Package etomica.normalmode

Interface NormalModes

All Known Implementing Classes:

NormalModes1DHR, NormalModes2D, NormalModes3D, NormalModesFromFile, NormalModesMolecular, NormalModesPotential, NormalModesSoftSpherical

public interface NormalModes

Provides information about all the normal modes for a periodic system. The periodicity is described by a set of wave vectors, which are provided via a WaveVectorFactory. For each wave vector there is a set of coupled degrees of freedom (e.g., xyz motions) that have been further decomposed into normal modes with corresponding frequencies and eigenvectors. In most cases these frequencies/vectors are determined via a simulation and recorded to file; the implmentation of this class then reads the data and provides it via the interface methods.

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.

Method Detail

getWaveVectorFactory

WaveVectorFactory getWaveVectorFactory()

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

getOmegaSquared

double[][] getOmegaSquared()

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.

getEigenvectors

double[][][] getEigenvectors()

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.

setHarmonicFudge

void setHarmonicFudge(double newHarmonicFudge)

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.

setTemperature

void setTemperature(double newTemperature)

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