Package etomica.normalmode

Class NormalModes1DHR

java.lang.Object

etomica.normalmode.NormalModes1DHR

All Implemented Interfaces:

NormalModes

public class NormalModes1DHR
extends java.lang.Object
implements NormalModes

Normal-mode quantities for a 1-dimensional system of hard rods. Frequencies are defined in terms of pair correlations (S matrix), which is given using an analytic solution.

Field Summary

Fields

Modifier and Type	Field	Description
protected Boundary	boundary
protected double	harmonicFudge
protected int	nA
protected double	temperature

Constructor Summary

Constructors

Constructor	Description
NormalModes1DHR(Boundary boundary, int numMolecules)

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.
static void	main(java.lang.String[] args)
static double	S1DHR(int m, double L, int N)	Returns the analytical result for the S matrix (just a scalar in this case) for the 1D HR system with PBC
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

harmonicFudge

protected double harmonicFudge

temperature

protected double temperature

boundary

protected final Boundary boundary

nA

protected final int nA

Constructor Detail

NormalModes1DHR

public NormalModes1DHR(Boundary boundary,
                       int numMolecules)

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

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

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

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

S1DHR

public static double S1DHR(int m,
                           double L,
                           int N)

Returns the analytical result for the S matrix (just a scalar in this case) for the 1D HR system with PBC

Parameters:

m - specification of the wave vector, such that k = 2 Pi m rho/N

L - lenth of the system

N - number of rods

main

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