Data Structures | |
| struct | AtomForce |
| Structure to hold atomic forces. More... | |
Files | |
| file | routines.h |
Header file for front end auxiliary routines. | |
Defines | |
| #define | APBSRC 13 |
| Return code for APBS during failure. | |
Typedefs | |
| typedef struct AtomForce | AtomForce |
| Define AtomForce type. | |
Functions | |
| int | main (int argc, char **argv) |
| The main APBS function. | |
| VEXTERNC Vparam * | loadParameter (NOsh *nosh) |
| Loads and returns parameter object. | |
| VEXTERNC int | loadMolecules (NOsh *nosh, Vparam *param, Valist *alist[NOSH_MAXMOL]) |
| Load the molecules given in NOsh into atom lists. | |
| VEXTERNC void | killMolecules (NOsh *nosh, Valist *alist[NOSH_MAXMOL]) |
| Destroy the loaded molecules. | |
| 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. | |
| VEXTERNC void | killDielMaps (NOsh *nosh, Vgrid *dielXMap[NOSH_MAXMOL], Vgrid *dielYMap[NOSH_MAXMOL], Vgrid *dielZMap[NOSH_MAXMOL]) |
| Destroy the loaded dielectric. | |
| VEXTERNC int | loadKappaMaps (NOsh *nosh, Vgrid *kappa[NOSH_MAXMOL]) |
| Load the kappa maps given in NOsh into grid objects. | |
| VEXTERNC void | killKappaMaps (NOsh *nosh, Vgrid *kappa[NOSH_MAXMOL]) |
| Destroy the loaded kappa maps. | |
| VEXTERNC int | loadPotMaps (NOsh *nosh, Vgrid *pot[NOSH_MAXMOL]) |
| Load the potential maps given in NOsh into grid objects. | |
| VEXTERNC void | killPotMaps (NOsh *nosh, Vgrid *pot[NOSH_MAXMOL]) |
| Destroy the loaded potential maps. | |
| VEXTERNC int | loadChargeMaps (NOsh *nosh, Vgrid *charge[NOSH_MAXMOL]) |
| Load the charge maps given in NOsh into grid objects. | |
| VEXTERNC void | killChargeMaps (NOsh *nosh, Vgrid *charge[NOSH_MAXMOL]) |
| Destroy the loaded charge maps. | |
| VEXTERNC void | printPBEPARM (PBEparm *pbeparm) |
| Print out generic PBE params loaded from input. | |
| VEXTERNC void | printMGPARM (MGparm *mgparm, double realCenter[3]) |
| Print out MG-specific params loaded from input. | |
| 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. | |
| VEXTERNC void | killMG (NOsh *nosh, Vpbe *pbe[NOSH_MAXCALC], Vpmgp *pmgp[NOSH_MAXCALC], Vpmg *pmg[NOSH_MAXCALC]) |
| Kill structures initialized during an MG calculation. | |
| VEXTERNC int | solveMG (NOsh *nosh, Vpmg *pmg, MGparm_CalcType type) |
| Solve the PBE with MG. | |
| VEXTERNC int | setPartMG (NOsh *nosh, MGparm *mgparm, Vpmg *pmg) |
| Set MG partitions for calculating observables and performing I/O. | |
| 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. | |
| VEXTERNC void | killEnergy () |
| Kill arrays allocated for energies. | |
| 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. | |
| VEXTERNC void | killForce (Vmem *mem, NOsh *nosh, int nforce[NOSH_MAXCALC], AtomForce *atomForce[NOSH_MAXCALC]) |
| Free memory from MG force calculation. | |
| VEXTERNC void | storeAtomEnergy (Vpmg *pmg, int icalc, double **atomEnergy, int *nenergy) |
| Store energy in arrays for future use. | |
| 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. | |
| 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. | |
| VEXTERNC int | writedataMG (int rank, NOsh *nosh, PBEparm *pbeparm, Vpmg *pmg) |
| Write out observables from MG calculation to file. | |
| VEXTERNC int | writematMG (int rank, NOsh *nosh, PBEparm *pbeparm, Vpmg *pmg) |
| Write out operator matrix from MG calculation to file. | |
| VEXTERNC double | returnEnergy (Vcom *com, NOsh *nosh, double totEnergy[NOSH_MAXCALC], int iprint) |
| Access net local energy. | |
| VEXTERNC int | printEnergy (Vcom *com, NOsh *nosh, double totEnergy[NOSH_MAXCALC], int iprint) |
| Combine and pretty-print energy data (deprecated...see printElecEnergy) | |
| VEXTERNC int | printElecEnergy (Vcom *com, NOsh *nosh, double totEnergy[NOSH_MAXCALC], int iprint) |
| Combine and pretty-print energy data. | |
| VEXTERNC int | printApolEnergy (NOsh *nosh, int iprint) |
| Combine and pretty-print energy data. | |
| 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) | |
| VEXTERNC int | printElecForce (Vcom *com, NOsh *nosh, int nforce[NOSH_MAXCALC], AtomForce *atomForce[NOSH_MAXCALC], int i) |
| Combine and pretty-print force data. | |
| VEXTERNC int | printApolForce (Vcom *com, NOsh *nosh, int nforce[NOSH_MAXCALC], AtomForce *atomForce[NOSH_MAXCALC], int i) |
| Combine and pretty-print force data. | |
| VEXTERNC void | startVio () |
| Wrapper to start MALOC Vio layer. | |
| VEXTERNC int | energyAPOL (APOLparm *apolparm, double sasa, double sav, double atomsasa[], double atomwcaEnergy[], int numatoms) |
| Calculate non-polar energies. | |
| VEXTERNC int | forceAPOL (Vacc *acc, Vmem *mem, APOLparm *apolparm, int *nforce, AtomForce **atomForce, Valist *alist, Vclist *clist) |
| Calculate non-polar forces. | |
| 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. | |
| VEXTERNC void | printFEPARM (int icalc, NOsh *nosh, FEMparm *feparm, Vfetk *fetk[NOSH_MAXCALC]) |
| Print out FE-specific params loaded from input. | |
| 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. | |
| VEXTERNC 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. | |
| VEXTERNC void | killFE (NOsh *nosh, Vpbe *pbe[NOSH_MAXCALC], Vfetk *fetk[NOSH_MAXCALC], Gem *gem[NOSH_MAXMOL]) |
| Kill structures initialized during an FE calculation. | |
| VEXTERNC int | preRefineFE (int i, NOsh *nosh, FEMparm *feparm, Vfetk *fetk[NOSH_MAXCALC]) |
| Pre-refine mesh before solve. | |
| VEXTERNC int | partFE (int i, NOsh *nosh, FEMparm *feparm, Vfetk *fetk[NOSH_MAXCALC]) |
| Partition mesh (if applicable) | |
| VEXTERNC int | solveFE (int i, NOsh *nosh, PBEparm *pbeparm, FEMparm *feparm, Vfetk *fetk[NOSH_MAXCALC]) |
| Solve-estimate-refine. | |
| VEXTERNC int | postRefineFE (int icalc, NOsh *nosh, FEMparm *feparm, Vfetk *fetk[NOSH_MAXCALC]) |
| Estimate error, mark mesh, and refine mesh after solve. | |
| VEXTERNC int | writedataFE (int rank, NOsh *nosh, PBEparm *pbeparm, Vfetk *fetk) |
| Write FEM data to files. | |
| VEXTERNC Vrc_Codes | loadMeshes (NOsh *nosh, Gem *gm[NOSH_MAXMOL]) |
| Load the meshes given in NOsh into geometry objects. | |
| VEXTERNC void | killMeshes (NOsh *nosh, Gem *alist[NOSH_MAXMOL]) |
| Destroy the loaded meshes. | |
| VEXTERNC int energyAPOL | ( | APOLparm * | apolparm, |
| double | sasa, | ||
| double | sav, | ||
| double | atomsasa[], | ||
| double | atomwcaEnergy[], | ||
| int | numatoms | ||
| ) |
Calculate non-polar energies.
| sasa | APOLparm object |
| sav | Solvent accessible surface area |
| atomsasa | Solvent accessible volume |
| atomwcaEnergy | Array for SASA per atom * |
| numatoms | Array for WCA energy per atom * Number of atoms (or size of the above arrays) * |
Definition at line 4146 of file routines.c.


| 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.
| nosh | Object with parsed input file parameters |
| icalc | Index of calculation |
| fetk | FE object array |
| nenergy | Set to number of entries in energy arrays |
| totEnergy | Set to total energy (in kT) |
| qfEnergy | Set to charge-potential energy (in kT) |
| qmEnergy | Set to mobile ion energy (in kT) |
| dielEnergy | Set to polarization energy (in kT) |
Definition at line 3710 of file routines.c.


| 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.
| nosh | Object with parsed input file parameters |
| icalc | Index of calculation |
| pmg | MG object |
| nenergy | Set to number of entries in energy arrays |
| totEnergy | Set to total energy (in kT) |
| qfEnergy | Set to charge-potential energy (in kT) |
| qmEnergy | Set to mobile ion energy (in kT) |
| dielEnergy | Set to polarization energy (in kT) |
Definition at line 1263 of file routines.c.


| VEXTERNC int forceAPOL | ( | Vacc * | acc, |
| Vmem * | mem, | ||
| APOLparm * | apolparm, | ||
| int * | nforce, | ||
| AtomForce ** | atomForce, | ||
| Valist * | alist, | ||
| Vclist * | clist | ||
| ) |
Calculate non-polar forces.
| acc | Accessiblity object |
| mem | Memory manager |
| apolparm | Apolar calculation parameter object |
| nforce | Number of atomic forces to calculate statements for |
| atomForce | Object for storing atom forces |
| alist | Atom list |
| clist | Cell list for accessibility object |
Definition at line 4195 of file routines.c.


| 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.
| mem | Memory management object |
| nosh | Parameters from input file |
| pbeparm | Generic PBE parameters |
| mgparm | MG-specific parmaeters |
| pmg | MG object |
| nforce | Set to number of forces in arrays |
| atomForce | List of atom forces |
| alist | List of atom lists |
Definition at line 1327 of file routines.c.


| 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.
| nosh | Input parameter object |
| mem | Memory manager |
| param | Atom parameters |
| apolparm | Apolar calculation parameters |
| nforce | Number of force calculations |
| atomForce | Atom force storage object |
| alist | Atom list |
Definition at line 3971 of file routines.c.


| VEXTERNC 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.
| nosh | Index in pb, fetk to initialize (calculation index) |
| feparm | Master parmaeter object |
| pbeparm | FE-specific parameters |
| pbe | Generic PBE parameters |
| alist | Array of PBE objects |
| fetk | Array of atom lists |
| gm | Array of finite element objects Array of geometry objects |

| 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.
| icalc | Index of calculation in pmg/pmpg arrays |
| nosh | Object with parsed input file parameters |
| mgparm | Object with MG-specific parameters |
| pbeparm | Object with generic PBE parameters |
| realCenter | The actual center of the current mesh |
| pbe | Array of Vpbe objects (one for each calc) |
| alist | Array of atom lists |
| dielXMap | Array of x-shifted dielectric maps |
| dielYMap | Array of y-shifted dielectric maps |
| dielZMap | Array of z-shifted dielectric maps |
| kappaMap | Array of kappa maps |
| chargeMap | Array of charge maps |
| pmgp | Array of MG parameter objects (one for each calc) |
| pmg | Array of MG objects (one for each calc) |
| potMap | Array of potential maps |
Definition at line 945 of file routines.c.


Destroy the loaded charge maps.
| nosh | NOsh object with input file information |
| charge | List of charge maps |
Definition at line 725 of file routines.c.


| VEXTERNC void killDielMaps | ( | NOsh * | nosh, |
| Vgrid * | dielXMap[NOSH_MAXMOL], | ||
| Vgrid * | dielYMap[NOSH_MAXMOL], | ||
| Vgrid * | dielZMap[NOSH_MAXMOL] | ||
| ) |
Destroy the loaded dielectric.
| nosh | NOsh object with input file information |
| dielXMap | List of x-shifted dielectric maps |
| dielYMap | List of y-shifted dielectric maps |
| dielZMap | List of x-shifted dielectric maps |
Definition at line 489 of file routines.c.


| VEXTERNC void killEnergy | ( | ) |
Kill arrays allocated for energies.
Definition at line 1456 of file routines.c.


| VEXTERNC void killFE | ( | NOsh * | nosh, |
| Vpbe * | pbe[NOSH_MAXCALC], | ||
| Vfetk * | fetk[NOSH_MAXCALC], | ||
| Gem * | gem[NOSH_MAXMOL] | ||
| ) |
Kill structures initialized during an FE calculation.
| pbe | Object with parsed input file parameters |
| fetk | Array of Vpbe objects for each calc |
| gem | Array of FEtk objects for each calc Array of geometry manager objects for each calc |
Definition at line 3283 of file routines.c.


| VEXTERNC void killForce | ( | Vmem * | mem, |
| NOsh * | nosh, | ||
| int | nforce[NOSH_MAXCALC], | ||
| AtomForce * | atomForce[NOSH_MAXCALC] | ||
| ) |
Free memory from MG force calculation.
| mem | Memory management object |
| nosh | Parameters from input file |
| nforce | Number of forces in arrays |
| atomForce | List of atom forces |
Definition at line 1464 of file routines.c.


Destroy the loaded kappa maps.
| nosh | NOsh object with input file information |
| kappa | List of kappa maps |
Definition at line 564 of file routines.c.


| VEXTERNC void killMeshes | ( | NOsh * | nosh, |
| Gem * | alist[NOSH_MAXMOL] | ||
| ) |
Destroy the loaded meshes.
| nosh | NOsh object with input file information |
| alist | Populated list of geometry objects to be destroyed |
| VEXTERNC void killMG | ( | NOsh * | nosh, |
| Vpbe * | pbe[NOSH_MAXCALC], | ||
| Vpmgp * | pmgp[NOSH_MAXCALC], | ||
| Vpmg * | pmg[NOSH_MAXCALC] | ||
| ) |
Kill structures initialized during an MG calculation.
| pbe | Object with parsed input file parameters |
| pmgp | Array of Vpbe objects for each calc |
| pmg | Array of MG parameter objects for each calc Array of MG objects for each calc |
Definition at line 1161 of file routines.c.


Destroy the loaded molecules.
| nosh | NOsh object with input file information |
| alist | List of atom list objects |
Definition at line 248 of file routines.c.


Destroy the loaded potential maps.
| nosh | NOsh object with input file information |
| pot | List of potential maps |
Definition at line 640 of file routines.c.

Load the charge maps given in NOsh into grid objects.
| nosh | NOsh object with input file information |
| charge | List of kappa maps |
Definition at line 654 of file routines.c.


| 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.
| nosh | NOsh object with input file information |
| dielXMap | List of x-shifted dielectric maps |
| dielYMap | List of y-shifted dielectric maps |
| dielZMap | List of x-shifted dielectric maps |
Definition at line 260 of file routines.c.


Load the kappa maps given in NOsh into grid objects.
| nosh | NOsh object with input file information |
| kappa | List of kappa maps |
Definition at line 511 of file routines.c.


| VEXTERNC Vrc_Codes loadMeshes | ( | NOsh * | nosh, |
| Gem * | gm[NOSH_MAXMOL] | ||
| ) |
Load the meshes given in NOsh into geometry objects.
| nosh | NOsh object with input file information |
| gm | List of geometry objects (to be populated) |
Load the molecules given in NOsh into atom lists.
| nosh | NOsh object with input file information |
| param | NULL (if PQR files only) or pointer to parameter object |
| alist | List of atom list objects (to be populated) |
Definition at line 112 of file routines.c.


Loads and returns parameter object.
| nosh | Pointer to NOsh object with input file information |
Definition at line 77 of file routines.c.


Load the potential maps given in NOsh into grid objects.
| nosh | NOsh object with input file information |
| pot | List of potential maps |
Definition at line 578 of file routines.c.


| int main | ( | int | argc, |
| char ** | argv | ||
| ) |
Partition mesh (if applicable)
| i | Calculation index |
| nosh | Master parameter object |
| feparm | FE-specific parameters |
| fetk | Array of FE solver objects |
Definition at line 3599 of file routines.c.

Estimate error, mark mesh, and refine mesh after solve.
| icalc | Calculation index |
| nosh | Master parameter object |
| feparm | FE-specific parameters |
| fetk | Array of FE solver objects |
Definition at line 3752 of file routines.c.


Pre-refine mesh before solve.
| i | Calculation index |
| nosh | Master parameter object |
| feparm | FE-specific parameters |
| fetk | Array of FE solver objects |
Definition at line 3606 of file routines.c.


| VEXTERNC int printApolEnergy | ( | NOsh * | nosh, |
| int | iprint | ||
| ) |
Combine and pretty-print energy data.
| nosh | Parameters from input file |
| iprint | Index of energy statement to print |
Definition at line 2555 of file routines.c.


| VEXTERNC int printApolForce | ( | Vcom * | com, |
| NOsh * | nosh, | ||
| int | nforce[NOSH_MAXCALC], | ||
| AtomForce * | atomForce[NOSH_MAXCALC], | ||
| int | i | ||
| ) |
Combine and pretty-print force data.
| nosh | Communications object |
| nforce | Parameters from input file |
| atomForce | Number of forces calculated |
| i | Array of force structures Index of force statement to print |
Definition at line 3083 of file routines.c.


| VEXTERNC int printElecEnergy | ( | Vcom * | com, |
| NOsh * | nosh, | ||
| double | totEnergy[NOSH_MAXCALC], | ||
| int | iprint | ||
| ) |
Combine and pretty-print energy data.
| nosh | Communications object |
| totEnergy | Parameters from input file |
| iprint | Array of energies from different calculations Index of energy statement to print |
Definition at line 2496 of file routines.c.


| VEXTERNC int printElecForce | ( | Vcom * | com, |
| NOsh * | nosh, | ||
| int | nforce[NOSH_MAXCALC], | ||
| AtomForce * | atomForce[NOSH_MAXCALC], | ||
| int | i | ||
| ) |
Combine and pretty-print force data.
| nosh | Communications object |
| nforce | Parameters from input file |
| atomForce | Number of forces calculated |
| i | Array of force structures Index of force statement to print |
Definition at line 2850 of file routines.c.


Combine and pretty-print energy data (deprecated...see printElecEnergy)
| nosh | Communications object |
| totEnergy | Parameters from input file |
| iprint | Array of energies from different calculations Index of energy statement to print |
Definition at line 2434 of file routines.c.


Print out FE-specific params loaded from input.
| icalc | Calculation index |
| nosh | Master parameter object |
| feparm | FE-specific parameters |
| fetk | Array of FE solver objects |
Definition at line 3466 of file routines.c.


| 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)
| nosh | Communications object |
| nforce | Parameters from input file |
| atomForce | Number of forces calculated |
| i | Array of force structures Index of force statement to print |
Definition at line 2614 of file routines.c.


| VEXTERNC void printMGPARM | ( | MGparm * | mgparm, |
| double | realCenter[3] | ||
| ) |
Print out MG-specific params loaded from input.
| realCenter | Center of mesh for actual calculation |
| mgparm | MGparm object |
Definition at line 915 of file routines.c.


| VEXTERNC void printPBEPARM | ( | PBEparm * | pbeparm ) |
Print out generic PBE params loaded from input.
| pbeparm | PBEparm object |
Definition at line 741 of file routines.c.


| VEXTERNC double returnEnergy | ( | Vcom * | com, |
| NOsh * | nosh, | ||
| double | totEnergy[NOSH_MAXCALC], | ||
| int | iprint | ||
| ) |
Access net local energy.
| com | Communications object |
| nosh | Parameters from input file |
| totEnergy | Array of energies from different calculations |
| iprint | Index of energy statement to print |
Definition at line 2408 of file routines.c.

Set MG partitions for calculating observables and performing I/O.
| nosh | Object with parsed input file parameters |
| mgparm | MG parameters from input file |
| pmg | MG object |
Definition at line 1221 of file routines.c.


| VEXTERNC int solveFE | ( | int | i, |
| NOsh * | nosh, | ||
| PBEparm * | pbeparm, | ||
| FEMparm * | feparm, | ||
| Vfetk * | fetk[NOSH_MAXCALC] | ||
| ) |
Solve-estimate-refine.
| i | Calculation index |
| nosh | Master parameter object |
| feparm | FE-specific parameters |
| pbeparm | Generic PBE parameters |
| fetk | Array of FE solver objects |
< AM_hPcg
< Coarse-grid solver; 0 = SLU, 1 = MG, 2 = CG, 3 = BCG, 4 = PCG, 5 = PBCG
< Primal problem
< Preconditioner; 0 = identity.
Definition at line 3660 of file routines.c.


| VEXTERNC int solveMG | ( | NOsh * | nosh, |
| Vpmg * | pmg, | ||
| MGparm_CalcType | type | ||
| ) |
Solve the PBE with MG.
| nosh | Object with parsed input file parameters |
| pmg | MG objects for this calculation |
| type | Type of MG calculation |
Definition at line 1187 of file routines.c.


| VEXTERNC void startVio | ( | ) |
Wrapper to start MALOC Vio layer.
Definition at line 75 of file routines.c.
| VEXTERNC void storeAtomEnergy | ( | Vpmg * | pmg, |
| int | icalc, | ||
| double ** | atomEnergy, | ||
| int * | nenergy | ||
| ) |
Store energy in arrays for future use.
| pmg | MG object |
| icalc | Calculation number |
| atomEnergy | Pointer to storage array of doubles |
| nenergy | Stores number of atoms per calc |
Definition at line 1552 of file routines.c.


Write FEM data to files.
| rank | Rank of processor (for parallel runs) |
| nosh | NOsh object |
| pbeparm | PBEparm object |
| fetk | FEtk object (with solution) |
Definition at line 3807 of file routines.c.


| 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.
| nosh | Parameters from input file |
| com | The communications object |
| fname | The target XML file name |
| totEnergy | An array with per-calc total energies (in kT) |
| qfEnergy | An array with per-calc charge-potential energies (in kT) |
| qmEnergy | An array with per-calc mobile energies (in kT) |
| dielEnergy | An array with per-calc polarization energies (in kT) |
| nenergy | An array containing the number of atoms per-calc |
| atomEnergy | An array containing per-atom energies (in KT) per calc |
| nforce | An array containing the number of forces calculated per-calc |
| atomForce | An array containing per-atom forces per calc |
Definition at line 1569 of file routines.c.


Write out observables from MG calculation to file.
| rank | Processor rank (if parallel calculation) |
| nosh | Parameters from input file |
| pbeparm | Generic PBE parameters |
| pmg | MG object |
Definition at line 2065 of file routines.c.


| 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.
| nosh | Parameters from input file |
| com | The communications object |
| fname | The target XML file name |
| totEnergy | An array with per-calc total energies (in kT) |
| qfEnergy | An array with per-calc charge-potential energies (in kT) |
| qmEnergy | An array with per-calc mobile energies (in kT) |
| dielEnergy | An array with per-calc polarization energies (in kT) |
| nenergy | An array containing the number of atoms per-calc |
| atomEnergy | An array containing per-atom energies (in KT) per calc |
| nforce | An array containing the number of forces calculated per-calc |
| atomForce | An array containing per-atom forces per calc |
Definition at line 1805 of file routines.c.

Write out operator matrix from MG calculation to file.
| rank | Processor rank (if parallel calculation) |
| nosh | Parameters from input file |
| pbeparm | Generic PBE parameters |
| pmg | MG object |
Definition at line 1481 of file routines.c.


1.7.2