Package ffx.numerics.multipole

Class QIFrame

java.lang.Object

ffx.numerics.multipole.QIFrame

public class QIFrame
extends Object

The QIFrame class defines a quasi-internal frame between two atoms.

The Z-axis of the QI frame is defined as the vector between the two atoms. The X- and Y-axes are then defined to create a right-handed coordinate system.

A rotation matrix from the global frame to the QI frame is constructed, and vice versa. Using the rotation matrices, methods are provided to rotate vectors and multipoles between the two frames.

Since:

1.0

Author:

Michael J. Schnieders

Constructor Summary

Constructors

Constructor	Description
QIFrame()	QIFrame constructor
QIFrame(double[] r)	QIFrame constructor.
QIFrame(double dx, double dy, double dz)	QIFrame constructor.

Method Summary

Modifier and Type	Method	Description
void	rotateInducedDipoles(PolarizableMultipole m)	Rotate the induced dipoles components.
void	rotatePermanentMultipole(PolarizableMultipole m)	Rotate the permanent multipole.
void	rotatePolarizableMultipole(PolarizableMultipole m)	Rotate the permanent multipole and induced dipole.
void	setAndRotate(double[] r, PolarizableMultipole mI, PolarizableMultipole mK)	Update the QIFrame rotation matrix and rotate the multipoles.
void	setAndRotate(double dx, double dy, double dz, PolarizableMultipole mI, PolarizableMultipole mK)	Update the QIFrame rotation matrix and rotate the multipoles.
void	setQIVector(double[] r)	Update the QIFrame rotation matrix.
final void	setQIVector(double dx, double dy, double dz)	Update the QIFrame rotation matrix.
void	toGlobal(double[] v)	Rotate a vector in the QI frame into the global frame.

Methods inherited from class java.lang.Object

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

Constructor Details

QIFrame

public QIFrame()

QIFrame constructor

(dx = 0, dy = 0, dz = 1).

QIFrame

public QIFrame(double dx,
 double dy,
 double dz)

QIFrame constructor.

Parameters:

dx - Separation along the x-axis.

dy - Separation along the y-axis.

dz - Separation along the z-axis.

QIFrame

public QIFrame(double[] r)

QIFrame constructor.

Parameters:

r - Separation along each axis.

Method Details

setQIVector

public void setQIVector(double[] r)

Update the QIFrame rotation matrix.

Parameters:

r - Separation along each axis.

setQIVector

public final void setQIVector(double dx,
 double dy,
 double dz)

Update the QIFrame rotation matrix.

Parameters:

dx - Separation along the x-axis.

dy - Separation along the y-axis.

dz - Separation along the z-axis.

setAndRotate

public void setAndRotate(double[] r,
 PolarizableMultipole mI,
 PolarizableMultipole mK)

Update the QIFrame rotation matrix and rotate the multipoles.

Parameters:

r - Separation along each axis.

mI - PolarizableMultipole for site I.

mK - PolarizableMultipole for site K.

setAndRotate

public void setAndRotate(double dx,
 double dy,
 double dz,
 PolarizableMultipole mI,
 PolarizableMultipole mK)

Update the QIFrame rotation matrix and rotate the multipoles.

Parameters:

dx - Separation along the x-axis.

dy - Separation along the y-axis.

dz - Separation along the z-axis.

mI - PolarizableMultipole for site I.

mK - PolarizableMultipole for site K.

rotatePolarizableMultipole

public void rotatePolarizableMultipole(PolarizableMultipole m)

Rotate the permanent multipole and induced dipole.

Parameters:

m - PolarizableMultipole to rotate.

rotatePermanentMultipole

public void rotatePermanentMultipole(PolarizableMultipole m)

Rotate the permanent multipole.

Parameters:

m - PolarizableMultipole to rotate.

rotateInducedDipoles

public void rotateInducedDipoles(PolarizableMultipole m)

Rotate the induced dipoles components.

Parameters:

m - PolarizableMultipole to rotate.

toGlobal

public void toGlobal(double[] v)

Rotate a vector in the QI frame into the global frame.

Parameters:

v - The vector to rotate (in-place).