Package ffx.numerics.multipole

Class PolarizableMultipoleSIMD

java.lang.Object

ffx.numerics.multipole.PolarizableMultipoleSIMD

public class PolarizableMultipoleSIMD
extends Object

The PolarizableMultipole class defines a polarizable multipole.

Since:

1.0

Author:

Michael J. Schnieders

Field Summary

Fields

Modifier and Type	Field	Description
protected DoubleVector	dx	Dipole x-component.
protected DoubleVector	dy	Dipole y-component.
protected DoubleVector	dz	Dipole z-component.
protected DoubleVector	px	Induced dipole chain rule x-component.
protected DoubleVector	py	Induced dipole chain rule y-component.
protected DoubleVector	pz	Induced dipole chain rule z-component.
protected DoubleVector	q	Partial charge.
protected DoubleVector	qxx	Quadrupole xx-component multiplied by 1/3.
protected DoubleVector	qxy	Quadrupole xy-component multiplied by 2/3.
protected DoubleVector	qxz	Quadrupole xz-component multiplied by 2/3.
protected DoubleVector	qyy	Quadrupole yy-component multiplied by 1/3.
protected DoubleVector	qyz	Quadrupole xz-component multiplied by 2/3.
protected DoubleVector	qzz	Quadrupole zz-component multiplied by 1/3.
protected DoubleVector	sx	Averaged induced dipole + induced dipole chain-rule x-component: sx = 0.5 * (ux + px).
protected DoubleVector	sy	Averaged induced dipole + induced dipole chain-rule y-component: sy = 0.5 * (uy + py).
protected DoubleVector	sz	Averaged induced dipole + induced dipole chain-rule z-component: sz = 0.5 * (uz + pz).
protected DoubleVector	ux	Induced dipole x-component.
protected DoubleVector	uy	Induced dipole y-component.
protected DoubleVector	uz	Induced dipole z-component.

Constructor Summary

Constructors

Constructor	Description
PolarizableMultipoleSIMD()	PolarizableMultipole constructor with zero moments.
PolarizableMultipoleSIMD(double[][] Q, double[][] u, double[][] uCR)	PolarizableMultipole constructor.

Method Summary

Modifier and Type	Method	Description
final void	applyMasks(DoubleVector scaleInduction, DoubleVector scaleEnergy)	Compute the scaled and averaged induced dipole.
void	set(double[][] Q, double[][] u, double[][] uCR)	Set the permanent multipole.
final void	setInducedDipole(double[][] u, double[][] uCR)	Set the induced dipole.
final void	setPermanentMultipole(double[][] Q)	Set the permanent multipole.

Methods inherited from class java.lang.Object

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

Field Details

q

protected DoubleVector q

Partial charge.

dx

protected DoubleVector dx

Dipole x-component.

dy

protected DoubleVector dy

Dipole y-component.

dz

protected DoubleVector dz

Dipole z-component.

qxx

protected DoubleVector qxx

Quadrupole xx-component multiplied by 1/3.

qyy

protected DoubleVector qyy

Quadrupole yy-component multiplied by 1/3.

qzz

protected DoubleVector qzz

Quadrupole zz-component multiplied by 1/3.

qxy

protected DoubleVector qxy

Quadrupole xy-component multiplied by 2/3.

qxz

protected DoubleVector qxz

Quadrupole xz-component multiplied by 2/3.

qyz

protected DoubleVector qyz

Quadrupole xz-component multiplied by 2/3.

ux

protected DoubleVector ux

Induced dipole x-component.

uy

protected DoubleVector uy

Induced dipole y-component.

uz

protected DoubleVector uz

Induced dipole z-component.

px

protected DoubleVector px

Induced dipole chain rule x-component.

py

protected DoubleVector py

Induced dipole chain rule y-component.

pz

protected DoubleVector pz

Induced dipole chain rule z-component.

sx

protected DoubleVector sx

Averaged induced dipole + induced dipole chain-rule x-component: sx = 0.5 * (ux + px).

sy

protected DoubleVector sy

Averaged induced dipole + induced dipole chain-rule y-component: sy = 0.5 * (uy + py).

sz

protected DoubleVector sz

Averaged induced dipole + induced dipole chain-rule z-component: sz = 0.5 * (uz + pz).

Constructor Details

PolarizableMultipoleSIMD

public PolarizableMultipoleSIMD()

PolarizableMultipole constructor with zero moments.

PolarizableMultipoleSIMD

public PolarizableMultipoleSIMD(double[][] Q,
 double[][] u,
 double[][] uCR)

PolarizableMultipole constructor.

Parameters:

Q - Multipoles Q[q, dx, dy, dz, qxx, qyy, qzz, qxy, qxz, qyz]

u - Induced dipoles u[ux, uy, uz]

uCR - Induced dipole chain-rules uCR[ux, uy, uz]

Method Details

set

public void set(double[][] Q,
 double[][] u,
 double[][] uCR)

Set the permanent multipole.

Note that the quadrupole trace components are multiplied by 1/3 and the off-diagonal components are multiplied by 2/3.

Parameters:

Q - Multipoles Q[q, dx, dy, dz, qxx, qyy, qzz, qxy, qxz, qyz]

u - Induced dipoles u[ux, uy, uz]

uCR - Induced dipole chain-rules uCR[ux, uy, uz]

setPermanentMultipole

public final void setPermanentMultipole(double[][] Q)

Set the permanent multipole.

Note that the quadrupole trace components are multiplied by 1/3 and the off-diagonal components are multiplied by 2/3.

Parameters:

Q - Multipole Q[q, dx, dy, dz, qxx, qyy, qzz, qxy, qxz, qyz]

setInducedDipole

public final void setInducedDipole(double[][] u,
 double[][] uCR)

Set the induced dipole.

Parameters:

u - Induced dipole u[ux, uy, uz]

uCR - Induced dipole chain-rule uCR[ux, uy, uz]

applyMasks

public final void applyMasks(DoubleVector scaleInduction,
 DoubleVector scaleEnergy)

Compute the scaled and averaged induced dipole.

Parameters:

scaleInduction - Induction mask scale factor.

scaleEnergy - Energy mask scale factor.