High-level front-end routines

Data Structures
struct	AtomForce
	Structure to hold atomic forces. More...
Files
file	main.c
	APBS "front end" program using formatted input 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.
Vparam *	loadParameter (NOsh *nosh)
	Loads and returns parameter object.
int	loadMolecules (NOsh *nosh, Vparam *param, Valist *alist[NOSH_MAXMOL])
	Load the molecules given in NOsh into atom lists.
void	killMolecules (NOsh *nosh, Valist *alist[NOSH_MAXMOL])
	Destroy the loaded molecules.
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.
void	killDielMaps (NOsh *nosh, Vgrid *dielXMap[NOSH_MAXMOL], Vgrid *dielYMap[NOSH_MAXMOL], Vgrid *dielZMap[NOSH_MAXMOL])
	Destroy the loaded dielectric.
int	loadKappaMaps (NOsh *nosh, Vgrid *kappa[NOSH_MAXMOL])
	Load the kappa maps given in NOsh into grid objects.
void	killKappaMaps (NOsh *nosh, Vgrid *kappa[NOSH_MAXMOL])
	Destroy the loaded kappa maps.
int	loadChargeMaps (NOsh *nosh, Vgrid *charge[NOSH_MAXMOL])
	Load the charge maps given in NOsh into grid objects.
void	killChargeMaps (NOsh *nosh, Vgrid *charge[NOSH_MAXMOL])
	Destroy the loaded charge maps.
void	printPBEPARM (PBEparm *pbeparm)
	Print out generic PBE params loaded from input.
void	printMGPARM (MGparm *mgparm, double realCenter[3])
	Print out MG-specific params loaded from input.
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.
void	killMG (NOsh *nosh, Vpbe *pbe[NOSH_MAXCALC], Vpmgp *pmgp[NOSH_MAXCALC], Vpmg *pmg[NOSH_MAXCALC])
	Kill structures initialized during an MG calculation.
int	solveMG (NOsh *nosh, Vpmg *pmg, MGparm_CalcType type)
	Solve the PBE with MG.
int	setPartMG (NOsh *nosh, MGparm *mgparm, Vpmg *pmg)
	Set MG partitions for calculating observables and performing I/O.
int	energyMG (NOsh *nosh, int icalc, Vpmg *pmg, int *nenergy, double *totEnergy, double *qfEnergy, double *qmEnergy, double *dielEnergy)
	Calculate electrostatic energies from MG solution.
void	killEnergy ()
	Kill arrays allocated for energies.
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.
void	killForce (Vmem *mem, NOsh *nosh, int nforce[NOSH_MAXCALC], AtomForce *atomForce[NOSH_MAXCALC])
	Free memory from MG force calculation.
void	storeAtomEnergy (Vpmg *pmg, int icalc, double **atomEnergy, int *nenergy)
	Store energy in arrays for future use.
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.
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.
int	writedataMG (int rank, NOsh *nosh, PBEparm *pbeparm, Vpmg *pmg)
	Write out observables from MG calculation to file.
int	writematMG (int rank, NOsh *nosh, PBEparm *pbeparm, Vpmg *pmg)
	Write out operator matrix from MG calculation to file.
double	returnEnergy (Vcom *com, NOsh *nosh, double totEnergy[NOSH_MAXCALC], int iprint)
	Access net local energy.
int	printEnergy (Vcom *com, NOsh *nosh, double totEnergy[NOSH_MAXCALC], int iprint)
	Combine and pretty-print energy data (deprecated...see printElecEnergy).
int	printElecEnergy (Vcom *com, NOsh *nosh, double totEnergy[NOSH_MAXCALC], int iprint)
	Combine and pretty-print energy data.
int	printApolEnergy (NOsh *nosh, int iprint)
	Combine and pretty-print energy data.
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).
int	printElecForce (Vcom *com, NOsh *nosh, int nforce[NOSH_MAXCALC], AtomForce *atomForce[NOSH_MAXCALC], int i)
	Combine and pretty-print force data.
int	printApolForce (Vcom *com, NOsh *nosh, int nforce[NOSH_MAXCALC], AtomForce *atomForce[NOSH_MAXCALC], int i)
	Combine and pretty-print force data.
void	startVio ()
	Wrapper to start MALOC Vio layer.
void	printFEPARM (int icalc, NOsh *nosh, FEMparm *feparm, Vfetk *fetk[NOSH_MAXCALC])
	Print out FE-specific params loaded from input.
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.
void	killFE (NOsh *nosh, Vpbe *pbe[NOSH_MAXCALC], Vfetk *fetk[NOSH_MAXCALC], Gem *gem[NOSH_MAXMOL])
	Kill structures initialized during an FE calculation.
int	preRefineFE (int i, NOsh *nosh, FEMparm *feparm, Vfetk *fetk[NOSH_MAXCALC])
	Pre-refine mesh before solve.
int	partFE (int i, NOsh *nosh, FEMparm *feparm, Vfetk *fetk[NOSH_MAXCALC])
	Partition mesh (if applicable).
int	solveFE (int i, NOsh *nosh, PBEparm *pbeparm, FEMparm *feparm, Vfetk *fetk[NOSH_MAXCALC])
	Solve-estimate-refine.
int	postRefineFE (int icalc, NOsh *nosh, FEMparm *feparm, Vfetk *fetk[NOSH_MAXCALC])
	Estimate error, mark mesh, and refine mesh after solve.
int	writedataFE (int rank, NOsh *nosh, PBEparm *pbeparm, Vfetk *fetk)
	Write FEM data to files.
int	energyAPOL (APOLparm *apolparm, double sasa, double sav, double atomsasa[], double atomwcaEnergy[], int numatoms)
	Calculate non-polar energies.
int	forceAPOL (Vacc *acc, Vmem *mem, APOLparm *apolparm, int *nforce, AtomForce **atomForce, Valist *alist, Vclist *clist)
	Calculate non-polar forces.
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

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) *

References ACE_COMPS, ACE_NO, ACE_TOTAL, sAPOLparm::calcenergy, sAPOLparm::gamma, sAPOLparm::press, and VRC_SUCCESS.

Referenced by initAPOL().

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

References sNOsh::bogus, sNOsh::calc, sPBEparm::calcenergy, sNOsh_calc::femparm, PBE_LPBE, PBE_LRPBE, PBE_NPBE, PBE_SMPBE, sNOsh_calc::pbeparm, sPBEparm::pbetype, PCE_COMPS, sPBEparm::temp, Vfetk_energy(), Vunit_kb, and Vunit_Na.

Referenced by main().

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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

References sVpbe::alist, APBS_TIMER_ENERGY, sNOsh::bogus, sNOsh::calc, sPBEparm::calcenergy, extEnergy(), sNOsh_calc::mgparm, sVpmg::pbe, sNOsh_calc::pbeparm, PCE_COMPS, PCE_TOTAL, sPBEparm::temp, Valist_getAtom(), Valist_getNumberAtoms(), Vpmg_dielEnergy(), Vpmg_energy(), Vpmg_qfAtomEnergy(), Vpmg_qfEnergy(), Vpmg_qmEnergy(), Vunit_kb, and Vunit_Na.

Referenced by main().

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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

References ACF_COMPS, ACF_TOTAL, sVacc::alist, sAPOLparm::bconc, sAPOLparm::calcforce, sAPOLparm::dpos, sAPOLparm::gamma, sVacc::mem, sAPOLparm::press, sVacc::refSphere, sAPOLparm::srad, sPBEparm::srad, sVacc::surf, Vacc_atomdSASA(), Vacc_atomdSAV(), Vacc_atomSurf(), Vacc_wcaForceAtom(), Valist_getAtom(), Valist_getNumberAtoms(), Vatom_getPosition(), and VRC_SUCCESS.

Referenced by initAPOL().

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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

References APBS_TIMER_FORCE, sNOsh::bogus, sPBEparm::calcforce, sMGparm::chgm, sPBEparm::molid, PCF_COMPS, PCF_TOTAL, AtomForce::qfForce, sPBEparm::srfm, sPBEparm::temp, Valist_getNumberAtoms(), Vpmg_dbForce(), Vpmg_ibForce(), Vpmg_qfForce(), Vunit_kb, and Vunit_Na.

Referenced by main().

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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

References sAPOLparm::bconc, sAPOLparm::calcenergy, sAPOLparm::calcforce, CLIST_AUTO_DOMAIN, sAPOLparm::dpos, energyAPOL(), sVparam_AtomData::epsilon, forceAPOL(), sAPOLparm::gamma, sAPOLparm::press, sVparam_AtomData::radius, sAPOLparm::sasa, sAPOLparm::sav, sAPOLparm::sdens, sAPOLparm::setwat, sAPOLparm::srad, sPBEparm::srad, Vacc_atomSASA(), Vacc_ctor(), Vacc_dtor(), Vacc_totalSASA(), Vacc_totalSAV(), Vacc_wcaEnergy(), Valist_getAtom(), Valist_getNumberAtoms(), Vatom_getCharge(), Vatom_getPosition(), Vatom_getRadius(), Vclist_ctor(), Vclist_dtor(), Vparam_getAtomData(), VRC_FAILURE, VRC_SUCCESS, sAPOLparm::watepsilon, and sAPOLparm::watsigma.

Referenced by main().

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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

Referenced by main().

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)

References APBS_TIMER_SETUP, sPBEparm::bcfl, BCFL_FOCUS, sPBEparm::calcenergy, sMGparm::center, sPBEparm::chargeMapID, sMGparm::chgm, sPBEparm::dielMapID, sPBEparm::ionc, sPBEparm::ionq, sPBEparm::ionr, sPBEparm::kappaMapID, sPBEparm::Lmem, sPBEparm::mdie, sPBEparm::memv, sMGparm::method, sPBEparm::molid, sNOsh::ncharge, sNOsh::ndiel, sPBEparm::nion, sNOsh::nkappa, sMGparm::nonlintype, PBE_LPBE, PBE_LRPBE, PBE_NPBE, PBE_SMPBE, sPBEparm::pbetype, PCE_NO, sPBEparm::pdie, sPBEparm::sdens, sPBEparm::sdie, sPBEparm::smsize, sPBEparm::smvolume, sPBEparm::srad, sPBEparm::srfm, sPBEparm::swin, sPBEparm::temp, sMGparm::useAqua, sPBEparm::useChargeMap, sPBEparm::useDielMap, sPBEparm::useKappaMap, Valist_getAtom(), Valist_getNumberAtoms(), Vatom_getCharge(), Vpbe_ctor(), Vpbe_dtor(), Vpbe_getDeblen(), Vpmg_ctor(), Vpmg_dtor(), Vpmg_fillco(), Vpmgp_ctor(), Vpmgp_dtor(), VSM_SPLINE, and sPBEparm::zmem.

Referenced by main().

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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

References sNOsh::ncharge, and Vgrid_dtor().

Referenced by main().

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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

References sNOsh::ndiel, and Vgrid_dtor().

Referenced by main().

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void killEnergy

(

)

Kill arrays allocated for energies.

Author:

Nathan Baker

Referenced by main().

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
	gem	Array of FEtk objects for each calc Array of geometry manager objects for each calc

References sNOsh::ncalc, sNOsh::nmesh, Vfetk_dtor(), and Vpbe_dtor().

Referenced by main().

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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

References sNOsh::ncalc.

Referenced by main().

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

References sNOsh::nkappa, and Vgrid_dtor().

Referenced by main().

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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

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

References sNOsh::ncalc, Vpbe_dtor(), Vpmg_dtor(), and Vpmgp_dtor().

Referenced by main().

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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

References sNOsh::nmol, and Valist_dtor().

Referenced by main().

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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

References sNOsh::chargefmt, sNOsh::chargepath, sNOsh::kappafmt, sNOsh::ncharge, VDF_AVS, VDF_DX, VDF_MCSF, VDF_UHBD, Vgrid_ctor(), and Vgrid_readDX().

Referenced by main().

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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

References sNOsh::dielfmt, sNOsh::dielXpath, sNOsh::dielYpath, sNOsh::dielZpath, sNOsh::ndiel, VDF_AVS, VDF_DX, VDF_MCSF, VDF_UHBD, Vgrid_ctor(), and Vgrid_readDX().

Referenced by main().

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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

References sNOsh::kappafmt, sNOsh::kappapath, sNOsh::nkappa, VDF_AVS, VDF_DX, VDF_MCSF, VDF_UHBD, Vgrid_ctor(), and Vgrid_readDX().

Referenced by main().

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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)

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)

References sNOsh::gotparm, sNOsh::molfmt, sNOsh::molpath, NMF_PDB, NMF_PQR, NMF_XML, sNOsh::nmol, sNOsh::parmpath, Valist_ctor(), Valist_getNumberAtoms(), Valist_readPDB(), Valist_readPQR(), and Valist_readXML().

Referenced by main().

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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

References sNOsh::gotparm, NPF_FLAT, NPF_XML, sNOsh::parmfmt, sNOsh::parmpath, Vparam_ctor(), Vparam_readFlatFile(), and Vparam_readXMLFile().

Referenced by main().

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int main	(	int	argc,
		char **	argv
	)

The main APBS function.

Author:

Nathan Baker, Dave Gohara, Todd Dolinsky

Returns:

Status code (0 for success)

Parameters:

	argc	Number of arguments
	argv	Argument strings

References ACD_ERROR, APBS_TIMER_WALL_CLOCK, APBSRC, sNOsh::apol2calc, sNOsh::apolname, sNOsh_calc::apolparm, sNOsh::calc, sPBEparm::calcenergy, sNOsh_calc::calctype, sNOsh::elec2calc, sNOsh::elecname, energyFE(), energyMG(), sNOsh_calc::femparm, forceMG(), initAPOL(), initFE(), initMG(), killChargeMaps(), killDielMaps(), killEnergy(), killFE(), killForce(), killKappaMaps(), killMG(), killMolecules(), loadChargeMaps(), loadDielMaps(), loadKappaMaps(), loadMolecules(), loadParameter(), sFEMparm::maxsolve, sNOsh_calc::mgparm, sAPOLparm::molid, sNOsh::napol, sNOsh::ncalc, NCT_APOL, NCT_FEM, NCT_MG, sNOsh::nelec, NOsh_ctor(), NOsh_dtor(), NOSH_MAXCALC, NOSH_MAXMOL, NOsh_parseInput(), NOsh_setupApolCalc(), NOsh_setupElecCalc(), sNOsh::nprint, NPT_APOLENERGY, NPT_APOLFORCE, NPT_ELECENERGY, NPT_ELECFORCE, NPT_ENERGY, NPT_FORCE, OUTPUT_FLAT, OUTPUT_NULL, sNOsh_calc::pbeparm, PCE_COMPS, postRefineFE(), preRefineFE(), printApolEnergy(), printApolForce(), printElecEnergy(), printElecForce(), printEnergy(), printFEPARM(), printForce(), printMGPARM(), printPBEPARM(), sNOsh::printwhat, setPartMG(), solveFE(), solveMG(), startVio(), storeAtomEnergy(), sMGparm::type, Vparam_dtor(), VRC_SUCCESS, Vstring_strcasecmp(), writedataFE(), writedataFlat(), writedataMG(), and writematMG().

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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

References Vfetk_setAtomColors().

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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.

References sFEMparm::akeySOLVE, sFEMparm::ekey, sFEMparm::etol, FRT_DUAL, FRT_GEOM, FRT_LOCA, FRT_RESI, FRT_UNIF, sFEMparm::maxvert, and sFEMparm::pkey.

Referenced by main().

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

References sFEMparm::akeyPRE, sFEMparm::ekey, sFEMparm::etol, FRT_DUAL, FRT_GEOM, FRT_LOCA, FRT_RESI, FRT_UNIF, sFEMparm::pkey, sFEMparm::targetNum, and sFEMparm::targetRes.

Referenced by main().

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

References ACE_TOTAL, sNOsh::apol2calc, sNOsh::apolname, sNOsh_calc::apolparm, sNOsh::calc, sAPOLparm::calcenergy, sAPOLparm::gamma, sAPOLparm::press, sNOsh::printcalc, sNOsh::printnarg, sNOsh::printop, sAPOLparm::sasa, sAPOLparm::sav, and Vstring_strcasecmp().

Referenced by main().

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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
	i	Array of force structures Index of force statement to print

References ACF_COMPS, ACF_NO, ACF_TOTAL, sNOsh::apol2calc, sNOsh::apolname, sNOsh_calc::apolparm, sNOsh::calc, sAPOLparm::calcforce, sNOsh::printcalc, sNOsh::printnarg, sNOsh::printop, AtomForce::sasaForce, AtomForce::savForce, sAPOLparm::temp, sPBEparm::temp, Vstring_strcasecmp(), and AtomForce::wcaForce.

Referenced by main().

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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

References sNOsh::calc, sPBEparm::calcenergy, sNOsh::elec2calc, sNOsh::elecname, sNOsh_calc::pbeparm, PCE_NO, sNOsh::printcalc, sNOsh::printnarg, sNOsh::printop, sPBEparm::temp, Vstring_strcasecmp(), Vunit_kb, and Vunit_Na.

Referenced by main().

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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
	i	Array of force structures Index of force statement to print

References sNOsh::calc, sPBEparm::calcforce, AtomForce::dbForce, sNOsh::elec2calc, sNOsh::elecname, AtomForce::ibForce, sNOsh_calc::pbeparm, PCF_COMPS, PCF_NO, PCF_TOTAL, sNOsh::printcalc, sNOsh::printnarg, sNOsh::printop, AtomForce::qfForce, sPBEparm::temp, Vstring_strcasecmp(), Vunit_kb, and Vunit_Na.

Referenced by main().

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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

References sNOsh::calc, sPBEparm::calcenergy, sNOsh::elec2calc, sNOsh::elecname, sNOsh_calc::pbeparm, PCE_NO, sNOsh::printcalc, sNOsh::printnarg, sNOsh::printop, sPBEparm::temp, Vstring_strcasecmp(), Vunit_kb, and Vunit_Na.

Referenced by main().

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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

References sFEMparm::akeyPRE, sFEMparm::akeySOLVE, sNOsh::bogus, sFEMparm::ekey, sFEMparm::etol, FET_FRAC, FET_GLOB, FET_SIMP, FRT_DUAL, FRT_GEOM, FRT_LOCA, FRT_RESI, FRT_UNIF, sFEMparm::glen, sFEMparm::maxsolve, sFEMparm::maxvert, sFEMparm::targetNum, sFEMparm::targetRes, VGT_DIRI, VGT_PREV, VGT_ZERO, VLT_BCG, VLT_CG, VLT_MG, VLT_SLU, VNT_ARC, VNT_INC, VNT_NEW, VPT_DIAG, VPT_IDEN, and VPT_MG.

Referenced by main().

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
	i	Array of force structures Index of force statement to print

References sNOsh::calc, sPBEparm::calcforce, AtomForce::dbForce, sNOsh::elec2calc, sNOsh::elecname, AtomForce::ibForce, sNOsh_calc::pbeparm, PCF_COMPS, PCF_NO, PCF_TOTAL, sNOsh::printcalc, sNOsh::printnarg, sNOsh::printop, AtomForce::qfForce, sPBEparm::temp, Vstring_strcasecmp(), Vunit_kb, and Vunit_Na.

Referenced by main().

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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

References sMGparm::chgm, sMGparm::dime, sMGparm::glen, sMGparm::grid, MCT_PARALLEL, sMGparm::nlev, sMGparm::ofrac, sMGparm::pdime, and sMGparm::type.

Referenced by main().

void printPBEPARM

(

PBEparm *

pbeparm

)

Print out generic PBE params loaded from input.

Author:

Nathan Baker

Parameters:

pbeparm

PBEparm object

References sPBEparm::bcfl, BCFL_FOCUS, BCFL_MDH, BCFL_MEM, BCFL_SDH, BCFL_ZERO, sPBEparm::calcenergy, sPBEparm::calcforce, sPBEparm::ionc, sPBEparm::ionq, sPBEparm::ionr, sPBEparm::molid, sPBEparm::nion, sPBEparm::numwrite, PBE_LPBE, PBE_LRPBE, PBE_NPBE, PBE_SMPBE, sPBEparm::pbetype, PCE_NO, PCF_COMPS, PCF_TOTAL, sPBEparm::pdie, sPBEparm::sdie, sPBEparm::smsize, sPBEparm::smvolume, sPBEparm::srad, sPBEparm::srfm, sPBEparm::swin, sPBEparm::temp, VDF_AVS, VDF_DX, VDF_MCSF, VDF_UHBD, VDT_CHARGE, VDT_DIELX, VDT_DIELY, VDT_DIELZ, VDT_EDENS, VDT_IVDW, VDT_KAPPA, VDT_LAP, VDT_NDENS, VDT_POT, VDT_QDENS, VDT_SMOL, VDT_SSPL, VDT_VDW, sPBEparm::writefmt, sPBEparm::writestem, and sPBEparm::writetype.

Referenced by main().

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

References sNOsh::calc, sPBEparm::calcenergy, sNOsh::elec2calc, sNOsh_calc::pbeparm, PCE_NO, sNOsh::printcalc, sNOsh::printnarg, sNOsh::printop, sPBEparm::temp, Vunit_kb, and Vunit_Na.

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

References sNOsh::bogus, sMGparm::center, sMGparm::glen, MCT_PARALLEL, sMGparm::partDisjCenter, sMGparm::partDisjLength, sMGparm::partDisjOwnSide, sMGparm::type, and Vpmg_setPart().

Referenced by main().

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int solveFE	(	int	i,
		NOsh *	nosh,
		PBEparm *	pbeparm,
		FEMparm *	feparm,
		Vfetk *	fetk[NOSH_MAXCALC]
	)

Solve-estimate-refine.

Author:

Nathan Baker

Parameters:

	i	Calculation index
	nosh	Master parameter object
	feparm	FE-specific parameters
	pbeparm	Generic PBE parameters
	fetk	Array of FE solver objects

Returns:

1 if successful, 0 otherwise

< AM_hPcg

< Coarse-grid solver; 0 = SLU, 1 = MG, 2 = CG, 3 = BCG, 4 = PCG, 5 = PBCG

< Primal problem

< Preconditioner; 0 = identity.

References PBE_LPBE, PBE_LRPBE, PBE_NPBE, PBE_SMPBE, and sPBEparm::pbetype.

Referenced by main().

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

References APBS_TIMER_SOLVER, sNOsh::bogus, MCT_DUMMY, sVpmgp::nx, sVpmgp::ny, sVpmgp::nz, sVpmg::pmgp, sVpmg::u, and Vpmg_solve().

Referenced by main().

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void startVio

(

)

Wrapper to start MALOC Vio layer.

Author:

Nathan Baker and Robert Konecny

Referenced by main().

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

References sVpbe::alist, sVpmg::pbe, Valist_getAtom(), Valist_getNumberAtoms(), sVpmg::vmem, and Vpmg_qfAtomEnergy().

Referenced by main().

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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

References sVfetk::am, sNOsh::bogus, sNOsh::ispara, sPBEparm::numwrite, sNOsh::proc_rank, VDF_AVS, VDF_DX, VDF_MCSF, VDF_UHBD, VDT_CHARGE, VDT_DIELX, VDT_DIELY, VDT_DIELZ, VDT_EDENS, VDT_IVDW, VDT_KAPPA, VDT_LAP, VDT_NDENS, VDT_POT, VDT_QDENS, VDT_SMOL, VDT_SSPL, VDT_VDW, Vfetk_fillArray(), Vfetk_write(), sPBEparm::writefmt, sPBEparm::writestem, and sPBEparm::writetype.

Referenced by main().

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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

References sPBEparm::bcfl, BCFL_FOCUS, BCFL_MDH, BCFL_MEM, BCFL_SDH, BCFL_ZERO, sNOsh::bogus, sNOsh::calc, sPBEparm::calcenergy, sPBEparm::calcforce, sMGparm::dime, sNOsh::elec2calc, sNOsh::elecname, sMGparm::glen, sMGparm::grid, sPBEparm::ionc, sPBEparm::ionq, sPBEparm::ionr, MCT_AUTO, MCT_DUMMY, MCT_MANUAL, MCT_PARALLEL, sNOsh_calc::mgparm, sPBEparm::molid, sNOsh::nelec, sPBEparm::nion, sNOsh::nprint, NPT_ENERGY, PBE_LPBE, PBE_NPBE, sNOsh_calc::pbeparm, sPBEparm::pbetype, PCE_COMPS, PCE_TOTAL, PCF_TOTAL, sPBEparm::pdie, sNOsh::printcalc, sNOsh::printnarg, sNOsh::printop, sNOsh::printwhat, sPBEparm::sdie, sPBEparm::srad, sPBEparm::srfm, sPBEparm::temp, sMGparm::type, Vstring_strcasecmp(), Vunit_kb, and Vunit_Na.

Referenced by main().

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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

References sNOsh::bogus, sVpmgp::hx, sVpmgp::hy, sVpmgp::hzed, sNOsh::ispara, sVpbe::maxIonRadius, sPBEparm::numwrite, sVpmgp::nx, sVpmgp::ny, sVpmgp::nz, sVpmg::pbe, sPBEparm::pbetype, sVpmg::pmgp, sNOsh::proc_rank, sVpmg::pvec, sVpmg::rwork, sPBEparm::srad, sPBEparm::swin, VDF_AVS, VDF_DX, VDF_MCSF, VDF_UHBD, VDT_CHARGE, VDT_DIELX, VDT_DIELY, VDT_DIELZ, VDT_EDENS, VDT_IVDW, VDT_KAPPA, VDT_LAP, VDT_NDENS, VDT_POT, VDT_QDENS, VDT_SMOL, VDT_SSPL, VDT_VDW, Vgrid_ctor(), Vgrid_dtor(), Vgrid_writeDX(), Vgrid_writeUHBD(), Vpmg_fillArray(), sPBEparm::writefmt, sPBEparm::writestem, sPBEparm::writetype, sVpmgp::xcent, sVpmgp::ycent, and sVpmgp::zcent.

Referenced by main().

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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

References sPBEparm::bcfl, BCFL_FOCUS, BCFL_MDH, BCFL_MEM, BCFL_SDH, BCFL_ZERO, sNOsh::bogus, sNOsh::calc, sPBEparm::calcenergy, sPBEparm::calcforce, sMGparm::dime, sNOsh::elec2calc, sNOsh::elecname, sMGparm::glen, sMGparm::grid, sPBEparm::ionc, sPBEparm::ionq, sPBEparm::ionr, MCT_AUTO, MCT_DUMMY, MCT_MANUAL, MCT_PARALLEL, sNOsh_calc::mgparm, sPBEparm::molid, sNOsh::nelec, sPBEparm::nion, sNOsh::nprint, NPT_ENERGY, PBE_LPBE, PBE_NPBE, sNOsh_calc::pbeparm, sPBEparm::pbetype, PCE_COMPS, PCE_TOTAL, PCF_TOTAL, sPBEparm::pdie, sNOsh::printcalc, sNOsh::printnarg, sNOsh::printop, sNOsh::printwhat, sPBEparm::sdie, sPBEparm::srad, sPBEparm::srfm, sPBEparm::temp, sMGparm::type, Vstring_strcasecmp(), Vunit_kb, and Vunit_Na.

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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

References sNOsh::bogus, sNOsh::ispara, sNOsh::proc_rank, Vpmg_printColComp(), sPBEparm::writemat, sPBEparm::writematflag, and sPBEparm::writematstem.

Referenced by main().

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