apbs_driver.h File Reference

Header file for the main iAPBS driver. More...

Go to the source code of this file.

Defines
#define	NATOMS   150000
	Maximum number of atoms.
Functions
VEXTERNC int	apbsdrv_ (int *nat, double x[NATOMS], double y[NATOMS], double z[NATOMS], double radius[NATOMS], double charge[NATOMS], double r_param[9], int i_param[25], double grid[3], int dime[3], int pdime[3], double glen[3], double center[3], double cglen[3], double fglen[3], double ccenter[3], double fcenter[3], double *ofrac, int *dbg, double ionq[MAXION], double ionc[MAXION], double ionr[MAXION], double esEnergy[NOSH_MAXCALC], double npEnergy[NOSH_MAXCALC], double apbsdx[NATOMS], double apbsdy[NATOMS], double apbsdz[NATOMS], double apbsqfx[NATOMS], double apbsqfy[NATOMS], double apbsqfz[NATOMS], double apbsibx[NATOMS], double apbsiby[NATOMS], double apbsibz[NATOMS], double apbsnpx[NATOMS], double apbsnpy[NATOMS], double apbsnpz[NATOMS], double apbsdbx[NATOMS], double apbsdby[NATOMS], double apbsdbz[NATOMS])
	Wrapper iAPBS function.
VEXTERNC int	iforceMG (Vmem *mem, NOsh *nosh, PBEparm *pbeparm, MGparm *mgparm, Vpmg *pmg, int *nforce, AtomForce **atomForce, Valist *alist[NOSH_MAXMOL], int debug)
	Calculate forces from MG solution.
double	getElecEnergy (Vcom *com, NOsh *nosh, double totEnergy[NOSH_MAXCALC], int iprint)
	Combine and pretty-print energy data.
char *	setupString (double r_param[9], int i_param[25], double grid[3], int dime[3], double ionq[MAXION], double ionc[MAXION], double ionr[MAXION], double glen[3], double center[3], double cglen[3], double fglen[3], double ccenter[3], double fcenter[3], double *ofrac, int pdime[3], int debug)
	Creates APBS input string.

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Detailed Description

Header file for the main iAPBS driver.

Author:

Robert Konecny

Version:

Id

apbs_driver.h 389 2010-03-29 20:18:15Z rok

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Function Documentation

VEXTERNC int apbsdrv_	(	int *	nat,
		double	x[NATOMS],
		double	y[NATOMS],
		double	z[NATOMS],
		double	radius[NATOMS],
		double	charge[NATOMS],
		double	r_param[9],
		int	i_param[25],
		double	grid[3],
		int	dime[3],
		int	pdime[3],
		double	glen[3],
		double	center[3],
		double	cglen[3],
		double	fglen[3],
		double	ccenter[3],
		double	fcenter[3],
		double *	ofrac,
		int *	dbg,
		double	ionq[MAXION],
		double	ionc[MAXION],
		double	ionr[MAXION],
		double	esEnergy[NOSH_MAXCALC],
		double	npEnergy[NOSH_MAXCALC],
		double	apbsdx[NATOMS],
		double	apbsdy[NATOMS],
		double	apbsdz[NATOMS],
		double	apbsqfx[NATOMS],
		double	apbsqfy[NATOMS],
		double	apbsqfz[NATOMS],
		double	apbsibx[NATOMS],
		double	apbsiby[NATOMS],
		double	apbsibz[NATOMS],
		double	apbsnpx[NATOMS],
		double	apbsnpy[NATOMS],
		double	apbsnpz[NATOMS],
		double	apbsdbx[NATOMS],
		double	apbsdby[NATOMS],
		double	apbsdbz[NATOMS]
	)

Wrapper iAPBS function.

Author:

Robert Konecny

Parameters:

	nat	Number of atoms
	x	Atomic coordinate (x)
	y	Atomic coordinate (y)
	z	Atomic coordinate (z)
	radius	Atomic radii
	charge	Atomic charges
	r_param	Input APBS parameters (real values)
	i_param	Input APBS parameters (integer values)
	grid	Grid spacing
	dime	Grid dimensions
	pdime	Grid of processors to be used in calculation
	glen	Grid side lengths
	center	Grid center
	cglen	Coarse grid side lengths
	fglen	Fine grid side lengths
	ccenter	Coarse grid center
	fcenter	Fine grid center
	ofrac	Overlap fraction between procs
	dbg	Debug verbosity flag
	ionq	Mobile ion charge
	ionc	Mobile ion concentration
	ionr	Mobile ion radius
	esEnergy	Electrostatic energy
	npEnergy	Non-polar energy
	apbsdx	Total electrostatic force per atom (x coordinate)
	apbsdy	Total electrostatic force per atom (y coordinate)
	apbsdz	Total electrostatic force per atom (z coordinate)
	apbsqfx	Fixed charge force (x)
	apbsqfy	Fixed charge force (y)
	apbsqfz	Fixed charge force (z)
	apbsibx	Ionic boundary force (x)
	apbsiby	Ionic boundary force (y)
	apbsibz	Ionic boundary force (z)
	apbsnpx	Non-polar force (x)
	apbsnpy	Non-polar force (y)
	apbsnpz	Non-polar force (z)
	apbsdbx	Dielectric boundary force (x)
	apbsdby	Dielectric boundary force (y)
	apbsdbz	Dielectric boundary force (z)

Returns:

1 if successful, 0 otherwise

double getElecEnergy	(	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

Note:

Collect Elect Energy

Author:

Robert Konecny

Parameters:

	nosh	Communications object
	totEnergy	Parameters from input file
	iprint	Array of energies from different calculations Index of energy statement to print

Referenced by apbsdrv_().

VEXTERNC int iforceMG	(	Vmem *	mem,
		NOsh *	nosh,
		PBEparm *	pbeparm,
		MGparm *	mgparm,
		Vpmg *	pmg,
		int *	nforce,
		AtomForce **	atomForce,
		Valist *	alist[NOSH_MAXMOL],
		int	debug
	)

Calculate forces from MG solution.

Author:

Robert Konecny (based on forceMG)

Parameters:

	mem	Memory management object
	nosh	Parameters from input file
	pbeparm	Generic PBE parameters
	mgparm	MG-specific parmaeters
	pmg	MG object
	nforce	0 => no forces, 1 => net forces, >1 => number of forces (1 per atom)
	atomForce	Pointer to array of force objects
	alist	List of atom lists
	debug	verbosity flag

Returns:

1 if successful, 0 otherwise

char* setupString	(	double	r_param[9],
		int	i_param[25],
		double	grid[3],
		int	dime[3],
		double	ionq[MAXION],
		double	ionc[MAXION],
		double	ionr[MAXION],
		double	glen[3],
		double	center[3],
		double	cglen[3],
		double	fglen[3],
		double	ccenter[3],
		double	fcenter[3],
		double *	ofrac,
		int	pdime[3],
		int	debug
	)

Creates APBS input string.

Author:

Robert Konecny

Parameters:

	r_param	Input APBS parameters (real values)
	i_param	Input APBS parameters (integer values)
	grid	Grid spacing
	dime	Grid dimensions
	ionq	Mobile ion charge
	ionc	Mobile ion concentration
	ionr	Mobile ion radius
	glen	Grid side lengths
	center	Grid center
	cglen	Coarse grid side lengths
	fglen	Fine grid side lengths
	ccenter	Coarse grid center
	fcenter	Fine grid center
	ofrac	Overlap fraction between procs
	pdime	Grid of processors to be used in calculation
	debug	Debug verbosity level.

Returns:

the input string

Author:

Robert Konecny

References MAX_BUF_SIZE.

Referenced by apbsdrv_().