vpmg.c File Reference

Class Vpmg methods. More...

#include "apbscfg.h"
#include "vpmg-private.h"
#include "apbs/vpmg.h"
#include "apbs/vhal.h"

Include dependency graph for vpmg.c:

Functions
VPUBLIC unsigned long int	Vpmg_memChk (Vpmg *thee)
	Return the memory used by this structure (and its contents) in bytes.
VPUBLIC void	Vpmg_printColComp (Vpmg *thee, char path[72], char title[72], char mxtype[3], int flag)
	Print out a column-compressed sparse matrix in Harwell-Boeing format.
VPUBLIC Vpmg *	Vpmg_ctor (Vpmgp pmgp, Vpbe pbe, int focusFlag, Vpmg pmgOLD, MGparm mgparm, PBEparm_calcEnergy energyFlag)
	Constructor for the Vpmg class (allocates new memory).
VPUBLIC int	Vpmg_ctor2 (Vpmg thee, Vpmgp pmgp, Vpbe pbe, int focusFlag, Vpmg pmgOLD, MGparm *mgparm, PBEparm_calcEnergy energyFlag)
	FORTRAN stub constructor for the Vpmg class (uses previously-allocated memory).
VPUBLIC int	Vpmg_solve (Vpmg *thee)
	Solve the PBE using PMG.
VPUBLIC void	Vpmg_dtor (Vpmg **thee)
	Object destructor.
VPUBLIC void	Vpmg_dtor2 (Vpmg *thee)
	FORTRAN stub object destructor.
VPUBLIC void	Vpmg_setPart (Vpmg *thee, double lowerCorner[3], double upperCorner[3], int bflags[6])
	Set partition information which restricts the calculation of observables to a (rectangular) subset of the problem domain.
VPUBLIC void	Vpmg_unsetPart (Vpmg *thee)
	Remove partition restrictions.
VPUBLIC int	Vpmg_fillArray (Vpmg thee, double vec, Vdata_Type type, double parm, Vhal_PBEType pbetype)
	Fill the specified array with accessibility values.
VPRIVATE double	Vpmg_polarizEnergy (Vpmg *thee, int extFlag)
	Determines energy from polarizeable charge and interaction with fixed charges according to Rocchia et al.
VPUBLIC double	Vpmg_energy (Vpmg *thee, int extFlag)
	Get the total electrostatic energy.
VPUBLIC double	Vpmg_dielEnergy (Vpmg *thee, int extFlag)
	Get the "polarization" contribution to the electrostatic energy.
VPUBLIC double	Vpmg_dielGradNorm (Vpmg *thee)
	Get the integral of the gradient of the dielectric function.
VPUBLIC double	Vpmg_qmEnergy (Vpmg *thee, int extFlag)
	Get the "mobile charge" contribution to the electrostatic energy.
VPUBLIC double	Vpmg_qmEnergySMPBE (Vpmg *thee, int extFlag)
	Vpmg_qmEnergy for SMPBE.
VPUBLIC double	Vpmg_qfEnergy (Vpmg *thee, int extFlag)
	Get the "fixed charge" contribution to the electrostatic energy.
VPRIVATE double	Vpmg_qfEnergyPoint (Vpmg *thee, int extFlag)
	Calculates charge-potential energy using summation over delta function positions (i.e. something like an Linf norm).
VPUBLIC double	Vpmg_qfAtomEnergy (Vpmg thee, Vatom atom)
	Get the per-atom "fixed charge" contribution to the electrostatic energy.
VPRIVATE double	Vpmg_qfEnergyVolume (Vpmg *thee, int extFlag)
	Calculates charge-potential energy as integral over a volume.
VPRIVATE void	Vpmg_splineSelect (int srfm, Vacc acc, double gpos, double win, double infrad, Vatom atom, double force)
	Selects a spline based surface method from either VSM_SPLINE, VSM_SPLINE5 or VSM_SPLINE7.
VPRIVATE void	focusFillBound (Vpmg thee, Vpmg pmgOLD)
	For focusing, fill in the boundaries of the new mesh based on the potential values in the old mesh.
VPRIVATE void	extEnergy (Vpmg thee, Vpmg pmgOLD, PBEparm_calcEnergy extFlag, double partMin[3], double partMax[3], int bflags[6])
	For focusing, set external energy data members in new Vpmg object based on energy calculations on old Vpmg object from regions outside the indicated partition.
VPRIVATE double	bcfl1sp (double size, double apos, double charge, double xkappa, double pre1, double pos)
	Calculate pre1(charge/d)(exp(-xkappa(d-size))/(1+xkappasize) due to a specific ion at a specific point.
VPRIVATE void	bcfl1 (double size, double apos, double charge, double xkappa, double pre1, double gxcf, double gycf, double gzcf, double xf, double yf, double *zf, int nx, int ny, int nz)
	Increment all boundary points by pre1(charge/d)(exp(-xkappa(d-size))/(1+xkappasize) to add the effect of the Debye-Huckel potential due to a single charge.
VPRIVATE void	bcfl2 (double size, double apos, double charge, double dipole, double quad, double xkappa, double eps_p, double eps_w, double T, double gxcf, double gycf, double gzcf, double xf, double yf, double *zf, int nx, int ny, int nz)
	Increment all boundary points to include the Debye-Huckel potential due to a single multipole site. (truncated at quadrupole).
VPRIVATE void	multipolebc (double r, double kappa, double eps_p, double eps_w, double rad, double tsr[3])
	This routine serves bcfl2. It returns (in tsr) the contraction independent portion of the Debye-Huckel potential tensor for a spherical ion with a central charge, dipole and quadrupole. See the code for an in depth description.
VPRIVATE void	bcCalc (Vpmg *thee)
	Fill boundary condition arrays.
VPRIVATE void	fillcoCoefMap (Vpmg *thee)
	Fill operator coefficient arrays from pre-calculated maps.
VPRIVATE void	fillcoCoefMol (Vpmg *thee)
	Fill operator coefficient arrays from a molecular surface calculation.
VPRIVATE void	fillcoCoefMolIon (Vpmg *thee)
	Fill ion (nonlinear) operator coefficient array from a molecular surface calculation.
VPRIVATE void	fillcoCoefMolDiel (Vpmg *thee)
	Fill differential operator coefficient arrays from a molecular surface calculation.
VPRIVATE void	fillcoCoefMolDielNoSmooth (Vpmg *thee)
	Fill differential operator coefficient arrays from a molecular surface calculation without smoothing.
VPRIVATE void	fillcoCoefMolDielSmooth (Vpmg *thee)
	Fill differential operator coefficient arrays from a molecular surface calculation with smoothing.
VPRIVATE void	fillcoCoefSpline (Vpmg *thee)
	Fill operator coefficient arrays from a spline-based surface calculation.
VPRIVATE void	fillcoCoef (Vpmg *thee)
	Top-level driver to fill all operator coefficient arrays.
VPRIVATE Vrc_Codes	fillcoCharge (Vpmg *thee)
	Top-level driver to fill source term charge array.
VPRIVATE Vrc_Codes	fillcoChargeMap (Vpmg *thee)
	Fill source term charge array from a pre-calculated map.
VPRIVATE void	fillcoChargeSpline1 (Vpmg *thee)
	Fill source term charge array from linear interpolation.
VPRIVATE double	bspline2 (double x)
	Evaluate a cubic B-spline.
VPRIVATE double	dbspline2 (double x)
	Evaluate a cubic B-spline derivative.
VPRIVATE void	fillcoChargeSpline2 (Vpmg *thee)
	Fill source term charge array from cubic spline interpolation.
VPUBLIC int	Vpmg_fillco (Vpmg thee, Vsurf_Meth surfMeth, double splineWin, Vchrg_Meth chargeMeth, int useDielXMap, Vgrid dielXMap, int useDielYMap, Vgrid dielYMap, int useDielZMap, Vgrid dielZMap, int useKappaMap, Vgrid kappaMap, int useChargeMap, Vgrid chargeMap)
	Fill the coefficient arrays prior to solving the equation.
VPUBLIC int	Vpmg_force (Vpmg thee, double force, int atomID, Vsurf_Meth srfm, Vchrg_Meth chgm)
	Calculate the total force on the specified atom in units of k_B T/AA.
VPUBLIC int	Vpmg_ibForce (Vpmg thee, double force, int atomID, Vsurf_Meth srfm)
	Calculate the osmotic pressure on the specified atom in units of k_B T/AA.
VPUBLIC int	Vpmg_dbForce (Vpmg thee, double dbForce, int atomID, Vsurf_Meth srfm)
	Calculate the dielectric boundary forces on the specified atom in units of k_B T/AA.
VPUBLIC int	Vpmg_qfForce (Vpmg thee, double force, int atomID, Vchrg_Meth chgm)
	Calculate the "charge-field" force on the specified atom in units of k_B T/AA.
VPRIVATE void	qfForceSpline1 (Vpmg thee, double force, int atomID)
	Charge-field force due to a linear spline charge function.
VPRIVATE void	qfForceSpline2 (Vpmg thee, double force, int atomID)
	Charge-field force due to a cubic spline charge function.
VPRIVATE void	qfForceSpline4 (Vpmg thee, double force, int atomID)
	Charge-field force due to a quintic spline charge function.
VPRIVATE void	markSphere (double rtot, double tpos, int nx, int ny, int nz, double hx, double hy, double hz, double xmin, double ymin, double zmin, double array, double markVal)
	Mark the grid points inside a sphere with a particular value. This marks by resetting the the grid points inside the sphere to the specified value.
VPRIVATE void	zlapSolve (Vpmg thee, double solution, double source, double *work1)
	Calculate the solution to Poisson's equation with a simple Laplacian operator and zero-valued Dirichlet boundary conditions. Store the solution in thee->u.
VPUBLIC int	Vpmg_solveLaplace (Vpmg *thee)
	Solve Poisson's equation with a homogeneous Laplacian operator using the solvent dielectric constant. This solution is performed by a sine wave decomposition.
VPRIVATE double	VFCHI4 (int i, double f)
	Return 2.5 plus difference of i - f.
VPRIVATE double	bspline4 (double x)
	Evaluate a 5th Order B-Spline (4th order polynomial).
VPUBLIC double	dbspline4 (double x)
	Evaluate a 5th Order B-Spline derivative (4th order polynomial).
VPUBLIC double	d2bspline4 (double x)
	Evaluate the 2nd derivative of a 5th Order B-Spline.
VPUBLIC double	d3bspline4 (double x)
	Evaluate the 3rd derivative of a 5th Order B-Spline.
VPUBLIC void	fillcoPermanentMultipole (Vpmg *thee)
	Fill source term charge array for the use of permanent multipoles.
VPRIVATE void	fillcoCoefSpline4 (Vpmg *thee)
	Fill operator coefficient arrays from a 7th order polynomial based surface calculation.
VPRIVATE void	fillcoCoefSpline3 (Vpmg *thee)
	Fill operator coefficient arrays from a 5th order polynomial based surface calculation.

Detailed Description

Class Vpmg methods.

Author:: Nathan Baker

Version:

Id: vpmg.c 1538 2009-12-21 20:31:00Z yhuang01

Attention:

 *
 * APBS -- Adaptive Poisson-Boltzmann Solver
 *
 * Nathan A. Baker (baker@biochem.wustl.edu)
 * Dept. of Biochemistry and Molecular Biophysics
 * Center for Computational Biology
 * Washington University in St. Louis
 *
 * Additional contributing authors listed in the code documentation.
 *
 * Copyright (c) 2002-2009, Washington University in St. Louis.
 * Portions Copyright (c) 2002-2009.  Nathan A. Baker
 * Portions Copyright (c) 1999-2002.  The Regents of the University of California.
 * Portions Copyright (c) 1995.  Michael Holst
 *
 * All rights reserved.
 * 
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are met: 
 *
 * -  Redistributions of source code must retain the above copyright notice, this
 * list of conditions and the following disclaimer.  
 * 
 * - Redistributions in binary form must reproduce the above copyright notice,
 * this list of conditions and the following disclaimer in the documentation
 * and/or other materials provided with the distribution.
 * 
 * - Neither the name of Washington University in St. Louis nor the names of its
 * contributors may be used to endorse or promote products derived from this
 * software without specific prior written permission.
 * 
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
 * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
 * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
 * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
 * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
 * EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
 * PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
 * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
 * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
 * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 *
 *

Function Documentation

VPRIVATE void bcCalc ( Vpmg * thee )

Fill boundary condition arrays.

Author:: Nathan Baker

References sVpmgp::bcfl, BCFL_FOCUS, BCFL_MDH, BCFL_MEM, BCFL_SDH, BCFL_UNUSED, BCFL_ZERO, sVpmg::gxcf, sVpmg::gycf, sVpmg::gzcf, sVpmgp::nx, sVpmgp::ny, sVpmgp::nz, sVpmg::pbe, sVpmg::pmgp, Vpbe_getLmem(), Vpbe_getmembraneDiel(), Vpbe_getmemv(), Vpbe_getSolventDiel(), Vpbe_getXkappa(), Vpbe_getzmem(), sVpmg::xf, sVpmg::yf, and sVpmg::zf.

Referenced by Vpmg_fillco().

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VPRIVATE void bcfl1	(	double	size,
		double *	apos,
		double	charge,
		double	xkappa,
		double	pre1,
		double *	gxcf,
		double *	gycf,
		double *	gzcf,
		double *	xf,
		double *	yf,
		double *	zf,
		int	nx,
		int	ny,
		int	nz
	)

Increment all boundary points by pre1*(charge/d)*(exp(-xkappa*(d-size))/(1+xkappa*size) to add the effect of the Debye-Huckel potential due to a single charge.

Author:: Nathan Baker

Parameters:

	apos	Size of the ion
	charge	Position of the ion
	xkappa	Charge of the ion
	pre1	Exponential screening factor
	gxcf	Unit- and dielectric-dependent prefactor
	gycf	Set to x-boundary values
	gzcf	Set to y-boundary values
	xf	Set to z-boundary values
	yf	Boundary point x-coordinates
	zf	Boundary point y-coordinates
	nx	Boundary point z-coordinates
	ny	Number of grid points in x-direction
	nz	Number of grid points in y-direction Number of grid points in y-direction

VPRIVATE double bcfl1sp	(	double	size,
		double *	apos,
		double	charge,
		double	xkappa,
		double	pre1,
		double *	pos
	)

Calculate pre1*(charge/d)*(exp(-xkappa*(d-size))/(1+xkappa*size) due to a specific ion at a specific point.

Author:: Nathan Baker

Returns:: Value of above function in arbitrary units (dependent on pre-factor)

Parameters:

	apos	Atom size
	charge	Atom position
	xkappa	Atom charge
	pre1	Exponential screening factor
	pos	Unit- and dielectric-dependent prefactor Function evaluation position

VPRIVATE void bcfl2	(	double	size,
		double *	apos,
		double	charge,
		double *	dipole,
		double *	quad,
		double	xkappa,
		double	eps_p,
		double	eps_w,
		double	T,
		double *	gxcf,
		double *	gycf,
		double *	gzcf,
		double *	xf,
		double *	yf,
		double *	zf,
		int	nx,
		int	ny,
		int	nz
	)

Increment all boundary points to include the Debye-Huckel potential due to a single multipole site. (truncated at quadrupole).

Author:: Michael Schnieders

Parameters:

	apos	Size of the ion
	charge	Position of the ion
	dipole	Charge of the ion
	quad	Dipole of the ion
	xkappa	Traceless Quadrupole of the ion
	eps_p	Exponential screening factor
	eps_w	Solute dielectric
	T	Solvent dielectric
	gxcf	Temperature
	gycf	Set to x-boundary values
	gzcf	Set to y-boundary values
	xf	Set to z-boundary values
	yf	Boundary point x-coordinates
	zf	Boundary point y-coordinates
	nx	Boundary point z-coordinates
	ny	Number of grid points in x-direction
	nz	Number of grid points in y-direction Number of grid points in y-direction

References multipolebc(), Vunit_ec, Vunit_eps0, and Vunit_kb.

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VPRIVATE double bspline2 ( double x )

Evaluate a cubic B-spline.

Author:: Nathan Baker

Returns:: Cubic B-spline value

Parameters:

x

Position

Referenced by fillcoChargeSpline2(), and qfForceSpline2().

VPRIVATE double bspline4 ( double x )

Evaluate a 5th Order B-Spline (4th order polynomial).

Author:: : Michael Schnieders

Returns:: 5th Order B-Spline

Parameters:

x

Position

Referenced by fillcoPermanentMultipole(), and qfForceSpline4().

VPUBLIC double d2bspline4 ( double x )

Evaluate the 2nd derivative of a 5th Order B-Spline.

Author:: : Michael Schnieders

Returns:: 2nd derivative of a 5th Order B-Spline

Parameters:

x

Position

Referenced by fillcoPermanentMultipole().

VPUBLIC double d3bspline4 ( double x )

Evaluate the 3rd derivative of a 5th Order B-Spline.

Author:: : Michael Schnieders

Returns:: 3rd derivative of a 5th Order B-Spline

Parameters:

x

Position

VPRIVATE double dbspline2 ( double x )

Evaluate a cubic B-spline derivative.

Author:: Nathan Baker

Returns:: Cubic B-spline derivative

Parameters:

x

Position

Referenced by qfForceSpline2().

VPUBLIC double dbspline4 ( double x )

Evaluate a 5th Order B-Spline derivative (4th order polynomial).

Author:: : Michael Schnieders

Returns:: 5th Order B-Spline derivative

Parameters:

x

Position

Referenced by fillcoPermanentMultipole(), and qfForceSpline4().

VPRIVATE void extEnergy	(	Vpmg *	thee,
		Vpmg *	pmgOLD,
		PBEparm_calcEnergy	extFlag,
		double	partMin[3],
		double	partMax[3],
		int	bflags[6]
	)

For focusing, set external energy data members in new Vpmg object based on energy calculations on old Vpmg object from regions outside the indicated partition.

Author:: Nathan Baker, Todd Dolinsky

Parameters:

	pmgOLD	Newly created PMG manager
	extFlag	Old PMG manager, source of energies
	partMin	Energy calculation flag
	partMax	Partition lower corner
	bflags	Partition upper corner Which boundaries to include the calculation

References sVpbe::alist, sVpmg::extDiEnergy, sVpmg::extQfEnergy, sVpmg::extQmEnergy, sVpmgp::hx, sVpmgp::hy, sVpmgp::hzed, sVpmgp::nx, sVpmgp::ny, sVpmgp::nz, sVatom::partID, sVpmg::pbe, sVpmg::pmgp, sVatom::position, sVpmg::pvec, Valist_getAtom(), Valist_getNumberAtoms(), VAPBS_BACK, VAPBS_DOWN, VAPBS_FRONT, VAPBS_LEFT, VAPBS_RIGHT, VAPBS_UP, Vpmg_dielEnergy(), Vpmg_qfEnergy(), Vpmg_qmEnergy(), Vpmg_setPart(), Vpmg_unsetPart(), sVpmgp::xcent, sVpmgp::ycent, and sVpmgp::zcent.

Referenced by energyMG(), and Vpmg_ctor2().

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VPRIVATE Vrc_Codes fillcoCharge ( Vpmg * thee )

Top-level driver to fill source term charge array.

Returns:: Success/failure status

Author:: Nathan Baker

References sVpmg::chargeMeth, sVpmg::chargeSrc, fillcoChargeMap(), fillcoChargeSpline1(), fillcoChargeSpline2(), fillcoInducedDipole(), fillcoNLInducedDipole(), fillcoPermanentMultipole(), sVpmg::useChargeMap, VCM_BSPL2, VCM_BSPL4, VCM_CHARGE, VCM_INDUCED, VCM_NLINDUCED, VCM_PERMANENT, VCM_TRIL, VRC_FAILURE, and VRC_SUCCESS.

Referenced by Vpmg_fillco().

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VPRIVATE Vrc_Codes fillcoChargeMap ( Vpmg * thee )

Fill source term charge array from a pre-calculated map.

Returns:: Success/failure status

Author:: Nathan Baker

References sVpmg::charge, sVpmg::chargeMap, sVpmgp::hx, sVpmgp::hy, sVpmgp::hzed, sVpmgp::nx, sVpmgp::ny, sVpmgp::nz, sVpmg::pbe, sVpmg::pmgp, Vgrid_value(), Vpbe_getZmagic(), VRC_FAILURE, VRC_SUCCESS, sVpmg::xf, sVpmg::yf, and sVpmg::zf.

Referenced by fillcoCharge().

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VPRIVATE void fillcoChargeSpline1 ( Vpmg * thee )

Fill source term charge array from linear interpolation.

Author:: Nathan Baker

References sVpbe::alist, sVpmgp::bcfl, BCFL_FOCUS, sVpmg::charge, sVpmgp::hx, sVpmgp::hy, sVpmgp::hzed, sVpmgp::nx, sVpmgp::ny, sVpmgp::nz, sVpmg::pbe, sVpmg::pmgp, Valist_getAtom(), Valist_getNumberAtoms(), Vatom_getCharge(), Vatom_getPosition(), Vpbe_getZmagic(), sVpmgp::xcent, sVpmgp::xlen, sVpmgp::ycent, sVpmgp::ylen, sVpmgp::zcent, and sVpmgp::zlen.

Referenced by fillcoCharge().

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VPRIVATE void fillcoChargeSpline2 ( Vpmg * thee )

Fill source term charge array from cubic spline interpolation.

Author:: Nathan Baker

References sVpbe::alist, sVpmgp::bcfl, BCFL_FOCUS, bspline2(), sVpmg::charge, sVpmgp::hx, sVpmgp::hy, sVpmgp::hzed, sVpmgp::nx, sVpmgp::ny, sVpmgp::nz, sVpmg::pbe, sVpmg::pmgp, Valist_getAtom(), Valist_getNumberAtoms(), Vatom_getCharge(), Vatom_getPosition(), Vpbe_getZmagic(), sVpmgp::xcent, sVpmgp::xlen, sVpmgp::ycent, sVpmgp::ylen, sVpmgp::zcent, and sVpmgp::zlen.

Referenced by fillcoCharge().

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VPRIVATE void fillcoCoef ( Vpmg * thee )

Top-level driver to fill all operator coefficient arrays.

Author:: Nathan Baker

References fillcoCoefMap(), fillcoCoefMol(), fillcoCoefSpline(), fillcoCoefSpline3(), fillcoCoefSpline4(), sVpmg::surfMeth, sVpmg::useDielXMap, sVpmg::useDielYMap, sVpmg::useDielZMap, sVpmg::useKappaMap, VSM_MOL, VSM_MOLSMOOTH, VSM_SPLINE, VSM_SPLINE3, and VSM_SPLINE4.

Referenced by Vpmg_fillco().

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VPRIVATE void fillcoCoefMap ( Vpmg * thee )

Fill operator coefficient arrays from pre-calculated maps.

Author:: Nathan Baker

References sVpmg::dielXMap, sVpmg::dielYMap, sVpmg::dielZMap, sVpmg::epsx, sVpmg::epsy, sVpmg::epsz, sVpmgp::hx, sVpmgp::hy, sVpmgp::hzed, sVpmg::kappa, sVpmg::kappaMap, sVpmgp::nx, sVpmgp::ny, sVpmgp::nz, sVpmg::pbe, sVpmg::pmgp, sVpmg::useDielXMap, sVpmg::useDielYMap, sVpmg::useDielZMap, sVpmg::useKappaMap, Vgrid_value(), Vpbe_getBulkIonicStrength(), VPMGSMALL, sVpmg::xf, sVpmg::yf, and sVpmg::zf.

Referenced by fillcoCoef(), and fillcoCoefMol().

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VPRIVATE void fillcoCoefMol ( Vpmg * thee )

Fill operator coefficient arrays from a molecular surface calculation.

Author:: Nathan Baker

References fillcoCoefMap(), fillcoCoefMolDiel(), fillcoCoefMolIon(), sVpmg::useDielXMap, sVpmg::useDielYMap, sVpmg::useDielZMap, and sVpmg::useKappaMap.

Referenced by fillcoCoef().

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VPRIVATE void fillcoCoefMolDiel ( Vpmg * thee )

Fill differential operator coefficient arrays from a molecular surface calculation.

Author:: Nathan Baker

References fillcoCoefMolDielNoSmooth(), fillcoCoefMolDielSmooth(), sVpmg::surfMeth, and VSM_MOLSMOOTH.

Referenced by fillcoCoefMol().

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VPRIVATE void fillcoCoefMolDielNoSmooth ( Vpmg * thee )

Fill differential operator coefficient arrays from a molecular surface calculation without smoothing.

Author:: Nathan Baker

References sVpbe::acc, sVpbe::alist, sVpmgp::bcfl, BCFL_FOCUS, sVpmg::epsx, sVpmg::epsy, sVpmg::epsz, sVpmgp::hx, sVpmgp::hy, sVpmgp::hzed, markSphere(), sVaccSurf::npts, sVpmgp::nx, sVpmgp::ny, sVpmgp::nz, sVpmg::pbe, sVpmg::pmgp, Vacc_atomSASA(), Vacc_atomSASPoints(), Vacc_SASA(), Valist_getAtom(), Valist_getNumberAtoms(), Vatom_getPosition(), Vatom_getRadius(), Vpbe_getSoluteDiel(), Vpbe_getSolventDiel(), Vpbe_getSolventRadius(), sVpmgp::xcent, sVpmgp::xlen, sVaccSurf::xpts, sVpmgp::ycent, sVpmgp::ylen, sVaccSurf::ypts, sVpmgp::zcent, sVpmgp::zlen, and sVaccSurf::zpts.

Referenced by fillcoCoefMolDiel().

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VPRIVATE void fillcoCoefMolDielSmooth ( Vpmg * thee )

Fill differential operator coefficient arrays from a molecular surface calculation with smoothing.

Molecular surface, dielectric smoothing following an implementation of Bruccoleri, et al. J Comput Chem 18 268-276 (1997).

This algorithm uses a 9 point harmonic smoothing technique - the point in question and all grid points 1/sqrt(2) grid spacings away.

Note:: This uses thee->a1cf, thee->a2cf, thee->a3cf as temporary storage.

Author:: Todd Dolinsky

References sVpmg::a1cf, sVpmg::a2cf, sVpmg::a3cf, sVpmg::epsx, sVpmg::epsy, sVpmg::epsz, sVpmgp::nx, sVpmgp::ny, sVpmgp::nz, sVpmg::pbe, sVpmg::pmgp, and Vpbe_getSolventDiel().

Referenced by fillcoCoefMolDiel().

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VPRIVATE void fillcoCoefMolIon ( Vpmg * thee )

Fill ion (nonlinear) operator coefficient array from a molecular surface calculation.

Author:: Nathan Baker

References sVpbe::acc, sVpbe::alist, sVpmgp::bcfl, BCFL_FOCUS, sVpmgp::hx, sVpmgp::hy, sVpmgp::hzed, sVpmg::kappa, markSphere(), sVpmgp::nx, sVpmgp::ny, sVpmgp::nz, sVpmg::pbe, sVpmg::pmgp, sVpmg::surfMeth, Valist_getAtom(), Valist_getNumberAtoms(), Vatom_getPosition(), Vatom_getRadius(), Vpbe_getBulkIonicStrength(), Vpbe_getMaxIonRadius(), VPMGSMALL, sVpmgp::xcent, sVpmgp::xlen, sVpmgp::ycent, sVpmgp::ylen, sVpmgp::zcent, and sVpmgp::zlen.

Referenced by fillcoCoefMol().

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VPRIVATE void fillcoCoefSpline ( Vpmg * thee )

Fill operator coefficient arrays from a spline-based surface calculation.

Author:: Nathan Baker

References sVpbe::alist, sVpmgp::bcfl, BCFL_FOCUS, sVpmg::epsx, sVpmg::epsy, sVpmg::epsz, sVpmgp::hx, sVpmgp::hy, sVpmgp::hzed, sVpmg::kappa, sVpmgp::nx, sVpmgp::ny, sVpmgp::nz, sVpmg::pbe, sVpmg::pmgp, sVpmg::splineWin, Valist_getAtom(), Valist_getNumberAtoms(), Vatom_getPosition(), Vatom_getRadius(), Vpbe_getBulkIonicStrength(), Vpbe_getMaxIonRadius(), Vpbe_getSoluteDiel(), Vpbe_getSolventDiel(), VPMGSMALL, sVpmgp::xcent, sVpmgp::xlen, sVpmgp::ycent, sVpmgp::ylen, sVpmgp::zcent, and sVpmgp::zlen.

Referenced by fillcoCoef().

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VPRIVATE void fillcoCoefSpline3 ( Vpmg * thee )

Fill operator coefficient arrays from a 5th order polynomial based surface calculation.

Author:: Michael Schnieders

References sVpbe::alist, sVpmgp::bcfl, BCFL_FOCUS, sVpmg::epsx, sVpmg::epsy, sVpmg::epsz, sVpmgp::hx, sVpmgp::hy, sVpmgp::hzed, sVpmg::kappa, sVpmgp::nx, sVpmgp::ny, sVpmgp::nz, sVpmg::pbe, sVpmg::pmgp, sVpmg::splineWin, Valist_getAtom(), Valist_getNumberAtoms(), Vatom_getPosition(), Vatom_getRadius(), Vpbe_getBulkIonicStrength(), Vpbe_getMaxIonRadius(), Vpbe_getSoluteDiel(), Vpbe_getSolventDiel(), VPMGSMALL, sVpmgp::xcent, sVpmgp::xlen, sVpmgp::ycent, sVpmgp::ylen, sVpmgp::zcent, and sVpmgp::zlen.

Referenced by fillcoCoef().

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VPRIVATE void fillcoCoefSpline4 ( Vpmg * thee )

Fill operator coefficient arrays from a 7th order polynomial based surface calculation.

Author:: Michael Schnieders

References sVpbe::alist, sVpmgp::bcfl, BCFL_FOCUS, sVpmg::epsx, sVpmg::epsy, sVpmg::epsz, sVpmgp::hx, sVpmgp::hy, sVpmgp::hzed, sVpmg::kappa, sVpmgp::nx, sVpmgp::ny, sVpmgp::nz, sVpmg::pbe, sVpmg::pmgp, sVpmg::splineWin, Valist_getAtom(), Valist_getNumberAtoms(), Vatom_getPosition(), Vatom_getRadius(), Vpbe_getBulkIonicStrength(), Vpbe_getMaxIonRadius(), Vpbe_getSoluteDiel(), Vpbe_getSolventDiel(), VPMGSMALL, sVpmgp::xcent, sVpmgp::xlen, sVpmgp::ycent, sVpmgp::ylen, sVpmgp::zcent, and sVpmgp::zlen.

Referenced by fillcoCoef().

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VPUBLIC void fillcoPermanentMultipole ( Vpmg * thee )

Fill source term charge array for the use of permanent multipoles.

Author:: Michael Schnieders

References sVpbe::alist, bspline4(), sVpmg::charge, d2bspline4(), dbspline4(), sVpmgp::hx, sVpmgp::hy, sVpmgp::hzed, sVpmgp::nx, sVpmgp::ny, sVpmgp::nz, sVpmg::pbe, sVpmg::pmgp, Valist_getAtom(), Valist_getNumberAtoms(), Vatom_getCharge(), Vatom_getPosition(), VFCHI4(), Vpbe_getZmagic(), sVpmgp::xcent, sVpmgp::xlen, sVpmgp::ycent, sVpmgp::ylen, sVpmgp::zcent, and sVpmgp::zlen.

Referenced by fillcoCharge().

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VPRIVATE void focusFillBound	(	Vpmg *	thee,
		Vpmg *	pmg
	)

For focusing, fill in the boundaries of the new mesh based on the potential values in the old mesh.

Author:: Nathan Baker

Parameters:

pmgOLD

New PMG object (the one just created) Old PMG object

References sVpmg::gxcf, sVpmg::gycf, sVpmg::gzcf, sVpmgp::hx, sVpmgp::hy, sVpmgp::hzed, sVpmgp::nx, sVpmgp::ny, sVpmgp::nz, sVpmg::pbe, sVpmg::pmgp, SINH_MIN, sVpmg::u, Vpbe_getSoluteCenter(), Vpbe_getSoluteCharge(), Vpbe_getSoluteRadius(), Vpbe_getSolventDiel(), Vpbe_getTemperature(), Vpbe_getXkappa(), VPMGSMALL, Vunit_ec, Vunit_eps0, Vunit_kb, sVpmgp::xcent, sVpmgp::ycent, and sVpmgp::zcent.

Referenced by Vpmg_ctor2().

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VPRIVATE void markSphere	(	double	rtot,
		double *	tpos,
		int	nx,
		int	ny,
		int	nz,
		double	hx,
		double	hy,
		double	hzed,
		double	xmin,
		double	ymin,
		double	zmin,
		double *	array,
		double	markVal
	)

Mark the grid points inside a sphere with a particular value. This marks by resetting the the grid points inside the sphere to the specified value.

Author:: Nathan Baker

Parameters:

	tpos	Sphere radius
	nx	Sphere position
	ny	Number of grid points
	nz	Number of grid points
	hx	Number of grid points
	hy	Grid spacing
	hz	Grid spacing
	xmin	Grid spacing
	ymin	Grid lower corner
	zmin	Grid lower corner
	array	Grid lower corner
	markVal	Grid values Value to mark with

Referenced by fillcoCoefMolDielNoSmooth(), and fillcoCoefMolIon().

VPRIVATE void multipolebc	(	double	r,
		double	kappa,
		double	eps_p,
		double	eps_w,
		double	rad,
		double	tsr[3]
	)

This routine serves bcfl2. It returns (in tsr) the contraction independent portion of the Debye-Huckel potential tensor for a spherical ion with a central charge, dipole and quadrupole. See the code for an in depth description.

Author:: Michael Schnieders

Parameters:

	kappa	Distance to the boundary
	eps_p	Exponential screening factor
	eps_w	Solute dielectric
	rad	Solvent dielectric
	tsr	Radius of the sphere Contraction-independent portion of each tensor

Referenced by bcfl2().

VPRIVATE void qfForceSpline1	(	Vpmg *	thee,
		double *	force,
		int	atomID
	)

Charge-field force due to a linear spline charge function.

Author:: Nathan Baker

Parameters:

atomID

Set to force Valist atom ID

References sVpbe::alist, sVpmgp::bcfl, BCFL_FOCUS, sVpmgp::hx, sVpmgp::hy, sVpmgp::hzed, sVpmgp::nx, sVpmgp::ny, sVpmgp::nz, sVatom::partID, sVpmg::pbe, sVpmg::pmgp, sVpmg::u, Valist_getAtom(), Vatom_getCharge(), Vatom_getPosition(), VPMGSMALL, sVpmgp::xmax, sVpmgp::xmin, sVpmgp::ymax, sVpmgp::ymin, sVpmgp::zmax, and sVpmgp::zmin.

Referenced by Vpmg_qfForce().

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VPRIVATE void qfForceSpline2	(	Vpmg *	thee,
		double *	force,
		int	atomID
	)

Charge-field force due to a cubic spline charge function.

Author:: Nathan Baker

Parameters:

atomID

Set to force Valist atom ID

References sVpbe::alist, sVpmgp::bcfl, BCFL_FOCUS, bspline2(), dbspline2(), sVpmgp::hx, sVpmgp::hy, sVpmgp::hzed, sVpmgp::nx, sVpmgp::ny, sVpmgp::nz, sVatom::partID, sVpmg::pbe, sVpmg::pmgp, sVpmg::u, Valist_getAtom(), Vatom_getCharge(), Vatom_getPosition(), sVpmgp::xlen, sVpmgp::xmax, sVpmgp::xmin, sVpmgp::ylen, sVpmgp::ymax, sVpmgp::ymin, sVpmgp::zlen, sVpmgp::zmax, and sVpmgp::zmin.

Referenced by Vpmg_qfForce().

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VPRIVATE void qfForceSpline4	(	Vpmg *	thee,
		double *	force,
		int	atomID
	)

Charge-field force due to a quintic spline charge function.

Author:: Michael Schnieders

Parameters:

atomID

Set to force Valist atom ID

References sVpbe::alist, bspline4(), dbspline4(), sVpmg::filled, sVpmgp::hx, sVpmgp::hy, sVpmgp::hzed, sVpmgp::nx, sVpmgp::ny, sVpmgp::nz, sVpmg::pbe, sVpmg::pmgp, sVpmg::u, Valist_getAtom(), Vatom_getCharge(), Vatom_getPosition(), VFCHI4(), sVpmgp::xlen, sVpmgp::xmax, sVpmgp::xmin, sVpmgp::ylen, sVpmgp::ymax, sVpmgp::ymin, sVpmgp::zlen, sVpmgp::zmax, and sVpmgp::zmin.

Referenced by Vpmg_qfForce().

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VPRIVATE double VFCHI4	(	int	i,
		double	f
	)

Return 2.5 plus difference of i - f.

Author:: Michael Schnieders

Returns:: (2.5+((double)(i)-(f)))

Referenced by fillcoPermanentMultipole(), and qfForceSpline4().

VPRIVATE double Vpmg_polarizEnergy	(	Vpmg *	thee,
		int	extFlag
	)

Determines energy from polarizeable charge and interaction with fixed charges according to Rocchia et al.

Author:: Nathan Baker

Returns:: Energy in kT

Parameters:

extFlag

If 1, add external energy contributions to result

References sVpbe::alist, sVpmg::charge, sVpmgp::hx, sVpmgp::hy, sVpmgp::hzed, sVpmgp::nx, sVpmgp::ny, sVpmgp::nz, sVpmg::pbe, sVpmg::pmgp, sVpmg::u, Valist_getAtom(), Valist_getNumberAtoms(), Vatom_getCharge(), Vatom_getPosition(), Vgrid_ctor(), Vgrid_curvature(), Vpbe_getSoluteDiel(), Vpbe_getSolventDiel(), Vpbe_getTemperature(), Vunit_ec, Vunit_eps0, Vunit_kb, sVpmgp::xmin, and sVpmgp::ymin.

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VPRIVATE double Vpmg_qfEnergyPoint	(	Vpmg *	thee,
		int	extFlag
	)

Calculates charge-potential energy using summation over delta function positions (i.e. something like an Linf norm).

Author:: Nathan Baker

Returns:: Energy in kT

Parameters:

extFlag

If 1, add external energy contributions to result

References sVpbe::alist, sVpmgp::bcfl, BCFL_FOCUS, sVpmg::extQfEnergy, sVpmgp::hx, sVpmgp::hy, sVpmgp::hzed, sVpmgp::nx, sVpmgp::ny, sVpmgp::nz, sVatom::partID, sVpmg::pbe, sVpmg::pmgp, sVpmg::pvec, sVpmg::u, Valist_getAtom(), Valist_getNumberAtoms(), Vatom_getCharge(), Vatom_getPosition(), sVpmgp::xmax, sVpmgp::xmin, sVpmgp::ymax, sVpmgp::ymin, sVpmgp::zmax, and sVpmgp::zmin.

Referenced by Vpmg_qfEnergy().

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VPRIVATE double Vpmg_qfEnergyVolume	(	Vpmg *	thee,
		int	extFlag
	)

Calculates charge-potential energy as integral over a volume.

Author:: Nathan Baker

Returns:: Energy in kT

Parameters:

extFlag

If 1, add external energy contributions to result

References sVpmg::charge, sVpmg::extQfEnergy, sVpmg::filled, sVpmgp::hx, sVpmgp::hy, sVpmgp::hzed, sVpmgp::nx, sVpmgp::ny, sVpmgp::nz, sVpmg::pbe, sVpmg::pmgp, sVpmg::pvec, sVpmg::u, and Vpbe_getZmagic().

Referenced by Vpmg_qfEnergy().

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VPUBLIC double Vpmg_qmEnergySMPBE	(	Vpmg *	thee,
		int	extFlag
	)

Vpmg_qmEnergy for SMPBE.

Author:: Vincent Chu

References sVpmg::extQmEnergy, sVpmg::filled, sVpmgp::hx, sVpmgp::hy, sVpmgp::hzed, sVpmg::kappa, MAXION, sVpmgp::nonlin, sVpmgp::nx, sVpmgp::ny, sVpmgp::nz, sVpmg::pbe, sVpmg::pmgp, sVpmg::pvec, sVpbe::smsize, sVpbe::smvolume, sVpmg::u, Vcap_exp(), Vpbe_getBulkIonicStrength(), Vpbe_getIons(), and Vpbe_getZkappa2().

Referenced by Vpmg_qmEnergy().

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VPRIVATE void Vpmg_splineSelect	(	int	srfm,
		Vacc *	acc,
		double *	gpos,
		double	win,
		double	infrad,
		Vatom *	atom,
		double *	force
	)

Selects a spline based surface method from either VSM_SPLINE, VSM_SPLINE5 or VSM_SPLINE7.

Author:: David Gohara

Parameters:

	acc	Surface method, currently VSM_SPLINE, VSM_SPLINE5, or VSM_SPLINE7
	gpos	Accessibility object
	win	Position array -> array[3]
	infrad	Spline window
	atom	Inflation radius
	force	Atom object Force array -> array[3]

References Vacc_splineAccGradAtomNorm(), Vacc_splineAccGradAtomNorm3(), Vacc_splineAccGradAtomNorm4(), VSM_SPLINE, VSM_SPLINE3, and VSM_SPLINE4.

Referenced by Vpmg_dbForce(), and Vpmg_ibForce().

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VPRIVATE void zlapSolve	(	Vpmg *	thee,
		double **	solution,
		double **	source,
		double **	work1
	)

Calculate the solution to Poisson's equation with a simple Laplacian operator and zero-valued Dirichlet boundary conditions. Store the solution in thee->u.

Author:: Nathan Baker

Note:: Vpmg_fillco must be called first

Parameters:

	source	Solution term vector
	work1	Source term vector Work vector

References sVpmgp::hx, sVpmgp::hy, sVpmgp::hzed, sVpmgp::nx, sVpmgp::ny, sVpmgp::nz, sVpmg::pmgp, sVpmg::u, sVpmgp::xlen, sVpmgp::ylen, and sVpmgp::zlen.

Referenced by Vpmg_solveLaplace().

vpmg.c File Reference

Functions

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