Interface  Description 

DiagramSource 
Class  Description 

BondConnectedSubstitution 
If Wertheim diagrams have bond connected network, fR bond is split into eR and one bond.

BondConnectedSubstitution.BondConnectedSubstitutionParameters2Site  
BondConnectedSubstitution3Site 
If Wertheim diagrams have bond connected network, fR bond is split into eR and one bond.

BondConnectedSubstitution3Site.BondConnectedSubstitutionParameters3Site  
BondConnectedSubstitutionNaphthalene 
revised from Hye Min's "BondConnectedSubstitution"
If Wertheim diagrams have bond connected network, fR bond is split into eR and one bond.

BondConnectedSubstitutionNaphthalene.BondConnectedSubstitutionParameters2SiteNa  
Chain  
ClusterAssociation  
ClusterCollapsedTreeNode  
ClusterDiagram 
Holds information about a cluster diagram, including the bonds, root points,
and score.

ClusterDiagramTree 
Holds information about a cluster diagram, including the bonds, root points,
and score.

ClusterGenerator 
Generates all clusters matching certain criteria.

ClusterOperations  
ClusterTreeNode  
CondenseExchange 
This operation replaces groups of points connected (internally) by
eexchange bonds with a single point.

CondenseExchange.CondenseExchangeParameters  
DCF 
Main method that simply generates and displays the graphs in the direct
correlation function.

ExchangeSplit 
This operation splits each ebond component into a sum of permuted
(exchanged) nodes.

ExchangeSplit.ExchangeSplitParameters  
ExternalVirialDiagrams  
Full  
MayerIonicDiagram1qbond 
modified from WertheimNaphthalene class
cluster diagrams generator for ionic solutions, based on Mayer's theory
fbond is splitted to kbond, (kg1+g1)
diagrams with g chain(s) are reduced to lower order of diagrams(here they are just simply discarded)
g1/kg1 is magically changed to represent q1bond [exp(kappa * r / (4*pi*r)] with different domain, but g1 is still in use
kg1 represents [exp(kappa * r / (4*pi*r)] instead of [exp(alpha * r / (4*pi*r)] (kq1 essentially)
===> then q1 is substituted by (xq1kg1), where xq1 has domain:[sigmaHS, infinity]
qi represent xqi bonds, gi represent REAL q bonds
the final result contains q1(represent xq1) and kg1(represent q1)
can handle 4pt
just xq1 & kq1 & k in the final set of S

MayerIonicDiagram2qbonds 
Mayer's theory on ionic solution
fbond is splitted to kbond, (kg+g),(kg2+g2)
diagrams with g chain(s) are reduced to lower order of diagrams(here they are just simply discarded)
gi is substituted by (qi  kgi)
qi represent modified q bonds, gi represent REAL q bonds
even number of q bonds , the final result contains q1,q2,kg1,kg2bonds

MayerIonicDiagram4qbonds 
cluster diagrams generator for ionic solutions, based on Mayer's theory
fbond is split into kbond(HS fhond), (kg+g),(kg2+g2),(kg3+g3),(kg4+g4)truncation
diagrams with g chain(s) are reduced to lower order of diagrams(here they are just simply discarded)
gi is substituted by (qi  kgi), where qi represents modified q bonds( domain [sigmaHS,infinity), gi represent REAL q bonds, i represents q bonds power
the final sets of diagrams contains q1,q2,q3,q4;kg1,kg2,kg3,kg4 bonds
2 pt diagrams with q2 bond is discarded ( cycle diagram)
cannot handle 4 points due to the insufficiency of calculations

PermutationIterator  
Ring  
Standard  
VirialDiagrams  
VirialDiagrams.ArticulatedAt0  
VirialDiagrams.ComparatorNumFieldNodesExchange  
VirialDiagramsMix  
VirialDiagramsMix2  
VirialDiagramsMix2.MaxIsomorphCriteriaMixture  
VirialDiagramsPT  
VirialDiagramsPT.ArticulatedAt0  
VirialDiagramsPT.ComparatorNumFieldNodesExchange  
VirialDiagramsPT.DiscardCriteria  
WertheimDiagrams2SiteRho 
Wertheim diagram generator for 2 site model

WertheimDiagrams3SiteRho 
Wertheim diagram generator for GCPM water (3 site model)
