) detected at line 649 [][][] [284] [285] Underfull \hbox (badness 10000) detected at line 719 [][][] Underfull \hbox (badness 10000) detected at line 722 [][][] Underfull \hbox (badness 10000) detected at line 772 [][][] Underfull \hbox (badness 10000) detected at line 775 [][][] Underfull \hbox (badness 10000) detected at line 778 [][][] [286] Overfull \hbox (304.08286pt too wide) in paragraph at lines 788--788 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 825 [][][] Underfull \hbox (badness 10000) detected at line 828 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 837--837 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [287] [288] Underfull \hbox (badness 10000) detected at line 907 [][][] Underfull \hbox (badness 10000) detected at line 910 [][][] [289] [290] [291] Underfull \hbox (badness 10000) detected at line 1050 [][][] Underfull \hbox (badness 10000) detected at line 1053 [][][] [292] [293] [294] Underfull \hbox (badness 10000) detected at line 1229 [][][] Underfull \hbox (badness 10000) detected at line 1232 [][][] [295] [296] Underfull \hbox (badness 10000) detected at line 1382 [][][] Underfull \hbox (badness 10000) detected at line 1385 [][][] Underfull \hbox (badness 10000) detected at line 1388 [][][] [297] [298] Underfull \hbox (badness 10000) detected at line 1446 [][][] Underfull \hbox (badness 10000) detected at line 1449 [][][] Underfull \hbox (badness 10000) detected at line 1452 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 1462--1462 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 1501 [][][] Underfull \hbox (badness 10000) detected at line 1504 [][][] [299] [300] Underfull \hbox (badness 10000) detected at line 1584 [][][] Underfull \hbox (badness 10000) detected at line 1587 [][][] Underfull \hbox (badness 10000) detected at line 1590 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 1600--1600 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 1637 [][][] Underfull \hbox (badness 10000) detected at line 1640 [][][] [301] Underfull \hbox (badness 10000) detected at line 1643 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 1652--1652 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Overfull \vbox (9.44278pt too high) has occurred while \output is active [302] Underfull \hbox (badness 10000) detected at line 1730 [][][] Underfull \hbox (badness 10000) detected at line 1735 [][][] Underfull \hbox (badness 10000) detected at line 1738 [][][] Underfull \hbox (badness 10000) detected at line 1768 [][][] Underfull \hbox (badness 10000) detected at line 1771 [][][] [303] Underfull \hbox (badness 10000) detected at line 1805 [][][] Underfull \hbox (badness 10000) detected at line 1808 [][][] [304] Underfull \hbox (badness 10000) detected at line 1842 [][][] Underfull \hbox (badness 10000) detected at line 1845 [][][] Underfull \hbox (badness 10000) detected at line 1879 [][][] Underfull \hbox (badness 10000) detected at line 1882 [][][] [305] Underfull \hbox (badness 10000) detected at line 1885 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 1895--1895 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 1932 [][][] Underfull \hbox (badness 10000) detected at line 1935 [][][] Underfull \hbox (badness 10000) detected at line 1938 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 1947--1947 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [306] [307] Underfull \hbox (badness 10000) detected at line 2033 [][][] Underfull \hbox (badness 10000) detected at line 2036 [][][] Underfull \hbox (badness 10000) detected at line 2070 [][][] Underfull \hbox (badness 10000) detected at line 2073 [][][] Underfull \hbox (badness 10000) detected at line 2076 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 2086--2086 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [308] Underfull \hbox (badness 10000) detected at line 2123 [][][] Underfull \hbox (badness 10000) detected at line 2126 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2135--2135 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [309] Underfull \hbox (badness 10000) detected at line 2170 [][][] Underfull \hbox (badness 10000) detected at line 2173 [][][] Underfull \hbox (badness 10000) detected at line 2205 [][][] [310] Underfull \hbox (badness 10000) detected at line 2208 [][][] Underfull \hbox (badness 10000) detected at line 2244 [][][] Underfull \hbox (badness 10000) detected at line 2247 [][][] [311] Underfull \hbox (badness 10000) detected at line 2283 [][][] Underfull \hbox (badness 10000) detected at line 2286 [][][] [312] Underfull \hbox (badness 10000) detected at line 2314 [][][] Underfull \hbox (badness 10000) detected at line 2317 [][][] Underfull \hbox (badness 10000) detected at line 2320 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 2330--2330 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [313] Underfull \hbox (badness 10000) detected at line 2367 [][][] Underfull \hbox (badness 10000) detected at line 2370 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2379--2379 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 2414 [][][] Underfull \hbox (badness 10000) detected at line 2417 [][][] [314] [315] Underfull \hbox (badness 10000) detected at line 2503 [][][] Underfull \hbox (badness 10000) detected at line 2506 [][][] Underfull \hbox (badness 10000) detected at line 2509 [][][] [316] Underfull \hbox (badness 10000) detected at line 2557 [][][] Underfull \hbox (badness 10000) detected at line 2560 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2569--2569 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [317] Underfull \hbox (badness 10000) detected at line 2604 [][][] Underfull \hbox (badness 10000) detected at line 2607 [][][] [318] Underfull \hbox (badness 10000) detected at line 2697 [][][] Underfull \hbox (badness 10000) detected at line 2700 [][][] [319] Underfull \hbox (badness 10000) detected at line 2746 [][][] Underfull \hbox (badness 10000) detected at line 2749 [][][] Underfull \hbox (badness 10000) detected at line 2752 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 2762--2762 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [320] Underfull \hbox (badness 10000) detected at line 2799 [][][] Underfull \hbox (badness 10000) detected at line 2802 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2811--2811 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 2846 [][][] Underfull \hbox (badness 10000) detected at line 2849 [][][] [321] Underfull \hbox (badness 10000) detected at line 2905 [][][] Underfull \hbox (badness 10000) detected at line 2908 [][][] Overfull \vbox (18.98318pt too high) has occurred while \output is active [322] Underfull \hbox (badness 10000) detected at line 2946 [][][] Underfull \hbox (badness 10000) detected at line 2957 [][][] [323] Underfull \hbox (badness 10000) detected at line 2960 [][][] [324] Underfull \hbox (badness 10000) detected at line 3046 [][][] Underfull \hbox (badness 10000) detected at line 3049 [][][] Underfull \hbox (badness 10000) detected at line 3052 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3062--3062 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 3099 [][][] Underfull \hbox (badness 10000) detected at line 3102 [][][] [325] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 3111--3111 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 3146 [][][] Underfull \hbox (badness 10000) detected at line 3149 [][][] [326] Underfull \hbox (badness 10000) detected at line 3187 [][][] Underfull \hbox (badness 10000) detected at line 3190 [][][] Underfull \hbox (badness 10000) detected at line 3193 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3203--3203 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [327] Underfull \hbox (badness 10000) detected at line 3240 [][][] Underfull \hbox (badness 10000) detected at line 3243 [][][] Underfull \hbox (badness 10000) detected at line 3246 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 3255--3255 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [328] Underfull \hbox (badness 10000) detected at line 3288 [][][] [329] Underfull \hbox (badness 10000) detected at line 3342 [][][] [330] [331] Underfull \hbox (badness 10000) detected at line 3484 [][][] [332] Underfull \hbox (badness 10000) detected at line 3542 [][][] Underfull \hbox (badness 10000) detected at line 3545 [][][] [333] Underfull \hbox (badness 10000) detected at line 3585 [][][] Underfull \hbox (badness 10000) detected at line 3588 [][][] Underfull \hbox (badness 10000) detected at line 3591 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3601--3601 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [334] Underfull \hbox (badness 10000) detected at line 3638 [][][] Underfull \hbox (badness 10000) detected at line 3641 [][][] Underfull \hbox (badness 10000) detected at line 3644 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 3653--3653 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [335] Underfull \hbox (badness 10000) detected at line 3702 [][][] Underfull \hbox (badness 10000) detected at line 3705 [][][] [336] [337] Underfull \hbox (badness 10000) detected at line 3789 [][][] Underfull \hbox (badness 10000) detected at line 3792 [][][] [338] Underfull \hbox (badness 10000) detected at line 3890 [][][] Underfull \hbox (badness 10000) detected at line 3893 [][][] Underfull \hbox (badness 10000) detected at line 3896 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3906--3906 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [339] Underfull \hbox (badness 10000) detected at line 3943 [][][] Underfull \hbox (badness 10000) detected at line 3946 [][][] Underfull \hbox (badness 10000) detected at line 3972 [][][] Underfull \hbox (badness 10000) detected at line 3975 [][][] [340] Underfull \hbox (badness 10000) detected at line 4001 [][][] Underfull \hbox (badness 10000) detected at line 4004 [][][] [341] Underfull \hbox (badness 10000) detected at line 4034 [][][] Underfull \hbox (badness 10000) detected at line 4037 [][][] Underfull \hbox (badness 10000) detected at line 4040 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 4050--4050 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 4087 [][][] [342] Underfull \hbox (badness 10000) detected at line 4090 [][][] Underfull \hbox (badness 10000) detected at line 4093 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 4102--4102 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 4137 [][][] Underfull \hbox (badness 10000) detected at line 4140 [][][] [343] Underfull \hbox (badness 10000) detected at line 4194 [][][] [344] Underfull \hbox (badness 10000) detected at line 4216 [][][] Overfull \vbox (38.14133pt too high) has occurred while \output is active [345] Underfull \hbox (badness 10000) detected at line 4290 [][][] Underfull \hbox (badness 10000) detected at line 4293 [][][] [346] [347] Underfull \hbox (badness 10000) detected at line 4383 [][][] Underfull \hbox (badness 10000) detected at line 4386 [][][] Underfull \hbox (badness 10000) detected at line 4426 [][][] Underfull \hbox (badness 10000) detected at line 4429 [][][] [348] Underfull \hbox (badness 10000) detected at line 4471 [][][] Underfull \hbox (badness 10000) detected at line 4474 [][][] [349] Underfull \hbox (badness 10000) detected at line 4532 [][][] Underfull \hbox (badness 10000) detected at line 4535 [][][] Underfull \hbox (badness 10000) detected at line 4538 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 4548--4548 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [350] Underfull \hbox (badness 10000) detected at line 4585 [][][] Underfull \hbox (badness 10000) detected at line 4588 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 4597--4597 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [351] Underfull \hbox (badness 10000) detected at line 4630 [][][] Underfull \hbox (badness 10000) detected at line 4633 [][][] Underfull \hbox (badness 10000) detected at line 4636 [][][] [352] Underfull \hbox (badness 10000) detected at line 4692 [][][] Underfull \hbox (badness 10000) detected at line 4695 [][][] Underfull \hbox (badness 10000) detected at line 4727 [][][] Underfull \hbox (badness 10000) detected at line 4730 [][][] [353] Underfull \hbox (badness 10000) detected at line 4768 [][][] Underfull \hbox (badness 10000) detected at line 4771 [][][] Underfull \hbox (badness 10000) detected at line 4774 [][][] Overfull \hbox (20.88268pt too wide) in paragraph at lines 4784--4784 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute,[] [354] Underfull \hbox (badness 10000) detected at line 4822 [][][] Underfull \hbox (badness 10000) detected at line 4825 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 4834--4834 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [355] Underfull \hbox (badness 10000) detected at line 4869 [][][] Underfull \hbox (badness 10000) detected at line 4872 [][][] [356] Underfull \hbox (badness 10000) detected at line 4930 [][][] Underfull \hbox (badness 10000) detected at line 4933 [][][] Underfull \hbox (badness 10000) detected at line 4965 [][][] Underfull \hbox (badness 10000) detected at line 4968 [][][] Underfull \hbox (badness 10000) detected at line 4971 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 4981--4981 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [357] Underfull \hbox (badness 10000) detected at line 5018 [][][] Underfull \hbox (badness 10000) detected at line 5021 [][][] Underfull \hbox (badness 10000) detected at line 5024 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 5033--5033 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [358] Underfull \hbox (badness 10000) detected at line 5068 [][][] Underfull \hbox (badness 10000) detected at line 5071 [][][] Underfull \hbox (badness 10000) detected at line 5101 [][][] Underfull \hbox (badness 10000) detected at line 5104 [][][] Underfull \hbox (badness 10000) detected at line 5107 [][][] [359] Underfull \hbox (badness 10000) detected at line 5137 [][][] Underfull \hbox (badness 10000) detected at line 5140 [][][] Underfull \hbox (badness 10000) detected at line 5170 [][][] [360] Underfull \hbox (badness 10000) detected at line 5173 [][][] Underfull \hbox (badness 10000) detected at line 5203 [][][] Underfull \hbox (badness 10000) detected at line 5206 [][][] Underfull \hbox (badness 10000) detected at line 5234 [][][] [361] Underfull \hbox (badness 10000) detected at line 5237 [][][] Underfull \hbox (badness 10000) detected at line 5265 [][][] Underfull \hbox (badness 10000) detected at line 5268 [][][] ) (./group___frontend.tex [362] Underfull \hbox (badness 2495) in paragraph at lines 32--33 []\T1/phv/m/n/10 VPUBLIC Vrc[]_[][]Codes [] (int icalc, [] $\OMS/cmsy/m/n/10 ^^ C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 feparm, [] $\OMS /cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbeparm, [] Overfull \hbox (16.65858pt too wide) in paragraph at lines 40--41 []\T1/phv/m/n/10 VEXTERNC int [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], Overfull \hbox (16.91972pt too wide) in paragraph at lines 42--43 []\T1/phv/m/n/10 VEXTERNC void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh , [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/1 0 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], Underfull \hbox (badness 1910) in paragraph at lines 60--61 [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1 /phv/m/n/10 alist[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][] [], [] Underfull \hbox (badness 1237) in paragraph at lines 60--61 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 charge[]Map[][][], [] $\OMS/cmsy/m/n/10 ^^C $\T1/phv/m/n/10 pmgp[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pmg[][][], [] [363] Underfull \hbox (badness 5817) in paragraph at lines 78--79 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], Underfull \hbox (badness 5817) in paragraph at lines 80--81 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], [364] [365] Underfull \hbox (badness 10000) detected at line 178 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 211 [][][] [366] Underfull \hbox (badness 10000) detected at line 235 [][][] [367] Underfull \hbox (badness 10000) detected at line 275 [][][] Underfull \hbox (badness 10000) detected at line 297 [][][] Underfull \hbox (badness 10000) detected at line 314 [][][] Underfull \hbox (badness 10000) detected at line 317 [][][] [368] Underfull \hbox (badness 10000) detected at line 351 [][][] Underfull \hbox (badness 10000) detected at line 373 [][][] Underfull \hbox (badness 10000) detected at line 390 [][][] Underfull \hbox (badness 10000) detected at line 393 [][][] [369] [370] Underfull \hbox (badness 10000) detected at line 495 [][][] Underfull \hbox (badness 10000) detected at line 502 [][][] [371] Underfull \hbox (badness 10000) detected at line 572 [][][] Underfull \hbox (badness 10000) detected at line 575 [][][] [372] Underfull \hbox (badness 10000) detected at line 625 [][][] Underfull \hbox (badness 10000) detected at line 649 [][][] Underfull \hbox (badness 10000) detected at line 677 [][][] [373] Underfull \hbox (badness 10000) detected at line 694 [][][] Underfull \hbox (badness 10000) detected at line 720 [][][] Underfull \hbox (badness 10000) detected at line 748 [][][] [374] Underfull \hbox (badness 10000) detected at line 772 [][][] Underfull \hbox (badness 10000) detected at line 792 [][][] Underfull \hbox (badness 10000) detected at line 818 [][][] [375] Underfull \hbox (badness 10000) detected at line 842 [][][] Underfull \hbox (badness 10000) detected at line 866 [][][] Underfull \hbox (badness 10000) detected at line 876 [][][] Underfull \hbox (badness 10000) detected at line 895 [][][] [376] Underfull \hbox (badness 10000) detected at line 909 [][][] Underfull \hbox (badness 10000) detected at line 912 [][][] Underfull \hbox (badness 10000) detected at line 929 [][][] Underfull \hbox (badness 10000) detected at line 939 [][][] Underfull \hbox (badness 10000) detected at line 958 [][][] Underfull \hbox (badness 10000) detected at line 961 [][][] [377] Underfull \hbox (badness 10000) detected at line 981 [][][] Underfull \hbox (badness 10000) detected at line 984 [][][] Underfull \hbox (badness 10000) detected at line 1010 [][][] Underfull \hbox (badness 10000) detected at line 1013 [][][] [378] Underfull \hbox (badness 10000) detected at line 1035 [][][] Underfull \hbox (badness 10000) detected at line 1045 [][][] Underfull \hbox (badness 10000) detected at line 1064 [][][] Underfull \hbox (badness 10000) detected at line 1067 [][][] Underfull \hbox (badness 10000) detected at line 1091 [][][] [379] Underfull \hbox (badness 10000) detected at line 1105 [][][] Underfull \hbox (badness 10000) detected at line 1122 [][][] Underfull \hbox (badness 10000) detected at line 1134 [][][] Underfull \hbox (badness 10000) in paragraph at lines 1135--1136 Underfull \hbox (badness 10000) detected at line 1138 [][][] [380] Underfull \hbox (badness 10000) detected at line 1166 [][][] Underfull \hbox (badness 10000) detected at line 1180 [][][] Underfull \hbox (badness 10000) detected at line 1201 [][][] Underfull \hbox (badness 10000) detected at line 1204 [][][] [381] Underfull \hbox (badness 10000) detected at line 1228 [][][] Underfull \hbox (badness 10000) detected at line 1231 [][][] Underfull \hbox (badness 10000) detected at line 1259 [][][] Underfull \hbox (badness 10000) detected at line 1262 [][][] [382] Underfull \hbox (badness 10000) detected at line 1288 [][][] Underfull \hbox (badness 10000) detected at line 1291 [][][] Underfull \hbox (badness 10000) detected at line 1319 [][][] Underfull \hbox (badness 10000) detected at line 1322 [][][] [383] Underfull \hbox (badness 10000) detected at line 1348 [][][] Underfull \hbox (badness 10000) detected at line 1377 [][][] Underfull \hbox (badness 10000) detected at line 1380 [][][] Underfull \hbox (badness 10000) detected at line 1408 [][][] [384] Underfull \hbox (badness 10000) detected at line 1432 [][][] Underfull \hbox (badness 10000) detected at line 1454 [][][] Underfull \hbox (badness 10000) detected at line 1468 [][][] [385] Underfull \hbox (badness 10000) detected at line 1485 [][][] Underfull \hbox (badness 10000) detected at line 1497 [][][] Underfull \hbox (badness 10000) detected at line 1514 [][][] Underfull \hbox (badness 10000) detected at line 1528 [][][] [386] Underfull \hbox (badness 10000) detected at line 1562 [][][] Underfull \hbox (badness 10000) detected at line 1574 [][][] Underfull \hbox (badness 10000) detected at line 1591 [][][] Underfull \hbox (badness 10000) detected at line 1608 [][][] [387] Underfull \hbox (badness 10000) detected at line 1636 [][][] Underfull \hbox (badness 10000) detected at line 1650 [][][] [388] Underfull \hbox (badness 10000) detected at line 1688 [][][] Underfull \hbox (badness 10000) detected at line 1716 [][][] Underfull \hbox (badness 10000) detected at line 1733 [][][] [389] Underfull \hbox (badness 10000) detected at line 1747 [][][] Underfull \hbox (badness 10000) detected at line 1764 [][][] Underfull \hbox (badness 10000) detected at line 1792 [][][] [390] Underfull \hbox (badness 10000) detected at line 1809 [][][] Underfull \hbox (badness 10000) detected at line 1823 [][][] ) [391] [392] Chapter 8. (./struct_atom_force.tex Underfull \hbox (badness 10000) detected at line 32 [][][] [393]) (./structs_a_p_o_lparm.tex [394] Underfull \hbox (badness 10000) detected at line 88 [][][] [395] Underfull \hbox (badness 10000) detected at line 224 [][][] [396] Underfull \hbox (badness 10000) detected at line 237 [][][] Underfull \hbox (badness 10000) detected at line 250 [][][] Underfull \hbox (badness 10000) detected at line 263 [][][] Underfull \hbox (badness 10000) detected at line 276 [][][] Underfull \hbox (badness 10000) detected at line 289 [][][] Underfull \hbox (badness 10000) detected at line 302 [][][] [397] Underfull \hbox (badness 10000) detected at line 315 [][][] Underfull \hbox (badness 10000) detected at line 328 [][][] Underfull \hbox (badness 10000) detected at line 341 [][][] Underfull \hbox (badness 10000) detected at line 354 [][][] Underfull \hbox (badness 10000) detected at line 367 [][][] Underfull \hbox (badness 10000) detected at line 380 [][][] [398]) (./structs_b_e_mparm.tex [399] Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 53 [][][] [400] Underfull \hbox (badness 10000) detected at line 129 [][][] Underfull \hbox (badness 10000) detected at line 142 [][][] Underfull \hbox (badness 10000) detected at line 155 [][][] [401] Underfull \hbox (badness 10000) detected at line 168 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 194 [][][] ) (./structs_f_e_mparm.tex [402] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) in paragraph at lines 84--85 [403] [404] [405]) (./structs_g_e_o_f_l_o_wparm.tex Underfull \hbox (badness 10000) detected at line 30 [][][] Underfull \hbox (badness 10000) detected at line 33 [][][] [406]) (./structs_m_gparm.tex [407] Underfull \hbox (badness 10000) detected at line 120 [][][] Underfull \hbox (badness 10000) detected at line 123 [][][] [408] Underfull \hbox (badness 10000) in paragraph at lines 149--150 Underfull \hbox (badness 10000) in paragraph at lines 180--181 [409] Underfull \hbox (badness 10000) in paragraph at lines 261--262 [410] [411] Underfull \hbox (badness 10000) detected at line 434 [][][] Underfull \hbox (badness 10000) detected at line 447 [][][] Underfull \hbox (badness 10000) detected at line 460 [][][] Underfull \hbox (badness 10000) detected at line 473 [][][] [412] Underfull \hbox (badness 10000) detected at line 486 [][][] Underfull \hbox (badness 10000) detected at line 499 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] Underfull \hbox (badness 10000) detected at line 538 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] [413] Underfull \hbox (badness 10000) detected at line 564 [][][] Underfull \hbox (badness 10000) detected at line 577 [][][] Underfull \hbox (badness 10000) detected at line 590 [][][] Underfull \hbox (badness 10000) detected at line 603 [][][] Underfull \hbox (badness 10000) detected at line 616 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] [414] Underfull \hbox (badness 10000) detected at line 642 [][][] Underfull \hbox (badness 10000) detected at line 655 [][][] Underfull \hbox (badness 10000) detected at line 668 [][][] ) (./structs_n_osh.tex [415] Underfull \hbox (badness 10000) detected at line 108 [][][] [416] [417] [418] [419] [420]) (./structs_n_osh__calc.tex [421] Underfull \hbox (badness 10000) detected at line 38 [][][] [422]) (./structs_p_b_a_mparm.tex [423] Underfull \hbox (badness 10000) detected at line 106 [][][] Underfull \hbox (badness 10000) detected at line 109 [][][] [424] [425] [426] [427]) (./structs_p_b_eparm.tex [428] [429] Underfull \hbox (badness 10000) detected at line 142 [][][] Underfull \hbox (badness 10000) detected at line 145 [][][] [430] [431] [432] Underfull \hbox (badness 10000) detected at line 391 [][][] Underfull \hbox (badness 10000) detected at line 404 [][][] Underfull \hbox (badness 10000) detected at line 417 [][][] Underfull \hbox (badness 10000) detected at line 430 [][][] [433] Underfull \hbox (badness 10000) detected at line 473 [][][] Underfull \hbox (badness 10000) detected at line 486 [][][] Underfull \hbox (badness 10000) detected at line 499 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Underfull \hbox (badness 10000) detected at line 525 [][][] [434] Underfull \hbox (badness 10000) detected at line 538 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] Underfull \hbox (badness 10000) detected at line 564 [][][] Underfull \hbox (badness 10000) detected at line 577 [][][] Underfull \hbox (badness 10000) detected at line 590 [][][] Underfull \hbox (badness 10000) detected at line 603 [][][] [435] Underfull \hbox (badness 10000) detected at line 616 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] [436] [437]) (./structs_p_b_s_a_mparm.tex [438] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] [439]) (./structs_vacc.tex [440] Underfull \hbox (badness 10000) detected at line 36 [][][] [441]) (./structs_vacc_surf.tex Underfull \hbox (badness 10000) detected at line 36 [][][] [442]) (./structs_valist.tex [443] Underfull \hbox (badness 10000) detected at line 36 [][][] [444]) (./structs_vatom.tex Underfull \hbox (badness 10000) detected at line 36 [][][] Underfull \hbox (badness 10000) in paragraph at lines 62--63 [445] Underfull \hbox (badness 10000) in paragraph at lines 93--94 Underfull \hbox (badness 10000) in paragraph at lines 114--115 ) (./structs_vclist.tex [446] Underfull \hbox (badness 10000) detected at line 40 [][][] [447]) (./structs_vclist_cell.tex Underfull \hbox (badness 10000) detected at line 24 [][][] ) (./structs_vcsm.tex [448] Underfull \hbox (badness 10000) detected at line 42 [][][] [449]) (./structs_vfetk.tex [450] Underfull \hbox (badness 10000) detected at line 60 [][][] [451] Underfull \hbox (badness 10000) in paragraph at lines 116--117 [452]) (./structs_vfetk___local_var.tex [453] Underfull \hbox (badness 10000) detected at line 86 [][][] [454] [455] [456] [457]) (./structs_vgreen.tex Underfull \hbox (badness 10000) detected at line 34 [][][] [458]) (./structs_vgrid.tex [459] Underfull \hbox (badness 10000) detected at line 52 [][][] [460] [461]) (./structs_vmgrid.tex Underfull \hbox (badness 10000) detected at line 24 [][][] ) (./structs_vopot.tex [462] Underfull \hbox (badness 10000) detected at line 26 [][][] ) (./structs_vparam___atom_data.tex [463] Underfull \hbox (badness 10000) detected at line 30 [][][] Underfull \hbox (badness 10000) detected at line 33 [][][] ) (./structs_vpbe.tex [464] Underfull \hbox (badness 10000) detected at line 86 [][][] [465] [466] [467] [468]) (./structs_vpee.tex [469] Underfull \hbox (badness 10000) detected at line 34 [][][] ) (./structs_vpmg.tex [470] [471] Underfull \hbox (badness 10000) detected at line 116 [][][] [472] [473] [474] [475] [476]) (./structs_vpmgp.tex [477] Underfull \hbox (badness 10000) detected at line 126 [][][] [478] Underfull \hbox (badness 10000) in paragraph at lines 164--165 Underfull \hbox (badness 10000) in paragraph at lines 175--176 Underfull \hbox (badness 10000) in paragraph at lines 186--187 [479] Underfull \hbox (badness 10000) in paragraph at lines 234--235 [480] [481] [482] [483] Underfull \hbox (badness 10000) in paragraph at lines 506--507 Underfull \hbox (badness 10000) in paragraph at lines 527--528 [484] Underfull \hbox (badness 10000) in paragraph at lines 548--549 Underfull \hbox (badness 10000) in paragraph at lines 589--590 [485] Underfull \hbox (badness 10000) in paragraph at lines 630--631 Underfull \hbox (badness 10000) in paragraph at lines 671--672 ) (./struct_vparam.tex [486] Underfull \hbox (badness 10000) detected at line 26 [][][] ) (./struct_vparam___res_data.tex [487] Underfull \hbox (badness 10000) detected at line 28 [][][] ) [488] Chapter 9. (./mainpage_8h_source.tex) (./apbs_8h.tex <./apbs_8h__incl.pdf> <./apbs_8h__dep __incl.pdf> [489] Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 53 [][][] Underfull \hbox (badness 10000) detected at line 56 [][][] [490]) (./apbs_8h_source.tex) (./vcsm_8c.tex [491] <./vcsm_8c__incl.pdf> [492] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] Underfull \hbox (badness 10000) detected at line 58 [][][] [493]) (./vcsm_8c_source.tex [494] [495] [496] [497] [498] [499]) (./vcsm_8h.tex <./vcsm_8h__incl.pdf> <./vcsm_8h__dep__incl.pdf> [500] [501] Underfull \hbox (badness 10000) detected at line 75 [][][] Underfull \hbox (badness 10000) detected at line 78 [][][] Underfull \hbox (badness 10000) detected at line 81 [][][] [502]) (./vcsm_8h_source.tex [503]) (./vfetk_8c.tex [504] <./vfetk_8c__incl.pdf > [505] [506] Underfull \hbox (badness 10000) detected at line 162 [][][] Underfull \hbox (badness 10000) detected at line 165 [][][] [507] Underfull \hbox (badness 10000) detected at line 168 [][][] [508] [509] [510] [511]) (./vfetk_8c_source.tex [512] [513] [514] [515] [516] [517] [518] [519] [520] [521] [522] [523] [524] [525] [526] [527] [528] [529] [530] [531] [532] [533] [534] [535] [536] [537] [538] [539] [540] [541]) (./vfetk_8h.tex [542] <./vfetk_8h__incl.pdf> <./vfetk_8h__dep__inc l.pdf> [543] [544] [545] Underfull \hbox (badness 10000) detected at line 187 [][][] [546] Underfull \hbox (badness 10000) detected at line 190 [][][] Underfull \hbox (badness 10000) detected at line 193 [][][] ) (./vfetk_8h_source.tex [547] [548] [549] [550] [551] [552]) (./vpee_8c.tex <. /vpee_8c__incl.pdf> [553] Underfull \hbox (badness 10000) detected at line 49 [][][] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] [554]) (./vpee_8c_source.tex [555] [556] [557] [558] [559] [560]) (./vpee_8h.tex [561] <./vpee_8h__incl.pdf> <./vpee_8h__dep__incl.pdf> [562] Underfull \hbox (badness 10000) detected at line 55 [][][] Underfull \hbox (badness 10000) detected at line 58 [][][] Underfull \hbox (badness 10000) detected at line 61 [][][] [563]) (./vpee_8h_source.tex [564]) (./apolparm_8c.tex <./apolparm_8c__incl.pdf > [565] Underfull \hbox (badness 10000) detected at line 64 [][][] Underfull \hbox (badness 10000) detected at line 67 [][][] Underfull \hbox (badness 10000) detected at line 70 [][][] [566] [567]) (./apolparm_8c_source.tex [568] [569] [570] [571] [572] [573] [574] [575]) (./apolparm_8h_source.tex [576]) (./bemparm_8c.tex <./bemparm_8c__ incl.pdf> [577] [578] Underfull \hbox (badness 10000) detected at line 48 [][][] Underfull \hbox (badness 10000) detected at line 51 [][][] Underfull \hbox (badness 10000) detected at line 54 [][][] [579] Underfull \hbox (badness 10000) detected at line 120 [][][] ) (./bemparm_8c_source.tex [580] [581] [582] [583]) (./bemparm_8h_source.tex [584]) (./femparm_8c.tex <./femparm_8c__incl.pdf> [585] [586] Underfull \hbox (badness 10000) detected at line 58 [][][] Underfull \hbox (badness 10000) detected at line 61 [][][] Underfull \hbox (badness 10000) detected at line 64 [][][] [587] [588]) (./femparm_8c_source.tex [589] [590] [591] [592] [593]) (./femparm_8h.tex <./femparm_8h__incl.pdf> [594] <./femparm_8h__dep__incl.pdf> [595] Underfull \hbox (badness 10000) detected at line 87 [][][] Underfull \hbox (badness 10000) detected at line 90 [][][] Underfull \hbox (badness 10000) detected at line 93 [][][] [596]) (./femparm_8h_source.tex [597]) (./geoflowparm_8c.tex [598] <./geoflowpa rm_8c__incl.pdf> [599] Underfull \hbox (badness 10000) detected at line 46 [][][] Underfull \hbox (badness 10000) detected at line 49 [][][] Underfull \hbox (badness 10000) detected at line 52 [][][] [600]) (./geoflowparm_8c_source.tex [601] [602]) (./geoflowparm_8h.tex [603] <. /geoflowparm_8h__incl.pdf> <./geoflowparm_8h__dep__incl.pdf> [604] [605] Underfull \hbox (badness 10000) detected at line 69 [][][] Underfull \hbox (badness 10000) detected at line 72 [][][] Underfull \hbox (badness 10000) detected at line 75 [][][] [606]) (./geoflowparm_8h_source.tex [607]) (./mgparm_8c.tex <./mgparm_8c__incl. pdf> [608] [609] Underfull \hbox (badness 10000) detected at line 94 [][][] Underfull \hbox (badness 10000) detected at line 97 [][][] Underfull \hbox (badness 10000) detected at line 100 [][][] [610] [611]) (./mgparm_8c_source.tex [612] [613] [614] [615] [616] [617] [618] [619] [620] [621] [622] [623]) (./mgparm_8h.tex <./mgparm_8h__incl.pdf> [624] <./mgparm_8h__dep__incl.pdf> [625] [626] Underfull \hbox (badness 10000) detected at line 102 [][][] Underfull \hbox (badness 10000) detected at line 105 [][][] Underfull \hbox (badness 10000) detected at line 108 [][][] [627]) (./mgparm_8h_source.tex [628]) (./nosh_8c.tex <./nosh_8c__incl.pdf> [629] [630] [631] Underfull \hbox (badness 10000) detected at line 150 [][][] Underfull \hbox (badness 10000) detected at line 153 [][][] Underfull \hbox (badness 10000) detected at line 156 [][][] [632] [633] [634] [635] [636]) (./nosh_8c_source.tex [637] [638] [639] [640] [641] [642] [643] [644] [645] [646] [647] [648] [649] [650] [651] [652] [653] [654] [655] [656] [657] [658] [659] [660] [661] [662] [663] [664] [665] [666] [667] [668] [669] [670] [671] [672] [673] [674] [675] [676]) (./nosh_8h.tex <./nosh_8h__incl.pdf> [677] <./nosh_8h__dep__incl.pdf> [678] [679] [680] Underfull \hbox (badness 10000) detected at line 169 [][][] Underfull \hbox (badness 10000) detected at line 172 [][][] Underfull \hbox (badness 10000) detected at line 175 [][][] ) (./nosh_8h_source.tex [681] [682] [683]) (./pbamparm_8c.tex <./pbamparm_8c__i ncl.pdf> [684] [685] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) detected at line 71 [][][] Underfull \hbox (badness 10000) detected at line 74 [][][] [686]) (./pbamparm_8c_source.tex [687] [688] [689] [690] [691] [692] [693] [694] [695]) (./pbamparm_8h.tex <./pbamparm_8h__incl.pdf> <./pbamparm_8h__dep__ incl.pdf> [696] [697] Underfull \hbox (badness 10000) detected at line 100 [][][] [698] Underfull \hbox (badness 10000) detected at line 103 [][][] Underfull \hbox (badness 10000) detected at line 106 [][][] [699]) (./pbamparm_8h_source.tex [700]) (./pbeparm_8c.tex [701] <./pbeparm_8c__ incl.pdf> [702] Underfull \hbox (badness 10000) detected at line 100 [][][] Underfull \hbox (badness 10000) detected at line 103 [][][] Underfull \hbox (badness 10000) detected at line 106 [][][] [703] [704] [705] [706] [707]) (./pbeparm_8c_source.tex [708] [709] [710] [711] [712] [713] [714] [715] [716] [717] [718] [719] [720] [721] [722]) (./pbeparm_8h.tex <./pbeparm_8h__incl.pdf> [723] <./pbeparm_8h__dep__incl.pdf> [724] Underfull \hbox (badness 10000) detected at line 86 [][][] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 92 [][][] [725]) (./pbeparm_8h_source.tex [726] [727]) (./pbsamparm_8c.tex <./pbsamparm_8 c__incl.pdf> [728] [729] Underfull \hbox (badness 10000) detected at line 48 [][][] Underfull \hbox (badness 10000) detected at line 51 [][][] Underfull \hbox (badness 10000) detected at line 54 [][][] [730]) (./pbsamparm_8c_source.tex [731] [732]) (./pbsamparm_8h.tex [733] <./pbs amparm_8h__incl.pdf> <./pbsamparm_8h__dep__incl.pdf> [734] [735] Underfull \hbox (badness 10000) detected at line 84 [][][] Underfull \hbox (badness 10000) detected at line 87 [][][] Underfull \hbox (badness 10000) detected at line 90 [][][] [736]) (./pbsamparm_8h_source.tex [737]) (./vacc_8c.tex <./vacc_8c__incl.pdf> [738] [739] [740] Underfull \hbox (badness 10000) detected at line 106 [][][] Underfull \hbox (badness 10000) detected at line 109 [][][] Underfull \hbox (badness 10000) detected at line 112 [][][] [741] Underfull \hbox (badness 10000) detected at line 178 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 207 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] [742] [743]) (./vacc_8c_source.tex [744] [745] [746] [747] [748] [749] [750] [751] [752] [753] [754] [755] [756] [757] [758] [759] [760] [761] [762] [763] [764] [765] [766]) (./vacc_8h.tex <./vacc_8h__incl.pdf> <./vacc_8h__dep__ incl.pdf> [767] [768] [769] Underfull \hbox (badness 10000) detected at line 121 [][][] Underfull \hbox (badness 10000) detected at line 124 [][][] Underfull \hbox (badness 10000) detected at line 127 [][][] [770]) (./vacc_8h_source.tex [771] [772] [773]) (./valist_8c.tex <./valist_8c__ incl.pdf> [774] [775] Underfull \hbox (badness 2293) in paragraph at lines 53--55 []\T1/phv/m/n/10 VPRIVATE Vrc[]_[][]Codes [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/ m/n/10 thee, Vio $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 sock, int $\OMS/cmsy/m/n/ 10 ^^C$\T1/phv/m/n/10 serial, char atom[] Underfull \hbox (badness 10000) detected at line 81 [][][] Underfull \hbox (badness 10000) detected at line 84 [][][] Underfull \hbox (badness 10000) detected at line 87 [][][] [776] [777] [778]) (./valist_8c_source.tex [779] [780] [781] [782] [783] [784] [785] [786] [787] [788]) (./valist_8h.tex [789] <./valist_8h__incl.pdf> < ./valist_8h__dep__incl.pdf> [790] Underfull \hbox (badness 10000) detected at line 75 [][][] Underfull \hbox (badness 10000) detected at line 78 [][][] Underfull \hbox (badness 10000) detected at line 81 [][][] [791]) (./valist_8h_source.tex [792] [793]) (./vatom_8c.tex <./vatom_8c__incl.p df> [794] Underfull \hbox (badness 10000) detected at line 70 [][][] Underfull \hbox (badness 10000) detected at line 73 [][][] Underfull \hbox (badness 10000) detected at line 76 [][][] [795]) (./vatom_8c_source.tex [796] [797] [798]) (./vatom_8h.tex <./vatom_8h__i ncl.pdf> [799] <./vatom_8h__dep__incl.pdf> [800] [801] Underfull \hbox (badness 10000) detected at line 94 [][][] Underfull \hbox (badness 10000) detected at line 97 [][][] Underfull \hbox (badness 10000) detected at line 100 [][][] ) (./vatom_8h_source.tex [802] [803]) (./vcap_8c.tex <./vcap_8c__incl.pdf> [804] Underfull \hbox (badness 10000) detected at line 30 [][][] Underfull \hbox (badness 10000) detected at line 33 [][][] Underfull \hbox (badness 10000) detected at line 36 [][][] [805]) (./vcap_8c_source.tex [806]) (./vcap_8h.tex <./vcap_8h__incl.pdf> <./vca p_8h__dep__incl.pdf> [807] Underfull \hbox (badness 10000) detected at line 45 [][][] Underfull \hbox (badness 10000) detected at line 48 [][][] [808] Underfull \hbox (badness 10000) detected at line 51 [][][] ) (./vcap_8h_source.tex [809]) (./vclist_8c.tex <./vclist_8c__incl.pdf> Underfull \hbox (badness 4060) in paragraph at lines 31--33 []\T1/phv/m/n/10 VPRIVATE void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 thee , dou-ble lower[]_[]corner[][][], dou-ble upper[]_[] [810] Underfull \hbox (badness 10000) detected at line 64 [][][] Underfull \hbox (badness 10000) detected at line 67 [][][] Underfull \hbox (badness 10000) detected at line 70 [][][] [811] [812]) (./vclist_8c_source.tex [813] [814] [815] [816] [817]) (./vclist_8h.tex [818] <./vclist_8h__incl.pdf> <./vclist_8h__dep__incl.pdf> [819] [820] Underfull \hbox (badness 10000) detected at line 82 [][][] Underfull \hbox (badness 10000) detected at line 85 [][][] Underfull \hbox (badness 10000) detected at line 88 [][][] [821]) (./vclist_8h_source.tex [822]) (./vgreen_8c.tex [823] <./vgreen_8c__incl .pdf> [824] Underfull \hbox (badness 10000) detected at line 54 [][][] Underfull \hbox (badness 10000) detected at line 57 [][][] Underfull \hbox (badness 10000) detected at line 60 [][][] [825]) (./vgreen_8c_source.tex [826] [827] [828] [829] [830] [831]) (./vgreen_8h.tex <./vgreen_8h__incl.pdf> [832] <./vgreen_8h__dep__incl.pdf> [833] Underfull \hbox (badness 10000) detected at line 70 [][][] Underfull \hbox (badness 10000) detected at line 73 [][][] ) (./vgreen_8h_source.tex [834]) (./vhal_8h.tex [835] <./vhal_8h__incl.pdf> <./ vhal_8h__dep__incl.pdf> [836] [837] [838] [839] Underfull \hbox (badness 10000) detected at line 301 [][][] Underfull \hbox (badness 10000) detected at line 304 [][][] Underfull \hbox (badness 10000) detected at line 307 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 316--316 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [840] [841] [842] [843] [844] [845] [846]) (./vhal_8h_source.tex [847] [848] [849] [850] [851] [852] [853] [854]) (./vmatrix_8h.tex [855] <./vmatrix_8h__dep __incl.pdf> Underfull \hbox (badness 10000) detected at line 35 [][][] Underfull \hbox (badness 10000) detected at line 38 [][][] Underfull \hbox (badness 10000) detected at line 41 [][][] [856] [857]) (./vmatrix_8h_source.tex [858]) (./vparam_8c.tex <./vparam_8c__inc l.pdf> [859] Underfull \hbox (badness 10000) detected at line 77 [][][] Underfull \hbox (badness 10000) detected at line 80 [][][] [860] Underfull \hbox (badness 10000) detected at line 83 [][][] ) (./vparam_8c_source.tex [861] [862] [863] [864] [865] [866] [867] [868]) (./vparam_8h.tex [869] <./vparam_8h__incl.pdf> <./vparam_8h__dep__incl.pdf> [870] [871] Underfull \hbox (badness 10000) detected at line 94 [][][] Underfull \hbox (badness 10000) detected at line 97 [][][] Underfull \hbox (badness 10000) detected at line 100 [][][] [872]) (./vparam_8h_source.tex [873]) (./vpbe_8c.tex <./vpbe_8c__incl.pdf> [874] [875] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 92 [][][] [876] Underfull \hbox (badness 10000) detected at line 95 [][][] ) (./vpbe_8c_source.tex [877] [878] [879] [880] [881] [882] [883]) (./vpbe_8h.tex <./vpbe_8h__incl.pdf> <./vpbe_8h__dep__incl.pdf> [884] [885] Underfull \hbox (badness 10000) detected at line 109 [][][] Underfull \hbox (badness 10000) detected at line 112 [][][] Underfull \hbox (badness 10000) detected at line 115 [][][] [886]) (./vpbe_8h_source.tex [887] [888] [889]) (./vstring_8c.tex <./vstring_8c __incl.pdf> [890] Underfull \hbox (badness 10000) detected at line 30 [][][] Underfull \hbox (badness 10000) detected at line 33 [][][] Underfull \hbox (badness 10000) detected at line 36 [][][] ) (./vstring_8c_source.tex [891] [892] [893]) (./vstring_8h.tex <./vstring_8h__ incl.pdf> <./vstring_8h__dep__incl.pdf> [894] Underfull \hbox (badness 10000) detected at line 39 [][][] Underfull \hbox (badness 10000) detected at line 42 [][][] Underfull \hbox (badness 10000) detected at line 45 [][][] [895]) (./vstring_8h_source.tex) (./vunit_8h.tex <./vunit_8h__dep__incl.pdf> [896] LaTeX Warning: Command \r invalid in math mode on input line 41. Missing character: There is no Å in font cmr9! Underfull \hbox (badness 10000) detected at line 49 [][][] Underfull \hbox (badness 10000) detected at line 54 [][][] Underfull \hbox (badness 10000) detected at line 57 [][][] [897]) (./vunit_8h_source.tex) (./main_8c.tex [898] <./main_8c__incl.pdf> Underfull \hbox (badness 10000) detected at line 27 [][][] Underfull \hbox (badness 10000) detected at line 40 [][][] Underfull \hbox (badness 10000) detected at line 43 [][][] [899]) (./main_8c_source.tex [900] [901] [902] [903] [904] [905] [906] [907] [908] [909] [910]) (./vgrid_8c.tex <./vgrid_8c__incl.pdf> [911] [912] Underfull \hbox (badness 10000) detected at line 83 [][][] Underfull \hbox (badness 10000) detected at line 86 [][][] Underfull \hbox (badness 10000) detected at line 89 [][][] [913] Underfull \hbox (badness 10000) detected at line 168 [][][] [914]) (./vgrid_8c_source.tex [915] [916] [917] [918] [919] [920] [921] [922] [923] [924] [925] [926] [927] [928] [929] [930] [931] [932] [933] [934] [935] [936] [937]) (./vgrid_8h.tex [938] <./vgrid_8h__incl.pdf> <./vgrid_ 8h__dep__incl.pdf> [939] [940] Underfull \hbox (badness 10000) detected at line 91 [][][] [941] Underfull \hbox (badness 10000) detected at line 94 [][][] Underfull \hbox (badness 10000) detected at line 97 [][][] [942] Underfull \hbox (badness 10000) detected at line 163 [][][] ) (./vgrid_8h_source.tex [943]) (./vmgrid_8c.tex [944] <./vmgrid_8c__incl.pdf> [945] Underfull \hbox (badness 10000) detected at line 40 [][][] Underfull \hbox (badness 10000) detected at line 43 [][][] Underfull \hbox (badness 10000) detected at line 46 [][][] Underfull \hbox (badness 10000) detected at line 49 [][][] Overfull \hbox (1024.08331pt too wide) in paragraph at lines 58--58 []\T1/pcr/m/n/8 * Copyright (c) 2010, Pacific Northwest National Laboratory. Portions Copyright (c) 2002-2020, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2020, T he Regents of the University of California. Portions Copyright (c) 1995, Michae l Holst.[] ) (./vmgrid_8c_source.tex [946] [947] [948]) (./vmgrid_8h.tex <./vmgrid_8h__inc l.pdf> <./vmgrid_8h__dep__incl.pdf> [949] [950] Underfull \hbox (badness 10000) detected at line 69 [][][] Underfull \hbox (badness 10000) detected at line 72 [][][] Underfull \hbox (badness 10000) detected at line 75 [][][] [951]) (./vmgrid_8h_source.tex) (./vopot_8c.tex [952] <./vopot_8c__incl.pdf> Underfull \hbox (badness 10000) detected at line 43 [][][] Underfull \hbox (badness 10000) detected at line 46 [][][] Underfull \hbox (badness 10000) detected at line 49 [][][] [953]) (./vopot_8c_source.tex [954] [955] [956] [957] [958]) (./vopot_8h.tex <. /vopot_8h__incl.pdf> <./vopot_8h__dep__incl.pdf> [959] [960] Underfull \hbox (badness 10000) detected at line 63 [][][] Underfull \hbox (badness 10000) detected at line 66 [][][] Underfull \hbox (badness 10000) detected at line 69 [][][] ) (./vopot_8h_source.tex [961]) (./vpmg_8c.tex <./vpmg_8c__incl.pdf> [962] [963] [964] [965] Underfull \hbox (badness 10000) detected at line 172 [][][] Underfull \hbox (badness 10000) detected at line 175 [][][] Underfull \hbox (badness 10000) detected at line 178 [][][] [966] Underfull \hbox (badness 10000) detected at line 260 [][][] [967] Underfull \hbox (badness 10000) detected at line 287 [][][] [968] Underfull \hbox (badness 10000) detected at line 383 [][][] Underfull \hbox (badness 10000) detected at line 386 [][][] Underfull \hbox (badness 10000) detected at line 408 [][][] Underfull \hbox (badness 10000) detected at line 411 [][][] [969] Underfull \hbox (badness 10000) detected at line 433 [][][] Underfull \hbox (badness 10000) detected at line 436 [][][] Underfull \hbox (badness 10000) detected at line 458 [][][] Underfull \hbox (badness 10000) detected at line 461 [][][] Underfull \hbox (badness 10000) detected at line 483 [][][] Underfull \hbox (badness 10000) detected at line 486 [][][] [970] Underfull \hbox (badness 10000) detected at line 508 [][][] Underfull \hbox (badness 10000) detected at line 511 [][][] Underfull \hbox (badness 10000) detected at line 533 [][][] Underfull \hbox (badness 10000) detected at line 536 [][][] Underfull \hbox (badness 10000) detected at line 553 [][][] Underfull \hbox (badness 10000) detected at line 556 [][][] [971] Underfull \hbox (badness 10000) detected at line 573 [][][] Underfull \hbox (badness 10000) detected at line 590 [][][] Underfull \hbox (badness 10000) detected at line 607 [][][] Underfull \hbox (badness 10000) detected at line 624 [][][] Underfull \hbox (badness 10000) detected at line 641 [][][] [972] Underfull \hbox (badness 10000) detected at line 658 [][][] Underfull \hbox (badness 10000) detected at line 675 [][][] Underfull \hbox (badness 10000) detected at line 696 [][][] Underfull \hbox (badness 10000) detected at line 699 [][][] Underfull \hbox (badness 10000) detected at line 716 [][][] [973] Underfull \hbox (badness 10000) detected at line 733 [][][] Underfull \hbox (badness 10000) detected at line 750 [][][] Underfull \hbox (badness 10000) detected at line 767 [][][] Underfull \hbox (badness 10000) detected at line 794 [][][] [974] Underfull \hbox (badness 10000) detected at line 831 [][][] [975] Underfull \hbox (badness 10000) detected at line 875 [][][] [976] Underfull \hbox (badness 10000) detected at line 925 [][][] Underfull \hbox (badness 10000) detected at line 947 [][][] [977] Underfull \hbox (badness 10000) detected at line 969 [][][] Underfull \hbox (badness 10000) detected at line 991 [][][] Underfull \hbox (badness 10000) detected at line 994 [][][] Underfull \hbox (badness 10000) detected at line 1011 [][][] Underfull \hbox (badness 10000) detected at line 1014 [][][] [978] Underfull \hbox (badness 10000) detected at line 1036 [][][] Underfull \hbox (badness 10000) detected at line 1039 [][][] Underfull \hbox (badness 10000) detected at line 1061 [][][] Underfull \hbox (badness 10000) detected at line 1064 [][][] Underfull \hbox (badness 10000) detected at line 1096 [][][] [979] Underfull \hbox (badness 10000) detected at line 1113 [][][] Underfull \hbox (badness 10000) detected at line 1145 [][][] Underfull \hbox (badness 10000) detected at line 1148 [][][] ) (./vpmg_8c_source.tex [980] [981] [982] [983] [984] [985] [986] [987] [988] [989] [990] [991] [992] [993] [994] [995] [996] [997] [998] [999] [1000] [1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008] [1009] [1010] [1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] [1021] [1022] [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] [1033] [1034] [1035] [1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] [1090] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112] [1113] [1114] [1115] [1116]) (./vpmg_8h.tex <./vpmg_8h__in cl.pdf> <./vpmg_8h__dep__incl.pdf> [1117] [1118] [1119] [1120] [1121] [1122] Underfull \hbox (badness 10000) detected at line 233 [][][] Underfull \hbox (badness 10000) detected at line 236 [][][] Underfull \hbox (badness 10000) detected at line 239 [][][] [1123] [1124] Underfull \hbox (badness 10000) detected at line 404 [][][] Underfull \hbox (badness 10000) detected at line 421 [][][] [1125] Underfull \hbox (badness 10000) detected at line 467 [][][] Underfull \hbox (badness 10000) detected at line 470 [][][] Underfull \hbox (badness 10000) detected at line 492 [][][] Underfull \hbox (badness 10000) detected at line 495 [][][] [1126] Underfull \hbox (badness 10000) detected at line 517 [][][] Underfull \hbox (badness 10000) detected at line 520 [][][] Underfull \hbox (badness 10000) detected at line 542 [][][] Underfull \hbox (badness 10000) detected at line 545 [][][] Underfull \hbox (badness 10000) detected at line 567 [][][] Underfull \hbox (badness 10000) detected at line 570 [][][] [1127] Underfull \hbox (badness 10000) detected at line 592 [][][] Underfull \hbox (badness 10000) detected at line 595 [][][] Underfull \hbox (badness 10000) detected at line 617 [][][] Underfull \hbox (badness 10000) detected at line 620 [][][] Underfull \hbox (badness 10000) detected at line 637 [][][] Underfull \hbox (badness 10000) detected at line 640 [][][] [1128] Underfull \hbox (badness 10000) detected at line 657 [][][] Underfull \hbox (badness 10000) detected at line 674 [][][] Underfull \hbox (badness 10000) detected at line 691 [][][] Underfull \hbox (badness 10000) detected at line 708 [][][] Underfull \hbox (badness 10000) detected at line 725 [][][] [1129] Underfull \hbox (badness 10000) detected at line 742 [][][] Underfull \hbox (badness 10000) detected at line 759 [][][] Underfull \hbox (badness 10000) detected at line 780 [][][] Underfull \hbox (badness 10000) detected at line 783 [][][] Underfull \hbox (badness 10000) detected at line 800 [][][] [1130] Underfull \hbox (badness 10000) detected at line 817 [][][] Underfull \hbox (badness 10000) detected at line 834 [][][] Underfull \hbox (badness 10000) detected at line 851 [][][] Underfull \hbox (badness 10000) detected at line 868 [][][] Underfull \hbox (badness 10000) detected at line 881 [][][] [1131] Underfull \hbox (badness 10000) detected at line 894 [][][] Underfull \hbox (badness 10000) detected at line 911 [][][] [1132] Underfull \hbox (badness 10000) detected at line 955 [][][] Underfull \hbox (badness 10000) detected at line 985 [][][] [1133] Underfull \hbox (badness 10000) detected at line 1007 [][][] Underfull \hbox (badness 10000) detected at line 1029 [][][] Underfull \hbox (badness 10000) detected at line 1051 [][][] Underfull \hbox (badness 10000) detected at line 1054 [][][] Underfull \hbox (badness 10000) detected at line 1071 [][][] [1134] Underfull \hbox (badness 10000) detected at line 1074 [][][] Underfull \hbox (badness 10000) detected at line 1096 [][][] Underfull \hbox (badness 10000) detected at line 1099 [][][] Underfull \hbox (badness 10000) detected at line 1121 [][][] Underfull \hbox (badness 10000) detected at line 1124 [][][] [1135] Underfull \hbox (badness 10000) detected at line 1156 [][][] Underfull \hbox (badness 10000) detected at line 1173 [][][] [1136] Underfull \hbox (badness 10000) detected at line 1205 [][][] Underfull \hbox (badness 10000) detected at line 1208 [][][] ) (./vpmg_8h_source.tex [1137] [1138] [1139] [1140] [1141] [1142] [1143] [1144]) (./vpmgp_8c.tex <./vpmgp_8c__incl.pdf> [1145] [1146] Underfull \hbox (badness 10000) detected at line 38 [][][] Underfull \hbox (badness 10000) detected at line 41 [][][] Underfull \hbox (badness 10000) detected at line 44 [][][] [1147]) (./vpmgp_8c_source.tex [1148] [1149] [1150]) (./vpmgp_8h.tex <./vpmgp_8 h__incl.pdf> [1151] <./vpmgp_8h__dep__incl.pdf> [1152] [1153] Underfull \hbox (badness 10000) detected at line 56 [][][] Underfull \hbox (badness 10000) detected at line 59 [][][] Underfull \hbox (badness 10000) detected at line 62 [][][] Underfull \hbox (badness 10000) detected at line 65 [][][] [1154]) (./vpmgp_8h_source.tex [1155]) (./build_ad_8c_source.tex [1156] [1157] [1158]) (./build_ad_8h_source.tex [1159]) (./build_bd_8c_source.tex [1160] [1161] [1162] [1163]) (./build_bd_8h_source.tex [1164]) (./build_gd_8c_source.tex [1165] [1166] [1167] [1168] [1169] [1170] [1171] [1172] [1173] [1174] [1175] [1176] [1177] [1178] [1179] [1180] [1181] [1182] [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] [1191] [1192] [1193] [1194] [1195] [1196] [1197] [1198] [1199] [1200] [1201] [1202]) (./build_gd_8h_source.tex [1203] [1204]) (./build_pd_8c_source.tex [1205] [1206] [1207] [1208] [1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216] [1217] [1218] [1219] [1220] [1221] [1222] [1223]) (./build_pd_8h_source.tex [1224] [1225] [1226]) (./cgd_8c_source.tex) (./cgd_8h_source.tex [1227]) (./gsd_8c_source.tex [1228] [1229] [1230] [1231]) (./gsd_8h_source.tex [1232]) (./matvecd_8c_source.tex [1233] [1234] [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242] [1243] [1244] [1245]) (./matvecd_8h_source.tex [1246] [1247] [1248] [1249] [1250] [1251]) (./mgcsd_8c_source.tex [1252] [1253] [1254] [1255] [1256] [1257]) (./mgcsd_8h_source.tex [1258]) (./mgdrvd_8c_source.tex [1259] [1260] [1261] [1262] [1263] [1264] [1265]) (./mgdrvd_8h_source.tex [1266] [1267]) (./mgfasd_8c_source.tex [1268] [1269] [1270] [1271] [1272] [1273]) (./mgfasd_8h_source.tex [1274] [1275]) (./mgsubd_8c_source.tex [1276] [1277] [1278] [1279] [1280] [1281] [1282] [1283] [1284] [1285] [1286]) (./mgsubd_8h_source.tex [1287] [1288] [1289] [1290]) (./mikpckd_8c_source.tex [1291] [1292] [1293] [1294]) (./mikpckd_8h_source.tex [1295] [1296] [1297]) (./mlinpckd_8c_source.tex [1298] [1299]) (./mlinpckd_8h_source.tex) (./mypdec_8c_source.tex [1300] [1301] [1302] [1303] [1304] [1305] [1306]) (./mypdec_8h_source.tex [1307]) (./newdrvd_8c_source.tex [1308] [1309] [1310] [1311]) (./newdrvd_8h_source.tex [1312]) (./newtond_8c_source.tex [1313] [1314] [1315] [1316] [1317] [1318] [1319]) (./newtond_8h_source.tex [1320]) (./powerd_8c_source.tex [1321] [1322] [1323] [1324] [1325]) (./powerd_8h_source.tex [1326]) (./smoothd_8c_source.tex [1327]) (./smoothd_8h_source.tex [1328]) (./routines_8c.tex <./routines_8c__incl.pdf> [1329] Underfull \hbox (badness 776) in paragraph at lines 47--48 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv /m/n/10 alist[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[] Underfull \hbox (badness 2856) in paragraph at lines 47--48 \T1/phv/m/n/10 YMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]ZMap[] [][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 kappa[]Map[][][], [] Underfull \hbox (badness 1237) in paragraph at lines 47--48 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 charge[]Map[][][], [] $\OMS/cmsy/m/n/10 ^^C $\T1/phv/m/n/10 pmgp[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pmg[][][], [] Underfull \hbox (badness 905) in paragraph at lines 61--62 []\T1/phv/m/n/10 VPUBLIC void [] (Vmem $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 mem , [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, int nforce[][][], [] $\OMS/cmsy /m/n/10 ^^C$\T1/phv/m/n/10 atom[] Underfull \hbox (badness 5817) in paragraph at lines 67--68 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], Underfull \hbox (badness 5817) in paragraph at lines 69--70 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], [1330] Underfull \hbox (badness 1442) in paragraph at lines 81--82 []\T1/phv/m/n/10 VPUBLIC int [] (Vcom $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 com, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, int nforce[][][], [] $\OMS/cmsy/ m/n/10 ^^C$\T1/phv/m/n/10 atom[] Underfull \hbox (badness 931) in paragraph at lines 87--88 []\T1/phv/m/n/10 VPUBLIC void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T 1/phv/m/n/10 fetk[][][], Gem Underfull \hbox (badness 2495) in paragraph at lines 89--90 []\T1/phv/m/n/10 VPUBLIC Vrc[]_[][]Codes [] (int icalc, [] $\OMS/cmsy/m/n/10 ^^ C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 feparm, [] $\OMS /cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbeparm, [] [1331] Underfull \hbox (badness 10000) detected at line 116 [][][] Underfull \hbox (badness 10000) detected at line 119 [][][] Underfull \hbox (badness 10000) detected at line 122 [][][] ) (./routines_8c_source.tex [1332] [1333] [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341] [1342] [1343] [1344] [1345] [1346] [1347] [1348] [1349] [1350] [1351] [1352] [1353] [1354] [1355] [1356] [1357] [1358] [1359] [1360] [1361] [1362] [1363] [1364] [1365] [1366] [1367] [1368] [1369] [1370] [1371] [1372] [1373] [1374] [1375] [1376] [1377] [1378] [1379] [1380] [1381] [1382] [1383] [1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] [1392] [1393] [1394] [1395] [1396] [1397] [1398] [1399] [1400]) (./routines_8h.tex <./routine s_8h__incl.pdf> <./routines_8h__dep__incl.pdf> [1401] Overfull \hbox (16.65858pt too wide) in paragraph at lines 50--51 []\T1/phv/m/n/10 VEXTERNC int [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], Overfull \hbox (16.91972pt too wide) in paragraph at lines 52--53 []\T1/phv/m/n/10 VEXTERNC void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh , [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][][], [] $\OMS/cmsy/m/n/1 0 ^^C$\T1/phv/m/n/10 diel[]YMap[][][], Underfull \hbox (badness 1910) in paragraph at lines 70--71 [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbe[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1 /phv/m/n/10 alist[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][] [], [] Underfull \hbox (badness 1237) in paragraph at lines 70--71 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 charge[]Map[][][], [] $\OMS/cmsy/m/n/10 ^^C $\T1/phv/m/n/10 pmgp[][][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pmg[][][], [] [1402] Underfull \hbox (badness 5817) in paragraph at lines 88--89 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], Underfull \hbox (badness 5817) in paragraph at lines 90--91 \T1/phv/m/n/10 int nenergy[][][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 atom[]Energy[][][], int nforce[][][], [1403] Underfull \hbox (badness 2495) in paragraph at lines 122--123 []\T1/phv/m/n/10 VPUBLIC Vrc[]_[][]Codes [] (int icalc, [] $\OMS/cmsy/m/n/10 ^^ C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 feparm, [] $\OMS /cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pbeparm, [] Underfull \hbox (badness 10000) detected at line 145 [][][] Underfull \hbox (badness 10000) detected at line 148 [][][] Underfull \hbox (badness 10000) detected at line 151 [][][] [1404]) (./routines_8h_source.tex [1405] [1406] [1407] [1408] [1409]) [1410] (./refman.ind [1411] [1412] [1413] [1414] [1415] [1416] [1417] [1418] [1419] [1420] [1421] [1422] [1423] [1424] [1425] [1426] [1427] [1428] [1429] [1430] [1431] [1432] [1433] [1434] [1435] [1436] [1437] [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] [1449] [1450] [1451] [1452] [1453] [1454] [1455] [1456] [1457] [1458] [1459]) (./refman.aux) ) (see the transcript file for additional information)< /usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrro8a.pfb> Output written on refman.pdf (1517 pages, 6288270 bytes). Transcript written on refman.log. [ 55%] Built target doc-pdf [ 57%] Built target mgmesh [ 59%] Built target smooth [ 62%] Built target dxmath [ 64%] Built target mergedx [ 66%] Built target mergedx2 [ 68%] Built target value [ 71%] Built target multivalue [ 73%] Built target benchmark [ 75%] Built target similarity [ 78%] Built target analysis [ 80%] Built target dx2mol [ 82%] Built target dx2uhbd [ 85%] Built target del2dx [ 87%] Built target tensor2dx [ 89%] Built target uhbd_asc2bin [ 91%] Built target coulomb [ 94%] Built target born [ 95%] Built target apbslib_swig_compilation [ 97%] Built target _apbslib [100%] Built target iapbs Install the project... -- Install configuration: "Release" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/share/apbs/doc/programmer -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/share/apbs/doc/programmer/programmer.pdf -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/share/apbs/doc/programmer/html -- Installing: 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/builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/share/apbs/tools/bin/del2dx -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/share/apbs/tools/bin/dx2uhbd -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/share/apbs/tools/bin/dx2mol -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/share/apbs/tools/bin/analysis -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/share/apbs/tools/bin/similarity -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/share/apbs/tools/bin/benchmark -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/share/apbs/tools/bin/multivalue -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/share/apbs/tools/bin/value -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/share/apbs/tools/bin/mergedx2 -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/share/apbs/tools/bin/mergedx -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/share/apbs/tools/bin/dxmath -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/share/apbs/tools/bin/smooth -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/share/apbs/tools/bin/mgmesh -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/lib64/libapbs.so.1 -- Set runtime path of "/builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/lib64/libapbs.so.1" to "/usr/lib" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/lib64/libapbs.so -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/include/apbs/apbscfg.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/include/apbs/apbs.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/include/apbs/routines.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs -- Set runtime path of "/builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs" to "/usr/lib" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/include/apbs/generic/nosh.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/include/apbs/generic/mgparm.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/include/apbs/generic/femparm.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/include/apbs/generic/pbamparm.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/include/apbs/generic/pbsamparm.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/include/apbs/generic/pbeparm.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/include/apbs/generic/bemparm.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/include/apbs/generic/geoflowparm.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/include/apbs/generic/apolparm.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/include/apbs/generic/vacc.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/include/apbs/generic/valist.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/include/apbs/generic/vatom.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/include/apbs/generic/vpbe.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/include/apbs/generic/vcap.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/include/apbs/generic/vclist.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/include/apbs/generic/vstring.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/include/apbs/generic/vparam.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/include/apbs/generic/vgreen.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/include/apbs/generic/vmatrix.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/include/apbs/generic/vhal.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/include/apbs/generic/vunit.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/include/apbs/pmgc/buildAd.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/include/apbs/pmgc/buildBd.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/include/apbs/pmgc/buildGd.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/include/apbs/pmgc/buildPd.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/include/apbs/pmgc/cgd.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/include/apbs/pmgc/gsd.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/include/apbs/pmgc/matvecd.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/include/apbs/pmgc/mgcsd.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/include/apbs/pmgc/mgdrvd.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/include/apbs/pmgc/mgsubd.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/include/apbs/pmgc/mikpckd.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/include/apbs/pmgc/mlinpckd.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/include/apbs/pmgc/mypdec.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/include/apbs/pmgc/newtond.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/include/apbs/pmgc/newdrvd.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/include/apbs/pmgc/powerd.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/include/apbs/pmgc/smoothd.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/include/apbs/pmgc/mgfasd.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/include/apbs/mg/vgrid.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/include/apbs/mg/vmgrid.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/include/apbs/mg/vopot.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/include/apbs/mg/vpmg.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/include/apbs/mg/vpmgp.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/mgmesh -- Set runtime path of "/builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/mgmesh" to "/usr/lib" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/smooth -- Set runtime path of "/builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/smooth" to "/usr/lib" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/dxmath -- Set runtime path of "/builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/dxmath" to "/usr/lib" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/mergedx -- Set runtime path of "/builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/mergedx" to "/usr/lib" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/mergedx2 -- Set runtime path of "/builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/mergedx2" to "/usr/lib" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/value -- Set runtime path of "/builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/value" to "/usr/lib" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/multivalue -- Set runtime path of "/builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/multivalue" to "/usr/lib" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/benchmark -- Set runtime path of "/builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/benchmark" to "/usr/lib" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/similarity -- Set runtime path of "/builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/similarity" to "/usr/lib" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/analysis -- Set runtime path of "/builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/analysis" to "/usr/lib" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/dx2mol -- Set runtime path of "/builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/dx2mol" to "/usr/lib" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/dx2uhbd -- Set runtime path of "/builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/dx2uhbd" to "/usr/lib" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/del2dx -- Set runtime path of "/builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/del2dx" to "/usr/lib" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/tensor2dx -- Set runtime path of "/builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/tensor2dx" to "/usr/lib" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/uhbd_asc2bin -- Set runtime path of "/builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/uhbd_asc2bin" to "/usr/lib" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/coulomb -- Set runtime path of "/builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/coulomb" to "/usr/lib" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/born -- Set runtime path of "/builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/born" to "/usr/lib" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/lib/libiapbs.a -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/include/iapbs/apbs_driver.h make: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/coulomb + cp -p /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/coulomb /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs-coulomb + rm -f /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/coulomb + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/born + cp -p /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/born /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs-born + rm -f /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/born + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/mgmesh + cp -p /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/mgmesh /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs-mgmesh + rm -f /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/mgmesh + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/dxmath + cp -p /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/dxmath /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs-dxmath + rm -f /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/dxmath + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/mergedx2 + cp -p /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/mergedx2 /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs-mergedx2 + rm -f /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/mergedx2 + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/mergedx + cp -p /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/mergedx /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs-mergedx + rm -f /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/mergedx + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/value + cp -p /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/value /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs-value + rm -f /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/value + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/uhbd_asc2bin + cp -p /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/uhbd_asc2bin /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs-uhbd_asc2bin + rm -f /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/uhbd_asc2bin + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/smooth + cp -p /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/smooth /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs-smooth + rm -f /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/smooth + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/dx2mol + cp -p /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/dx2mol /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs-dx2mol + rm -f /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/dx2mol + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/dx2uhbd + cp -p /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/dx2uhbd /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs-dx2uhbd + rm -f /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/dx2uhbd + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/similarity + cp -p /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/similarity /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs-similarity + rm -f /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/similarity + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/multivalue + cp -p /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/multivalue /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs-multivalue + rm -f /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/multivalue + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/benchmark + cp -p /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/benchmark /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs-benchmark + rm -f /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/benchmark + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/analysis + cp -p /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/analysis /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs-analysis + rm -f /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/analysis + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/del2dx + cp -p /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/del2dx /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs-del2dx + rm -f /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/del2dx + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/tensor2dx + cp -p /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/tensor2dx /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs-tensor2dx + rm -f /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/tensor2dx + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs-{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs-coulomb + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs-{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs-born + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs-{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs-mgmesh + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs-{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs-dxmath + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs-{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs-mergedx2 + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs-{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs-mergedx + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs-{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs-value + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs-{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs-uhbd_asc2bin + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs-{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs-smooth + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs-{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs-dx2mol + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs-{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs-dx2uhbd + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs-{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs-similarity + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs-{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs-multivalue + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs-{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs-benchmark + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs-{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs-analysis + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs-{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs-del2dx + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs-{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs-tensor2dx + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/lib64/libapbs.so.1 + mkdir -p /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/lib64/python3.12/site-packages/apbs + install -pm 755 tools/manip/psize.py /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/lib64/python3.12/site-packages/apbs/ + /usr/bin/python3 /usr/lib/rpm/redhat/pathfix.py -pn -i /usr/bin/python3 /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/lib64/python3.12/site-packages/apbs/psize.py /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/lib64/python3.12/site-packages/apbs/psize.py: updating + ln -s /usr/lib64/python3.12/site-packages/apbs/psize.py /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/bin/apbs-psize.py + install -pm 755 build/lib/_apbslib.so /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/lib64/python3.12/site-packages/apbs/ + rm -rf /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/share/apbs ++ find /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64 -type f '(' -name '*.a' ')' + for i in `find /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64 -type f \( -name "*.a" \)` + rm -f /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/lib/libiapbs.a + /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 3.0.0-22.fc39 --unique-debug-suffix -3.0.0-22.fc39.x86_64 --unique-debug-src-base apbs-3.0.0-22.fc39.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/apbs-3.0.0 find-debuginfo: starting Extracting debug info from 20 files DWARF-compressing 20 files sepdebugcrcfix: Updated 20 CRC32s, 0 CRC32s did match. Creating .debug symlinks for symlinks to ELF files Copying sources found by 'debugedit -l' to /usr/src/debug/apbs-3.0.0-22.fc39.x86_64 5148 blocks find-debuginfo: done + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/check-rpaths + /usr/lib/rpm/redhat/brp-mangle-shebangs + /usr/lib/rpm/brp-remove-la-files + env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j2 Bytecompiling .py files below /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/lib/debug/usr/lib64/python3.12 using python3.12 Bytecompiling .py files below /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/lib64/python3.12 using python3.12 + /usr/lib/rpm/redhat/brp-python-hardlink Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.5kRy3o + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS ~/build/BUILD/apbs-3.0.0/tests ~/build/BUILD/apbs-3.0.0 + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd apbs-3.0.0 + pushd tests + export LD_LIBRARY_PATH=/builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/lib64 + LD_LIBRARY_PATH=/builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/lib64 + /usr/bin/python3 ./apbs_tester.py Testing all sections The following sections will be tested: born, actin-dimer-auto, actin-dimer-parallel, alkanes, FKBP, hca-bind, ionize, ion-pmf, ion-protein, pka-lig, point-pmf, solv ================================================================================ Running tests for born section -------------------------------------------------------------------------------- Testing forces from apbs-forces.in Checking forces for input file apbs-forces.inChecking Polar ForcesChecking Apolar ForcesElapsed time: 0.000733 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-auto.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol-auto.in ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 22 2024 at 00:00:00 Parsing input file apbs-mol-auto.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading XML-format atom data from ion.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.607073836227E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.383 x 0.383 x 0.383 Grid lengths: 24.495 x 24.495 x 24.495 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.200266567971E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to potential.dx.gz Total electrostatic energy = 4.732245131587E+03 kJ/mol Calculating forces... Writing potential to potential.dx.gz ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.190871482831E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.383 x 0.383 x 0.383 Grid lengths: 24.495 x 24.495 x 24.495 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.430874049735E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.962018684215E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -2.297735526282E+02 kJ/mol Global net ELEC energy = -2.297735526282E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-auto.out RESULT 960.7073836227 RESULT 2200.266567971 RESULT 4732.245131587 RESULT 1190.871482831 RESULT 2430.874049735 RESULT 4962.018684215 RESULT -229.7735526282 Testing computed result 9.607073836227E+02 against expected result 9.607074E+02 *** PASSED *** Testing computed result 2.200266567971E+03 against expected result 2.200267E+03 *** PASSED *** Testing computed result 4.732245131587E+03 against expected result 4.732245E+03 *** PASSED *** Testing computed result 1.190871482831E+03 against expected result 1.190871E+03 *** PASSED *** Testing computed result 2.430874049735E+03 against expected result 2.430874E+03 *** PASSED *** Testing computed result 4.962018684215E+03 against expected result 4.962019E+03 *** PASSED *** Testing computed result -2.297735526282E+02 against expected result -2.297735E+02 *** PASSED *** Elapsed time: 0.832948 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-auto.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol-auto.in ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 22 2024 at 00:00:00 Parsing input file apbs-smol-auto.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading XML-format atom data from ion.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.532928767450E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.383 x 0.383 x 0.383 Grid lengths: 24.495 x 24.495 x 24.495 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.201243880085E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.733006258977E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.190871482831E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.383 x 0.383 x 0.383 Grid lengths: 24.495 x 24.495 x 24.495 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.430874049735E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.962018684215E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -2.290124252387E+02 kJ/mol Global net ELEC energy = -2.290124252387E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-auto.out RESULT 953.292876745 RESULT 2201.243880085 RESULT 4733.006258977 RESULT 1190.871482831 RESULT 2430.874049735 RESULT 4962.018684215 RESULT -229.0124252387 Testing computed result 9.532928767450E+02 against expected result 9.532929E+02 *** PASSED *** Testing computed result 2.201243880085E+03 against expected result 2.201244E+03 *** PASSED *** Testing computed result 4.733006258977E+03 against expected result 4.733006E+03 *** PASSED *** Testing computed result 1.190871482831E+03 against expected result 1.190871E+03 *** PASSED *** Testing computed result 2.430874049735E+03 against expected result 2.430874E+03 *** PASSED *** Testing computed result 4.962018684215E+03 against expected result 4.962019E+03 *** PASSED *** Testing computed result -2.290124252387E+02 against expected result -2.290124E+02 *** PASSED *** Elapsed time: 0.758953 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-parallel.in Splitting the input file into 4 separate files using the inputgen utility BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol-parallel-PE0.in ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 22 2024 at 00:00:00 Parsing input file apbs-mol-parallel-PE0.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading XML-format atom data from ion.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.401768459022E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.142935592471E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485255308186E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707009E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557588E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949131E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.761864094552E+01 kJ/mol Global net ELEC energy = -5.761864094552E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-parallel-PE0.out Processor 0 results: 2.401768459022E+02 8.142935592471E+02 1.485255308186E+03 2.977178707009E+02 8.799304557588E+02 1.542873949131E+03 -5.761864094552E+01 BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol-parallel-PE1.in ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 22 2024 at 00:00:00 Parsing input file apbs-mol-parallel-PE1.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading XML-format atom data from ion.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.401768459022E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.142778312125E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485246667424E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707009E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557588E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949131E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.762728170718E+01 kJ/mol Global net ELEC energy = -5.762728170718E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-parallel-PE1.out Processor 1 results: 2.401768459022E+02 8.142778312125E+02 1.485246667424E+03 2.977178707009E+02 8.799304557588E+02 1.542873949131E+03 -5.762728170718E+01 BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol-parallel-PE2.in ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 22 2024 at 00:00:00 Parsing input file apbs-mol-parallel-PE2.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading XML-format atom data from ion.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.401768459091E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.142935605696E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485255306569E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707146E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557596E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949141E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.761864257239E+01 kJ/mol Global net ELEC energy = -5.761864257239E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-parallel-PE2.out Processor 2 results: 2.401768459091E+02 8.142935605696E+02 1.485255306569E+03 2.977178707146E+02 8.799304557596E+02 1.542873949141E+03 -5.761864257239E+01 BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol-parallel-PE3.in ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 22 2024 at 00:00:00 Parsing input file apbs-mol-parallel-PE3.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading XML-format atom data from ion.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.401768459091E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.142778325440E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485246665692E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707146E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557596E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949141E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.762728344954E+01 kJ/mol Global net ELEC energy = -5.762728344954E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-parallel-PE3.out Processor 3 results: 2.401768459091E+02 8.142778325440E+02 1.485246665692E+03 2.977178707146E+02 8.799304557596E+02 1.542873949141E+03 -5.762728344954E+01 RESULT 960.7073836226 RESULT 3257.1427835731997 RESULT 5941.0039478710005 RESULT 1190.8714828309999 RESULT 3519.7218230368003 RESULT 6171.495796544 RESULT -230.49184867463003 Testing computed result 9.607073836226E+02 against expected result 9.607074E+02 *** PASSED *** Testing computed result 3.257142783573E+03 against expected result 3.257143E+03 *** PASSED *** Testing computed result 5.941003947871E+03 against expected result 5.941004E+03 *** PASSED *** Testing computed result 1.190871482831E+03 against expected result 1.190871E+03 *** PASSED *** Testing computed result 3.519721823037E+03 against expected result 3.519722E+03 *** PASSED *** Testing computed result 6.171495796544E+03 against expected result 6.171496E+03 *** PASSED *** Testing computed result -2.304918486746E+02 against expected result -2.304918E+02 *** PASSED *** Elapsed time: 3.596451 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-parallel.in Splitting the input file into 4 separate files using the inputgen utility BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol-parallel-PE0.in ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 22 2024 at 00:00:00 Parsing input file apbs-smol-parallel-PE0.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading XML-format atom data from ion.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.383232191816E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.145369591602E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485524998001E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707009E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557588E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949131E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.734895113069E+01 kJ/mol Global net ELEC energy = -5.734895113069E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-parallel-PE0.out Processor 0 results: 2.383232191816E+02 8.145369591602E+02 1.485524998001E+03 2.977178707009E+02 8.799304557588E+02 1.542873949131E+03 -5.734895113069E+01 BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol-parallel-PE1.in ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 22 2024 at 00:00:00 Parsing input file apbs-smol-parallel-PE1.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading XML-format atom data from ion.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.383232191816E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.145419898332E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485529328612E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707009E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557588E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949131E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.734462051928E+01 kJ/mol Global net ELEC energy = -5.734462051928E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-parallel-PE1.out Processor 1 results: 2.383232191816E+02 8.145419898332E+02 1.485529328612E+03 2.977178707009E+02 8.799304557588E+02 1.542873949131E+03 -5.734462051928E+01 BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol-parallel-PE2.in ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 22 2024 at 00:00:00 Parsing input file apbs-smol-parallel-PE2.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading XML-format atom data from ion.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.383232191909E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.145369593489E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485524997676E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707146E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557596E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949141E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.734895146550E+01 kJ/mol Global net ELEC energy = -5.734895146550E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-parallel-PE2.out Processor 2 results: 2.383232191909E+02 8.145369593489E+02 1.485524997676E+03 2.977178707146E+02 8.799304557596E+02 1.542873949141E+03 -5.734895146550E+01 BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol-parallel-PE3.in ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 22 2024 at 00:00:00 Parsing input file apbs-smol-parallel-PE3.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading XML-format atom data from ion.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.383232191909E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.145419900310E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485529328301E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707146E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557596E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949141E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.734462084052E+01 kJ/mol Global net ELEC energy = -5.734462084052E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-parallel-PE3.out Processor 3 results: 2.383232191909E+02 8.145419900310E+02 1.485529328301E+03 2.977178707146E+02 8.799304557596E+02 1.542873949141E+03 -5.734462084052E+01 RESULT 953.292876745 RESULT 3258.1578983732998 RESULT 5942.108652589999 RESULT 1190.8714828309999 RESULT 3519.7218230368003 RESULT 6171.495796544 RESULT -229.38714395599 Testing computed result 9.532928767450E+02 against expected result 9.532929E+02 *** PASSED *** Testing computed result 3.258157898373E+03 against expected result 3.258158E+03 *** PASSED *** Testing computed result 5.942108652590E+03 against expected result 5.942109E+03 *** PASSED *** Testing computed result 1.190871482831E+03 against expected result 1.190871E+03 *** PASSED *** Testing computed result 3.519721823037E+03 against expected result 3.519722E+03 *** PASSED *** Testing computed result 6.171495796544E+03 against expected result 6.171496E+03 *** PASSED *** Testing computed result -2.293871439560E+02 against expected result -2.293871E+02 *** PASSED *** Elapsed time: 3.497797 seconds -------------------------------------------------------------------------------- Total elapsed time: 8.686882 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for actin-dimer-auto section -------------------------------------------------------------------------------- Testing input file apbs-mol-auto.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol-auto.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 22 2024 at 00:00:00 Parsing input file apbs-mol-auto.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1028.322 MB total, 1028.322 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.527617850342E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1028.322 MB total, 2042.113 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.919510754196E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1030.291 MB total, 2042.113 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.527671844880E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1030.291 MB total, 2046.048 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.915468859278E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1046.446 MB total, 2046.048 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.056317807611E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1046.446 MB total, 2069.492 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 5.836028296532E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 2 (mol2) - 1 (mol1) end Local net energy (PE 0) = 1.048683058625E+02 kJ/mol Global net ELEC energy = 1.048683058625E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 2069.492 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-auto.out RESULT 152761.7850342 RESULT 291951.0754196 RESULT 152767.184488 RESULT 291546.8859278 RESULT 305631.7807611 RESULT 583602.8296532 RESULT 104.8683058625 Testing computed result 1.527617850342E+05 against expected result 1.527618E+05 *** PASSED *** Testing computed result 2.919510754196E+05 against expected result 2.919511E+05 *** PASSED *** Testing computed result 1.527671844880E+05 against expected result 1.527672E+05 *** PASSED *** Testing computed result 2.915468859278E+05 against expected result 2.915469E+05 *** PASSED *** Testing computed result 3.056317807611E+05 against expected result 3.056318E+05 *** PASSED *** Testing computed result 5.836028296532E+05 against expected result 5.836028E+05 *** PASSED *** Testing computed result 1.048683058625E+02 against expected result 1.048683E+02 *** PASSED *** Elapsed time: 46.999307 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-auto.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol-auto.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 22 2024 at 00:00:00 Parsing input file apbs-smol-auto.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1028.322 MB total, 1028.322 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.528632421825E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1028.322 MB total, 2042.113 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.920618662320E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1030.291 MB total, 2042.113 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.529297900572E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1030.291 MB total, 2046.048 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.916592202835E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1046.446 MB total, 2046.048 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.059244262535E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1046.446 MB total, 2069.492 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 5.838306706232E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 2 (mol2) - 1 (mol1) end Local net energy (PE 0) = 1.095841077691E+02 kJ/mol Global net ELEC energy = 1.095841077691E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 2069.492 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-auto.out RESULT 152863.2421825 RESULT 292061.866232 RESULT 152929.7900572 RESULT 291659.2202835 RESULT 305924.4262535 RESULT 583830.6706232 RESULT 109.5841077691 Testing computed result 1.528632421825E+05 against expected result 1.528632E+05 *** PASSED *** Testing computed result 2.920618662320E+05 against expected result 2.920619E+05 *** PASSED *** Testing computed result 1.529297900572E+05 against expected result 1.529298E+05 *** PASSED *** Testing computed result 2.916592202835E+05 against expected result 2.916592E+05 *** PASSED *** Testing computed result 3.059244262535E+05 against expected result 3.059244E+05 *** PASSED *** Testing computed result 5.838306706232E+05 against expected result 5.838307E+05 *** PASSED *** Testing computed result 1.095841077691E+02 against expected result 1.095841E+02 *** PASSED *** Elapsed time: 37.411679 seconds -------------------------------------------------------------------------------- Total elapsed time: 84.410986 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for actin-dimer-parallel section -------------------------------------------------------------------------------- Testing input file apbs-mol-parallel.in Splitting the input file into 8 separate files using the inputgen utility BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol-parallel-PE0.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 22 2024 at 00:00:00 Parsing input file apbs-mol-parallel-PE0.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.335181353180E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.307364282738E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.892640552270E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.287357981689E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.237489755360E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 3.595556713401E+04 kJ/mol Calculating forces... Writing potential to pot-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 8.344489735005E+00 kJ/mol Global net ELEC energy = 8.344489735005E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-parallel-PE0.out Processor 0 results: 1.335181353180E+03 1.307364282738E+04 2.892640552270E+03 2.287357981689E+04 4.237489755360E+03 3.595556713401E+04 8.344489735005E+00 BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol-parallel-PE1.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 22 2024 at 00:00:00 Parsing input file apbs-mol-parallel-PE1.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.161150884899E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.271349239954E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -1.084559511557E-01 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -9.159185455930E-02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.161009682231E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 9.271249973273E+04 kJ/mol Calculating forces... Writing potential to pot-PE1.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = -9.010749548674E-01 kJ/mol Global net ELEC energy = -9.010749548674E-01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-parallel-PE1.out Processor 1 results: 1.161150884899E+04 9.271349239954E+04 1.084559511557E-01 9.159185455930E-02 1.161009682231E+04 9.271249973273E+04 -9.010749548674E-01 BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol-parallel-PE2.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 22 2024 at 00:00:00 Parsing input file apbs-mol-parallel-PE2.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -1.533327920982E+01 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.349327483109E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.753646268927E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.716901575464E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.760706267384E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 3.753396861378E+04 kJ/mol Calculating forces... Writing potential to pot-PE2.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 3.002011083293E+01 kJ/mol Global net ELEC energy = 3.002011083293E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-parallel-PE2.out Processor 2 results: 1.533327920982E+01 3.349327483109E+02 4.753646268927E+03 3.716901575464E+04 4.760706267384E+03 3.753396861378E+04 3.002011083293E+01 BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol-parallel-PE3.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 22 2024 at 00:00:00 Parsing input file apbs-mol-parallel-PE3.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.803290534287E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.400275505449E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -8.150603559111E-01 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -8.573366340513E-01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.804039178218E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 1.400354034488E+05 kJ/mol Calculating forces... Writing potential to pot-PE3.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 8.710240552123E+00 kJ/mol Global net ELEC energy = 8.710240552123E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-parallel-PE3.out Processor 3 results: 1.803290534287E+04 1.400275505449E+05 8.150603559111E-01 8.573366340513E-01 1.804039178218E+04 1.400354034488E+05 8.710240552123E+00 BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol-parallel-PE4.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 22 2024 at 00:00:00 Parsing input file apbs-mol-parallel-PE4.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.015087619451E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.216054441666E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.620207421716E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.273875050379E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.666622027749E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 1.306246439444E+05 kJ/mol Calculating forces... Writing potential to pot-PE4.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 2.108446480104E+01 kJ/mol Global net ELEC energy = 2.108446480104E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-parallel-PE4.out Processor 4 results: 4.015087619451E+02 3.216054441666E+03 1.620207421716E+04 1.273875050379E+05 1.666622027749E+04 1.306246439444E+05 2.108446480104E+01 BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol-parallel-PE5.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 22 2024 at 00:00:00 Parsing input file apbs-mol-parallel-PE5.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.100112513614E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.662571883858E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -4.370921758038E-01 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -4.013366922344E-01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.115105077953E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 1.662768924081E+04 kJ/mol Calculating forces... Writing potential to pot-PE5.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 2.371738924671E+00 kJ/mol Global net ELEC energy = 2.371738924671E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-parallel-PE5.out Processor 5 results: 2.100112513614E+03 1.662571883858E+04 4.370921758038E-01 4.013366922344E-01 2.115105077953E+03 1.662768924081E+04 2.371738924671E+00 BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol-parallel-PE6.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 22 2024 at 00:00:00 Parsing input file apbs-mol-parallel-PE6.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -2.817378781616E+00 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -1.959534462269E+00 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.176793266728E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.643533578081E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.176229449467E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 9.643148330287E+04 kJ/mol Calculating forces... Writing potential to pot-PE6.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = -1.892943480882E+00 kJ/mol Global net ELEC energy = -1.892943480882E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-parallel-PE6.out Processor 6 results: 2.817378781616E+00 1.959534462269E+00 1.176793266728E+04 9.643533578081E+04 1.176229449467E+04 9.643148330287E+04 -1.892943480882E+00 BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol-parallel-PE7.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 22 2024 at 00:00:00 Parsing input file apbs-mol-parallel-PE7.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.428230292158E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.199832997920E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.881300088062E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.152799174875E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.847712854852E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 2.618156668929E+04 kJ/mol Calculating forces... Writing potential to pot-PE7.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 3.043753521012E+01 kJ/mol Global net ELEC energy = 3.043753521012E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-parallel-PE7.out Processor 7 results: 2.428230292158E+03 2.199832997920E+04 3.881300088062E+02 4.152799174875E+03 2.847712854852E+03 2.618156668929E+04 3.043753521012E+01 RESULT 35927.59777074854 RESULT 287991.6813140391 RESULT 36005.78432292607 RESULT 288019.58583029587 RESULT 72040.017332199 RESULT 576102.8221066899 RESULT 98.17456162013961 Testing computed result 3.592759777075E+04 against expected result 3.592760E+04 *** PASSED *** Testing computed result 2.879916813140E+05 against expected result 2.879917E+05 *** PASSED *** Testing computed result 3.600578432293E+04 against expected result 3.600578E+04 *** PASSED *** Testing computed result 2.880195858303E+05 against expected result 2.880196E+05 *** PASSED *** Testing computed result 7.204001733220E+04 against expected result 7.204002E+04 *** PASSED *** Testing computed result 5.761028221067E+05 against expected result 5.761028E+05 *** PASSED *** Testing computed result 9.817456162014E+01 against expected result 9.817456E+01 *** PASSED *** Elapsed time: 149.471162 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-parallel.in Splitting the input file into 8 separate files using the inputgen utility BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol-parallel-PE0.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 22 2024 at 00:00:00 Parsing input file apbs-smol-parallel-PE0.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.371266245949E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.306912276054E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977036667733E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.288057348250E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.356039288708E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 3.595842845220E+04 kJ/mol Calculating forces... Writing potential to pot-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 8.732209150865E+00 kJ/mol Global net ELEC energy = 8.732209150865E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-parallel-PE0.out Processor 0 results: 1.371266245949E+03 1.306912276054E+04 2.977036667733E+03 2.288057348250E+04 4.356039288708E+03 3.595842845220E+04 8.732209150865E+00 BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol-parallel-PE1.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 22 2024 at 00:00:00 Parsing input file apbs-smol-parallel-PE1.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.183935033618E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.276168507128E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -1.420924995464E-01 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -1.129046670919E-01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.183791435221E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 9.276041697078E+04 kJ/mol Calculating forces... Writing potential to pot-PE1.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = -1.155195837104E+00 kJ/mol Global net ELEC energy = -1.155195837104E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-parallel-PE1.out Processor 1 results: 1.183935033618E+04 9.276168507128E+04 1.420924995464E-01 1.129046670919E-01 1.183791435221E+04 9.276041697078E+04 -1.155195837104E+00 BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol-parallel-PE2.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 22 2024 at 00:00:00 Parsing input file apbs-smol-parallel-PE2.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -9.992726432058E+00 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.375960934473E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.863608503641E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.720602537782E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.896854387650E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 3.757590620855E+04 kJ/mol Calculating forces... Writing potential to pot-PE2.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 3.228473728523E+01 kJ/mol Global net ELEC energy = 3.228473728523E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-parallel-PE2.out Processor 2 results: 9.992726432058E+00 3.375960934473E+02 4.863608503641E+03 3.720602537782E+04 4.896854387650E+03 3.757590620855E+04 3.228473728523E+01 BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol-parallel-PE3.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 22 2024 at 00:00:00 Parsing input file apbs-smol-parallel-PE3.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.826846317904E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.401007397614E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -9.966525690477E-01 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -8.961424692860E-01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.827933209233E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 1.401092487740E+05 kJ/mol Calculating forces... Writing potential to pot-PE3.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 9.405155088028E+00 kJ/mol Global net ELEC energy = 9.405155088028E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-parallel-PE3.out Processor 3 results: 1.826846317904E+04 1.401007397614E+05 9.966525690477E-01 8.961424692860E-01 1.827933209233E+04 1.401092487740E+05 9.405155088028E+00 BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol-parallel-PE4.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 22 2024 at 00:00:00 Parsing input file apbs-smol-parallel-PE4.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.021998204986E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.215581388579E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.644646339930E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.274227930024E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.689865332202E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 1.306747503910E+05 kJ/mol Calculating forces... Writing potential to pot-PE4.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 3.637600005488E+01 kJ/mol Global net ELEC energy = 3.637600005488E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-parallel-PE4.out Processor 4 results: 4.021998204986E+02 3.215581388579E+03 1.644646339930E+04 1.274227930024E+05 1.689865332202E+04 1.306747503910E+05 3.637600005488E+01 BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol-parallel-PE5.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 22 2024 at 00:00:00 Parsing input file apbs-smol-parallel-PE5.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.187673595319E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.663590032901E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -4.710032885061E-01 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -4.849499127484E-01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.189033693728E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 1.663641996916E+04 kJ/mol Calculating forces... Writing potential to pot-PE5.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 1.004590063261E+00 kJ/mol Global net ELEC energy = 1.004590063261E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-parallel-PE5.out Processor 5 results: 2.187673595319E+03 1.663590032901E+04 4.710032885061E-01 4.849499127484E-01 2.189033693728E+03 1.663641996916E+04 1.004590063261E+00 BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol-parallel-PE6.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 22 2024 at 00:00:00 Parsing input file apbs-smol-parallel-PE6.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -4.897659240526E+00 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -2.552765434658E+00 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.200266111088E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.646358551314E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.199560371894E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 9.645933328248E+04 kJ/mol Calculating forces... Writing potential to pot-PE6.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = -1.699465221478E+00 kJ/mol Global net ELEC energy = -1.699465221478E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-parallel-PE6.out Processor 6 results: 4.897659240526E+00 2.552765434658E+00 1.200266111088E+04 9.646358551314E+04 1.199560371894E+04 9.645933328248E+04 -1.699465221478E+00 BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol-parallel-PE7.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 22 2024 at 00:00:00 Parsing input file apbs-smol-parallel-PE7.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.521894873214E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.200161660501E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.033680106430E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.154432431334E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.960165191413E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 2.618664307349E+04 kJ/mol Calculating forces... Writing potential to pot-PE7.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 3.059403714563E+01 kJ/mol Global net ELEC energy = 3.059403714563E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-parallel-PE7.out Processor 7 results: 2.521894873214E+03 2.200161660501E+04 4.033680106430E+02 4.154432431334E+03 2.960165191413E+03 2.618664307349E+04 3.059403714563E+01 RESULT 36605.73843587318 RESULT 288124.794774701 RESULT 36694.74744055409 RESULT 288128.90380424313 RESULT 73413.59604699901 RESULT 576361.14712166 RESULT 115.54206772931201 Testing computed result 3.660573843587E+04 against expected result 3.660574E+04 *** PASSED *** Testing computed result 2.881247947747E+05 against expected result 2.881248E+05 *** PASSED *** Testing computed result 3.669474744055E+04 against expected result 3.669475E+04 *** PASSED *** Testing computed result 2.881289038042E+05 against expected result 2.881289E+05 *** PASSED *** Testing computed result 7.341359604700E+04 against expected result 7.341360E+04 *** PASSED *** Testing computed result 5.763611471217E+05 against expected result 5.763611E+05 *** PASSED *** Testing computed result 1.155420677293E+02 against expected result 1.155421E+02 *** PASSED *** Elapsed time: 127.022622 seconds -------------------------------------------------------------------------------- Total elapsed time: 276.493784 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for alkanes section -------------------------------------------------------------------------------- Testing input file alkanes.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: alkanes.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 22 2024 at 00:00:00 Parsing input file alkanes.in... rank 0 size 1... Parsed input file. Reading parameter data from parm.dat. Got paths for 11 molecules Reading PDB-format atom data from 2-methylbutane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 17 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 4.33e+00 e Reading PDB-format atom data from butane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 14 atoms Centered at (3.917e+00, 7.025e-01, -8.575e+00) Net charge 3.51e+00 e Reading PDB-format atom data from cyclohexane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 18 atoms Centered at (1.123e+00, 5.880e-01, 7.680e-01) Net charge 4.93e+00 e Reading PDB-format atom data from cyclopentane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 13 atoms Centered at (1.320e+00, 5.255e-01, 1.289e+00) Net charge 3.88e+00 e Reading PDB-format atom data from ethane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 8 atoms Centered at (2.210e-01, -2.100e-02, 7.650e-01) Net charge 1.87e+00 e Reading PDB-format atom data from hexane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 20 atoms Centered at (4.951e+00, -9.500e-03, -8.406e+00) Net charge 5.16e+00 e Reading PDB-format atom data from isobutane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 14 atoms Centered at (1.859e+01, 1.864e+01, 1.921e+01) Net charge 3.51e+00 e Reading PDB-format atom data from methane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5 atoms Centered at (1.803e+01, 1.779e+01, 1.782e+01) Net charge 1.05e+00 e Reading PDB-format atom data from neopentane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 17 atoms Centered at (1.867e+01, 1.894e+01, 1.920e+01) Net charge 4.33e+00 e Reading PDB-format atom data from pentane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 17 atoms Centered at (4.460e+00, 1.615e-01, -8.566e+00) Net charge 4.33e+00 e Reading PDB-format atom data from propane.pdb. 11 atoms Centered at (1.836e+01, 1.896e+01, 1.861e+01) Net charge 2.69e+00 e Preparing to run 11 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated-2-methylbutane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 3.815624614267E+00 SASA for atom 1: 0.000000000000E+00 SASA for atom 2: 6.122920124655E-01 SASA for atom 3: 3.957497153740E+00 SASA for atom 4: 4.308445014544E+00 SASA for atom 5: 1.843264951960E+01 SASA for atom 6: 1.837011296483E+01 SASA for atom 7: 1.666599184724E+01 SASA for atom 8: 1.480031796315E+01 SASA for atom 9: 1.603020354037E+01 SASA for atom 10: 1.473778140838E+01 SASA for atom 11: 1.611879699297E+01 SASA for atom 12: 1.810954398660E+01 SASA for atom 13: 1.420100931324E+01 SASA for atom 14: 1.437298483886E+01 SASA for atom 15: 1.814081226399E+01 SASA for atom 16: 2.152820898091E+01 Total solvent accessible surface area: 214.202 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 3.243280922127E-02 Surface tension*area energy for atom 1: 0.000000000000E+00 Surface tension*area energy for atom 2: 5.204482105957E-03 Surface tension*area energy for atom 3: 3.363872580679E-02 Surface tension*area energy for atom 4: 3.662178262362E-02 Surface tension*area energy for atom 5: 1.566775209166E-01 Surface tension*area energy for atom 6: 1.561459602010E-01 Surface tension*area energy for atom 7: 1.416609307015E-01 Surface tension*area energy for atom 8: 1.258027026868E-01 Surface tension*area energy for atom 9: 1.362567300932E-01 Surface tension*area energy for atom 10: 1.252711419712E-01 Surface tension*area energy for atom 11: 1.370097744402E-01 Surface tension*area energy for atom 12: 1.539311238861E-01 Surface tension*area energy for atom 13: 1.207085791625E-01 Surface tension*area energy for atom 14: 1.221703711303E-01 Surface tension*area energy for atom 15: 1.541969042439E-01 Surface tension*area energy for atom 16: 1.829897763377E-01 Total surface tension energy: 1.82072 kJ/mol Total solvent accessible volume: 253.665 A^3 Total pressure*volume energy: 60.7274 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.271287875274E+00 WCA energy for atom 1: -5.600872869478E+00 WCA energy for atom 2: -5.773775123943E+00 WCA energy for atom 3: -6.072801488986E+00 WCA energy for atom 4: -6.378470721845E+00 WCA energy for atom 5: -1.573474558351E+00 WCA energy for atom 6: -1.582338715648E+00 WCA energy for atom 7: -1.504044838266E+00 WCA energy for atom 8: -1.351002262819E+00 WCA energy for atom 9: -1.437367175239E+00 WCA energy for atom 10: -1.384626257493E+00 WCA energy for atom 11: -1.468867560891E+00 WCA energy for atom 12: -1.557005662832E+00 WCA energy for atom 13: -1.473759654043E+00 WCA energy for atom 14: -1.502261431335E+00 WCA energy for atom 15: -1.550940901474E+00 WCA energy for atom 16: -1.667828659696E+00 Total WCA energy: -48.1507 kJ/mol Total non-polar energy = 1.439739455792E+01 kJ/mol ---------------------------------------- CALCULATION #2 (solvated-butane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 4.405515699447E+00 SASA for atom 1: 8.213673337951E-01 SASA for atom 2: 8.064333822716E-01 SASA for atom 3: 4.375647796400E+00 SASA for atom 4: 1.855251124959E+01 SASA for atom 5: 2.147609518526E+01 SASA for atom 6: 1.852645435176E+01 SASA for atom 7: 1.660345529247E+01 SASA for atom 8: 1.658782115377E+01 SASA for atom 9: 1.658260977421E+01 SASA for atom 10: 1.658260977421E+01 SASA for atom 11: 2.145003828744E+01 SASA for atom 12: 1.852124297220E+01 SASA for atom 13: 1.856293400871E+01 Total solvent accessible surface area: 193.855 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 3.744688344530E-02 Surface tension*area energy for atom 1: 6.981622337259E-03 Surface tension*area energy for atom 2: 6.854683749309E-03 Surface tension*area energy for atom 3: 3.719300626940E-02 Surface tension*area energy for atom 4: 1.576963456215E-01 Surface tension*area energy for atom 5: 1.825468090747E-01 Surface tension*area energy for atom 6: 1.574748619900E-01 Surface tension*area energy for atom 7: 1.411293699860E-01 Surface tension*area energy for atom 8: 1.409964798071E-01 Surface tension*area energy for atom 9: 1.409521830808E-01 Surface tension*area energy for atom 10: 1.409521830808E-01 Surface tension*area energy for atom 11: 1.823253254433E-01 Surface tension*area energy for atom 12: 1.574305652637E-01 Surface tension*area energy for atom 13: 1.577849390741E-01 Total surface tension energy: 1.64777 kJ/mol Total solvent accessible volume: 217.863 A^3 Total pressure*volume energy: 52.1564 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.728858147814E+00 WCA energy for atom 1: -6.204037472587E+00 WCA energy for atom 2: -6.202937735018E+00 WCA energy for atom 3: -6.728762249931E+00 WCA energy for atom 4: -1.623549989062E+00 WCA energy for atom 5: -1.709092300778E+00 WCA energy for atom 6: -1.625196457114E+00 WCA energy for atom 7: -1.484289341167E+00 WCA energy for atom 8: -1.485410538626E+00 WCA energy for atom 9: -1.485593139015E+00 WCA energy for atom 10: -1.484878734279E+00 WCA energy for atom 11: -1.708585062695E+00 WCA energy for atom 12: -1.625094916482E+00 WCA energy for atom 13: -1.624416805392E+00 Total WCA energy: -41.7207 kJ/mol Total non-polar energy = 1.208346456826E+01 kJ/mol ---------------------------------------- CALCULATION #3 (solvated-cyclohexane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 7.840324549863E-01 SASA for atom 1: 8.064333822716E-01 SASA for atom 2: 8.288343095569E-01 SASA for atom 3: 7.840324549863E-01 SASA for atom 4: 7.989664065098E-01 SASA for atom 5: 8.363012853187E-01 SASA for atom 6: 2.001169752764E+01 SASA for atom 7: 1.616048802948E+01 SASA for atom 8: 2.001169752764E+01 SASA for atom 9: 1.619175630687E+01 SASA for atom 10: 1.616048802948E+01 SASA for atom 11: 1.993352683418E+01 SASA for atom 12: 2.001169752764E+01 SASA for atom 13: 1.618133354774E+01 SASA for atom 14: 1.617091078861E+01 SASA for atom 15: 2.001690890721E+01 SASA for atom 16: 1.993873821374E+01 SASA for atom 17: 1.617091078861E+01 Total solvent accessible surface area: 221.799 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 6.664275867383E-03 Surface tension*area energy for atom 1: 6.854683749309E-03 Surface tension*area energy for atom 2: 7.045091631234E-03 Surface tension*area energy for atom 3: 6.664275867383E-03 Surface tension*area energy for atom 4: 6.791214455333E-03 Surface tension*area energy for atom 5: 7.108560925209E-03 Surface tension*area energy for atom 6: 1.700994289850E-01 Surface tension*area energy for atom 7: 1.373641482506E-01 Surface tension*area energy for atom 8: 1.700994289850E-01 Surface tension*area energy for atom 9: 1.376299286084E-01 Surface tension*area energy for atom 10: 1.373641482506E-01 Surface tension*area energy for atom 11: 1.694349780905E-01 Surface tension*area energy for atom 12: 1.700994289850E-01 Surface tension*area energy for atom 13: 1.375413351558E-01 Surface tension*area energy for atom 14: 1.374527417032E-01 Surface tension*area energy for atom 15: 1.701437257113E-01 Surface tension*area energy for atom 16: 1.694792748168E-01 Surface tension*area energy for atom 17: 1.374527417032E-01 Total surface tension energy: 1.88529 kJ/mol Total solvent accessible volume: 267.435 A^3 Total pressure*volume energy: 64.0239 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -5.793234697241E+00 WCA energy for atom 1: -5.784370526583E+00 WCA energy for atom 2: -5.791799130412E+00 WCA energy for atom 3: -5.788504399087E+00 WCA energy for atom 4: -5.797319672490E+00 WCA energy for atom 5: -5.787358035342E+00 WCA energy for atom 6: -1.523887929614E+00 WCA energy for atom 7: -1.413678912317E+00 WCA energy for atom 8: -1.521751604392E+00 WCA energy for atom 9: -1.414741802525E+00 WCA energy for atom 10: -1.413367854344E+00 WCA energy for atom 11: -1.523407238081E+00 WCA energy for atom 12: -1.523000623583E+00 WCA energy for atom 13: -1.413922068538E+00 WCA energy for atom 14: -1.416316744211E+00 WCA energy for atom 15: -1.524577474659E+00 WCA energy for atom 16: -1.523300410052E+00 WCA energy for atom 17: -1.414522566061E+00 Total WCA energy: -52.3691 kJ/mol Total non-polar energy = 1.354016672221E+01 kJ/mol ---------------------------------------- CALCULATION #4 (solvated-cyclopentane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 9.490526193215E+00 SASA for atom 1: 9.512927120500E+00 SASA for atom 2: 2.299828534626E+00 SASA for atom 3: 1.919012770776E+00 SASA for atom 4: 2.307295510388E+00 SASA for atom 5: 2.325838699632E+01 SASA for atom 6: 2.325838699632E+01 SASA for atom 7: 2.045987617019E+01 SASA for atom 8: 2.067875411190E+01 SASA for atom 9: 2.028790064456E+01 SASA for atom 10: 1.897463299431E+01 SASA for atom 11: 2.048593306801E+01 SASA for atom 12: 2.070481100972E+01 Total solvent accessible surface area: 193.638 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 8.066947264233E-02 Surface tension*area energy for atom 1: 8.085988052425E-02 Surface tension*area energy for atom 2: 1.954854254432E-02 Surface tension*area energy for atom 3: 1.631160855160E-02 Surface tension*area energy for atom 4: 1.961201183830E-02 Surface tension*area energy for atom 5: 1.976962894687E-01 Surface tension*area energy for atom 6: 1.976962894687E-01 Surface tension*area energy for atom 7: 1.739089474466E-01 Surface tension*area energy for atom 8: 1.757694099511E-01 Surface tension*area energy for atom 9: 1.724471554788E-01 Surface tension*area energy for atom 10: 1.612843804516E-01 Surface tension*area energy for atom 11: 1.741304310781E-01 Surface tension*area energy for atom 12: 1.759908935826E-01 Total surface tension energy: 1.64593 kJ/mol Total solvent accessible volume: 217.998 A^3 Total pressure*volume energy: 52.1887 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.343496616804E+00 WCA energy for atom 1: -6.327869601807E+00 WCA energy for atom 2: -6.334858040579E+00 WCA energy for atom 3: -6.296075406417E+00 WCA energy for atom 4: -6.345600816761E+00 WCA energy for atom 5: -1.663697465126E+00 WCA energy for atom 6: -1.662444032853E+00 WCA energy for atom 7: -1.572325104493E+00 WCA energy for atom 8: -1.604626551065E+00 WCA energy for atom 9: -1.586431484963E+00 WCA energy for atom 10: -1.554291291374E+00 WCA energy for atom 11: -1.574315220751E+00 WCA energy for atom 12: -1.604941679892E+00 Total WCA energy: -44.471 kJ/mol Total non-polar energy = 9.363673200142E+00 kJ/mol ---------------------------------------- CALCULATION #5 (solvated-ethane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 5.995981536705E+00 SASA for atom 1: 5.966113633657E+00 SASA for atom 2: 2.121552620704E+01 SASA for atom 3: 2.124158310486E+01 SASA for atom 4: 2.125200586399E+01 SASA for atom 5: 2.123116034573E+01 SASA for atom 6: 2.125200586399E+01 SASA for atom 7: 2.127285138225E+01 Total solvent accessible surface area: 139.427 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 5.096584306199E-02 Surface tension*area energy for atom 1: 5.071196588609E-02 Surface tension*area energy for atom 2: 1.803319727598E-01 Surface tension*area energy for atom 3: 1.805534563913E-01 Surface tension*area energy for atom 4: 1.806420498439E-01 Surface tension*area energy for atom 5: 1.804648629387E-01 Surface tension*area energy for atom 6: 1.806420498439E-01 Surface tension*area energy for atom 7: 1.808192367491E-01 Total surface tension energy: 1.18513 kJ/mol Total solvent accessible volume: 140.346 A^3 Total pressure*volume energy: 33.5988 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -7.360066353115E+00 WCA energy for atom 1: -7.355483516201E+00 WCA energy for atom 2: -1.776106201066E+00 WCA energy for atom 3: -1.773973940651E+00 WCA energy for atom 4: -1.775401936843E+00 WCA energy for atom 5: -1.773464835521E+00 WCA energy for atom 6: -1.774382856097E+00 WCA energy for atom 7: -1.772366599434E+00 Total WCA energy: -25.3612 kJ/mol Total non-polar energy = 9.422717598546E+00 kJ/mol ---------------------------------------- CALCULATION #6 (solvated-hexane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 4.405515699447E+00 SASA for atom 1: 8.213673337951E-01 SASA for atom 2: 3.285469335181E-01 SASA for atom 3: 2.986790304710E-01 SASA for atom 4: 1.855251124959E+01 SASA for atom 5: 2.147609518526E+01 SASA for atom 6: 1.852645435176E+01 SASA for atom 7: 1.655655287639E+01 SASA for atom 8: 1.655134149682E+01 SASA for atom 9: 1.360170066332E+01 SASA for atom 10: 1.357043238593E+01 SASA for atom 11: 1.381536722546E+01 SASA for atom 12: 1.384142412329E+01 SASA for atom 13: 7.765654792245E-01 SASA for atom 14: 1.684839013200E+01 SASA for atom 15: 1.682233323417E+01 SASA for atom 16: 4.166572475070E+00 SASA for atom 17: 2.179398933870E+01 SASA for atom 18: 1.877660057086E+01 SASA for atom 19: 1.876096643216E+01 Total solvent accessible surface area: 250.291 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 3.744688344530E-02 Surface tension*area energy for atom 1: 6.981622337259E-03 Surface tension*area energy for atom 2: 2.792648934903E-03 Surface tension*area energy for atom 3: 2.538771759003E-03 Surface tension*area energy for atom 4: 1.576963456215E-01 Surface tension*area energy for atom 5: 1.825468090747E-01 Surface tension*area energy for atom 6: 1.574748619900E-01 Surface tension*area energy for atom 7: 1.407306994493E-01 Surface tension*area energy for atom 8: 1.406864027230E-01 Surface tension*area energy for atom 9: 1.156144556382E-01 Surface tension*area energy for atom 10: 1.153486752804E-01 Surface tension*area energy for atom 11: 1.174306214164E-01 Surface tension*area energy for atom 12: 1.176521050479E-01 Surface tension*area energy for atom 13: 6.600806573408E-03 Surface tension*area energy for atom 14: 1.432113161220E-01 Surface tension*area energy for atom 15: 1.429898324905E-01 Surface tension*area energy for atom 16: 3.541586603809E-02 Surface tension*area energy for atom 17: 1.852489093789E-01 Surface tension*area energy for atom 18: 1.596011048523E-01 Surface tension*area energy for atom 19: 1.594682146734E-01 Total surface tension energy: 2.12748 kJ/mol Total solvent accessible volume: 298.053 A^3 Total pressure*volume energy: 71.3539 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.635406071935E+00 WCA energy for atom 1: -5.957247427848E+00 WCA energy for atom 2: -5.524801144538E+00 WCA energy for atom 3: -5.522294168859E+00 WCA energy for atom 4: -1.605314409440E+00 WCA energy for atom 5: -1.701051761776E+00 WCA energy for atom 6: -1.606669162773E+00 WCA energy for atom 7: -1.442505934938E+00 WCA energy for atom 8: -1.443059002759E+00 WCA energy for atom 9: -1.328947132810E+00 WCA energy for atom 10: -1.328906972440E+00 WCA energy for atom 11: -1.331566344214E+00 WCA energy for atom 12: -1.328041776815E+00 WCA energy for atom 13: -5.937562025661E+00 WCA energy for atom 14: -1.442277774427E+00 WCA energy for atom 15: -1.442777091510E+00 WCA energy for atom 16: -6.602262542378E+00 WCA energy for atom 17: -1.698172146664E+00 WCA energy for atom 18: -1.600970858835E+00 WCA energy for atom 19: -1.600841970217E+00 Total WCA energy: -57.0807 kJ/mol Total non-polar energy = 1.640068943201E+01 kJ/mol ---------------------------------------- CALCULATION #7 (solvated-isobutane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 3.464676753463E+00 SASA for atom 1: 1.984493338158E+01 SASA for atom 2: 1.778643845361E+01 SASA for atom 3: 1.671289426332E+01 SASA for atom 4: 0.000000000000E+00 SASA for atom 5: 3.531879535319E+00 SASA for atom 6: 1.673895116114E+01 SASA for atom 7: 1.793756846098E+01 SASA for atom 8: 1.973549441072E+01 SASA for atom 9: 1.710895911022E+01 SASA for atom 10: 4.599657069253E+00 SASA for atom 11: 1.937069784121E+01 SASA for atom 12: 1.654613011726E+01 SASA for atom 13: 1.936548646165E+01 Total solvent accessible surface area: 192.744 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 2.944975240444E-02 Surface tension*area energy for atom 1: 1.686819337434E-01 Surface tension*area energy for atom 2: 1.511847268556E-01 Surface tension*area energy for atom 3: 1.420596012382E-01 Surface tension*area energy for atom 4: 0.000000000000E+00 Surface tension*area energy for atom 5: 3.002097605021E-02 Surface tension*area energy for atom 6: 1.422810848697E-01 Surface tension*area energy for atom 7: 1.524693319183E-01 Surface tension*area energy for atom 8: 1.677517024912E-01 Surface tension*area energy for atom 9: 1.454261524369E-01 Surface tension*area energy for atom 10: 3.909708508865E-02 Surface tension*area energy for atom 11: 1.646509316503E-01 Surface tension*area energy for atom 12: 1.406421059967E-01 Surface tension*area energy for atom 13: 1.646066349240E-01 Total surface tension energy: 1.63832 kJ/mol Total solvent accessible volume: 218.943 A^3 Total pressure*volume energy: 52.415 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.381016335247E+00 WCA energy for atom 1: -1.612317964554E+00 WCA energy for atom 2: -1.588013719598E+00 WCA energy for atom 3: -1.532162371190E+00 WCA energy for atom 4: -5.987950445279E+00 WCA energy for atom 5: -6.393089030861E+00 WCA energy for atom 6: -1.533454887042E+00 WCA energy for atom 7: -1.587650918485E+00 WCA energy for atom 8: -1.614083521570E+00 WCA energy for atom 9: -1.442402031577E+00 WCA energy for atom 10: -6.408813541353E+00 WCA energy for atom 11: -1.605830214390E+00 WCA energy for atom 12: -1.529385873788E+00 WCA energy for atom 13: -1.605662490385E+00 Total WCA energy: -40.8218 kJ/mol Total non-polar energy = 1.323144287435E+01 kJ/mol ---------------------------------------- CALCULATION #8 (solvated-methane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 1.231304303117E+01 SASA for atom 1: 2.323233009850E+01 SASA for atom 2: 2.345641941977E+01 SASA for atom 3: 2.377431357320E+01 SASA for atom 4: 2.264344420771E+01 Total solvent accessible surface area: 105.42 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 1.046608657649E-01 Surface tension*area energy for atom 1: 1.974748058372E-01 Surface tension*area energy for atom 2: 1.993795650680E-01 Surface tension*area energy for atom 3: 2.020816653722E-01 Surface tension*area energy for atom 4: 1.924692757655E-01 Total surface tension energy: 0.896066 kJ/mol Total solvent accessible volume: 95.985 A^3 Total pressure*volume energy: 22.9788 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -8.133807570805E+00 WCA energy for atom 1: -1.962181541765E+00 WCA energy for atom 2: -1.964078319162E+00 WCA energy for atom 3: -1.963015006647E+00 WCA energy for atom 4: -1.957425549100E+00 Total WCA energy: -15.9805 kJ/mol Total non-polar energy = 7.894367190329E+00 kJ/mol ---------------------------------------- CALCULATION #9 (solvated-neopentane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 2.441701074100E+00 SASA for atom 1: 1.663993494942E+01 SASA for atom 2: 1.715586152630E+01 SASA for atom 3: 1.645753666466E+01 SASA for atom 4: 0.000000000000E+00 SASA for atom 5: 2.389432243768E+00 SASA for atom 6: 1.638457735076E+01 SASA for atom 7: 1.667641460637E+01 SASA for atom 8: 1.721839808108E+01 SASA for atom 9: 2.419300146815E+00 SASA for atom 10: 1.640021148945E+01 SASA for atom 11: 1.666599184724E+01 SASA for atom 12: 1.719234118325E+01 SASA for atom 13: 2.449168049862E+00 SASA for atom 14: 1.723403221977E+01 SASA for atom 15: 1.639500010989E+01 SASA for atom 16: 1.663472356985E+01 Total solvent accessible surface area: 210.755 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 2.075445912985E-02 Surface tension*area energy for atom 1: 1.414394470700E-01 Surface tension*area energy for atom 2: 1.458248229736E-01 Surface tension*area energy for atom 3: 1.398890616496E-01 Surface tension*area energy for atom 4: 0.000000000000E+00 Surface tension*area energy for atom 5: 2.031017407203E-02 Surface tension*area energy for atom 6: 1.392689074814E-01 Surface tension*area energy for atom 7: 1.417495241541E-01 Surface tension*area energy for atom 8: 1.463563836891E-01 Surface tension*area energy for atom 9: 2.056405124793E-02 Surface tension*area energy for atom 10: 1.394017976603E-01 Surface tension*area energy for atom 11: 1.416609307015E-01 Surface tension*area energy for atom 12: 1.461349000577E-01 Surface tension*area energy for atom 13: 2.081792842383E-02 Surface tension*area energy for atom 14: 1.464892738680E-01 Surface tension*area energy for atom 15: 1.393575009340E-01 Surface tension*area energy for atom 16: 1.413951503437E-01 Total surface tension energy: 1.79141 kJ/mol Total solvent accessible volume: 251.127 A^3 Total pressure*volume energy: 60.1198 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.011082520236E+00 WCA energy for atom 1: -1.497367782613E+00 WCA energy for atom 2: -1.498546483218E+00 WCA energy for atom 3: -1.492562171495E+00 WCA energy for atom 4: -5.447325863939E+00 WCA energy for atom 5: -6.004516149175E+00 WCA energy for atom 6: -1.492776531092E+00 WCA energy for atom 7: -1.496078170066E+00 WCA energy for atom 8: -1.501529655270E+00 WCA energy for atom 9: -5.996267554365E+00 WCA energy for atom 10: -1.492194267752E+00 WCA energy for atom 11: -1.496027211216E+00 WCA energy for atom 12: -1.500561393960E+00 WCA energy for atom 13: -6.000218612907E+00 WCA energy for atom 14: -1.500859921426E+00 WCA energy for atom 15: -1.492908499790E+00 WCA energy for atom 16: -1.494057174414E+00 Total WCA energy: -47.4149 kJ/mol Total non-polar energy = 1.449633815052E+01 kJ/mol ---------------------------------------- CALCULATION #10 (solvated-pentane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 4.405515699447E+00 SASA for atom 1: 8.213673337951E-01 SASA for atom 2: 3.285469335181E-01 SASA for atom 3: 7.466975761774E-01 SASA for atom 4: 1.855251124959E+01 SASA for atom 5: 2.147609518526E+01 SASA for atom 6: 1.852645435176E+01 SASA for atom 7: 1.655655287639E+01 SASA for atom 8: 1.655134149682E+01 SASA for atom 9: 1.360170066332E+01 SASA for atom 10: 1.357043238593E+01 SASA for atom 11: 1.685881289113E+01 SASA for atom 12: 1.687444702982E+01 SASA for atom 13: 4.196440378117E+00 SASA for atom 14: 1.881308022781E+01 SASA for atom 15: 1.882350298694E+01 SASA for atom 16: 2.182004623652E+01 Total solvent accessible surface area: 222.524 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 3.744688344530E-02 Surface tension*area energy for atom 1: 6.981622337259E-03 Surface tension*area energy for atom 2: 2.792648934903E-03 Surface tension*area energy for atom 3: 6.346929397508E-03 Surface tension*area energy for atom 4: 1.576963456215E-01 Surface tension*area energy for atom 5: 1.825468090747E-01 Surface tension*area energy for atom 6: 1.574748619900E-01 Surface tension*area energy for atom 7: 1.407306994493E-01 Surface tension*area energy for atom 8: 1.406864027230E-01 Surface tension*area energy for atom 9: 1.156144556382E-01 Surface tension*area energy for atom 10: 1.153486752804E-01 Surface tension*area energy for atom 11: 1.432999095746E-01 Surface tension*area energy for atom 12: 1.434327997535E-01 Surface tension*area energy for atom 13: 3.566974321399E-02 Surface tension*area energy for atom 14: 1.599111819364E-01 Surface tension*area energy for atom 15: 1.599997753890E-01 Surface tension*area energy for atom 16: 1.854703930104E-01 Total surface tension energy: 1.89145 kJ/mol Total solvent accessible volume: 258.93 A^3 Total pressure*volume energy: 61.9878 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.655804319869E+00 WCA energy for atom 1: -6.027315962813E+00 WCA energy for atom 2: -5.696430965386E+00 WCA energy for atom 3: -6.016749084714E+00 WCA energy for atom 4: -1.608595384643E+00 WCA energy for atom 5: -1.703300955380E+00 WCA energy for atom 6: -1.609931495887E+00 WCA energy for atom 7: -1.457107525189E+00 WCA energy for atom 8: -1.457741620594E+00 WCA energy for atom 9: -1.354235498709E+00 WCA energy for atom 10: -1.354106470090E+00 WCA energy for atom 11: -1.456736412636E+00 WCA energy for atom 12: -1.455995435596E+00 WCA energy for atom 13: -6.633650611186E+00 WCA energy for atom 14: -1.605996088477E+00 WCA energy for atom 15: -1.606549890103E+00 WCA energy for atom 16: -1.700042300035E+00 Total WCA energy: -49.4003 kJ/mol Total non-polar energy = 1.447900211546E+01 kJ/mol ---------------------------------------- CALCULATION #11 (solvated-propane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 3.173464698754E+00 SASA for atom 1: 1.931858404557E+01 SASA for atom 2: 2.014198201675E+01 SASA for atom 3: 2.149694070352E+01 SASA for atom 4: 1.904078819252E+00 SASA for atom 5: 2.067354273233E+01 SASA for atom 6: 1.937590922077E+01 SASA for atom 7: 3.098794941136E+00 SASA for atom 8: 1.942802301642E+01 SASA for atom 9: 1.973028303116E+01 SASA for atom 10: 2.204934693736E+01 Total solvent accessible surface area: 170.391 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 2.697444993941E-02 Surface tension*area energy for atom 1: 1.642079643873E-01 Surface tension*area energy for atom 2: 1.712068471424E-01 Surface tension*area energy for atom 3: 1.827239959799E-01 Surface tension*area energy for atom 4: 1.618466996365E-02 Surface tension*area energy for atom 5: 1.757251132248E-01 Surface tension*area energy for atom 6: 1.646952283766E-01 Surface tension*area energy for atom 7: 2.633975699966E-02 Surface tension*area energy for atom 8: 1.651381956396E-01 Surface tension*area energy for atom 9: 1.677074057649E-01 Surface tension*area energy for atom 10: 1.874194489675E-01 Total surface tension energy: 1.44832 kJ/mol Total solvent accessible volume: 183.573 A^3 Total pressure*volume energy: 43.9474 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.818670105515E+00 WCA energy for atom 1: -1.641297645338E+00 WCA energy for atom 2: -1.649584120441E+00 WCA energy for atom 3: -1.711408141255E+00 WCA energy for atom 4: -6.624720142882E+00 WCA energy for atom 5: -1.610117050515E+00 WCA energy for atom 6: -1.596858009746E+00 WCA energy for atom 7: -6.816460624835E+00 WCA energy for atom 8: -1.642782751806E+00 WCA energy for atom 9: -1.645779566650E+00 WCA energy for atom 10: -1.714436154542E+00 Total WCA energy: -33.4721 kJ/mol Total non-polar energy = 1.192358496286E+01 kJ/mol ---------------------------------------- PRINT STATEMENTS print APOL energy 1 (solvated-2-methylbutane) end Global net APOL energy = 1.439739455792E+01 kJ/mol print APOL energy 2 (solvated-butane) end Global net APOL energy = 1.208346456826E+01 kJ/mol print APOL energy 3 (solvated-cyclohexane) end Global net APOL energy = 1.354016672221E+01 kJ/mol print APOL energy 4 (solvated-cyclopentane) end Global net APOL energy = 9.363673200142E+00 kJ/mol print APOL energy 5 (solvated-ethane) end Global net APOL energy = 9.422717598546E+00 kJ/mol print APOL energy 6 (solvated-hexane) end Global net APOL energy = 1.640068943201E+01 kJ/mol print APOL energy 7 (solvated-isobutane) end Global net APOL energy = 1.323144287435E+01 kJ/mol print APOL energy 8 (solvated-methane) end Global net APOL energy = 7.894367190329E+00 kJ/mol print APOL energy 9 (solvated-neopentane) end Global net APOL energy = 1.449633815052E+01 kJ/mol print APOL energy 10 (solvated-pentane) end Global net APOL energy = 1.447900211546E+01 kJ/mol print APOL energy 11 (solvated-propane) end Global net APOL energy = 1.192358496286E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 11 molecules Final memory usage: 0.001 MB total, 2.267 MB high water Thanks for using APBS! Checking for intermidiate energies in input file alkanes.out RESULT 14.39739455792 RESULT 12.08346456826 RESULT 13.54016672221 RESULT 9.363673200142 RESULT 9.422717598546 RESULT 16.40068943201 RESULT 13.23144287435 RESULT 7.894367190329 RESULT 14.49633815052 RESULT 14.47900211546 RESULT 11.92358496286 Testing computed result 1.439739455792E+01 against expected result 1.439739E+01 *** PASSED *** Testing computed result 1.208346456826E+01 against expected result 1.208346E+01 *** PASSED *** Testing computed result 1.354016672221E+01 against expected result 1.354017E+01 *** PASSED *** Testing computed result 9.363673200142E+00 against expected result 9.363673E+00 *** PASSED *** Testing computed result 9.422717598546E+00 against expected result 9.422718E+00 *** PASSED *** Testing computed result 1.640068943201E+01 against expected result 1.640069E+01 *** PASSED *** Testing computed result 1.323144287435E+01 against expected result 1.323144E+01 *** PASSED *** Testing computed result 7.894367190329E+00 against expected result 7.894367E+00 *** PASSED *** Testing computed result 1.449633815052E+01 against expected result 1.449634E+01 *** PASSED *** Testing computed result 1.447900211546E+01 against expected result 1.447900E+01 *** PASSED *** Testing computed result 1.192358496286E+01 against expected result 1.192358E+01 *** PASSED *** Elapsed time: 8.909410 seconds -------------------------------------------------------------------------------- Total elapsed time: 8.909410 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for FKBP section -------------------------------------------------------------------------------- Testing input file 1d7h-dmso-mol.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: 1d7h-dmso-mol.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 22 2024 at 00:00:00 Parsing input file 1d7h-dmso-mol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from 1d7h-dmso-complex.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1673 atoms Centered at (2.587e+01, 1.835e+01, 1.911e+01) Net charge 9.91e-01 e Reading PQR-format atom data from dmso-min.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 10 atoms Centered at (1.775e+01, 1.777e+01, 2.049e+01) Net charge 2.78e-17 e Reading PQR-format atom data from 1d7h-min.pqr. 1663 atoms Centered at (2.587e+01, 1.835e+01, 1.911e+01) Net charge 9.91e-01 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (complex-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.059 MB total, 122.059 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.060899690259E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (complex-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.059 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.276523673491E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.059 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.399234956777E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (complex-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.059 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.610066575192E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (dmso-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.961107503213E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (dmso-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 7.121048606059E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (dmso-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.751571424823E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #8 (dmso-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 7.339101343121E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (1d7h-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.058410584089E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #10 (1d7h-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.205385249581E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (1d7h-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.395961902233E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (1d7h-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.538248433997E+04 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end Local net energy (PE 0) = -3.335429017008E+03 kJ/mol Global net ELEC energy = -3.335429017008E+03 kJ/mol print energy 6 (dmso-solv-fine) - 8 (dmso-ref-fine) end Local net energy (PE 0) = -2.180527370616E+01 kJ/mol Global net ELEC energy = -2.180527370616E+01 kJ/mol print energy 10 (1d7h-solv-fine) - 12 (1d7h-ref-fine) end Local net energy (PE 0) = -3.328631844166E+03 kJ/mol Global net ELEC energy = -3.328631844166E+03 kJ/mol print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) - 6 (dmso-solv-fine) + 8 (dmso-ref-fine) - 10 (1d7h-solv-fine) + 12 (1d7h-ref-fine) end Local net energy (PE 0) = 1.500810086371E+01 kJ/mol Global net ELEC energy = 1.500810086371E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 221.696 MB high water Thanks for using APBS! Checking for intermidiate energies in input file 1d7h-dmso-mol.out RESULT 10608.99690259 RESULT 42765.23673491 RESULT 13992.34956777 RESULT 46100.66575192 RESULT 39.61107503213 RESULT 712.1048606059 RESULT 67.51571424823 RESULT 733.9101343121 RESULT 10584.10584089 RESULT 42053.85249581 RESULT 13959.61902233 RESULT 45382.48433997 RESULT -3335.429017008 RESULT -21.80527370616 RESULT -3328.631844166 RESULT 15.00810086371 Testing computed result 1.060899690259E+04 against expected result 1.060900E+04 *** PASSED *** Testing computed result 4.276523673491E+04 against expected result 4.276524E+04 *** PASSED *** Testing computed result 1.399234956777E+04 against expected result 1.399235E+04 *** PASSED *** Testing computed result 4.610066575192E+04 against expected result 4.610067E+04 *** PASSED *** Testing computed result 3.961107503213E+01 against expected result 3.961108E+01 *** PASSED *** Testing computed result 7.121048606059E+02 against expected result 7.121049E+02 *** PASSED *** Testing computed result 6.751571424823E+01 against expected result 6.751571E+01 *** PASSED *** Testing computed result 7.339101343121E+02 against expected result 7.339101E+02 *** PASSED *** Testing computed result 1.058410584089E+04 against expected result 1.058411E+04 *** PASSED *** Testing computed result 4.205385249581E+04 against expected result 4.205385E+04 *** PASSED *** Testing computed result 1.395961902233E+04 against expected result 1.395962E+04 *** PASSED *** Testing computed result 4.538248433997E+04 against expected result 4.538248E+04 *** PASSED *** Testing computed result 1.500810086371E+01 against expected result 1.500810E+01 *** PASSED *** Elapsed time: 6.349128 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file 1d7h-dmso-smol.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: 1d7h-dmso-smol.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 22 2024 at 00:00:00 Parsing input file 1d7h-dmso-smol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from 1d7h-dmso-complex.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1673 atoms Centered at (2.587e+01, 1.835e+01, 1.911e+01) Net charge 9.91e-01 e Reading PQR-format atom data from dmso-min.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 10 atoms Centered at (1.775e+01, 1.777e+01, 2.049e+01) Net charge 2.78e-17 e Reading PQR-format atom data from 1d7h-min.pqr. 1663 atoms Centered at (2.587e+01, 1.835e+01, 1.911e+01) Net charge 9.91e-01 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (complex-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.059 MB total, 122.059 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.074948704824E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (complex-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.059 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.289487256481E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.059 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.399234956777E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (complex-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.059 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.610066575192E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (dmso-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.719709905887E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (dmso-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 7.125747080979E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (dmso-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.751571424823E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #8 (dmso-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 7.339101343121E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (1d7h-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.071654753674E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #10 (1d7h-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.218178203716E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (1d7h-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.395961902233E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (1d7h-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.538248433997E+04 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end Local net energy (PE 0) = -3.205793187109E+03 kJ/mol Global net ELEC energy = -3.205793187109E+03 kJ/mol print energy 6 (dmso-solv-fine) - 8 (dmso-ref-fine) end Local net energy (PE 0) = -2.133542621421E+01 kJ/mol Global net ELEC energy = -2.133542621421E+01 kJ/mol print energy 10 (1d7h-solv-fine) - 12 (1d7h-ref-fine) end Local net energy (PE 0) = -3.200702302816E+03 kJ/mol Global net ELEC energy = -3.200702302816E+03 kJ/mol print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) - 6 (dmso-solv-fine) + 8 (dmso-ref-fine) - 10 (1d7h-solv-fine) + 12 (1d7h-ref-fine) end Local net energy (PE 0) = 1.624454192073E+01 kJ/mol Global net ELEC energy = 1.624454192073E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 221.696 MB high water Thanks for using APBS! Checking for intermidiate energies in input file 1d7h-dmso-smol.out RESULT 10749.48704824 RESULT 42894.87256481 RESULT 13992.34956777 RESULT 46100.66575192 RESULT 37.19709905887 RESULT 712.5747080979 RESULT 67.51571424823 RESULT 733.9101343121 RESULT 10716.54753674 RESULT 42181.78203716 RESULT 13959.61902233 RESULT 45382.48433997 RESULT -3205.793187109 RESULT -21.33542621421 RESULT -3200.702302816 RESULT 16.24454192073 Testing computed result 1.074948704824E+04 against expected result 1.074949E+04 *** PASSED *** Testing computed result 4.289487256481E+04 against expected result 4.289487E+04 *** PASSED *** Testing computed result 1.399234956777E+04 against expected result 1.399235E+04 *** PASSED *** Testing computed result 4.610066575192E+04 against expected result 4.610067E+04 *** PASSED *** Testing computed result 3.719709905887E+01 against expected result 3.719710E+01 *** PASSED *** Testing computed result 7.125747080979E+02 against expected result 7.125747E+02 *** PASSED *** Testing computed result 6.751571424823E+01 against expected result 6.751571E+01 *** PASSED *** Testing computed result 7.339101343121E+02 against expected result 7.339101E+02 *** PASSED *** Testing computed result 1.071654753674E+04 against expected result 1.071655E+04 *** PASSED *** Testing computed result 4.218178203716E+04 against expected result 4.218178E+04 *** PASSED *** Testing computed result 1.395961902233E+04 against expected result 1.395962E+04 *** PASSED *** Testing computed result 4.538248433997E+04 against expected result 4.538248E+04 *** PASSED *** Testing computed result 1.624454192073E+01 against expected result 1.624454E+01 *** PASSED *** Elapsed time: 6.198450 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file 1d7i-dss-mol.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: 1d7i-dss-mol.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 22 2024 at 00:00:00 Parsing input file 1d7i-dss-mol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from 1d7i-dss-complex.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1677 atoms Centered at (2.526e+01, 1.899e+01, 1.912e+01) Net charge 9.91e-01 e Reading PQR-format atom data from dss-min.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 14 atoms Centered at (1.734e+01, 1.921e+01, 2.050e+01) Net charge -8.33e-17 e Reading PQR-format atom data from 1d7i-min.pqr. 1663 atoms Centered at (2.526e+01, 1.899e+01, 1.912e+01) Net charge 9.91e-01 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (complex-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.425 MB total, 122.425 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.160578033846E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (complex-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.425 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.955701871716E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.425 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.264965939588E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (complex-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.425 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.301801664829E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (dss-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.431133325426E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (dss-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.677348113184E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (dss-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.171079106781E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #8 (dss-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.697869784185E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (1d7i-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.040108332204E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #10 (1d7i-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.787747796627E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (1d7i-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.252495566243E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (1d7i-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.133237922574E+04 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end Local net energy (PE 0) = -3.460997931137E+03 kJ/mol Global net ELEC energy = -3.460997931137E+03 kJ/mol print energy 6 (dss-solv-fine) - 8 (dss-ref-fine) end Local net energy (PE 0) = -2.052167100108E+01 kJ/mol Global net ELEC energy = -2.052167100108E+01 kJ/mol print energy 10 (1d7i-solv-fine) - 12 (1d7i-ref-fine) end Local net energy (PE 0) = -3.454901259473E+03 kJ/mol Global net ELEC energy = -3.454901259473E+03 kJ/mol print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) - 6 (dss-solv-fine) + 8 (dss-ref-fine) - 10 (1d7i-solv-fine) + 12 (1d7i-ref-fine) end Local net energy (PE 0) = 1.442499933668E+01 kJ/mol Global net ELEC energy = 1.442499933668E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 222.305 MB high water Thanks for using APBS! Checking for intermidiate energies in input file 1d7i-dss-mol.out RESULT 9160.578033846 RESULT 39557.01871716 RESULT 12649.65939588 RESULT 43018.01664829 RESULT 94.31133325426 RESULT 1677.348113184 RESULT 117.1079106781 RESULT 1697.869784185 RESULT 9040.108332204 RESULT 37877.47796627 RESULT 12524.95566243 RESULT 41332.37922574 RESULT -3460.997931137 RESULT -20.52167100108 RESULT -3454.901259473 RESULT 14.42499933668 Testing computed result 9.160578033846E+03 against expected result 9.160578E+03 *** PASSED *** Testing computed result 3.955701871716E+04 against expected result 3.955702E+04 *** PASSED *** Testing computed result 1.264965939588E+04 against expected result 1.264966E+04 *** PASSED *** Testing computed result 4.301801664829E+04 against expected result 4.301802E+04 *** PASSED *** Testing computed result 9.431133325426E+01 against expected result 9.431133E+01 *** PASSED *** Testing computed result 1.677348113184E+03 against expected result 1.677348E+03 *** PASSED *** Testing computed result 1.171079106781E+02 against expected result 1.171079E+02 *** PASSED *** Testing computed result 1.697869784185E+03 against expected result 1.697870E+03 *** PASSED *** Testing computed result 9.040108332204E+03 against expected result 9.040108E+03 *** PASSED *** Testing computed result 3.787747796627E+04 against expected result 3.787748E+04 *** PASSED *** Testing computed result 1.252495566243E+04 against expected result 1.252496E+04 *** PASSED *** Testing computed result 4.133237922574E+04 against expected result 4.133238E+04 *** PASSED *** Testing computed result 1.442499933668E+01 against expected result 1.442501E+01 *** PASSED *** Elapsed time: 6.347746 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file 1d7i-dss-smol.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: 1d7i-dss-smol.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 22 2024 at 00:00:00 Parsing input file 1d7i-dss-smol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from 1d7i-dss-complex.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1677 atoms Centered at (2.526e+01, 1.899e+01, 1.912e+01) Net charge 9.91e-01 e Reading PQR-format atom data from dss-min.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 14 atoms Centered at (1.734e+01, 1.921e+01, 2.050e+01) Net charge -8.33e-17 e Reading PQR-format atom data from 1d7i-min.pqr. 1663 atoms Centered at (2.526e+01, 1.899e+01, 1.912e+01) Net charge 9.91e-01 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (complex-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.425 MB total, 122.425 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.634884642408E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (complex-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.425 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.003177540425E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.425 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.264965939588E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (complex-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.425 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.301801664829E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (dss-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 7.942232645345E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (dss-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.677798535473E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (dss-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.171079106781E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #8 (dss-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.697869784185E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (1d7i-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.507068451372E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #10 (1d7i-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.835075772299E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (1d7i-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.252495566243E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (1d7i-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.133237922574E+04 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end Local net energy (PE 0) = -2.986241244040E+03 kJ/mol Global net ELEC energy = -2.986241244040E+03 kJ/mol print energy 6 (dss-solv-fine) - 8 (dss-ref-fine) end Local net energy (PE 0) = -2.007124871262E+01 kJ/mol Global net ELEC energy = -2.007124871262E+01 kJ/mol print energy 10 (1d7i-solv-fine) - 12 (1d7i-ref-fine) end Local net energy (PE 0) = -2.981621502756E+03 kJ/mol Global net ELEC energy = -2.981621502756E+03 kJ/mol print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) - 6 (dss-solv-fine) + 8 (dss-ref-fine) - 10 (1d7i-solv-fine) + 12 (1d7i-ref-fine) end Local net energy (PE 0) = 1.545150742844E+01 kJ/mol Global net ELEC energy = 1.545150742844E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 222.305 MB high water Thanks for using APBS! Checking for intermidiate energies in input file 1d7i-dss-smol.out RESULT 9634.884642408 RESULT 40031.77540425 RESULT 12649.65939588 RESULT 43018.01664829 RESULT 79.42232645345 RESULT 1677.798535473 RESULT 117.1079106781 RESULT 1697.869784185 RESULT 9507.068451372 RESULT 38350.75772299 RESULT 12524.95566243 RESULT 41332.37922574 RESULT -2986.24124404 RESULT -20.07124871262 RESULT -2981.621502756 RESULT 15.45150742844 Testing computed result 9.634884642408E+03 against expected result 9.634885E+03 *** PASSED *** Testing computed result 4.003177540425E+04 against expected result 4.003178E+04 *** PASSED *** Testing computed result 1.264965939588E+04 against expected result 1.264966E+04 *** PASSED *** Testing computed result 4.301801664829E+04 against expected result 4.301802E+04 *** PASSED *** Testing computed result 7.942232645345E+01 against expected result 7.942233E+01 *** PASSED *** Testing computed result 1.677798535473E+03 against expected result 1.677799E+03 *** PASSED *** Testing computed result 1.171079106781E+02 against expected result 1.171079E+02 *** PASSED *** Testing computed result 1.697869784185E+03 against expected result 1.697870E+03 *** PASSED *** Testing computed result 9.507068451372E+03 against expected result 9.507068E+03 *** PASSED *** Testing computed result 3.835075772299E+04 against expected result 3.835076E+04 *** PASSED *** Testing computed result 1.252495566243E+04 against expected result 1.252496E+04 *** PASSED *** Testing computed result 4.133237922574E+04 against expected result 4.133238E+04 *** PASSED *** Testing computed result 1.545150742844E+01 against expected result 1.545150E+01 *** PASSED *** Elapsed time: 6.272149 seconds -------------------------------------------------------------------------------- Total elapsed time: 25.167473 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for hca-bind section -------------------------------------------------------------------------------- Testing input file apbs-mol.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 22 2024 at 00:00:00 Parsing input file apbs-mol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from acet.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 18 atoms Centered at (-6.028e+00, 3.898e+00, 1.518e+01) Net charge -1.00e+00 e Reading PQR-format atom data from hca.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 2482 atoms Centered at (-7.196e+00, 4.070e-01, 1.704e+01) Net charge 1.00e+00 e Reading PQR-format atom data from complex.pqr. 2500 atoms Centered at (-7.196e+00, 4.070e-01, 1.704e+01) Net charge -1.02e-14 e Preparing to run 9 PBE calculations. ---------------------------------------- CALCULATION #1 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.727 MB total, 62.727 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.213600726771E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.727 MB total, 123.701 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.825764811255E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.727 MB total, 123.701 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 6.458471211905E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.516 MB total, 146.516 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.093606095527E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #5 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.516 MB total, 245.092 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.515433544464E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.516 MB total, 245.092 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.786369323561E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.926 MB total, 245.092 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.105322784838E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #8 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.926 MB total, 245.725 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.533304996252E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #9 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.926 MB total, 245.725 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.850429388099E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (acet) - 2 (hca) end Local net energy (PE 0) = -5.246475812665E+01 kJ/mol Global net ELEC energy = -5.246475812665E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 245.725 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol.out RESULT 221.3600726771 RESULT 1825.764811255 RESULT 6458.471211905 RESULT 20936.06095527 RESULT 151543.3544464 RESULT 178636.9323561 RESULT 21053.22784838 RESULT 153330.4996252 RESULT 185042.9388099 RESULT -52.46475812665 Testing computed result 2.213600726771E+02 against expected result 2.213601E+02 *** PASSED *** Testing computed result 1.825764811255E+03 against expected result 1.825765E+03 *** PASSED *** Testing computed result 6.458471211905E+03 against expected result 6.458471E+03 *** PASSED *** Testing computed result 2.093606095527E+04 against expected result 2.093606E+04 *** PASSED *** Testing computed result 1.515433544464E+05 against expected result 1.515434E+05 *** PASSED *** Testing computed result 1.786369323561E+05 against expected result 1.786369E+05 *** PASSED *** Testing computed result 2.105322784838E+04 against expected result 2.105323E+04 *** PASSED *** Testing computed result 1.533304996252E+05 against expected result 1.533305E+05 *** PASSED *** Testing computed result 1.850429388099E+05 against expected result 1.850429E+05 *** PASSED *** Testing computed result -5.246475812665E+01 against expected result -5.246476E+01 *** PASSED *** Elapsed time: 5.415817 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 22 2024 at 00:00:00 Parsing input file apbs-smol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from acet.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 18 atoms Centered at (-6.028e+00, 3.898e+00, 1.518e+01) Net charge -1.00e+00 e Reading PQR-format atom data from hca.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 2482 atoms Centered at (-7.196e+00, 4.070e-01, 1.704e+01) Net charge 1.00e+00 e Reading PQR-format atom data from complex.pqr. 2500 atoms Centered at (-7.196e+00, 4.070e-01, 1.704e+01) Net charge -1.02e-14 e Preparing to run 9 PBE calculations. ---------------------------------------- CALCULATION #1 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.727 MB total, 62.727 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.884888131017E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.727 MB total, 123.701 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.820045922544E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.727 MB total, 123.701 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 6.460002606908E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.516 MB total, 146.516 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.189161497021E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #5 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.516 MB total, 245.092 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.520000494925E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.516 MB total, 245.092 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.790436191580E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.926 MB total, 245.092 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.195842512312E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #8 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.926 MB total, 245.725 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.537771604355E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #9 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.926 MB total, 245.725 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.854495619747E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (acet) - 2 (hca) end Local net energy (PE 0) = -5.405979017066E+01 kJ/mol Global net ELEC energy = -5.405979017066E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 245.725 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol.out RESULT 188.4888131017 RESULT 1820.045922544 RESULT 6460.002606908 RESULT 21891.61497021 RESULT 152000.0494925 RESULT 179043.619158 RESULT 21958.42512312 RESULT 153777.1604355 RESULT 185449.5619747 RESULT -54.05979017066 Testing computed result 1.884888131017E+02 against expected result 1.884888E+02 *** PASSED *** Testing computed result 1.820045922544E+03 against expected result 1.820046E+03 *** PASSED *** Testing computed result 6.460002606908E+03 against expected result 6.460003E+03 *** PASSED *** Testing computed result 2.189161497021E+04 against expected result 2.189161E+04 *** PASSED *** Testing computed result 1.520000494925E+05 against expected result 1.520000E+05 *** PASSED *** Testing computed result 1.790436191580E+05 against expected result 1.790436E+05 *** PASSED *** Testing computed result 2.195842512312E+04 against expected result 2.195843E+04 *** PASSED *** Testing computed result 1.537771604355E+05 against expected result 1.537772E+05 *** PASSED *** Testing computed result 1.854495619747E+05 against expected result 1.854496E+05 *** PASSED *** Testing computed result -5.405979017066E+01 against expected result -5.405978E+01 *** PASSED *** Elapsed time: 4.979175 seconds -------------------------------------------------------------------------------- Total elapsed time: 10.394992 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for ionize section -------------------------------------------------------------------------------- Testing input file apbs-mol.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol.in ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 22 2024 at 00:00:00 Parsing input file apbs-mol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading XML-format atom data from acetic-acid.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 8 atoms Centered at (0.000e+00, -1.535e-01, 1.287e+00) Net charge -1.67e-16 e Reading XML-format atom data from acetate.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 8 atoms Centered at (0.000e+00, -1.535e-01, 1.287e+00) Net charge -1.00e+00 e Reading XML-format atom data from proton.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (1.780e-01, -1.286e+00, 2.937e+00) Net charge 1.00e+00 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (acetic-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 61.598 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 5.823898055191E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (acetic-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.793274462353E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (acetic-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 5.846917564309E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (acetic-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.815953282539E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (acetate-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 8.219846763777E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (acetate-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.392741988698E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (acetate-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 8.420373979905E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #8 (acetate-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.412716615065E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (proton-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.412 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.862359524598E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #10 (proton-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.412 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.288156251610E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (proton-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.373 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.162533113906E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (proton-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.373 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.585616091973E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (acetic-solv) - 2 (acetic-ref) end Local net energy (PE 0) = -2.267882018629E+01 kJ/mol Global net ELEC energy = -2.267882018629E+01 kJ/mol print energy 3 (acetate-solv) - 4 (acetate-ref) end Local net energy (PE 0) = -1.997462636633E+02 kJ/mol Global net ELEC energy = -1.997462636633E+02 kJ/mol print energy 5 (proton-solv) - 6 (proton-ref) end Local net energy (PE 0) = -2.974598403628E+02 kJ/mol Global net ELEC energy = -2.974598403628E+02 kJ/mol print energy 3 (acetate-solv) - 4 (acetate-ref) + 5 (proton-solv) - 6 (proton-ref) - 1 (acetic-solv) + 2 (acetic-ref) end Local net energy (PE 0) = -4.745272838398E+02 kJ/mol Global net ELEC energy = -4.745272838398E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 122.404 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol.out RESULT 5823.898055191 RESULT 9793.274462353 RESULT 5846.917564309 RESULT 9815.953282539 RESULT 8219.846763777 RESULT 13927.41988698 RESULT 8420.373979905 RESULT 14127.16615065 RESULT 3862.359524598 RESULT 6288.15625161 RESULT 4162.533113906 RESULT 6585.616091973 RESULT -22.67882018629 RESULT -199.7462636633 RESULT -297.4598403628 RESULT -474.5272838398 Testing computed result 5.823898055191E+03 against expected result 5.823898E+03 *** PASSED *** Testing computed result 9.793274462353E+03 against expected result 9.793274E+03 *** PASSED *** Testing computed result 5.846917564309E+03 against expected result 5.846918E+03 *** PASSED *** Testing computed result 9.815953282539E+03 against expected result 9.815953E+03 *** PASSED *** Testing computed result 8.219846763777E+03 against expected result 8.219847E+03 *** PASSED *** Testing computed result 1.392741988698E+04 against expected result 1.392742E+04 *** PASSED *** Testing computed result 8.420373979905E+03 against expected result 8.420374E+03 *** PASSED *** Testing computed result 1.412716615065E+04 against expected result 1.412717E+04 *** PASSED *** Testing computed result 3.862359524598E+03 against expected result 3.862360E+03 *** PASSED *** Testing computed result 6.288156251610E+03 against expected result 6.288156E+03 *** PASSED *** Testing computed result 4.162533113906E+03 against expected result 4.162533E+03 *** PASSED *** Testing computed result 6.585616091973E+03 against expected result 6.585616E+03 *** PASSED *** Testing computed result -2.267882018629E+01 against expected result -2.267882E+01 *** PASSED *** Testing computed result -1.997462636633E+02 against expected result -1.997463E+02 *** PASSED *** Testing computed result -2.974598403628E+02 against expected result -2.974598E+02 *** PASSED *** Testing computed result -4.745272838398E+02 against expected result -4.745273E+02 *** PASSED *** Elapsed time: 1.394246 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol.in ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 22 2024 at 00:00:00 Parsing input file apbs-smol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading XML-format atom data from acetic-acid.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 8 atoms Centered at (0.000e+00, -1.535e-01, 1.287e+00) Net charge -1.67e-16 e Reading XML-format atom data from acetate.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 8 atoms Centered at (0.000e+00, -1.535e-01, 1.287e+00) Net charge -1.00e+00 e Reading XML-format atom data from proton.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (1.780e-01, -1.286e+00, 2.937e+00) Net charge 1.00e+00 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (acetic-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 61.598 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 5.824172730822E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (acetic-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.793622759239E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (acetic-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 5.846917564309E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (acetic-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.815953282539E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (acetate-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 8.221328580569E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (acetate-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.392867783119E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (acetate-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 8.420373979905E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #8 (acetate-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.412716615065E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (proton-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.412 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.863066835285E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #10 (proton-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.412 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.289649216644E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (proton-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.373 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.162533113906E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (proton-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.373 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.585616091973E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (acetic-solv) - 2 (acetic-ref) end Local net energy (PE 0) = -2.233052329981E+01 kJ/mol Global net ELEC energy = -2.233052329981E+01 kJ/mol print energy 3 (acetate-solv) - 4 (acetate-ref) end Local net energy (PE 0) = -1.984883194538E+02 kJ/mol Global net ELEC energy = -1.984883194538E+02 kJ/mol print energy 5 (proton-solv) - 6 (proton-ref) end Local net energy (PE 0) = -2.959668753288E+02 kJ/mol Global net ELEC energy = -2.959668753288E+02 kJ/mol print energy 3 (acetate-solv) - 4 (acetate-ref) + 5 (proton-solv) - 6 (proton-ref) - 1 (acetic-solv) + 2 (acetic-ref) end Local net energy (PE 0) = -4.721246714828E+02 kJ/mol Global net ELEC energy = -4.721246714828E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 122.404 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol.out RESULT 5824.172730822 RESULT 9793.622759239 RESULT 5846.917564309 RESULT 9815.953282539 RESULT 8221.328580569 RESULT 13928.67783119 RESULT 8420.373979905 RESULT 14127.16615065 RESULT 3863.066835285 RESULT 6289.649216644 RESULT 4162.533113906 RESULT 6585.616091973 RESULT -22.33052329981 RESULT -198.4883194538 RESULT -295.9668753288 RESULT -472.1246714828 Testing computed result 5.824172730822E+03 against expected result 5.824173E+03 *** PASSED *** Testing computed result 9.793622759239E+03 against expected result 9.793623E+03 *** PASSED *** Testing computed result 5.846917564309E+03 against expected result 5.846918E+03 *** PASSED *** Testing computed result 9.815953282539E+03 against expected result 9.815953E+03 *** PASSED *** Testing computed result 8.221328580569E+03 against expected result 8.221329E+03 *** PASSED *** Testing computed result 1.392867783119E+04 against expected result 1.392868E+04 *** PASSED *** Testing computed result 8.420373979905E+03 against expected result 8.420374E+03 *** PASSED *** Testing computed result 1.412716615065E+04 against expected result 1.412717E+04 *** PASSED *** Testing computed result 3.863066835285E+03 against expected result 3.863067E+03 *** PASSED *** Testing computed result 6.289649216644E+03 against expected result 6.289649E+03 *** PASSED *** Testing computed result 4.162533113906E+03 against expected result 4.162533E+03 *** PASSED *** Testing computed result 6.585616091973E+03 against expected result 6.585616E+03 *** PASSED *** Testing computed result -2.233052329981E+01 against expected result -2.233050E+01 *** PASSED *** Testing computed result -1.984883194538E+02 against expected result -1.984883E+02 *** PASSED *** Testing computed result -2.959668753288E+02 against expected result -2.959669E+02 *** PASSED *** Testing computed result -4.721246714828E+02 against expected result -4.721247E+02 *** PASSED *** Elapsed time: 1.353078 seconds -------------------------------------------------------------------------------- Total elapsed time: 2.747324 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for ion-pmf section -------------------------------------------------------------------------------- Testing input file ion-pmf.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: ion-pmf.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 22 2024 at 00:00:00 Parsing input file ion-pmf.in... rank 0 size 1... Parsed input file. Reading parameter data from parm.dat. Got paths for 1 molecules Reading PDB-format atom data from ion-pmf.pdb. Vpmg_ibForce: No force for zero ionic strength! Vpmg_ibForce: No force for zero ionic strength! 2 atoms Centered at (-1.000e+00, 0.000e+00, 0.000e+00) Net charge 2.00e+00 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.106 MB total, 61.106 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated All-atom solvent forces will be calculated Total electrostatic energy = 7.839535983197E+03 kJ/mol Calculating forces... Printing per-atom forces for molecule 1 (kJ/mol/A) Legend: tot n -- total force for atom n qf n -- fixed charge force for atom n db n -- dielectric boundary force for atom n ib n -- ionic boundary force for atom n mgF tot 0 -3.760e+03 -4.398e-05 -7.763e-05 mgF qf 0 -3.767e+03 -1.730e-05 -2.384e-05 mgF ib 0 0.000e+00 0.000e+00 0.000e+00 mgF db 0 6.148e+00 -2.668e-05 -5.379e-05 mgF tot 1 -3.596e+03 -5.403e-05 -1.012e-04 mgF qf 1 -3.598e+03 -2.253e-05 -3.831e-05 mgF ib 1 0.000e+00 0.000e+00 0.000e+00 mgF db 1 2.883e+00 -3.150e-05 -6.291e-05 Vpmg_ibForce: No force for zero ionic strength! Vpmg_ibForce: No force for zero ionic strength! ---------------------------------------- CALCULATION #2 (ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.106 MB total, 61.155 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated All-atom solvent forces will be calculated Total electrostatic energy = 8.964727588811E+03 kJ/mol Calculating forces... Printing per-atom forces for molecule 1 (kJ/mol/A) Legend: tot n -- total force for atom n qf n -- fixed charge force for atom n db n -- dielectric boundary force for atom n ib n -- ionic boundary force for atom n mgF tot 0 -3.850e+03 -4.055e-06 -7.703e-06 mgF qf 0 -3.850e+03 -4.055e-06 -7.703e-06 mgF ib 0 0.000e+00 0.000e+00 0.000e+00 mgF db 0 0.000e+00 0.000e+00 0.000e+00 mgF tot 1 -3.514e+03 -4.163e-06 -7.690e-06 mgF qf 1 -3.514e+03 -4.163e-06 -7.690e-06 mgF ib 1 0.000e+00 0.000e+00 0.000e+00 mgF db 1 0.000e+00 0.000e+00 0.000e+00 ---------------------------------------- CALCULATION #3 (asolv): APOLAR Printing per atom forces (kJ/mol/A) Legend: tot n -- Total force for atom n sasa n -- SASA force for atom n sav n -- SAV force for atom n wca n -- WCA force for atom n gamma 0.000720 pressure 0.000000 bconc 0.033000 tot 0 2.715e-02 9.130e-07 9.130e-07 sasa 0 -1.100e+01 0.000e+00 0.000e+00 sav 0 0.000e+00 0.000e+00 0.000e+00 wca 0 -5.827e-01 -2.767e-05 -2.767e-05 tot 1 -2.723e-02 9.133e-07 9.133e-07 sasa 1 1.112e+01 0.000e+00 0.000e+00 sav 1 0.000e+00 0.000e+00 0.000e+00 wca 1 5.827e-01 -2.767e-05 -2.767e-05 Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 1.153275282828E+02 SASA for atom 1: 1.153114143344E+02 Total solvent accessible surface area: 230.639 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 8.303582036361E-02 Surface tension*area energy for atom 1: 8.302421832080E-02 Total surface tension energy: 0.16606 kJ/mol Total solvent accessible volume: 0 A^3 Total pressure*volume energy: 0 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.909718359932E+00 WCA energy for atom 1: -6.909422551724E+00 Total WCA energy: -13.8191 kJ/mol Total non-polar energy = -1.365308087297E+01 kJ/mol ---------------------------------------- PRINT STATEMENTS print energy 1 (solv) - 2 (ref) end Local net energy (PE 0) = -1.125191605614E+03 kJ/mol Global net ELEC energy = -1.125191605614E+03 kJ/mol print force 1 (solv) - 2 (ref) end Printing per-atom forces (kJ/mol/A). Legend: tot n -- Total force for atom n qf n -- Fixed charge force for atom n db n -- Dielectric boundary force for atom n ib n -- Ionic boundary force for atom n tot all -- Total force for system qf 0 8.398642197666E+01 -1.324564548552E-05 -1.613435632529E-05 ib 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 db 0 6.148357059184E+00 -2.667517425897E-05 -5.378919678211E-05 tot 0 9.013477903584E+01 -3.992081974449E-05 -6.992355310740E-05 qf 1 -8.466423642736E+01 -1.836748045969E-05 -3.062224428458E-05 ib 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 db 1 2.882739230548E+00 -3.149946357588E-05 -6.291495506459E-05 tot 1 -8.178149719681E+01 -4.986694403557E-05 -9.353719934917E-05 tot all 8.353281839029E+00 -8.978776378007E-05 -1.634607524566E-04 print APOL energy 1 (asolv) end Global net APOL energy = -1.365308087297E+01 kJ/mol print APOL force 1 (asolv) end Printing per atom forces (kJ/mol/A) Legend: tot n -- Total force for atom n sasa n -- SASA force for atom n sav n -- SAV force for atom n wca n -- WCA force for atom n tot all -- Total force for system sasa 0 -1.099776974333E+01 0.000000000000E+00 0.000000000000E+00 sav 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 wca 0 -5.826577086437E-01 -2.766670515801E-05 -2.766670515838E-05 tot 0 -1.158042745197E+01 -2.766670515801E-05 -2.766670515838E-05 sasa 1 1.111862435589E+01 0.000000000000E+00 0.000000000000E+00 sav 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 wca 1 5.826560767576E-01 -2.767485007141E-05 -2.767485007183E-05 tot 1 1.170128043265E+01 -2.767485007141E-05 -2.767485007183E-05 tot all 1.208529806779E-01 -5.534155522943E-05 -5.534155523021E-05 ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 60.711 MB total, 62.250 MB high water Thanks for using APBS! Checking for intermidiate energies in input file ion-pmf.out RESULT 7839.535983197 RESULT 8964.727588811 RESULT -1125.191605614 RESULT -13.65308087297 Testing computed result 7.839535983197E+03 against expected result 7.839536E+03 *** PASSED *** Testing computed result 8.964727588811E+03 against expected result 8.964728E+03 *** PASSED *** Testing computed result -1.125191605614E+03 against expected result -1.125192E+03 *** PASSED *** Elapsed time: 4.952024 seconds -------------------------------------------------------------------------------- Total elapsed time: 4.952024 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for ion-protein section -------------------------------------------------------------------------------- Testing input file apbs-mol-pdiel2.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol-pdiel2.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 22 2024 at 00:00:00 Parsing input file apbs-mol-pdiel2.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from small491.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 259 atoms Centered at (2.898e+02, 1.679e+02, 8.192e+01) Net charge 1.97e+01 e Reading PQR-format atom data from 491.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (2.998e+02, 1.629e+02, 8.934e+01) Net charge 2.00e+00 e Reading PQR-format atom data from complex.pqr. 260 atoms Centered at (2.898e+02, 1.679e+02, 8.192e+01) Net charge 2.17e+01 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (protein): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 518.491 MB total, 518.491 MB high water Using linear spline charge discretization. Grid dimensions: 129 x 129 x 129 Grid spacings: 0.523 x 0.523 x 0.586 Grid lengths: 67.000 x 67.000 x 75.000 Grid center: (289.756, 167.946, 81.925) Multigrid levels: 6 Molecule ID: 1 Nonlinear traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 7.525554553704E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (ion): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 499.862 MB total, 518.560 MB high water Using linear spline charge discretization. Grid dimensions: 129 x 129 x 129 Grid spacings: 0.523 x 0.523 x 0.586 Grid lengths: 67.000 x 67.000 x 75.000 Grid center: (289.756, 167.946, 81.925) Multigrid levels: 6 Molecule ID: 2 Nonlinear traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.967613272771E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 518.565 MB total, 518.565 MB high water Using linear spline charge discretization. Grid dimensions: 129 x 129 x 129 Grid spacings: 0.523 x 0.523 x 0.586 Grid lengths: 67.000 x 67.000 x 75.000 Grid center: (289.756, 167.946, 81.925) Multigrid levels: 6 Molecule ID: 3 Nonlinear traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.050875942181E+04 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (protein) - 2 (ion) end Local net energy (PE 0) = 1.559159533658E+01 kJ/mol Global net ELEC energy = 1.559159533658E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 518.565 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-pdiel2.out RESULT 7525.554553704 RESULT 2967.613272771 RESULT 10508.75942181 RESULT 15.59159533658 Testing computed result 7.525554553704E+03 against expected result 7.525555E+03 *** PASSED *** Testing computed result 2.967613272771E+03 against expected result 2.967613E+03 *** PASSED *** Testing computed result 1.050875942181E+04 against expected result 1.050876E+04 *** PASSED *** Testing computed result 1.559159533658E+01 against expected result 1.559160E+01 *** PASSED *** Elapsed time: 8.079475 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-pdiel2.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol-pdiel2.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 22 2024 at 00:00:00 Parsing input file apbs-smol-pdiel2.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from small491.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 259 atoms Centered at (2.898e+02, 1.679e+02, 8.192e+01) Net charge 1.97e+01 e Reading PQR-format atom data from 491.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (2.998e+02, 1.629e+02, 8.934e+01) Net charge 2.00e+00 e Reading PQR-format atom data from complex.pqr. 260 atoms Centered at (2.898e+02, 1.679e+02, 8.192e+01) Net charge 2.17e+01 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (protein): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 518.491 MB total, 518.491 MB high water Using linear spline charge discretization. Grid dimensions: 129 x 129 x 129 Grid spacings: 0.523 x 0.523 x 0.586 Grid lengths: 67.000 x 67.000 x 75.000 Grid center: (289.756, 167.946, 81.925) Multigrid levels: 6 Molecule ID: 1 Nonlinear traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 7.561237446444E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (ion): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 499.862 MB total, 518.560 MB high water Using linear spline charge discretization. Grid dimensions: 129 x 129 x 129 Grid spacings: 0.523 x 0.523 x 0.586 Grid lengths: 67.000 x 67.000 x 75.000 Grid center: (289.756, 167.946, 81.925) Multigrid levels: 6 Molecule ID: 2 Nonlinear traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.974076897757E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 518.565 MB total, 518.565 MB high water Using linear spline charge discretization. Grid dimensions: 129 x 129 x 129 Grid spacings: 0.523 x 0.523 x 0.586 Grid lengths: 67.000 x 67.000 x 75.000 Grid center: (289.756, 167.946, 81.925) Multigrid levels: 6 Molecule ID: 3 Nonlinear traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.055886976547E+04 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (protein) - 2 (ion) end Local net energy (PE 0) = 2.355542126539E+01 kJ/mol Global net ELEC energy = 2.355542126539E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 518.565 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-pdiel2.out RESULT 7561.237446444 RESULT 2974.076897757 RESULT 10558.86976547 RESULT 23.55542126539 Testing computed result 7.561237446444E+03 against expected result 7.561237E+03 *** PASSED *** Testing computed result 2.974076897757E+03 against expected result 2.974077E+03 *** PASSED *** Testing computed result 1.055886976547E+04 against expected result 1.055887E+04 *** PASSED *** Testing computed result 2.355542126539E+01 against expected result 2.355542E+01 *** PASSED *** Elapsed time: 6.743147 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-pdiel12.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol-pdiel12.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 22 2024 at 00:00:00 Parsing input file apbs-mol-pdiel12.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from small491.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 259 atoms Centered at (2.898e+02, 1.679e+02, 8.192e+01) Net charge 1.97e+01 e Reading PQR-format atom data from 491.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (2.998e+02, 1.629e+02, 8.934e+01) Net charge 2.00e+00 e Reading PQR-format atom data from complex.pqr. 260 atoms Centered at (2.898e+02, 1.679e+02, 8.192e+01) Net charge 2.17e+01 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (protein): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 518.491 MB total, 518.491 MB high water Using linear spline charge discretization. Grid dimensions: 129 x 129 x 129 Grid spacings: 0.523 x 0.523 x 0.586 Grid lengths: 67.000 x 67.000 x 75.000 Grid center: (289.756, 167.946, 81.925) Multigrid levels: 6 Molecule ID: 1 Nonlinear traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 12.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.363584355927E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (ion): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 499.862 MB total, 518.560 MB high water Using linear spline charge discretization. Grid dimensions: 129 x 129 x 129 Grid spacings: 0.523 x 0.523 x 0.586 Grid lengths: 67.000 x 67.000 x 75.000 Grid center: (289.756, 167.946, 81.925) Multigrid levels: 6 Molecule ID: 2 Nonlinear traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 12.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 5.110802147229E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 518.565 MB total, 518.565 MB high water Using linear spline charge discretization. Grid dimensions: 129 x 129 x 129 Grid spacings: 0.523 x 0.523 x 0.586 Grid lengths: 67.000 x 67.000 x 75.000 Grid center: (289.756, 167.946, 81.925) Multigrid levels: 6 Molecule ID: 3 Nonlinear traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 12.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.892691797082E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (protein) - 2 (ion) end Local net energy (PE 0) = 1.802722643145E+01 kJ/mol Global net ELEC energy = 1.802722643145E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 518.565 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-pdiel12.out RESULT 1363.584355927 RESULT 511.0802147229 RESULT 1892.691797082 RESULT 18.02722643145 Testing computed result 1.363584355927E+03 against expected result 1.363584E+03 *** PASSED *** Testing computed result 5.110802147229E+02 against expected result 5.110802E+02 *** PASSED *** Testing computed result 1.892691797082E+03 against expected result 1.892692E+03 *** PASSED *** Testing computed result 1.802722643145E+01 against expected result 1.802723E+01 *** PASSED *** Elapsed time: 5.992976 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-pdiel12.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol-pdiel12.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 22 2024 at 00:00:00 Parsing input file apbs-smol-pdiel12.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from small491.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 259 atoms Centered at (2.898e+02, 1.679e+02, 8.192e+01) Net charge 1.97e+01 e Reading PQR-format atom data from 491.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (2.998e+02, 1.629e+02, 8.934e+01) Net charge 2.00e+00 e Reading PQR-format atom data from complex.pqr. 260 atoms Centered at (2.898e+02, 1.679e+02, 8.192e+01) Net charge 2.17e+01 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (protein): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 518.491 MB total, 518.491 MB high water Using linear spline charge discretization. Grid dimensions: 129 x 129 x 129 Grid spacings: 0.523 x 0.523 x 0.586 Grid lengths: 67.000 x 67.000 x 75.000 Grid center: (289.756, 167.946, 81.925) Multigrid levels: 6 Molecule ID: 1 Nonlinear traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 12.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.366571366426E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (ion): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 499.862 MB total, 518.560 MB high water Using linear spline charge discretization. Grid dimensions: 129 x 129 x 129 Grid spacings: 0.523 x 0.523 x 0.586 Grid lengths: 67.000 x 67.000 x 75.000 Grid center: (289.756, 167.946, 81.925) Multigrid levels: 6 Molecule ID: 2 Nonlinear traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 12.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 5.108315415905E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 518.565 MB total, 518.565 MB high water Using linear spline charge discretization. Grid dimensions: 129 x 129 x 129 Grid spacings: 0.523 x 0.523 x 0.586 Grid lengths: 67.000 x 67.000 x 75.000 Grid center: (289.756, 167.946, 81.925) Multigrid levels: 6 Molecule ID: 3 Nonlinear traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 12.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.896685358215E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (protein) - 2 (ion) end Local net energy (PE 0) = 1.928245019843E+01 kJ/mol Global net ELEC energy = 1.928245019843E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 518.565 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-pdiel12.out RESULT 1366.571366426 RESULT 510.8315415905 RESULT 1896.685358215 RESULT 19.28245019843 Testing computed result 1.366571366426E+03 against expected result 1.366571E+03 *** PASSED *** Testing computed result 5.108315415905E+02 against expected result 5.108315E+02 *** PASSED *** Testing computed result 1.896685358215E+03 against expected result 1.896685E+03 *** PASSED *** Testing computed result 1.928245019843E+01 against expected result 1.928245E+01 *** PASSED *** Elapsed time: 6.448725 seconds -------------------------------------------------------------------------------- Total elapsed time: 27.264323 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for pka-lig section -------------------------------------------------------------------------------- Testing input file apbs-mol-vdw.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol-vdw.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 22 2024 at 00:00:00 Parsing input file apbs-mol-vdw.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from bx6_7_lig_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 47 atoms Centered at (2.482e+01, -3.315e+01, 2.154e+01) Net charge 1.11e-16 e Reading PQR-format atom data from bx6_7_apo_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3423 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 3470 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (lig-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 204.292 MB total, 204.292 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.224988750664E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (lig-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 204.292 MB total, 406.001 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.049695084686E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (pka-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 291.151 MB total, 406.001 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.818450789522E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (pka-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 291.151 MB total, 533.426 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.008254338259E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 292.063 MB total, 533.426 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.840918409896E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 292.063 MB total, 534.806 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.113304681884E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end Local net energy (PE 0) = 8.083515648730E+00 kJ/mol Global net ELEC energy = 8.083515648730E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 534.806 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-vdw.out RESULT 2224.988750664 RESULT 10496.95084686 RESULT 181845.0789522 RESULT 300825.4338259 RESULT 184091.8409896 RESULT 311330.4681884 RESULT 8.08351564873 Testing computed result 2.224988750664E+03 against expected result 2.224989E+03 *** PASSED *** Testing computed result 1.049695084686E+04 against expected result 1.049695E+04 *** PASSED *** Testing computed result 1.818450789522E+05 against expected result 1.818451E+05 *** PASSED *** Testing computed result 3.008254338259E+05 against expected result 3.008254E+05 *** PASSED *** Testing computed result 1.840918409896E+05 against expected result 1.840918E+05 *** PASSED *** Testing computed result 3.113304681884E+05 against expected result 3.113305E+05 *** PASSED *** Testing computed result 8.083515648730E+00 against expected result 8.083516E+00 *** PASSED *** Elapsed time: 7.000559 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-vdw.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol-vdw.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 22 2024 at 00:00:00 Parsing input file apbs-smol-vdw.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from bx6_7_lig_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 47 atoms Centered at (2.482e+01, -3.315e+01, 2.154e+01) Net charge 1.11e-16 e Reading PQR-format atom data from bx6_7_apo_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3423 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 3470 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (lig-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 204.292 MB total, 204.292 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.226793167046E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (lig-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 204.292 MB total, 406.001 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.050504485887E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (pka-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 291.151 MB total, 406.001 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.827976621645E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (pka-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 291.151 MB total, 533.426 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.017228546773E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 292.063 MB total, 533.426 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.850819075387E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 292.063 MB total, 534.806 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.122488625388E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end Local net energy (PE 0) = 2.096300255723E+01 kJ/mol Global net ELEC energy = 2.096300255723E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 534.806 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-vdw.out RESULT 2226.793167046 RESULT 10505.04485887 RESULT 182797.6621645 RESULT 301722.8546773 RESULT 185081.9075387 RESULT 312248.8625388 RESULT 20.96300255723 Testing computed result 2.226793167046E+03 against expected result 2.226793E+03 *** PASSED *** Testing computed result 1.050504485887E+04 against expected result 1.050504E+04 *** PASSED *** Testing computed result 1.827976621645E+05 against expected result 1.827977E+05 *** PASSED *** Testing computed result 3.017228546773E+05 against expected result 3.017229E+05 *** PASSED *** Testing computed result 1.850819075387E+05 against expected result 1.850819E+05 *** PASSED *** Testing computed result 3.122488625388E+05 against expected result 3.122489E+05 *** PASSED *** Testing computed result 2.096300255723E+01 against expected result 2.096296E+01 *** PASSED *** Elapsed time: 6.058695 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-surf.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol-surf.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 22 2024 at 00:00:00 Parsing input file apbs-mol-surf.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from bx6_7_lig_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 47 atoms Centered at (2.482e+01, -3.315e+01, 2.154e+01) Net charge 1.11e-16 e Reading PQR-format atom data from bx6_7_apo_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3423 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 3470 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (lig-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 203.877 MB total, 203.877 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.244350164274E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (lig-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 203.877 MB total, 405.586 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.052149475373E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (pka-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.521 MB total, 405.586 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.862615690066E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (pka-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.521 MB total, 493.795 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.051810884053E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.858 MB total, 493.795 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.886625455219E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.858 MB total, 494.601 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.158218439277E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end Local net energy (PE 0) = 1.192607686581E+02 kJ/mol Global net ELEC energy = 1.192607686581E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 494.601 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-surf.out RESULT 2244.350164274 RESULT 10521.49475373 RESULT 186261.5690066 RESULT 305181.0884053 RESULT 188662.5455219 RESULT 315821.8439277 RESULT 119.2607686581 Testing computed result 2.244350164274E+03 against expected result 2.244350E+03 *** PASSED *** Testing computed result 1.052149475373E+04 against expected result 1.052149E+04 *** PASSED *** Testing computed result 1.862615690066E+05 against expected result 1.862616E+05 *** PASSED *** Testing computed result 3.051810884053E+05 against expected result 3.051811E+05 *** PASSED *** Testing computed result 1.886625455219E+05 against expected result 1.886625E+05 *** PASSED *** Testing computed result 3.158218439277E+05 against expected result 3.158218E+05 *** PASSED *** Testing computed result 1.192607686581E+02 against expected result 1.192608E+02 *** PASSED *** Elapsed time: 6.246888 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-surf.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol-surf.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 22 2024 at 00:00:00 Parsing input file apbs-smol-surf.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from bx6_7_lig_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 47 atoms Centered at (2.482e+01, -3.315e+01, 2.154e+01) Net charge 1.11e-16 e Reading PQR-format atom data from bx6_7_apo_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3423 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 3470 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (lig-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 203.877 MB total, 203.877 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.251466789420E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (lig-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 203.877 MB total, 405.586 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.052814502873E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (pka-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.521 MB total, 405.586 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.864071689626E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (pka-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.521 MB total, 493.795 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.053319953673E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.858 MB total, 493.795 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.888027142979E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.858 MB total, 494.601 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.159690177241E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end Local net energy (PE 0) = 1.088773280806E+02 kJ/mol Global net ELEC energy = 1.088773280806E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 494.601 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-surf.out RESULT 2251.46678942 RESULT 10528.14502873 RESULT 186407.1689626 RESULT 305331.9953673 RESULT 188802.7142979 RESULT 315969.0177241 RESULT 108.8773280806 Testing computed result 2.251466789420E+03 against expected result 2.251467E+03 *** PASSED *** Testing computed result 1.052814502873E+04 against expected result 1.052815E+04 *** PASSED *** Testing computed result 1.864071689626E+05 against expected result 1.864072E+05 *** PASSED *** Testing computed result 3.053319953673E+05 against expected result 3.053320E+05 *** PASSED *** Testing computed result 1.888027142979E+05 against expected result 1.888027E+05 *** PASSED *** Testing computed result 3.159690177241E+05 against expected result 3.159690E+05 *** PASSED *** Testing computed result 1.088773280806E+02 against expected result 1.088773E+02 *** PASSED *** Elapsed time: 6.074869 seconds -------------------------------------------------------------------------------- Total elapsed time: 25.381011 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for point-pmf section -------------------------------------------------------------------------------- Testing input file complex-0_1.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: complex-0_1.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 22 2024 at 00:00:00 Parsing input file complex-0_1.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol0.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-3.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-2.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from complex-0_1.pqr. 2 atoms Centered at (-2.500e+00, 0.000e+00, 0.000e+00) Net charge 2.00e+00 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (point1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.060 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.776035707281E+01 kJ/mol Fixed charge energy = 97.7604 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 96.5336 kJ/mol Per-atom energies: Atom 0: 9.776035707281E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (point2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.067 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.975920687031E+01 kJ/mol Fixed charge energy = 89.7592 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 88.6151 kJ/mol Per-atom energies: Atom 0: 8.975920687031E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.067 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.058277719334E+02 kJ/mol Fixed charge energy = 205.828 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 201.106 kJ/mol Per-atom energies: Atom 0: 1.069144350786E+02 kJ/mol Atom 1: 9.891333685475E+01 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (point1) - 2 (point2) end Local net energy (PE 0) = 1.830820799027E+01 kJ/mol Global net ELEC energy = 1.830820799027E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 61.067 MB high water Thanks for using APBS! Checking for intermidiate energies in input file complex-0_1.out RESULT 97.76035707281 RESULT 89.75920687031 RESULT 205.8277719334 RESULT 0.0 RESULT 0.0 RESULT 0.0 RESULT 97.7604 RESULT 89.7592 RESULT 205.828 RESULT 96.5336 RESULT 88.6151 RESULT 201.106 RESULT 18.30820799027 Testing computed result 9.776035707281E+01 against expected result 9.776036E+01 *** PASSED *** Testing computed result 8.975920687031E+01 against expected result 8.975921E+01 *** PASSED *** Testing computed result 2.058277719334E+02 against expected result 2.058278E+02 *** PASSED *** Testing computed result 9.776040000000E+01 against expected result 9.776040E+01 *** PASSED *** Testing computed result 8.975920000000E+01 against expected result 8.975920E+01 *** PASSED *** Testing computed result 2.058280000000E+02 against expected result 2.058280E+02 *** PASSED *** Testing computed result 9.653360000000E+01 against expected result 9.653360E+01 *** PASSED *** Testing computed result 8.861510000000E+01 against expected result 8.861510E+01 *** PASSED *** Testing computed result 2.011060000000E+02 against expected result 2.011060E+02 *** PASSED *** Testing computed result 1.830820799027E+01 against expected result 1.830821E+01 *** PASSED *** Elapsed time: 0.337952 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file complex-0_2.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: complex-0_2.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 22 2024 at 00:00:00 Parsing input file complex-0_2.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol0.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-3.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-1.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from complex-0_2.pqr. 2 atoms Centered at (-2.000e+00, 0.000e+00, 0.000e+00) Net charge 2.00e+00 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (point1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.060 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.776035707281E+01 kJ/mol Fixed charge energy = 97.7604 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 96.5336 kJ/mol Per-atom energies: Atom 0: 9.776035707281E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (point2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.067 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.017611498797E+02 kJ/mol Fixed charge energy = 101.761 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 100.656 kJ/mol Per-atom energies: Atom 0: 1.017611498797E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.068 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.084282010393E+02 kJ/mol Fixed charge energy = 208.428 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 203.83 kJ/mol Per-atom energies: Atom 0: 1.022136878480E+02 kJ/mol Atom 1: 1.062145131913E+02 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (point1) - 2 (point2) end Local net energy (PE 0) = 8.906694086750E+00 kJ/mol Global net ELEC energy = 8.906694086750E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 61.068 MB high water Thanks for using APBS! Checking for intermidiate energies in input file complex-0_2.out RESULT 97.76035707281 RESULT 101.7611498797 RESULT 208.4282010393 RESULT 0.0 RESULT 0.0 RESULT 0.0 RESULT 97.7604 RESULT 101.761 RESULT 208.428 RESULT 96.5336 RESULT 100.656 RESULT 203.83 RESULT 8.90669408675 Testing computed result 9.776035707281E+01 against expected result 9.776036E+01 *** PASSED *** Testing computed result 1.017611498797E+02 against expected result 1.017611E+02 *** PASSED *** Testing computed result 2.084282010393E+02 against expected result 2.084282E+02 *** PASSED *** Testing computed result 9.776040000000E+01 against expected result 9.776040E+01 *** PASSED *** Testing computed result 1.017610000000E+02 against expected result 1.017610E+02 *** PASSED *** Testing computed result 2.084280000000E+02 against expected result 2.084280E+02 *** PASSED *** Testing computed result 9.653360000000E+01 against expected result 9.653360E+01 *** PASSED *** Testing computed result 1.006560000000E+02 against expected result 1.006560E+02 *** PASSED *** Testing computed result 2.038300000000E+02 against expected result 2.038300E+02 *** PASSED *** Testing computed result 8.906694086750E+00 against expected result 8.906694E+00 *** PASSED *** Elapsed time: 0.342091 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file complex-0_3.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: complex-0_3.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 22 2024 at 00:00:00 Parsing input file complex-0_3.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol0.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-3.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from mol3.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from complex-0_3.pqr. 2 atoms Centered at (-1.500e+00, 0.000e+00, 0.000e+00) Net charge 2.00e+00 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (point1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.060 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.776035707281E+01 kJ/mol Fixed charge energy = 97.7604 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 96.5336 kJ/mol Per-atom energies: Atom 0: 9.776035707281E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (point2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.067 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.337661883222E+02 kJ/mol Fixed charge energy = 133.766 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 132.672 kJ/mol Per-atom energies: Atom 0: 1.337661883222E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.068 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.374361452120E+02 kJ/mol Fixed charge energy = 237.436 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 232.924 kJ/mol Per-atom energies: Atom 0: 1.007151570480E+02 kJ/mol Atom 1: 1.367209881640E+02 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (point1) - 2 (point2) end Local net energy (PE 0) = 5.909599816984E+00 kJ/mol Global net ELEC energy = 5.909599816984E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 61.068 MB high water Thanks for using APBS! Checking for intermidiate energies in input file complex-0_3.out RESULT 97.76035707281 RESULT 133.7661883222 RESULT 237.436145212 RESULT 0.0 RESULT 0.0 RESULT 0.0 RESULT 97.7604 RESULT 133.766 RESULT 237.436 RESULT 96.5336 RESULT 132.672 RESULT 232.924 RESULT 5.909599816984 Testing computed result 9.776035707281E+01 against expected result 9.776036E+01 *** PASSED *** Testing computed result 1.337661883222E+02 against expected result 1.337662E+02 *** PASSED *** Testing computed result 2.374361452120E+02 against expected result 2.374361E+02 *** PASSED *** Testing computed result 9.776040000000E+01 against expected result 9.776040E+01 *** PASSED *** Testing computed result 1.337660000000E+02 against expected result 1.337660E+02 *** PASSED *** Testing computed result 2.374360000000E+02 against expected result 2.374360E+02 *** PASSED *** Testing computed result 9.653360000000E+01 against expected result 9.653360E+01 *** PASSED *** Testing computed result 1.326720000000E+02 against expected result 1.326720E+02 *** PASSED *** Testing computed result 2.329240000000E+02 against expected result 2.329240E+02 *** PASSED *** Testing computed result 5.909599816984E+00 against expected result 5.909600E+00 *** PASSED *** Elapsed time: 0.341768 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file complex-0_4.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: complex-0_4.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 22 2024 at 00:00:00 Parsing input file complex-0_4.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol0.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-3.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from mol4.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (1.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from complex-0_4.pqr. 2 atoms Centered at (-1.000e+00, 0.000e+00, 0.000e+00) Net charge 2.00e+00 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (point1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.060 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.776035707281E+01 kJ/mol Fixed charge energy = 97.7604 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 96.5336 kJ/mol Per-atom energies: Atom 0: 9.776035707281E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (point2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.067 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.017611498797E+02 kJ/mol Fixed charge energy = 101.761 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 100.654 kJ/mol Per-atom energies: Atom 0: 1.017611498797E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.061 MB total, 61.068 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.039516519000E+02 kJ/mol Fixed charge energy = 203.952 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 199.493 kJ/mol Per-atom energies: Atom 0: 9.997541697022E+01 kJ/mol Atom 1: 1.039762349297E+02 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (point1) - 2 (point2) end Local net energy (PE 0) = 4.430144947418E+00 kJ/mol Global net ELEC energy = 4.430144947418E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 61.068 MB high water Thanks for using APBS! Checking for intermidiate energies in input file complex-0_4.out RESULT 97.76035707281 RESULT 101.7611498797 RESULT 203.9516519 RESULT 0.0 RESULT 0.0 RESULT 0.0 RESULT 97.7604 RESULT 101.761 RESULT 203.952 RESULT 96.5336 RESULT 100.654 RESULT 199.493 RESULT 4.430144947418 Testing computed result 9.776035707281E+01 against expected result 9.776036E+01 *** PASSED *** Testing computed result 1.017611498797E+02 against expected result 1.017611E+02 *** PASSED *** Testing computed result 2.039516519000E+02 against expected result 2.039517E+02 *** PASSED *** Testing computed result 9.776040000000E+01 against expected result 9.776040E+01 *** PASSED *** Testing computed result 1.017610000000E+02 against expected result 1.017610E+02 *** PASSED *** Testing computed result 2.039520000000E+02 against expected result 2.039520E+02 *** PASSED *** Testing computed result 9.653360000000E+01 against expected result 9.653360E+01 *** PASSED *** Testing computed result 1.006540000000E+02 against expected result 1.006540E+02 *** PASSED *** Testing computed result 1.994930000000E+02 against expected result 1.994930E+02 *** PASSED *** Testing computed result 4.430144947418E+00 against expected result 4.430145E+00 *** PASSED *** Elapsed time: 0.338242 seconds -------------------------------------------------------------------------------- Total elapsed time: 1.360053 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for solv section -------------------------------------------------------------------------------- Testing input file apbs-mol.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 22 2024 at 00:00:00 Parsing input file apbs-mol.in... rank 0 size 1... Parsed input file. Got paths for 2 molecules Reading PQR-format atom data from methanol.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3 atoms Centered at (3.086e-01, 0.000e+00, -2.417e-01) Net charge 5.55e-17 e Reading PQR-format atom data from methoxide.pqr. 2 atoms Centered at (0.000e+00, 0.000e+00, -1.279e-01) Net charge -1.00e+00 e Preparing to run 4 PBE calculations. ---------------------------------------- CALCULATION #1 (methanol-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.253 MB total, 61.253 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.309, 0.000, -0.242) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.847663548071E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (methanol-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.253 MB total, 61.328 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.309, 0.000, -0.242) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.883912182952E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (methoxide-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.250 MB total, 61.328 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.000, 0.000, -0.128) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 2.732623683321E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (methoxide-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.250 MB total, 61.328 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.000, 0.000, -0.128) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.123035854133E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (methanol-solv) - 2 (methanol-ref) end Local net energy (PE 0) = -3.624863488074E+01 kJ/mol Global net ELEC energy = -3.624863488074E+01 kJ/mol print energy 3 (methoxide-solv) - 4 (methoxide-ref) end Local net energy (PE 0) = -3.904121708125E+02 kJ/mol Global net ELEC energy = -3.904121708125E+02 kJ/mol print energy 3 (methoxide-solv) - 4 (methoxide-ref) - 1 (methanol-solv) + 2 (methanol-ref) end Local net energy (PE 0) = -3.541635359318E+02 kJ/mol Global net ELEC energy = -3.541635359318E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 2 molecules Final memory usage: 0.001 MB total, 61.328 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol.out RESULT 1847.663548071 RESULT 1883.912182952 RESULT 2732.623683321 RESULT 3123.035854133 RESULT -36.24863488074 RESULT -390.4121708125 RESULT -354.1635359318 Testing computed result 1.847663548071E+03 against expected result 1.847664E+03 *** PASSED *** Testing computed result 1.883912182952E+03 against expected result 1.883912E+03 *** PASSED *** Testing computed result 2.732623683321E+03 against expected result 2.732624E+03 *** PASSED *** Testing computed result 3.123035854133E+03 against expected result 3.123036E+03 *** PASSED *** Testing computed result -3.624863488074E+01 against expected result -3.624863E+01 *** PASSED *** Testing computed result -3.904121708125E+02 against expected result -3.904121E+02 *** PASSED *** Testing computed result -3.541635359318E+02 against expected result -3.541635E+02 *** PASSED *** Elapsed time: 0.503154 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 22 2024 at 00:00:00 Parsing input file apbs-smol.in... rank 0 size 1... Parsed input file. Got paths for 2 molecules Reading PQR-format atom data from methanol.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3 atoms Centered at (3.086e-01, 0.000e+00, -2.417e-01) Net charge 5.55e-17 e Reading PQR-format atom data from methoxide.pqr. 2 atoms Centered at (0.000e+00, 0.000e+00, -1.279e-01) Net charge -1.00e+00 e Preparing to run 4 PBE calculations. ---------------------------------------- CALCULATION #1 (methanol-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.253 MB total, 61.253 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.309, 0.000, -0.242) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.847860440020E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (methanol-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.253 MB total, 61.328 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.309, 0.000, -0.242) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.885436377745E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (methoxide-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.250 MB total, 61.328 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.000, 0.000, -0.128) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 2.734040568569E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (methoxide-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.250 MB total, 61.328 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.000, 0.000, -0.128) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.125279428954E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (methanol-solv) - 2 (methanol-ref) end Local net energy (PE 0) = -3.757593772493E+01 kJ/mol Global net ELEC energy = -3.757593772493E+01 kJ/mol print energy 3 (methoxide-solv) - 4 (methoxide-ref) end Local net energy (PE 0) = -3.912388603848E+02 kJ/mol Global net ELEC energy = -3.912388603848E+02 kJ/mol print energy 3 (methoxide-solv) - 4 (methoxide-ref) - 1 (methanol-solv) + 2 (methanol-ref) end Local net energy (PE 0) = -3.536629226599E+02 kJ/mol Global net ELEC energy = -3.536629226599E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 2 molecules Final memory usage: 0.001 MB total, 61.328 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol.out RESULT 1847.86044002 RESULT 1885.436377745 RESULT 2734.040568569 RESULT 3125.279428954 RESULT -37.57593772493 RESULT -391.2388603848 RESULT -353.6629226599 Testing computed result 1.847860440020E+03 against expected result 1.847860E+03 *** PASSED *** Testing computed result 1.885436377745E+03 against expected result 1.885436E+03 *** PASSED *** Testing computed result 2.734040568569E+03 against expected result 2.734041E+03 *** PASSED *** Testing computed result 3.125279428954E+03 against expected result 3.125279E+03 *** PASSED *** Testing computed result -3.757593772493E+01 against expected result -3.757594E+01 *** PASSED *** Testing computed result -3.912388603848E+02 against expected result -3.912388E+02 *** PASSED *** Testing computed result -3.536629226599E+02 against expected result -3.536629E+02 *** PASSED *** Elapsed time: 0.495636 seconds -------------------------------------------------------------------------------- Total elapsed time: 0.998790 seconds Test results have been logged -------------------------------------------------------------------------------- + RPM_EC=0 ++ jobs -p + exit 0 Processing files: apbs-3.0.0-22.fc39.x86_64 Provides: apbs = 3.0.0-22.fc39 apbs(x86-64) = 3.0.0-22.fc39 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: libapbs.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.4)(64bit) libm.so.6()(64bit) libmaloc.so.1()(64bit) rtld(GNU_HASH) Processing files: apbs-tools-3.0.0-22.fc39.x86_64 warning: absolute symlink: /usr/bin/apbs-psize.py -> /usr/lib64/python3.12/site-packages/apbs/psize.py Provides: apbs-tools = 3.0.0-22.fc39 apbs-tools(x86-64) = 3.0.0-22.fc39 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: libapbs.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.29)(64bit) libmaloc.so.1()(64bit) rtld(GNU_HASH) Processing files: apbs-libs-3.0.0-22.fc39.x86_64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.YpREXh + umask 022 + cd /builddir/build/BUILD + cd apbs-3.0.0 + DOCDIR=/builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/share/doc/apbs-libs + export LC_ALL= + LC_ALL= + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/share/doc/apbs-libs + cp -pr /builddir/build/BUILD/apbs-3.0.0/README.md /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/share/doc/apbs-libs + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.AFD807 + umask 022 + cd /builddir/build/BUILD + cd apbs-3.0.0 + LICENSEDIR=/builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/share/licenses/apbs-libs + export LC_ALL= + LC_ALL= + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/share/licenses/apbs-libs + cp -pr /builddir/build/BUILD/apbs-3.0.0/LICENSE.md /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/share/licenses/apbs-libs + cp -pr /builddir/build/BUILD/apbs-3.0.0/COPYING /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/share/licenses/apbs-libs + cp -pr /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/iapbs-COPYING /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/share/licenses/apbs-libs + cp -pr /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/iapbs-LGPLv2 /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/share/licenses/apbs-libs + RPM_EC=0 ++ jobs -p + exit 0 Provides: apbs-libs = 3.0.0-22.fc39 apbs-libs(x86-64) = 3.0.0-22.fc39 libapbs.so.1()(64bit) Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: libc.so.6()(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.3.1)(64bit) libgomp.so.1()(64bit) libgomp.so.1(GOMP_4.0)(64bit) libgomp.so.1(OMP_1.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.29)(64bit) rtld(GNU_HASH) Processing files: apbs-devel-3.0.0-22.fc39.x86_64 Provides: apbs-devel = 3.0.0-22.fc39 apbs-devel(x86-64) = 3.0.0-22.fc39 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: libapbs.so.1()(64bit) Processing files: apbs-doc-3.0.0-22.fc39.noarch Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.6dz5ZI + umask 022 + cd /builddir/build/BUILD + cd apbs-3.0.0 + DOCDIR=/builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/share/doc/apbs-doc + export LC_ALL= + LC_ALL= + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/share/doc/apbs-doc + cp -pr /builddir/build/BUILD/apbs-3.0.0/build/doc /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/share/doc/apbs-doc + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.Z3gmIH + umask 022 + cd /builddir/build/BUILD + cd apbs-3.0.0 + LICENSEDIR=/builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/share/licenses/apbs-doc + export LC_ALL= + LC_ALL= + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/share/licenses/apbs-doc + cp -pr /builddir/build/BUILD/apbs-3.0.0/LICENSE.md /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64/usr/share/licenses/apbs-doc + RPM_EC=0 ++ jobs -p + exit 0 Provides: apbs-doc = 3.0.0-22.fc39 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: python3-apbs-3.0.0-22.fc39.x86_64 Provides: python-apbs = 3.0.0-22.fc39 python3-apbs = 3.0.0-22.fc39 python3-apbs(x86-64) = 3.0.0-22.fc39 python3.12-apbs = 3.0.0-22.fc39 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PartialHardlinkSets) <= 4.0.4-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: /usr/bin/python3 libc.so.6()(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.3.1)(64bit) libgomp.so.1()(64bit) libgomp.so.1(GOMP_4.0)(64bit) libgomp.so.1(OMP_1.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.29)(64bit) libmaloc.so.1()(64bit) libpython3.12.so.1.0()(64bit) python(abi) = 3.12 rtld(GNU_HASH) Obsoletes: apbs-libs < 0:3.0.0-11 python-apbs < 3.0.0-22.fc39 Processing files: apbs-debugsource-3.0.0-22.fc39.x86_64 Provides: apbs-debugsource = 3.0.0-22.fc39 apbs-debugsource(x86-64) = 3.0.0-22.fc39 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: apbs-debuginfo-3.0.0-22.fc39.x86_64 Provides: apbs-debuginfo = 3.0.0-22.fc39 apbs-debuginfo(x86-64) = 3.0.0-22.fc39 debuginfo(build-id) = 1d2a35c1f6950821545f2d79451f8bf6fde613e9 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: apbs-debugsource(x86-64) = 3.0.0-22.fc39 Processing files: apbs-tools-debuginfo-3.0.0-22.fc39.x86_64 Provides: apbs-tools-debuginfo = 3.0.0-22.fc39 apbs-tools-debuginfo(x86-64) = 3.0.0-22.fc39 debuginfo(build-id) = 07aa86fa28aca9d9f177b00c1ec7f8a7abf18464 debuginfo(build-id) = 28fe4628f96439f2fe6ddb821e1aab951525d177 debuginfo(build-id) = 2e32c285ea2ab49af390e8a8719ef1a427283136 debuginfo(build-id) = 49ade9cd8177d10110542ef423d283855e485d19 debuginfo(build-id) = 51608f3aea5dbbeb5f6b57c678a3e997cd717ffe debuginfo(build-id) = 5c00d9b1b82930f565e45c28f6ecb275ab22edf1 debuginfo(build-id) = 63c1bf41647fd7a30f69e48161db0c72ebeafd31 debuginfo(build-id) = 71dfce80bfeaf41ab2c9ca65bfb87d7edfe9c492 debuginfo(build-id) = 778425ef58bf4c360a7d36b108d172c591942272 debuginfo(build-id) = 8a1f121b66255aa3a9b01aec24733b8c371c012c debuginfo(build-id) = 8ebea0544f63355ce276db0f849f2d28fa7e1137 debuginfo(build-id) = a3c0d81cb171ef5f04fcc3edeb6feabb03586dc3 debuginfo(build-id) = b66d902b150d088d6b9e535536677334bdc578cc debuginfo(build-id) = d08057b2191e3e2b557e1479fda4fd3154fe01d7 debuginfo(build-id) = e6ac60bf92f7b2d1cb22afab77b1810cf6fe3b60 debuginfo(build-id) = f8713f7caef5319b85a7eeda2068b5d5b9cf8388 debuginfo(build-id) = fa24f361a24a2e1c8e85c83f4f3d51b501e2f3e7 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: apbs-debugsource(x86-64) = 3.0.0-22.fc39 Processing files: apbs-libs-debuginfo-3.0.0-22.fc39.x86_64 Provides: apbs-libs-debuginfo = 3.0.0-22.fc39 apbs-libs-debuginfo(x86-64) = 3.0.0-22.fc39 debuginfo(build-id) = be833bd7769b543c65a1a7ada8c9961cd6c11b6c libapbs.so.1-3.0.0-22.fc39.x86_64.debug()(64bit) Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: apbs-debugsource(x86-64) = 3.0.0-22.fc39 Processing files: python3-apbs-debuginfo-3.0.0-22.fc39.x86_64 Provides: debuginfo(build-id) = 560d746beee25da24edec719dba1756ac3bf660a python-apbs-debuginfo = 3.0.0-22.fc39 python3-apbs-debuginfo = 3.0.0-22.fc39 python3-apbs-debuginfo(x86-64) = 3.0.0-22.fc39 python3.12-apbs-debuginfo = 3.0.0-22.fc39 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: apbs-debugsource(x86-64) = 3.0.0-22.fc39 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64 Wrote: /builddir/build/RPMS/apbs-debugsource-3.0.0-22.fc39.x86_64.rpm Wrote: /builddir/build/RPMS/python3-apbs-debuginfo-3.0.0-22.fc39.x86_64.rpm Wrote: /builddir/build/RPMS/apbs-libs-debuginfo-3.0.0-22.fc39.x86_64.rpm Wrote: /builddir/build/RPMS/python3-apbs-3.0.0-22.fc39.x86_64.rpm Wrote: /builddir/build/RPMS/apbs-libs-3.0.0-22.fc39.x86_64.rpm Wrote: /builddir/build/RPMS/apbs-devel-3.0.0-22.fc39.x86_64.rpm Wrote: /builddir/build/RPMS/apbs-tools-debuginfo-3.0.0-22.fc39.x86_64.rpm Wrote: /builddir/build/RPMS/apbs-debuginfo-3.0.0-22.fc39.x86_64.rpm Wrote: /builddir/build/RPMS/apbs-tools-3.0.0-22.fc39.x86_64.rpm Wrote: /builddir/build/RPMS/apbs-3.0.0-22.fc39.x86_64.rpm Wrote: /builddir/build/RPMS/apbs-doc-3.0.0-22.fc39.noarch.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.kefVzs + umask 022 + cd /builddir/build/BUILD + cd apbs-3.0.0 + /usr/bin/rm -rf /builddir/build/BUILDROOT/apbs-3.0.0-22.fc39.x86_64 + RPM_EC=0 ++ jobs -p + exit 0 Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.xveoRJ + umask 022 + cd /builddir/build/BUILD + rm -rf /builddir/build/BUILD/apbs-3.0.0-SPECPARTS + rm -rf apbs-3.0.0 apbs-3.0.0.gemspec + RPM_EC=0 ++ jobs -p + exit 0 RPM build warnings: %patchN is deprecated (4 usages found), use %patch N (or %patch -P N) absolute symlink: /usr/bin/apbs-psize.py -> /usr/lib64/python3.12/site-packages/apbs/psize.py Finish: rpmbuild apbs-3.0.0-22.fc39.src.rpm Finish: build phase for apbs-3.0.0-22.fc39.src.rpm INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-39-x86_64-1705965440.204976/root/var/log/dnf.rpm.log /var/lib/mock/fedora-39-x86_64-1705965440.204976/root/var/log/dnf.librepo.log /var/lib/mock/fedora-39-x86_64-1705965440.204976/root/var/log/dnf.log INFO: Done(/var/lib/copr-rpmbuild/results/apbs-3.0.0-22.fc39.src.rpm) Config(child) 16 minutes 43 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot Finish: run Running RPMResults tool Package info: { "packages": [ { "name": "apbs-tools-debuginfo", "epoch": null, "version": "3.0.0", "release": "22.fc39", "arch": "x86_64" }, { "name": "apbs", "epoch": null, "version": "3.0.0", "release": "22.fc39", "arch": "x86_64" }, { "name": "apbs-debuginfo", "epoch": null, "version": "3.0.0", "release": "22.fc39", "arch": "x86_64" }, { "name": "python3-apbs-debuginfo", "epoch": null, "version": "3.0.0", "release": "22.fc39", "arch": "x86_64" }, { "name": "apbs-libs", "epoch": null, "version": "3.0.0", "release": "22.fc39", "arch": "x86_64" }, { "name": "python3-apbs", "epoch": null, "version": "3.0.0", "release": "22.fc39", "arch": "x86_64" }, { "name": "apbs-devel", "epoch": null, "version": "3.0.0", "release": "22.fc39", "arch": "x86_64" }, { "name": "apbs-doc", "epoch": null, "version": "3.0.0", "release": "22.fc39", "arch": "noarch" }, { "name": "apbs", "epoch": null, "version": "3.0.0", "release": "22.fc39", "arch": "src" }, { "name": "apbs-tools", "epoch": null, "version": "3.0.0", "release": "22.fc39", "arch": "x86_64" }, { "name": "apbs-libs-debuginfo", "epoch": null, "version": "3.0.0", "release": "22.fc39", "arch": "x86_64" }, { "name": "apbs-debugsource", "epoch": null, "version": "3.0.0", "release": "22.fc39", "arch": "x86_64" } ] } RPMResults finished