Package etomica.virial.cluster

Class ClusterGenerator

java.lang.Object

etomica.virial.cluster.ClusterGenerator

All Implemented Interfaces:

java.io.Serializable

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

Generates all clusters matching certain criteria.

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
ClusterDiagram	mCluster

Constructor Summary

Constructors

Constructor	Description
ClusterGenerator(ClusterDiagram aCluster)

Method Summary

Modifier and Type	Method	Description
boolean	advance()	Advances the cluster to the next cluster matching the given criteria.
void	calcReeHoover()	Calculates the Ree-Hoover coefficient (coefficient for Ree-Hoover diagram / coefficient for Mayer diagram) for mCluster and sets mCluster's mReeHooverFactor to it.
static void	findMaxScore(boolean excludeRootPermutations, ClusterDiagram cluster, int[] score)	Determines whether any cluster permuted from the given one by exchanging points from startPoint to stopPoint (inclusive) has a higher score than that passed in.
boolean	isArticulationPair(int exclude1, int exclude2)	determines if the given pair of points is an articulation pair.
boolean	isArticulationPoint(int exclude)	Determines if the given point is an articulation point.
boolean	isConnected()	Determines if the cluster is connected.
boolean	isConnected(int exclude)	Determines if the cluster is connected after removal of the given node.
boolean	isElementary()	Convenience method to determine whether the cluster is elementary or not.
boolean	isMaximumScore()	Determines if the cluster has a maximum score.
boolean	isNodalPoint(int exclude)	Determines if the given node is a nodal point.
static void	main(java.lang.String[] args)	Demonstrates how to use this class.
void	reset()	Resets the cluster generator.
void	setAllPermutations(boolean flag)	Set whether to generate all permutations.
void	setExcludeArticulationPair(boolean flag)	Set whether to exclude clusters having an articulation pair.
void	setExcludeArticulationPoint(boolean flag)	Set whether to exclude clusters having an articulation point.
void	setExcludeNodalPoint(boolean flag)	Set whether to exclude clusters having a nodal point.
void	setMakeReeHover(boolean flag)	Set whether to generate Ree-Hoover diagrams.
void	setOnlyConnected(boolean flag)	Set whether to only generate clusters that are singly-connected.
void	setOnlyDoublyConnected(boolean flag)	Set whether to only generate clusters that are doubly-connected.
void	setStartConnection(int i)
void	setStopConnection(int i)
static boolean	swapAllAndCompare(boolean excludeRootPermutations, ClusterDiagram cluster, int[] score)

Methods inherited from class java.lang.Object

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

Field Detail

mCluster

public final ClusterDiagram mCluster

Constructor Detail

ClusterGenerator

public ClusterGenerator(ClusterDiagram aCluster)

Method Detail

setOnlyConnected

public void setOnlyConnected(boolean flag)

Set whether to only generate clusters that are singly-connected.

setOnlyDoublyConnected

public void setOnlyDoublyConnected(boolean flag)

Set whether to only generate clusters that are doubly-connected.

setExcludeNodalPoint

public void setExcludeNodalPoint(boolean flag)

Set whether to exclude clusters having a nodal point.

setExcludeArticulationPoint

public void setExcludeArticulationPoint(boolean flag)

Set whether to exclude clusters having an articulation point.

setExcludeArticulationPair

public void setExcludeArticulationPair(boolean flag)

Set whether to exclude clusters having an articulation pair.

setAllPermutations

public void setAllPermutations(boolean flag)

Set whether to generate all permutations. If false, only one cluster from each set of permutations will be generated. That cluster has the greatest "score" among its set of permutations, and the number of identical permutations will be calculated and stored in the mNumIdenticalPermutations field.

setMakeReeHover

public void setMakeReeHover(boolean flag)

Set whether to generate Ree-Hoover diagrams. If set, then connected points have an f-bond and all others have an e-bond.

swapAllAndCompare

public static boolean swapAllAndCompare(boolean excludeRootPermutations,
                                        ClusterDiagram cluster,
                                        int[] score)

findMaxScore

public static void findMaxScore(boolean excludeRootPermutations,
                                ClusterDiagram cluster,
                                int[] score)

Determines whether any cluster permuted from the given one by exchanging points from startPoint to stopPoint (inclusive) has a higher score than that passed in. If such a cluster is located, the method returns true immediately. The method always restores the connections to their state when the method was called. If the permutations of the given cluster do not have a higher score, the cluster's mNumIdenticalPermutations field is updated to include the number of identical permutations encountered while swapping.

isConnected

public boolean isConnected(int exclude)

Determines if the cluster is connected after removal of the given node.

isConnected

public boolean isConnected()

Determines if the cluster is connected.

isElementary

public boolean isElementary()

Convenience method to determine whether the cluster is elementary or not.

isNodalPoint

public boolean isNodalPoint(int exclude)

Determines if the given node is a nodal point.

isArticulationPoint

public boolean isArticulationPoint(int exclude)

Determines if the given point is an articulation point.

isArticulationPair

public boolean isArticulationPair(int exclude1,
                                  int exclude2)

determines if the given pair of points is an articulation pair.

isMaximumScore

public boolean isMaximumScore()

Determines if the cluster has a maximum score. If the score can be increased by swapping filled points or by swapping reference nodes, then one of its permutations must have a higher score and the method returns false. If the cluster does have a maximum score, the mNumIdenticalPermutations is calculated as 1 + the number of permuted clusters with the same score as the unpermuted cluster.

calcReeHoover

public void calcReeHoover()

Calculates the Ree-Hoover coefficient (coefficient for Ree-Hoover diagram / coefficient for Mayer diagram) for mCluster and sets mCluster's mReeHooverFactor to it.

reset

public void reset()

Resets the cluster generator. This resets the cluster, and prepares the generator to generate clusters matching the appropriate criteria.

setStartConnection

public void setStartConnection(int i)

setStopConnection

public void setStopConnection(int i)

advance

public boolean advance()

Advances the cluster to the next cluster matching the given criteria. Returns false if no more clusters exist.

main

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

Demonstrates how to use this class.