NonlinearPCM Class Reference

Nonlinear solvation models: shared electrostatic part implementation. More...

#include <NonlinearPCM.h>

Inheritance diagram for NonlinearPCM:

Public Member Functions
	NonlinearPCM (const Everything &e, const FluidSolverParams &params)
	See createFluidSolver()
bool	prefersGummel () const
	Specify whether fluid prefers a gummel loop (true) or is minimized each time (false)
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
void	minimizeFluid ()
	Converge using nonlinear conjugate gradients.
void	step (const ScalarFieldTilde &dir, double alpha)
	Move the state in parameter space along direction dir with scale alpha.
double	compute (ScalarFieldTilde *grad, ScalarFieldTilde *Kgrad)
	Returns the objective function at the current state and store the gradient in grad and preconditioned gradient in Kgrad, if non-null.
bool	report (int iter)
Public Member Functions inherited from PCM
	PCM (const Everything &e, const FluidSolverParams &fsp)
void	dumpDensities (const char *filenamePattern) const
	dump cavity shape functions
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 Minimizable< ScalarFieldTilde >
virtual void	constrain (ScalarFieldTilde &)
	Constrain search directions to the space of free directions for minimize.
virtual double	sync (double x) const
	Override to synchronize scalars over MPI processes (if the same minimization is happening in sync over many processes)
virtual double	safeStepSize (const ScalarFieldTilde &dir) const
	Override to return maximum safe step size along a given direction. Steps can be arbitrarily large by default.
double	minimize (const MinimizeParams &params)
	Minimize this objective function with algorithm controlled by params and return the minimized value.
void	fdTest (const MinimizeParams &params)

Public Attributes
ScalarFieldTilde	phiTot
	State of the solver = total electrostatic potential.
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)

Protected Member Functions
void	set_internal (const ScalarFieldTilde &rhoExplicitTilde, const ScalarFieldTilde &nCavityTilde)
	Fluid-dependent implementation of set()
double	get_Adiel_and_grad_internal (ScalarFieldTilde &Adiel_rhoExplicitTilde, ScalarFieldTilde &Adiel_nCavityTilde, IonicGradient *extraForces, matrix3<> *Adiel_RRT) const
	Fluid-dependent implementation of get_Adiel_and_grad()
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
Protected Member Functions inherited from FluidSolver
virtual void	getSusceptibility_internal (const std::vector< complex > &omega, std::vector< SusceptibilityTerm > &susceptibility, ScalarFieldArray &sArr, bool elecOnly) const
	Fluid-dependent implementation of getSusceptibility()

Additional Inherited Members
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

Nonlinear solvation models: shared electrostatic part implementation.

Member Function Documentation

dumpDensities()

void NonlinearPCM::dumpDensities ( const char *  filenamePattern ) const

virtual

Dump relevant fluid densities (eg. NO and NH) to file(s) the provided pattern will have a single s which may be substituted Fluid solver implementations may override to dump fluid densities, no dumping by default

Reimplemented from FluidSolver.

report()

bool NonlinearPCM::report ( int  iter )

virtual

Override for optional processing/reporting after each/every few iterations It should return whether the state was modified

Reimplemented from Minimizable< ScalarFieldTilde >.

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

• fluid/NonlinearPCM.h