Interface  Description 

ClusterAbstract  
ClusterSumAssociation.ClusterCriteria  
ClusterWeight  
ClusterWeight.Factory  
ClusterWeightSumWall.DataSourceClusterWall  
ClusterWheatley  
CoordinatePairSet  
IntSet.PropertyBin  
MayerFunction  
MayerFunctionNonAdditive 
Interface for a Mayer ffunction, which takes 3+ atoms and
returns exp((u(atoms)u(pairs))/kT)  1

SpeciesFactory 
Class  Description 

AtomPairSet 
Class that holds a set of atom pairs.

B2ForSphericallySymmetricUByTrapezoidRule  
B2Ionic 
two points cluster diagrams calculation
Integral I2,S2,mean activity coefficient,osmotic coefficient of ionic solution via single integrals
include cycle diagram(=>DHLL); (k0); (k2);(kn+n)
=0, kbond, =1, modified qbond,etc, m>3,two diagrams are added up to evaluate
s = parameter * c^2 * I
ds/dc = parameter * ( 2*c*I + c^2 * dI/dc)
all are in simulation units
contains "linear step in sqrt(c)" && "linear step in c"

B3ForSphericallySymmetricU 
Compute B3 for a spherically symmetric potential to within a given tolerance, specified with getConvergece(), by
either FFT or FFT and one layer of quadrature.

B3ForSphericallySymmetricU.DampingParams  
B3LJ 
This is a main method to compute B3 and dB3/dT for LennardJones via FFT
It creates a discretization of the LennardJones Mayer function, and computes
B3 via FFT.

B3NonAddForSphericallySymmetricU 
Computes the classical, nonadditive component of B3 for a spherically symmetric potential using quadrature.

B4FFTLJ 
Computes four approximations of B4 by FFT: HNC(C), HNC(V), PY(C), and PY(V).

B5FFTLJ 
Computes four approximations of B5 by FFT: HNC(C), HNC(V), PY(C), and PY(V).

B6FFTLJ 
Modification of FFT Program of B4

BnHNCLJ 
This is just a main method for HypernettedChain.java...

BnHSIonic 
ionic solution, restrictive primitive model (RPM)
compute s, (phi[osmotic coefficient]1) and ln(gamma) from HARD SPHERE interaction(from Standard class)
2nd ~ 5th order integrals are included
p[] (<==> HSB[]) ==> integral = HSB[]* n! / (1n)
s[n] = c^n * HSB[n] / (1n)
ds[n]/dc = n * c ^ (n1) * HSB[n] / (1n) = s[n] * n/c cuz integral is independent of concentration
in simulation units
contains "linear step in sqrt(c)" && "linear step in c"

BnIETP2Spherical 
This is just a main method for HypernettedChain.java or PercusYevick.java...

BnJHBVArgon_Analytic 
Computes virial coefficients for argon using the analytical expressions
developed by Jaeger, Hellmann, Bich, and Vogel (2011), JCP, 135: 084308.

BnPY_1QC_Helium 
Computes the PercusYevick compressibilityroute approximation for to the
first quantum correction of Bn, where the first quantum correction is
as defined Kim and Henderson (1968,1966).

BnPYHardSphere 
This is just a main method for PercusYevick.java...

BnPYLJ 
This is just a main method for PercusYevick.java.

BnSCALJ 
Combines the PercusYevick and hypernettedchain approximations to the virial coefficients to
generate a selfconsistent (thermodynamically consistent) approximation.

BoxCluster  
CalcFFT 
CalcFFT can calculate distribution functions using FFT.

ClusterBonds  
ClusterBondsNonAdditive 
Subclass of ClusterBonds capable of handling nonadditive Mayer functions.

ClusterChainHS 
This class calculates the sum of all chain and/or ring clusters for hard potentials, for which the Mayer function
can take values of only 1 or 0.

ClusterChainSoft 
This class calculates the sum of all chain clusters.

ClusterCoupledAtomFlipped  
ClusterCoupledFlipped  
ClusterCoupledFlippedPartial  
ClusterDifference 
This class holds multiple clusters and returns the value from one minus the
average value from the others.

ClusterExchange  
ClusterICPYC 
Cluster class that computes the correction to the ICPY (incrementally
corrected PercusYevick) formulation.

ClusterPY  
ClusterSinglyConnected 
This class calculates the sum of all tree clusters using an adaptation of Wheatley's
recursive formulation.

ClusterSum  
ClusterSumAssociation 
repulsive potential: LennardJones potential
attractive potential: shorthanded square well potential
Wertheim's double attractionsite model, hyperpoint diagram
2 Fbond, 1 f_R bond diagram

ClusterSumEF  
ClusterSumExternalField  
ClusterSumHS 
This class calculates the sum of all biconnected clusters for hard spheres.

ClusterSumIC  
ClusterSumIC.FR2  
ClusterSumMultibody 
Cluster class capable of computing multibody (up to 6th order) contributions
to diagrams.

ClusterSumMultibodyShell  
ClusterSumNonAdditiveTrimerEnergy  
ClusterSumPolarizable  
ClusterSumPolarizableWertheimProduct  
ClusterSumPolarizableWertheimProduct4Pt  
ClusterSumPolarizableWertheimProduct4PtFinal  
ClusterSumShell  
ClusterSumStickyEF  
ClusterTree  
ClusterTreeBonds  
ClusterTreeEF  
ClusterWeightAbs  
ClusterWeightSumWall  
ClusterWeightUmbrella 
Umbrella cluster weight wrapper function.

ClusterWheatleyExtendSW  
ClusterWheatleyHS 
This class calculates the sum of all biconnected clusters using Wheatley's
recursive formulation.

ClusterWheatleyHS.AllSigs  
ClusterWheatleyMultibody 
This class uses Wheatley's recursion approach to calculating all biconnected
diagrams, but adds in nonadditive contributions.

ClusterWheatleyMultibodyBD 
This class uses Wheatley's recursion approach to calculating all biconnected
diagrams, but adds in nonadditive contributions.

ClusterWheatleyMultibodyMix 
This class uses Wheatley's recursion approach to calculating all biconnected
diagrams for a mixture, but adds in 3body contributions.

ClusterWheatleyPartitionScreening 
This class calculates the sum of all biconnected clusters using Wheatley's
recursive formulation.

ClusterWheatleySoft 
This class calculates the sum of all biconnected clusters using Wheatley's
recursive formulation.

ClusterWheatleySoftBD 
This class calculates the sum of all biconnected clusters using Wheatley's
recursive formulation.

ClusterWheatleySoftBDMix 
Cluster class using Whealtey's recursion with BigDecimal to handle mixtures.

ClusterWheatleySoftMix 
Cluster class using Whealtey's recursion to handle mixtures.

ConfigurationCluster  
ConfigurationClusterAceticAcid  
ConfigurationClusterChain  
ConfigurationClusterChainFourSites  
ConfigurationClusterMove  
ConfigurationClusterWertheimGCPM  
ConfigurationClusterWertheimGCPM4Pt  
ConfigurationClusterWertheimGCPMDirectSampling  
Conformation7SiteRigidSF6 
Conformation of SF6
7 LJ sites, rigid, no charge
Reference: Samios, Molecular force field investigation for sulfur hexafluoride: A computer simulation study

ConformationAlkaneEH 
Conformation for normal alkanes, explicit hydrogen
Siepmann, TraPPEEH

ConformationAnthracene3site 
Conformation for Anthracene
Reference paper: Iwai
3 site linear, group H to the two side benzene rings

ConformationAnthraceneTraPPE 
Conformation for Anthracene
Reference paper: TraPPE: 4 UA description of linear and branched alkanes and alkylbenzenes, Siepmann et al
modified from naphthalene conformation

ConformationCO2 
Conformation for CO2
Reference paper: Partial molar ~~, Stubbs DarkeWilhelm, Siepmann, JCP

ConformationMethane 
Conformation for TraPPEExplicit hydrogen methane
C site and H site, NOTE the H is located in the middle of CH bond

ConformationNaphthaleneTraPPE 
Conformation for Naphthalene
Reference paper: TraPPE: 4 UA description of linear and branched alkanes and alkylbenzenes, Siepmann et al

ConformationPh3site 
Conformation for Phenanthrene
Reference paper: Iwai
3 site group H to the two side benzene rings , eihter 464 or 545 model
modified from ConformationAnthracene

ConformationPhenanthreneTraPPE 
Conformation for Phenanthrene
Reference paper: TraPPE: 4 UA description of linear and branched alkanes and alkylbenzenes, Siepmann et al
modified from naphthalene
kept the axis and coorinated unchanged

CoordinatePairLeafSet  
CoordinatePairMoleculeSet  
HNCGenerator  
HypernettedChain 
Calculates the hypernettedchain (HNC) virial coefficients of second to Mth order for any sphericallysymmetric Mayer function, fr.

IEGenerator  
IntSet 
An IntSet holds an array of integers and can act as a has key.

IsFFT  
MayerD2FDT2Spherical 
Required for computing second derivatives of virial coefficients w/r to temperature

MayerDFDTSpherical 
Required for computing temperature derivatives of virial coefficients

MayerDFQFHDTSpherical 
Required for computing temperature derivatives of virial coefficients computed with quadratic FeynmannHibbs modification
to the potential.

MayerEGeneral  
MayerEHardSphere  
MayerENonGeneral  
MayerESpherical  
MayerFunctionMolecularThreeBody  
MayerFunctionNonAdditiveFull  
MayerFunctionProductGeneral  
MayerFunctionSphericalThreeBody 
Nonadditive Mayer function class for "spherical" potentials

MayerFunctionSum  
MayerFunctionSumGeneral  
MayerFunctionTemperature 
Mayer function that wraps another MayerFunction and ignores
the temperature passed to f(), asking the wrapped MayerFunction
for its value at the MayerFunction Temperature's temperature.

MayerFunctionThreeBody 
This class acts as a nonadditive Mayer function for molecules that
interact with only a 3body potential.

MayerGeneral  
MayerGeneralAtomic  
MayerGeneralSpherical  
MayerHardSphere  
MayerPTAtt 
Mayer function class that returns temperature expansion bond of the desired
order using molecular potentials.

MayerPUGeneral 
f + u
f: exp(beta U)
u: 0 for r < sigmaHS, dipole energy otherwise
a Potential2 object.

MayerSphericalPlus  
MayerSphericalPTAtt 
Mayer function class that returns temperature expansion bond of the desired
order.

MayerSSSeries  
MayerWell  
MayerXSpherical  
MCMoveChangeBondLength  
MCMoveClusterAngleBend 
An MC Move for cluster simulations that bends the bond angle for 3atom
molecule.

MCMoveClusterAngleBendAceticAcid 
An MC Move for cluster simulations that bends the bond angle for 3atom
molecule.

MCMoveClusterAtom 
Overrides MCMoveAtom to prevent index0 molecule from being displaced

MCMoveClusterAtomChainHSTail 
Grows configurations of chains with the pair probability distribution that
is flat for some distance and then has a powerlaw decay tail.

MCMoveClusterAtomDiscrete 
Extension of MCMoveClusterAtom that moves only the second atom and only
along the x axis.

MCMoveClusterAtomHSChain  
MCMoveClusterAtomHSRing  
MCMoveClusterAtomHSTree  
MCMoveClusterAtomMulti  
MCMoveClusterAtomQ  
MCMoveClusterAtomRotateMulti 
Extension of MCMoveAtom that does trial in which several atom orientations are
perturbed.

MCMoveClusterDiagram 
Move that attempts to perform changes in the cluster diagram.

MCMoveClusterMolecule 
Standard Monte Carlo moleculedisplacement trial move for cluster integrals.

MCMoveClusterMoleculeLayerMove 
Monte Carlo moleculedisplacement from 1 layer to the other layer trial move for cluster integrals.

MCMoveClusterMoleculeMulti  
MCMoveClusterPolyhedraChain  
MCMoveClusterPolyhedraTree  
MCMoveClusterReptateMulti 
An MC move for cluster simulations which performs reptation moves on molecules.

MCMoveClusterRingPartialRegrow 
MCMove that partially regrows the beads of a ring polymer, accepting or
rejecting the move based on the sampling weight.

MCMoveClusterRingRegrow 
MCMove that fully regrows the beads of a ring polymer, accepting or
rejecting the move based on the sampling weight.

MCMoveClusterRingRegrowExchange 
MCMove that fully regrows the beads of a ring polymer, accepting or
rejecting the move based on the sampling weight.

MCMoveClusterRingRegrowOrientation 
MCMove that fully regrows the beads of a ring polymer by rotating the images, accepting or
rejecting the move based on the sampling weight.

MCMoveClusterRingScale 
MCMove that scales the atoms of a molecule in or out.

MCMoveClusterRotateCH3 
Monte Carlo CH3 rotation for cluster integrals(Alkane TraPPEEH).

MCMoveClusterRotateMolecule3D 
MC move for Mayer Sampling that rotates a single molecule

MCMoveClusterRotateMoleculeMulti 
MCMove for use in a Mayer sampling simulation that rotates all molecules in
a Box except the first molecule, which is never moved.

MCMoveClusterTorsionAceticAcid 
An MC Move for cluster simulations that performs torsion moves on acetic acid.

MCMoveClusterTorsionAlkaneEH 
MC move for alkaneTraPPEEH torsion
pick up carbons in the box only, but move update all the atoms(carbons and hydrogens)

MCMoveClusterTorsionMulti 
An MC Move for cluster simulations that performs torsion moves on a chain
molecule (of length N>=4).

MCMoveClusterWiggleAceticAcid 
An MC Move for cluster simulations that "wiggles" a chain molecule.

MCMoveClusterWiggleAlkaneEH 
Wiggle move for alkane, TraPPEEH
hydrogens attached to the 3 carbons are updated, keeping bond lengths and angles fixed
*********** outline ************
// update j if j == 0 or j == n1
// update 3 H on j
// if j==0, update 2H on (j+1)
// if j==n1, update 2H on (j1)
&& 0 
MCMoveClusterWiggleMulti 
An MC Move for cluster simulations that "wiggles" a chain molecule.

MeterSamplingWeight 
Measures value of clusters in a box and returns the values
divided by the sampling bias from the sampling cluster.

MeterVirial 
Measures value of clusters in a box and returns the values
divided by the sampling bias from the sampling cluster.

MeterVirialBD 
This meter handles direct sampling with BigDecimal precision for averages.

MeterVirialBDBin 
Measures value of clusters in a box and returns the values
divided by the sampling bias from the sampling cluster.

MeterVirialBDBinMultiThreaded 
Measures cluster averages for virial coefficients.

MeterVirialBDBinMultiThreaded.MyData  
MeterVirialBinMultiThreaded 
Measures cluster averages for virial coefficients.

MeterVirialBinMultiThreaded.MyData  
MeterVirialEBinMultiThreaded 
Measures cluster averages for virial coefficients.

MeterVirialEBinMultiThreaded.MyData  
MeterVirialEBinMultiThreaded.MyDataCov  
MeterVirialExternalField 
Measures value of clusters in a box and returns the values
divided by the sampling bias from the sampling cluster.

MeterVirialExternalFieldConfined 
Measures value of clusters in a box and returns the values
divided by the sampling bias from the sampling cluster.

MeterVirialExternalFieldOverlapConfined 
Measures value of clusters in a box and returns the values
divided by the sampling bias from the sampling cluster.

MeterVirialExternalFieldOverlapConfined.RangeComparator  
MeterVirialExternalFieldOverlapConfinedRho 
Measures value of clusters in a box and returns the values
divided by the sampling bias from the sampling cluster.

MeterVirialExternalFieldOverlapConfinedSW 
Measures value of clusters in a box and returns the values
divided by the sampling bias from the sampling cluster.

MeterVirialExternalFieldOverlapRho 
Measures value of clusters in a box and returns the values
divided by the sampling bias from the sampling cluster.

MeterVirialExternalFieldRho 
Measures value of clusters in a box and returns the values
divided by the sampling bias from the sampling cluster.

MeterVirialExternalFieldSW 
Measures value of clusters in a box and returns the values
divided by the sampling bias from the sampling cluster.

MeterVirialExternalFieldSW.Near  
MeterVirialIC 
Returns cluster and distribution function values from ClusterSumIC

MeterVirialSWWE  
MoleculeActionRelaxWater3P  
MuFGeneral  
MuGeneral  
OrnsteinZernike  
P1IntraLambda  
PercusYevick 
Calculates the PercusYevick (PY) virial coefficients of second to Mth order for any sphericallysymmetric Mayer function, fr.

PercusYevick1QC 
Computes the PercusYevick compressibilityroute approximation to the
first quantum correction of Bn, where the first quantum correction is
as defined Kim and Henderson (1968,1966).

PotentialCommonAtomic  
PotentialEmulCached 
Potential class whose sole purpose is to remember previously calculated
energies and return them if no change has been made to the configuration.

PotentialGroup3PI 
PotentialGroup that calculates the energy between PI molecules triplets.

PotentialGroupPI 
PotentialGroup that calculates the energy between PI molecule pairs.

PotentialNonAdditive 
Potential class which computes nonadditive energies from potentials
that return the full energies for varioussized groups of molecules.

PYGenerator  
PYGenerator.IteratorEF  
Species7SiteRigidSF6 
Species SF6, 7 sites, LJ, rigid, no partial charge
Reference: Samios, Molecular force field investigation for sulfur hexafluoride: A computer simulation study

SpeciesAlkane  
SpeciesAlkaneEH 
Species for TraPPEExplicit hydrogen,Siepmann

SpeciesAnthracene3site464 
Species Anthracene molecule
rigid , LJ potential, no charge, this model is very similar to 3site 545 model, only the weight of the sites are different
reference: Iwai, monte carlo sim of Naphthalene, phenathlene,anthracene in SCF 1998
* @author shu
March, 7, 2011

SpeciesAnthracene3site545 
Species Anthracene molecule
rigid , LJ potential, no charge, 3 site model.each benzene ring is a site
reference: Iwai, monte carlo sim of Naphthalene, phenathlene,anthracene in SCF 1998
* @author shu
March, 7, 2011

SpeciesFactoryOrientedSpheres 
SpeciesFactory that makes SpeciesSpheresMono

SpeciesFactorySiepmannSpheres 
SpeciesFactory that makes Siepmann's alkane model.

SpeciesFactorySpheres 
SpeciesFactory that makes SpeciesSpheresMono

SpeciesFactorySpheres2  
SpeciesFactoryTangentSpheres 
SpeciesFactory that makes a tangent sphere species.

SpeciesFactoryWater3P 
SpeciesFactory that makes SpeciesWater

SpeciesFactoryWater4P 
SpeciesFactory that makes SpeciesWater

SpeciesFactoryWaterGCPM 
SpeciesFactory that makes SpeciesWater

SpeciesMethane 
Species for methane with explicit hydrogen
Bond angle = 109.5

SpeciesPh3site464 
Species Phenanthrene molecule
rigid , LJ potential, no charge, 3 site model.each benzene ring is a site, 464 model
reference: Iwai, monte carlo sim of Naphthalene, phenathlene,anthracene in SCF 1998

SpeciesPh3site545 
Species Phenanthrene molecule
rigid , LJ potential, no charge, 3 site model.each benzene ring is a site
reference: Iwai, monte carlo sim of Naphthalene, phenathlene,anthracene in SCF 1998

SpeciesTraPPEAnthracene 
Species Anthracene molecule
this is for TraPPE, the Anthracene is rigid , LJ potential, 10 interaction site
reference: TraPPE 4, UA description of linear and branched alkanes and alkylbenzenes, Siepmann
modified from Species Anthracene molecule class

SpeciesTraPPECO2 
Species CO2 molecule
this is for TraPPE, the CO2 is rigid , LJ potential + QQ

SpeciesTraPPENaphthalene 
Species Naphthalene molecule
this is for TraPPE, the Naphthalene is rigid , LJ potential
reference: TraPPE 4, UA description of linear and branched alkanes and alkylbenzenes, Siepmann

SpeciesTraPPEPhenanthrene 
Species Phenanthrene molecule
this is for TraPPE, the Phenanthrene is rigid , LJ potential
reference: TraPPE 4, UA description of linear and branched alkanes and alkylbenzenes, Siepmann
modified from species of phenanthrene C14H10
