energy
Class FDPoissonBoltzmann

java.lang.Object
  energy.FDPoissonBoltzmann

Direct Known Subclasses:

FDPoissonBoltzmann_Boundary, FDPoissonBoltzmann_ChargeGrid, FDPoissonBoltzmann_EpsGrid

public class FDPoissonBoltzmann

extends java.lang.Object

Field Summary

(package private) Particles	atoms
(package private) boolean	debug
protected double[]	epsCgrid epsCgrid[GPX*GPY*GPZ] stores the sum of the permittivities at the six faces plus @f$\varepsilon _{Solvent} \kappa ^2 h^2 @f$ times the number of solvent faces divided by six.
protected double[]	epsIgrid epsIgrid[GPX*GPY*GPZ] stores the permittivity surrounding each face of a gridpoint[I][J][K] shifted in direction I
protected double[]	epsJgrid epsJgrid[GPX*GPY*GPZ] stores the permittivity surrounding each face of a gridpoint[I][J][K] shifted in direction J
protected double[]	epsKgrid epsKgrid[GPX*GPY*GPZ] stores the permittivity surrounding each face of a gridpoint[I][J][K] shifted in direction K
protected static double	epssolute solute permittivity
protected static double	epssolvent solvent permittivity
(package private) static int	GPX number of grid points along X.
(package private) int	GPXGPY
(package private) int	GPXGPYGPZ
(package private) static int	GPY number of grid points along Y.
(package private) static int	GPZ number of grid points along Z.
protected static double	gridspacing gridspacing @f$ h @f$
protected static double[]	gridstart grid origin
(package private) boolean	havephi
(package private) FDPoissonBoltzmann_ICCG	iccg
protected static double	kappa
(package private) FDPoissonBoltzmann_Boundary	PBboundary
(package private) FDPoissonBoltzmann_ChargeGrid	PBcrgGrid
(package private) FDPoissonBoltzmann_EpsGrid	PBeps
protected double[]	phigrid phigrid[GPX*GPY*GPZ] will become the solution vector when solving for the electrostatic potential
protected double[]	rhogrid rhogrid[GPX*GPY*GPZ] stores the charges assigned to each grid point divided by the gridspacing @f$ h @f$
(package private) SimSystem	sys

Constructor Summary

FDPoissonBoltzmann()
The PoissonBoltzmann default class constructor.

FDPoissonBoltzmann(FDPoissonBoltzmann_Parameters parameters, boolean debug)

FDPoissonBoltzmann(Particles atoms, SimSystem sys, boolean debug)

FDPoissonBoltzmann(Particles atoms, SimSystem sys, FDPoissonBoltzmann_Parameters parameters, boolean debug)
The PoissonBoltzmann class constructor.

Method Summary

void	addParticles(Particles atoms, SimSystem sys)
double[]	dGelec(boolean green) public boolean dGelec calculates the electrostatic free energy [G] for the system from the electrostatic potential (phigrid) calculated above.
private double	getdG()
double[]	getgridstart()
double[]	getpotential()
(package private) void	gridcheck() static final void gridcheck checks whether any atom exceeds the grid
(package private) int	index(int x, int y, int z) static final int index converts 3D to 1D array index.
void	setpermittivity(double solute, double solvent) static setpermittivity.
void	setupGrid(FDPoissonBoltzmann_Parameters parameters, boolean newphi) public void method setupGrid sets up a grid around the solute particles using the center of geometry as the grid center, along with the given gridspacing, ionic strength, solute/solven permittivities and the number of gridpoints along X,Y and Z.
boolean	solveforpotential(int maxits, double acceptance) public boolean solveforpotential solves the linearized Poisson-Boltzmann equation for the electrostatic potential phigrid using the incomplete cholesky conjugate gradient algorithm

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

atoms

Particles atoms

sys

SimSystem sys

GPX

static int GPX

number of grid points along X.

GPY

static int GPY

number of grid points along Y.

GPZ

static int GPZ

number of grid points along Z.

GPXGPY

final int GPXGPY

GPXGPYGPZ

final int GPXGPYGPZ

rhogrid

protected double[] rhogrid

rhogrid[GPX*GPY*GPZ] stores the charges assigned to each grid point divided by the gridspacing @f$ h @f$

epsIgrid

protected double[] epsIgrid

epsIgrid[GPX*GPY*GPZ] stores the permittivity surrounding each face of a gridpoint[I][J][K] shifted in direction I

epsJgrid

protected double[] epsJgrid

epsJgrid[GPX*GPY*GPZ] stores the permittivity surrounding each face of a gridpoint[I][J][K] shifted in direction J

epsKgrid

protected double[] epsKgrid

epsKgrid[GPX*GPY*GPZ] stores the permittivity surrounding each face of a gridpoint[I][J][K] shifted in direction K

epsCgrid

protected double[] epsCgrid

epsCgrid[GPX*GPY*GPZ] stores the sum of the permittivities at the six faces plus @f$\varepsilon _{Solvent} \kappa ^2 h^2 @f$ times the number of solvent faces divided by six. This corresponds to the diagonal elements of the coefficient matrix A.

phigrid

protected double[] phigrid

phigrid[GPX*GPY*GPZ] will become the solution vector when solving for the electrostatic potential

gridspacing

protected static double gridspacing

gridspacing @f$ h @f$

epssolute

protected static double epssolute

solute permittivity

epssolvent

protected static double epssolvent

solvent permittivity

gridstart

protected static double[] gridstart

grid origin

kappa

protected static double kappa

PBboundary

FDPoissonBoltzmann_Boundary PBboundary

PBcrgGrid

FDPoissonBoltzmann_ChargeGrid PBcrgGrid

PBeps

FDPoissonBoltzmann_EpsGrid PBeps

iccg

FDPoissonBoltzmann_ICCG iccg

debug

final boolean debug

havephi

boolean havephi

Constructor Detail

FDPoissonBoltzmann

public FDPoissonBoltzmann()

The PoissonBoltzmann default class constructor.

FDPoissonBoltzmann

public FDPoissonBoltzmann(Particles atoms,
                          SimSystem sys,
                          boolean debug)

FDPoissonBoltzmann

public FDPoissonBoltzmann(FDPoissonBoltzmann_Parameters parameters,
                          boolean debug)

FDPoissonBoltzmann

public FDPoissonBoltzmann(Particles atoms,
                          SimSystem sys,
                          FDPoissonBoltzmann_Parameters parameters,
                          boolean debug)

The PoissonBoltzmann class constructor.

Parameters:

atoms - Particles in the system

sys - the SimSystem to be used

Method Detail

addParticles

public void addParticles(Particles atoms,
                         SimSystem sys)

setupGrid

public void setupGrid(FDPoissonBoltzmann_Parameters parameters,
                      boolean newphi)

public void method setupGrid sets up a grid around the solute particles using the center of geometry as the grid center, along with the given gridspacing, ionic strength, solute/solven permittivities and the number of gridpoints along X,Y and Z.

See Also:

PositionUtils, FDPoissonBoltzmann_Boundary, FDPoissonBoltzmann_ChargeGrid, FDPoissonBoltzmann_EpsGrid

solveforpotential

public boolean solveforpotential(int maxits,
                                 double acceptance)

public boolean solveforpotential solves the linearized Poisson-Boltzmann equation for the electrostatic potential phigrid using the incomplete cholesky conjugate gradient algorithm

Parameters:

maxits - maximum number of iterations

acceptance - acceptance criterion for the norm of the residual

See Also:

jpb_solver_Math

dGelec

public double[] dGelec(boolean green)

public boolean dGelec calculates the electrostatic free energy [G] for the system from the electrostatic potential (phigrid) calculated above. It is possible to obtain an estimate of the electrostatic solvation free energy difference dGsolv by substracting the finite-difference Coulombic and self-energy correction in a medium of uniform dielectric permittivity (Green functions correction).

Parameters:

green - boolean to determine whether Green functions correction is applied or not.

See Also:

FDPoissonBoltzmann_GreenFunction

getdG

private final double getdG()

gridcheck

final void gridcheck()

static final void gridcheck checks whether any atom exceeds the grid

index

final int index(int x,
                int y,
                int z)

static final int index converts 3D to 1D array index.

Parameters:

x - index along x

y - index along y

z - index along z

setpermittivity

public void setpermittivity(double solute,
                            double solvent)

static setpermittivity.

Parameters:

solute - solute permittivity

solvent - solvent permittivity

getpotential

public double[] getpotential()

getgridstart

public double[] getgridstart()