VirialDiagramsPT

java.lang.Object
- etomica.virial.cluster.VirialDiagramsPT

public class VirialDiagramsPT
extends java.lang.Object

Nested Class Summary

Nested Classes
Modifier and Type	Class	Description
`static class`	`VirialDiagramsPT.ArticulatedAt0`
`static class`	`VirialDiagramsPT.ComparatorNumFieldNodesExchange`
`static class`	`VirialDiagramsPT.DiscardCriteria`

Field Summary

Fields
Modifier and Type	Field	Description
`char[]`	`aBonds`
`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`	`doExp`
`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 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 int`	`n`
`protected char`	`nodeColor`
`protected int`	`orderBeta`
`protected java.util.Set<Graph>`	`p`
`protected static int[][]`	`quadStart`
`protected static int[][]`	`quintStart`
`char`	`rBond`
`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
`VirialDiagramsPT(int n, boolean multibody, boolean flex)`
`VirialDiagramsPT(int n, boolean multibody, boolean flex, boolean interactive)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`java.util.Map<Graph,Graph>`	`getCancelMap()`
`java.util.Set<Graph>`	`getExtraDisconnectedVirialGraphs(int order)`
`static int`	`getGroupID(int[] ids, int n)`
`java.util.Set<Graph>`	`getMSMCGraphs(boolean connectedOnly, int order)`
`int`	`getOrderBeta()`
`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 r, MayerFunction[] a, int order)`
`ClusterSum`	`makeVirialCluster(MayerFunction r, MayerFunction[] a)`
`ClusterSum`	`makeVirialCluster(java.util.Set<Graph> graphs, MayerFunction r, MayerFunction[] a)`
`void`	`makeVirialDiagrams()`
`int`	`populateBonds(Graph g, java.util.List<ClusterBonds> allBonds, java.util.List<java.lang.Double> weights, 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`	`setDoExp(boolean newDoExp)`
`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)`
`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
`void`	`setOrderBeta(int newOrder)`
`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).
`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
```

rBond
```
public char rBond
```

aBonds
```
public char[] aBonds
```

orderBeta
```
protected int orderBeta
```

doExp
```
protected boolean doExp
```

tripletStart
```
protected static int[][] tripletStart
```

quadStart
```
protected static int[][] quadStart
```

quintStart
```
protected static int[][] quintStart
```

sixStart
```
protected static int[][] sixStart
```

Constructor Detail

VirialDiagramsPT

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

VirialDiagramsPT

public VirialDiagramsPT(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)

setDoMultiFromPair

public void setDoMultiFromPair(boolean newDoMultiFromPair)

setDoMinimalBC

public void setDoMinimalBC(boolean newDoMinimalBC)

setOrderBeta

public void setOrderBeta(int newOrder)

getOrderBeta
```
public int getOrderBeta()
```

setDoExp

public void setDoExp(boolean newDoExp)

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,
                                          int order)

getCancelMap

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

makeVirialCluster

public ClusterSum makeVirialCluster(MayerFunction r,
                                    MayerFunction[] a)

makeVirialCluster

public ClusterSum makeVirialCluster(java.util.Set<Graph> graphs,
                                    MayerFunction r,
                                    MayerFunction[] a)

swap0n
```
protected byte swap0n(byte i)
```

populateBonds

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

makeSingleVirialClusters

public ClusterSumShell[] makeSingleVirialClusters(ClusterSum coreCluster,
                                                  MayerFunction r,
                                                  MayerFunction[] a,
                                                  int order)

getExtraDisconnectedVirialGraphs

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

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)

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.

Class VirialDiagramsPT

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

n

flex

multibody

isInteractive

doReeHoover

p

disconnectedP

minMultiP

fullMultiP

trueMultiP

rho

lnfXi

fullLnXi

cancelMap

doShortcut

doMinimalMulti

doMultiFromPair

doMinimalBC

doKeepEBonds

doExchange

doExchangeF

doExchangeCondensing

doDisconnectedMatching

doNegativeExchange

doHB

flexCancelOnly

nodeColor

flexColors

allPermutations

fBond

bBond

eBond

excBond

mBond

mmBond

fmBond

efbcBond

ffBond

mxcBond

MxcBond

rBond

aBonds

orderBeta

doExp

tripletStart

quadStart

quintStart

sixStart

Constructor Detail

VirialDiagramsPT

VirialDiagramsPT

Method Detail

main

setDoReeHoover

setDoShortcut

setDoKeepEBonds

setDoHB

setDoExchange

setDoDisconnectedMatching

setDoExchangeF

setDoExchangeCondensing

setDoNegativeExchange

setDoMinimalMulti

setDoMultiFromPair

setDoMinimalBC

setOrderBeta

getOrderBeta

setDoExp

init

setAllPermutations

getVirialGraphs

setFlexCancelOnly

getMSMCGraphs