Package etomica.virial.cluster

Class VirialDiagramsMix2

java.lang.Object

etomica.virial.cluster.VirialDiagramsMix2

public class VirialDiagramsMix2
extends java.lang.Object

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	VirialDiagramsMix2.MaxIsomorphCriteriaMixture

Field Summary

Fields

Modifier and Type	Field	Description
protected boolean	allPermutations
protected java.util.Map<Graph,Graph>	cancelMap
protected java.util.Set<Graph>	cancelP
protected java.util.Set<Graph>	disconnectedP
protected boolean	doDisconnectedMatching
protected boolean	doKeepEBonds
protected boolean	doReeHoover
protected boolean	doShortcut
char	eBond
char	efbcBond
char	excBond
char	fBond
protected boolean[]	flex
protected char[]	flexColors
protected boolean	isInteractive
protected java.util.Set<Graph>	lnfXi
protected int	n
protected char[]	nodeColors
protected java.util.Set<Graph>	p
protected java.util.Set<Graph>	rhoA
protected java.util.Set<Graph>	rhoB

Constructor Summary

Constructors

Constructor	Description
VirialDiagramsMix2(int n, boolean[] flex)
VirialDiagramsMix2(int n, boolean[] flex, boolean interactive)

Method Summary

Modifier and Type	Method	Description
java.util.Map<Graph,Graph>	getCancelMap()
java.util.Set<Graph>	getExtraDisconnectedVirialGraphs(int[] numPoints)
java.util.Set<Graph>	getMSMCGraphs(boolean connectedOnly, int flexID, int[] numPoints)
java.util.Set<Graph>	getSplitDisconnectedVirialGraphs(Graph g)
static boolean	graphHasEdgeColor(Graph g, char color)
static void	main(java.lang.String[] args)
GraphList	makeGraphList()
void	makeRhoDiagrams()
ClusterSumShell[]	makeSingleVirialClusters(ClusterSum coreCluster, MayerFunction[][] f, int flexID, int[] numPoints)
ClusterSum	makeVirialCluster(MayerFunction[][] f, int flexID, int[] numPoints)
ClusterSum	makeVirialCluster(java.util.Set<Graph> graphs, MayerFunction[][] f, int flexID, int[] numPoints)
void	makeVirialDiagrams()
int	populateEFBonds(Graph g, java.util.List<ClusterBonds> allBonds, java.util.List<java.lang.Double> weights, int firstPoint, int lastPoint, boolean swapControl, boolean connectedGraph, int flexID)
void	setDoDisconnectedMatching(boolean newDoDisconnectedMatching)
void	setDoKeepEBonds(boolean newDoKeepEBonds)
void	setDoReeHoover(boolean newDoReeHoover)
void	setDoShortcut(boolean newDoShortcut)
protected byte	swap0n(byte i, int firstPoint, int lastPoint, boolean connectedGraph)

Methods inherited from class java.lang.Object

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

Field Detail

n

protected final int n

nodeColors

protected char[] nodeColors

flex

protected final boolean[] flex

flexColors

protected char[] flexColors

isInteractive

protected final boolean isInteractive

doReeHoover

protected boolean doReeHoover

p

protected java.util.Set<Graph> p

cancelP

protected java.util.Set<Graph> cancelP

disconnectedP

protected java.util.Set<Graph> disconnectedP

rhoA

protected java.util.Set<Graph> rhoA

rhoB

protected java.util.Set<Graph> rhoB

lnfXi

protected java.util.Set<Graph> lnfXi

cancelMap

protected java.util.Map<Graph,Graph> cancelMap

doShortcut

protected boolean doShortcut

doKeepEBonds

protected boolean doKeepEBonds

doDisconnectedMatching

protected boolean doDisconnectedMatching

fBond

public char fBond

eBond

public char eBond

excBond

public char excBond

efbcBond

public char efbcBond

allPermutations

protected boolean allPermutations

Constructor Detail

VirialDiagramsMix2

public VirialDiagramsMix2(int n,
                          boolean[] flex)

VirialDiagramsMix2

public VirialDiagramsMix2(int n,
                          boolean[] flex,
                          boolean interactive)

Method Detail

main

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

setDoReeHoover

public void setDoReeHoover(boolean newDoReeHoover)

setDoShortcut

public void setDoShortcut(boolean newDoShortcut)

setDoKeepEBonds

public void setDoKeepEBonds(boolean newDoKeepEBonds)

setDoDisconnectedMatching

public void setDoDisconnectedMatching(boolean newDoDisconnectedMatching)

getExtraDisconnectedVirialGraphs

public java.util.Set<Graph> getExtraDisconnectedVirialGraphs(int[] numPoints)

getSplitDisconnectedVirialGraphs

public java.util.Set<Graph> getSplitDisconnectedVirialGraphs(Graph g)

makeGraphList

public GraphList makeGraphList()

graphHasEdgeColor

public static boolean graphHasEdgeColor(Graph g,
                                        char color)

makeRhoDiagrams

public void makeRhoDiagrams()

makeVirialDiagrams

public void makeVirialDiagrams()

getMSMCGraphs

public java.util.Set<Graph> getMSMCGraphs(boolean connectedOnly,
                                          int flexID,
                                          int[] numPoints)

getCancelMap

public java.util.Map<Graph,Graph> getCancelMap()

makeVirialCluster

public ClusterSum makeVirialCluster(MayerFunction[][] f,
                                    int flexID,
                                    int[] numPoints)

makeVirialCluster

public ClusterSum makeVirialCluster(java.util.Set<Graph> graphs,
                                    MayerFunction[][] f,
                                    int flexID,
                                    int[] numPoints)

swap0n

protected byte swap0n(byte i,
                      int firstPoint,
                      int lastPoint,
                      boolean connectedGraph)

populateEFBonds

public int populateEFBonds(Graph g,
                           java.util.List<ClusterBonds> allBonds,
                           java.util.List<java.lang.Double> weights,
                           int firstPoint,
                           int lastPoint,
                           boolean swapControl,
                           boolean connectedGraph,
                           int flexID)

makeSingleVirialClusters

public ClusterSumShell[] makeSingleVirialClusters(ClusterSum coreCluster,
                                                  MayerFunction[][] f,
                                                  int flexID,
                                                  int[] numPoints)