Package etomica.models.nitrogen

Class HarmonicAlphaNitrogenModelDecomposed

java.lang.Object

etomica.simulation.Simulation

etomica.models.nitrogen.HarmonicAlphaNitrogenModelDecomposed

public class HarmonicAlphaNitrogenModelDecomposed
extends Simulation

Class that constructs the Hessian Matrix Special features about this class is that: 1. each row of blocks can be calculated in separate simulations (to account for the expensive nature of constructing the Matrix in a single run) 2. you can combine all the row blocks into the (N*dof) x (N*dof) matrix once all the simulations are done N is the number of molecules and dof is the degrees of freedom for each molecule

Field Summary

Fields

Modifier and Type	Field	Description
protected Box	box
protected CoordinateDefinitionNitrogen	coordinateDef
protected P2Nitrogen	potential
protected PotentialMaster	potentialMaster
protected Space	space

Fields inherited from class etomica.simulation.Simulation

eventManager, random, seeds

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
double[][]	contructFullMatrix(CoordinateDefinition coordinateDef, java.lang.String fname)
void	doEigenDecompose(double[][] array, java.lang.String filename)
double[][]	get2ndDerivativeMoleculei(CoordinateDefinition coordinateDef, int iMolecule)
double[][]	getMatrixFromFile(java.lang.String fname, int iMolecule)
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

Constructor Detail

HarmonicAlphaNitrogenModelDecomposed

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

Method Detail

get2ndDerivativeMoleculei

public double[][] get2ndDerivativeMoleculei(CoordinateDefinition coordinateDef,
                                            int iMolecule)

contructFullMatrix

public double[][] contructFullMatrix(CoordinateDefinition coordinateDef,
                                     java.lang.String fname)

getMatrixFromFile

public double[][] getMatrixFromFile(java.lang.String fname,
                                    int iMolecule)

doEigenDecompose

public void doEigenDecompose(double[][] array,
                             java.lang.String filename)

main

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