Package ffx.potential.nonbonded

Class ReciprocalSpace

java.lang.Object

ffx.potential.nonbonded.ReciprocalSpace

public class ReciprocalSpace
extends Object

The Reciprocal Space class computes the reciprocal space contribution to ParticleMeshEwald for the AMOEBA force field.

1. Assignment of polarizable multipole charge density to the 3D grid, via b-Splines, is parallelized using a spatial decomposition.
2. The convolution depends on methods of the Real3DParallel and Complex3DParallel classes.
3. Finally, the electric potential and its gradients are collected, in parallel, off the grid using b-Splines.

Since:

1.0

Author:

Michael J. Schnieders

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
class	ReciprocalSpace.BSplineRegion	The class computes b-Splines that are used to spline multipoles and induced dipoles onto the PME grid.
static enum	ReciprocalSpace.GridMethod

Constructor Summary

Constructors

Constructor	Description
ReciprocalSpace(ParticleMeshEwald particleMeshEwald, Crystal crystal, ForceField forceField, Atom[] atoms, double aewald, ParallelTeam fftTeam, ParallelTeam parallelTeam)	Reciprocal Space PME contribution.

Method Summary

Modifier and Type	Method	Description
void	cartToFracInducedDipole(double[] inducedDipole, double[] inducedDipoleCR, double[] fracInducedDipole, double[] fracInducedDipoleCR)	cartToFracInducedDipoles
void	computeBSplines()	computeBSplines
void	computeInducedPhi(double[][] cartInducedDipolePhi, double[][] cartInducedDipoleCRPhi, double[][] fracInducedDipolePhi, double[][] fracInducedDipoleCRPhi)	computeInducedPhi
void	computePermanentPhi(double[][] cartPermanentPhi, double[][] fracPermanentPhi)	Compute the potential Phi and its derivatives for all atoms.
int	getXDim()	getXDim
int	getYDim()	getYDim
int	getZDim()	getZDim
void	initTimings()	initTimings.
void	performConvolution()	Compute the reciprocal space field using a convolution.
void	printTimings()	printTimings.
void	setAtoms(Atom[] atoms)	Setter for the field atoms.
void	setCrystal(Crystal crystal)	Setter for the field crystal.
void	splineInducedDipoles(double[][][] inducedDipole, double[][][] inducedDipoleCR, boolean[] use)	Place the induced dipoles onto the FFT grid for the atoms in use.
void	splinePermanentMultipoles(double[][][] globalMultipoles, double[][][] fracMultipoles, boolean[] use)	Use b-Splines to place the permanent multipoles onto the FFT grid for the atoms in use.
void	toFractionalDipole(double[] gd, double[] fd)	Convert a dipole in the global frame into a factional dipole.

Methods inherited from class java.lang.Object

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

Constructor Details

ReciprocalSpace

public ReciprocalSpace(ParticleMeshEwald particleMeshEwald,
 Crystal crystal,
 ForceField forceField,
 Atom[] atoms,
 double aewald,
 ParallelTeam fftTeam,
 ParallelTeam parallelTeam)

Reciprocal Space PME contribution.

Parameters:

particleMeshEwald - a ParticleMeshEwald object.

crystal - a Crystal object.

forceField - a ForceField object.

atoms - an array of Atom objects.

aewald - the Ewald parameter.

fftTeam - a ParallelTeam object.

parallelTeam - a ParallelTeam object.

Method Details

cartToFracInducedDipole

public void cartToFracInducedDipole(double[] inducedDipole,
 double[] inducedDipoleCR,
 double[] fracInducedDipole,
 double[] fracInducedDipoleCR)

cartToFracInducedDipoles

Parameters:

inducedDipole - Input Cartesian induced dipole.

inducedDipoleCR - Input Cartesian induced dipole CR.

fracInducedDipole - Output fractional induced dipole.

fracInducedDipoleCR - Output fractional induced dipole CR.

computeBSplines

public void computeBSplines()

computeBSplines

computeInducedPhi

public void computeInducedPhi(double[][] cartInducedDipolePhi,
 double[][] cartInducedDipoleCRPhi,
 double[][] fracInducedDipolePhi,
 double[][] fracInducedDipoleCRPhi)

computeInducedPhi

Parameters:

cartInducedDipolePhi - an array of double.

cartInducedDipoleCRPhi - an array of double.

fracInducedDipolePhi - an array of double.

fracInducedDipoleCRPhi - an array of double.

computePermanentPhi

public void computePermanentPhi(double[][] cartPermanentPhi,
 double[][] fracPermanentPhi)

Compute the potential Phi and its derivatives for all atoms.

Parameters:

cartPermanentPhi - an array of double.

fracPermanentPhi - an array of double.

getXDim

public int getXDim()

getXDim

Returns:

the X dimension of the FFT grid.

getYDim

public int getYDim()

getYDim

Returns:

the Y dimension of the FFT grid.

getZDim

public int getZDim()

getZDim

Returns:

the Z dimension of the FFT grid.

performConvolution

public void performConvolution()

Compute the reciprocal space field using a convolution.

initTimings

public void initTimings()

initTimings.

printTimings

public void printTimings()

printTimings.

setAtoms

public void setAtoms(Atom[] atoms)

Setter for the field atoms.

Parameters:

atoms - an array of Atom objects.

setCrystal

public void setCrystal(Crystal crystal)

Setter for the field crystal.

Parameters:

crystal - a Crystal object.

splineInducedDipoles

public void splineInducedDipoles(double[][][] inducedDipole,
 double[][][] inducedDipoleCR,
 boolean[] use)

Place the induced dipoles onto the FFT grid for the atoms in use.

Parameters:

inducedDipole - Induced dipoles.

inducedDipoleCR - Chain rule term for induced dipole gradient.

use - The atoms in use.

splinePermanentMultipoles

public void splinePermanentMultipoles(double[][][] globalMultipoles,
 double[][][] fracMultipoles,
 boolean[] use)

Use b-Splines to place the permanent multipoles onto the FFT grid for the atoms in use.

Parameters:

globalMultipoles - an array of double.

fracMultipoles - an array of double.

use - an array of boolean.

toFractionalDipole

public void toFractionalDipole(double[] gd,
 double[] fd)

Convert a dipole in the global frame into a factional dipole.

Parameters:

gd - an array of

invalid reference

double

objects.

fd - an array of

invalid reference

double

objects.