Files | |
file | routines.h |
Header file for front end auxiliary routines. | |
Data Structures | |
struct | AtomForce |
Structure to hold atomic forces. More... | |
Defines | |
#define | APBSRC 13 |
Return code for APBS during failure. | |
Typedefs | |
typedef AtomForce | AtomForce |
Define AtomForce type. | |
Functions | |
VPUBLIC Vparam * | loadParameter (NOsh *nosh) |
Loads and returns parameter object. | |
VPUBLIC int | loadMolecules (NOsh *nosh, Vparam *param, Valist *alist[NOSH_MAXMOL]) |
Load the molecules given in NOsh into atom lists. | |
VPUBLIC void | killMolecules (NOsh *nosh, Valist *alist[NOSH_MAXMOL]) |
Destroy the loaded molecules. | |
VPUBLIC 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. | |
VPUBLIC void | killDielMaps (NOsh *nosh, Vgrid *dielXMap[NOSH_MAXMOL], Vgrid *dielYMap[NOSH_MAXMOL], Vgrid *dielZMap[NOSH_MAXMOL]) |
Destroy the loaded dielectric. | |
VPUBLIC int | loadKappaMaps (NOsh *nosh, Vgrid *map[NOSH_MAXMOL]) |
Load the kappa maps given in NOsh into grid objects. | |
VPUBLIC void | killKappaMaps (NOsh *nosh, Vgrid *map[NOSH_MAXMOL]) |
Destroy the loaded kappa maps. | |
VPUBLIC int | loadChargeMaps (NOsh *nosh, Vgrid *map[NOSH_MAXMOL]) |
Load the charge maps given in NOsh into grid objects. | |
VPUBLIC void | killChargeMaps (NOsh *nosh, Vgrid *map[NOSH_MAXMOL]) |
Destroy the loaded charge maps. | |
VPUBLIC void | printPBEPARM (PBEparm *pbeparm) |
Print out generic PBE params loaded from input. | |
VPUBLIC void | printMGPARM (MGparm *mgparm, double realCenter[3]) |
Print out MG-specific params loaded from input. | |
VPUBLIC 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]) |
Initialize an MG calculation. | |
VPUBLIC void | killMG (NOsh *nosh, Vpbe *pbe[NOSH_MAXCALC], Vpmgp *pmgp[NOSH_MAXCALC], Vpmg *pmg[NOSH_MAXCALC]) |
Kill structures initialized during an MG calculation. | |
VPUBLIC int | solveMG (NOsh *nosh, Vpmg *pmg, MGparm_CalcType type) |
Solve the PBE with MG. | |
VPUBLIC int | setPartMG (NOsh *nosh, MGparm *mgparm, Vpmg *pmg) |
Set MG partitions for calculating observables and performing I/O. | |
VPUBLIC int | energyMG (NOsh *nosh, int icalc, Vpmg *pmg, int *nenergy, double *totEnergy, double *qfEnergy, double *qmEnergy, double *dielEnergy) |
Calculate electrostatic energies from MG solution. | |
VPUBLIC void | killEnergy () |
Kill arrays allocated for energies. | |
VPUBLIC 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. | |
VPUBLIC void | killForce (Vmem *mem, NOsh *nosh, int nforce[NOSH_MAXCALC], AtomForce *atomForce[NOSH_MAXCALC]) |
Free memory from MG force calculation. | |
VPUBLIC void | storeAtomEnergy (Vpmg *pmg, int icalc, double **atomEnergy, int *nenergy) |
Store energy in arrays for future use. | |
VPUBLIC 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. | |
VPUBLIC 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. | |
VPUBLIC int | writedataMG (int rank, NOsh *nosh, PBEparm *pbeparm, Vpmg *pmg) |
Write out observables from MG calculation to file. | |
VPUBLIC int | writematMG (int rank, NOsh *nosh, PBEparm *pbeparm, Vpmg *pmg) |
Write out operator matrix from MG calculation to file. | |
VPUBLIC double | returnEnergy (Vcom *com, NOsh *nosh, double totEnergy[NOSH_MAXCALC], int iprint) |
Access net local energy. | |
VPUBLIC int | printEnergy (Vcom *com, NOsh *nosh, double totEnergy[NOSH_MAXCALC], int iprint) |
Combine and pretty-print energy data (deprecated...see printElecEnergy). | |
VPUBLIC int | printElecEnergy (Vcom *com, NOsh *nosh, double totEnergy[NOSH_MAXCALC], int iprint) |
Combine and pretty-print energy data. | |
VPUBLIC int | printApolEnergy (NOsh *nosh, int iprint) |
Combine and pretty-print energy data. | |
VPUBLIC int | printForce (Vcom *com, NOsh *nosh, int nforce[NOSH_MAXCALC], AtomForce *atomForce[NOSH_MAXCALC], int iprint) |
Combine and pretty-print force data (deprecated...see printElecForce). | |
VPUBLIC int | printElecForce (Vcom *com, NOsh *nosh, int nforce[NOSH_MAXCALC], AtomForce *atomForce[NOSH_MAXCALC], int iprint) |
Combine and pretty-print force data. | |
VPUBLIC int | printApolForce (Vcom *com, NOsh *nosh, int nforce[NOSH_MAXCALC], AtomForce *atomForce[NOSH_MAXCALC], int iprint) |
Combine and pretty-print force data. | |
VPUBLIC void | startVio () |
Wrapper to start MALOC Vio layer. | |
VPUBLIC void | printFEPARM (int icalc, NOsh *nosh, FEMparm *feparm, Vfetk *fetk[NOSH_MAXCALC]) |
Print out FE-specific params loaded from input. | |
VPUBLIC 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. | |
Vrc_Codes | initFE (int icalc, NOsh *nosh, FEMparm *feparm, PBEparm *pbeparm, Vpbe *pbe[NOSH_MAXCALC], Valist *alist[NOSH_MAXMOL], Vfetk *fetk[NOSH_MAXCALC], Gem *gm[NOSH_MAXCALC]) |
Initialize FE solver objects. | |
VPUBLIC void | killFE (NOsh *nosh, Vpbe *pbe[NOSH_MAXCALC], Vfetk *fetk[NOSH_MAXCALC], Gem *gm[NOSH_MAXMOL]) |
Kill structures initialized during an FE calculation. | |
VPUBLIC int | preRefineFE (int icalc, NOsh *nosh, FEMparm *feparm, Vfetk *fetk[NOSH_MAXCALC]) |
Pre-refine mesh before solve. | |
VPUBLIC int | partFE (int icalc, NOsh *nosh, FEMparm *feparm, Vfetk *fetk[NOSH_MAXCALC]) |
Partition mesh (if applicable). | |
VPUBLIC int | solveFE (int icalc, NOsh *nosh, PBEparm *pbeparm, FEMparm *feparm, Vfetk *fetk[NOSH_MAXCALC]) |
Solve-estimate-refine. | |
VPUBLIC int | postRefineFE (int icalc, NOsh *nosh, FEMparm *feparm, Vfetk *fetk[NOSH_MAXCALC]) |
Estimate error, mark mesh, and refine mesh after solve. | |
VPUBLIC int | writedataFE (int rank, NOsh *nosh, PBEparm *pbeparm, Vfetk *fetk) |
Write FEM data to files. | |
VPUBLIC int | energyAPOL (APOLparm *apolparm, double sasa, double sav, double atomsasa[], double atomwcaEnergy[], int numatoms) |
Calculate non-polar energies. | |
VPUBLIC int | forceAPOL (Vacc *acc, Vmem *mem, APOLparm *apolparm, int *nforce, AtomForce **atomForce, Valist *alist, Vclist *clist) |
Calculate non-polar forces. | |
VPUBLIC 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. | |
Vrc_Codes | loadMeshes (NOsh *nosh, Gem *gm[NOSH_MAXMOL]) |
Load the meshes given in NOsh into geometry objects. | |
void | killMeshes (NOsh *nosh, Gem *alist[NOSH_MAXMOL]) |
Destroy the loaded meshes. |
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Calculate non-polar energies.
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Calculate electrostatic energies from FE solution.
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Calculate electrostatic energies from MG solution.
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Calculate non-polar forces.
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Calculate forces from MG solution.
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Upperlevel routine to the non-polar energy and force routines.
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Initialize FE solver objects.
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Initialize an MG calculation.
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Destroy the loaded charge maps.
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Destroy the loaded dielectric.
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Kill arrays allocated for energies.
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Kill structures initialized during an FE calculation.
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Free memory from MG force calculation.
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Destroy the loaded kappa maps.
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Destroy the loaded meshes.
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Kill structures initialized during an MG calculation.
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Destroy the loaded molecules.
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Load the charge maps given in NOsh into grid objects.
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Load the dielectric maps given in NOsh into grid objects.
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Load the kappa maps given in NOsh into grid objects.
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Load the meshes given in NOsh into geometry objects.
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Load the molecules given in NOsh into atom lists.
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Loads and returns parameter object.
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Partition mesh (if applicable).
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Estimate error, mark mesh, and refine mesh after solve.
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Pre-refine mesh before solve.
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Combine and pretty-print energy data.
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Combine and pretty-print force data.
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Combine and pretty-print energy data.
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Combine and pretty-print force data.
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Combine and pretty-print energy data (deprecated...see printElecEnergy).
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Print out FE-specific params loaded from input.
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Combine and pretty-print force data (deprecated...see printElecForce).
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Print out MG-specific params loaded from input.
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Print out generic PBE params loaded from input.
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Access net local energy.
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Set MG partitions for calculating observables and performing I/O.
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Solve-estimate-refine. < AM_hPcg < Coarse-grid solver; 0 = SLU, 1 = MG, 2 = CG, 3 = BCG, 4 = PCG, 5 = PBCG < Primal problem < Preconditioner; 0 = identity. |
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Solve the PBE with MG.
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Wrapper to start MALOC Vio layer.
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Store energy in arrays for future use.
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Write FEM data to files.
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Write out information to a flat file.
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Write out observables from MG calculation to file.
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Write out information to an XML file.
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Write out operator matrix from MG calculation to file.
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