APBS 3.0.0
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vclist.c File Reference

Class Vclist methods. More...

#include "vclist.h"
Include dependency graph for vclist.c:

Go to the source code of this file.

Macros

#define VCLIST_INFLATE   1.42
 

Functions

VPUBLIC unsigned long int Vclist_memChk (Vclist *thee)
 Get number of bytes in this object and its members.
 
VPUBLIC double Vclist_maxRadius (Vclist *thee)
 Get the max probe radius value (in A) the cell list was constructed with.
 
VPUBLIC VclistVclist_ctor (Valist *alist, double max_radius, int npts[VAPBS_DIM], Vclist_DomainMode mode, double lower_corner[VAPBS_DIM], double upper_corner[VAPBS_DIM])
 Construct the cell list object.
 
VPRIVATE void Vclist_getMolDims (Vclist *thee, double lower_corner[VAPBS_DIM], double upper_corner[VAPBS_DIM], double *r_max)
 
VPRIVATE Vrc_Codes Vclist_setupGrid (Vclist *thee)
 
VPRIVATE Vrc_Codes 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])
 
VPRIVATE void Vclist_gridSpan (Vclist *thee, Vatom *atom, int imin[VAPBS_DIM], int imax[VAPBS_DIM])
 
VPRIVATE int Vclist_arrayIndex (Vclist *thee, int i, int j, int k)
 
VPRIVATE Vrc_Codes Vclist_assignAtoms (Vclist *thee)
 
VPUBLIC Vrc_Codes Vclist_ctor2 (Vclist *thee, Valist *alist, double max_radius, int npts[VAPBS_DIM], Vclist_DomainMode mode, double lower_corner[VAPBS_DIM], double upper_corner[VAPBS_DIM])
 FORTRAN stub to construct the cell list object.
 
VPUBLIC void Vclist_dtor (Vclist **thee)
 Destroy object.
 
VPUBLIC void Vclist_dtor2 (Vclist *thee)
 FORTRAN stub to destroy object.
 
VPUBLIC VclistCellVclist_getCell (Vclist *thee, double pos[VAPBS_DIM])
 Return cell corresponding to specified position or return VNULL.
 
VPUBLIC VclistCellVclistCell_ctor (int natoms)
 Allocate and construct a cell list cell object.
 
VPUBLIC Vrc_Codes VclistCell_ctor2 (VclistCell *thee, int natoms)
 Construct a cell list object.
 
VPUBLIC void VclistCell_dtor (VclistCell **thee)
 Destroy object.
 
VPUBLIC void VclistCell_dtor2 (VclistCell *thee)
 FORTRAN stub to destroy object.
 

Detailed Description

Class Vclist methods.

Author
Nathan Baker
Version
$Id$
Attention
*
* APBS -- Adaptive Poisson-Boltzmann Solver
*
*  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.
*
* 

Definition in file vclist.c.

Function Documentation

◆ Vclist_arrayIndex()

VPRIVATE int Vclist_arrayIndex ( Vclist * thee,
int i,
int j,
int k )

Definition at line 262 of file vclist.c.

◆ Vclist_assignAtoms()

VPRIVATE Vrc_Codes Vclist_assignAtoms ( Vclist * thee)

Definition at line 270 of file vclist.c.

◆ Vclist_getMolDims()

VPRIVATE void Vclist_getMolDims ( Vclist * thee,
double lower_corner[VAPBS_DIM],
double upper_corner[VAPBS_DIM],
double * r_max )

Definition at line 90 of file vclist.c.

◆ Vclist_gridSpan()

VPRIVATE void Vclist_gridSpan ( Vclist * thee,
Vatom * atom,
int imin[VAPBS_DIM],
int imax[VAPBS_DIM] )

Definition at line 231 of file vclist.c.

◆ Vclist_setupGrid()

VPRIVATE Vrc_Codes Vclist_setupGrid ( Vclist * thee)

Definition at line 125 of file vclist.c.

◆ Vclist_storeParms()

VPRIVATE Vrc_Codes 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] )

Definition at line 174 of file vclist.c.