Package etomica.models.nitrogen

Class FindPairMoleculeIndex

java.lang.Object

etomica.models.nitrogen.FindPairMoleculeIndex

public class FindPairMoleculeIndex
extends java.lang.Object

Class to identify the pair of molecules that are the same in terms of displacement vector and orientation This is done to speed up the construction of the Hessian Matrix such that we do not have to recalculate the block matrix that is the same. The index field is a 5-dimensional array index[0] is x-direction displacement index[1] is y-direction displacement index[2] is z-direction displacement index[3] is the orientation of moleculeA index[4] is the orientation of moleculeB The isNewPair array is to keep track whether the pair with index[][][][][] has been looped over or not.

Field Summary

Fields

Modifier and Type	Field	Description
protected CoordinateDefinitionNitrogen	coordinateDef
protected double	halfUnitCellLength
protected int[]	index
protected boolean[][][][][]	isNewPair
protected Vector	molAVec
protected Vector	molBVec
protected int	nCell
protected IMoleculePositionDefinition	positionDefinition
protected double[][][]	siteDisplacement
protected Vector	tempOrientA
protected Vector	tempOrientB
protected Vector	tempVec

Constructor Summary

Constructors

Constructor	Description
FindPairMoleculeIndex(Space space, CoordinateDefinitionNitrogen coordinateDefination)

Method Summary

Modifier and Type	Method	Description
boolean	getIsNewPair(int[] index)
int	getOrientationIndex(Vector orientation)
int[]	getPairMoleculesIndex(IMolecule moleculeA, IMolecule moleculeB, boolean isReverseOrder)
int[]	getSiteDisplacementIndex()
void	resetNewMoleculePair()
void	updateNewMoleculePair(int[] index)

Methods inherited from class java.lang.Object

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

Field Detail

index

protected int[] index

coordinateDef

protected CoordinateDefinitionNitrogen coordinateDef

positionDefinition

protected IMoleculePositionDefinition positionDefinition

tempVec

protected Vector tempVec

tempOrientA

protected Vector tempOrientA

tempOrientB

protected Vector tempOrientB

molAVec

protected Vector molAVec

molBVec

protected Vector molBVec

halfUnitCellLength

protected double halfUnitCellLength

siteDisplacement

protected double[][][] siteDisplacement

isNewPair

protected boolean[][][][][] isNewPair

nCell

protected int nCell

Constructor Detail

FindPairMoleculeIndex

public FindPairMoleculeIndex(Space space,
                             CoordinateDefinitionNitrogen coordinateDefination)

Method Detail

getPairMoleculesIndex

public int[] getPairMoleculesIndex(IMolecule moleculeA,
                                   IMolecule moleculeB,
                                   boolean isReverseOrder)

getSiteDisplacementIndex

public int[] getSiteDisplacementIndex()

updateNewMoleculePair

public void updateNewMoleculePair(int[] index)

resetNewMoleculePair

public void resetNewMoleculePair()

getOrientationIndex

public int getOrientationIndex(Vector orientation)

getIsNewPair

public boolean getIsNewPair(int[] index)