APBS 3.0.0
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routines.h
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1
61#ifndef _APBSROUTINES_H_
62#define _APBSROUTINES_H_
63
64#include "apbs.h"
65
66#ifdef HAVE_MC_H
67# include "mc/mc.h"
68# include "fem/vfetk.h"
69#endif
70#ifdef HAVE_MCX_H
71# include "mcx/mcx.h"
72#endif
73
74#ifdef ENABLE_BEM
75 #include "TABIPBstruct.h"
76#endif
77
78#ifdef ENABLE_GEOFLOW
79 #include "GeometricFlowWrap.h"
80#endif
81
82#if defined(ENABLE_PBAM) || defined(ENABLE_PBSAM)
83 #include "PBAMWrap.h"
84#endif
85
86#ifdef ENABLE_PBSAM
87 #include "PBSAMWrap.h"
88#endif
89
93#define APBSRC 13
94
99struct AtomForce {
100 double ibForce[3];
101 double qfForce[3];
102 double dbForce[3];
103 double sasaForce[3];
104 double savForce[3];
105 double wcaForce[3];
106};
107
111typedef struct AtomForce AtomForce;
112
118VEXTERNC Vparam* loadParameter(
119 NOsh *nosh
121 );
122
128VEXTERNC int loadMolecules(
129 NOsh *nosh,
130 Vparam *param,
132 Valist *alist[NOSH_MAXMOL]
134 );
135
142VEXTERNC void killMolecules(NOsh *nosh, Valist *alist[NOSH_MAXMOL]);
143
153VEXTERNC int loadDielMaps(NOsh *nosh,
154 Vgrid *dielXMap[NOSH_MAXMOL],
155 Vgrid *dielYMap[NOSH_MAXMOL],
156 Vgrid *dielZMap[NOSH_MAXMOL]
157 );
158
167VEXTERNC void killDielMaps(NOsh *nosh, Vgrid *dielXMap[NOSH_MAXMOL],
168 Vgrid *dielYMap[NOSH_MAXMOL], Vgrid *dielZMap[NOSH_MAXMOL]);
169
177VEXTERNC int loadKappaMaps(NOsh *nosh, Vgrid *kappa[NOSH_MAXMOL]);
178
185VEXTERNC void killKappaMaps(NOsh *nosh, Vgrid *kappa[NOSH_MAXMOL]);
186
194VEXTERNC int loadPotMaps(NOsh *nosh, Vgrid *pot[NOSH_MAXMOL]);
195
202VEXTERNC void killPotMaps(NOsh *nosh, Vgrid *pot[NOSH_MAXMOL]);
203
211VEXTERNC int loadChargeMaps(NOsh *nosh, Vgrid *charge[NOSH_MAXMOL]);
212
219VEXTERNC void killChargeMaps(NOsh *nosh, Vgrid *charge[NOSH_MAXMOL]);
220
226VEXTERNC void printPBEPARM(PBEparm *pbeparm);
227
234VEXTERNC void printMGPARM(MGparm *mgparm, double realCenter[3]);
235
241VEXTERNC int initMG(
242 int icalc,
243 NOsh *nosh,
244 MGparm *mgparm,
245 PBEparm *pbeparm,
246 double realCenter[3],
247 Vpbe *pbe[NOSH_MAXCALC],
248 Valist *alist[NOSH_MAXMOL],
249 Vgrid *dielXMap[NOSH_MAXMOL],
250 Vgrid *dielYMap[NOSH_MAXMOL],
251 Vgrid *dielZMap[NOSH_MAXMOL],
252 Vgrid *kappaMap[NOSH_MAXMOL],
253 Vgrid *chargeMap[NOSH_MAXMOL],
254 Vpmgp *pmgp[NOSH_MAXCALC],
255 Vpmg *pmg[NOSH_MAXCALC],
256 Vgrid *potMap[NOSH_MAXMOL]
257 );
258
264VEXTERNC void killMG(
265 NOsh *nosh,
266 Vpbe *pbe[NOSH_MAXCALC],
267 Vpmgp *pmgp[NOSH_MAXCALC],
268 Vpmg *pmg[NOSH_MAXCALC]
269);
270
279VEXTERNC int solveMG(NOsh *nosh, Vpmg *pmg, MGparm_CalcType type);
280
289VEXTERNC int setPartMG(NOsh *nosh, MGparm *mgparm, Vpmg *pmg);
290
304VEXTERNC int energyMG(NOsh* nosh, int icalc, Vpmg *pmg,
305 int *nenergy, double *totEnergy, double *qfEnergy, double *qmEnergy,
306 double *dielEnergy);
307
312VEXTERNC void killEnergy();
313
327VEXTERNC int forceMG(Vmem *mem, NOsh *nosh, PBEparm *pbeparm, MGparm *mgparm,
328 Vpmg *pmg, int *nforce, AtomForce **atomForce, Valist *alist[NOSH_MAXMOL]);
329
338VEXTERNC void killForce(Vmem *mem, NOsh *nosh, int nforce[NOSH_MAXCALC],
339 AtomForce *atomForce[NOSH_MAXCALC]);
340
345VEXTERNC void storeAtomEnergy(
346 Vpmg *pmg,
347 int icalc,
348 double **atomEnergy,
349 int *nenergy
350 );
351
368VEXTERNC int writedataFlat(NOsh *nosh, Vcom *com, const char *fname,
369 double totEnergy[NOSH_MAXCALC], double qfEnergy[NOSH_MAXCALC],
370 double qmEnergy[NOSH_MAXCALC], double dielEnergy[NOSH_MAXCALC],
371 int nenergy[NOSH_MAXCALC], double *atomEnergy[NOSH_MAXCALC],
372 int nforce[NOSH_MAXCALC], AtomForce *atomForce[NOSH_MAXCALC]);
373
390VEXTERNC int writedataXML(NOsh *nosh, Vcom *com, const char *fname,
391 double totEnergy[NOSH_MAXCALC], double qfEnergy[NOSH_MAXCALC],
392 double qmEnergy[NOSH_MAXCALC], double dielEnergy[NOSH_MAXCALC],
393 int nenergy[NOSH_MAXCALC], double *atomEnergy[NOSH_MAXCALC],
394 int nforce[NOSH_MAXCALC], AtomForce *atomForce[NOSH_MAXCALC]);
395
405VEXTERNC int writedataMG(int rank, NOsh *nosh, PBEparm *pbeparm, Vpmg *pmg);
406
416VEXTERNC int writematMG(int rank, NOsh *nosh, PBEparm *pbeparm, Vpmg *pmg);
417
427VEXTERNC double returnEnergy(Vcom *com, NOsh *nosh, double totEnergy[NOSH_MAXCALC], int iprint);
428
434VEXTERNC int printEnergy(
435 Vcom *com,
436 NOsh *nosh,
437 double totEnergy[NOSH_MAXCALC],
439 int iprint
440 );
441
447VEXTERNC int printElecEnergy(
448 Vcom *com,
449 NOsh *nosh,
450 double totEnergy[NOSH_MAXCALC],
452 int iprint
453 );
454
460VEXTERNC int printApolEnergy(
461 NOsh *nosh,
462 int iprint
463 );
464
470VEXTERNC int printForce(
471 Vcom *com,
472 NOsh *nosh,
473 int nforce[NOSH_MAXCALC],
474 AtomForce *atomForce[NOSH_MAXCALC],
475 int i
476 );
477
483VEXTERNC int printElecForce(
484 Vcom *com,
485 NOsh *nosh,
486 int nforce[NOSH_MAXCALC],
487 AtomForce *atomForce[NOSH_MAXCALC],
488 int i
489 );
490
496VEXTERNC int printApolForce(
497 Vcom *com,
498 NOsh *nosh,
499 int nforce[NOSH_MAXCALC],
500 AtomForce *atomForce[NOSH_MAXCALC],
501 int i
502 );
503
508VEXTERNC void startVio();
509
515VEXTERNC int energyAPOL(
516 APOLparm *apolparm,
517 double sasa,
518 double sav,
519 double atomsasa[],
520 double atomwcaEnergy[],
521 int numatoms
522 );
523
529VEXTERNC int forceAPOL(
530 Vacc *acc,
531 Vmem *mem,
532 APOLparm *apolparm,
534 int *nforce,
536 AtomForce **atomForce,
538 Valist *alist,
539 Vclist *clist
540 );
541
547VEXTERNC int initAPOL(
548 NOsh *nosh,
549 Vmem *mem,
550 Vparam *param,
551 APOLparm *apolparm,
552 int *nforce,
553 AtomForce **atomForce,
554 Valist *alist
555 );
556
557
558#ifdef HAVE_MC_H
559#include "fem/vfetk.h"
560
569VEXTERNC void printFEPARM(int icalc, NOsh *nosh, FEMparm *feparm,
570 Vfetk *fetk[NOSH_MAXCALC]);
571
586VEXTERNC int energyFE(NOsh* nosh, int icalc, Vfetk *fetk[NOSH_MAXCALC],
587 int *nenergy, double *totEnergy, double *qfEnergy, double *qmEnergy,
588 double *dielEnergy);
589
597VEXTERNC Vrc_Codes initFE(
598 int icalc,
599 NOsh *nosh,
600 FEMparm *feparm,
601 PBEparm *pbeparm,
602 Vpbe *pbe[NOSH_MAXCALC],
603 Valist *alist[NOSH_MAXMOL],
604 Vfetk *fetk[NOSH_MAXCALC]
605);
606
612VEXTERNC void killFE(
613 NOsh *nosh,
614 Vpbe *pbe[NOSH_MAXCALC],
615 Vfetk *fetk[NOSH_MAXCALC],
616 Gem *gem[NOSH_MAXMOL]
617);
618
628VEXTERNC int preRefineFE(int i,
629 FEMparm *feparm,
630 Vfetk *fetk[NOSH_MAXCALC]
631);
632
642VEXTERNC int partFE(int i, NOsh *nosh, FEMparm *feparm,
643 Vfetk *fetk[NOSH_MAXCALC]);
644
654VEXTERNC int solveFE(int i,
655 PBEparm *pbeparm,
656 FEMparm *feparm,
657 Vfetk *fetk[NOSH_MAXCALC]
658);
659
671VEXTERNC int postRefineFE(int icalc,
672 FEMparm *feparm,
673 Vfetk *fetk[NOSH_MAXCALC]
674);
675
685VEXTERNC int writedataFE(int rank, NOsh *nosh, PBEparm *pbeparm, Vfetk *fetk);
686
692VEXTERNC Vrc_Codes loadMeshes(
693 NOsh *nosh,
694 Gem *gm[NOSH_MAXMOL]
696 );
697
702VEXTERNC void killMeshes(
703 NOsh *nosh,
704 Gem *alist[NOSH_MAXMOL]
705 );
706#endif
707
708#endif
709
710
711
712VEXTERNC void printMGPARM(MGparm *mgparm, double realCenter[3]);
713
714#ifdef ENABLE_BEM
720VEXTERNC int initBEM(
721 int icalc,
722 NOsh *nosh,
723 BEMparm *bemparm,
724 PBEparm *pbeparm,
725 Vpbe *pbe[NOSH_MAXCALC]
726 );
727
733VEXTERNC void killBEM(
734 NOsh *nosh,
735 Vpbe *pbe[NOSH_MAXCALC]
736);
737
746VEXTERNC int solveBEM(Valist* molecules[NOSH_MAXMOL],NOsh *nosh, PBEparm *pbeparm, BEMparm *bemparm, BEMparm_CalcType type);
747
756VEXTERNC int setPartBEM(NOsh *nosh, BEMparm *bemparm);
757
771VEXTERNC int energyBEM(NOsh* nosh, int icalc,
772 int *nenergy, double *totEnergy, double *qfEnergy, double *qmEnergy,
773 double *dielEnergy);
774
788VEXTERNC int forceBEM(NOsh *nosh, PBEparm *pbeparm, BEMparm *bemparm,
789 int *nforce, AtomForce **atomForce, Valist *alist[NOSH_MAXMOL]);
790
797VEXTERNC void printBEMPARM(BEMparm *bemparm);
798
808VEXTERNC int writedataBEM(int rank, NOsh *nosh, PBEparm *pbeparm);
809
819VEXTERNC int writematBEM(int rank, NOsh *nosh, PBEparm *pbeparm);
820#endif
821
822#ifdef ENABLE_GEOFLOW
830VEXTERNC int solveGeometricFlow(
831 Valist* molecules[NOSH_MAXMOL],
832 NOsh *nosh,
833 PBEparm *pbeparm,
834 APOLparm *apolparm,
835 GEOFLOWparm *parm
836);
837#endif
838
839#ifdef ENABLE_PBAM
847VEXTERNC int solvePBAM(
848 Valist* molecules[NOSH_MAXMOL],
849 NOsh *nosh,
850 PBEparm *pbeparm,
851 PBAMparm *parm
852);
853#endif
854
855#ifdef ENABLE_PBSAM
863VEXTERNC int solvePBSAM(
864 Valist* molecules[NOSH_MAXMOL],
865 NOsh *nosh,
866 PBEparm *pbeparm,
867 PBAMparm *parm,
868 PBSAMparm *samparm
869);
870#endif
Header file for header dependencies.
enum eBEMparm_CalcType BEMparm_CalcType
Declare BEMparm_CalcType type.
Definition bemparm.h:86
VEXTERNC void printPBEPARM(PBEparm *pbeparm)
Print out generic PBE params loaded from input.
Definition routines.c:1002
VEXTERNC int loadPotMaps(NOsh *nosh, Vgrid *pot[NOSH_MAXMOL])
Load the potential maps given in NOsh into grid objects.
Definition routines.c:793
VEXTERNC void killForce(Vmem *mem, NOsh *nosh, int nforce[NOSH_MAXCALC], AtomForce *atomForce[NOSH_MAXCALC])
Free memory from MG force calculation.
Definition routines.c:1782
VEXTERNC void storeAtomEnergy(Vpmg *pmg, int icalc, double **atomEnergy, int *nenergy)
Store energy in arrays for future use.
Definition routines.c:1870
VEXTERNC int solveMG(NOsh *nosh, Vpmg *pmg, MGparm_CalcType type)
Solve the PBE with MG.
Definition routines.c:1487
VEXTERNC int postRefineFE(int icalc, FEMparm *feparm, Vfetk *fetk[NOSH_MAXCALC])
Estimate error, mark mesh, and refine mesh after solve.
Definition routines.c:4239
VEXTERNC int partFE(int i, NOsh *nosh, FEMparm *feparm, Vfetk *fetk[NOSH_MAXCALC])
Partition mesh (if applicable)
Definition routines.c:4039
VPUBLIC Vrc_Codes initFE(int icalc, NOsh *nosh, FEMparm *feparm, PBEparm *pbeparm, Vpbe *pbe[NOSH_MAXCALC], Valist *alist[NOSH_MAXMOL], Vfetk *fetk[NOSH_MAXCALC])
Initialize FE solver objects.
Definition routines.c:3711
VEXTERNC int preRefineFE(int i, FEMparm *feparm, Vfetk *fetk[NOSH_MAXCALC])
Pre-refine mesh before solve.
Definition routines.c:4046
VEXTERNC void startVio()
Wrapper to start MALOC Vio layer.
Definition routines.c:58
VEXTERNC void killKappaMaps(NOsh *nosh, Vgrid *kappa[NOSH_MAXMOL])
Destroy the loaded kappa maps.
Definition routines.c:776
VEXTERNC double returnEnergy(Vcom *com, NOsh *nosh, double totEnergy[NOSH_MAXCALC], int iprint)
Access net local energy.
Definition routines.c:2753
VEXTERNC int printElecEnergy(Vcom *com, NOsh *nosh, double totEnergy[NOSH_MAXCALC], int iprint)
Combine and pretty-print energy data.
Definition routines.c:2853
VEXTERNC int printForce(Vcom *com, NOsh *nosh, int nforce[NOSH_MAXCALC], AtomForce *atomForce[NOSH_MAXCALC], int i)
Combine and pretty-print force data (deprecated...see printElecForce)
Definition routines.c:2980
VEXTERNC int writedataXML(NOsh *nosh, Vcom *com, const char *fname, double totEnergy[NOSH_MAXCALC], double qfEnergy[NOSH_MAXCALC], double qmEnergy[NOSH_MAXCALC], double dielEnergy[NOSH_MAXCALC], int nenergy[NOSH_MAXCALC], double *atomEnergy[NOSH_MAXCALC], int nforce[NOSH_MAXCALC], AtomForce *atomForce[NOSH_MAXCALC])
Write out information to an XML file.
Definition routines.c:2123
VEXTERNC int setPartMG(NOsh *nosh, MGparm *mgparm, Vpmg *pmg)
Set MG partitions for calculating observables and performing I/O.
Definition routines.c:1523
VEXTERNC void killMeshes(NOsh *nosh, Gem *alist[NOSH_MAXMOL])
Destroy the loaded meshes.
VEXTERNC void killDielMaps(NOsh *nosh, Vgrid *dielXMap[NOSH_MAXMOL], Vgrid *dielYMap[NOSH_MAXMOL], Vgrid *dielZMap[NOSH_MAXMOL])
Destroy the loaded dielectric.
Definition routines.c:639
VEXTERNC void killMG(NOsh *nosh, Vpbe *pbe[NOSH_MAXCALC], Vpmgp *pmgp[NOSH_MAXCALC], Vpmg *pmg[NOSH_MAXCALC])
Kill structures initialized during an MG calculation.
Definition routines.c:1461
VEXTERNC int writedataFlat(NOsh *nosh, Vcom *com, const char *fname, double totEnergy[NOSH_MAXCALC], double qfEnergy[NOSH_MAXCALC], double qmEnergy[NOSH_MAXCALC], double dielEnergy[NOSH_MAXCALC], int nenergy[NOSH_MAXCALC], double *atomEnergy[NOSH_MAXCALC], int nforce[NOSH_MAXCALC], AtomForce *atomForce[NOSH_MAXCALC])
Write out information to a flat file.
Definition routines.c:1887
VEXTERNC int solveFE(int i, PBEparm *pbeparm, FEMparm *feparm, Vfetk *fetk[NOSH_MAXCALC])
Solve-estimate-refine.
Definition routines.c:4116
VEXTERNC void killEnergy()
Kill arrays allocated for energies.
Definition routines.c:1774
VEXTERNC int loadChargeMaps(NOsh *nosh, Vgrid *charge[NOSH_MAXMOL])
Load the charge maps given in NOsh into grid objects.
Definition routines.c:884
VEXTERNC int printElecForce(Vcom *com, NOsh *nosh, int nforce[NOSH_MAXCALC], AtomForce *atomForce[NOSH_MAXCALC], int i)
Combine and pretty-print force data.
Definition routines.c:3228
VEXTERNC void killMolecules(NOsh *nosh, Valist *alist[NOSH_MAXMOL])
Destroy the loaded molecules.
Definition routines.c:233
VEXTERNC void printFEPARM(int icalc, NOsh *nosh, FEMparm *feparm, Vfetk *fetk[NOSH_MAXCALC])
Print out FE-specific params loaded from input.
Definition routines.c:3903
VEXTERNC int writedataMG(int rank, NOsh *nosh, PBEparm *pbeparm, Vpmg *pmg)
Write out observables from MG calculation to file.
Definition routines.c:2383
VEXTERNC int forceAPOL(Vacc *acc, Vmem *mem, APOLparm *apolparm, int *nforce, AtomForce **atomForce, Valist *alist, Vclist *clist)
Calculate non-polar forces.
Definition routines.c:4729
VEXTERNC int printEnergy(Vcom *com, NOsh *nosh, double totEnergy[NOSH_MAXCALC], int iprint)
Combine and pretty-print energy data (deprecated...see printElecEnergy)
Definition routines.c:2785
VEXTERNC int initMG(int icalc, NOsh *nosh, MGparm *mgparm, PBEparm *pbeparm, double realCenter[3], Vpbe *pbe[NOSH_MAXCALC], Valist *alist[NOSH_MAXMOL], Vgrid *dielXMap[NOSH_MAXMOL], Vgrid *dielYMap[NOSH_MAXMOL], Vgrid *dielZMap[NOSH_MAXMOL], Vgrid *kappaMap[NOSH_MAXMOL], Vgrid *chargeMap[NOSH_MAXMOL], Vpmgp *pmgp[NOSH_MAXCALC], Vpmg *pmg[NOSH_MAXCALC], Vgrid *potMap[NOSH_MAXMOL])
Initialize an MG calculation.
Definition routines.c:1212
VEXTERNC int printApolForce(Vcom *com, NOsh *nosh, int nforce[NOSH_MAXCALC], AtomForce *atomForce[NOSH_MAXCALC], int i)
Combine and pretty-print force data.
Definition routines.c:3471
VEXTERNC int writematMG(int rank, NOsh *nosh, PBEparm *pbeparm, Vpmg *pmg)
Write out operator matrix from MG calculation to file.
Definition routines.c:1799
VEXTERNC int writedataFE(int rank, NOsh *nosh, PBEparm *pbeparm, Vfetk *fetk)
Write FEM data to files.
Definition routines.c:4300
VEXTERNC int initAPOL(NOsh *nosh, Vmem *mem, Vparam *param, APOLparm *apolparm, int *nforce, AtomForce **atomForce, Valist *alist)
Upperlevel routine to the non-polar energy and force routines.
Definition routines.c:4475
VEXTERNC void printMGPARM(MGparm *mgparm, double realCenter[3])
Print out MG-specific params loaded from input.
Definition routines.c:1179
VEXTERNC void killPotMaps(NOsh *nosh, Vgrid *pot[NOSH_MAXMOL])
Destroy the loaded potential maps.
Definition routines.c:865
VEXTERNC void killFE(NOsh *nosh, Vpbe *pbe[NOSH_MAXCALC], Vfetk *fetk[NOSH_MAXCALC], Gem *gem[NOSH_MAXMOL])
Kill structures initialized during an FE calculation.
Definition routines.c:3683
VEXTERNC int energyAPOL(APOLparm *apolparm, double sasa, double sav, double atomsasa[], double atomwcaEnergy[], int numatoms)
Calculate non-polar energies.
Definition routines.c:4674
VEXTERNC int energyMG(NOsh *nosh, int icalc, Vpmg *pmg, int *nenergy, double *totEnergy, double *qfEnergy, double *qmEnergy, double *dielEnergy)
Calculate electrostatic energies from MG solution.
Definition routines.c:1569
VEXTERNC int forceMG(Vmem *mem, NOsh *nosh, PBEparm *pbeparm, MGparm *mgparm, Vpmg *pmg, int *nforce, AtomForce **atomForce, Valist *alist[NOSH_MAXMOL])
Calculate forces from MG solution.
Definition routines.c:1636
VEXTERNC int energyFE(NOsh *nosh, int icalc, Vfetk *fetk[NOSH_MAXCALC], int *nenergy, double *totEnergy, double *qfEnergy, double *qmEnergy, double *dielEnergy)
Calculate electrostatic energies from FE solution.
Definition routines.c:4179
VEXTERNC int printApolEnergy(NOsh *nosh, int iprint)
Combine and pretty-print energy data.
Definition routines.c:2918
VEXTERNC Vrc_Codes loadMeshes(NOsh *nosh, Gem *gm[NOSH_MAXMOL])
Load the meshes given in NOsh into geometry objects.
VEXTERNC int loadKappaMaps(NOsh *nosh, Vgrid *kappa[NOSH_MAXMOL])
Load the kappa maps given in NOsh into grid objects.
Definition routines.c:664
VEXTERNC int loadDielMaps(NOsh *nosh, Vgrid *dielXMap[NOSH_MAXMOL], Vgrid *dielYMap[NOSH_MAXMOL], Vgrid *dielZMap[NOSH_MAXMOL])
Load the dielectric maps given in NOsh into grid objects.
Definition routines.c:250
VEXTERNC Vparam * loadParameter(NOsh *nosh)
Loads and returns parameter object.
Definition routines.c:60
VEXTERNC void killChargeMaps(NOsh *nosh, Vgrid *charge[NOSH_MAXMOL])
Destroy the loaded charge maps.
Definition routines.c:984
VEXTERNC int loadMolecules(NOsh *nosh, Vparam *param, Valist *alist[NOSH_MAXMOL])
Load the molecules given in NOsh into atom lists.
Definition routines.c:95
enum eMGparm_CalcType MGparm_CalcType
Declare MGparm_CalcType type.
Definition mgparm.h:89
#define NOSH_MAXCALC
Maximum number of calculations in a run.
Definition nosh.h:87
#define NOSH_MAXMOL
Maximum number of molecules in a run.
Definition nosh.h:83
Structure to hold atomic forces.
Definition routines.h:99
double ibForce[3]
Definition routines.h:100
double wcaForce[3]
Definition routines.h:105
double dbForce[3]
Definition routines.h:102
double sasaForce[3]
Definition routines.h:103
double qfForce[3]
Definition routines.h:101
double savForce[3]
Definition routines.h:104
Reads and assigns charge/radii parameters.
Definition vparam.h:135
Parameter structure for APOL-specific variables from input files.
Definition apolparm.h:129
Parameter structure for BEM-specific variables from input files.
Definition bemparm.h:96
Parameter structure for FEM-specific variables from input files.
Definition femparm.h:133
Parameter structure for GEOFLOW-specific variables from input files.
Definition geoflowparm.h:98
Parameter structure for MG-specific variables from input files.
Definition mgparm.h:114
Class for parsing fixed format input files.
Definition nosh.h:195
Parameter structure for PBAM-specific variables from input files.
Definition pbamparm.h:105
Parameter structure for PBE variables from input files.
Definition pbeparm.h:117
Parameter structure for PBSAM-specific variables from input files.
Definition pbsamparm.h:105
Oracle for solvent- and ion-accessibility around a biomolecule.
Definition vacc.h:108
Container class for list of atom objects.
Definition valist.h:78
Atom cell list.
Definition vclist.h:117
Contains public data members for Vfetk class/module.
Definition vfetk.h:176
Electrostatic potential oracle for Cartesian mesh data.
Definition vgrid.h:81
Contains public data members for Vpbe class/module.
Definition vpbe.h:84
Contains public data members for Vpmg class/module.
Definition vpmg.h:116
Contains public data members for Vpmgp class/module.
Definition vpmgp.h:80
Contains declarations for class Vfetk.