etomica.normalmode

Class NormalModesMolecular

java.lang.Object

etomica.normalmode.NormalModesMolecular

All Implemented Interfaces:

NormalModes

public class NormalModesMolecular
extends java.lang.Object
implements NormalModes

Uses analysis of 2nd derivatives to compute the normal modes for a Bravais lattice with a basis, occupied by atoms that interact with a simple, spherically-symmetric soft potential.

Field Summary

Fields

Modifier and Type	Field and Description
protected LatticeSumMolecularCrystal.AtomicTensorAtomicPair	atomicTensorAtomicPair
protected int	basisDim
protected IBox	box
protected int[]	nC
protected IPotentialMaster	potentialMaster
protected Primitive	primitive
protected ISpace	space
protected SpeciesWater4P	species
protected LatticeSumMolecularCrystal	summer
protected boolean	waveVectorMethod

Constructor Summary

Constructors

Constructor and Description
NormalModesMolecular(SpeciesWater4P species, boolean waveVectorMethod, IPotentialMaster potentialMaster, IBox box, int[] nUniyCellsInSupBox, Primitive primitive, int basisDim, LatticeSumMolecularCrystal.AtomicTensorAtomicPair atomicTensorAtomicPair, ISpace space)

Method Summary

Modifier and Type	Method and Description
void	calculateModes()
double[][][]	getEigenvectors() First index corresponds to the wave vector; second index gives the eigenvector, and third index gives the elements of the vector.
java.lang.String	getFileName()
double[][]	getOmegaSquared() Returns an array giving the frequencies (squared) corresponding to the normal-mode motions.
WaveVectorFactory	getWaveVectorFactory() Returns a factory that provides the wave vectors and coefficients for the periodic system.
void	setFileName(java.lang.String filename)
void	setHarmonicFudge(double newHarmonicFudge) Set the fudge factor applied to frequencies.
void	setTemperature(double newTemperature) Set the temperature used for calculating omega-squared.

Methods inherited from class java.lang.Object

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

Field Detail

space

protected final ISpace space

box

protected IBox box

basisDim

protected int basisDim

atomicTensorAtomicPair

protected final LatticeSumMolecularCrystal.AtomicTensorAtomicPair atomicTensorAtomicPair

primitive

protected final Primitive primitive

summer

protected LatticeSumMolecularCrystal summer

potentialMaster

protected IPotentialMaster potentialMaster

waveVectorMethod

protected final boolean waveVectorMethod

species

protected SpeciesWater4P species

nC

protected int[] nC

Constructor Detail

NormalModesMolecular

public NormalModesMolecular(SpeciesWater4P species,
                            boolean waveVectorMethod,
                            IPotentialMaster potentialMaster,
                            IBox box,
                            int[] nUniyCellsInSupBox,
                            Primitive primitive,
                            int basisDim,
                            LatticeSumMolecularCrystal.AtomicTensorAtomicPair atomicTensorAtomicPair,
                            ISpace space)

Method Detail

calculateModes

public void calculateModes()

setHarmonicFudge

public void setHarmonicFudge(double newHarmonicFudge)

Description copied from interface: NormalModes

Set the fudge factor applied to frequencies. The squared-frequencies returned by getOmegaSquared will be the nominal values divided by the given fudge factor. Thus a smaller value of this fudge factor will make for "tighter" harmonic springs, corresponding to to smaller deviation from the lattice sites.

Specified by:

setHarmonicFudge in interface NormalModes

setTemperature

public void setTemperature(double newTemperature)

Description copied from interface: NormalModes

Set the temperature used for calculating omega-squared. Omega-squared is kT/eigenvalue.

Specified by:

setTemperature in interface NormalModes

getFileName

public java.lang.String getFileName()

setFileName

public void setFileName(java.lang.String filename)

getWaveVectorFactory

public WaveVectorFactory getWaveVectorFactory()

Description copied from interface: NormalModes

Returns a factory that provides the wave vectors and coefficients for the periodic system.

Specified by:

getWaveVectorFactory in interface NormalModes

getOmegaSquared

public double[][] getOmegaSquared()

Description copied from interface: NormalModes

Returns an array giving the frequencies (squared) corresponding to the normal-mode motions. First index indicates the wave vector, and second index indicates the eigenvector. Length of second index is coordinateDim.

Specified by:

getOmegaSquared in interface NormalModes

getEigenvectors

public double[][][] getEigenvectors()

Description copied from interface: NormalModes

First index corresponds to the wave vector; second index gives the eigenvector, and third index gives the elements of the vector. Length of 2nd and 3rd dimensions is coordinateDim.

Specified by:

getEigenvectors in interface NormalModes