Package ffx.numerics.multipole

Class PolarizableMultipole

java.lang.Object

ffx.numerics.multipole.PolarizableMultipole

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

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
final void	applyMasks(double scaleInduction, double scaleEnergy)	Compute the scaled and averaged induced dipole.
void	clearInducedDipoles()	Clear the induced dipoles.
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 double q

Partial charge.

dx

protected double dx

Dipole x-component.

dy

protected double dy

Dipole y-component.

dz

protected double dz

Dipole z-component.

qxx

protected double qxx

Quadrupole xx-component multiplied by 1/3.

qyy

protected double qyy

Quadrupole yy-component multiplied by 1/3.

qzz

protected double qzz

Quadrupole zz-component multiplied by 1/3.

qxy

protected double qxy

Quadrupole xy-component multiplied by 2/3.

qxz

protected double qxz

Quadrupole xz-component multiplied by 2/3.

qyz

protected double qyz

Quadrupole xz-component multiplied by 2/3.

ux

protected double ux

Induced dipole x-component.

uy

protected double uy

Induced dipole y-component.

uz

protected double uz

Induced dipole z-component.

px

protected double px

Induced dipole chain rule x-component.

py

protected double py

Induced dipole chain rule y-component.

pz

protected double pz

Induced dipole chain rule z-component.

sx

protected double sx

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

sy

protected double sy

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

sz

protected double sz

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

Z

protected double Z

Constructor Details

PolarizableMultipole

public PolarizableMultipole()

PolarizableMultipole constructor with zero moments.

PolarizableMultipole

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

PolarizableMultipole constructor.

Parameters:

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

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

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

PolarizableMultipole

public PolarizableMultipole(double[] Q,
 double[] u,
 double[] uCR,
 double Z)

PolarizableMultipole constructor.

Parameters:

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

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

uCR - Induced dipole chain-rule 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 - Multipole Q[q, dx, dy, dz, qxx, qyy, qzz, qxy, qxz, qyz]

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

uCR - Induced dipole chain-rule 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]

clearInducedDipoles

public void clearInducedDipoles()

Clear the induced dipoles.

applyMasks

public final void applyMasks(double scaleInduction,
 double scaleEnergy)

Compute the scaled and averaged induced dipole.

Parameters:

scaleInduction - Induction mask scale factor.

scaleEnergy - Energy mask scale factor.