Package etomica.models.nitrogen

Class HarmonicAlphaNitrogenModelPairMoleculeSequential

java.lang.Object

etomica.simulation.Simulation

etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequential

public class HarmonicAlphaNitrogenModelPairMoleculeSequential
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.

Field Summary

Fields

Modifier and Type	Field	Description
protected Box	box
protected CalcAnalytical2ndDerivativeNitrogen	cA2nD
protected CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen	cAN2nD
protected CoordinateDefinitionNitrogen	coordinateDef
protected FindPairMoleculeIndex	findPair
protected double[][][][][][][]	pairMatrix
protected P2Nitrogen	potential
protected PotentialMaster	potentialMaster
protected Space	space

Fields inherited from class etomica.simulation.Simulation

eventManager, random, seeds

Constructor Summary

Constructors

Constructor	Description
HarmonicAlphaNitrogenModelPairMoleculeSequential(Space space, int numMolecule, double density)

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

cAN2nD

protected CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen cAN2nD

cA2nD

protected CalcAnalytical2ndDerivativeNitrogen cA2nD

findPair

protected FindPairMoleculeIndex findPair

Constructor Detail

HarmonicAlphaNitrogenModelPairMoleculeSequential

public HarmonicAlphaNitrogenModelPairMoleculeSequential(Space space,
                                                        int numMolecule,
                                                        double density)

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)