Package etomica.virial.cluster

Class VirialDiagrams

java.lang.Object

etomica.virial.cluster.VirialDiagrams

Direct Known Subclasses:

ExternalVirialDiagrams

public class VirialDiagrams
extends java.lang.Object

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	VirialDiagrams.ArticulatedAt0
static class	VirialDiagrams.ComparatorNumFieldNodesExchange

Field Summary

Fields

Modifier and Type	Field	Description
protected boolean	allPermutations
char	bBond
protected java.util.Map<Graph,Graph>	cancelMap
protected java.util.Set<Graph>	disconnectedP
protected boolean	doDisconnectedMatching
protected boolean	doExchange
protected boolean	doExchangeCondensing
protected boolean	doExchangeF
protected boolean	doHB
protected boolean	doKeepEBonds
protected boolean	doMinimalBC
protected boolean	doMinimalMulti
protected boolean	doMultiFromPair
protected boolean	doNegativeExchange
protected boolean	doReeHoover
protected boolean	doShortcut
char	eBond
char	efbcBond
char	excBond
char	fBond
char	ffBond
protected boolean	flex
protected boolean	flexCancelOnly
protected char[]	flexColors
char	fmBond
protected java.util.Set<Graph>	fullLnXi
protected java.util.Set<Graph>	fullMultiP
protected static int[][][]	groupStart
protected boolean	isInteractive
protected java.util.Set<Graph>	lnfXi
char	mBond
protected java.util.Set<Graph>	minMultiP
char	mmBond
protected boolean	multibody
char	mxcBond
char	MxcBond
protected static int[][]	myIds
protected int	n
protected char	nodeColor
protected java.util.Set<Graph>	p
protected static int[][]	quadStart
protected static int[][]	quintStart
protected java.util.Set<Graph>	rho
protected static int[][]	sixStart
protected static int[][]	tripletStart
protected java.util.Set<Graph>	trueMultiP

Constructor Summary

Constructors

Constructor	Description
VirialDiagrams(int n, boolean multibody, boolean flex)
VirialDiagrams(int n, boolean multibody, boolean flex, boolean interactive)

Method Summary

Modifier and Type	Method	Description
java.util.Map<Graph,Graph>	getCancelMap()
java.util.Set<Graph>	getExtraDisconnectedVirialGraphs()
static int	getGroupID(int[] ids, int n)
java.util.Set<Graph>	getMSMCGraphs(boolean connectedOnly, boolean getMultiGraphs)
java.util.Set<Graph>	getSplitDisconnectedVirialGraphs(Graph g)
java.util.Set<Graph>	getVirialGraphs()
static boolean	graphHasEdgeColor(Graph g, char color)
protected void	init()
static java.util.HashMap<java.lang.Character,java.lang.Integer>	initMetaDataComparator()
static void	main(java.lang.String[] args)
static GraphList	makeGraphList()
void	makeRhoDiagrams()
ClusterSumShell[]	makeSingleVirialClusters(ClusterSum coreCluster, MayerFunction e, MayerFunction f)
ClusterSumMultibodyShell[]	makeSingleVirialClustersMulti(ClusterSumMultibody coreCluster, MayerFunction f, MayerFunctionNonAdditive fMulti)
ClusterSum	makeVirialCluster(MayerFunction f)
ClusterSum	makeVirialCluster(MayerFunction f, MayerFunctionNonAdditive fMulti)
ClusterSum	makeVirialCluster(MayerFunction f, MayerFunctionNonAdditive fMulti, boolean doTotal)
ClusterSum	makeVirialCluster(java.util.Set<Graph> graphs, MayerFunction f, MayerFunctionNonAdditive fMulti)
ClusterSumHS	makeVirialClusterHS(java.util.Set<Graph> graphs, MayerFunction f)
ClusterSum	makeVirialClusterSecondTemperatureDerivative(MayerFunction f, MayerFunction e, MayerFunction dfdT, MayerFunction d2fdT2)
ClusterSum	makeVirialClusterTempDeriv(MayerFunction f, MayerFunction e, MayerFunction dfdT)
void	makeVirialDiagrams()
static int	pairId(int id0, int id1, int n)	Returns the pair ID for the given indices (id0, id1, id2)
int	populateEFBonds(Graph g, java.util.List<ClusterBonds> allBonds, java.util.List<java.lang.Double> weights, boolean swap)
void	populateEFdfdTBonds(Graph g, java.util.ArrayList<ClusterBonds> allBonds, boolean swap)
void	populateEFdfdTdf2dT2Bonds(Graph g, java.util.ArrayList<ClusterBonds> allBonds, boolean swap)
static int	quadId(int id0, int id1, int id2, int id3, int n)	Returns the quad ID for the given indices (id0, id1, id2, id3) and given number of molecules (n).
static int	quintId(int id0, int id1, int id2, int id3, int id4, int n)	Returns the quint ID for the given indices (id0, id1, id2, id3, id4) and given number of molecules (n).
void	setAllPermutations(boolean newAllPermutations)
void	setDoDisconnectedMatching(boolean newDoDisconnectedMatching)
void	setDoExchange(boolean newDoExchange)
void	setDoExchangeCondensing(boolean newDoExchangeCondensing)	Turn on replacement of exchanged groups of nodes with a single node (of a different color)
void	setDoExchangeF(boolean newDoExchangeF)	Turn on replacement of eBonds with bonds that represent a single fBond between an exchange group and another molecule (or another exchange group).
void	setDoHB(boolean newDoHB)	Enable construction of diagrams from the Hellmann-Bich formulation
void	setDoKeepEBonds(boolean newDoKeepEBonds)
void	setDoMinimalBC(boolean newDoMinimalBC)
void	setDoMinimalMulti(boolean newDoMinimalMulti)	Only include graphs with nonadditive bonds.
void	setDoMultiFromPair(boolean newDoMultiFromPair)
void	setDoNegativeExchange(boolean newDoNegativeExchange)
void	setDoReeHoover(boolean newDoReeHoover)
void	setDoShortcut(boolean newDoShortcut)
void	setFlexCancelOnly(boolean newFlexCancelOnly)	This method only effects the graphs returned by getMSMCGraphs
static int	singletId(int id0, int n)
static int	sixId(int id0, int id1, int id2, int id3, int id4, int id5, int n)	Returns the six-molecule ID for the given indices (id0, id1, id2, id3, id4, id5) and given number of molecules (n).
java.util.Set<Graph>	substMinMulti(Graph g)
protected byte	swap0n(byte i)
static int	tripletId(int id0, int id1, int id2, int n)	Returns the triplet ID for the given indices (id0, id1, id2) and given number of molecules (n).

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

flex

protected final boolean flex

multibody

protected final boolean multibody

isInteractive

protected final boolean isInteractive

doReeHoover

protected boolean doReeHoover

p

protected java.util.Set<Graph> p

disconnectedP

protected java.util.Set<Graph> disconnectedP

minMultiP

protected java.util.Set<Graph> minMultiP

fullMultiP

protected java.util.Set<Graph> fullMultiP

trueMultiP

protected java.util.Set<Graph> trueMultiP

rho

protected java.util.Set<Graph> rho

lnfXi

protected java.util.Set<Graph> lnfXi

fullLnXi

protected java.util.Set<Graph> fullLnXi

cancelMap

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

doShortcut

protected boolean doShortcut

doMinimalMulti

protected boolean doMinimalMulti

doMultiFromPair

protected boolean doMultiFromPair

doMinimalBC

protected boolean doMinimalBC

doKeepEBonds

protected boolean doKeepEBonds

doExchange

protected boolean doExchange

doExchangeF

protected boolean doExchangeF

doExchangeCondensing

protected boolean doExchangeCondensing

doDisconnectedMatching

protected boolean doDisconnectedMatching

doNegativeExchange

protected boolean doNegativeExchange

doHB

protected boolean doHB

flexCancelOnly

protected boolean flexCancelOnly

nodeColor

protected final char nodeColor

See Also:

Constant Field Values

flexColors

protected char[] flexColors

allPermutations

protected boolean allPermutations

fBond

public char fBond

bBond

public char bBond

eBond

public char eBond

excBond

public char excBond

mBond

public char mBond

mmBond

public char mmBond

fmBond

public char fmBond

efbcBond

public char efbcBond

ffBond

public char ffBond

mxcBond

public char mxcBond

MxcBond

public char MxcBond

groupStart

protected static int[][][] groupStart

myIds

protected static int[][] myIds

tripletStart

protected static int[][] tripletStart

quadStart

protected static int[][] quadStart

quintStart

protected static int[][] quintStart

sixStart

protected static int[][] sixStart

Constructor Detail

VirialDiagrams

public VirialDiagrams(int n,
                      boolean multibody,
                      boolean flex)

VirialDiagrams

public VirialDiagrams(int n,
                      boolean multibody,
                      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)

setDoHB

public void setDoHB(boolean newDoHB)

Enable construction of diagrams from the Hellmann-Bich formulation

setDoExchange

public void setDoExchange(boolean newDoExchange)

setDoDisconnectedMatching

public void setDoDisconnectedMatching(boolean newDoDisconnectedMatching)

setDoExchangeF

public void setDoExchangeF(boolean newDoExchangeF)

Turn on replacement of eBonds with bonds that represent a single fBond between an exchange group and another molecule (or another exchange group).

setDoExchangeCondensing

public void setDoExchangeCondensing(boolean newDoExchangeCondensing)

Turn on replacement of exchanged groups of nodes with a single node (of a different color)

setDoNegativeExchange

public void setDoNegativeExchange(boolean newDoNegativeExchange)

setDoMinimalMulti

public void setDoMinimalMulti(boolean newDoMinimalMulti)

Only include graphs with nonadditive bonds.

setDoMultiFromPair

public void setDoMultiFromPair(boolean newDoMultiFromPair)

setDoMinimalBC

public void setDoMinimalBC(boolean newDoMinimalBC)

init

protected void init()

setAllPermutations

public void setAllPermutations(boolean newAllPermutations)

getVirialGraphs

public java.util.Set<Graph> getVirialGraphs()

setFlexCancelOnly

public void setFlexCancelOnly(boolean newFlexCancelOnly)

This method only effects the graphs returned by getMSMCGraphs

getMSMCGraphs

public java.util.Set<Graph> getMSMCGraphs(boolean connectedOnly,
                                          boolean getMultiGraphs)

getCancelMap

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

makeVirialCluster

public ClusterSum makeVirialCluster(MayerFunction f)

makeVirialCluster

public ClusterSum makeVirialCluster(MayerFunction f,
                                    MayerFunctionNonAdditive fMulti)

makeVirialCluster

public ClusterSum makeVirialCluster(MayerFunction f,
                                    MayerFunctionNonAdditive fMulti,
                                    boolean doTotal)

makeVirialCluster

public ClusterSum makeVirialCluster(java.util.Set<Graph> graphs,
                                    MayerFunction f,
                                    MayerFunctionNonAdditive fMulti)

makeVirialClusterHS

public ClusterSumHS makeVirialClusterHS(java.util.Set<Graph> graphs,
                                        MayerFunction f)

makeVirialClusterTempDeriv

public ClusterSum makeVirialClusterTempDeriv(MayerFunction f,
                                             MayerFunction e,
                                             MayerFunction dfdT)

makeVirialClusterSecondTemperatureDerivative

public ClusterSum makeVirialClusterSecondTemperatureDerivative(MayerFunction f,
                                                               MayerFunction e,
                                                               MayerFunction dfdT,
                                                               MayerFunction d2fdT2)

swap0n

protected byte swap0n(byte i)

populateEFBonds

public int populateEFBonds(Graph g,
                           java.util.List<ClusterBonds> allBonds,
                           java.util.List<java.lang.Double> weights,
                           boolean swap)

populateEFdfdTBonds

public void populateEFdfdTBonds(Graph g,
                                java.util.ArrayList<ClusterBonds> allBonds,
                                boolean swap)

populateEFdfdTdf2dT2Bonds

public void populateEFdfdTdf2dT2Bonds(Graph g,
                                      java.util.ArrayList<ClusterBonds> allBonds,
                                      boolean swap)

makeSingleVirialClusters

public ClusterSumShell[] makeSingleVirialClusters(ClusterSum coreCluster,
                                                  MayerFunction e,
                                                  MayerFunction f)

substMinMulti

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

makeSingleVirialClustersMulti

public ClusterSumMultibodyShell[] makeSingleVirialClustersMulti(ClusterSumMultibody coreCluster,
                                                                MayerFunction f,
                                                                MayerFunctionNonAdditive fMulti)

getExtraDisconnectedVirialGraphs

public java.util.Set<Graph> getExtraDisconnectedVirialGraphs()

getSplitDisconnectedVirialGraphs

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

makeGraphList

public static GraphList makeGraphList()

initMetaDataComparator

public static java.util.HashMap<java.lang.Character,java.lang.Integer> initMetaDataComparator()

makeRhoDiagrams

public void makeRhoDiagrams()

makeVirialDiagrams

public void makeVirialDiagrams()

graphHasEdgeColor

public static boolean graphHasEdgeColor(Graph g,
                                        char color)

getGroupID

public static int getGroupID(int[] ids,
                             int n)

singletId

public static int singletId(int id0,
                            int n)

pairId

public static int pairId(int id0,
                         int id1,
                         int n)

Returns the pair ID for the given indices (id0, id1, id2)

tripletId

public static int tripletId(int id0,
                            int id1,
                            int id2,
                            int n)

Returns the triplet ID for the given indices (id0, id1, id2) and given number of molecules (n). Triplets are ordered as (0,1,2), (0,1,3), (0,1,4)... (0,1,n-1) (0,2,3), (0,2,4), (0,2,5)... (0,2,n-1) ... (0,n-3,n-2),(0,n-3,n-1) (0,n-2,n-1) Indices must be given in order. If idx < 0 or idx >= n, the id returned will be nonsense (or there will be an exception).

quadId

public static int quadId(int id0,
                         int id1,
                         int id2,
                         int id3,
                         int n)

Returns the quad ID for the given indices (id0, id1, id2, id3) and given number of molecules (n). Quads are ordered the same as triplets.

quintId

public static int quintId(int id0,
                          int id1,
                          int id2,
                          int id3,
                          int id4,
                          int n)

Returns the quint ID for the given indices (id0, id1, id2, id3, id4) and given number of molecules (n). Quints are ordered the same as triplets.

sixId

public static int sixId(int id0,
                        int id1,
                        int id2,
                        int id3,
                        int id4,
                        int id5,
                        int n)

Returns the six-molecule ID for the given indices (id0, id1, id2, id3, id4, id5) and given number of molecules (n). Sixes are ordered the same as triplets.