Nonlocal SaLSA [37] solvation model implementation (electrostatic part) More...

#include <SaLSA.h>

Inheritance diagram for SaLSA:

Public Member Functions
	SaLSA (const Everything &e, const FluidSolverParams &fsp)
	Parameters same as createFluidSolver()

bool	prefersGummel () const
	Specify whether fluid prefers a gummel loop (true) or is minimized each time (false)

ScalarFieldTilde	chi (const ScalarFieldTilde &) const
	Apply the non-local chi (i.e. compute induced charge density given a potential)

ScalarFieldTilde	hessian (const ScalarFieldTilde &) const
	Implements LinearSolvable::hessian for the non-local poisson-like equation.

ScalarFieldTilde	precondition (const ScalarFieldTilde &) const
	Implements a modified inverse kinetic preconditioner.

double	sync (double x) const
	All processes minimize together; make sure scalars are in sync to round-off error.

void	minimizeFluid ()
	Converge using linear conjugate gradients.

void	loadState (const char *filename)
	Load state from file.

void	saveState (const char *filename) const
	Save state to file.

void	dumpDensities (const char *filenamePattern) const
	dump cavity shape functions

Public Member Functions inherited from PCM
	PCM (const Everything &e, const FluidSolverParams &fsp)

void	dumpDebug (const char *filenamePattern) const
	generate fluidDebug text file with common info to all PCMs

Public Member Functions inherited from FluidSolver
	FluidSolver (const Everything &e, const FluidSolverParams &fsp)
	Any non-electrostatic contributions to A_rhoExplicitTilde (removed from dumped d_fluid / d_tot) More...

double	ionWidthMuCorrection () const
	correction to electron chemical potential due to finite ion width in fluid interaction

bool	useGummel () const

void	set (const ScalarFieldTilde &rhoExplicitTilde, const ScalarFieldTilde &nCavityTilde)

double	get_Adiel_and_grad (ScalarFieldTilde Adiel_rhoExplicitTilde=0, ScalarFieldTilde Adiel_nCavityTilde=0, IonicGradient extraForces=0, matrix3<> Adiel_RRT=0) const

void	getSusceptibility (const std::vector< complex > &omega, std::vector< SusceptibilityTerm > &susceptibility, ScalarFieldTildeArray &sTilde, bool elecOnly) const
	Get susceptibility for a list of specified (complex) frequencies.

virtual double	bulkPotential ()

Public Member Functions inherited from LinearSolvable< ScalarFieldTilde >
int	solve (const ScalarFieldTilde &rhs, const MinimizeParams &params)

Protected Member Functions
void	set_internal (const ScalarFieldTilde &rhoExplicitTilde, const ScalarFieldTilde &nCavityTilde)
	Fluid-dependent implementation of set()

double	get_Adiel_and_grad_internal (ScalarFieldTilde &grad_rhoExplicitTilde, ScalarFieldTilde &grad_nCavityTilde, IonicGradient extraForces, matrix3<> Adiel_RRT) const
	Fluid-dependent implementation of get_Adiel_and_grad()

void	getSusceptibility_internal (const std::vector< complex > &omega, std::vector< SusceptibilityTerm > &susceptibility, ScalarFieldArray &sArr, bool elecOnly) const
	Fluid-dependent implementation of getSusceptibility()

Protected Member Functions inherited from PCM
virtual void	printDebug (FILE *fp) const
	over-ride to get extra PCM-specific output in fluidDebug text file

void	updateCavity ()
	update shape function(s) from nCavity, and energies dependent upon shape alone

void	propagateCavityGradients (const ScalarFieldArray &A_shape, ScalarField &A_nCavity, ScalarFieldTilde &A_rhoExplicitTilde, IonicGradient forces, matrix3<> Adiel_RRT) const

void	accumExtraForces (IonicGradient *forces, const ScalarFieldTilde &A_nCavityTilde) const
	Accumulate extra fluid forces (vdw and full-core forces, when applicable)

ScalarFieldTilde	getFullCore () const
	get full core correction for PCM variants that need them

Additional Inherited Members
Public Attributes inherited from FluidSolver
const Everything &	e

const GridInfo &	gInfo

const FluidSolverParams &	fsp

double	epsBulk

double	epsInf
	bulk dielectric constants of fluid

double	k2factor
	prefactor to screening term (0 => no ionic screening)

std::vector< std::vector< vector3<> > >	atpos

ScalarFieldTilde	A_rhoNonES
	atomic positions per species in the relevant coordinate system (depending on embedding option)

Public Attributes inherited from LinearSolvable< ScalarFieldTilde >
ScalarFieldTilde	state
	the location of the minimum, obtained by solving hessian * state == rhs

Static Protected Member Functions inherited from PCM
static ScalarFieldTilde	coulomb (const ScalarFieldTilde &rho)

static matrix3	coulombStress (const ScalarFieldTilde &X, const ScalarFieldTilde &Y)

Protected Attributes inherited from PCM
EnergyComponents	Adiel
	PCM energy components.

ScalarFieldTilde	rhoExplicitTilde
	Charge density of explicit (electronic) system.

ScalarField	nCavity

ScalarField	tauCavity

ScalarField	nCavityEx [2]
	Cavity determining electron density (or product for SaLSA, or KE density for SG14tauVW, and expanded electron densities for the SGA13 variant)

ScalarFieldArray	shape
	Electrostatic cavity shape function. Second component, if any, is separate ionic cavity.

ScalarField	shapeVdw
	Separate cavitation/dispersion shape function for the SGA13 variant.

std::vector< RadialFunctionG >	Sf
	spherically-averaged structure factors for each solvent site

std::vector< int >	atomicNumbers
	atomic number for each solvent site (for dispersion interactions)

Detailed Description

Nonlocal SaLSA [37] solvation model implementation (electrostatic part)

The documentation for this class was generated from the following file:

fluid/SaLSA.h

Public Member Functions

Protected Member Functions

Additional Inherited Members

Detailed Description