| Interface | Description |
|---|---|
| ClusterAbstract | |
| ClusterAbstractMultivalue | |
| ClusterSumAssociation.ClusterCriteria | |
| ClusterWeight | |
| ClusterWeight.Factory | |
| ClusterWeightSumWall.DataSourceClusterWall | |
| ClusterWheatley | |
| CoordinatePairSet | |
| IntSet.PropertyBin | |
| MayerFunction | |
| MayerFunctionNonAdditive |
Interface for a Mayer f-function, 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, k-bond, =1, modified q-bond,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 Lennard-Jones via FFT
It creates a discretization of the Lennard-Jones Mayer function, and computes
B3 via FFT.
|
| B3NonAddForSphericallySymmetricU |
Computes the classical, non-additive 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! / (1-n)
s[n] = c^n * HSB[n] / (1-n)
ds[n]/dc = n * c ^ (n-1) * HSB[n] / (1-n) = 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.
|
| BnPCJSDHe |
This is just a main method for PercusYevick.java.
|
| BnPCJSDHe.BnPCJSDHeParams | |
| BnPY_1QC_Helium |
Computes the Percus-Yevick compressibility-route approximation for to the
first quantum correction of Bn, where the first quantum correction is
as defined Kim and Henderson (1968,1966).
|
| BnPYCHe |
This is just a main method for PercusYevick.java.
|
| BnPYCHe.BnPYHeParams | |
| BnPYHardSphere |
This is just a main method for PercusYevick.java...
|
| BnPYLJ |
This is just a main method for PercusYevick.java.
|
| BnSCALJ |
Combines the Percus-Yevick and hypernetted-chain approximations to the virial coefficients to
generate a self-consistent (thermodynamically consistent) approximation.
|
| BoxCluster | |
| CalcFFT |
CalcFFT can calculate distribution functions using FFT.
|
| ClusterBonds | |
| ClusterBondsNonAdditive |
Subclass of ClusterBonds capable of handling non-additive 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.
|
| ClusterConstant |
This class returns a constant value needed when using random placement of atoms in a box to sample the target system.
|
| ClusterCoupledAtomFlipped | |
| ClusterCoupledFlipped | |
| ClusterCoupledFlippedMultivalue | |
| 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 Percus-Yevick) formulation.
|
| ClusterMultiToSingle | |
| ClusterMultivalueUmbrella |
Umbrella cluster wraps a ClusterAbstractMultivalue.
|
| ClusterPY | |
| ClusterSinglyConnected |
This class calculates the sum of all tree clusters using an adaptation of Wheatley's
recursive formulation.
|
| ClusterSum | |
| ClusterSumAssociation |
repulsive potential: Lennard-Jones potential
attractive potential: short-handed square well potential
Wertheim's double attraction-site model, hyper-point diagram
2 F-bond, 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 non-additive contributions.
|
| ClusterWheatleyMultibodyBD |
This class uses Wheatley's recursion approach to calculating all biconnected
diagrams, but adds in non-additive contributions.
|
| ClusterWheatleyMultibodyDerivatives |
This class uses Wheatley's recursion approach to calculating all biconnected
diagrams, but adds in non-additive contributions.
|
| ClusterWheatleyMultibodyDerivatives.ClusterRetrievePrimes | |
| ClusterWheatleyMultibodyDerivativesBD |
This class uses Wheatley's recursion approach to calculating all biconnected
diagrams, but adds in non-additive contributions.
|
| ClusterWheatleyMultibodyDerivativesBD.ClusterRetrievePrimes | |
| ClusterWheatleyMultibodyMix |
This class uses Wheatley's recursion approach to calculating all biconnected
diagrams for a mixture, but adds in 3-body contributions.
|
| ClusterWheatleyPartitionScreening |
This class calculates the sum of all biconnected clusters using Wheatley's
recursive formulation.
|
| ClusterWheatleyPT |
Cluster that uses recursion to compute temperature perturbation coefficients.
|
| ClusterWheatleyPT.ClusterRetrievePrimesBD |
Cluster returns only BD values.
|
| 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.
|
| ClusterWheatleySoftDerivatives |
This class calculates the sum of all biconnected clusters using Wheatley's
recursive formulation.
|
| ClusterWheatleySoftDerivatives.ClusterRetrievePrimes | |
| ClusterWheatleySoftDerivatives.ClusterRetrievePrimesBD |
Cluster returns only BD values.
|
| ClusterWheatleySoftDerivativesBD |
This class calculates the sum of all biconnected clusters using Wheatley's
recursive formulation.
|
| ClusterWheatleySoftDerivativesBD.ClusterRetrievePrimes | |
| ClusterWheatleySoftDerivativesMix | |
| ClusterWheatleySoftDerivativesMixBD | |
| ClusterWheatleySoftMix |
Cluster class using Whealtey's recursion to handle mixtures.
|
| ClusterWheatleySoftMixBD |
Cluster class using Whealtey's recursion with BigDecimal 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
|
| 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
|
| 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 hypernetted-chain (HNC) virial coefficients of second to Mth order for any spherically-symmetric 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 Feynmann-Hibbs modification
to the potential.
|
| MayerEGeneral | |
| MayerEHardSphere | |
| MayerENonGeneral | |
| MayerESpherical | |
| MayerFunctionMolecularThreeBody | |
| MayerFunctionNonAdditiveFull | |
| MayerFunctionProductGeneral | |
| MayerFunctionSphericalThreeBody |
Non-additive 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 non-additive Mayer function for molecules that
interact with only a 3-body potential.
|
| MayerGeneral | |
| MayerGeneralAtomic | |
| MayerGeneralSpherical | |
| MayerHardSphere | |
| MayerHSMixture |
This class represents a Mayer function for any pair of species from a
hard sphere mixture.
|
| 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 3-atom
molecule.
|
| MCMoveClusterAngleBendAceticAcid |
An MC Move for cluster simulations that bends the bond angle for 3-atom
molecule.
|
| MCMoveClusterAtom |
Overrides MCMoveAtom to prevent index-0 molecule from being displaced
|
| MCMoveClusterAtomChainHSTail |
Grows configurations of chains with the pair probability distribution that
is flat for some distance and then has a power-law decay tail.
|
| MCMoveClusterAtomDiscrete |
Extension of MCMoveClusterAtom that moves only the second atom and only
along the x axis.
|
| MCMoveClusterAtomHSChain |
Class that samples molecule positions based on a chain of hard spheres of
diameter sigma.
|
| MCMoveClusterAtomHSChainMix |
Class that samples molecule positions based on a chain of hard spheres of
various sizes.
|
| MCMoveClusterAtomHSRing | |
| MCMoveClusterAtomHSTree |
Class that samples molecule positions based on a tree of hard spheres of
diameter sigma.
|
| MCMoveClusterAtomHSTreeMix |
Class that samples molecule positions based on a tree of hard spheres of
various sizes.
|
| MCMoveClusterAtomInBox |
Class that samples molecule positions by randomly placing hard spheres
in the box.
|
| MCMoveClusterAtomMulti | |
| MCMoveClusterAtomQ | |
| MCMoveClusterAtomRotateMulti |
Extension of MCMoveAtom that does trial in which several atom orientations are
perturbed.
|
| MCMoveClusterAtomSQWChain | |
| MCMoveClusterAtomSQWTree | |
| MCMoveClusterDiagram |
Move that attempts to perform changes in the cluster diagram.
|
| MCMoveClusterMolecule |
Standard Monte Carlo molecule-displacement trial move for cluster integrals.
|
| MCMoveClusterMoleculeHSChain |
Class that samples molecule positions based on a chain of hard spheres of
diameter sigma.
|
| MCMoveClusterMoleculeLayerMove |
Monte Carlo molecule-displacement 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 TraPPE-EH).
|
| 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 alkane-TraPPE-EH 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, TraPPE-EH
hydrogens attached to the 3 carbons are updated, keeping bond lengths and angles fixed
*********** outline ************
// update j if j == 0 or j == n-1
// update 3 H on j
// if j==0, update 2H on (j+1)
// if j==n-1, update 2H on (j-1)
&& 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 Percus-Yevick (PY) virial coefficients of second to Mth order for any spherically-symmetric Mayer function, fr.
|
| PercusYevick1QC |
Computes the Percus-Yevick compressibility-route 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 non-additive energies from potentials
that return the full energies for various-sized 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 | |
| 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
|
| SpeciesFactorySpheres |
SpeciesFactory that makes SpeciesSpheresMono
|
| SpeciesFactoryWaterGCPM |
SpeciesFactory that makes SpeciesWater
|
| 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
|
| 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
|