Package etomica.virial

Class ClusterBonds

java.lang.Object

etomica.virial.ClusterBonds

All Implemented Interfaces:

java.io.Serializable

Direct Known Subclasses:

Chain, ClusterBondsNonAdditive, Full, Ring

public class ClusterBonds
extends java.lang.Object
implements java.io.Serializable

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
protected int[][]	bondIndexArray
protected int	nPermutations
protected int	nPoints
protected int[][]	permutations
protected double	rPermutations
protected boolean	usePermutations

Constructor Summary

Constructors

Constructor	Description
ClusterBonds(int[][] bondIndexArray, boolean usePermutations)
ClusterBonds(int n, int[][][] bonds)	Constructor for Cluster, with default to not using permutations (this can be changed after construction if desired).
ClusterBonds(int n, int[][][] bonds, boolean usePermutations)	Constructor for Cluster.

Method Summary

Modifier and Type	Method	Description
int[][]	getBondIndexArray()
boolean	isUsePermutations()	Returns the usePermutations flag.
static void	main(java.lang.String[] args)
int	nPermutations()	Number of permutations of (and including) the basic cluster used when calculating its value for a configuration
int	pointCount()
void	setUsePermutations(boolean usePermutations)	Sets the usePermutations flag.
java.lang.String	toString()
double	value(double[][][] fValues)	Returns the value of the cluster for the given set of atom pairs at the given value of beta = 1/kT.
protected double	valueUsingPermutations(double[][][] fValues)	Returns value obtained by averaging over all unique permutations of the point indices.

Methods inherited from class java.lang.Object

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

Field Detail

nPoints

protected final int nPoints

bondIndexArray

protected final int[][] bondIndexArray

usePermutations

protected boolean usePermutations

permutations

protected int[][] permutations

nPermutations

protected int nPermutations

rPermutations

protected double rPermutations

Constructor Detail

ClusterBonds

public ClusterBonds(int n,
                    int[][][] bonds)

Constructor for Cluster, with default to not using permutations (this can be changed after construction if desired).

ClusterBonds

public ClusterBonds(int n,
                    int[][][] bonds,
                    boolean usePermutations)

Constructor for Cluster. Each BondGroup in the given array defines a set of pairs and a single bond function defined between each.

ClusterBonds

public ClusterBonds(int[][] bondIndexArray,
                    boolean usePermutations)

Method Detail

getBondIndexArray

public int[][] getBondIndexArray()

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

pointCount

public int pointCount()

value

public double value(double[][][] fValues)

Returns the value of the cluster for the given set of atom pairs at the given value of beta = 1/kT. It is expected that the pairs in the given PairSet will have all be reset (i.e., their r2 values already computed).

Parameters:

pairs - PairSet defining current configuration. Does not call reset for atom pairs, so this must be done before calling the method (accomplished by invoking pairs.resetPairs() method).

beta - reciprocal temperature, 1/kT

Returns:

double value of the cluster

valueUsingPermutations

protected double valueUsingPermutations(double[][][] fValues)

Returns value obtained by averaging over all unique permutations of the point indices.

Parameters:

fValues -

Returns:

double

isUsePermutations

public boolean isUsePermutations()

Returns the usePermutations flag.

Returns:

boolean

setUsePermutations

public void setUsePermutations(boolean usePermutations)

Sets the usePermutations flag.

Parameters:

usePermutations - The usePermutations to set

nPermutations

public int nPermutations()

Number of permutations of (and including) the basic cluster used when calculating its value for a configuration

Returns:

int the number of permutations

main

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