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.

double	operator() (const ScalarFieldMuEps &state, ScalarFieldMuEps &Adiel_state, ScalarFieldTilde Adiel_rhoExplicitTilde=0, ScalarFieldTilde Adiel_nCavityTilde=0, IonicGradient *forces=0) const
	Compute gradient and free energy (with optional outputs)

void	step (const ScalarFieldMuEps &dir, double alpha)
	Move the state in parameter space along direction dir with scale alpha.

double	compute (ScalarFieldMuEps grad, ScalarFieldMuEps Kgrad)
	Returns the objective function at the current state and store the gradient in grad and preconditioned gradient in Kgrad, if non-null.

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) const

virtual double	bulkPotential ()

Public Member Functions inherited from Minimizable< ScalarFieldMuEps >
virtual bool	report (int iter)

virtual void	constrain (ScalarFieldMuEps &)
	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 ScalarFieldMuEps &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 Member Functions inherited from Pulay< ScalarFieldTilde >
	Pulay (const PulayParams &pp)

double	minimize (double Eprev=+DBL_MAX, std::vector< string > extraNames=std::vector< string >(), std::vector< double > extraThresh=std::vector< double >())
	Minimize energy using a self-consistent iteration. More...

void	loadState (const char *filename)
	Load the state from a single binary file.

void	saveState (const char *filename) const
	Save the state to a single binary file.

void	clearState ()
	remove past variables and residuals

virtual double	sync (double x) const
	Override to synchronize scalars over MPI processes (if the same minimization is happening in sync over many processes)

Public Attributes
ScalarFieldMuEps	state
	State of the solver = ion chemical potentials and effective local electric field.

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) const
	Fluid-dependent implementation of get_Adiel_and_grad()

double	cycle (double dEprev, std::vector< double > &extraValues)
	Single cycle of the self-consistency loop. In each subsequent cycle, Pulay will try to zero the difference between getVariable() before and after the cycle. The implementation should only do the work of computing the updated variable; debug printing and I/O, if any, should occur in report() instead. More...

void	axpy (double alpha, const ScalarFieldTilde &X, ScalarFieldTilde &Y) const
	Scaled accumulate on variable.

double	dot (const ScalarFieldTilde &X, const ScalarFieldTilde &Y) const
	Euclidean dot product. Metric applied separately for efficiency.

size_t	variableSize () const
	Number of bytes per variable.

void	readVariable (ScalarFieldTilde &X, FILE *fp) const
	Read variable from stream.

void	writeVariable (const ScalarFieldTilde &X, FILE *fp) const

ScalarFieldTilde	getVariable () const
	Write variable to stream. More...

void	setVariable (const ScalarFieldTilde &)
	Set the state of system to specified variable.

ScalarFieldTilde	precondition (const ScalarFieldTilde &) const
	Apply preconditioner to variable/residual.

ScalarFieldTilde	applyMetric (const ScalarFieldTilde &) const
	Apply metric to variable/residual.

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) 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 Pulay< ScalarFieldTilde >
virtual void	report (int iter)
	Override to perform optional reporting.

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

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

double NonlinearPCM::cycle	(	double	dEprev,
		std::vector< double > &	extraValues
	)

protectedvirtual

Single cycle of the self-consistency loop. In each subsequent cycle, Pulay will try to zero the difference between getVariable() before and after the cycle. The implementation should only do the work of computing the updated variable; debug printing and I/O, if any, should occur in report() instead.

Parameters

dEprev	energy change at previous cycle, which may be used to adjust accuracy of any inner optimizations
extraValues	Specify the values of any extra convergence parameters specified in minimize()

Returns: Energy at end of cycle

Implements Pulay< ScalarFieldTilde >.

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.

ScalarFieldTilde NonlinearPCM::getVariable ( ) const

protectedvirtual

Write variable to stream.

Get the current variable from state of system

Implements Pulay< ScalarFieldTilde >.

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

fluid/NonlinearPCM.h

Public Member Functions

Public Attributes

Protected Member Functions

Additional Inherited Members

Detailed Description

Member Function Documentation