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High-level front-end routines


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 VparamloadParameter (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.


Function Documentation

VPUBLIC int energyAPOL APOLparm apolparm,
double  sasa,
double  sav,
double  atomsasa[],
double  atomwcaEnergy[],
int  numatoms
 

Calculate non-polar energies.

Author:
David Gohara
Returns:
1 if successful, 0 otherwise
Parameters:
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) *

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.

Author:
Nathan Baker
Parameters:
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)
Bug:
"calcenergy 2" does not work
Returns:
1 if successful, 0 otherwise

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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.

Author:
Nathan Baker
Parameters:
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)
Returns:
1 if successful, 0 otherwise

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VPUBLIC int forceAPOL Vacc acc,
Vmem *  mem,
APOLparm apolparm,
int *  nforce,
AtomForce **  atomForce,
Valist alist,
Vclist clist
 

Calculate non-polar forces.

Author:
David Gohara
Returns:
1 if successful, 0 otherwise
Parameters:
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

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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.

Author:
Nathan Baker
Parameters:
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
Returns:
1 if successful, 0 otherwise

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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.

Author:
David Gohara
Returns:
1 if successful, 0 otherwise
Parameters:
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

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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.

Author:
Nathan Baker
Bug:
THIS FUNCTION IS HARD-CODED TO SOLVE LRPBE

Todo:
THIS FUNCTION IS HARD-CODED TO SOLVE LRPBE
Parameters:
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

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.

Author:
Nathan Baker
Returns:
1 if succesful, 0 otherwise
Parameters:
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)

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VPUBLIC void killChargeMaps NOsh nosh,
Vgrid charge[NOSH_MAXMOL]
 

Destroy the loaded charge maps.

Author:
Nathan Baker
Parameters:
nosh NOsh object with input file information
charge List of charge maps

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VPUBLIC void killDielMaps NOsh nosh,
Vgrid dielXMap[NOSH_MAXMOL],
Vgrid dielYMap[NOSH_MAXMOL],
Vgrid dielZMap[NOSH_MAXMOL]
 

Destroy the loaded dielectric.

Author:
Nathan Baker
Parameters:
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

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VPUBLIC void killEnergy  ) 
 

Kill arrays allocated for energies.

Author:
Nathan Baker

VPUBLIC void killFE NOsh nosh,
Vpbe pbe[NOSH_MAXCALC],
Vfetk fetk[NOSH_MAXCALC],
Gem *  gem[NOSH_MAXMOL]
 

Kill structures initialized during an FE calculation.

Author:
Nathan Baker
Parameters:
pbe  Object with parsed input file parameters
fetk  Array of Vpbe objects for each calc
gm  Array of FEtk objects for each calc Array of geometry manager objects for each calc

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VPUBLIC void killForce Vmem *  mem,
NOsh nosh,
int  nforce[NOSH_MAXCALC],
AtomForce atomForce[NOSH_MAXCALC]
 

Free memory from MG force calculation.

Author:
Nathan Baker
Parameters:
mem Memory management object
nosh Parameters from input file
nforce Number of forces in arrays
atomForce List of atom forces

VPUBLIC void killKappaMaps NOsh nosh,
Vgrid kappa[NOSH_MAXMOL]
 

Destroy the loaded kappa maps.

Author:
Nathan Baker
Parameters:
nosh NOsh object with input file information
kappa List of kappa maps

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void killMeshes NOsh nosh,
Gem *  alist[NOSH_MAXMOL]
 

Destroy the loaded meshes.

Author:
Nathan Baker
Parameters:
nosh  NOsh object with input file information
alist  Populated list of geometry objects to be destroyed

VPUBLIC void killMG NOsh nosh,
Vpbe pbe[NOSH_MAXCALC],
Vpmgp pmgp[NOSH_MAXCALC],
Vpmg pmg[NOSH_MAXCALC]
 

Kill structures initialized during an MG calculation.

Author:
Nathan Baker
Parameters:
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

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VPUBLIC void killMolecules NOsh nosh,
Valist alist[NOSH_MAXMOL]
 

Destroy the loaded molecules.

Author:
Nathan Baker
Parameters:
nosh NOsh object with input file information
alist List of atom list objects

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VPUBLIC int loadChargeMaps NOsh nosh,
Vgrid charge[NOSH_MAXMOL]
 

Load the charge maps given in NOsh into grid objects.

Author:
Nathan Baker
Parameters:
nosh NOsh object with input file information
charge List of kappa maps
Returns:
1 if successful, 0 otherwise

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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.

Author:
Nathan Baker
Parameters:
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
Returns:
1 if successful, 0 otherwise

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VPUBLIC int loadKappaMaps NOsh nosh,
Vgrid kappa[NOSH_MAXMOL]
 

Load the kappa maps given in NOsh into grid objects.

Author:
Nathan Baker
Parameters:
nosh NOsh object with input file information
kappa List of kappa maps
Returns:
1 if successful, 0 otherwise

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Vrc_Codes loadMeshes NOsh nosh,
Gem *  gm[NOSH_MAXMOL]
 

Load the meshes given in NOsh into geometry objects.

Author:
Nathan Baker
Returns:
Error code on success/failure
Parameters:
nosh  NOsh object with input file information
gm  List of geometry objects (to be populated)

VPUBLIC int loadMolecules NOsh nosh,
Vparam param,
Valist alist[NOSH_MAXMOL]
 

Load the molecules given in NOsh into atom lists.

Author:
Nathan Baker
Returns:
1 if successful, 0 otherwise
Parameters:
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)

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VPUBLIC Vparam* loadParameter NOsh nosh  ) 
 

Loads and returns parameter object.

Author:
Nathan Baker
Returns:
Pointer to parameter object or NULL
Parameters:
nosh  Pointer to NOsh object with input file information

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VPUBLIC int partFE int  i,
NOsh nosh,
FEMparm feparm,
Vfetk fetk[NOSH_MAXCALC]
 

Partition mesh (if applicable).

Author:
Nathan Baker
Parameters:
i Calculation index
nosh Master parameter object
feparm FE-specific parameters
fetk Array of FE solver objects
Returns:
1 if successful, 0 otherwise

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VPUBLIC int postRefineFE int  icalc,
NOsh nosh,
FEMparm feparm,
Vfetk fetk[NOSH_MAXCALC]
 

Estimate error, mark mesh, and refine mesh after solve.

Author:
Nathan Baker
Parameters:
icalc Calculation index
nosh Master parameter object
feparm FE-specific parameters
fetk Array of FE solver objects
Returns:
1 if successful, 0 otherwise -- note that a 0 will likely imply that either the max number of vertices have been met or no vertices were marked for refinement. In either case, this should not be treated as a fatal error.

VPUBLIC int preRefineFE int  i,
NOsh nosh,
FEMparm feparm,
Vfetk fetk[NOSH_MAXCALC]
 

Pre-refine mesh before solve.

Author:
Nathan Baker
Parameters:
i Calculation index
nosh Master parameter object
feparm FE-specific parameters
fetk Array of FE solver objects
Returns:
1 if successful, 0 otherwise

VPUBLIC int printApolEnergy NOsh nosh,
int  iprint
 

Combine and pretty-print energy data.

Author:
David Gohara
Returns:
1 if successful, 0 otherwise
Parameters:
nosh  Parameters from input file
iprint  Index of energy statement to print

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VPUBLIC int printApolForce Vcom *  com,
NOsh nosh,
int  nforce[NOSH_MAXCALC],
AtomForce atomForce[NOSH_MAXCALC],
int  i
 

Combine and pretty-print force data.

Author:
David Gohara
Returns:
1 if successful, 0 otherwise
Parameters:
nosh  Communications object
nforce  Parameters from input file
atomForce  Number of forces calculated
iprint  Array of force structures Index of force statement to print

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VPUBLIC int printElecEnergy Vcom *  com,
NOsh nosh,
double  totEnergy[NOSH_MAXCALC],
int  iprint
 

Combine and pretty-print energy data.

Author:
David Gohara
Returns:
1 if successful, 0 otherwise
Parameters:
nosh  Communications object
totEnergy  Parameters from input file
iprint  Array of energies from different calculations Index of energy statement to print

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VPUBLIC int printElecForce Vcom *  com,
NOsh nosh,
int  nforce[NOSH_MAXCALC],
AtomForce atomForce[NOSH_MAXCALC],
int  i
 

Combine and pretty-print force data.

Author:
David Gohara
Returns:
1 if successful, 0 otherwise
Parameters:
nosh  Communications object
nforce  Parameters from input file
atomForce  Number of forces calculated
iprint  Array of force structures Index of force statement to print

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VPUBLIC int printEnergy Vcom *  com,
NOsh nosh,
double  totEnergy[NOSH_MAXCALC],
int  iprint
 

Combine and pretty-print energy data (deprecated...see printElecEnergy).

Author:
Nathan Baker
Returns:
1 if successful, 0 otherwise
Parameters:
nosh  Communications object
totEnergy  Parameters from input file
iprint  Array of energies from different calculations Index of energy statement to print

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VPUBLIC void printFEPARM int  icalc,
NOsh nosh,
FEMparm feparm,
Vfetk fetk[NOSH_MAXCALC]
 

Print out FE-specific params loaded from input.

Author:
Nathan Baker
Parameters:
icalc Calculation index
nosh Master parameter object
feparm FE-specific parameters
fetk Array of FE solver objects

VPUBLIC 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).

Author:
Nathan Baker
Returns:
1 if successful, 0 otherwise
Parameters:
nosh  Communications object
nforce  Parameters from input file
atomForce  Number of forces calculated
iprint  Array of force structures Index of force statement to print

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VPUBLIC void printMGPARM MGparm mgparm,
double  realCenter[3]
 

Print out MG-specific params loaded from input.

Author:
Nathan Baker
Parameters:
realCenter Center of mesh for actual calculation
mgparm MGparm object

VPUBLIC void printPBEPARM PBEparm pbeparm  ) 
 

Print out generic PBE params loaded from input.

Author:
Nathan Baker
Parameters:
pbeparm PBEparm object

VPUBLIC double returnEnergy Vcom *  com,
NOsh nosh,
double  totEnergy[NOSH_MAXCALC],
int  iprint
 

Access net local energy.

Author:
Justin Xiang
Parameters:
com Communications object
nosh Parameters from input file
totEnergy Array of energies from different calculations
iprint Index of energy statement to print
Returns:
Net local energy

VPUBLIC int setPartMG NOsh nosh,
MGparm mgparm,
Vpmg pmg
 

Set MG partitions for calculating observables and performing I/O.

Author:
Nathan Baker
Parameters:
nosh Object with parsed input file parameters
mgparm MG parameters from input file
pmg MG object
Returns:
1 if successful, 0 otherwise

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VPUBLIC int solveFE int  icalc,
NOsh nosh,
PBEparm pbeparm,
FEMparm feparm,
Vfetk fetk[NOSH_MAXCALC]
 

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.

VPUBLIC int solveMG NOsh nosh,
Vpmg pmg,
MGparm_CalcType  type
 

Solve the PBE with MG.

Author:
Nathan Baker
Parameters:
nosh Object with parsed input file parameters
pmg MG objects for this calculation
type Type of MG calculation
Returns:
1 if successful, 0 otherwise

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VPUBLIC void startVio  ) 
 

Wrapper to start MALOC Vio layer.

Author:
Nathan Baker and Robert Konecny

VPUBLIC void storeAtomEnergy Vpmg pmg,
int  icalc,
double **  atomEnergy,
int *  nenergy
 

Store energy in arrays for future use.

Author:
Todd Dolinsky
Parameters:
pmg  MG object
icalc  Calculation number
atomEnergy  Pointer to storage array of doubles
nenergy  Stores number of atoms per calc

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VPUBLIC int writedataFE int  rank,
NOsh nosh,
PBEparm pbeparm,
Vfetk fetk
 

Write FEM data to files.

Author:
Nathan Baker
Parameters:
rank Rank of processor (for parallel runs)
nosh NOsh object
pbeparm PBEparm object
fetk FEtk object (with solution)
Returns:
1 if successful, 0 otherwise

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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.

Author:
Todd Dolinsky
Parameters:
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
Returns:
1 if successful, 0 otherwise

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VPUBLIC int writedataMG int  rank,
NOsh nosh,
PBEparm pbeparm,
Vpmg pmg
 

Write out observables from MG calculation to file.

Author:
Nathan Baker
Parameters:
rank Processor rank (if parallel calculation)
nosh Parameters from input file
pbeparm Generic PBE parameters
pmg MG object
Returns:
1 if successful, 0 otherwise

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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.

Author:
Todd Dolinsky
Parameters:
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
Returns:
1 if successful, 0 otherwise

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VPUBLIC int writematMG int  rank,
NOsh nosh,
PBEparm pbeparm,
Vpmg pmg
 

Write out operator matrix from MG calculation to file.

Author:
Nathan Baker
Parameters:
rank Processor rank (if parallel calculation)
nosh Parameters from input file
pbeparm Generic PBE parameters
pmg MG object
Returns:
1 if successful, 0 otherwise

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