Package etomica.models.nitrogen

Class HarmonicAlphaNitrogenModelPairMoleculeSequentialLS

java.lang.Object

etomica.simulation.Simulation

etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialLS

public class HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
extends Simulation

This class is created to take care of Java out of memory problem when creating a 2D array that is gigantic [~10000][~10000] The class is write a 5 x (nA * dof) Matrix to file while looping through the molecules This class also applied the molecules pair identification algorithm to speed up the matrix construction. with lattice sum

Field Summary

Fields

Modifier and Type	Field	Description
protected double[][][]	array
protected MoleculeChildAtomAction	atomGroupActionTranslate
protected Box	box
protected CalcAnalytical2ndDerivativeNitrogen	cA2nD
protected CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen	cAN2nD
protected CalcNumerical2ndDerivativeNitrogen	cm2ndD
protected CoordinateDefinitionNitrogen	coordinateDef
protected FindPairMoleculeIndex	findPair
protected boolean[][][][][]	isFoundReverse
protected Vector	lsPosition
protected int	nLayer
protected double[][][][][][][]	pairMatrix
protected P2Nitrogen	potential
protected PotentialMaster	potentialMaster
protected double	rC
protected Space	space
protected AtomActionTranslateBy	translateBy
protected double	xVecBox
protected double	yVecBox
protected double	zVecBox

Fields inherited from class etomica.simulation.Simulation

eventManager, random, seeds

Constructor Summary

Constructors

Constructor	Description
HarmonicAlphaNitrogenModelPairMoleculeSequentialLS(Space space, int numMolecule, double density, double rC)

Method Summary

Modifier and Type	Method	Description
void	constructHessianMatrix(int nCell)
void	constructHessianMatrix(java.lang.String fname, int nCell)
double[][]	get2ndDerivative(int molec0)
static void	main(java.lang.String[] args)

Methods inherited from class java.lang.Object

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

Methods inherited from class etomica.simulation.Simulation

addBox, addSpecies, box, getBox, getBoxCount, getBoxes, getController, getEventManager, getIntegrator, getRandom, getRandomSeeds, getSpace, getSpecies, getSpeciesCount, getSpeciesList, makeBox, makeBox, makeUniqueElementSymbol, removeBox, setRandom, species

Field Detail

box

protected Box box

space

protected Space space

potential

protected P2Nitrogen potential

coordinateDef

protected CoordinateDefinitionNitrogen coordinateDef

potentialMaster

protected PotentialMaster potentialMaster

pairMatrix

protected double[][][][][][][] pairMatrix

cm2ndD

protected CalcNumerical2ndDerivativeNitrogen cm2ndD

cAN2nD

protected CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen cAN2nD

cA2nD

protected CalcAnalytical2ndDerivativeNitrogen cA2nD

findPair

protected FindPairMoleculeIndex findPair

translateBy

protected AtomActionTranslateBy translateBy

atomGroupActionTranslate

protected MoleculeChildAtomAction atomGroupActionTranslate

lsPosition

protected Vector lsPosition

xVecBox

protected double xVecBox

yVecBox

protected double yVecBox

zVecBox

protected double zVecBox

rC

protected double rC

nLayer

protected int nLayer

isFoundReverse

protected boolean[][][][][] isFoundReverse

array

protected double[][][] array

Constructor Detail

HarmonicAlphaNitrogenModelPairMoleculeSequentialLS

public HarmonicAlphaNitrogenModelPairMoleculeSequentialLS(Space space,
                                                          int numMolecule,
                                                          double density,
                                                          double rC)

Method Detail

get2ndDerivative

public double[][] get2ndDerivative(int molec0)

constructHessianMatrix

public void constructHessianMatrix(java.lang.String fname,
                                   int nCell)

constructHessianMatrix

public void constructHessianMatrix(int nCell)

main

public static void main(java.lang.String[] args)