Interface  Description 

CoordinateDefinitionHSDimer.IntegerFunction  
IAPIPotential 
Preliminary interface for proposed IPotential interface

LatticeSumMolecularCrystal.AtomicTensorAtomicPair  
NormalModes 
Provides information about all the normal modes for a periodic system.

WaveVectorFactory 
Interface for a class the returns the appropriate wave vectors for a box
and primitive

Class  Description 

ArrayA2B 
Reads a file containing n mxm matrices as ASCII and serializes them to
another file.

ArrayB2A 
Reads a file containing n mxm matrices as (serialized) binary data and
writes them to another file as text (ASCII).

ArrayReader1D 
Reads in lots of 1D arrays from a file.

ArrayReader2D 
Reads in lots of 2D arrays from a file.

BasisBigCell  
BoltzmannProcessor 
DataProcessor that returns the Boltzmann factor of the incoming energy.

CalcHarmonicA 
Convenience class to calculate the Helmholtz free energy based on the
normal mode description of the system with harmonic springs governing the
system's exploration of the modes.

CalcJacobian 
Class that calculates the dq/dx Jacobian.

ConformationHSDimer 
Conformation for HS Dimer

CoordinateDefinition 
An abstract class that defines the realspace generalized coordinates that are
summed (over molecules) to form collective coordinates (from which normal
coordinates are determined).

CoordinateDefinition.BasisCell  
CoordinateDefinition.SiteSource  
CoordinateDefinitionHSDimer 
CoordinateDefinition implementation for HS Dimer.

CoordinateDefinitionLeaf 
CoordinateDefinition implementation for monatomic molecules that are simply
leaf atoms.

CoordinateDefinitionLeafSuperBox  
CoordinateDefinitionMolecule 
CoordinateDefinition implementation for molecules.

CoordinateDefinitionMolecule.MoleculeSiteSource  
CoordinateDefinitionMoleculeVolumeFluctuation 
CoordinateDefinition implementation for molecules.

CoordinateDefinitionMoleculeVolumeFluctuation.MoleculeSiteSource  
DataProcessorBoltzmannFactor  
DataProcessorSum 
DataProcessor that sends on the sum of the incoming data values as a scalar.

DataSourceAvgPressure 
Averages the measured pressures for various N.

DataSourceAvgPressure2 
Computes pressure from the grand canonical route based on measured free
energy differences and simulation parameters.

DataSourceFE 
Free energy data source that computes free energy differences based on
overlap sampling performed by an MCMoveOverlapListener.

DataSourceFEHistogram 
Returns a histogram of # of atoms based on free energy results and the given
chemical potential.

DataSourceImposedFEFit 
Like DataSourceFEHistogram, returns a probability histogram for N based on
free energies.

DataSourceImposedFEHistogram 
This is a strange creature...

DataSourceMuRoot 
Datasource that returns an estimate of mu based on thermodynamic
selfconsistency of pressure measurements and defect free energies.

DataSourceMuRoot1 
Datasource that returns an estimate of mu based on thermodynamic
selfconsistency of pressure measurements and defect free energies.

DataSourceMuRootPMatch 
Datasource that returns an estimate of mu based on thermodynamic
selfconsistency of pressure measurements and defect free energies.

DataSourcePMu 
DataSource that returns P2P1 or mumu* as a function of mu.

DataSourcePN 
DataSource that returns measured pressure as a function of N

DeviceCellNum3DSlider  
DeviceCellNumXYSlider  
DeviceEigenvaluesSlider  
DeviceWaveVectorSlider  
HarmonicCrystal 
Properties of a system of monatomic molecules occupying a lattice and interacting according
to a sphericallysymmetric pair potential.

HarmonicCrystalSoftSphereBCC 
Properties of a system of monatomic molecules occupying a lattice and interacting according
to a softsphere sphericallysymmetric pair potential.

HarmonicCrystalSoftSphereFCC 
Properties of a system of monatomic molecules occupying a lattice and interacting according
to a softsphere sphericallysymmetric pair potential.

HarmonicCrystalSoftSphereHCP 
Properties of a system of monatomic molecules occupying a lattice and interacting according
to a softsphere sphericallysymmetric pair potential.

HarmonicCrystalSsFccNxy 
Properties of a system of monatomic molecules occupying a lattice and
interacting according to a sphericallysymmetric pair potential.

HarmonicCrystalSsFccNxy.Params  
HessianDB 
MC simulation of FCC softsphere model in 3D with tabulation of the
collectivecoordinate Smatrix.

HessianFromFile 
MC simulation of FCC softsphere model in 3D with tabulation of the
collectivecoordinate Smatrix.

HSDimerNPT 
NPT simulation for hard sphere solid using an MCMove that does coordinate
scaling with volume changes.

HSDimerNPT.HSMD3DParameters  
HSNPT 
NPT simulation for hard sphere solid using an MCMove that does coordinate
scaling with volume changes.

HSNPT.ActionSummer  
HSNPT.ColorSchemeDisplacement  
HSNPT.HSMD3DParameters  
HSNPT.MyAgent  
HTTPSoftSphereApplet 
Applet to illustrate HTTP method

HTTPSoftSphereApplet.Applet  
HTTPSoftSphereApplet.SimOverlapTPSSParams  
HTTPSoftSphereSim 
Applet to illustrate HTTP method

IntegratorHardMDMC 
Custom DMD integrator that handles hybrid simulations with
insertion/deletions.

IntegratorHarmonic 
Integrator that is used for the harmonic osciallating system

LatticeSumMolecularCrystal  
LJVacancyMin  
LJVacancyMin.SimOverlapParam 
Inner class for parameters understood by the HSMD3D constructor

LJVacancyMin.VectorForce  
MCMoveAtomCoupled 
Standard Monte Carlo atomdisplacement trial move.

MCMoveAtomCoupledBennet 
Standard Monte Carlo atomdisplacement trial move.

MCMoveAtomCoupledUmbrella 
Standard Monte Carlo atomdisplacement trial move.

MCMoveAtomSuperBox 
Standard Monte Carlo atomdisplacement trial move.

MCMoveEinsteinCrystal 
MC move whose purpose in life is to sample an Einstein crystal.

MCMoveHarmonic  
MCMoveHarmonicEin 
MC move whose purpose in life is to sample a system whose energy is a
combination of normal mode contributions and Einstein crystal
contributions.

MCMoveHarmonicStep 
MCMove that performs random displacements in the harmonic coordinates for
the k=0 wave vector.

MCMoveMoleculeCoupled 
Standard Monte Carlo moleculedisplacement trial move.

MCMovePhaseAngle  
MCMoveRotateMoleculePhiTheta  
MCMoveSingleMode 
A Monte Carlo move which selects each individual modes to move
the atoms accordingly

MCMoveVolumeMonoclinic 
Standard Monte Carlo volumechange move for simulations in the NPT ensemble.

MCMoveVolumeMonoclinicAngle 
Standard Monte Carlo volumechange move for simulations in the NPT ensemble.

MCMoveVolumeMonoclinicScaled 
Monte Carlo volumechange move for simulations of crystalline solids in the
NPT ensemble (molecular model).

MCMoveVolumeSolid 
Monte Carlo volumechange move for simulations of crystalline solids in the
NPT ensemble.

MCMoveVolumeSolidNPTMolecular 
Monte Carlo volumechange move for simulations of crystalline solids in the
NPT ensemble (molecular model).

MCMoveVolumeSolidNPTMolecularOriented 
Class which handles orientation of linear molecules during volume change
trials.

MCMoveWV  
MeterAPIPotentialEnergy 
Meter that returns the potential energy using an IAPIPotential.

MeterAtomicDisplacement 
Calculates the average atomic displacement from their lattice sites

MeterBoltzmann 
Meter used for overlap sampling in the targetsampled system.

MeterBoltzmannHarmonic 
Meter used for overlap sampling in the harmonicsampled system.

MeterBoltzmannHTTP 
Same as TargetTP class but is used by MethodBoltzmannHTTP
It is to illustrate the idea of HTTP method.

MeterBoltzmannTarget 
Meter used for overlap sampling in the targetsampled system.

MeterDADB  
MeterDDP 
Meter that measures the overlap averages for perturbing from a solid at one
density into other densities.

MeterDirectSamplingHarmonic 
Meter used for overlap sampling in the harmonicsampled system.

MeterDirectSamplingTarget 
Meter used for overlap sampling in the targetsampled system.

MeterDisplacementMoleculeRMS  
MeterDisplacementRMS  
MeterDP 
Meter that measures the overlap averages for perturbing from a solid at one
density into other densities.

MeterHarmonicCoordinate  
MeterHarmonicEnergy 
Meter that calculates the harmonic energy of a configuration given
eigenvectors and omegas corresponding to wave vectors.

MeterHarmonicEnergyFromMove 
Meter that returns the harmonic energy from the MC move as a data source.

MeterHarmonicSingleEnergy 
Meter that calculates the Boltzmannfactored harmonic energy of each normal mode for a
configuration given eigenvectors and omegas corresponding to wave vectors.

MeterJacobian  
MeterMaxExpansion 
measures the maximum amount by which by which the HS diameter could increase
without causing overlap

MeterNormalMode 
Calculates the Smatrix for a configuration.

MeterOverlapSwitch 
Meter whose purpose in life is to measure the overlap between systems
defined by a combination of two energy meters.

MeterPhiDeviation 
Meter that measures the average tilt angle (not the angle of average tilt!)

MeterPlaneSlip 
Meter that measures the average tilt angle (not the angle of average tilt!)

MeterPressureSuperBox 
Meter for evaluation of the softpotential pressure in a box.

MeterSamplingHarmonic 
Meter used for compute for the probability of the harmonic sampling
< e0 / (e1 + alpha * e0)>umb

MeterSamplingTarget 
Meter used for compute for the probability of the target system sampling
< e1 / (e1 + alpha * e0)>umb

MeterSolidDA 
Meter for evaluation of the softpotential pressure in a box.

MeterSolidDACut 
Meter for evaluation of the softpotential pressure in a box.

MeterSolidMirror 
Meter uses harmonicallymapped averages to compute properties and also
couples configurations with their mirror images to obtain cancellation
of error at very low temperatures.

MeterSolidProps  
MeterSolidPropsLJ  
MeterTargetTP 
Meter that measures the overlap averages for perturbing from a solid at one
temperature into other the system at other temperatures.

MeterThetaDeviation 
Meter that measures the average tilt angle (not the angle of average tilt!)

MeterTilt 
Meter that measures the average tilt angle (not the angle of average tilt!)

MeterTiltHistogram 
Meter that measures the average tilt angle (not the angle of average tilt!)

MeterTiltRotation 
Meter that measures the average tilt angle (not the angle of average tilt!)

MeterTiltRotationHistogram 
Meter that measures the average tilt angle (not the angle of average tilt!)

MeterTiltRotationStdev 
Meter that measures the average tilt angle (not the angle of average tilt!)

MeterWorkBennetHarmonic 
Meter used for direct sampling in the harmonicsampled system.

MeterWorkBennetTarget 
Meter used for direct sampling in the targetsampled system.

MeterWorkHarmonicBennet 
Meter used for overlap sampling in the harmonicsampled system.

MeterWorkHarmonicPhaseSpace 
Meter used for overlap sampling in the harmonicsampled system.

MeterWorkHarmonicTargetandReweighting 
Meter used for overlap sampling in the harmonicsampled system.

MeterWorkHarmonicUmbrella 
Meter used for direct sampling in the harmonicsampled system.

MeterWorkTargetBennet 
Meter used for overlap sampling in the targetsampled system.

MeterWorkTargetHarmonicandReweighting 
Meter used for overlap sampling in the targetsampled system.

MeterWorkTargetPhaseSpace 
Meter used for overlap sampling in the targetsampled system.

MeterWorkTargetUmbrella 
Meter used for direct sampling in the targetsampled system.

MeterWorkUmbrellaHarmonic 
Meter used for direct sampling in the harmonicsampled system.

MeterWorkUmbrellaTarget 
Meter used for direct sampling in the targetsampled system.

MinimizeHCP 
Determines c/a ratio of primitive vector lengths corresponding to the
minimum energy HCP structure.

MinimizeHCP.SimOverlapParam 
Inner class for parameters understood by the HSMD3D constructor

ModifierCells3D 
Modifier class that enables change of the number of cells in 2D

ModifierXCells2D 
Modifier class that enables change of the number of cells in 2D

ModifierYCells2D 
Modifier class that enables change of the number of cells in 2D

NormalModeAnalysisDisplay1D  
NormalModeAnalysisDisplay1D.Applet  
NormalModeAnalysisDisplay1DGraphic  
NormalModeAnalysisDisplay1DGraphic.Applet  
NormalModeAnalysisDisplay2D 
Harmonic anaylsis for 2D softsphere model

NormalModeAnalysisDisplay2DGraphic  
NormalModeAnalysisDisplay2DGraphic.Applet  
NormalModeAnalysisDisplay3D  
NormalModeAnalysisDisplay3D.Applet  
NormalModeAnalysisDisplay3DGraphic 
Harmonic Oscillator 3D

NormalModeAnalysisDisplay3DGraphic.Applet  
NormalModeEigenGetter  
NormalModes1DHR 
Normalmode quantities for a 1dimensional system of hard rods.

NormalModes2D  
NormalModes3D  
NormalModesFromFile 
Provides normalmode information as obtained from a file read at
construction.

NormalModesMolecular 
Uses analysis of 2nd derivatives to compute the normal modes for a Bravais lattice with a basis,
occupied by atoms that interact with a simple, sphericallysymmetric soft potential.

NormalModesPotential 
Uses analysis of 2nd derivatives to compute the normal modes for a Bravais lattice with a basis,
occupied by atoms that interact with a simple, sphericallysymmetric soft potential.

NormalModesSoftSpherical 
Computes the normal modes for a Bravais lattice occupied by atoms that interact
with a simple, sphericallysymmetric soft potential, using analysis of second
derivatives.

NormalModesVariable  
P1Constraint  
P1ConstraintNbr  
P1ConstraintNbrHcp  
P2XOrder 
Hard potential that enforces ordering of the xcoordinates of the
pairs.

PotentialCalculationEFSSP  
PotentialCalculationLJSP  
PotentialCalculationSolidSuper 
Sums the force on each iterated atom and adds it to the integrator agent
associated with the atom.

PotentialCalculationSolidSuperCut 
Sums the force on each iterated atom and adds it to the integrator agent
associated with the atom.

PotentialCalculationSolidSuperCutLS 
Sums the force on each iterated atom and adds it to the integrator agent
associated with the atom.

SimBennet 
Simulation to sample Bennet's Overlap Region

SimBennet.SimBennetParam  
SimCalcJ 
Simulation class of hard spheres in 1D or 3D that calculates the dq/dx
Jacobian.

SimCalcS 
MD simulation of hard spheres in 1D or 3D with tabulation of the
collectivecoordinate Smatrix.

SimCalcSLJ 
MD simulation of hard spheres in 1D or 3D with tabulation of the
collectivecoordinate Smatrix.

SimCalcSMorse 
MC simulation of Morse model in 3D with tabulation of the
collectivecoordinate Smatrix.

SimCalcSSoftSphere2D 
MC simulation of FCC softsphere model in 2D with tabulation of the
collectivecoordinate Smatrix.

SimCalcSSoftSphereFCC 
MC simulation of FCC softsphere model in 3D with tabulation of the
collectivecoordinate Smatrix.

SimCalcSSoftSphereFCCSuperBox 
MC simulation of FCC softsphere model in 3D with tabulation of the
collectivecoordinate Smatrix.

SimEinStep1 
Simulation that samples a composite energy function (soft sphere and
Einstein crystal) and perturbs into overlap regions shared by systems with
more or less soft sphere contributions.

SimEinStep1.SimOverlapParam 
Inner class for parameters understood by the HSMD3D constructor

SimEinStep1HCP 
Simulation that samples a composite energy function (soft sphere and
Einstein crystal) and perturbs into overlap regions shared by systems with
more or less soft sphere contributions.

SimEinStep1HCP.SimOverlapParam 
Inner class for parameters understood by the HSMD3D constructor

SimEinStep2 
Simulation that samples a composite energy function (soft sphere and
Einstein crystal) and perturbs into overlap regions shared by systems with
more or less soft sphere contributions.

SimEinStep2.MeterPotentialEnergyComposite  
SimEinStep2.SimOverlapParam 
Inner class for parameters understood by the HSMD3D constructor

SimEinStep2HCP 
Simulation that samples a composite energy function (soft sphere and
Einstein crystal) and perturbs into overlap regions shared by systems with
more or less soft sphere contributions.

SimEinStep2HCP.MeterPotentialEnergyComposite  
SimEinStep2HCP.SimOverlapParam 
Inner class for parameters understood by the HSMD3D constructor

SimFluidSoftSphere 
MC simulation of softsphere fluid model

SimHarmonic 
Simulation to sample harmonic potential

SimHarmonicUmbrella 
Simulation to sample harmonic system and perturbing into
the umbrella sampling region

SimHarmonicUmbrella.SimBennetParam  
SimHSMDVacancy 
Simple LennardJones molecular dynamics simulation in 3D

SimHSMDVacancy.HSMDVParams  
SimLJHTTISuper  
SimLJHTTISuper.SimOverlapParam 
Inner class for parameters understood by the HSMD3D constructor

SimLJHTTISuperHCP  
SimLJHTTISuperHCP.SimOverlapParam 
Inner class for parameters understood by the HSMD3D constructor

SimLJVacancy 
Simple LennardJones molecular dynamics simulation in 3D

SimLJVacancy.LJParams  
SimModesJ 
Simulation class of hard spheres in 1D or 3D that calculates the dq/dx
Jacobian.

SimOverlap 
Simulation to run sampling with the hard sphere potential, but measuring
the harmonic potential based on normal mode data from a previous simulation.

SimOverlap.SimOverlapParam 
Inner class for parameters understood by the HSMD3D constructor

SimOverlapLJ 
Simulation to run sampling with the LJ potential, but measuring
the harmonic potential based on normal mode data from a previous simulation.

SimOverlapLJ.SimOverlapParam 
Inner class for parameters understood by the HSMD3D constructor

SimOverlapLJModule 
Main method that constructs an overlap sampling module to calculate the free
energy difference between a harmonic system and a lennard jones solid.

SimOverlapLJModule.APIPotentialReference  
SimOverlapLJModule.APIPotentialTarget  
SimOverlapLJModule.MeterPotentialEnergyDifference  
SimOverlapLJModule.SimOverlapParam 
Inner class for parameters understood by the HSMD3D constructor

SimOverlapModule 
Overlap sampling "module" to calculate free energy difference.

SimOverlapSoftSphere 
Simulation to run sampling with the hard sphere potential, but measuring
the harmonic potential based on normal mode data from a previous simulation.

SimOverlapSoftSphere.SimOverlapParam 
Inner class for parameters understood by the HSMD3D constructor

SimOverlapSoftSphereDP 
Simulation to run density perturbation for soft spheres.

SimOverlapSoftSphereDP.SimOverlapParam 
Inner class for parameters understood by the HSMD3D constructor

SimOverlapSoftSphereEin 
Simulation that samples a composite energy function (soft sphere and
Einstein crystal) and perturbs into overlap regions shared by systems with
more or less soft sphere contributions.

SimOverlapSoftSphereEin.MeterPotentialEnergyComposite  
SimOverlapSoftSphereEin.SimOverlapParam 
Inner class for parameters understood by the HSMD3D constructor

SimOverlapSoftSphereEinHarm 
Overlap sampling simulation whose target system has a composite energy
function (soft sphere and Einstein crystal) and whose reference system is
defined by (harmonically coupled) normal modes and Einstein crystal.

SimOverlapSoftSphereEinHarm.MeterPotentialEnergyComposite  
SimOverlapSoftSphereEinHarm.SimOverlapParam 
Inner class for parameters understood by the HSMD3D constructor

SimOverlapSoftSphereHCP 
Simulation to run sampling with the softsphere potential, but measuring
the harmonic potential based on normal mode data from a previous simulation.

SimOverlapSoftSphereHCP.SimOverlapParam 
Inner class for parameters understood by the HSMD3D constructor

SimOverlapSoftSphereReweighting 
Simulation to run sampling with the hard sphere potential, but measuring
the harmonic potential based on normal mode data from a previous simulation.

SimOverlapSoftSphereReweighting.SimOverlapParam 
Inner class for parameters understood by the HSMD3D constructor

SimOverlapSoftSphereSoftness 
Conduct Bennett's Overlap Sampling to quantify the freeenergy difference
between softsphere model with different softness
SoftSphere potential: U = epsilon*(sigma/r)^n
where n is the exponent, s = 1/n (where s is softness)
epsilon and sigma is set to 1

SimOverlapSoftSphereSoftness.SimOverlapParam 
Inner class for parameters understood by the HSMD3D constructor

SimOverlapSoftSphereSuperBox 
Simulation to run sampling with the hard sphere potential, but measuring
the harmonic potential based on normal mode data from a previous simulation.

SimOverlapSoftSphereSuperBox.SimOverlapParam 
Inner class for parameters understood by the HSMD3D constructor

SimOverlapSoftSphereTP 
Simulation to run sampling with the hard sphere potential, but measuring
the harmonic potential based on normal mode data from a previous simulation.

SimOverlapSoftSphereTP.SimOverlapParam 
Inner class for parameters understood by the HSMD3D constructor

SimOverlapSoftSphereTPHCP 
The original Bennett's Overlapping Sampling Simulation
 used to check for the computation time

SimOverlapSoftSphereTPHCP.SimOverlapParam 
Inner class for parameters understood by the HSMD3D constructor

SimOverlapSoftSphereTPSlantedBox 
Simulation to run sampling with the hard sphere potential, but measuring
the harmonic potential based on normal mode data from a previous simulation.

SimOverlapSoftSphereTPSlantedBox.SimOverlapParam 
Inner class for parameters understood by the HSMD3D constructor

SimOverlapSSnxy 
Simulation to run sampling with the hard sphere potential, but measuring
the harmonic potential based on normal mode data from a previous simulation.

SimOverlapSSnxy.SimOverlapParam 
Inner class for parameters understood by the HSMD3D constructor

SimTarget 
Simulation to run sampling with the hard sphere potential, but measuring
the harmonic potential based on normal mode data from a previous simulation.

SimTargetUmbrella 
Simulation to sample target system and perturbing into
the umbrella sampling region

SimTargetUmbrella.SimBennetParam  
SimUmbrella 
Simulation to sample Umbrella Sampling

SimUmbrella.SimBennetParam  
SimUmbrellaSoftSphere 
Simulation to sample Umbrella Overlap Sampling
The original Umbrella Sampling Simulation
 used to check for the computation time

SimUmbrellaSoftSphere.SimBennetParam  
SoftSphereSolidEOS 
SoftSphere Solid Equation of State
for n = 12, 9 and 6
Reference: Tan, Schultz and Kofke, J Chem.

SoftSphereSolidEOSCalculator  
SpeciesHSDimer 
Species hardsphere dimer molecule

WaveVectorFactory1D 
Wave vector factory that returns wave vectors for a 1D system.

WaveVectorFactory2D 
Wave vector factory that returns wave vectors appropriate for a box with
a singleatom basis.

WaveVectorFactoryFcc 
WaveVectorFactory implementation that returns wave vectors appropriate for
a cubic FCC lattice.

WaveVectorFactoryFromFile 
Obtains wave vectors and coefficients from a file.

WaveVectorFactorySimple 
Wave vector factory that returns wave vectors appropriate for a box with
a singleatom basis.

WaveVectorFactorySuperBox  
WriteS 
Class that writes out S from the MeterNormalMode, calculates
eigenvectors/values (writes them out) and calculates the harmonic free
energy from them.
