Vpmg class

A wrapper for Mike Holst's PMG multigrid code. More...

Data Structures
struct	sVpmg
	Contains public data members for Vpmg class/module. More...
Files
file	vpmg.h
	Contains declarations for class Vpmg.
file	vpmg-private.h
	Class Vpmg private method declaration.
file	vpmg.c
	Class Vpmg methods.
Typedefs
typedef struct sVpmg	Vpmg
	Declaration of the Vpmg class as the Vpmg structure.
Functions
unsigned long int	Vpmg_memChk (Vpmg *thee)
	Return the memory used by this structure (and its contents) in bytes.
Vpmg *	Vpmg_ctor (Vpmgp parms, Vpbe pbe, int focusFlag, Vpmg pmgOLD, MGparm mgparm, PBEparm_calcEnergy energyFlag)
	Constructor for the Vpmg class (allocates new memory).
int	Vpmg_ctor2 (Vpmg thee, Vpmgp parms, Vpbe pbe, int focusFlag, Vpmg pmgOLD, MGparm *mgparm, PBEparm_calcEnergy energyFlag)
	FORTRAN stub constructor for the Vpmg class (uses previously-allocated memory).
void	Vpmg_dtor (Vpmg **thee)
	Object destructor.
void	Vpmg_dtor2 (Vpmg *thee)
	FORTRAN stub object destructor.
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.
int	Vpmg_solve (Vpmg *thee)
	Solve the PBE using PMG.
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.
double	Vpmg_energy (Vpmg *thee, int extFlag)
	Get the total electrostatic energy.
double	Vpmg_qfEnergy (Vpmg *thee, int extFlag)
	Get the "fixed charge" contribution to the electrostatic energy.
double	Vpmg_qfAtomEnergy (Vpmg thee, Vatom atom)
	Get the per-atom "fixed charge" contribution to the electrostatic energy.
double	Vpmg_qmEnergy (Vpmg *thee, int extFlag)
	Get the "mobile charge" contribution to the electrostatic energy.
double	Vpmg_dielEnergy (Vpmg *thee, int extFlag)
	Get the "polarization" contribution to the electrostatic energy.
double	Vpmg_dielGradNorm (Vpmg *thee)
	Get the integral of the gradient of the dielectric function.
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.
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.
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.
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.
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.
void	Vpmg_unsetPart (Vpmg *thee)
	Remove partition restrictions.
int	Vpmg_fillArray (Vpmg thee, double vec, Vdata_Type type, double parm, Vhal_PBEType pbetype)
	Fill the specified array with accessibility values.
VPUBLIC void	Vpmg_fieldSpline4 (Vpmg *thee, int atomID, double field[3])
	Computes the field at an atomic center using a stencil based on the first derivative of a 5th order B-spline.
double	Vpmg_qfPermanentMultipoleEnergy (Vpmg *thee, int atomID)
	Computes the permanent multipole electrostatic hydration energy (the polarization component of the hydration energy currently computed in TINKER).
void	Vpmg_qfPermanentMultipoleForce (Vpmg *thee, int atomID, double force[3], double torque[3])
	Computes the q-Phi Force for permanent multipoles based on 5th order B-splines.
void	Vpmg_ibPermanentMultipoleForce (Vpmg *thee, int atomID, double force[3])
	Compute the ionic boundary force for permanent multipoles.
void	Vpmg_dbPermanentMultipoleForce (Vpmg *thee, int atomID, double force[3])
	Compute the dielectric boundary force for permanent multipoles.
void	Vpmg_qfDirectPolForce (Vpmg thee, Vgrid perm, Vgrid *induced, int atomID, double force[3], double torque[3])
	q-Phi direct polarization force between permanent multipoles and induced dipoles, which are induced by the sum of the permanent intramolecular field and the permanent reaction field.
void	Vpmg_qfNLDirectPolForce (Vpmg thee, Vgrid perm, Vgrid *nlInduced, int atomID, double force[3], double torque[3])
	q-Phi direct polarization force between permanent multipoles and non-local induced dipoles based on 5th Order B-Splines. Keep in mind that the "non-local" induced dipooles are just a mathematical quantity that result from differentiation of the AMOEBA polarization energy.
void	Vpmg_ibDirectPolForce (Vpmg thee, Vgrid perm, Vgrid *induced, int atomID, double force[3])
	Ionic boundary direct polarization force between permanent multipoles and induced dipoles, which are induced by the sum of the permanent intramolecular field and the permanent reaction field.
void	Vpmg_ibNLDirectPolForce (Vpmg thee, Vgrid perm, Vgrid *nlInduced, int atomID, double force[3])
	Ionic boundary direct polarization force between permanent multipoles and non-local induced dipoles based on 5th order Keep in mind that the "non-local" induced dipooles are just a mathematical quantity that result from differentiation of the AMOEBA polarization energy.
void	Vpmg_dbDirectPolForce (Vpmg thee, Vgrid perm, Vgrid *induced, int atomID, double force[3])
	Dielectric boundary direct polarization force between permanent multipoles and induced dipoles, which are induced by the sum of the permanent intramolecular field and the permanent reaction field.
void	Vpmg_dbNLDirectPolForce (Vpmg thee, Vgrid perm, Vgrid *nlInduced, int atomID, double force[3])
	Dielectric bounday direct polarization force between permanent multipoles and non-local induced dipoles. Keep in mind that the "non-local" induced dipooles are just a mathematical quantity that result from differentiation of the AMOEBA polarization energy.
void	Vpmg_qfMutualPolForce (Vpmg thee, Vgrid induced, Vgrid *nlInduced, int atomID, double force[3])
	Mutual polarization force for induced dipoles based on 5th order B-Splines. This force arises due to self-consistent convergence of the solute induced dipoles and reaction field.
void	Vpmg_ibMutualPolForce (Vpmg thee, Vgrid induced, Vgrid *nlInduced, int atomID, double force[3])
	Ionic boundary mutual polarization force for induced dipoles based on 5th order B-Splines. This force arises due to self-consistent convergence of the solute induced dipoles and reaction field.
void	Vpmg_dbMutualPolForce (Vpmg thee, Vgrid induced, Vgrid *nlInduced, int atomID, double force[3])
	Dielectric boundary mutual polarization force for induced dipoles based on 5th order B-Splines. This force arises due to self-consistent convergence of the solute induced dipoles and reaction field.
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.

Detailed Description

A wrapper for Mike Holst's PMG multigrid code.

Note:: Many of the routines and macros are borrowed from the main.c driver (written by Mike Holst) provided with the PMG code.

Function Documentation

Vpmg* Vpmg_ctor	(	Vpmgp *	parms,
		Vpbe *	pbe,
		int	focusFlag,
		Vpmg *	pmgOLD,
		MGparm *	mgparm,
		PBEparm_calcEnergy	energyFlag
	)

Constructor for the Vpmg class (allocates new memory).

Author:: Nathan Baker

Returns:: Pointer to newly allocated Vpmg object

Parameters:

	pbe	PMG parameter object
	focusFlag	PBE-specific variables
	pmgOLD	1 for focusing, 0 otherwise
	mgparm	Old Vpmg object to use for boundary conditions
	energyFlag	MGparm parameter object for boundary conditions What types of energies to calculate

References Vpmg_ctor2().

Referenced by initMG().

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int Vpmg_ctor2	(	Vpmg *	thee,
		Vpmgp *	parms,
		Vpbe *	pbe,
		int	focusFlag,
		Vpmg *	pmgOLD,
		MGparm *	mgparm,
		PBEparm_calcEnergy	energyFlag
	)

FORTRAN stub constructor for the Vpmg class (uses previously-allocated memory).

Author:: Nathan Baker

Returns:: 1 if successful, 0 otherwise

Parameters:

	parms	Memory location for object
	pbe	PMG parameter object
	focusFlag	PBE-specific variables
	pmgOLD	1 for focusing, 0 otherwise
	mgparm	Old Vpmg object to use for boundary conditions (can be VNULL if focusFlag = 0)
	energyFlag	MGparm parameter object for boundary conditions (can be VNULL if focusFlag = 0) What types of energies to calculate (ignored if focusFlag = 0)

References sVpmg::a1cf, sVpmg::a2cf, sVpmg::a3cf, sVpmgp::bcfl, BCFL_FOCUS, sVpmg::ccf, sMGparm::center, sVpmg::charge, sVpmg::chargeSrc, sMGparm::chgs, sVpmg::epsx, sVpmg::epsy, sVpmg::epsz, sVpmgp::errtol, sVpmg::extDiEnergy, extEnergy(), sVpmg::extQfEnergy, sVpmg::extQmEnergy, sVpmg::fcf, sVpmg::filled, focusFillBound(), sMGparm::glen, sVpmg::gxcf, sVpmg::gycf, sVpmg::gzcf, sVpmgp::iinfo, sVpmg::iparm, sVpmgp::ipcon, sVpmgp::iperf, sVpmgp::ipkey, IPKEY_LPBE, IPKEY_NPBE, IPKEY_SMPBE, sVpmgp::irite, sVpmgp::istop, sVpmgp::itmax, sVpmg::iwork, sVpmg::kappa, MAXION, MCT_PARALLEL, sVpmgp::meth, sVpmgp::mgcoar, sVpmgp::mgdisc, sVpmgp::mgkey, sVpmgp::mgprol, sVpmgp::mgsmoo, sVpmgp::mgsolv, sVpmgp::n_ipc, sVpmgp::n_iz, sVpmgp::n_rpc, sVpmgp::narr, sVpmgp::narrc, sVpmgp::nc, sVpmgp::nf, sVpmgp::niwk, sVpmgp::nlev, sVpmgp::nonlin, sVpmgp::nrwk, sVpmgp::nu1, sVpmgp::nu2, sVpmgp::nx, sVpmgp::nxc, sVpmgp::ny, sVpmgp::nyc, sVpmgp::nz, sVpmgp::nzc, sVpmgp::omegal, sVpmgp::omegan, sMGparm::partDisjCenter, sMGparm::partDisjLength, sMGparm::partDisjOwnSide, sVpmg::pbe, PCE_NO, sVpmg::pmgp, sVpmg::pvec, sVpmg::rparm, sVpmg::rwork, sVpbe::smsize, sVpbe::smvolume, sVpmg::tcf, sMGparm::type, sVpmg::u, sMGparm::useAqua, sVpmg::vmem, Vpbe_getBulkIonicStrength(), Vpbe_getIons(), Vpbe_getZkappa2(), Vpmg_dtor(), Vpmg_unsetPart(), sVpmg::xf, sVpmg::yf, and sVpmg::zf.

Referenced by Vpmg_ctor().

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void Vpmg_dbDirectPolForce	(	Vpmg *	thee,
		Vgrid *	perm,
		Vgrid *	induced,
		int	atomID,
		double	force[3]
	)

Dielectric boundary direct polarization force between permanent multipoles and induced dipoles, which are induced by the sum of the permanent intramolecular field and the permanent reaction field.

Author:: Michael Schnieders

Parameters:

	perm	Vpmg object
	induced	Permanent multipole potential
	atomID	Induced dipole potential
	force	Atom index (returned) force

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.

Author:: Nathan Baker

Note:

Using the force evaluation methods of Im et al (Roux group), Comput Phys Commun, 111, 59--75 (1998). However, this gives the whole (self-interactions included) force -- reaction field forces will have to be calculated at higher level.
No contributions are made from higher levels of focusing.

Returns:: 1 if successful, 0 otherwise

Parameters:

	dbForce	Vpmg object
	atomID	3*sizeof(double) space to hold the dielectric boundary force in units of k_B T/AA
	srfm	Valist ID of desired atom Surface discretization method

References sVpbe::acc, sVpbe::alist, sVpmgp::bcfl, BCFL_FOCUS, sVpmg::epsx, sVpmg::epsy, sVpmg::epsz, sVpmg::filled, sVpmgp::hx, sVpmgp::hy, sVpmgp::hzed, sVpmgp::nx, sVpmgp::ny, sVpmgp::nz, sVatom::partID, sVpmg::pbe, sVpmg::pmgp, sVpmg::splineWin, sVpmg::u, Valist_getAtom(), Vatom_getPosition(), Vatom_getRadius(), Vpbe_getSoluteDiel(), Vpbe_getSolventDiel(), Vpbe_getSolventRadius(), Vpbe_getTemperature(), Vpbe_getZmagic(), Vpmg_splineSelect(), VPMGSMALL, VSM_SPLINE, VSM_SPLINE3, VSM_SPLINE4, Vunit_kb, Vunit_Na, sVpmgp::xlen, sVpmgp::xmax, sVpmgp::xmin, sVpmgp::ylen, sVpmgp::ymax, sVpmgp::ymin, sVpmgp::zlen, sVpmgp::zmax, and sVpmgp::zmin.

Referenced by forceMG(), and Vpmg_force().

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void Vpmg_dbMutualPolForce	(	Vpmg *	thee,
		Vgrid *	induced,
		Vgrid *	nlInduced,
		int	atomID,
		double	force[3]
	)

Dielectric boundary mutual polarization force for induced dipoles based on 5th order B-Splines. This force arises due to self-consistent convergence of the solute induced dipoles and reaction field.

Author:: Michael Schnieders

Parameters:

	induced	Vpmg object
	nlInduced	Induced dipole potential
	atomID	Non-local induced dipole potential
	force	Atom index (returned) force

void Vpmg_dbNLDirectPolForce	(	Vpmg *	thee,
		Vgrid *	perm,
		Vgrid *	nlInduced,
		int	atomID,
		double	force[3]
	)

Dielectric bounday direct polarization force between permanent multipoles and non-local induced dipoles. Keep in mind that the "non-local" induced dipooles are just a mathematical quantity that result from differentiation of the AMOEBA polarization energy.

Author:: Michael Schnieders

Parameters:

	perm	Vpmg object
	nlInduced	Permanent multipole potential
	atomID	Non-local induced dipole potential
	force	Atom index (returned) force

void Vpmg_dbPermanentMultipoleForce	(	Vpmg *	thee,
		int	atomID,
		double	force[3]
	)

Compute the dielectric boundary force for permanent multipoles.

Author:: Michael Schnieders

Parameters:

	atomID	Vpmg object
	force	Atom index (returned) force

double Vpmg_dielEnergy	(	Vpmg *	thee,
		int	extFlag
	)

Get the "polarization" contribution to the electrostatic energy.

Using the solution at the finest mesh level, get the electrostatic energy due to the interaction of the mobile charges with the potential:

$G = \frac{1}{2} \int \epsilon (\nabla u)^2 dx$

where epsilon is the dielectric parameter and u(x) is the dimensionless electrostatic potential. The energy is scaled to units of k_b T.

Author:: Nathan Baker

Note:: The value of this observable may be modified by setting restrictions on the subdomain over which it is calculated. Such limits can be set via Vpmg_setPart and are generally useful for parallel runs.

Returns:: The polarization electrostatic energy in units of k_B T.

Parameters:

extFlag

Vpmg object If this was a focused calculation, include (1 -- for serial calculations) or ignore (0 -- for parallel calculations) energy contributions from outside the focusing domain

References sVpmg::epsx, sVpmg::epsy, sVpmg::epsz, sVpmg::extDiEnergy, 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 energyMG(), extEnergy(), and Vpmg_energy().

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double Vpmg_dielGradNorm ( Vpmg * thee )

Get the integral of the gradient of the dielectric function.

Using the dielectric map at the finest mesh level, calculate the integral of the norm of the dielectric function gradient routines of Im et al (see Vpmg_dbForce for reference):

$\int \| \nabla \epsilon \| dx$

where epsilon is the dielectric parameter. The integral is returned in units of A^2.

Author:: Nathan Baker restrictions on the subdomain over which it is calculated. Such limits can be set via Vpmg_setPart and are generally useful for parallel runs.

Returns:: The integral in units of A^2.

Parameters:

thee

Vpmg object

References sVpmg::epsx, sVpmg::epsy, sVpmg::epsz, sVpmg::filled, sVpmgp::hx, sVpmgp::hy, sVpmgp::hzed, sVpmgp::nx, sVpmgp::ny, sVpmgp::nz, sVpmg::pmgp, and sVpmg::pvec.

void Vpmg_dtor ( Vpmg ** thee )

Object destructor.

Author:: Nathan Baker

Parameters:

thee

Pointer to memory location of object to be destroyed

References Vpmg_dtor2().

Referenced by initMG(), killMG(), and Vpmg_ctor2().

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void Vpmg_dtor2 ( Vpmg * thee )

FORTRAN stub object destructor.

Author:: Nathan Baker

Parameters:

thee

Pointer to object to be destroyed

References sVpmg::a1cf, sVpmg::a2cf, sVpmg::a3cf, sVpmg::ccf, sVpmg::charge, sVpmg::epsx, sVpmg::epsy, sVpmg::epsz, sVpmg::fcf, sVpmg::gxcf, sVpmg::gycf, sVpmg::gzcf, sVpmg::iparm, sVpmg::iwork, sVpmg::kappa, sVpmgp::narr, sVpmgp::niwk, sVpmgp::nrwk, sVpmgp::nx, sVpmgp::ny, sVpmgp::nz, sVpmg::pmgp, sVpmg::pvec, sVpmg::rparm, sVpmg::rwork, sVpmg::tcf, sVpmg::u, sVpmg::vmem, sVpmg::xf, sVpmg::yf, and sVpmg::zf.

Referenced by Vpmg_dtor().

double Vpmg_energy	(	Vpmg *	thee,
		int	extFlag
	)

Get the total electrostatic energy.

Author:: Nathan Baker

Note:: The value of this observable may be modified by setting restrictions on the subdomain over which it is calculated. Such limits can be set via Vpmg_setPart and are generally useful for parallel runs.

Returns:: The electrostatic energy in units of k_B T.

Parameters:

extFlag

Vpmg object If this was a focused calculation, include (1 -- for serial calculations) or ignore (0 -- for parallel calculations) energy contributions from outside the focusing domain

References sVpmgp::nonlin, sVpmg::pbe, sVpmg::pmgp, Vpbe_getBulkIonicStrength(), Vpmg_dielEnergy(), Vpmg_qfEnergy(), and Vpmg_qmEnergy().

Referenced by energyMG().

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VPUBLIC void Vpmg_fieldSpline4	(	Vpmg *	thee,
		int	atomID,
		double	field[3]
	)

Computes the field at an atomic center using a stencil based on the first derivative of a 5th order B-spline.

Author:: Michael Schnieders

Parameters:

	atomID	Vpmg object
	field	Atom index The (returned) electric field

int Vpmg_fillArray	(	Vpmg *	thee,
		double *	vec,
		Vdata_Type	type,
		double	parm,
		Vhal_PBEType	pbetype
	)

Fill the specified array with accessibility values.

Author:: Nathan Baker

Returns:: 1 if successful, 0 otherwise

Parameters:

	vec	Vpmg object
	type	A nxnynz*sizeof(double) array to contain the values to be written
	parm	What to write
	pbetype	Parameter for data type definition (if needed) Parameter for PBE type (if needed)

References sVpmg::charge, sVpmg::epsx, sVpmg::epsy, sVpmg::epsz, sVpmg::filled, sVpmgp::hx, sVpmgp::hy, sVpmgp::hzed, sVpbe::ionConc, sVpbe::ionQ, sVpmg::kappa, sVpbe::maxIonRadius, sVpbe::numIon, sVpmgp::nx, sVpmgp::ny, sVpmgp::nz, sVpmg::pbe, PBE_LPBE, PBE_NPBE, PBE_SMPBE, sVpmg::pmgp, sVpbe::solventRadius, sVpmg::u, Vacc_ivdwAcc(), Vacc_molAcc(), Vacc_splineAcc(), Vacc_vdwAcc(), Vcap_exp(), 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_curvature(), Vgrid_dtor(), Vgrid_gradient(), Vpbe_getSoluteDiel(), Vpbe_getSolventDiel(), Vpbe_getVacc(), Vpbe_getZmagic(), sVpmgp::xmin, sVpmgp::ymin, and sVpmgp::zmin.

Referenced by writedataMG().

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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.

Author:: Nathan Baker

Returns:: 1 if successful, 0 otherwise

Parameters:

	surfMeth	Vpmg object
	splineWin	Surface discretization method
	chargeMeth	Spline window (in A) for surfMeth = VSM_SPLINE
	useDielXMap	Charge discretization method
	dielXMap	Boolean to use dielectric map argument
	useDielYMap	External dielectric map
	dielYMap	Boolean to use dielectric map argument
	useDielZMap	External dielectric map
	dielZMap	Boolean to use dielectric map argument
	useKappaMap	External dielectric map
	kappaMap	Boolean to use kappa map argument
	useChargeMap	External kappa map
	chargeMap	Boolean to use charge map argument External charge map

References bcCalc(), sVpmgp::bcfl, BCFL_FOCUS, sVpmg::chargeMap, sVpmg::chargeMeth, sVpmg::dielXMap, sVpmg::dielYMap, sVpmg::dielZMap, sVpmg::epsx, sVpmg::epsy, sVpmg::epsz, fillcoCharge(), fillcoCoef(), sVpmg::filled, sVpmgp::hx, sVpmgp::hy, sVpmgp::hzed, sVpmg::kappa, sVpmg::kappaMap, sVpmgp::nx, sVpmgp::ny, sVpmgp::nz, sVpmg::pbe, sVpmg::pmgp, sVpmg::rparm, sVpmg::splineWin, sVpmg::surfMeth, sVpmg::tcf, sVpmg::useChargeMap, sVpmg::useDielXMap, sVpmg::useDielYMap, sVpmg::useDielZMap, sVpmg::useKappaMap, Vpbe_getBulkIonicStrength(), Vpbe_getSoluteDiel(), Vpbe_getSolventDiel(), VPMGSMALL, VRC_FAILURE, VRC_SUCCESS, sVpmgp::xcent, sVpmg::xf, sVpmgp::xlen, sVpmgp::xmax, sVpmgp::xmin, sVpmgp::ycent, sVpmg::yf, sVpmgp::ylen, sVpmgp::ymax, sVpmgp::ymin, sVpmgp::zcent, sVpmg::zf, sVpmgp::zlen, sVpmgp::zmax, and sVpmgp::zmin.

Referenced by initMG().

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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.

Author:: Nathan Baker

Note:

Using the force evaluation methods of Im et al (Roux group), Comput Phys Commun, 111, 59--75 (1998). However, this gives the whole (self-interactions included) force -- reaction field forces will have to be calculated at higher level.
No contributions are made from higher levels of focusing.

Returns:: 1 if successful, 0 otherwise

Parameters:

	force	Vpmg object
	atomID	3*sizeof(double) space to hold the force in units of k_B T/AA
	srfm	Valist ID of desired atom
	chgm	Surface discretization method Charge discretization method

References Vpmg_dbForce(), Vpmg_ibForce(), and Vpmg_qfForce().

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void Vpmg_ibDirectPolForce	(	Vpmg *	thee,
		Vgrid *	perm,
		Vgrid *	induced,
		int	atomID,
		double	force[3]
	)

Ionic boundary direct polarization force between permanent multipoles and induced dipoles, which are induced by the sum of the permanent intramolecular field and the permanent reaction field.

Author:: Michael Schnieders

Parameters:

	perm	Vpmg object
	induced	Permanent multipole potential
	atomID	Induced dipole potential
	force	Atom index (returned) force

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.

Author:: Nathan Baker

Note:

Using the force evaluation methods of Im et al (Roux group), Comput Phys Commun, 111, 59--75 (1998). However, this gives the whole (self-interactions included) force -- reaction field forces will have to be calculated at higher level.
No contributions are made from higher levels of focusing.

Returns:: 1 if successful, 0 otherwise

Parameters:

	force	Vpmg object
	atomID	3*sizeof(double) space to hold the boundary force in units of k_B T/AA
	srfm	Valist ID of desired atom Surface discretization method

References sVpbe::acc, sVpbe::alist, sVpmgp::bcfl, BCFL_FOCUS, sVpmgp::hx, sVpmgp::hy, sVpmgp::hzed, sVpmg::kappa, MAXION, sVpmgp::nonlin, sVpmgp::nx, sVpmgp::ny, sVpmgp::nz, sVatom::partID, sVpmg::pbe, sVpmg::pmgp, sVpmg::splineWin, sVpmg::u, Valist_getAtom(), Vatom_getPosition(), Vatom_getRadius(), Vcap_exp(), Vpbe_getBulkIonicStrength(), Vpbe_getIons(), Vpbe_getMaxIonRadius(), Vpbe_getZkappa2(), Vpbe_getZmagic(), Vpmg_splineSelect(), VPMGSMALL, VSM_SPLINE, VSM_SPLINE3, VSM_SPLINE4, sVpmgp::xlen, sVpmgp::xmax, sVpmgp::xmin, sVpmgp::ylen, sVpmgp::ymax, sVpmgp::ymin, sVpmgp::zlen, sVpmgp::zmax, and sVpmgp::zmin.

Referenced by forceMG(), and Vpmg_force().

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void Vpmg_ibMutualPolForce	(	Vpmg *	thee,
		Vgrid *	induced,
		Vgrid *	nlInduced,
		int	atomID,
		double	force[3]
	)

Ionic boundary mutual polarization force for induced dipoles based on 5th order B-Splines. This force arises due to self-consistent convergence of the solute induced dipoles and reaction field.

Author:: Michael Schnieders

Parameters:

	induced	Vpmg object
	nlInduced	Induced dipole potential
	atomID	Non-local induced dipole potential
	force	Atom index (returned) force

void Vpmg_ibNLDirectPolForce	(	Vpmg *	thee,
		Vgrid *	perm,
		Vgrid *	nlInduced,
		int	atomID,
		double	force[3]
	)

Ionic boundary direct polarization force between permanent multipoles and non-local induced dipoles based on 5th order Keep in mind that the "non-local" induced dipooles are just a mathematical quantity that result from differentiation of the AMOEBA polarization energy.

Author:: Michael Schnieders

Parameters:

	perm	Vpmg object
	nlInduced	Permanent multipole potential
	atomID	Induced dipole potential
	force	Atom index (returned) force

void Vpmg_ibPermanentMultipoleForce	(	Vpmg *	thee,
		int	atomID,
		double	force[3]
	)

Compute the ionic boundary force for permanent multipoles.

Author:: Michael Schnieders

Parameters:

	atomID	Vpmg object
	force	Atom index (returned) force

unsigned long int Vpmg_memChk ( Vpmg * thee )

Return the memory used by this structure (and its contents) in bytes.

Author:: Nathan Baker

Returns:: The memory used by this structure and its contents in bytes

Parameters:

thee

Object for memory check

References sVpmg::vmem.

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.

Author:: Nathan Baker

Bug:: Can this path variable be replaced with a Vio socket?

Parameters:

	path	Vpmg object
	title	The file to which the matrix is to be written
	mxtype	The title of the matrix
	flag	The type of REAL-valued matrix, a 3-character string of the form "R_A" where the '_' can be one of: S: symmetric matrix U: unsymmetric matrix H: Hermitian matrix Z: skew-symmetric matrix R: rectangular matrix The operator to compress: 0: Poisson operator 1: Linearization of the full Poisson-Boltzmann operator around the current solution

References sVpmg::iparm, sVpmg::iwork, sVpmgp::nx, sVpmgp::ny, sVpmgp::nz, sVpmg::pmgp, sVpmg::rparm, sVpmg::rwork, and sVpmg::vmem.

Referenced by writematMG().

double Vpmg_qfAtomEnergy	(	Vpmg *	thee,
		Vatom *	atom
	)

Get the per-atom "fixed charge" contribution to the electrostatic energy.

Using the solution at the finest mesh level, get the electrostatic energy due to the interaction of the fixed charges with the potential:

$G = q u(r),$

where q$ is the charge and r is the location of the atom of interest. The result is returned in units of k_B T. Clearly, no self-interaction terms are removed. A factor a 1/2 has to be included to convert this to a real energy.

Author:: Nathan Baker

Note:: The value of this observable may be modified by setting restrictions on the subdomain over which it is calculated. Such limits can be set via Vpmg_setPart and are generally useful for parallel runs.

Returns:: The fixed charge electrostatic energy in units of k_B T.

Parameters:

atom

The Vpmg object The atom for energy calculations

References sVpmgp::bcfl, BCFL_FOCUS, sVpmgp::hx, sVpmgp::hy, sVpmgp::hzed, sVpmgp::nx, sVpmgp::ny, sVpmgp::nz, sVatom::partID, sVpmg::pmgp, sVpmg::u, Vatom_getCharge(), Vatom_getPosition(), sVpmg::xf, sVpmg::yf, and sVpmg::zf.

Referenced by energyMG(), and storeAtomEnergy().

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void Vpmg_qfDirectPolForce	(	Vpmg *	thee,
		Vgrid *	perm,
		Vgrid *	induced,
		int	atomID,
		double	force[3],
		double	torque[3]
	)

q-Phi direct polarization force between permanent multipoles and induced dipoles, which are induced by the sum of the permanent intramolecular field and the permanent reaction field.

Author:: Michael Schnieders

Parameters:

	perm	Vpmg object
	induced	Permanent multipole potential
	atomID	Induced dipole potential
	force	Atom index
	torque	(returned) force (returned) torque

double Vpmg_qfEnergy	(	Vpmg *	thee,
		int	extFlag
	)

Get the "fixed charge" contribution to the electrostatic energy.

Using the solution at the finest mesh level, get the electrostatic energy due to the interaction of the fixed charges with the potential:

$G = \sum_i q_i u(r_i)$

and return the result in units of k_B T. Clearly, no self-interaction terms are removed. A factor a 1/2 has to be included to convert this to a real energy.

Author:: Nathan Baker

Note:: The value of this observable may be modified by setting restrictions on the subdomain over which it is calculated. Such limits can be set via Vpmg_setPart and are generally useful for parallel runs.

Returns:: The fixed charge electrostatic energy in units of k_B T.

Parameters:

extFlag

Vpmg object If this was a focused calculation, include (1 -- for serial calculations) or ignore (0 -- for parallel calculations) energy contributions from outside the focusing domain

References sVpmg::chargeMeth, sVpmg::useChargeMap, VCM_BSPL2, Vpmg_qfEnergyPoint(), and Vpmg_qfEnergyVolume().

Referenced by energyMG(), extEnergy(), and Vpmg_energy().

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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.

Author:: Nathan Baker

Note:

Using the force evaluation methods of Im et al (Roux group), Comput Phys Commun, 111, 59--75 (1998). However, this gives the whole (self-interactions included) force -- reaction field forces will have to be calculated at higher level.
No contributions are made from higher levels of focusing.

Returns:: 1 if sucessful, 0 otherwise

Parameters:

	force	Vpmg object
	atomID	3*sizeof(double) space to hold the force in units of k_B T/A
	chgm	Valist ID of desired atom Charge discretization method

References qfForceSpline1(), qfForceSpline2(), qfForceSpline4(), VCM_BSPL2, VCM_BSPL4, and VCM_TRIL.

Referenced by forceMG(), and Vpmg_force().

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void Vpmg_qfMutualPolForce	(	Vpmg *	thee,
		Vgrid *	induced,
		Vgrid *	nlInduced,
		int	atomID,
		double	force[3]
	)

Mutual polarization force for induced dipoles based on 5th order B-Splines. This force arises due to self-consistent convergence of the solute induced dipoles and reaction field.

Author:: Michael Schnieders

Parameters:

	induced	Vpmg object
	nlInduced	Induced dipole potential
	atomID	Non-local induced dipole potential
	force	Atom index (returned) force

void Vpmg_qfNLDirectPolForce	(	Vpmg *	thee,
		Vgrid *	perm,
		Vgrid *	nlInduced,
		int	atomID,
		double	force[3],
		double	torque[3]
	)

q-Phi direct polarization force between permanent multipoles and non-local induced dipoles based on 5th Order B-Splines. Keep in mind that the "non-local" induced dipooles are just a mathematical quantity that result from differentiation of the AMOEBA polarization energy.

Author:: Michael Schnieders

Parameters:

	perm	Vpmg object
	nlInduced	Permanent multipole potential
	atomID	Non-local induced dipole potential
	force	Atom index
	torque	(returned) force (returned) torque

double Vpmg_qfPermanentMultipoleEnergy	(	Vpmg *	thee,
		int	atomID
	)

Computes the permanent multipole electrostatic hydration energy (the polarization component of the hydration energy currently computed in TINKER).

Author:: Michael Schnieders

Returns:: The permanent multipole electrostatic hydration energy

Parameters:

atomID

Vpmg object Atom index

void Vpmg_qfPermanentMultipoleForce	(	Vpmg *	thee,
		int	atomID,
		double	force[3],
		double	torque[3]
	)

Computes the q-Phi Force for permanent multipoles based on 5th order B-splines.

Author:: Michael Schnieders

Parameters:

	atomID	Vpmg object
	force	Atom index
	torque	(returned) force (returned) torque

double Vpmg_qmEnergy	(	Vpmg *	thee,
		int	extFlag
	)

Get the "mobile charge" contribution to the electrostatic energy.

Using the solution at the finest mesh level, get the electrostatic energy due to the interaction of the mobile charges with the potential:

$G = \frac{1}{4 I_s} \sum_i c_i q_i^2 \int \kappa^2(x) e^{-q_i u(x)} dx$

for the NPBE and

$G = \frac{1}{2} \int \overline{\kappa}^2(x) u^2(x) dx$

for the LPBE. Here i denotes the counterion species, I_s is the bulk ionic strength, kappa^2(x) is the modified Debye-Huckel parameter, c_i is the concentration of species i, q_i is the charge of species i, and u(x) is the dimensionless electrostatic potential. The energy is scaled to units of k_b T.

Author:: Nathan Baker

Note:: The value of this observable may be modified by setting restrictions on the subdomain over which it is calculated. Such limits can be set via Vpmg_setPart and are generally useful for parallel runs.

Returns:: The mobile charge electrostatic energy in units of k_B T.

Parameters:

extFlag

Vpmg object If this was a focused calculation, include (1 -- for serial calculations) or ignore (0 -- for parallel calculations) energy contributions from outside the focusing domain

References sVpbe::ipkey, IPKEY_SMPBE, sVpmg::pbe, and Vpmg_qmEnergySMPBE().

Referenced by energyMG(), extEnergy(), and Vpmg_energy().

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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.

Author:: Nathan Baker

Parameters:

	lowerCorner	Vpmg object
	upperCorner	Partition lower corner
	bflags	Partition upper corner Booleans indicating whether a particular processor is on the boundary with another partition. 0 if the face is not bounded (next to) another partition, and 1 otherwise.

References sVpbe::alist, 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, VPMGSMALL, sVpmgp::xcent, sVpmgp::ycent, and sVpmgp::zcent.

Referenced by extEnergy(), and setPartMG().

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int Vpmg_solve ( Vpmg * thee )

Solve the PBE using PMG.

Author:: Nathan Baker

Returns:: 1 if successful, 0 otherwise

Parameters:

thee

Vpmg object

References sVpmg::a1cf, sVpmg::a2cf, sVpmg::a3cf, sVpmg::ccf, sVpmg::charge, sVpmg::epsx, sVpmg::epsy, sVpmg::epsz, sVpmg::fcf, sVpmg::filled, sVpmg::gxcf, sVpmg::gycf, sVpmg::gzcf, sVpmg::iparm, sVpmg::iwork, sVpmg::kappa, sVpmgp::key, sVpmgp::meth, sVpmgp::nx, sVpmgp::ny, sVpmgp::nz, sVpmg::pbe, sVpmg::pmgp, sVpmg::rparm, sVpmg::rwork, sVpmg::tcf, sVpmg::u, Vpbe_getZkappa2(), VPMGSMALL, sVpmg::xf, sVpmg::yf, and sVpmg::zf.

Referenced by solveMG().

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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.

Author:: Nathan Baker

Returns:: 1 if successful, 0 otherwise

Note:: This function is really only for testing purposes as the PMG multigrid solver can solve the homogeneous system much more quickly. Perhaps we should implement an FFT version at some point...

Parameters:

thee

Vpmg object

References sVpmg::charge, sVpmg::fcf, sVpmg::filled, sVpmg::gxcf, sVpmg::gycf, sVpmg::gzcf, sVpmgp::hx, sVpmgp::hy, sVpmgp::hzed, sVpmgp::nx, sVpmgp::ny, sVpmgp::nz, sVpmg::pbe, sVpmg::pmgp, sVpmg::tcf, sVpmg::u, Vpbe_getSolventDiel(), and zlapSolve().