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.
#define	USEHB   1
	Set this macro to 1 for hierarchical basis, 0 for normal solver.
Typedefs
typedef AtomForce	AtomForce
	Define AtomForce type.
Functions
int	loadMolecules (NOsh *nosh, 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.
int	npenergyMG (NOsh *nosh, int icalc, Vpmg *pmg, int *nenergy, double *npEnergy)
	Calculate apolar 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.
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.
int	printEnergy (Vcom *com, NOsh *nosh, double totEnergy[NOSH_MAXCALC], int i)
	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.
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.
int	initFE (int icalc, NOsh *nosh, FEMparm *feparm, PBEparm *pbeparm, Vpbe *pbe[NOSH_MAXCALC], Valist *alist[NOSH_MAXMOL], Vfetk *fetk[NOSH_MAXCALC])
	Initialize FE solver objects.
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.

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Function Documentation

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

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

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

int initFE (  int  icalc, NOsh *  nosh, FEMparm *  feparm, PBEparm *  pbeparm, Vpbe *  pbe[NOSH_MAXCALC], Valist *  alist[NOSH_MAXMOL], Vfetk *  fetk[NOSH_MAXCALC] )

Initialize FE solver objects. Author: Nathan Baker Parameters: icalc  Index in pbe, fetk to initialize -- calculation index nosh  Master parameter object feparm  FE-specific parameters pbeparm  Generic PBE parameters pbe  Array of PBE objects alist  Array of atom lists fetk  Array of FE solver objects Bug: THIS FUNCTION IS HARD-CODED TO SOLVE LRPBE Todo: THIS FUNCTION IS HARD-CODED TO SOLVE LRPBE Returns: 1 if successful, 0 otherwise

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 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) Returns: 1 if succesful, 0 otherwise

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

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

void killEnergy (   )

Kill arrays allocated for energies. Author: Nathan Baker

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

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

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: nosh  Object with parsed input file parameters pbe  Array of Vpbe objects (one for each calc) pmgp  Array of MG parameter objects (one for each calc) pmg  Array of MG objects (one for each calc)

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

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

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

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

int loadMolecules (  NOsh *  nosh, Valist *  alist[NOSH_MAXMOL] )

Load the molecules given in NOsh into atom lists. Author: Nathan Baker Parameters: nosh  NOsh object with input file information alist  List of atom list objects Returns: 1 if successful, 0 otherwise

int npenergyMG (  NOsh *  nosh, int  icalc, Vpmg *  pmg, int *  nenergy, double *  npEnergy )

Calculate apolar 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 npEnergy  Set to apolar energy (in kT) Returns: 1 if successful, 0 otherwise

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

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.

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

int printEnergy (  Vcom *  com, NOsh *  nosh, double  totEnergy[NOSH_MAXCALC], int  i )

Combine and pretty-print energy data. Author: Nathan Baker Parameters: com  Communications object nosh  Parameters from input file totEnergy  Array of energies from different calculations i  Index of energy statement to print Returns: 1 if successful, 0 otherwise

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

int printForce (  Vcom *  com, NOsh *  nosh, int  nforce[NOSH_MAXCALC], AtomForce *  atomForce[NOSH_MAXCALC], int  i )

Combine and pretty-print force data. Author: Nathan Baker Parameters: com  Communications object nosh  Parameters from input file nforce  Number of forces calculated atomForce  Array of force structures i  Index of force statement to print Returns: 1 if successful, 0 otherwise

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

void printPBEPARM (  PBEparm *  pbeparm  )

Print out generic PBE params loaded from input. Author: Nathan Baker Parameters: pbeparm  PBEparm object

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

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

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

void startVio (   )

Wrapper to start MALOC Vio layer. Author: Nathan Baker and Robert Konecny

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

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

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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