Package etomica.normalmode

Class NormalModesFromFile

java.lang.Object

etomica.normalmode.NormalModesFromFile

All Implemented Interfaces:

NormalModes

public class NormalModesFromFile
extends java.lang.Object
implements NormalModes

Provides normal-mode information as obtained from a file read at construction. File is expected to contain information about eigenvectors and eigenvalues of pair correlations. Reciprocal of eigenvalues gives frequencies defined by this implementation.

Constructor Summary

Constructors

Constructor	Description
NormalModesFromFile(java.lang.String filename, int D)

Method Summary

Modifier and Type	Method	Description
double[][][]	getEigenvectors()	First index corresponds to the wave vector; second index gives the eigenvector, and third index gives the elements of the vector.
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	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

Constructor Detail

NormalModesFromFile

public NormalModesFromFile(java.lang.String filename,
                           int D)

Parameters:

filename - Root of file name where normal mode information may be found. Wavevectors will be taken filename.k, eigenvalues from filename.val, and eigenvectors from filename.vec.

D - spatial dimension of the system (not necessarily coordinate dimension).

Method Detail

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

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

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