ClusterWheatleyPartitionScreening

java.lang.Object
- etomica.virial.ClusterWheatleyPartitionScreening

All Implemented Interfaces:

ClusterAbstract, ClusterWheatley
```
public class ClusterWheatleyPartitionScreening
extends java.lang.Object
implements ClusterWheatley
```
This class calculates the sum of all biconnected clusters using Wheatley's recursive formulation.

Nested Class Summary

Nested Classes
Modifier and Type Class Description

class ClusterWheatleyPartitionScreening.FrequencyCounter

Nested Classes
Modifier and Type	Class	Description
`class`	`ClusterWheatleyPartitionScreening.FrequencyCounter`

Field Summary

Fields
Modifier and Type	Field	Description
`protected int[]`	`allZero`
`protected double`	`beta`
`protected static boolean`	`checkme`
`protected int`	`cliqueCount`
`protected int[]`	`cliqueList`
`protected boolean[]`	`cliqueSet`
`protected long`	`cPairID`
`protected boolean`	`doStatistics`
`protected int`	`eCliqueCount`
`protected int[]`	`eCliqueList`
`protected int`	`edgeCount`
`protected MayerFunction`	`f`
`protected int[]`	`fA`
`protected int[]`	`fAB`
`protected int[][][]`	`fABList`
`protected int[][]`	`fABValues`
`protected int[][][]`	`fAList`
`protected int[][]`	`fAValues`
`protected int[]`	`fB`
`protected int[]`	`fC`
`protected int[][]`	`fCList`
`protected boolean[]`	`fQ`
`protected int[]`	`fullBondMask`
`protected long`	`lastCPairID`
`protected double`	`lastValue`
`protected int`	`n`
`protected int`	`nf`
`protected long`	`notzero`
`protected int[]`	`nPts`
`protected int`	`nPtsTabulated`
`protected byte[]`	`outDegree`
`protected int[][][]`	`partitionsA`
`protected int[][]`	`partitionsC`
`protected boolean`	`precalcQ`
`protected long`	`screened`
`protected int[]`	`sig`
`ClusterWheatleyPartitionScreening.FrequencyCounter[]`	`sigCounter`
`protected long`	`total`
`protected double`	`value`
`protected int[]`	`vCount`

Constructor Summary

Constructors
Constructor	Description
`ClusterWheatleyPartitionScreening(int nPoints, MayerFunction f)`
`ClusterWheatleyPartitionScreening(int nPoints, MayerFunction f, int nPtsTabulated)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected void`	`calcfAB(int v, boolean useTable)`
`protected void`	`calcfAB0(boolean useTable)`
`protected void`	`calcfC(boolean useTable)`
`protected void`	`calcfQ(BoxCluster box)`	This calculates all fQ values given that the entries for pairs have already been populated.
`long`	`calcSignature(BoxCluster box)`
`protected void`	`calcSignatures()`	Compute signatures used for lookup tables of fA, fAB, fC
`double`	`calcValue(BoxCluster box)`	Returns the cluster value for the given configuration.
`protected void`	`calcValue(BoxCluster box, boolean doCheck)`
`boolean`	`checkConfig(BoxCluster box)`	Determines whether the configuration is zero-valued or not.
`protected boolean`	`cliqueCheck(int clique, int nfm1)`	Checks to see if the set \|clique\| is a clique separator.
`protected int[]`	`computeAPartitions(int vs1, int i)`
`int`	`getCliqueCount()`	Returns number of cliques for the configuration passed to checkConfig
`int[]`	`getCliques()`	Returns an array containing the clique sets for the configuration passed to checkConfig.
`long`	`getCPairID()`
`int`	`getECliqueCount()`	Returns number of e-bond cliques for the configuration passed to checkConfig
`int[]`	`getECliques()`	Returns an array containing the clique sets (based on e-bonds) for the configuration passed to checkConfig.
`int`	`getEdgeCount()`	Returns edgeCount (number of overlaps) of configuration passed to checkConfig
`int[]`	`getFullBondMask()`	Returns number bond mask for all points for the configuration passed to checkConfig
`long`	`getLastCPairID()`
`double`	`getLastValue()`
`byte[]`	`getOutDegree()`	Returns outDegee (number of bonds for each point) of the configuration passed to checkConfig
`static void`	`main(java.lang.String[] args)`
`ClusterAbstract`	`makeCopy()`	Returns another instance of an identical cluster (shallow copy).
`int`	`pointCount()`	Number of points in the cluster.
`void`	`setTemperature(double temperature)`
`protected void`	`updateF()`
`protected void`	`updateF(BoxCluster box)`
`double`	`value(BoxCluster box)`	Value of this cluster for the given pairset at the specified reciprocal temperature.

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
```
  - nf
```
protected final int nf
```
  - f
```
protected final MayerFunction f
```
  - fQ
```
protected final boolean[] fQ
```
  - fA
```
protected final int[] fA
```
  - fB
```
protected final int[] fB
```
  - fAB
```
protected final int[] fAB
```
  - fC
```
protected final int[] fC
```
  - cPairID
```
protected long cPairID
```
  - lastCPairID
```
protected long lastCPairID
```
  - value
```
protected double value
```
  - lastValue
```
protected double lastValue
```
  - beta
```
protected double beta
```
  - outDegree
```
protected final byte[] outDegree
```
  - fullBondMask
```
protected final int[] fullBondMask
```
  - cliqueSet
```
protected final boolean[] cliqueSet
```
  - cliqueCount
```
protected int cliqueCount
```
  - eCliqueCount
```
protected int eCliqueCount
```
  - precalcQ
```
protected boolean precalcQ
```
  - cliqueList
```
protected final int[] cliqueList
```
  - eCliqueList
```
protected final int[] eCliqueList
```
  - nPts
```
protected final int[] nPts
```
  - vCount
```
protected final int[] vCount
```
  - sig
```
protected final int[] sig
```
  - partitionsA
```
protected final int[][][] partitionsA
```
  - partitionsC
```
protected final int[][] partitionsC
```
  - fAList
```
protected final int[][][] fAList
```
  - fABList
```
protected final int[][][] fABList
```
  - fCList
```
protected final int[][] fCList
```
  - allZero
```
protected final int[] allZero
```
  - fAValues
```
protected final int[][] fAValues
```
  - fABValues
```
protected final int[][] fABValues
```
  - nPtsTabulated
```
protected final int nPtsTabulated
```
  - checkme
```
protected static final boolean checkme
```
    See Also:
    
    Constant Field Values
  - doStatistics
```
protected final boolean doStatistics
```
    See Also:
    
    Constant Field Values
  - sigCounter
```
public final ClusterWheatleyPartitionScreening.FrequencyCounter[] sigCounter
```
  - total
```
protected long total
```
  - notzero
```
protected long notzero
```
  - screened
```
protected long screened
```
  - edgeCount
```
protected int edgeCount
```
- Constructor Detail
  - ClusterWheatleyPartitionScreening
```
public ClusterWheatleyPartitionScreening(int nPoints,
                                         MayerFunction f)
```
  - ClusterWheatleyPartitionScreening
```
public ClusterWheatleyPartitionScreening(int nPoints,
                                         MayerFunction f,
                                         int nPtsTabulated)
```
- Method Detail
  - computeAPartitions
```
protected int[] computeAPartitions(int vs1,
                                   int i)
```
  - makeCopy
```
public ClusterAbstract makeCopy()
```
    Description copied from interface: ClusterAbstract
    
    Returns another instance of an identical cluster (shallow copy).
    
    Specified by:
    
    makeCopy in interface ClusterAbstract
  - pointCount
```
public int pointCount()
```
    Description copied from interface: ClusterAbstract
    
    Number of points in the cluster.
    
    Specified by:
    
    pointCount in interface ClusterAbstract
    
    Returns:
    
    int
  - value
```
public double value(BoxCluster box)
```
    Description copied from interface: ClusterAbstract
    
    Value of this cluster for the given pairset at the specified reciprocal temperature.
    
    Specified by:
    
    value in interface ClusterAbstract
  - getCPairID
```
public long getCPairID()
```
  - getLastCPairID
```
public long getLastCPairID()
```
  - getLastValue
```
public double getLastValue()
```
  - calcfQ
```
protected void calcfQ(BoxCluster box)
```
    This calculates all fQ values given that the entries for pairs have already been populated.
  - calcSignatures
```
protected void calcSignatures()
```
    Compute signatures used for lookup tables of fA, fAB, fC
  - checkConfig
```
public boolean checkConfig(BoxCluster box)
```
    Description copied from interface: ClusterWheatley
    
    Determines whether the configuration is zero-valued or not. If not zero, this method also computes various quantities returnable through other methods.
    
    Specified by:
    
    checkConfig in interface ClusterWheatley
  - cliqueCheck
```
protected boolean cliqueCheck(int clique,
                              int nfm1)
```
    Checks to see if the set |clique| is a clique separator. The graph connectivity is described by the fullBondMask array.
  - calcValue
```
public double calcValue(BoxCluster box)
```
    Returns the cluster value for the given configuration. You must call doCheck(BoxCluster) before calling this method.
    
    Specified by:
    
    calcValue in interface ClusterWheatley
  - calcValue
```
protected void calcValue(BoxCluster box,
                         boolean doCheck)
```
  - calcfC
```
protected final void calcfC(boolean useTable)
```
  - calcfAB
```
protected final void calcfAB(int v,
                             boolean useTable)
```
  - calcfAB0
```
protected final void calcfAB0(boolean useTable)
```
  - getEdgeCount
```
public int getEdgeCount()
```
    Returns edgeCount (number of overlaps) of configuration passed to checkConfig
    
    Specified by:
    
    getEdgeCount in interface ClusterWheatley
  - getCliqueCount
```
public int getCliqueCount()
```
    Description copied from interface: ClusterWheatley
    
    Returns number of cliques for the configuration passed to checkConfig
    
    Specified by:
    
    getCliqueCount in interface ClusterWheatley
  - getECliqueCount
```
public int getECliqueCount()
```
    Description copied from interface: ClusterWheatley
    
    Returns number of e-bond cliques for the configuration passed to checkConfig
    
    Specified by:
    
    getECliqueCount in interface ClusterWheatley
  - getFullBondMask
```
public int[] getFullBondMask()
```
    Description copied from interface: ClusterWheatley
    
    Returns number bond mask for all points for the configuration passed to checkConfig
    
    Specified by:
    
    getFullBondMask in interface ClusterWheatley
  - getCliques
```
public int[] getCliques()
```
    Description copied from interface: ClusterWheatley
    
    Returns an array containing the clique sets for the configuration passed to checkConfig. The array is filled from the beginning and may contain cruft at the end (use getCliqueCount to know where to stop).
    
    Specified by:
    
    getCliques in interface ClusterWheatley
  - getECliques
```
public int[] getECliques()
```
    Description copied from interface: ClusterWheatley
    
    Returns an array containing the clique sets (based on e-bonds) for the configuration passed to checkConfig. The array is filled from the beginning and may contain cruft at the end (use getCliqueCount to know where to stop).
    
    Specified by:
    
    getECliques in interface ClusterWheatley
  - getOutDegree
```
public byte[] getOutDegree()
```
    Returns outDegee (number of bonds for each point) of the configuration passed to checkConfig
    
    Specified by:
    
    getOutDegree in interface ClusterWheatley
  - updateF
```
protected void updateF(BoxCluster box)
```
  - calcSignature
```
public long calcSignature(BoxCluster box)
```
  - updateF
```
protected void updateF()
```
  - setTemperature
```
public void setTemperature(double temperature)
```
    Specified by:
    
    setTemperature in interface ClusterAbstract
  - main
```
public static void main(java.lang.String[] args)
```

Class ClusterWheatleyPartitionScreening

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

n

nf

f

fQ

fA

fB

fAB

fC

cPairID

lastCPairID

value

lastValue

beta

outDegree

fullBondMask

cliqueSet

cliqueCount

eCliqueCount

precalcQ

cliqueList

eCliqueList

nPts

vCount

sig

partitionsA

partitionsC

fAList

fABList

fCList

allZero

fAValues

fABValues

nPtsTabulated

checkme

doStatistics

sigCounter

total

notzero

screened

edgeCount

Constructor Detail

ClusterWheatleyPartitionScreening

ClusterWheatleyPartitionScreening

Method Detail

computeAPartitions

makeCopy

pointCount

value

getCPairID

getLastCPairID

getLastValue

calcfQ

calcSignatures

checkConfig

cliqueCheck

calcValue

calcValue

calcfC

calcfAB

calcfAB0

getEdgeCount

getCliqueCount

getECliqueCount

getFullBondMask

getCliques

getECliques

getOutDegree

updateF

calcSignature

updateF

setTemperature

main