Package etomica.models.nitrogen

Class HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS

java.lang.Object

etomica.simulation.Simulation

etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS

public class HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
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. Additional: For larger system size, the matrix can be broken down into smaller matrices and then can be summed up later, and it is called the Half2 with lattice sum

Field Summary

Fields

Modifier and Type	Field	Description
protected MoleculeChildAtomAction	atomGroupActionTranslate
protected Box	box
protected CalcAnalytical2ndDerivativeNitrogen	cA2nD
protected CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen	cAN2nD
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 SpeciesGeneral	species
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
HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS(Space space, int numMolecule, double density, double rC)

Method Summary

Modifier and Type	Method	Description
void	constructHessianMatrix(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

cAN2nD

protected CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen cAN2nD

cA2nD

protected CalcAnalytical2ndDerivativeNitrogen cA2nD

findPair

protected FindPairMoleculeIndex findPair

species

protected SpeciesGeneral species

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

Constructor Detail

HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS

public HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS(Space space,
                                                               int numMolecule,
                                                               double density,
                                                               double rC)

Method Detail

get2ndDerivative

public double[][] get2ndDerivative(int molec0)

constructHessianMatrix

public void constructHessianMatrix(int nCell)

main

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