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A

A - Variable in class etomica.conjugategradient.ConjugateGradients
 
A - Variable in class etomica.conjugategradient.PreconditionedConjugateGradient
 
A - Variable in class etomica.conjugategradient.SteepestDescent
 
a - Variable in class etomica.dimer.P1LepsHarmonic
 
A - Variable in class etomica.meam.ParameterSetMEAM
 
a - Variable in class etomica.meam.ParameterSetMEAM
 
A - Variable in class etomica.meam.PotentialCuLREP
 
A - Variable in class etomica.meam.PotentialEFS
 
a - Variable in class etomica.meam.PotentialFeEAM
 
a - Variable in class etomica.paracetamol.AnalyticalDerivativeEnergyParacetamol
 
a - Static variable in class etomica.virial.ConformationAnthraceneTraPPE
 
a - Static variable in class etomica.virial.ConformationPhenanthreneTraPPE
 
a - Variable in class etomica.virial.MCMoveClusterAtomHSTree
 
a - Variable in class etomica.virial.MCMoveClusterPolyhedraTree
 
a0 - Variable in class etomica.meam.PotentialFeEAM_LS
 
A1 - Variable in class etomica.dimer.P1LepsHarmonic
 
a1 - Variable in class etomica.virial.B3ForSphericallySymmetricU.DampingParams
 
A2 - Variable in class etomica.dimer.P1LepsHarmonic
 
a2 - Variable in class etomica.virial.B3ForSphericallySymmetricU.DampingParams
 
aBonds - Variable in class etomica.virial.cluster.VirialDiagramsPT
 
acceptNotify() - Method in class etomica.models.hexane.MCMoveCBMC
 
acceptNotify() - Method in class etomica.models.hexane.MCMoveCombinedCbmcTranslation
 
acceptNotify() - Method in class etomica.models.hexane.MCMoveReptate
 
acceptNotify() - Method in class etomica.normalmode.MCMoveAtomCoupled
Method called by IntegratorMC in the event that the most recent trial is accepted.
acceptNotify() - Method in class etomica.normalmode.MCMoveAtomCoupledBennet
Method called by IntegratorMC in the event that the most recent trial is accepted.
acceptNotify() - Method in class etomica.normalmode.MCMoveAtomCoupledUmbrella
Method called by IntegratorMC in the event that the most recent trial is accepted.
acceptNotify() - Method in class etomica.normalmode.MCMoveAtomSuperBox
Method called by IntegratorMC in the event that the most recent trial is accepted.
acceptNotify() - Method in class etomica.normalmode.MCMoveEinsteinCrystal
 
acceptNotify() - Method in class etomica.normalmode.MCMoveHarmonic
 
acceptNotify() - Method in class etomica.normalmode.MCMoveHarmonicStep
 
acceptNotify() - Method in class etomica.normalmode.MCMoveMoleculeCoupled
 
acceptNotify() - Method in class etomica.normalmode.MCMovePhaseAngle
 
acceptNotify() - Method in class etomica.normalmode.MCMoveRotateMoleculePhiTheta
 
acceptNotify() - Method in class etomica.normalmode.MCMoveSingleMode
 
acceptNotify() - Method in class etomica.normalmode.MCMoveVolumeMonoclinic
 
acceptNotify() - Method in class etomica.normalmode.MCMoveVolumeMonoclinicAngle
 
acceptNotify() - Method in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
 
acceptNotify() - Method in class etomica.normalmode.MCMoveVolumeSolid
 
acceptNotify() - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
 
acceptNotify() - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecularOriented
 
acceptNotify() - Method in class etomica.normalmode.MCMoveWV
 
acceptNotify() - Method in class etomica.paracetamol.MCMoveMoleculeCoupledDLPOLY
 
acceptNotify() - Method in class etomica.spin.MCMoveSpinFlip
 
acceptNotify() - Method in class etomica.virial.BoxCluster
Informs the box that the trial was accepted so it will keep the new coordinate pairs.
acceptNotify() - Method in class etomica.virial.MCMoveChangeBondLength
 
acceptNotify() - Method in class etomica.virial.MCMoveClusterAngleBend
 
acceptNotify() - Method in class etomica.virial.MCMoveClusterAngleBendAceticAcid
 
acceptNotify() - Method in class etomica.virial.MCMoveClusterAtom
 
acceptNotify() - Method in class etomica.virial.MCMoveClusterAtomChainHSTail
 
acceptNotify() - Method in class etomica.virial.MCMoveClusterAtomDiscrete
 
acceptNotify() - Method in class etomica.virial.MCMoveClusterAtomHSChain
 
acceptNotify() - Method in class etomica.virial.MCMoveClusterAtomHSRing
 
acceptNotify() - Method in class etomica.virial.MCMoveClusterAtomHSTree
 
acceptNotify() - Method in class etomica.virial.MCMoveClusterAtomMulti
 
acceptNotify() - Method in class etomica.virial.MCMoveClusterAtomQ
 
acceptNotify() - Method in class etomica.virial.MCMoveClusterAtomRotateMulti
 
acceptNotify() - Method in class etomica.virial.MCMoveClusterDiagram
 
acceptNotify() - Method in class etomica.virial.MCMoveClusterMolecule
 
acceptNotify() - Method in class etomica.virial.MCMoveClusterMoleculeMulti
 
acceptNotify() - Method in class etomica.virial.MCMoveClusterPolyhedraChain
 
acceptNotify() - Method in class etomica.virial.MCMoveClusterPolyhedraTree
 
acceptNotify() - Method in class etomica.virial.MCMoveClusterReptateMulti
 
acceptNotify() - Method in class etomica.virial.MCMoveClusterRingPartialRegrow
 
acceptNotify() - Method in class etomica.virial.MCMoveClusterRingRegrow
 
acceptNotify() - Method in class etomica.virial.MCMoveClusterRingRegrowExchange
 
acceptNotify() - Method in class etomica.virial.MCMoveClusterRingRegrowOrientation
 
acceptNotify() - Method in class etomica.virial.MCMoveClusterRingScale
 
acceptNotify() - Method in class etomica.virial.MCMoveClusterRotateCH3
 
acceptNotify() - Method in class etomica.virial.MCMoveClusterRotateMolecule3D
 
acceptNotify() - Method in class etomica.virial.MCMoveClusterRotateMoleculeMulti
 
acceptNotify() - Method in class etomica.virial.MCMoveClusterTorsionAceticAcid
 
acceptNotify() - Method in class etomica.virial.MCMoveClusterTorsionAlkaneEH
 
acceptNotify() - Method in class etomica.virial.MCMoveClusterTorsionMulti
 
acceptNotify() - Method in class etomica.virial.MCMoveClusterWiggleAceticAcid
 
acceptNotify() - Method in class etomica.virial.MCMoveClusterWiggleAlkaneEH
 
acceptNotify() - Method in class etomica.virial.MCMoveClusterWiggleMulti
 
acceptNotify() - Method in class etomica.virial.paralleltempering.MCMoveSwapCluster
Swaps positions of molecules in two boxes.
accumulator - Variable in class etomica.normalmode.SimOverlapSoftSphereDP
 
accumulator - Variable in class etomica.normalmode.SimOverlapSoftSphereEin
 
accumulator - Variable in class etomica.normalmode.SimOverlapSoftSphereTP
 
accumulator - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP
 
accumulator - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox
 
accumulator - Variable in class etomica.virial.simulations.SimulationVirial
 
accumulator - Variable in class etomica.virial.simulations.SimulationVirialPT
 
accumulatorPump - Variable in class etomica.normalmode.SimOverlapSoftSphereDP
 
accumulatorPump - Variable in class etomica.normalmode.SimOverlapSoftSphereEin
 
accumulatorPump - Variable in class etomica.normalmode.SimOverlapSoftSphereTP
 
accumulatorPump - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP
 
accumulatorPump - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox
 
accumulatorPump - Variable in class etomica.virial.simulations.SimulationVirial
 
accumulatorPump - Variable in class etomica.virial.simulations.SimulationVirialPT
 
accumulatorPumps - Variable in class etomica.normalmode.SimOverlap
 
accumulatorPumps - Variable in class etomica.normalmode.SimOverlapLJ
 
accumulatorPumps - Variable in class etomica.normalmode.SimOverlapLJModule
 
accumulatorPumps - Variable in class etomica.normalmode.SimOverlapModule
 
accumulatorPumps - Variable in class etomica.normalmode.SimOverlapSoftSphere
 
accumulatorPumps - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
 
accumulatorPumps - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
 
accumulatorPumps - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting
 
accumulatorPumps - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
 
accumulatorPumps - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox
 
accumulatorPumps - Variable in class etomica.normalmode.SimOverlapSSnxy
 
accumulatorPumps - Variable in class etomica.virial.simulations.SimulationVirialMultiOverlap
 
accumulatorPumps - Variable in class etomica.virial.simulations.SimulationVirialOverlap
 
accumulatorPumps - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
 
accumulators - Variable in class etomica.normalmode.SimOverlap
 
accumulators - Variable in class etomica.normalmode.SimOverlapLJ
 
accumulators - Variable in class etomica.normalmode.SimOverlapLJModule
 
accumulators - Variable in class etomica.normalmode.SimOverlapSoftSphere
 
accumulators - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
 
accumulators - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
 
accumulators - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting
 
accumulators - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
 
accumulators - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox
 
accumulators - Variable in class etomica.normalmode.SimOverlapSSnxy
 
accumulators - Variable in class etomica.virial.MeterVirialBDBin
 
accumulators - Variable in class etomica.virial.simulations.SimulationVirialMultiOverlap
 
accumulators - Variable in class etomica.virial.simulations.SimulationVirialOverlap
 
accumulators - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
 
AccumulatorVirialOverlapSingleAverage - Class in etomica.virial.overlap
Accumulator for taking ratio between two sums (and pretend it's an "average") Data added to this accumulator must be a 2-element DataDoubleArray
AccumulatorVirialOverlapSingleAverage(int, boolean) - Constructor for class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage
 
AccumulatorVirialOverlapSingleAverage(long, int, boolean) - Constructor for class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage
 
ACollectionBondedPotential - Class in etomica.virial.GUI.components
 
ACollectionBondedPotential() - Constructor for class etomica.virial.GUI.components.ACollectionBondedPotential
 
actionIntegrate - Variable in class etomica.paracetamol.MCParacetamolMonoclinicDLMULTI
 
actionIntegrate - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicDLMULTI
 
actionIntegrate - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
 
actionIntegrate - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
 
actionIntegrator - Variable in class etomica.virial.simulations.TestLJAssociationMC3D_NPT
 
actionPerformed() - Method in class etomica.models.hexane.CheckCBMCHexane
 
actionPerformed() - Method in class etomica.models.hexane.ShowStep
 
actionPerformed() - Method in class etomica.normalmode.HSNPT.ActionSummer
 
actionPerformed() - Method in class etomica.normalmode.MeterAtomicDisplacement
 
actionPerformed() - Method in class etomica.normalmode.MeterNormalMode
Calculating things and adds terms to the sums
actionPerformed() - Method in class etomica.normalmode.MeterTiltHistogram
 
actionPerformed() - Method in class etomica.normalmode.MeterTiltRotationHistogram
 
actionPerformed() - Method in class etomica.normalmode.WriteS
 
actionPerformed(IAtom) - Method in class etomica.paracetamol.AtomActionTransformed
 
actionPerformed(ActionEvent) - Method in class etomica.virial.GUI.controllers.ControllerAlertMsgBox.CloseWindowButtonListener
 
actionPerformed(ActionEvent) - Method in class etomica.virial.GUI.controllers.ControllerAlertMsgBoxSpeciesRemoval.NoDoNotRemoveSpeciesButtonListener
 
actionPerformed(ActionEvent) - Method in class etomica.virial.GUI.controllers.ControllerAlertMsgBoxSpeciesRemoval.YesRemoveSpeciesButtonListener
 
actionPerformed(ActionEvent) - Method in class etomica.virial.GUI.views.ViewConsoleOutputBox
 
actionPerformed() - Method in class etomica.virial.MeterVirialBDBin
 
actionPerformed() - Method in class etomica.virial.MeterVirialBDBinMultiThreaded
 
actionPerformed() - Method in class etomica.virial.MeterVirialBinMultiThreaded
 
actionPerformed() - Method in class etomica.virial.MeterVirialEBinMultiThreaded
 
actionPerformed(IMolecule) - Method in class etomica.virial.MoleculeActionRelaxWater3P
 
actionPerformed() - Method in class etomica.zeolite.MSDCoordWriter
 
actionPerformed(IEvent) - Method in class etomica.zeolite.MSDCoordWriter
 
actionPerformed() - Method in class etomica.zeolite.ZeoliteSimStart
 
ActionSummer(IBox, ISpace) - Constructor for class etomica.normalmode.HSNPT.ActionSummer
 
active - Variable in class etomica.threaded.atom.PotentialMasterListWorker
 
active - Variable in class etomica.threaded.domain.PotentialMasterListWorker
 
activity - Variable in class etomica.conjugategradient.DerivativeEnergyFunction
 
activity - Variable in class etomica.conjugategradient.FiniteDifferenceDerivativeCG
 
activityIntegrate - Variable in class etomica.densityofstate.DensityOfState
 
activityIntegrate - Variable in class etomica.densityofstate.DensityOfStatesPolynomial
 
activityIntegrate - Variable in class etomica.dimer.IntegratorDimerMin
 
activityIntegrate - Variable in class etomica.dimer.IntegratorDimerRT
 
activityIntegrate - Variable in class etomica.meam.EFSTungsten
 
activityIntegrate - Variable in class etomica.meam.MEAM_3DMDwithGB
 
activityIntegrate - Variable in class etomica.meam.MEAM_3DMDwithSnAgGB
 
activityIntegrate - Variable in class etomica.meam.MEAM_3DMDwithSnCuGB
 
activityIntegrate - Variable in class etomica.meam.MEAM_MC
 
activityIntegrate - Variable in class etomica.meam.MEAMMd3D
 
activityIntegrate - Variable in class etomica.models.hexane.HexaneVolumeFraction
 
activityIntegrate - Variable in class etomica.models.hexane.SimHarmonicHexane
 
activityIntegrate - Variable in class etomica.models.hexane.TestHexane
 
activityIntegrate - Variable in class etomica.models.hexane.TestHexaneCBMCOnly
 
activityIntegrate - Variable in class etomica.models.hexane.TestHexaneFileConfig
 
activityIntegrate - Variable in class etomica.models.hexane.TestHexaneHarmonic
 
activityIntegrate - Variable in class etomica.models.hexane.TestSetToUHexane
 
activityIntegrate - Variable in class etomica.normalmode.HessianDB
 
activityIntegrate - Variable in class etomica.normalmode.HSDimerNPT
 
activityIntegrate - Variable in class etomica.normalmode.HSNPT
 
activityIntegrate - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1D
 
activityIntegrate - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2D
 
activityIntegrate - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3D
 
activityIntegrate - Variable in class etomica.normalmode.SimBennet
 
activityIntegrate - Variable in class etomica.normalmode.SimCalcJ
 
activityIntegrate - Variable in class etomica.normalmode.SimCalcS
 
activityIntegrate - Variable in class etomica.normalmode.SimCalcSLJ
 
activityIntegrate - Variable in class etomica.normalmode.SimCalcSMorse
 
activityIntegrate - Variable in class etomica.normalmode.SimCalcSSoftSphere2D
 
activityIntegrate - Variable in class etomica.normalmode.SimCalcSSoftSphereFCC
 
activityIntegrate - Variable in class etomica.normalmode.SimCalcSSoftSphereFCCSuperBox
 
activityIntegrate - Variable in class etomica.normalmode.SimEinStep1
 
activityIntegrate - Variable in class etomica.normalmode.SimEinStep1HCP
 
activityIntegrate - Variable in class etomica.normalmode.SimEinStep2
 
activityIntegrate - Variable in class etomica.normalmode.SimEinStep2HCP
 
activityIntegrate - Variable in class etomica.normalmode.SimFluidSoftSphere
 
activityIntegrate - Variable in class etomica.normalmode.SimHarmonic
 
activityIntegrate - Variable in class etomica.normalmode.SimHarmonicUmbrella
 
activityIntegrate - Variable in class etomica.normalmode.SimLJHTTISuper
 
activityIntegrate - Variable in class etomica.normalmode.SimLJHTTISuperHCP
 
activityIntegrate - Variable in class etomica.normalmode.SimModesJ
 
activityIntegrate - Variable in class etomica.normalmode.SimOverlap
 
activityIntegrate - Variable in class etomica.normalmode.SimOverlapLJ
 
activityIntegrate - Variable in class etomica.normalmode.SimOverlapLJModule
 
activityIntegrate - Variable in class etomica.normalmode.SimOverlapModule
 
activityIntegrate - Variable in class etomica.normalmode.SimOverlapSoftSphere
 
activityIntegrate - Variable in class etomica.normalmode.SimOverlapSoftSphereDP
 
activityIntegrate - Variable in class etomica.normalmode.SimOverlapSoftSphereEin
 
activityIntegrate - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
 
activityIntegrate - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
 
activityIntegrate - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting
 
activityIntegrate - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
 
activityIntegrate - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox
 
activityIntegrate - Variable in class etomica.normalmode.SimOverlapSoftSphereTP
 
activityIntegrate - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP
 
activityIntegrate - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox
 
activityIntegrate - Variable in class etomica.normalmode.SimOverlapSSnxy
 
activityIntegrate - Variable in class etomica.normalmode.SimTarget
 
activityIntegrate - Variable in class etomica.normalmode.SimTargetUmbrella
 
activityIntegrate - Variable in class etomica.normalmode.SimUmbrella
 
activityIntegrate - Variable in class etomica.normalmode.SimUmbrellaSoftSphere
 
activityIntegrate - Variable in class etomica.threaded.atom.LJMD3DThreaded
 
activityIntegrate - Variable in class etomica.threaded.domain.LJMD3DThreaded
 
activityIntegrate - Variable in class etomica.threaded.domain.MEAMMd3DThreaded
 
activityIntegrate - Variable in class etomica.zeolite.ZeoliteSimulation
 
activityIntegrateDimer - Variable in class etomica.dimer.SimDimerLJadatom
 
activityIntegrateDimer - Variable in class etomica.dimer.SimDimerLJgb
 
activityIntegrateDimer - Variable in class etomica.dimer.SimDimerMEAMadatom
 
activityIntegrateDimer - Variable in class etomica.dimer.SimDimerMEAMGB
 
activityIntegrateMAP - Variable in class etomica.dimer.EnergyMap
 
activityIntegrateMD - Variable in class etomica.dimer.SimDimerLJadatom
 
activityIntegrateMD - Variable in class etomica.dimer.SimDimerLJgb
 
activityIntegrateMD - Variable in class etomica.dimer.SimDimerMEAMadatom
 
activityIntegrateMD - Variable in class etomica.dimer.SimDimerMEAMGB
 
activityIntegrateMin - Variable in class etomica.dimer.SimDimerLJadatom
 
activityIntegrateMin - Variable in class etomica.dimer.SimDimerMEAMadatom
 
activityIntegrateMin - Variable in class etomica.dimer.SimDimerMEAMGB
 
actualFlipList - Variable in class etomica.virial.ClusterCoupledFlippedPartial
 
adAtomPos - Variable in class etomica.dimer.SimDimerLJadatom
 
adAtomPos - Variable in class etomica.dimer.SimDimerMEAMadatom
 
adAtomPos - Variable in class etomica.dimer.SimDimerMEAMGB
 
addAddSpecies1ButtonListener(ActionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
 
addAddSpecies2ButtonListener(ActionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
 
addAddSpecies3ButtonListener(ActionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
 
addAlkaneLengthViewListener(int) - Method in class etomica.virial.GUI.controllers.ControllerAlkaneLengthSelection
 
addAlterSimEnvButtonListener(ActionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
 
addAlterSimEnvButtonListener(ActionListener) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
 
addAnotherSpeciesButtonListener(ActionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
 
addBondedPotentialSets(CollectionPotentialAtomicLike, ISpace, int) - Method in class etomica.virial.GUI.components.ACollectionBondedPotential
 
addBondedPotentialSets(CollectionPotentialAtomicLike, ISpace, int) - Method in class etomica.virial.GUI.components.CollectionBondedPotentialAlcohols
 
addBondedPotentialSets(CollectionPotentialAtomicLike, ISpace, int) - Method in class etomica.virial.GUI.components.CollectionBondedPotentialAlkanes
 
addCellNumSliderListener(ChangeListener) - Method in class etomica.normalmode.DeviceCellNum3DSlider
Add the specified listener to the list of listeners that will get invoked when the 'nCell #' slider value changes.
addChooseOkayButtonListener(ActionListener) - Method in class etomica.virial.GUI.views.ViewSimEnvironmentSelection
 
addCloseWindowButtonListener(ActionListener) - Method in class etomica.virial.GUI.views.ViewAlertMsgBox
 
addCloseWindowButtonListener(ActionListener) - Method in class etomica.virial.GUI.views.ViewAlkaneLengthSelection
 
addCloseWindowButtonListener(ActionListener) - Method in class etomica.virial.GUI.views.ViewSimEnvironmentSelection
 
addClusterDiagram(ClusterDiagram) - Method in class etomica.virial.cluster.ClusterDiagramTree
Adds the given diagram to the tree, adding nodes as needed
addConnection(int, int) - Method in class etomica.virial.cluster.ClusterDiagram
Adds a connection between the node1 and node2.
addCountOfSpeciesSLMListener(ChangeListener, int) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
 
addData(BigDecimal, MathContext) - Method in class etomica.virial.MeterVirialBDBinMultiThreaded.MyData
 
addData(double) - Method in class etomica.virial.MeterVirialBinMultiThreaded.MyData
 
addData(double[]) - Method in class etomica.virial.MeterVirialEBinMultiThreaded.MyData
 
addData(double[]) - Method in class etomica.virial.MeterVirialEBinMultiThreaded.MyDataCov
 
addData(IData) - Method in class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage
Add the given values to the sums and block sums
addEditVariablesButtonListener(ActionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
 
addEditVariablesButtonListener(ActionListener) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
 
addEquivalents(ArrayList<ClusterDiagram>) - Static method in class etomica.virial.cluster.ClusterOperations
Replaces all isomorphic clusters in the given list by a single cluster with weight given by their sum.
addEValNumSliderListener(ChangeListener) - Method in class etomica.normalmode.DeviceEigenvaluesSlider
Add the specified listener to the list of listeners that will get invoked when the 'eigenvalues #' slider value changes.
additive - Variable in class etomica.virial.simulations.VirialGCPM.VirialGCPMParam
 
addMoleculeListDisplayLSMListener(ListSelectionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
 
addMoleculeListDisplayLSMListener(ListSelectionListener) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
 
addMoleculeListDisplayTMListener(TableModelListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
 
addMoleculeListDisplayTMListener(TableModelListener) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
 
addNoDoNotRemoveSpeciesButtonListener(ActionListener) - Method in class etomica.virial.GUI.views.ViewAlertMsgBoxSpeciesRemoval
 
addPotentialButtonListener(ActionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
 
addPotentialButtonListener(ActionListener) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
 
addPotentialsJListListener(ListSelectionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
 
addPotentialsJListListener(ListSelectionListener) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
 
addPotParamDisplayLSMListener(ListSelectionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
 
addPotParamDisplayLSMListener(ListSelectionListener) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
 
addPotParamDisplayTMListener(TableModelListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
 
addPotParamDisplayTMListener(TableModelListener) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
 
addProgressListener(double) - Method in class etomica.virial.simulations.SimulationVirialOverlap2
Causes a progress report (coefficient value and uncertainty) 10 times during the course of the simulation.
addProgressListener(double, boolean) - Method in class etomica.virial.simulations.SimulationVirialOverlap2
Causes a progress report (coefficient value and uncertainty) 10 times during the course of the simulation.
addRadioGroupActionListener(ActionListener) - Method in class etomica.normalmode.DeviceCellNumXYSlider
Add the specified listener to the list of listeners that will get invoked when the "x-axis" or "y-axis" radio button is pushed.
addRadioGroupActionListener(ActionListener) - Method in class etomica.normalmode.DeviceEigenvaluesSlider
Add the specified listener to the list of listeners that will get invoked when the "Eigenvalue" or "All Eigenvalues" radio button is pushed.
addRadioGroupActionListener(ActionListener) - Method in class etomica.normalmode.DeviceWaveVectorSlider
Add the specified listener to the list of listeners that will get invoked when the "Wave Vector" or "All Wave Vectors" radio button is pushed.
addRemoveButtonListener(ActionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
 
addRemoveSpecies1ButtonListener(ActionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
 
addRemoveSpecies2ButtonListener(ActionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
 
addRemoveSpecies3ButtonListener(ActionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
 
addResetButtonListener(ActionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
 
addResetButtonListener(ActionListener) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
 
addRunButtonListener(ActionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
 
addRunButtonListener(ActionListener) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
 
addSameSpeciesButtonListener(ActionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
 
addSaveValuesButtonListener(ActionListener) - Method in class etomica.virial.GUI.views.ViewAlkaneLengthSelection
 
addSaveValuesButtonListener(ActionListener) - Method in class etomica.virial.GUI.views.ViewSimEnvironmentSelection
 
addSpecies(Object) - Method in class etomica.virial.GUI.components.ArrayMoleculeDisplayList
 
addSpeciesButtonListener(ActionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
 
addSpeciesIndextoSites(String[], int) - Method in class etomica.virial.GUI.components.BuilderCollectionPotential
 
addSpeciesJListListener(ListSelectionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
 
addSpeciesJListListener(ListSelectionListener) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
 
addSpeciesMolecule(int) - Method in class etomica.virial.GUI.models.ModelSelectedSpecies
 
addThermostatAction(IAction) - Method in class etomica.normalmode.IntegratorHardMDMC
 
addToHashMapPotentialNonBonded(String[], IPotential) - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicLike
 
addToHashMapPotentialNonBonded(String[], IPotential) - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicUnlike
 
addWaveVectorNumSliderListener(ChangeListener) - Method in class etomica.normalmode.DeviceWaveVectorSlider
Add the specified listener to the list of listeners that will get invoked when the 'wave vectors #' slider value changes.
addXYCellNumSliderListener(ChangeListener) - Method in class etomica.normalmode.DeviceCellNumXYSlider
Add the specified listener to the list of listeners that will get invoked when the 'xCell #' and 'yCell #' slider value changes.
addYesRemoveSpeciesButtonListener(ActionListener) - Method in class etomica.virial.GUI.views.ViewAlertMsgBoxSpeciesRemoval
 
adjustStepFreq() - Method in class etomica.virial.overlap.IntegratorOverlap
Adjusts the frequency with which steps for each sub-integrator are performed.
adjustStepFreq - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical.VirialParam
 
adjustStepFreq - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical_Correction.VirialParam
 
adjustStepFrequency - Variable in class etomica.virial.simulations.VirialHePCKLJS.VirialParam
 
adjustStepFrequency - Variable in class etomica.virial.simulations.VirialHePCKLJSCHNCCorrection.VirialLJParam
 
adjustStepFrequency - Variable in class etomica.virial.simulations.VirialHePCKLJSPYCorrection.VirialLJParam
 
advance() - Method in class etomica.virial.cluster.ClusterGenerator
Advances the cluster to the next cluster matching the given criteria.
Aelement - Variable in class etomica.virial.GUI.components.SimpleElementForSimilarSpecies
 
aFe - Variable in class etomica.meam.PotentialFeEAM_LS
 
affectedAtomIterator - Variable in class etomica.normalmode.MCMoveAtomCoupled
 
affectedAtomIterator - Variable in class etomica.normalmode.MCMoveAtomCoupledBennet
 
affectedAtomIterator - Variable in class etomica.normalmode.MCMoveAtomCoupledUmbrella
 
affectedAtomIterator - Variable in class etomica.normalmode.MCMoveAtomSuperBox
 
affectedAtomIterator - Variable in class etomica.normalmode.MCMoveVolumeMonoclinic
 
affectedAtomIterator - Variable in class etomica.normalmode.MCMoveVolumeMonoclinicAngle
 
affectedAtomIterator - Variable in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
 
affectedAtomIterator - Variable in class etomica.normalmode.MCMoveVolumeSolid
 
affectedAtomIterator - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
 
affectedAtomIterator - Variable in class etomica.spin.MCMoveSpinFlip
 
affectedAtomIterator - Variable in class etomica.virial.MCMoveClusterAngleBend
 
affectedAtomIterator - Variable in class etomica.virial.MCMoveClusterAngleBendAceticAcid
 
affectedAtomList - Variable in class etomica.normalmode.MCMoveAtomCoupled
 
affectedAtomList - Variable in class etomica.normalmode.MCMoveAtomCoupledBennet
 
affectedAtomList - Variable in class etomica.normalmode.MCMoveAtomCoupledUmbrella
 
affectedAtomList - Variable in class etomica.normalmode.MCMoveAtomSuperBox
 
affectedAtoms() - Method in class etomica.models.hexane.MCMoveCBMC
 
affectedAtoms() - Method in class etomica.models.hexane.MCMoveCombinedCbmcTranslation
 
affectedAtoms() - Method in class etomica.models.hexane.MCMoveReptate
 
affectedAtoms() - Method in class etomica.normalmode.MCMoveAtomCoupled
 
affectedAtoms() - Method in class etomica.normalmode.MCMoveAtomCoupledBennet
 
affectedAtoms() - Method in class etomica.normalmode.MCMoveAtomCoupledUmbrella
 
affectedAtoms() - Method in class etomica.normalmode.MCMoveAtomSuperBox
 
affectedAtoms() - Method in class etomica.normalmode.MCMoveEinsteinCrystal
 
affectedAtoms() - Method in class etomica.normalmode.MCMoveHarmonic
 
affectedAtoms() - Method in class etomica.normalmode.MCMoveHarmonicStep
 
affectedAtoms() - Method in class etomica.normalmode.MCMoveMoleculeCoupled
 
affectedAtoms() - Method in class etomica.normalmode.MCMovePhaseAngle
 
affectedAtoms() - Method in class etomica.normalmode.MCMoveSingleMode
 
affectedAtoms() - Method in class etomica.normalmode.MCMoveVolumeMonoclinic
 
affectedAtoms() - Method in class etomica.normalmode.MCMoveVolumeMonoclinicAngle
 
affectedAtoms() - Method in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
 
affectedAtoms() - Method in class etomica.normalmode.MCMoveVolumeSolid
 
affectedAtoms() - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
 
affectedAtoms() - Method in class etomica.normalmode.MCMoveWV
 
affectedAtoms() - Method in class etomica.paracetamol.MCMoveMoleculeCoupledDLPOLY
 
affectedAtoms() - Method in class etomica.spin.MCMoveSpinFlip
 
affectedAtoms() - Method in class etomica.virial.MCMoveChangeBondLength
 
affectedAtoms() - Method in class etomica.virial.MCMoveClusterAngleBend
 
affectedAtoms() - Method in class etomica.virial.MCMoveClusterAngleBendAceticAcid
 
affectedAtoms() - Method in class etomica.virial.MCMoveClusterAtomQ
 
affectedAtoms(IBox) - Method in class etomica.virial.MCMoveClusterAtomQ
 
affectedAtoms() - Method in class etomica.virial.MCMoveClusterDiagram
 
affectedAtoms() - Method in class etomica.virial.MCMoveClusterReptateMulti
 
affectedAtoms() - Method in class etomica.virial.MCMoveClusterRingPartialRegrow
 
affectedAtoms() - Method in class etomica.virial.MCMoveClusterRingRegrow
 
affectedAtoms() - Method in class etomica.virial.MCMoveClusterRingRegrowExchange
 
affectedAtoms() - Method in class etomica.virial.MCMoveClusterRingRegrowOrientation
 
affectedAtoms() - Method in class etomica.virial.MCMoveClusterRingScale
 
affectedAtoms(IBox) - Method in class etomica.virial.paralleltempering.MCMoveSwapCluster
 
affectedMoleculeIterator - Variable in class etomica.normalmode.MCMoveMoleculeCoupled
 
affectedMoleculeIterator - Variable in class etomica.paracetamol.MCMoveMoleculeCoupledDLPOLY
 
affectedMoleculeList - Variable in class etomica.normalmode.MCMoveMoleculeCoupled
 
affectedMoleculeList - Variable in class etomica.paracetamol.MCMoveMoleculeCoupledDLPOLY
 
ag - Variable in class etomica.meam.MEAM_MC
 
ag - Variable in class etomica.meam.MEAMMd3D
 
Ag - Static variable in class etomica.meam.ParameterSetMEAM
 
ag - Variable in class etomica.threaded.domain.MEAMMd3DThreaded
 
Ag3Sn - Static variable in class etomica.meam.ParameterSetMEAM
 
agB - Variable in class etomica.meam.MEAM_3DMDwithSnAgGB
 
agentManager - Variable in class etomica.conjugategradient.DerivativeEnergyFunction
 
agentManager - Variable in class etomica.conjugategradient.FiniteDifferenceDerivativeCG
 
agentManager - Variable in class etomica.normalmode.HSNPT.ActionSummer
 
agentManager - Variable in class etomica.normalmode.HSNPT.ColorSchemeDisplacement
 
agFixedB - Variable in class etomica.meam.MEAM_3DMDwithSnAgGB
 
AHarm - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1DGraphic
 
AHarm - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2DGraphic
 
AHarm - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
 
ai - Variable in class etomica.normalmode.nptdemo.HSNPT2DSim
 
ai - Variable in class etomica.normalmode.SimHSMDVacancy
 
ai - Variable in class etomica.normalmode.SimLJVacancy
 
ai - Variable in class etomica.virial.simulations.SimulationVirial
 
ai - Variable in class etomica.virial.simulations.SimulationVirialMultiOverlap
 
ai - Variable in class etomica.virial.simulations.SimulationVirialOverlap
 
ai - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
 
ai - Variable in class etomica.virial.simulations.SimulationVirialPT
 
akimaSpline - Variable in class etomica.normalmode.SoftSphereSolidEOS
 
Alat - Variable in class etomica.normalmode.SimHSMDVacancy.HSMDVParams
 
alkaneSpherePanel - Variable in class etomica.virial.GUI.views.ViewAlkaneLengthSelection
 
allAtoms - Variable in class etomica.conjugategradient.DerivativeEnergyFunction
 
allAtoms - Variable in class etomica.conjugategradient.FiniteDifferenceDerivativeCG
 
allatoms - Variable in class etomica.dimer.IntegratorDimerMin
 
allatoms - Variable in class etomica.dimer.IntegratorDimerRT
 
allMyData - Variable in class etomica.virial.MeterVirialBDBinMultiThreaded
 
allMyData - Variable in class etomica.virial.MeterVirialBinMultiThreaded
 
allMyData - Variable in class etomica.virial.MeterVirialEBinMultiThreaded
 
allMyData - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.SimulationWorker
 
allMyData - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.SimulationWorker
 
allPermutations - Variable in class etomica.virial.cluster.VirialDiagrams
 
allPermutations - Variable in class etomica.virial.cluster.VirialDiagramsMix2
 
allPermutations - Variable in class etomica.virial.cluster.VirialDiagramsPT
 
allPermutations - Variable in class etomica.virial.ClusterICPYC
 
AllSigs(int) - Constructor for class etomica.virial.ClusterWheatleyHS.AllSigs
 
allValueClusters - Variable in class etomica.virial.simulations.SimulationVirial
 
allValueClusters - Variable in class etomica.virial.simulations.SimulationVirialPT
 
allZero - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
 
alpha - Variable in class etomica.dimer.P1LepsHarmonic
 
alpha - Variable in class etomica.normalmode.MCMoveEinsteinCrystal
 
alpha - Variable in class etomica.normalmode.MCMoveHarmonicEin
 
alpha - Variable in class etomica.normalmode.MeterOverlapSwitch
 
alpha - Variable in class etomica.normalmode.MeterTargetTP
 
alpha - Variable in class etomica.normalmode.SimLJHTTISuperHCP.SimOverlapParam
 
alpha - Variable in class etomica.normalmode.SimOverlapSoftSphereEin.SimOverlapParam
 
alpha - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness.SimOverlapParam
 
alpha - Variable in class etomica.normalmode.SimOverlapSoftSphereTP.SimOverlapParam
 
alpha - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP.SimOverlapParam
 
alpha - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox.SimOverlapParam
 
alphaCenter - Variable in class etomica.normalmode.MeterOverlapSwitch
 
alphaCenter - Variable in class etomica.normalmode.MeterTargetTP
 
alphaCenter - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
 
alphaCenter - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm.SimOverlapParam
 
alphaCenter - Variable in class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage
 
alphaCenter - Variable in class etomica.virial.overlap.DataProcessorVirialOverlap
 
alphaSource - Variable in class etomica.virial.overlap.DataVirialOverlap
 
alphaSpan - Variable in class etomica.normalmode.MeterOverlapSwitch
 
alphaSpan - Variable in class etomica.normalmode.MeterTargetTP
 
alphaSpan - Variable in class etomica.normalmode.SimOverlapSoftSphereEin.SimOverlapParam
 
alphaSpan - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
 
alphaSpan - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm.SimOverlapParam
 
alphaSpan - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness.SimOverlapParam
 
alphaSpan - Variable in class etomica.normalmode.SimOverlapSoftSphereTP.SimOverlapParam
 
alphaSpan - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP.SimOverlapParam
 
alphaSpan - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox.SimOverlapParam
 
alphaSpan - Variable in class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage
 
alphaSpan - Variable in class etomica.virial.overlap.DataProcessorVirialOverlap
 
AnalyticalDerivativeEnergyParacetamol - Class in etomica.paracetamol
 
AnalyticalDerivativeEnergyParacetamol(IBox, PotentialMaster, ISpace) - Constructor for class etomica.paracetamol.AnalyticalDerivativeEnergyParacetamol
 
angleCCC - Variable in class etomica.virial.ConformationAlkaneEH
 
angleCCC_half - Variable in class etomica.virial.ConformationAlkaneEH
 
angleCCH - Variable in class etomica.virial.ConformationAlkaneEH
 
angleHCH - Variable in class etomica.virial.ConformationAlkaneEH
 
angleHCH_half - Variable in class etomica.virial.ConformationAlkaneEH
 
aPair - Variable in class etomica.virial.MayerGeneralAtomic
 
aPairSet - Variable in class etomica.virial.BoxCluster
 
APIPotentialReference(MeterHarmonicEnergy[]) - Constructor for class etomica.normalmode.SimOverlapLJModule.APIPotentialReference
 
APIPotentialTarget(IPotentialMaster) - Constructor for class etomica.normalmode.SimOverlapLJModule.APIPotentialTarget
 
AppControllerMixtureBuilder - Class in etomica.virial.GUI.controllers
 
AppControllerMixtureBuilder(AppViewMixtureBuilder, AppModelMixtureBuilder) - Constructor for class etomica.virial.GUI.controllers.AppControllerMixtureBuilder
 
append(ClusterBonds[], ClusterBonds[]) - Static method in class etomica.virial.simulations.VirialAlkaneEHTest
 
append(double[], double[]) - Static method in class etomica.virial.simulations.VirialAlkaneEHTest
 
append(ClusterBonds[], ClusterBonds[]) - Static method in class etomica.virial.simulations.VirialAlkaneFlex
 
append(double[], double[]) - Static method in class etomica.virial.simulations.VirialAlkaneFlex
 
append(ClusterBonds[], ClusterBonds[]) - Static method in class etomica.virial.simulations.VirialCO2PI
 
append(double[], double[]) - Static method in class etomica.virial.simulations.VirialCO2PI
 
append(ClusterBonds[], ClusterBonds[]) - Static method in class etomica.virial.simulations.VirialH2PI
 
append(double[], double[]) - Static method in class etomica.virial.simulations.VirialH2PI
 
append(ClusterBonds[], ClusterBonds[]) - Static method in class etomica.virial.simulations.VirialH2PIBoltzmann
 
append(double[], double[]) - Static method in class etomica.virial.simulations.VirialH2PIBoltzmann
 
append(ClusterBonds[], ClusterBonds[]) - Static method in class etomica.virial.simulations.VirialH2PIXC
 
append(double[], double[]) - Static method in class etomica.virial.simulations.VirialH2PIXC
 
append(ClusterBonds[], ClusterBonds[]) - Static method in class etomica.virial.simulations.VirialHePI
 
append(double[], double[]) - Static method in class etomica.virial.simulations.VirialHePI
 
append(ClusterBonds[], ClusterBonds[]) - Static method in class etomica.virial.simulations.VirialHePI_PotentialCorrection
 
append(double[], double[]) - Static method in class etomica.virial.simulations.VirialHePI_PotentialCorrection
 
append(ClusterBonds[], ClusterBonds[]) - Static method in class etomica.virial.simulations.VirialHePIXC
 
append(double[], double[]) - Static method in class etomica.virial.simulations.VirialHePIXC
 
append(ClusterBonds[], ClusterBonds[]) - Static method in class etomica.virial.simulations.VirialHePIXCEven
 
append(double[], double[]) - Static method in class etomica.virial.simulations.VirialHePIXCEven
 
append(ClusterBonds[], ClusterBonds[]) - Static method in class etomica.virial.simulations.VirialHePIXCOdd
 
append(double[], double[]) - Static method in class etomica.virial.simulations.VirialHePIXCOdd
 
AppFrameMixtureBuilder - Class in etomica.virial.GUI.containers
 
AppFrameMixtureBuilder(String) - Constructor for class etomica.virial.GUI.containers.AppFrameMixtureBuilder
 
Applet() - Constructor for class etomica.normalmode.HTTPSoftSphereApplet.Applet
 
Applet() - Constructor for class etomica.normalmode.NormalModeAnalysisDisplay1D.Applet
 
Applet() - Constructor for class etomica.normalmode.NormalModeAnalysisDisplay1DGraphic.Applet
 
Applet() - Constructor for class etomica.normalmode.NormalModeAnalysisDisplay2DGraphic.Applet
 
Applet() - Constructor for class etomica.normalmode.NormalModeAnalysisDisplay3D.Applet
 
Applet() - Constructor for class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic.Applet
 
Applet() - Constructor for class etomica.normalmode.nptdemo.HSNPT2DGraphic.Applet
 
ApplicationMixtureBuilder - Class in etomica.virial.GUI
 
ApplicationMixtureBuilder() - Constructor for class etomica.virial.GUI.ApplicationMixtureBuilder
 
apply(Set<Graph>, Parameters) - Method in class etomica.virial.cluster.BondConnectedSubstitution
 
apply(Graph, BondConnectedSubstitution.BondConnectedSubstitutionParameters2Site) - Method in class etomica.virial.cluster.BondConnectedSubstitution
 
apply(Set<Graph>, Parameters) - Method in class etomica.virial.cluster.BondConnectedSubstitution3Site
 
apply(Graph, BondConnectedSubstitution3Site.BondConnectedSubstitutionParameters3Site) - Method in class etomica.virial.cluster.BondConnectedSubstitution3Site
 
apply(Set<Graph>, Parameters) - Method in class etomica.virial.cluster.BondConnectedSubstitutionNaphthalene
 
apply(Graph, BondConnectedSubstitutionNaphthalene.BondConnectedSubstitutionParameters2SiteNa) - Method in class etomica.virial.cluster.BondConnectedSubstitutionNaphthalene
 
apply(Set<Graph>, Parameters) - Method in class etomica.virial.cluster.CondenseExchange
 
apply(Graph, CondenseExchange.CondenseExchangeParameters) - Method in class etomica.virial.cluster.CondenseExchange
 
apply(Set<Graph>, Parameters) - Method in class etomica.virial.cluster.ExchangeSplit
 
AppModelMixtureBuilder - Class in etomica.virial.GUI.models
 
AppModelMixtureBuilder() - Constructor for class etomica.virial.GUI.models.AppModelMixtureBuilder
 
AppViewMixtureBuilder - Class in etomica.virial.GUI.views
 
AppViewMixtureBuilder(AppFrameMixtureBuilder, AppModelMixtureBuilder) - Constructor for class etomica.virial.GUI.views.AppViewMixtureBuilder
 
aProj - Variable in class etomica.paracetamol.AnalyticalDerivativeEnergyParacetamol
 
aRef - Variable in class etomica.virial.simulations.VirialH2PIBoltzmann.VirialHePIParam
 
aRef - Variable in class etomica.virial.simulations.VirialH2PIXC.VirialHePIParam
 
aRef - Variable in class etomica.virial.simulations.VirialHePIXC.VirialHePIParam
 
aRef - Variable in class etomica.virial.simulations.VirialHePIXCEven.VirialHePIParam
 
ArrayA2B - Class in etomica.normalmode
Reads a file containing n mxm matrices as ASCII and serializes them to another file.
ArrayA2B() - Constructor for class etomica.normalmode.ArrayA2B
 
ArrayB2A - Class in etomica.normalmode
Reads a file containing n mxm matrices as (serialized) binary data and writes them to another file as text (ASCII).
ArrayB2A() - Constructor for class etomica.normalmode.ArrayB2A
 
ArrayMoleculeDisplayList - Class in etomica.virial.GUI.components
 
ArrayMoleculeDisplayList() - Constructor for class etomica.virial.GUI.components.ArrayMoleculeDisplayList
 
ArrayReader1D - Class in etomica.normalmode
Reads in lots of 1D arrays from a file.
ArrayReader1D() - Constructor for class etomica.normalmode.ArrayReader1D
 
ArrayReader2D - Class in etomica.normalmode
Reads in lots of 2D arrays from a file.
ArrayReader2D() - Constructor for class etomica.normalmode.ArrayReader2D
 
ArticulatedAt0(boolean) - Constructor for class etomica.virial.cluster.VirialDiagrams.ArticulatedAt0
 
ArticulatedAt0(boolean, char) - Constructor for class etomica.virial.cluster.VirialDiagrams.ArticulatedAt0
 
ArticulatedAt0(boolean) - Constructor for class etomica.virial.cluster.VirialDiagramsPT.ArticulatedAt0
 
ArticulatedAt0(boolean, char) - Constructor for class etomica.virial.cluster.VirialDiagramsPT.ArticulatedAt0
 
association(MayerFunction, MoleculePair, IBox) - Method in class etomica.virial.ConfigurationClusterAceticAcid
 
association(MoleculePair, IBox) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM
 
association(MoleculePair, IBox) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
 
association(MoleculePair, IBox) - Method in class etomica.virial.ConfigurationClusterWertheimGCPMDirectSampling
 
association2(MoleculePair, IBox) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM
 
association2(MoleculePair, IBox) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
 
association2(MoleculePair, IBox) - Method in class etomica.virial.ConfigurationClusterWertheimGCPMDirectSampling
 
association3(MoleculePair, IBox) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM
 
association3(MoleculePair, IBox) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
 
association3(MoleculePair, IBox) - Method in class etomica.virial.ConfigurationClusterWertheimGCPMDirectSampling
 
association4(MoleculePair, MoleculePair, IBox) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM
 
association4(MoleculePair, MoleculePair, IBox) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
 
association4(MoleculePair, IBox) - Method in class etomica.virial.ConfigurationClusterWertheimGCPMDirectSampling
 
association5(MoleculePair, MoleculePair, IBox) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM
 
association5(MoleculePair, MoleculePair, IBox) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
 
association6(MoleculePair, MoleculePair, IBox) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM
 
associationPotential - Variable in class etomica.virial.ConfigurationClusterWertheimGCPM
 
associationPotential - Variable in class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
 
associationPotential - Variable in class etomica.virial.ConfigurationClusterWertheimGCPMDirectSampling
 
associationPotential2 - Variable in class etomica.virial.ConfigurationClusterWertheimGCPM
 
associationPotential2 - Variable in class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
 
associationPotential2 - Variable in class etomica.virial.ConfigurationClusterWertheimGCPMDirectSampling
 
associationPotential3 - Variable in class etomica.virial.ConfigurationClusterWertheimGCPM
 
associationPotential3 - Variable in class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
 
associationPotential3 - Variable in class etomica.virial.ConfigurationClusterWertheimGCPMDirectSampling
 
aTarget - Variable in class etomica.virial.simulations.VirialH2PIBoltzmann.VirialHePIParam
 
aTarget - Variable in class etomica.virial.simulations.VirialH2PIXC.VirialHePIParam
 
aTarget - Variable in class etomica.virial.simulations.VirialHePIXC.VirialHePIParam
 
aTarget - Variable in class etomica.virial.simulations.VirialHePIXCEven.VirialHePIParam
 
atom - Variable in class etomica.models.hexane.MCMoveCBMC
 
atom - Variable in class etomica.spin.MCMoveSpinFlip
 
atom - Variable in class etomica.virial.MeterVirialExternalFieldSW.Near
 
atom0 - Variable in class etomica.normalmode.MCMoveAtomCoupled
 
atom0 - Variable in class etomica.normalmode.MCMoveAtomCoupledBennet
 
atom0 - Variable in class etomica.normalmode.MCMoveAtomCoupledUmbrella
 
atom0 - Variable in class etomica.normalmode.MCMoveAtomSuperBox
 
atom1 - Variable in class etomica.normalmode.MCMoveAtomCoupled
 
atom1 - Variable in class etomica.normalmode.MCMoveAtomCoupledBennet
 
atom1 - Variable in class etomica.normalmode.MCMoveAtomCoupledUmbrella
 
atom1 - Variable in class etomica.normalmode.MCMoveAtomSuperBox
 
AtomActionTransformed - Class in etomica.paracetamol
Moves (translates) an atom by a specified vector amount.
AtomActionTransformed(ISpace) - Constructor for class etomica.paracetamol.AtomActionTransformed
 
atomActionTranslateTo - Variable in class etomica.normalmode.CoordinateDefinition
 
atomActionTranslateTo - Variable in class etomica.paracetamol.ConfigurationMonoclinicLattice
 
atomActionTranslateTo - Variable in class etomica.paracetamol.ConfigurationOrthorhombicLattice
 
atomAgent0 - Variable in class etomica.dimer.IntegratorDimerMin
 
atomAgent0 - Variable in class etomica.dimer.IntegratorDimerRT
 
atomAgent1 - Variable in class etomica.dimer.IntegratorDimerRT
 
atomAgent2 - Variable in class etomica.dimer.IntegratorDimerRT
 
atomAgentManager - Variable in class etomica.normalmode.LatticeSumMolecularCrystal
 
atomAgentManager - Variable in class etomica.threaded.PotentialCalculationForceSumThreaded
 
atomAgentMin - Variable in class etomica.dimer.IntegratorDimerMin
 
AtomDecompositionMD - Class in etomica.threads
 
AtomDecompositionMD() - Constructor for class etomica.threads.AtomDecompositionMD
 
atomGroupAction - Variable in class etomica.normalmode.CoordinateDefinitionHSDimer
 
atomGroupAction - Variable in class etomica.paracetamol.ConfigurationMonoclinicLattice
 
atomGroupAction - Variable in class etomica.paracetamol.ConfigurationOrthorhombicLattice
 
atomGroupAction - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
 
atomicTensor(IAtom, IAtom) - Method in interface etomica.normalmode.LatticeSumMolecularCrystal.AtomicTensorAtomicPair
 
atomicTensorAtomicPair - Variable in class etomica.normalmode.NormalModesMolecular
 
atomicToMolecularD(LatticeSumMolecularCrystal.AtomicTensorAtomicPair, IMolecule, IMolecule) - Method in class etomica.normalmode.LatticeSumMolecularCrystal
 
atomIterator - Variable in class etomica.threaded.atom.PotentialMasterListWorker
 
atomIterator - Variable in class etomica.threaded.domain.PotentialMasterListWorker
 
atomList - Variable in class etomica.models.hexane.MCMoveCBMC
 
atomMove - Variable in class etomica.normalmode.SimEinStep1
 
atomMove - Variable in class etomica.normalmode.SimEinStep1HCP
 
atomMove - Variable in class etomica.normalmode.SimEinStep2
 
atomMove - Variable in class etomica.normalmode.SimEinStep2HCP
 
atomMove - Variable in class etomica.normalmode.SimLJHTTISuper
 
atomMove - Variable in class etomica.normalmode.SimLJHTTISuperHCP
 
atomMove - Variable in class etomica.normalmode.SimOverlapSoftSphere
 
atomMove - Variable in class etomica.normalmode.SimOverlapSoftSphereDP
 
atomMove - Variable in class etomica.normalmode.SimOverlapSoftSphereEin
 
atomMove - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
 
atomMove - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
 
atomMove - Variable in class etomica.normalmode.SimOverlapSoftSphereTP
 
atomMove - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP
 
atomMove - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox
 
atomMove - Variable in class etomica.normalmode.SimOverlapSSnxy
 
atomMoveRef - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
 
atomMoveTarg - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
 
atomPair - Variable in class etomica.threaded.atom.PotentialMasterListWorker
 
atomPair - Variable in class etomica.threaded.domain.PotentialMasterListWorker
 
AtomPairSet - Class in etomica.virial
Class that holds a set of atom pairs.
AtomPairSet(IMoleculeList) - Constructor for class etomica.virial.AtomPairSet
Constructor for AtomPairSet.
atomPosDef - Variable in class etomica.normalmode.LatticeSumMolecularCrystal
 
atoms - Variable in class etomica.virial.ClusterSumNonAdditiveTrimerEnergy
 
atoms - Variable in class etomica.virial.CoordinatePairMoleculeSet
 
atoms - Variable in class etomica.virial.MCMoveClusterRingPartialRegrow
 
atoms - Variable in class etomica.virial.MCMoveClusterRingScale
 
atomsetArrayList - Variable in class etomica.threaded.atom.PotentialMasterListWorker
 
atomsetArrayList - Variable in class etomica.threaded.domain.PotentialMasterListWorker
 
atomSetSinglet - Variable in class etomica.threaded.atom.PotentialMasterListWorker
 
atomSetSinglet - Variable in class etomica.threaded.domain.PotentialMasterListWorker
 
atomSinglet - Variable in class etomica.normalmode.MCMoveAtomCoupled
 
atomSource - Variable in class etomica.models.hexane.MCMoveReptate
 
atomSource - Variable in class etomica.normalmode.MCMoveAtomCoupled
 
atomSource - Variable in class etomica.normalmode.MCMoveAtomCoupledBennet
 
atomSource - Variable in class etomica.normalmode.MCMoveAtomCoupledUmbrella
 
atomSpeciesA - Variable in class etomica.normalmode.MCMoveAtomSuperBox
 
atomSpeciesB - Variable in class etomica.normalmode.MCMoveAtomSuperBox
 
avgStat - Variable in class etomica.virial.overlap.DataVirialOverlap
 
axes - Variable in class etomica.normalmode.CoordinateDefinitionHSDimer
 
axes - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
 
axis - Variable in class etomica.normalmode.CoordinateDefinitionHSDimer
 
axis - Variable in class etomica.virial.ClusterCoupledAtomFlipped
 
axis - Variable in class etomica.virial.MCMoveClusterRotateCH3
 
axis0 - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
 
axis0 - Variable in class etomica.virial.MCMoveClusterAtomHSRing
 
axis0Prime - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
 
axisNorm - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
 
axisNormPrime - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
 

B

B - Variable in class etomica.conjugategradient.ConjugateGradients
 
B - Variable in class etomica.conjugategradient.PreconditionedConjugateGradient
 
B - Variable in class etomica.conjugategradient.SteepestDescent
 
b - Variable in class etomica.dimer.P1LepsHarmonic
 
B - Variable in class etomica.meam.PotentialCuLREP
 
B - Variable in class etomica.meam.PotentialEFS
 
b - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
 
b0 - Variable in class etomica.meam.ParameterSetMEAM
 
b1 - Variable in class etomica.meam.ParameterSetMEAM
 
B10HS(double) - Static method in class etomica.virial.cluster.Standard
 
B11HS(double) - Static method in class etomica.virial.cluster.Standard
 
B12HS(double) - Static method in class etomica.virial.cluster.Standard
 
b2 - Variable in class etomica.meam.ParameterSetMEAM
 
B2 - Static variable in class etomica.virial.cluster.Standard
 
B2 - Variable in class etomica.virial.simulations.ShapeParser.ShapeData
 
B2ForSphericallySymmetricUByTrapezoidRule - Class in etomica.virial
 
B2ForSphericallySymmetricUByTrapezoidRule() - Constructor for class etomica.virial.B2ForSphericallySymmetricUByTrapezoidRule
 
B2HS(double) - Static method in class etomica.virial.cluster.Standard
 
B2Ionic - Class in etomica.virial
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"
B2Ionic() - Constructor for class etomica.virial.B2Ionic
 
B2SW(double, double, double) - Static method in class etomica.virial.cluster.Standard
 
b3 - Variable in class etomica.meam.ParameterSetMEAM
 
B3ForSphericallySymmetricU - Class in etomica.virial
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() - Constructor for class etomica.virial.B3ForSphericallySymmetricU
 
B3ForSphericallySymmetricU.DampingParams - Class in etomica.virial
 
B3HS(double) - Static method in class etomica.virial.cluster.Standard
 
B3LJ - Class in etomica.virial
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.
B3LJ() - Constructor for class etomica.virial.B3LJ
 
B3NonAddForSphericallySymmetricU - Class in etomica.virial
Computes the classical, non-additive component of B3 for a spherically symmetric potential using quadrature.
B3NonAddForSphericallySymmetricU() - Constructor for class etomica.virial.B3NonAddForSphericallySymmetricU
 
B3SW(double, double, double) - Static method in class etomica.virial.cluster.Standard
 
B4FFTLJ - Class in etomica.virial
Computes four approximations of B4 by FFT: HNC(C), HNC(V), PY(C), and PY(V).
B4FFTLJ() - Constructor for class etomica.virial.B4FFTLJ
 
B4HS(double) - Static method in class etomica.virial.cluster.Standard
 
B5FFTLJ - Class in etomica.virial
Computes four approximations of B5 by FFT: HNC(C), HNC(V), PY(C), and PY(V).
B5FFTLJ() - Constructor for class etomica.virial.B5FFTLJ
 
B5HS(double) - Static method in class etomica.virial.cluster.Standard
 
B6FFTLJ - Class in etomica.virial
Modification of FFT Program of B4
B6FFTLJ() - Constructor for class etomica.virial.B6FFTLJ
 
B6HS(double) - Static method in class etomica.virial.cluster.Standard
 
B7HS(double) - Static method in class etomica.virial.cluster.Standard
 
B8HS(double) - Static method in class etomica.virial.cluster.Standard
 
B9HS(double) - Static method in class etomica.virial.cluster.Standard
 
bALattice - Variable in class etomica.normalmode.DataSourceAvgPressure2
 
bALattice - Variable in class etomica.normalmode.DataSourceMuRoot1
 
bALattice - Variable in class etomica.normalmode.DataSourceMuRootPMatch
 
bALattice - Variable in class etomica.normalmode.DataSourcePMu
 
basis - Variable in class etomica.normalmode.CoordinateDefinition
 
basis - Variable in class etomica.normalmode.HessianDB
 
basis - Variable in class etomica.normalmode.LJVacancyMin
 
basis - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1D
 
basis - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2D
 
basis - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3D
 
basis - Variable in class etomica.normalmode.NormalModes2D
 
basis - Variable in class etomica.normalmode.NormalModes3D
 
basis - Variable in class etomica.normalmode.SimBennet
 
basis - Variable in class etomica.normalmode.SimCalcSLJ
 
basis - Variable in class etomica.normalmode.SimCalcSMorse
 
basis - Variable in class etomica.normalmode.SimCalcSSoftSphere2D
 
basis - Variable in class etomica.normalmode.SimCalcSSoftSphereFCC
 
basis - Variable in class etomica.normalmode.SimCalcSSoftSphereFCCSuperBox
 
basis - Variable in class etomica.normalmode.SimEinStep1
 
basis - Variable in class etomica.normalmode.SimEinStep1HCP
 
basis - Variable in class etomica.normalmode.SimEinStep2
 
basis - Variable in class etomica.normalmode.SimEinStep2HCP
 
basis - Variable in class etomica.normalmode.SimHarmonicUmbrella
 
basis - Variable in class etomica.normalmode.SimLJHTTISuper
 
basis - Variable in class etomica.normalmode.SimLJHTTISuperHCP
 
basis - Variable in class etomica.normalmode.SimOverlap
 
basis - Variable in class etomica.normalmode.SimOverlapLJ
 
basis - Variable in class etomica.normalmode.SimOverlapLJModule
 
basis - Variable in class etomica.normalmode.SimOverlapSoftSphere
 
basis - Variable in class etomica.normalmode.SimOverlapSoftSphereDP
 
basis - Variable in class etomica.normalmode.SimOverlapSoftSphereEin
 
basis - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
 
basis - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
 
basis - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting
 
basis - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
 
basis - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox
 
basis - Variable in class etomica.normalmode.SimOverlapSoftSphereTP
 
basis - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP
 
basis - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox
 
basis - Variable in class etomica.normalmode.SimOverlapSSnxy
 
basis - Variable in class etomica.normalmode.SimTargetUmbrella
 
basis - Variable in class etomica.normalmode.SimUmbrella
 
basis - Variable in class etomica.normalmode.SimUmbrellaSoftSphere
 
BasisBigCell - Class in etomica.normalmode
 
BasisBigCell(ISpace, Basis, int[]) - Constructor for class etomica.normalmode.BasisBigCell
 
BasisCell(IMoleculeList, IVectorMutable) - Constructor for class etomica.normalmode.CoordinateDefinition.BasisCell
 
basisDim - Variable in class etomica.normalmode.NormalModesMolecular
 
basisFCC - Variable in class etomica.normalmode.HessianDB
 
BasisMonoclinicParacetamol - Class in etomica.paracetamol
An 4-atom basis that for a monoclinic paracetamol crystal.
BasisMonoclinicParacetamol() - Constructor for class etomica.paracetamol.BasisMonoclinicParacetamol
Makes a monoclinic-crystal paracetamol 4-atom basis.
basisOrientation - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
 
basisOrientation - Variable in class etomica.paracetamol.LatticeSumCrystalParacetamol
 
BasisOrthorhombicParacetamol - Class in etomica.paracetamol
An 8-atom basis that for a orthorhombic paracetamol crystal.
BasisOrthorhombicParacetamol() - Constructor for class etomica.paracetamol.BasisOrthorhombicParacetamol
Makes a orthorhombic-crystal paracetamol 8-atom basis.
bBond - Variable in class etomica.virial.cluster.VirialDiagrams
 
bBond - Variable in class etomica.virial.cluster.VirialDiagramsPT
 
BCC - Static variable in class etomica.normalmode.SoftSphereSolidEOS
 
BCC - Static variable in class etomica.normalmode.SoftSphereSolidEOSCalculator
 
BDONE - Static variable in class etomica.virial.ClusterWheatleySoftBD
 
BDONE - Static variable in class etomica.virial.MeterVirialBDBin
 
bdry - Variable in class etomica.models.hexane.HexaneVolumeFraction
 
bdry - Variable in class etomica.models.hexane.SimHarmonicHexane
 
bdry - Variable in class etomica.models.hexane.TestHexane
 
bdry - Variable in class etomica.models.hexane.TestHexaneCBMCOnly
 
bdry - Variable in class etomica.models.hexane.TestHexaneFileConfig
 
bdry - Variable in class etomica.models.hexane.TestHexaneHarmonic
 
bdry - Variable in class etomica.models.hexane.TestSetToUHexane
 
bdry - Variable in class etomica.normalmode.SimCalcJ
 
bdry - Variable in class etomica.normalmode.SimCalcS
 
bdry - Variable in class etomica.normalmode.SimModesJ
 
bdry - Variable in class etomica.paracetamol.MCParacetamolMonoclinicDLMULTI
 
bdry - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicDLMULTI
 
bdry - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
 
bdry - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
 
bdry - Variable in class etomica.paracetamol.MDParacetamolMonoclinic
 
bdry - Variable in class etomica.paracetamol.MDParacetamolOrthorhombic
 
BDZERO - Static variable in class etomica.virial.ClusterWheatleySoftBD
 
BDZERO - Static variable in class etomica.virial.MeterVirialBD
 
BDZERO - Static variable in class etomica.virial.MeterVirialBDBin
 
BDZERO - Static variable in class etomica.virial.MeterVirialBDBinMultiThreaded
 
BDZERO - Static variable in class etomica.virial.MeterVirialSWWE
 
beadFac - Variable in class etomica.virial.simulations.VirialH2PI.VirialH2PIParam
 
beadFac - Variable in class etomica.virial.simulations.VirialH2PISimple.VirialH2PISimpleParam
 
beadFac - Variable in class etomica.virial.simulations.VirialHePIXCOdd.VirialHePIParam
 
beadFac - Variable in class etomica.virial.simulations.VirialN2PI.VirialN2Param
 
beadFac - Variable in class etomica.virial.simulations.VirialO2PI.VirialO2Param
 
bennetUDiff - Variable in class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage
 
beta - Variable in class etomica.models.hexane.MCMoveCBMC
 
beta - Variable in class etomica.virial.ClusterChainSoft
 
beta - Variable in class etomica.virial.ClusterExchange
 
beta - Variable in class etomica.virial.ClusterSinglyConnected
 
beta - Variable in class etomica.virial.ClusterSum
 
beta - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct
 
beta - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
 
beta - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
 
beta - Variable in class etomica.virial.ClusterTree
 
beta - Variable in class etomica.virial.ClusterWheatleyExtendSW
 
beta - Variable in class etomica.virial.ClusterWheatleyHS
 
beta - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
 
beta - Variable in class etomica.virial.ClusterWheatleySoft
 
beta - Variable in class etomica.virial.ClusterWheatleySoftBD
 
betaUAB - Variable in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
 
betaUAW - Variable in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
 
betaUAWf - Variable in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
 
betaUBA - Variable in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
 
betaUBW - Variable in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
 
betaUBWf - Variable in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
 
BHS(int, double) - Static method in class etomica.virial.cluster.Standard
Returns the nth virial coefficient for hard spheres of diameter sigma.
bias - Variable in class etomica.virial.MCMoveClusterTorsionAlkaneEH
 
bias - Variable in class etomica.virial.MCMoveClusterTorsionMulti
 
binSize - Variable in class etomica.virial.MCMoveClusterTorsionAlkaneEH
 
binSize - Variable in class etomica.virial.MCMoveClusterTorsionMulti
 
blN2 - Static variable in class etomica.virial.simulations.VirialN2
 
blN2 - Static variable in class etomica.virial.simulations.VirialN2PI
 
blO2 - Static variable in class etomica.virial.simulations.VirialO2PI
 
blockAccumulator - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
 
blockCounter - Variable in class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage
 
blocks - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical.VirialParam
 
blocks - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical_Correction.VirialParam
 
blocks - Variable in class etomica.virial.simulations.VirialHePI_PotentialCorrection.VirialHePIParam
 
blocks - Variable in class etomica.virial.simulations.VirialHePIXCOdd.VirialHePIParam
 
blocksEq - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical.VirialParam
 
blocksEq - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical_Correction.VirialParam
 
blocksEq - Variable in class etomica.virial.simulations.VirialHePI_PotentialCorrection.VirialHePIParam
 
blocksEq - Variable in class etomica.virial.simulations.VirialHePIXCOdd.VirialHePIParam
 
blockSize - Variable in class etomica.virial.simulations.SimulationVirialMultiOverlap
 
blockSize - Variable in class etomica.virial.simulations.SimulationVirialOverlap
 
blockSize - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
 
blOption - Variable in class etomica.virial.simulations.VirialH2PI.VirialH2PIParam
 
blOption - Variable in class etomica.virial.simulations.VirialH2PISimple.VirialH2PISimpleParam
 
bmu - Variable in class etomica.normalmode.DataSourceAvgPressure
 
bmu - Variable in class etomica.normalmode.DataSourceAvgPressure2
 
bmu - Variable in class etomica.normalmode.DataSourceFEHistogram
 
bmu - Variable in class etomica.normalmode.DataSourceImposedFEFit
 
bmu - Variable in class etomica.normalmode.DataSourceImposedFEHistogram
 
bmu - Variable in class etomica.normalmode.DataSourceMuRoot
 
bmu - Variable in class etomica.normalmode.DataSourceMuRoot1
 
bmu - Variable in class etomica.normalmode.DataSourceMuRootPMatch
 
bmu - Variable in class etomica.normalmode.DataSourcePMu
 
bmuLat - Variable in class etomica.normalmode.DataSourceMuRoot
 
BnFlexibleContributionTraPPEUAMethanol - Class in etomica.virial.simulations
Computes (part of) the flexible contribution to the virial coefficient for the TraPPE-UA model of methanol (http://www.chem.umn.edu/groups/siepmann/trappe/intro.php) K.R.S.
BnFlexibleContributionTraPPEUAMethanol() - Constructor for class etomica.virial.simulations.BnFlexibleContributionTraPPEUAMethanol
 
BnFlexibleContributionTraPPEUAMethanol.VirialParam - Class in etomica.virial.simulations
Inner class for parameters
BnHNCLJ - Class in etomica.virial
This is just a main method for HypernettedChain.java...
BnHNCLJ() - Constructor for class etomica.virial.BnHNCLJ
 
BnHSIonic - Class in etomica.virial
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"
BnHSIonic() - Constructor for class etomica.virial.BnHSIonic
 
BnIETP2Spherical - Class in etomica.virial
This is just a main method for HypernettedChain.java or PercusYevick.java...
BnIETP2Spherical() - Constructor for class etomica.virial.BnIETP2Spherical
 
BnJHBVArgon_Analytic - Class in etomica.virial
Computes virial coefficients for argon using the analytical expressions developed by Jaeger, Hellmann, Bich, and Vogel (2011), JCP, 135: 084308.
BnJHBVArgon_Analytic() - Constructor for class etomica.virial.BnJHBVArgon_Analytic
 
BnPY_1QC_Helium - Class in etomica.virial
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).
BnPY_1QC_Helium() - Constructor for class etomica.virial.BnPY_1QC_Helium
 
BnPYHardSphere - Class in etomica.virial
This is just a main method for PercusYevick.java...
BnPYHardSphere() - Constructor for class etomica.virial.BnPYHardSphere
 
BnPYLJ - Class in etomica.virial
This is just a main method for PercusYevick.java.
BnPYLJ() - Constructor for class etomica.virial.BnPYLJ
 
BnSCALJ - Class in etomica.virial
Combines the Percus-Yevick and hypernetted-chain approximations to the virial coefficients to generate a self-consistent (thermodynamically consistent) approximation.
BnSCALJ() - Constructor for class etomica.virial.BnSCALJ
 
BoltzmannProcessor - Class in etomica.normalmode
DataProcessor that returns the Boltzmann factor of the incoming energy.
BoltzmannProcessor() - Constructor for class etomica.normalmode.BoltzmannProcessor
 
bond - Static variable in class etomica.virial.ConformationAnthraceneTraPPE
 
bond - Static variable in class etomica.virial.ConformationPhenanthreneTraPPE
 
BondConnectedSubstitution - Class in etomica.virial.cluster
If Wertheim diagrams have bond connected network, fR bond is split into eR and -one bond.
BondConnectedSubstitution() - Constructor for class etomica.virial.cluster.BondConnectedSubstitution
 
BondConnectedSubstitution.BondConnectedSubstitutionParameters2Site - Class in etomica.virial.cluster
 
BondConnectedSubstitution3Site - Class in etomica.virial.cluster
If Wertheim diagrams have bond connected network, fR bond is split into eR and -one bond.
BondConnectedSubstitution3Site() - Constructor for class etomica.virial.cluster.BondConnectedSubstitution3Site
 
BondConnectedSubstitution3Site.BondConnectedSubstitutionParameters3Site - Class in etomica.virial.cluster
 
BondConnectedSubstitutionNaphthalene - Class in etomica.virial.cluster
revised from Hye Min's "BondConnectedSubstitution" If Wertheim diagrams have bond connected network, fR bond is split into eR and -one bond.
BondConnectedSubstitutionNaphthalene() - Constructor for class etomica.virial.cluster.BondConnectedSubstitutionNaphthalene
 
BondConnectedSubstitutionNaphthalene.BondConnectedSubstitutionParameters2SiteNa - Class in etomica.virial.cluster
 
BondConnectedSubstitutionParameters2Site(char, char) - Constructor for class etomica.virial.cluster.BondConnectedSubstitution.BondConnectedSubstitutionParameters2Site
 
BondConnectedSubstitutionParameters2SiteNa(char, char, List<Character>, List<Character>, List<Character>, List<Character>) - Constructor for class etomica.virial.cluster.BondConnectedSubstitutionNaphthalene.BondConnectedSubstitutionParameters2SiteNa
 
BondConnectedSubstitutionParameters3Site(char, char) - Constructor for class etomica.virial.cluster.BondConnectedSubstitution3Site.BondConnectedSubstitutionParameters3Site
 
bondDecomp - Variable in class etomica.virial.cluster.MayerIonicDiagram1qbond
 
bondDecomp - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
 
bondDecomp - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
 
bondDecomp - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
 
bondDecomp - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
 
bondedAtoms - Variable in class etomica.virial.MCMoveClusterWiggleAceticAcid
 
bondIndexArray - Variable in class etomica.virial.ClusterBonds
 
bondL - Variable in class etomica.virial.Conformation7SiteRigidSF6
 
bondL - Variable in class etomica.virial.SpeciesFactorySiepmannSpheres
 
bondL - Variable in class etomica.virial.SpeciesFactorySpheres2
 
bondlength - Variable in class etomica.models.hexane.CBMCGrowStraightAlkane
 
bondlength - Static variable in class etomica.virial.ConformationAnthracene3site
 
bondlength - Static variable in class etomica.virial.ConformationCO2
 
bondlength - Static variable in class etomica.virial.ConformationNaphthaleneTraPPE
 
bondlength - Static variable in class etomica.virial.ConformationPh3site
 
bondLength - Variable in class etomica.virial.MCMoveClusterTorsionAlkaneEH
 
bondLength - Variable in class etomica.virial.MCMoveClusterTorsionMulti
 
bondList - Variable in class etomica.virial.simulations.VirialLJSeries.VirialLJParam
 
bonds - Variable in class etomica.virial.MCMoveClusterAtomHSTree
 
bonds - Variable in class etomica.virial.MCMoveClusterPolyhedraTree
 
bondsTree - Variable in class etomica.virial.ClusterTree
 
bondTheta - Variable in class etomica.virial.SpeciesFactorySiepmannSpheres
 
bondTheta - Variable in class etomica.virial.SpeciesFactorySpheres2
 
boundary - Variable in class etomica.meam.PotentialCuLREP
 
boundary - Variable in class etomica.meam.PotentialEFS
 
boundary - Variable in class etomica.meam.PotentialFeEAM
 
boundary - Variable in class etomica.meam.PotentialFeEAM_LS
 
boundary - Variable in class etomica.meam.PotentialMEAM
 
boundary - Variable in class etomica.normalmode.HessianDB
 
boundary - Variable in class etomica.normalmode.LJVacancyMin
 
boundary - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1D
 
boundary - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2D
 
boundary - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3D
 
boundary - Variable in class etomica.normalmode.NormalModes1DHR
 
boundary - Variable in class etomica.normalmode.NormalModes2D
 
boundary - Variable in class etomica.normalmode.P1ConstraintNbr
 
boundary - Variable in class etomica.normalmode.P1ConstraintNbrHcp
 
boundary - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
 
boundary - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
 
boundary - Variable in class etomica.normalmode.SimBennet
 
boundary - Variable in class etomica.normalmode.SimCalcSLJ
 
boundary - Variable in class etomica.normalmode.SimCalcSMorse
 
boundary - Variable in class etomica.normalmode.SimCalcSSoftSphere2D
 
boundary - Variable in class etomica.normalmode.SimCalcSSoftSphereFCC
 
boundary - Variable in class etomica.normalmode.SimCalcSSoftSphereFCCSuperBox
 
boundary - Variable in class etomica.normalmode.SimEinStep1
 
boundary - Variable in class etomica.normalmode.SimEinStep1HCP
 
boundary - Variable in class etomica.normalmode.SimEinStep2
 
boundary - Variable in class etomica.normalmode.SimEinStep2HCP
 
boundary - Variable in class etomica.normalmode.SimHarmonic
 
boundary - Variable in class etomica.normalmode.SimHarmonicUmbrella
 
boundary - Variable in class etomica.normalmode.SimLJHTTISuper
 
boundary - Variable in class etomica.normalmode.SimLJHTTISuperHCP
 
boundary - Variable in class etomica.normalmode.SimOverlapSoftSphereDP
 
boundary - Variable in class etomica.normalmode.SimOverlapSoftSphereEin
 
boundary - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
 
boundary - Variable in class etomica.normalmode.SimOverlapSoftSphereTP
 
boundary - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP
 
boundary - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox
 
boundary - Variable in class etomica.normalmode.SimTarget
 
boundary - Variable in class etomica.normalmode.SimTargetUmbrella
 
boundary - Variable in class etomica.normalmode.SimUmbrella
 
boundary - Variable in class etomica.normalmode.SimUmbrellaSoftSphere
 
boundary - Variable in class etomica.paracetamol.SimulationOrthorhombicParacetamol
 
boundaryHarmonic - Variable in class etomica.normalmode.SimOverlap
 
boundaryHarmonic - Variable in class etomica.normalmode.SimOverlapLJ
 
boundaryHarmonic - Variable in class etomica.normalmode.SimOverlapLJModule
 
boundaryHarmonic - Variable in class etomica.normalmode.SimOverlapSoftSphere
 
boundaryHarmonic - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
 
boundaryHarmonic - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting
 
boundaryHarmonic - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox
 
boundaryHarmonic - Variable in class etomica.normalmode.SimOverlapSSnxy
 
boundaryRef - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
 
boundaryRef - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
 
boundaryTarg - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
 
boundaryTarget - Variable in class etomica.normalmode.SimOverlap
 
boundaryTarget - Variable in class etomica.normalmode.SimOverlapLJ
 
boundaryTarget - Variable in class etomica.normalmode.SimOverlapLJModule
 
boundaryTarget - Variable in class etomica.normalmode.SimOverlapSoftSphere
 
boundaryTarget - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
 
boundaryTarget - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting
 
boundaryTarget - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox
 
boundaryTarget - Variable in class etomica.normalmode.SimOverlapSSnxy
 
box - Variable in class etomica.conjugategradient.DerivativeEnergyFunction
 
box - Variable in class etomica.conjugategradient.FiniteDifferenceDerivativeCG
 
box - Variable in class etomica.densityofstate.DensityOfState
 
box - Variable in class etomica.densityofstate.DensityOfStatesPolynomial
 
box - Variable in class etomica.dimer.EnergyMap
 
box - Variable in class etomica.dimer.PotentialCalculationForcePressureSumGB
 
box - Variable in class etomica.dimer.SimDimerLJadatom
 
box - Variable in class etomica.dimer.SimDimerLJgb
 
box - Variable in class etomica.dimer.SimDimerMEAMadatom
 
box - Variable in class etomica.dimer.SimDimerMEAMGB
 
box - Variable in class etomica.meam.EFSTungsten
 
box - Variable in class etomica.meam.MEAM_3DMDwithGB
 
box - Variable in class etomica.meam.MEAM_3DMDwithSnAgGB
 
box - Variable in class etomica.meam.MEAM_3DMDwithSnCuGB
 
box - Variable in class etomica.meam.MEAM_MC
 
box - Variable in class etomica.meam.MEAMMd3D
 
box - Variable in class etomica.models.hexane.HexaneVolumeFraction
 
box - Variable in class etomica.models.hexane.SimHarmonicHexane
 
box - Variable in class etomica.models.hexane.TestHexane
 
box - Variable in class etomica.models.hexane.TestHexaneCBMCOnly
 
box - Variable in class etomica.models.hexane.TestHexaneFileConfig
 
box - Variable in class etomica.models.hexane.TestHexaneHarmonic
 
box - Variable in class etomica.normalmode.CoordinateDefinition
 
box - Variable in class etomica.normalmode.DeviceCellNum3DSlider
 
box - Variable in class etomica.normalmode.DeviceCellNumXYSlider
 
box - Variable in class etomica.normalmode.HessianDB
 
box - Variable in class etomica.normalmode.HSDimerNPT
 
box - Variable in class etomica.normalmode.HSNPT
 
box - Variable in class etomica.normalmode.LatticeSumMolecularCrystal
 
box - Variable in class etomica.normalmode.LJVacancyMin
 
box - Variable in class etomica.normalmode.MeterAPIPotentialEnergy
 
box - Variable in class etomica.normalmode.MeterMaxExpansion
 
box - Variable in class etomica.normalmode.MeterPhiDeviation
 
box - Variable in class etomica.normalmode.MeterPlaneSlip
 
box - Variable in class etomica.normalmode.MeterSolidDA
 
box - Variable in class etomica.normalmode.MeterSolidDACut
 
box - Variable in class etomica.normalmode.MeterSolidMirror
 
box - Variable in class etomica.normalmode.MeterThetaDeviation
 
box - Variable in class etomica.normalmode.MeterTilt
 
box - Variable in class etomica.normalmode.MeterTiltHistogram
 
box - Variable in class etomica.normalmode.MeterTiltRotation
 
box - Variable in class etomica.normalmode.MeterTiltRotationHistogram
 
box - Variable in class etomica.normalmode.MeterTiltRotationStdev
 
box - Variable in class etomica.normalmode.MinimizeHCP
 
box - Variable in class etomica.normalmode.ModifierCells3D
 
box - Variable in class etomica.normalmode.ModifierXCells2D
 
box - Variable in class etomica.normalmode.ModifierYCells2D
 
box - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1D
 
box - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2D
 
box - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3D
 
box - Variable in class etomica.normalmode.NormalModesMolecular
 
box - Variable in class etomica.normalmode.nptdemo.HSNPT2DSim
 
box - Variable in class etomica.normalmode.P2XOrder
 
box - Variable in class etomica.normalmode.PotentialCalculationEFSSP
 
box - Variable in class etomica.normalmode.PotentialCalculationLJSP
 
box - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
 
box - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
 
box - Variable in class etomica.normalmode.SimBennet
 
box - Variable in class etomica.normalmode.SimCalcJ
 
box - Variable in class etomica.normalmode.SimCalcS
 
box - Variable in class etomica.normalmode.SimCalcSLJ
 
box - Variable in class etomica.normalmode.SimCalcSMorse
 
box - Variable in class etomica.normalmode.SimCalcSSoftSphere2D
 
box - Variable in class etomica.normalmode.SimCalcSSoftSphereFCC
 
box - Variable in class etomica.normalmode.SimCalcSSoftSphereFCCSuperBox
 
box - Variable in class etomica.normalmode.SimEinStep1
 
box - Variable in class etomica.normalmode.SimEinStep1HCP
 
box - Variable in class etomica.normalmode.SimEinStep2
 
box - Variable in class etomica.normalmode.SimEinStep2HCP
 
box - Variable in class etomica.normalmode.SimFluidSoftSphere
 
box - Variable in class etomica.normalmode.SimHarmonic
 
box - Variable in class etomica.normalmode.SimHarmonicUmbrella
 
box - Variable in class etomica.normalmode.SimHSMDVacancy
 
box - Variable in class etomica.normalmode.SimLJHTTISuper
 
box - Variable in class etomica.normalmode.SimLJHTTISuperHCP
 
box - Variable in class etomica.normalmode.SimLJVacancy
 
box - Variable in class etomica.normalmode.SimModesJ
 
box - Variable in class etomica.normalmode.SimOverlapSoftSphereDP
 
box - Variable in class etomica.normalmode.SimOverlapSoftSphereEin
 
box - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
 
box - Variable in class etomica.normalmode.SimOverlapSoftSphereTP
 
box - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP
 
box - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox
 
box - Variable in class etomica.normalmode.SimTarget
 
box - Variable in class etomica.normalmode.SimTargetUmbrella
 
box - Variable in class etomica.normalmode.SimUmbrella
 
box - Variable in class etomica.normalmode.SimUmbrellaSoftSphere
 
box - Variable in class etomica.paracetamol.MCParacetamolMonoclinicDLMULTI
 
box - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicDLMULTI
 
box - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
 
box - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
 
box - Variable in class etomica.paracetamol.MDParacetamolMonoclinic
The Box holding the atoms.
box - Variable in class etomica.paracetamol.MDParacetamolOrthorhombic
The Box holding the atoms.
box - Variable in class etomica.paracetamol.NumericalDerivativeEnergyParacetamol
 
box - Variable in class etomica.paracetamol.SimulationOrthorhombicParacetamol
 
box - Variable in class etomica.spin.Heisenberg
 
box - Variable in class etomica.threaded.atom.LJMD3DThreaded
 
box - Variable in class etomica.threaded.domain.LJMD3DThreaded
 
box - Variable in class etomica.threaded.domain.MEAMMd3DThreaded
 
box - Variable in class etomica.virial.MeterVirialBDBinMultiThreaded
 
box - Variable in class etomica.virial.MeterVirialBinMultiThreaded
 
box - Variable in class etomica.virial.MeterVirialEBinMultiThreaded
 
box - Variable in class etomica.virial.simulations.SimulationVirial
 
box - Variable in class etomica.virial.simulations.SimulationVirialMultiOverlap
 
box - Variable in class etomica.virial.simulations.SimulationVirialOverlap
 
box - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
 
box - Variable in class etomica.virial.simulations.SimulationVirialPT
 
box - Variable in class etomica.virial.simulations.TestLJAssociationMC3D_NPT
 
box - Variable in class etomica.yukawa.TestHC2YukawaMC3D
 
box - Variable in class etomica.yukawa.TestYukawaMC3D
 
box - Variable in class etomica.yukawa.TestYukawaMD3D
 
box - Variable in class etomica.zeolite.ZeoliteSimulation
The Box holding the atoms.
box1 - Variable in class etomica.dimer.IntegratorDimerRT
 
box1 - Variable in class etomica.virial.PotentialCommonAtomic
 
box2 - Variable in class etomica.dimer.IntegratorDimerRT
 
BoxAgentSourceCellManagerThreaded - Class in etomica.threaded.domain
BoxAgentSource responsible for creating a NeighborCellManager.
BoxAgentSourceCellManagerThreaded(ISimulation, IAtomPositionDefinition, ISpace) - Constructor for class etomica.threaded.domain.BoxAgentSourceCellManagerThreaded
 
boxCells - Variable in class etomica.normalmode.MCMoveAtomSuperBox
 
BoxCluster - Class in etomica.virial
 
BoxCluster(ClusterWeight, ISpace) - Constructor for class etomica.virial.BoxCluster
Constructor for BoxCluster.
BoxClusterFactory() - Constructor for class etomica.virial.simulations.SimulationVirialOverlap2.BoxClusterFactory
 
boxFactory - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
 
boxHarmonic - Variable in class etomica.normalmode.SimOverlap
 
boxHarmonic - Variable in class etomica.normalmode.SimOverlapLJ
 
boxHarmonic - Variable in class etomica.normalmode.SimOverlapLJModule
 
boxHarmonic - Variable in class etomica.normalmode.SimOverlapSoftSphere
 
boxHarmonic - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
 
boxHarmonic - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting
 
boxHarmonic - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox
 
boxHarmonic - Variable in class etomica.normalmode.SimOverlapSSnxy
 
boxIndex - Variable in class etomica.normalmode.P1ConstraintNbr
 
boxManager - Variable in class etomica.normalmode.P1ConstraintNbr
 
boxMin - Variable in class etomica.dimer.IntegratorDimerMin
 
boxRef - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
 
boxRef - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
 
boxSize - Variable in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
 
boxSize - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
 
boxSize0 - Variable in class etomica.normalmode.MeterDisplacementRMS
 
boxTarg - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
 
boxTarget - Variable in class etomica.normalmode.SimOverlap
 
boxTarget - Variable in class etomica.normalmode.SimOverlapLJ
 
boxTarget - Variable in class etomica.normalmode.SimOverlapLJModule
 
boxTarget - Variable in class etomica.normalmode.SimOverlapSoftSphere
 
boxTarget - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
 
boxTarget - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting
 
boxTarget - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox
 
boxTarget - Variable in class etomica.normalmode.SimOverlapSSnxy
 
bpharm - Variable in class etomica.normalmode.SimLJHTTISuper.SimOverlapParam
 
bpharm - Variable in class etomica.normalmode.SimLJHTTISuperHCP.SimOverlapParam
 
bpharmLJ - Variable in class etomica.normalmode.SimLJHTTISuper.SimOverlapParam
 
bpharmLJ - Variable in class etomica.normalmode.SimLJHTTISuperHCP.SimOverlapParam
 
bpRes - Variable in class etomica.normalmode.MeterSolidDACut
 
bpResDADv2 - Variable in class etomica.normalmode.MeterSolidDACut
 
bprime - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
 
bSum - Variable in class etomica.virial.ClusterSinglyConnected
 
BuilderCollectionPotential - Class in etomica.virial.GUI.components
 
BuilderCollectionPotential() - Constructor for class etomica.virial.GUI.components.BuilderCollectionPotential
 
bump(IAtomList, double) - Method in class etomica.normalmode.P2XOrder
 
button - Variable in class etomica.zeolite.DeviceButtonSingle
 

C

c - Variable in class etomica.dimer.P1LepsHarmonic
 
C - Variable in class etomica.meam.PotentialFeEAM
 
c - Variable in class etomica.normalmode.SoftSphereSolidEOS
 
c - Variable in class etomica.normalmode.SoftSphereSolidEOSCalculator
 
c - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
 
c - Variable in class etomica.virial.ClusterPY
 
c0 - Variable in class etomica.meam.PotentialCuLREP
 
c0 - Variable in class etomica.meam.PotentialEFS
 
c1 - Variable in class etomica.meam.PotentialCuLREP
 
c1 - Variable in class etomica.meam.PotentialEFS
 
c2 - Variable in class etomica.meam.PotentialCuLREP
 
c2 - Variable in class etomica.meam.PotentialEFS
 
c2 - Static variable in class etomica.virial.BnJHBVArgon_Analytic
 
c2_sqrt - Static variable in class etomica.virial.BnJHBVArgon_Analytic
 
c3 - Variable in class etomica.meam.PotentialCuLREP
 
c3 - Variable in class etomica.meam.PotentialEFS
 
c3 - Static variable in class etomica.virial.BnJHBVArgon_Analytic
 
C3 - Static variable in class etomica.virial.cluster.Standard
 
c3_sqrt - Static variable in class etomica.virial.BnJHBVArgon_Analytic
 
c3Add - Static variable in class etomica.virial.BnJHBVArgon_Analytic
 
c3Add_sqrt - Static variable in class etomica.virial.BnJHBVArgon_Analytic
 
c4 - Variable in class etomica.meam.PotentialCuLREP
 
c4 - Variable in class etomica.meam.PotentialEFS
 
c4 - Static variable in class etomica.virial.BnJHBVArgon_Analytic
 
c4_sqrt - Static variable in class etomica.virial.BnJHBVArgon_Analytic
 
c4Add - Static variable in class etomica.virial.BnJHBVArgon_Analytic
 
c4Add_sqrt - Static variable in class etomica.virial.BnJHBVArgon_Analytic
 
c5 - Static variable in class etomica.virial.BnJHBVArgon_Analytic
 
c5_sqrt - Static variable in class etomica.virial.BnJHBVArgon_Analytic
 
c5Add - Static variable in class etomica.virial.BnJHBVArgon_Analytic
 
c5Add_sqrt - Static variable in class etomica.virial.BnJHBVArgon_Analytic
 
c6 - Static variable in class etomica.virial.BnJHBVArgon_Analytic
 
c6_sqrt - Static variable in class etomica.virial.BnJHBVArgon_Analytic
 
c6Add - Static variable in class etomica.virial.BnJHBVArgon_Analytic
 
c6Add_sqrt - Static variable in class etomica.virial.BnJHBVArgon_Analytic
 
c7Add - Static variable in class etomica.virial.BnJHBVArgon_Analytic
 
c7Add_sqrt - Static variable in class etomica.virial.BnJHBVArgon_Analytic
 
calcApprox - Variable in class etomica.virial.simulations.VirialHeNonAdditive.VirialParam
 
calcApprox - Variable in class etomica.virial.simulations.VirialHeNonAdditiveWheatley.VirialParam
 
calcApprox - Variable in class etomica.virial.simulations.VirialHePI.VirialHePIParam
 
calcApprox - Variable in class etomica.virial.simulations.VirialHePIXCEven.VirialHePIParam
 
calcApprox - Variable in class etomica.virial.simulations.VirialHePIXCOdd.VirialHePIParam
 
calcApprox - Variable in class etomica.virial.simulations.VirialHePYCorrection.VirialHePYCParam
 
calcApprox - Variable in class etomica.virial.simulations.VirialHeSC.VirialHePYCParam
 
calcBondAngleEnergy(double) - Method in class etomica.models.hexane.CBMCGrowSolidHexane
 
calcBondAngleEnergy(double) - Method in class etomica.models.hexane.CBMCGrowStraightAlkane
 
calcBondL() - Method in class etomica.models.hexane.CBMCGrowSolidHexane
 
calcBondL() - Method in class etomica.models.hexane.CBMCGrowStraightAlkane
Returns the bond length for the new atom in a test Should take bonded potential into account.
calcBondTorsionalEnergy(IVectorMutable) - Method in class etomica.models.hexane.CBMCGrowSolidHexane
 
calcBondTorsionalEnergy(IVectorMutable) - Method in class etomica.models.hexane.CBMCGrowStraightAlkane
 
calcExternalEnergy(IAtom) - Method in class etomica.models.hexane.CBMCGrowSolidHexane
 
calcExternalEnergy(IAtom) - Method in class etomica.models.hexane.CBMCGrowStraightAlkane
 
calcF(double) - Method in class etomica.virial.MayerFunctionThreeBody
Returns exp(x)-1 computed directly or using a series expansion
calcfAB(int, boolean) - Method in class etomica.virial.ClusterWheatleyPartitionScreening
 
calcfAB0(boolean) - Method in class etomica.virial.ClusterWheatleyPartitionScreening
 
calcfC(boolean) - Method in class etomica.virial.ClusterWheatleyPartitionScreening
 
CalcFFT - Class in etomica.virial
CalcFFT can calculate distribution functions using FFT.
CalcFFT(IFunction, double, int) - Constructor for class etomica.virial.CalcFFT
 
calcForce(int, double) - Method in class etomica.threads.ThreadsMD
 
calcfQ(BoxCluster) - Method in class etomica.virial.ClusterWheatleyPartitionScreening
This calculates all fQ values given that the entries for pairs have already been populated.
calcFullFQ(BoxCluster) - Method in class etomica.virial.ClusterSumHS
This calculates all FQ values given that the entries for pairs have already been populated.
calcFullFQ(BoxCluster) - Method in class etomica.virial.ClusterWheatleyExtendSW
This calculates all FQ values given that the entries for pairs have already been populated.
calcFullFQ(BoxCluster) - Method in class etomica.virial.ClusterWheatleyHS
This calculates all FQ values given that the entries for pairs have already been populated.
calcFullFQ(BoxCluster) - Method in class etomica.virial.ClusterWheatleyMultibody
 
calcFullFQ(BoxCluster) - Method in class etomica.virial.ClusterWheatleyMultibodyBD
 
calcFullFQ(BoxCluster) - Method in class etomica.virial.ClusterWheatleyMultibodyMix
 
calcFullFQ(BoxCluster) - Method in class etomica.virial.ClusterWheatleySoft
This calculates all FQ values given that the entries for pairs have already been populated.
calcFullFQ(BoxCluster) - Method in class etomica.virial.ClusterWheatleySoftBD
This calculates all FQ values given that the entries for pairs have already been populated.
calcGradientDifferentiable - Variable in class etomica.dimer.SimDimerLJadatom
 
calcGradientDifferentiable - Variable in class etomica.dimer.SimDimerMEAMadatom
 
calcGradientDifferentiable - Variable in class etomica.dimer.SimDimerMEAMGB
 
CalcHarmonicA - Class in etomica.normalmode
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.
CalcHarmonicA() - Constructor for class etomica.normalmode.CalcHarmonicA
 
CalcJacobian - Class in etomica.normalmode
Class that calculates the dq/dx Jacobian.
CalcJacobian() - Constructor for class etomica.normalmode.CalcJacobian
 
calcModes - Variable in class etomica.dimer.SimDimerLJadatom
 
calcRandomBond() - Method in class etomica.models.hexane.CBMCGrowStraightAlkane
Generates a random bond.
calcRandomBondWithAngle(IAtom, IAtom) - Method in class etomica.models.hexane.CBMCGrowSolidHexane
 
calcRandomBondWithAngle(IAtom, IAtom) - Method in class etomica.models.hexane.CBMCGrowStraightAlkane
XXX METHOD NOT TESTED! USE AT OWN PERIL! Generates a random bond that accounts for bond angle in the calculation This method will change its parameter.
calcRandomBondWithAngleAndTorsion(IAtom, IAtom, IAtom) - Method in class etomica.models.hexane.CBMCGrowSolidHexane
 
calcRandomBondWithAngleAndTorsion(IAtom, IAtom, IAtom) - Method in class etomica.models.hexane.CBMCGrowStraightAlkane
XXX METHOD NOT TESTED! USE AT OWN PERIL!l dy Generates a random bond that accounts for bond angle and torsion in the calculation.
calcReeHoover() - Method in class etomica.virial.cluster.ClusterGenerator
Calculates the Ree-Hoover coefficient (coefficient for Ree-Hoover diagram / coefficient for Mayer diagram) for mCluster and sets mCluster's mReeHooverFactor to it.
calcRosenbluthFactors() - Method in class etomica.models.hexane.CBMCGrowStraightAlkane
Calculates wOld and wNew
calcRosenbluthFactors() - Method in class etomica.models.hexane.MCMoveCBMC
 
calcScore(int[]) - Method in class etomica.virial.cluster.ClusterDiagram
compute a score for the cluster.
calcSignature(BoxCluster) - Method in class etomica.virial.ClusterWheatleyPartitionScreening
 
calcSignatures() - Method in class etomica.virial.ClusterWheatleyPartitionScreening
Compute signatures used for lookup tables of fA, fAB, fC
calcStartIndex() - Method in class etomica.models.hexane.CBMCGrowSolidHexane
 
calcStartIndex() - Method in class etomica.models.hexane.CBMCGrowStraightAlkane
 
calcSums(IAtomList) - Method in class etomica.meam.PotentialMEAM
 
calcT(IVector, double[], double[]) - Method in class etomica.normalmode.CoordinateDefinition
Calculates the complex "T vector", which is collective coordinate given by the Fourier sum (over atoms) of the generalized coordinate vector.
calcU(IMoleculeList) - Method in class etomica.models.hexane.CoordinateDefinitionHexane
 
calcU(IMoleculeList) - Method in class etomica.normalmode.CoordinateDefinition
Calculates the generalized coordinates for the given molecules in their current position and orientation.
calcU(IMoleculeList) - Method in class etomica.normalmode.CoordinateDefinitionHSDimer
 
calcU(IMoleculeList) - Method in class etomica.normalmode.CoordinateDefinitionLeaf
Assigns the given array u to be the current position of the atom minus its lattice position
calcU(IMoleculeList) - Method in class etomica.normalmode.CoordinateDefinitionMolecule
 
calcU(IMoleculeList) - Method in class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation
 
calcU(IMoleculeList) - Method in class etomica.paracetamol.CoordinateDefinitionParacetamol
 
calculate(IBox, IteratorDirective, PotentialCalculation) - Method in class etomica.dimer.PotentialMasterListDimer
 
calculate(IBox, IteratorDirective, PotentialCalculation) - Method in class etomica.threaded.atom.PotentialMasterListThreaded
 
calculate(IAtom, IteratorDirective, PotentialCalculation) - Method in class etomica.threaded.atom.PotentialMasterListWorker
 
calculate(IBox, IteratorDirective, PotentialCalculation) - Method in class etomica.threaded.domain.PotentialMasterListThreaded
 
calculate(IAtom, IteratorDirective, PotentialCalculation) - Method in class etomica.threaded.domain.PotentialMasterListWorker
 
calculateEnergy(IBox) - Method in interface etomica.normalmode.IAPIPotential
Returns the potential energy of the given box.
calculateEnergy(IBox) - Method in class etomica.normalmode.SimOverlapLJModule.APIPotentialReference
 
calculateEnergy(IBox) - Method in class etomica.normalmode.SimOverlapLJModule.APIPotentialTarget
 
calculateLatticeDimensions(int, IVectorMutable) - Method in class etomica.paracetamol.ConfigurationMonoclinicLattice
 
calculateLatticeDimensions(int, IVectorMutable) - Method in class etomica.paracetamol.ConfigurationOrthorhombicLattice
 
calculateLatticeDimensions(int, IVector) - Method in class etomica.threaded.domain.NeighborCellManagerThreaded
 
calculateModes() - Method in class etomica.normalmode.NormalModesMolecular
 
calculateModes() - Method in class etomica.normalmode.NormalModesPotential
 
calculateModes() - Method in class etomica.normalmode.NormalModesSoftSpherical
 
calculateModes() - Method in class etomica.paracetamol.NormalModesPotentialParacetamol
 
calculateSum(LatticeSumMolecularCrystal.AtomicTensorAtomicPair) - Method in class etomica.normalmode.LatticeSumMolecularCrystal
 
calculateSum(LatticeEnergyParacetamol) - Method in class etomica.paracetamol.LatticeSumCrystalParacetamol
 
calculateSystemSigmaHSRef(ModelSelectedSpecies) - Method in class etomica.virial.GUI.models.ModelSimulationEnvironment
 
calculateSystemSigmaHSRef(IMolecularModel_SpeciesFactory[], int[]) - Method in class etomica.virial.GUI.models.ModelSimulationEnvironment
 
calculateThreaded(IBox, IteratorDirective, IPotentialCalculationThreaded, NeighborListManager) - Method in class etomica.threaded.atom.PotentialMasterListThreaded
 
calculateThreaded(IBox, IteratorDirective, IPotentialCalculationThreaded, NeighborListManager) - Method in class etomica.threaded.domain.PotentialMasterListThreaded
 
calcValue() - Method in class etomica.virial.ClusterChainHS
 
calcValue() - Method in class etomica.virial.ClusterChainSoft
 
calcValue(BoxCluster) - Method in class etomica.virial.ClusterICPYC
 
calcValue(BoxCluster) - Method in class etomica.virial.ClusterPY
 
calcValue() - Method in class etomica.virial.ClusterSinglyConnected
 
calcValue() - Method in class etomica.virial.ClusterSum
 
calcValue() - Method in class etomica.virial.ClusterSumAssociation
 
calcValue() - Method in class etomica.virial.ClusterSumExternalField
 
calcValue(BoxCluster) - Method in class etomica.virial.ClusterSumHS
Returns the cluster value for the given configuration.
calcValue() - Method in class etomica.virial.ClusterSumIC
 
calcValue() - Method in class etomica.virial.ClusterSumMultibody
 
calcValue() - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct
 
calcValue() - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
 
calcValue() - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
 
calcValue() - Method in class etomica.virial.ClusterSumStickyEF
 
calcValue(BoxCluster) - Method in interface etomica.virial.ClusterWheatley
Calculates the value of the configuration.
calcValue(BoxCluster) - Method in class etomica.virial.ClusterWheatleyExtendSW
Returns the cluster value for the given configuration.
calcValue(BoxCluster) - Method in class etomica.virial.ClusterWheatleyHS
Returns the cluster value for the given configuration.
calcValue(BoxCluster, boolean) - Method in class etomica.virial.ClusterWheatleyHS
 
calcValue(BoxCluster) - Method in class etomica.virial.ClusterWheatleyMultibody
 
calcValue(BoxCluster) - Method in class etomica.virial.ClusterWheatleyMultibodyBD
 
calcValue(BoxCluster) - Method in class etomica.virial.ClusterWheatleyMultibodyMix
 
calcValue(BoxCluster) - Method in class etomica.virial.ClusterWheatleyPartitionScreening
Returns the cluster value for the given configuration.
calcValue(BoxCluster, boolean) - Method in class etomica.virial.ClusterWheatleyPartitionScreening
 
calcValue(BoxCluster) - Method in class etomica.virial.ClusterWheatleySoft
Returns the cluster value for the given configuration.
calcValue(BoxCluster) - Method in class etomica.virial.ClusterWheatleySoftBD
Returns the cluster value for the given configuration.
calcVibrationalModes - Variable in class etomica.dimer.SimDimerLJadatom
 
calcVibrationalModes - Variable in class etomica.dimer.SimDimerMEAMadatom
 
calcVibrationalModes - Variable in class etomica.dimer.SimDimerMEAMGB
 
calcWeight() - Method in class etomica.virial.MCMoveClusterRingPartialRegrow
 
cancelMap - Variable in class etomica.virial.cluster.MayerIonicDiagram1qbond
 
cancelMap - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
 
cancelMap - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
 
cancelMap - Variable in class etomica.virial.cluster.VirialDiagrams
 
cancelMap - Variable in class etomica.virial.cluster.VirialDiagramsMix
 
cancelMap - Variable in class etomica.virial.cluster.VirialDiagramsMix2
 
cancelMap - Variable in class etomica.virial.cluster.VirialDiagramsPT
 
cancelMap - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
 
cancelMap - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
 
cancelP - Variable in class etomica.virial.cluster.MayerIonicDiagram1qbond
 
cancelP - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
 
cancelP - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
 
cancelP - Variable in class etomica.virial.cluster.VirialDiagramsMix
 
cancelP - Variable in class etomica.virial.cluster.VirialDiagramsMix2
 
cancelP - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
 
cancelP - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
 
capF1Bond - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
 
capF2Bond - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
 
capFABBond - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
 
capFACBond - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
 
capFBABond - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
 
capFBCBond - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
 
capFBond - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
 
capFBond - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
 
capFCABond - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
 
capFCBBond - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
 
CBMCGrowSolidHexane - Class in etomica.models.hexane
Contains specifics for the solid hexane model: bond length = 0.4 rejects moving the whole molecule as a CBMC move
CBMCGrowSolidHexane(IPotentialMaster, IRandom, ISpace, IntegratorMC, IBox, ISpecies, int) - Constructor for class etomica.models.hexane.CBMCGrowSolidHexane
 
CBMCGrowStraightAlkane - Class in etomica.models.hexane
Grows a straight-chain alkane of specified length.
CBMCGrowStraightAlkane(IPotentialMaster, IRandom, IntegratorMC, IBox, ISpecies, ISpace, int, int) - Constructor for class etomica.models.hexane.CBMCGrowStraightAlkane
 
cbmcMove - Variable in class etomica.models.hexane.MCMoveCombinedCbmcTranslation
 
CCbondL - Variable in class etomica.virial.ConformationAlkaneEH
 
cctMove - Variable in class etomica.models.hexane.TestHexane
 
cctMove - Variable in class etomica.models.hexane.TestHexaneFileConfig
 
cctMove - Variable in class etomica.models.hexane.TestSetToUHexane
 
cellPosition - Variable in class etomica.normalmode.CoordinateDefinition.BasisCell
 
cells - Variable in class etomica.normalmode.CoordinateDefinition
 
cells - Variable in class etomica.normalmode.MCMoveAtomSuperBox
 
centerer - Variable in class etomica.models.hexane.MCMoveCombinedCbmcTranslation
 
cFe - Variable in class etomica.meam.PotentialFeEAM_LS
 
CH2element - Variable in class etomica.virial.GUI.components.SimpleElementForSimilarSpecies
 
CH3element - Variable in class etomica.virial.GUI.components.SimpleElementForSimilarSpecies
 
Chain - Class in etomica.virial.cluster
 
Chain(int) - Constructor for class etomica.virial.cluster.Chain
Constructor for Chain.
chain(int) - Static method in class etomica.virial.cluster.Standard
Returns a chain of bonds, {{0,1},{1,2},...{n-2,n-1}}
CHAIN_TAIL - Static variable in class etomica.virial.simulations.VirialHS.VirialHSParam
 
CHAIN_TAIL - Static variable in class etomica.virial.simulations.VirialSWWE.VirialSWWEParam
 
CHAIN_TREE - Static variable in class etomica.virial.simulations.VirialHS.VirialHSParam
 
CHAIN_TREE - Static variable in class etomica.virial.simulations.VirialPolyhedra.VirialHSParam
 
CHAIN_TREE - Static variable in class etomica.virial.simulations.VirialPolyhedra2.VirialHSParam
 
CHAIN_TREE - Static variable in class etomica.virial.simulations.VirialSWWE.VirialSWWEParam
 
chainFrac - Variable in class etomica.virial.ClusterChainHS
 
chainFrac - Variable in class etomica.virial.simulations.VirialHS.VirialHSParam
 
chainFrac - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.SimulationWorker
 
chainFrac - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.VirialHSBinParam
 
chainFrac - Variable in class etomica.virial.simulations.VirialPolyhedra.VirialHSParam
 
chainFrac - Variable in class etomica.virial.simulations.VirialPolyhedra2.VirialHSParam
 
chainFrac - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.SimulationWorker
 
chainFrac - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.VirialHSBinParam
 
chainFrac - Variable in class etomica.virial.simulations.VirialSWWE.VirialSWWEParam
 
chainlength - Variable in class etomica.models.hexane.MCMoveCBMC
 
CHAINS - Static variable in class etomica.virial.simulations.VirialHS.VirialHSParam
 
CHAINS - Static variable in class etomica.virial.simulations.VirialPolyhedra.VirialHSParam
 
CHAINS - Static variable in class etomica.virial.simulations.VirialPolyhedra2.VirialHSParam
 
CHAINS - Static variable in class etomica.virial.simulations.VirialSWWE.VirialSWWEParam
 
characterEndA - Variable in class etomica.virial.cluster.BondConnectedSubstitutionNaphthalene.BondConnectedSubstitutionParameters2SiteNa
 
characterEndB - Variable in class etomica.virial.cluster.BondConnectedSubstitutionNaphthalene.BondConnectedSubstitutionParameters2SiteNa
 
characterStartA - Variable in class etomica.virial.cluster.BondConnectedSubstitutionNaphthalene.BondConnectedSubstitutionParameters2SiteNa
 
characterStartB - Variable in class etomica.virial.cluster.BondConnectedSubstitutionNaphthalene.BondConnectedSubstitutionParameters2SiteNa
 
charge - Variable in class etomica.virial.simulations.VirialN2TraPPE.VirialN2Param
 
ChargeAgentSourceParacetamol - Class in etomica.paracetamol
 
ChargeAgentSourceParacetamol() - Constructor for class etomica.paracetamol.ChargeAgentSourceParacetamol
 
CHbondL - Variable in class etomica.virial.ConformationAlkaneEH
 
check(Graph) - Method in class etomica.virial.cluster.VirialDiagrams.ArticulatedAt0
 
check(Graph) - Method in class etomica.virial.cluster.VirialDiagramsMix2.MaxIsomorphCriteriaMixture
 
check(Graph) - Method in class etomica.virial.cluster.VirialDiagramsPT.ArticulatedAt0
 
check(Graph) - Method in class etomica.virial.cluster.VirialDiagramsPT.DiscardCriteria
 
check(Graph) - Method in class etomica.virial.IsFFT
 
CheckCBMCHexane - Class in etomica.models.hexane
 
CheckCBMCHexane(IBox, PotentialMaster, ISpace) - Constructor for class etomica.models.hexane.CheckCBMCHexane
 
checkConfig(BoxCluster) - Method in class etomica.virial.ClusterSumHS
 
checkConfig(BoxCluster) - Method in interface etomica.virial.ClusterWheatley
Determines whether the configuration is zero-valued or not.
checkConfig(BoxCluster) - Method in class etomica.virial.ClusterWheatleyExtendSW
 
checkConfig(BoxCluster) - Method in class etomica.virial.ClusterWheatleyHS
 
checkConfig(BoxCluster) - Method in class etomica.virial.ClusterWheatleyPartitionScreening
 
checkDimensions() - Method in class etomica.threaded.domain.NeighborCellManagerThreaded
 
checkForSimilarSites(String[], String[], IMolecularModel_SpeciesFactory[]) - Method in class etomica.virial.GUI.components.BuilderCollectionPotential
 
checkIfCompatible(ModelSelectedSpecies, ModelSimulationEnvironment) - Method in class etomica.virial.GUI.components.BuilderCollectionPotential
 
checkIfSameSpeciesWithSimilarPotentials(IMolecularModel_SpeciesFactory, IMolecularModel_SpeciesFactory, int, int) - Method in class etomica.virial.GUI.controllers.ControllerSpeciesSelection
 
checkIndexOfSpeciesSelected() - Method in class etomica.virial.GUI.controllers.ControllerSpeciesSelection
 
checkme - Static variable in class etomica.virial.ClusterWheatleyPartitionScreening
 
children - Variable in class etomica.virial.cluster.ClusterTreeNode
 
chopF(MayerFunction[]) - Static method in class etomica.virial.ClusterSumStickyEF
 
chType - Variable in class etomica.virial.SpeciesAnthracene3site464
 
chType - Variable in class etomica.virial.SpeciesAnthracene3site545
 
chType - Variable in class etomica.virial.SpeciesPh3site464
 
chType - Variable in class etomica.virial.SpeciesPh3site545
 
chType - Variable in class etomica.virial.SpeciesTraPPEAnthracene
 
chType - Variable in class etomica.virial.SpeciesTraPPENaphthalene
 
chType - Variable in class etomica.virial.SpeciesTraPPEPhenanthrene
 
cliqueCheck(int, int) - Method in class etomica.virial.ClusterSumHS
Checks to see if the set |clique| is a clique separator.
cliqueCheck(int, int) - Method in class etomica.virial.ClusterWheatleyHS
Checks to see if the set |clique| is a clique separator.
cliqueCheck(int, int) - Method in class etomica.virial.ClusterWheatleyPartitionScreening
Checks to see if the set |clique| is a clique separator.
cliqueCount - Variable in class etomica.virial.ClusterSumHS
 
cliqueCount - Variable in class etomica.virial.ClusterWheatleyHS
 
cliqueCount - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
 
cliqueCountE2 - Variable in class etomica.virial.ClusterWheatleyExtendSW
 
cliqueCountEF - Variable in class etomica.virial.ClusterWheatleyExtendSW
 
cliqueCountF1 - Variable in class etomica.virial.ClusterWheatleyExtendSW
 
cliqueCountNone - Variable in class etomica.virial.ClusterWheatleyExtendSW
 
cliqueList - Variable in class etomica.virial.ClusterSumHS
 
cliqueList - Variable in class etomica.virial.ClusterWheatleyHS
 
cliqueList - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
 
cliqueListE2 - Variable in class etomica.virial.ClusterWheatleyExtendSW
 
cliqueListEF - Variable in class etomica.virial.ClusterWheatleyExtendSW
 
cliqueListF1 - Variable in class etomica.virial.ClusterWheatleyExtendSW
 
cliqueListNone - Variable in class etomica.virial.ClusterWheatleyExtendSW
 
cliqueSet - Variable in class etomica.virial.ClusterSumHS
 
cliqueSet - Variable in class etomica.virial.ClusterWheatleyHS
 
cliqueSet - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
 
cliqueSetE2 - Variable in class etomica.virial.ClusterWheatleyExtendSW
 
cliqueSetEF - Variable in class etomica.virial.ClusterWheatleyExtendSW
 
cliqueSetF1 - Variable in class etomica.virial.ClusterWheatleyExtendSW
 
cliqueSetNone - Variable in class etomica.virial.ClusterWheatleyExtendSW
 
clone() - Method in interface etomica.virial.GUI.models.IMolecularModel_SpeciesFactory
 
clone() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
 
clone() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
 
clone() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
 
clone() - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
 
clone() - Method in class etomica.virial.GUI.models.MolecularModelLJ_SpeciesLJ
 
clone() - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
 
clone() - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
 
clone() - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
 
clone() - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
 
clone() - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
 
closeAlkaneView() - Method in class etomica.virial.GUI.views.ViewAlkaneLengthSelection
 
closeFile() - Method in class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage
 
closeFile() - Method in class etomica.zeolite.MSDCoordWriter
 
closeFW() - Method in class etomica.normalmode.MeterTargetTP
Closes file with overlap data.
closeSimEnvParamView() - Method in class etomica.virial.GUI.views.ViewSimEnvironmentSelection
 
closeWindow - Variable in class etomica.virial.GUI.views.ViewAlkaneLengthSelection
 
CloseWindowButtonListener() - Constructor for class etomica.virial.GUI.controllers.ControllerAlertMsgBox.CloseWindowButtonListener
 
cluster - Variable in class etomica.virial.MeterVirialExternalField
 
cluster - Variable in class etomica.virial.MeterVirialExternalFieldConfined
 
cluster - Variable in class etomica.virial.MeterVirialExternalFieldSW
 
ClusterAbstract - Interface in etomica.virial
 
clusterAdd - Variable in class etomica.virial.ClusterDifference
 
ClusterAssociation - Class in etomica.virial.cluster
 
ClusterAssociation() - Constructor for class etomica.virial.cluster.ClusterAssociation
 
clusterBD - Variable in class etomica.virial.ClusterWheatleySoft
 
ClusterBonds - Class in etomica.virial
 
ClusterBonds(int, int[][][]) - Constructor for class etomica.virial.ClusterBonds
Constructor for Cluster, with default to not using permutations (this can be changed after construction if desired).
ClusterBonds(int, int[][][], boolean) - Constructor for class etomica.virial.ClusterBonds
Constructor for Cluster.
ClusterBonds(int[][], boolean) - Constructor for class etomica.virial.ClusterBonds
 
ClusterBondsNonAdditive - Class in etomica.virial
Subclass of ClusterBonds capable of handling non-additive Mayer functions.
ClusterBondsNonAdditive(int, int[][][], int[][]) - Constructor for class etomica.virial.ClusterBondsNonAdditive
Construct a ClusterBondsNonAdditive of size n, using the given list of pair and multibonds.
ClusterBondsNonAdditive(int[][], int[][]) - Constructor for class etomica.virial.ClusterBondsNonAdditive
 
ClusterChainHS - Class in etomica.virial
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.
ClusterChainHS(int, MayerFunction) - Constructor for class etomica.virial.ClusterChainHS
Constructs with default to perform chain-only calculation, with chainFrac = 1.0
ClusterChainHS(int, MayerFunction, boolean) - Constructor for class etomica.virial.ClusterChainHS
Constructs to perform either chain-only or ring-only calculation, as directed by doRing (true for ring-only)
ClusterChainHS(int, MayerFunction, double, double) - Constructor for class etomica.virial.ClusterChainHS
Constructs to perform linear combination of chain and ring values, with computed cluster values each weighted by given fractions, and summed to get total value
ClusterChainSoft - Class in etomica.virial
This class calculates the sum of all chain clusters.
ClusterChainSoft(int, MayerFunction) - Constructor for class etomica.virial.ClusterChainSoft
 
ClusterChainSoft(int, MayerFunction, boolean) - Constructor for class etomica.virial.ClusterChainSoft
 
ClusterCollapsedTreeNode - Class in etomica.virial.cluster
 
ClusterCollapsedTreeNode(int, int) - Constructor for class etomica.virial.cluster.ClusterCollapsedTreeNode
 
ClusterCollapsedTreeNode(ClusterTreeNode, ClusterTreeNode) - Constructor for class etomica.virial.cluster.ClusterCollapsedTreeNode
 
ClusterCoupledAtomFlipped - Class in etomica.virial
 
ClusterCoupledAtomFlipped(ClusterAbstract, ISpace) - Constructor for class etomica.virial.ClusterCoupledAtomFlipped
 
ClusterCoupledAtomFlipped(ClusterAbstract, ISpace, double) - Constructor for class etomica.virial.ClusterCoupledAtomFlipped
 
ClusterCoupledFlipped - Class in etomica.virial
 
ClusterCoupledFlipped(ClusterAbstract, ISpace) - Constructor for class etomica.virial.ClusterCoupledFlipped
cluster must have caching disabled
ClusterCoupledFlipped(ClusterAbstract, ISpace, double) - Constructor for class etomica.virial.ClusterCoupledFlipped
cluster must have caching disabled configurations will be flipped when the minimum distance between any two molecules exceeds minFlipDistance.
ClusterCoupledFlippedPartial - Class in etomica.virial
 
ClusterCoupledFlippedPartial(ClusterAbstract, ISpace, int[][]) - Constructor for class etomica.virial.ClusterCoupledFlippedPartial
 
clusterCriteria - Variable in class etomica.virial.ClusterSumAssociation
 
ClusterDiagram - Class in etomica.virial.cluster
Holds information about a cluster diagram, including the bonds, root points, and score.
ClusterDiagram(int, int) - Constructor for class etomica.virial.cluster.ClusterDiagram
Constructs a cluster having numBody points of which numRootPoints are root points, with bonds between each pair of points (full star).
ClusterDiagram(int, int, int[][]) - Constructor for class etomica.virial.cluster.ClusterDiagram
Constructs a cluster having numBody points of which numRootPoints are root points, with bonds as given by the array bonds.
ClusterDiagram(int, int, int[][], Rational) - Constructor for class etomica.virial.cluster.ClusterDiagram
 
ClusterDiagram(ClusterDiagram) - Constructor for class etomica.virial.cluster.ClusterDiagram
Creates a copy of the given cluster
ClusterDiagramTree - Class in etomica.virial.cluster
Holds information about a cluster diagram, including the bonds, root points, and score.
ClusterDiagramTree(int, int) - Constructor for class etomica.virial.cluster.ClusterDiagramTree
Constructs a cluster having numBody points and numRootPoints root points.
ClusterDifference - Class in etomica.virial
This class holds multiple clusters and returns the value from one minus the average value from the others.
ClusterDifference(ClusterAbstract, ClusterAbstract[]) - Constructor for class etomica.virial.ClusterDifference
 
ClusterExchange - Class in etomica.virial
 
ClusterExchange(IPotentialAtomic) - Constructor for class etomica.virial.ClusterExchange
 
ClusterGenerator - Class in etomica.virial.cluster
Generates all clusters matching certain criteria.
ClusterGenerator(ClusterDiagram) - Constructor for class etomica.virial.cluster.ClusterGenerator
 
ClusterICPYC - Class in etomica.virial
Cluster class that computes the correction to the ICPY (incrementally corrected Percus-Yevick) formulation.
ClusterICPYC(int, MayerFunction) - Constructor for class etomica.virial.ClusterICPYC
 
clusterMultiBD - Variable in class etomica.virial.ClusterWheatleyMultibody
 
ClusterOperations - Class in etomica.virial.cluster
 
ClusterOperations() - Constructor for class etomica.virial.cluster.ClusterOperations
 
ClusterPY - Class in etomica.virial
 
ClusterPY(int, MayerFunction) - Constructor for class etomica.virial.ClusterPY
 
clusterRadius - Variable in class etomica.dimer.SimDimerMEAMGB
 
clusters - Variable in class etomica.virial.ClusterSum
 
clusters - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct
 
clusters - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
 
clusters - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
 
clusters - Variable in class etomica.virial.MeterVirial
 
clusters - Variable in class etomica.virial.MeterVirialBD
 
clusters - Variable in class etomica.virial.MeterVirialExternalFieldOverlapConfined
 
clusters - Variable in class etomica.virial.MeterVirialExternalFieldOverlapConfinedRho
 
clusters - Variable in class etomica.virial.MeterVirialExternalFieldOverlapConfinedSW
 
clusters - Variable in class etomica.virial.MeterVirialExternalFieldOverlapRho
 
clusters - Variable in class etomica.virial.MeterVirialExternalFieldRho
 
clusters - Variable in class etomica.virial.MeterVirialSWWE
 
ClusterSinglyConnected - Class in etomica.virial
This class calculates the sum of all tree clusters using an adaptation of Wheatley's recursive formulation.
ClusterSinglyConnected(int, MayerFunction) - Constructor for class etomica.virial.ClusterSinglyConnected
 
clusterSubtract - Variable in class etomica.virial.ClusterDifference
 
ClusterSum - Class in etomica.virial
 
ClusterSum(ClusterBonds[], double[], MayerFunction[]) - Constructor for class etomica.virial.ClusterSum
Constructor for ClusterSum.
ClusterSumAssociation - Class in etomica.virial
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
ClusterSumAssociation(ClusterBonds[], double[], MayerFunction[], ClusterSumAssociation.ClusterCriteria) - Constructor for class etomica.virial.ClusterSumAssociation
Constructor for ClusterSum.
ClusterSumAssociation.ClusterCriteria - Interface in etomica.virial
 
ClusterSumEF - Class in etomica.virial
 
ClusterSumEF(ClusterBonds[], double[], MayerFunction[]) - Constructor for class etomica.virial.ClusterSumEF
Constructs a Cluster sum of the given cluster and weights.
ClusterSumExternalField - Class in etomica.virial
 
ClusterSumExternalField(ClusterBonds[], double[], MayerFunction[]) - Constructor for class etomica.virial.ClusterSumExternalField
 
ClusterSumHS - Class in etomica.virial
This class calculates the sum of all biconnected clusters for hard spheres.
ClusterSumHS(ClusterBonds[], double[], MayerFunction) - Constructor for class etomica.virial.ClusterSumHS
 
ClusterSumIC - Class in etomica.virial
 
ClusterSumIC(ClusterBonds[], double[], MayerFunction[], MayerFunction[]) - Constructor for class etomica.virial.ClusterSumIC
 
ClusterSumIC.FR2 - Class in etomica.virial
 
ClusterSumMultibody - Class in etomica.virial
Cluster class capable of computing multibody (up to 6th order) contributions to diagrams.
ClusterSumMultibody(ClusterBonds[], double[], MayerFunction[], MayerFunctionNonAdditive[]) - Constructor for class etomica.virial.ClusterSumMultibody
 
ClusterSumMultibodyShell - Class in etomica.virial
 
ClusterSumMultibodyShell(ClusterSumMultibody, ClusterBonds[], double[], MayerFunction[], MayerFunctionNonAdditive[]) - Constructor for class etomica.virial.ClusterSumMultibodyShell
Constructs a cluster (shell) that depends on another ClusterSumMultibody instance (the core) to do the actual work of calculating all the f values.
ClusterSumNonAdditiveTrimerEnergy - Class in etomica.virial
 
ClusterSumNonAdditiveTrimerEnergy(ClusterBonds[], double[], MayerFunction[], Potential) - Constructor for class etomica.virial.ClusterSumNonAdditiveTrimerEnergy
Adapted by Kate from ClusterSumPolarizable (simplification for nonadditive trimer energy only).
ClusterSumPolarizable - Class in etomica.virial
 
ClusterSumPolarizable(ClusterBonds[], double[], MayerFunction[]) - Constructor for class etomica.virial.ClusterSumPolarizable
Constructor for ClusterSum.
ClusterSumPolarizableWertheimProduct - Class in etomica.virial
 
ClusterSumPolarizableWertheimProduct(ClusterBonds[], double[], MayerFunction[]) - Constructor for class etomica.virial.ClusterSumPolarizableWertheimProduct
Constructor for ClusterSum for Wertheim diagram including multi body term.
ClusterSumPolarizableWertheimProduct4Pt - Class in etomica.virial
 
ClusterSumPolarizableWertheimProduct4Pt(ClusterBonds[], double[], MayerFunction[]) - Constructor for class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
Constructor for ClusterSum for Wertheim diagram including multi body term.
ClusterSumPolarizableWertheimProduct4PtFinal - Class in etomica.virial
 
ClusterSumPolarizableWertheimProduct4PtFinal(ClusterBonds[], double[], MayerFunction[]) - Constructor for class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
Constructor for ClusterSum for Wertheim diagram including multi body term.
ClusterSumShell - Class in etomica.virial
 
ClusterSumShell(ClusterSum, ClusterBonds[], double[], MayerFunction[]) - Constructor for class etomica.virial.ClusterSumShell
Constructs a cluster (shell) that depends on another ClusterSum instance (the core) to do the actual work of calculating all the f values.
ClusterSumStickyEF - Class in etomica.virial
 
ClusterSumStickyEF(ClusterBonds[], double[], MayerFunction[], ClusterSumStickyEF[], IRandom) - Constructor for class etomica.virial.ClusterSumStickyEF
 
ClusterSumStickyEF(ClusterSumEF, ClusterSumStickyEF[], IRandom) - Constructor for class etomica.virial.ClusterSumStickyEF
 
ClusterTree - Class in etomica.virial
 
ClusterTree(ClusterDiagramTree, MayerFunction[]) - Constructor for class etomica.virial.ClusterTree
 
ClusterTreeBonds - Class in etomica.virial
 
ClusterTreeBonds() - Constructor for class etomica.virial.ClusterTreeBonds
 
ClusterTreeEF - Class in etomica.virial
 
ClusterTreeEF(ClusterDiagramTree, MayerFunction[]) - Constructor for class etomica.virial.ClusterTreeEF
 
ClusterTreeNode - Class in etomica.virial.cluster
 
ClusterTreeNode(int) - Constructor for class etomica.virial.cluster.ClusterTreeNode
 
ClusterWeight - Interface in etomica.virial
 
ClusterWeight.Factory - Interface in etomica.virial
 
ClusterWeightAbs - Class in etomica.virial
 
ClusterWeightAbs(ClusterAbstract) - Constructor for class etomica.virial.ClusterWeightAbs
 
clusterWeights - Variable in class etomica.virial.ClusterSum
 
clusterWeights - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct
 
clusterWeights - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
 
clusterWeights - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
 
ClusterWeightSumWall - Class in etomica.virial
 
ClusterWeightSumWall(ClusterWeightSumWall.DataSourceClusterWall, int) - Constructor for class etomica.virial.ClusterWeightSumWall
 
ClusterWeightSumWall.DataSourceClusterWall - Interface in etomica.virial
 
ClusterWeightUmbrella - Class in etomica.virial
Umbrella cluster weight wrapper function.
ClusterWeightUmbrella(ClusterAbstract[]) - Constructor for class etomica.virial.ClusterWeightUmbrella
Contructs an umbrella cluster from the given clusters.
ClusterWheatley - Interface in etomica.virial
 
clusterWheatleyBDBD - Variable in class etomica.virial.ClusterWheatleyMultibodyBD
 
ClusterWheatleyExtendSW - Class in etomica.virial
 
ClusterWheatleyExtendSW(int, MayerFunction, MayerFunction) - Constructor for class etomica.virial.ClusterWheatleyExtendSW
 
ClusterWheatleyHS - Class in etomica.virial
This class calculates the sum of all biconnected clusters using Wheatley's recursive formulation.
ClusterWheatleyHS(int, MayerFunction) - Constructor for class etomica.virial.ClusterWheatleyHS
 
ClusterWheatleyHS.AllSigs - Class in etomica.virial
 
ClusterWheatleyMultibody - Class in etomica.virial
This class uses Wheatley's recursion approach to calculating all biconnected diagrams, but adds in non-additive contributions.
ClusterWheatleyMultibody(int, MayerFunction, MayerFunctionNonAdditive[]) - Constructor for class etomica.virial.ClusterWheatleyMultibody
 
ClusterWheatleyMultibody(int, MayerFunction, MayerFunctionNonAdditive) - Constructor for class etomica.virial.ClusterWheatleyMultibody
 
ClusterWheatleyMultibody(int, MayerFunction, MayerFunctionNonAdditive, MayerFunctionNonAdditive[], double) - Constructor for class etomica.virial.ClusterWheatleyMultibody
 
ClusterWheatleyMultibodyBD - Class in etomica.virial
This class uses Wheatley's recursion approach to calculating all biconnected diagrams, but adds in non-additive contributions.
ClusterWheatleyMultibodyBD(int, MayerFunction, MayerFunctionNonAdditive[], int) - Constructor for class etomica.virial.ClusterWheatleyMultibodyBD
 
ClusterWheatleyMultibodyBD(int, MayerFunction, MayerFunctionNonAdditive, int) - Constructor for class etomica.virial.ClusterWheatleyMultibodyBD
 
ClusterWheatleyMultibodyBD(int, MayerFunction, MayerFunctionNonAdditive, MayerFunctionNonAdditive[], int) - Constructor for class etomica.virial.ClusterWheatleyMultibodyBD
 
ClusterWheatleyMultibodyMix - Class in etomica.virial
This class uses Wheatley's recursion approach to calculating all biconnected diagrams for a mixture, but adds in 3-body contributions.
ClusterWheatleyMultibodyMix(int, int[], MayerFunction[][], MayerFunctionNonAdditive[][][], double, boolean) - Constructor for class etomica.virial.ClusterWheatleyMultibodyMix
Constructs a cluster capable of handling mixtures of nonadditive molecules.
ClusterWheatleyPartitionScreening - Class in etomica.virial
This class calculates the sum of all biconnected clusters using Wheatley's recursive formulation.
ClusterWheatleyPartitionScreening(int, MayerFunction) - Constructor for class etomica.virial.ClusterWheatleyPartitionScreening
 
ClusterWheatleyPartitionScreening(int, MayerFunction, int) - Constructor for class etomica.virial.ClusterWheatleyPartitionScreening
 
ClusterWheatleyPartitionScreening.FrequencyCounter - Class in etomica.virial
 
ClusterWheatleySoft - Class in etomica.virial
This class calculates the sum of all biconnected clusters using Wheatley's recursive formulation.
ClusterWheatleySoft(int, MayerFunction, double) - Constructor for class etomica.virial.ClusterWheatleySoft
 
ClusterWheatleySoftBD - Class in etomica.virial
This class calculates the sum of all biconnected clusters using Wheatley's recursive formulation.
ClusterWheatleySoftBD(int, MayerFunction, int) - Constructor for class etomica.virial.ClusterWheatleySoftBD
 
ClusterWheatleySoftBDMix - Class in etomica.virial
Cluster class using Whealtey's recursion with BigDecimal to handle mixtures.
ClusterWheatleySoftBDMix(int, int[], MayerFunction[][], int) - Constructor for class etomica.virial.ClusterWheatleySoftBDMix
 
ClusterWheatleySoftMix - Class in etomica.virial
Cluster class using Whealtey's recursion to handle mixtures.
ClusterWheatleySoftMix(int, int[], MayerFunction[][], double) - Constructor for class etomica.virial.ClusterWheatleySoftMix
 
Cmax - Variable in class etomica.meam.ParameterSetMEAM
 
Cmin - Variable in class etomica.meam.ParameterSetMEAM
 
coefficient - Variable in class etomica.virial.cluster.ClusterTreeNode
 
coefficients - Variable in class etomica.normalmode.WaveVectorFactory1D
 
coefficients - Variable in class etomica.normalmode.WaveVectorFactory2D
 
coefficients - Variable in class etomica.normalmode.WaveVectorFactoryFcc
 
coefficients - Variable in class etomica.normalmode.WaveVectorFactorySimple
 
coefficients - Variable in class etomica.virial.MayerFunctionProductGeneral
 
coefficients - Variable in class etomica.virial.MayerFunctionSum
 
coefficients - Variable in class etomica.virial.MayerFunctionSumGeneral
 
coeffs - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1DGraphic
 
coeffs - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2DGraphic
 
coeffs - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
 
collapse() - Method in class etomica.virial.cluster.ClusterDiagramTree
 
CollectionBondedPotentialAlcohols - Class in etomica.virial.GUI.components
 
CollectionBondedPotentialAlcohols() - Constructor for class etomica.virial.GUI.components.CollectionBondedPotentialAlcohols
 
CollectionBondedPotentialAlkanes - Class in etomica.virial.GUI.components
 
CollectionBondedPotentialAlkanes(int) - Constructor for class etomica.virial.GUI.components.CollectionBondedPotentialAlkanes
 
CollectionPotentialAtomicLike - Class in etomica.virial.GUI.components
 
CollectionPotentialAtomicLike(int) - Constructor for class etomica.virial.GUI.components.CollectionPotentialAtomicLike
 
CollectionPotentialAtomicUnlike - Class in etomica.virial.GUI.components
 
CollectionPotentialAtomicUnlike(int, int) - Constructor for class etomica.virial.GUI.components.CollectionPotentialAtomicUnlike
 
CollectionPotentialMolecularLike - Class in etomica.virial.GUI.components
 
CollectionPotentialMolecularLike(int) - Constructor for class etomica.virial.GUI.components.CollectionPotentialMolecularLike
 
CollectionPotentialMolecularUnlike - Class in etomica.virial.GUI.components
 
CollectionPotentialMolecularUnlike(int, int) - Constructor for class etomica.virial.GUI.components.CollectionPotentialMolecularUnlike
 
collisionTime(IAtomList, double) - Method in class etomica.normalmode.P2XOrder
 
color1 - Variable in class etomica.virial.cluster.CondenseExchange.CondenseExchangeParameters
 
colorAllAtoms() - Method in class etomica.normalmode.nptdemo.ColorSchemeScaledOverlap
 
colors - Variable in class etomica.normalmode.nptdemo.ColorSchemeScaledOverlap
 
ColorSchemeDisplacement(CoordinateDefinition, ISpace, HSNPT.ActionSummer) - Constructor for class etomica.normalmode.HSNPT.ColorSchemeDisplacement
 
colorSchemeOverlap - Variable in class etomica.normalmode.nptdemo.HSNPT2DGraphic
 
colorSchemeScaled - Variable in class etomica.normalmode.nptdemo.HSNPT2DGraphic
 
ColorSchemeScaledOverlap - Class in etomica.normalmode.nptdemo
Color atoms based on being neighbors of the reference atom
ColorSchemeScaledOverlap(ISpace, PotentialMasterList, CoordinateDefinition) - Constructor for class etomica.normalmode.nptdemo.ColorSchemeScaledOverlap
 
columnNames - Variable in class etomica.virial.GUI.models.ModelMoleculeListDisplayTable
 
columnNames - Variable in class etomica.virial.GUI.models.ModelMoleculeListDisplayTable_new
 
columnNames - Variable in class etomica.virial.GUI.models.ModelPotParamDisplayTable
 
com - Variable in class etomica.normalmode.MCMoveRotateMoleculePhiTheta
 
com - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecularOriented
 
com - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
 
com - Variable in class etomica.virial.MCMoveClusterRingRegrow
 
com - Variable in class etomica.virial.MCMoveClusterRingRegrowExchange
 
com - Variable in class etomica.virial.MCMoveClusterRingScale
 
com0 - Variable in class etomica.normalmode.LatticeSumMolecularCrystal
 
com0 - Variable in class etomica.virial.MCMoveClusterRingRegrow
 
com0 - Variable in class etomica.virial.MCMoveClusterRingRegrowExchange
 
com1 - Variable in class etomica.normalmode.LatticeSumMolecularCrystal
 
comOld - Variable in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
 
comOld - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
 
comparator - Variable in class etomica.virial.MeterVirialExternalFieldOverlapConfined
 
ComparatorNumFieldNodesExchange() - Constructor for class etomica.virial.cluster.VirialDiagrams.ComparatorNumFieldNodesExchange
 
ComparatorNumFieldNodesExchange() - Constructor for class etomica.virial.cluster.VirialDiagramsPT.ComparatorNumFieldNodesExchange
 
compare(Graph, Graph) - Method in class etomica.virial.cluster.VirialDiagrams.ComparatorNumFieldNodesExchange
 
compare(Graph, Graph) - Method in class etomica.virial.cluster.VirialDiagramsPT.ComparatorNumFieldNodesExchange
 
compare(DoubleRange, DoubleRange) - Method in class etomica.virial.MeterVirialExternalFieldOverlapConfined.RangeComparator
 
compareTo(IntSet) - Method in class etomica.virial.IntSet
 
compareTo(MeterVirialExternalFieldSW.Near) - Method in class etomica.virial.MeterVirialExternalFieldSW.Near
 
compressibility - Variable in class etomica.virial.HypernettedChain
 
compressibility - Variable in class etomica.virial.PercusYevick
 
compressibility - Variable in class etomica.virial.simulations.VirialHePCKLJSCHNCCorrection.VirialLJParam
 
compressibility - Variable in class etomica.virial.simulations.VirialHePCKLJSPYCorrection.VirialLJParam
 
compressibility - Variable in class etomica.virial.simulations.VirialLJCHNCCorrection.VirialLJParam
 
compressibility - Variable in class etomica.virial.simulations.VirialLJPYCorrection.VirialLJParam
 
computeAPartitions(int, int) - Method in class etomica.virial.ClusterWheatleyPartitionScreening
 
computeB(double[], int, double, boolean) - Static method in class etomica.virial.B3ForSphericallySymmetricU
 
computeB(int, int, double, double, Potential2SoftSpherical) - Static method in class etomica.virial.BnIETP2Spherical
 
computeB(int, int, double, double, Potential2SoftSpherical) - Static method in class etomica.virial.BnPY_1QC_Helium
 
computeB(double[], int, int, double, boolean) - Method in class etomica.virial.HypernettedChain
 
computeB(double[], int, int, double, boolean) - Method in class etomica.virial.PercusYevick
 
computeB(double[], int, int, double, boolean) - Method in class etomica.virial.PercusYevick1QC
 
computeB2QM(Potential2SoftSpherical, double) - Static method in class etomica.virial.B3ForSphericallySymmetricU
 
computeB3NonAdd(Potential2SoftSpherical, PotentialSoft, Space, double) - Static method in class etomica.virial.B3NonAddForSphericallySymmetricU
 
computePartitions(int, int) - Method in class etomica.virial.ClusterSinglyConnected
 
CondenseExchange - Class in etomica.virial.cluster
This operation replaces groups of points connected (internally) by e-exchange bonds with a single point.
CondenseExchange() - Constructor for class etomica.virial.cluster.CondenseExchange
 
CondenseExchange.CondenseExchangeParameters - Class in etomica.virial.cluster
 
CondenseExchangeParameters(char, char, char, char) - Constructor for class etomica.virial.cluster.CondenseExchange.CondenseExchangeParameters
 
configMonoLattice - Variable in class etomica.paracetamol.MDParacetamolMonoclinic
 
configOrthoLattice - Variable in class etomica.paracetamol.MDParacetamolOrthorhombic
 
configuration - Variable in class etomica.normalmode.CoordinateDefinitionHSDimer
 
configuration - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
 
ConfigurationAligned - Class in etomica.spin
Configuration used to align all atoms in a spin system, so all point in the same direction.
ConfigurationAligned() - Constructor for class etomica.spin.ConfigurationAligned
 
ConfigurationCluster - Class in etomica.virial
 
ConfigurationCluster(ISpace) - Constructor for class etomica.virial.ConfigurationCluster
 
ConfigurationClusterAceticAcid - Class in etomica.virial
 
ConfigurationClusterAceticAcid(ISpace, IRandom, MayerFunction) - Constructor for class etomica.virial.ConfigurationClusterAceticAcid
 
ConfigurationClusterAceticAcid(ISpace, IRandom, MayerFunction, MayerFunction) - Constructor for class etomica.virial.ConfigurationClusterAceticAcid
 
ConfigurationClusterAceticAcid(ISpace, IRandom, MayerFunction, MayerFunction, MayerFunction) - Constructor for class etomica.virial.ConfigurationClusterAceticAcid
 
ConfigurationClusterChain - Class in etomica.virial
 
ConfigurationClusterChain(ISpace) - Constructor for class etomica.virial.ConfigurationClusterChain
 
ConfigurationClusterChainFourSites - Class in etomica.virial
 
ConfigurationClusterChainFourSites(ISpace) - Constructor for class etomica.virial.ConfigurationClusterChainFourSites
 
ConfigurationClusterMove - Class in etomica.virial
 
ConfigurationClusterMove(ISpace, IRandom) - Constructor for class etomica.virial.ConfigurationClusterMove
 
ConfigurationClusterMove(ISpace, IRandom, double) - Constructor for class etomica.virial.ConfigurationClusterMove
 
ConfigurationClusterWertheimGCPM - Class in etomica.virial
 
ConfigurationClusterWertheimGCPM(ISpace, IRandom, PNWaterGCPMThreeSite) - Constructor for class etomica.virial.ConfigurationClusterWertheimGCPM
 
ConfigurationClusterWertheimGCPM(ISpace, IRandom, PNWaterGCPMThreeSite, PNWaterGCPMThreeSite) - Constructor for class etomica.virial.ConfigurationClusterWertheimGCPM
 
ConfigurationClusterWertheimGCPM(ISpace, IRandom, PNWaterGCPMThreeSite, PNWaterGCPMThreeSite, PNWaterGCPMThreeSite) - Constructor for class etomica.virial.ConfigurationClusterWertheimGCPM
 
ConfigurationClusterWertheimGCPM(ISpace, IRandom, PNWaterGCPMThreeSite, PNWaterGCPMThreeSite, double) - Constructor for class etomica.virial.ConfigurationClusterWertheimGCPM
 
ConfigurationClusterWertheimGCPM4Pt - Class in etomica.virial
 
ConfigurationClusterWertheimGCPM4Pt(ISpace, IRandom, PNWaterGCPMThreeSite) - Constructor for class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
 
ConfigurationClusterWertheimGCPM4Pt(ISpace, IRandom, PNWaterGCPMThreeSite, PNWaterGCPMThreeSite) - Constructor for class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
 
ConfigurationClusterWertheimGCPM4Pt(ISpace, IRandom, PNWaterGCPMThreeSite, PNWaterGCPMThreeSite, PNWaterGCPMThreeSite) - Constructor for class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
 
ConfigurationClusterWertheimGCPM4Pt(ISpace, IRandom, PNWaterGCPMThreeSite, PNWaterGCPMThreeSite, double) - Constructor for class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
 
ConfigurationClusterWertheimGCPMDirectSampling - Class in etomica.virial
 
ConfigurationClusterWertheimGCPMDirectSampling(ISpace, IRandom, PNWaterGCPMThreeSite) - Constructor for class etomica.virial.ConfigurationClusterWertheimGCPMDirectSampling
 
ConfigurationClusterWertheimGCPMDirectSampling(ISpace, IRandom, PNWaterGCPMThreeSite, PNWaterGCPMThreeSite) - Constructor for class etomica.virial.ConfigurationClusterWertheimGCPMDirectSampling
 
ConfigurationClusterWertheimGCPMDirectSampling(ISpace, IRandom, PNWaterGCPMThreeSite, PNWaterGCPMThreeSite, PNWaterGCPMThreeSite) - Constructor for class etomica.virial.ConfigurationClusterWertheimGCPMDirectSampling
 
ConfigurationClusterWertheimGCPMDirectSampling(ISpace, IRandom, PNWaterGCPMThreeSite, PNWaterGCPMThreeSite, double) - Constructor for class etomica.virial.ConfigurationClusterWertheimGCPMDirectSampling
 
ConfigurationFileXYZ - Class in etomica.zeolite
 
ConfigurationFileXYZ(String, ISpace) - Constructor for class etomica.zeolite.ConfigurationFileXYZ
 
ConfigurationMonoclinicLattice - Class in etomica.paracetamol
Constructs configuration that has the molecules placed on the sites of a lattice.
ConfigurationMonoclinicLattice(SpaceLattice, ISpace) - Constructor for class etomica.paracetamol.ConfigurationMonoclinicLattice
Constructs class using instance of IndexIteratorRectangular as the default index iterator.
ConfigurationMonoclinicLattice(SpaceLattice, IndexIteratorSizable, ISpace) - Constructor for class etomica.paracetamol.ConfigurationMonoclinicLattice
Construct class that will place atoms on sites of the given lattice, proceeding in the order resulting from iteration through the given index iterator.
ConfigurationMonoclinicLattice.MyLattice - Class in etomica.paracetamol
Used to store the state of a lattice.
ConfigurationOrthorhombicLattice - Class in etomica.paracetamol
Constructs configuration that has the molecules placed on the sites of a lattice.
ConfigurationOrthorhombicLattice(SpaceLattice, ISpace) - Constructor for class etomica.paracetamol.ConfigurationOrthorhombicLattice
Constructs class using instance of IndexIteratorRectangular as the default index iterator.
ConfigurationOrthorhombicLattice(SpaceLattice, IndexIteratorSizable, ISpace) - Constructor for class etomica.paracetamol.ConfigurationOrthorhombicLattice
Construct class that will place atoms on sites of the given lattice, proceeding in the order resulting from iteration through the given index iterator.
ConfigurationOrthorhombicLattice.MyLattice - Class in etomica.paracetamol
Used to store the state of a lattice.
conformation - Variable in class etomica.virial.SpeciesFactoryWater4P
 
Conformation7SiteRigidSF6 - Class in etomica.virial
Conformation of SF6 7 LJ sites, rigid, no charge Reference: Samios, Molecular force field investigation for sulfur hexafluoride: A computer simulation study
Conformation7SiteRigidSF6(ISpace) - Constructor for class etomica.virial.Conformation7SiteRigidSF6
 
ConformationAlkaneEH - Class in etomica.virial
Conformation for normal alkanes, explicit hydrogen Siepmann, TraPPE-EH
ConformationAlkaneEH(ISpace, SpeciesAlkaneEH) - Constructor for class etomica.virial.ConformationAlkaneEH
 
ConformationAnthracene3site - Class in etomica.virial
Conformation for Anthracene Reference paper: Iwai 3 site linear, group H to the two side benzene rings
ConformationAnthracene3site(ISpace) - Constructor for class etomica.virial.ConformationAnthracene3site
 
ConformationAnthraceneTraPPE - Class in etomica.virial
Conformation for Anthracene Reference paper: TraPPE: 4 UA description of linear and branched alkanes and alkylbenzenes, Siepmann et al modified from naphthalene conformation
ConformationAnthraceneTraPPE(ISpace) - Constructor for class etomica.virial.ConformationAnthraceneTraPPE
 
ConformationCO2 - Class in etomica.virial
Conformation for CO2 Reference paper: Partial molar ~~, Stubbs Darke-Wilhelm, Siepmann, JCP
ConformationCO2(ISpace) - Constructor for class etomica.virial.ConformationCO2
 
ConformationHexane - Class in etomica.models.hexane
Defines the vectors used to create a hexane molecule according to Dr.
ConformationHexane(ISpace) - Constructor for class etomica.models.hexane.ConformationHexane
 
ConformationHSDimer - Class in etomica.normalmode
Conformation for HS Dimer
ConformationHSDimer(ISpace, double) - Constructor for class etomica.normalmode.ConformationHSDimer
 
ConformationMethane - Class in etomica.virial
Conformation for TraPPE-Explicit hydrogen methane C site and H site, NOTE the H is located in the middle of C-H bond
ConformationMethane(ISpace) - Constructor for class etomica.virial.ConformationMethane
 
ConformationNaphthaleneTraPPE - Class in etomica.virial
Conformation for Naphthalene Reference paper: TraPPE: 4 UA description of linear and branched alkanes and alkylbenzenes, Siepmann et al
ConformationNaphthaleneTraPPE(ISpace) - Constructor for class etomica.virial.ConformationNaphthaleneTraPPE
 
ConformationParacetamol - Class in etomica.paracetamol
 
ConformationParacetamol(ISpace) - Constructor for class etomica.paracetamol.ConformationParacetamol
 
ConformationParacetamolMonoclinic - Class in etomica.paracetamol
 
ConformationParacetamolMonoclinic(ISpace) - Constructor for class etomica.paracetamol.ConformationParacetamolMonoclinic
 
ConformationParacetamolOrthorhombic - Class in etomica.paracetamol
 
ConformationParacetamolOrthorhombic(ISpace) - Constructor for class etomica.paracetamol.ConformationParacetamolOrthorhombic
 
ConformationPh3site - Class in etomica.virial
Conformation for Phenanthrene Reference paper: Iwai 3 site group H to the two side benzene rings , eihter 464 or 545 model modified from ConformationAnthracene
ConformationPh3site(ISpace) - Constructor for class etomica.virial.ConformationPh3site
 
ConformationPhenanthreneTraPPE - Class in etomica.virial
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
ConformationPhenanthreneTraPPE(ISpace) - Constructor for class etomica.virial.ConformationPhenanthreneTraPPE
 
ConjugateGradients - Class in etomica.conjugategradient
 
ConjugateGradients(Matrix, Matrix, Matrix, int) - Constructor for class etomica.conjugategradient.ConjugateGradients
 
ConjugateGradientsAlgorithm() - Method in class etomica.conjugategradient.ConjugateGradients
Conjugate Gradients solution for Ax = b
constraint - Variable in class etomica.normalmode.P1ConstraintNbr
 
constraintEnergy(IBox) - Method in class etomica.normalmode.MeterBoltzmannHTTP
Returns true if all atoms in the given box satisfy p1's constraint
constraintEnergy(IBox) - Method in class etomica.normalmode.MeterDDP
Returns true if all atoms in the given box satisfy p1's constraint
constraintEnergy(IBox) - Method in class etomica.normalmode.MeterDP
Returns true if all atoms in the given box satisfy p1's constraint
constraintEnergy(IBox) - Method in class etomica.normalmode.MeterTargetTP
Returns true if all atoms in the given box satisfy p1's constraint
constraintMap - Variable in class etomica.virial.MCMoveClusterMoleculeMulti
 
constraintMap - Variable in class etomica.virial.MCMoveClusterRotateMoleculeMulti
 
constraintPotential - Variable in class etomica.normalmode.MCMoveAtomCoupled
 
cont - Variable in class etomica.virial.simulations.VirialH2PISimple.VirialH2PISimpleParam
 
continuous - Variable in class etomica.virial.simulations.VirialCO2PI.VirialH2PIParam
 
continuous - Variable in class etomica.virial.simulations.VirialH2PI.VirialH2PIParam
 
controller - Variable in class etomica.densityofstate.DensityOfState
 
controller - Variable in class etomica.densityofstate.DensityOfStatesPolynomial
 
controller - Variable in class etomica.meam.EFSTungsten
 
controller - Variable in class etomica.meam.MEAM_3DMDwithGB
 
controller - Variable in class etomica.meam.MEAM_3DMDwithSnAgGB
 
controller - Variable in class etomica.meam.MEAM_3DMDwithSnCuGB
 
controller - Variable in class etomica.meam.MEAM_MC
 
controller - Variable in class etomica.meam.MEAMMd3D
 
controller - Variable in class etomica.normalmode.SimOverlapModule
 
controller - Variable in class etomica.paracetamol.MCParacetamolMonoclinicDLMULTI
 
controller - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicDLMULTI
 
controller - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
 
controller - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
 
controller - Variable in class etomica.threaded.atom.LJMD3DThreaded
 
controller - Variable in class etomica.threaded.domain.LJMD3DThreaded
 
controller - Variable in class etomica.threaded.domain.MEAMMd3DThreaded
 
controller - Variable in class etomica.yukawa.TestHC2YukawaMC3D
 
controller - Variable in class etomica.yukawa.TestYukawaMC3D
 
ControllerAlertMsgBox - Class in etomica.virial.GUI.controllers
 
ControllerAlertMsgBox(String, ModelSpeciesSelection) - Constructor for class etomica.virial.GUI.controllers.ControllerAlertMsgBox
 
ControllerAlertMsgBox.CloseWindowButtonListener - Class in etomica.virial.GUI.controllers
 
ControllerAlertMsgBoxSpeciesRemoval - Class in etomica.virial.GUI.controllers
 
ControllerAlertMsgBoxSpeciesRemoval(String, ModelSpeciesSelection, int) - Constructor for class etomica.virial.GUI.controllers.ControllerAlertMsgBoxSpeciesRemoval
 
ControllerAlertMsgBoxSpeciesRemoval.NoDoNotRemoveSpeciesButtonListener - Class in etomica.virial.GUI.controllers
 
ControllerAlertMsgBoxSpeciesRemoval.YesRemoveSpeciesButtonListener - Class in etomica.virial.GUI.controllers
 
ControllerAlkaneLengthSelection - Class in etomica.virial.GUI.controllers
 
ControllerAlkaneLengthSelection(ModelSelectedSpecies) - Constructor for class etomica.virial.GUI.controllers.ControllerAlkaneLengthSelection
 
ControllerSimEnvironmentSelection - Class in etomica.virial.GUI.controllers
 
ControllerSimEnvironmentSelection(ModelSimulationEnvironment) - Constructor for class etomica.virial.GUI.controllers.ControllerSimEnvironmentSelection
 
controllerSpeciesSelection - Variable in class etomica.virial.GUI.controllers.AppControllerMixtureBuilder
 
ControllerSpeciesSelection - Class in etomica.virial.GUI.controllers
 
Converter(String) - Static method in class etomica.zeolite.Zeolite
 
Converter(String) - Static method in class etomica.zeolite.ZeoliteSimulation
 
convolution(ClusterDiagram, ClusterDiagram) - Static method in class etomica.virial.cluster.ClusterOperations
Returns a new cluster that is a convolution of the given cluster, which is obtained by joining a root point from each diagram and turning it into a field point.
convolution(ClusterDiagram[], ClusterDiagram[]) - Static method in class etomica.virial.cluster.ClusterOperations
Returns an array of clusters formed from taking the convolution of each of the diagrams of the first set with each of the diagrams of the second set.
coordDef - Variable in class etomica.paracetamol.MCParacetamolMonoclinicDLMULTI
 
coordDef - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicDLMULTI
 
coordDef - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
 
coordinateDefinition - Variable in class etomica.conjugategradient.DerivativeEnergyFunction
 
coordinateDefinition - Variable in class etomica.meam.EFSTungsten
 
coordinateDefinition - Variable in class etomica.meam.PotentialFeEAM_LS
 
coordinateDefinition - Variable in class etomica.models.hexane.SimHarmonicHexane
 
coordinateDefinition - Variable in class etomica.models.hexane.TestHexane
 
coordinateDefinition - Variable in class etomica.models.hexane.TestHexaneFileConfig
 
coordinateDefinition - Variable in class etomica.models.hexane.TestHexaneHarmonic
 
coordinateDefinition - Variable in class etomica.normalmode.CalcJacobian
 
CoordinateDefinition - Class in etomica.normalmode
An abstract class that defines the real-space generalized coordinates that are summed (over molecules) to form collective coordinates (from which normal coordinates are determined).
CoordinateDefinition(IBox, int, Primitive, ISpace) - Constructor for class etomica.normalmode.CoordinateDefinition
 
CoordinateDefinition(IBox, int, Primitive, Basis, ISpace) - Constructor for class etomica.normalmode.CoordinateDefinition
 
coordinateDefinition - Variable in class etomica.normalmode.HessianDB
 
coordinateDefinition - Variable in class etomica.normalmode.HSDimerNPT
 
coordinateDefinition - Variable in class etomica.normalmode.HSNPT.ColorSchemeDisplacement
 
coordinateDefinition - Variable in class etomica.normalmode.HSNPT
 
coordinateDefinition - Variable in class etomica.normalmode.HTTPSoftSphereSim
 
coordinateDefinition - Variable in class etomica.normalmode.IntegratorHarmonic
 
coordinateDefinition - Variable in class etomica.normalmode.LJVacancyMin
 
coordinateDefinition - Variable in class etomica.normalmode.MCMoveAtomCoupledBennet
 
coordinateDefinition - Variable in class etomica.normalmode.MCMoveAtomCoupledUmbrella
 
coordinateDefinition - Variable in class etomica.normalmode.MCMoveAtomSuperBox
 
coordinateDefinition - Variable in class etomica.normalmode.MCMoveEinsteinCrystal
 
coordinateDefinition - Variable in class etomica.normalmode.MCMoveHarmonic
 
coordinateDefinition - Variable in class etomica.normalmode.MCMoveHarmonicStep
 
coordinateDefinition - Variable in class etomica.normalmode.MCMovePhaseAngle
 
coordinateDefinition - Variable in class etomica.normalmode.MCMoveSingleMode
 
coordinateDefinition - Variable in class etomica.normalmode.MCMoveVolumeSolid
 
coordinateDefinition - Variable in class etomica.normalmode.MCMoveWV
 
coordinateDefinition - Variable in class etomica.normalmode.MeterAtomicDisplacement
 
coordinateDefinition - Variable in class etomica.normalmode.MeterBoltzmannHTTP
 
coordinateDefinition - Variable in class etomica.normalmode.MeterDADB
 
coordinateDefinition - Variable in class etomica.normalmode.MeterDDP
 
coordinateDefinition - Variable in class etomica.normalmode.MeterDisplacementMoleculeRMS
 
coordinateDefinition - Variable in class etomica.normalmode.MeterDisplacementRMS
 
coordinateDefinition - Variable in class etomica.normalmode.MeterDP
 
coordinateDefinition - Variable in class etomica.normalmode.MeterHarmonicCoordinate
 
coordinateDefinition - Variable in class etomica.normalmode.MeterHarmonicEnergy
 
coordinateDefinition - Variable in class etomica.normalmode.MeterHarmonicSingleEnergy
 
coordinateDefinition - Variable in class etomica.normalmode.MeterJacobian
 
coordinateDefinition - Variable in class etomica.normalmode.MeterNormalMode
 
coordinateDefinition - Variable in class etomica.normalmode.MeterSolidMirror
 
coordinateDefinition - Variable in class etomica.normalmode.MeterSolidProps
 
coordinateDefinition - Variable in class etomica.normalmode.MeterSolidPropsLJ
 
coordinateDefinition - Variable in class etomica.normalmode.MeterTargetTP
 
coordinateDefinition - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1D
 
coordinateDefinition - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2D
 
coordinateDefinition - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3D
 
coordinateDefinition - Variable in class etomica.normalmode.nptdemo.ColorSchemeScaledOverlap
 
coordinateDefinition - Variable in class etomica.normalmode.nptdemo.DisplayBoxCanvas2DNpTScaling
 
coordinateDefinition - Variable in class etomica.normalmode.nptdemo.HSNPT2DSim
 
coordinateDefinition - Variable in class etomica.normalmode.PotentialCalculationEFSSP
 
coordinateDefinition - Variable in class etomica.normalmode.PotentialCalculationLJSP
 
coordinateDefinition - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
 
coordinateDefinition - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
 
coordinateDefinition - Variable in class etomica.normalmode.SimBennet
 
coordinateDefinition - Variable in class etomica.normalmode.SimCalcJ
 
coordinateDefinition - Variable in class etomica.normalmode.SimCalcS
 
coordinateDefinition - Variable in class etomica.normalmode.SimCalcSLJ
 
coordinateDefinition - Variable in class etomica.normalmode.SimCalcSMorse
 
coordinateDefinition - Variable in class etomica.normalmode.SimCalcSSoftSphere2D
 
coordinateDefinition - Variable in class etomica.normalmode.SimCalcSSoftSphereFCC
 
coordinateDefinition - Variable in class etomica.normalmode.SimCalcSSoftSphereFCCSuperBox
 
coordinateDefinition - Variable in class etomica.normalmode.SimHarmonic
 
coordinateDefinition - Variable in class etomica.normalmode.SimHarmonicUmbrella
 
coordinateDefinition - Variable in class etomica.normalmode.SimLJHTTISuper
 
coordinateDefinition - Variable in class etomica.normalmode.SimLJHTTISuperHCP
 
coordinateDefinition - Variable in class etomica.normalmode.SimModesJ
 
coordinateDefinition - Variable in class etomica.normalmode.SimOverlapSoftSphereTP
 
coordinateDefinition - Variable in class etomica.normalmode.SimTarget
 
coordinateDefinition - Variable in class etomica.normalmode.SimTargetUmbrella
 
coordinateDefinition - Variable in class etomica.normalmode.SimUmbrella
 
coordinateDefinition - Variable in class etomica.normalmode.SimUmbrellaSoftSphere
 
coordinateDefinition - Variable in class etomica.paracetamol.MDParacetamolMonoclinic
 
coordinateDefinition - Variable in class etomica.paracetamol.MDParacetamolOrthorhombic
 
coordinateDefinition - Variable in class etomica.paracetamol.NumericalDerivativeEnergyParacetamol
 
coordinateDefinition - Variable in class etomica.paracetamol.SimulationOrthorhombicParacetamol
 
CoordinateDefinition.BasisCell - Class in etomica.normalmode
 
CoordinateDefinition.SiteSource - Class in etomica.normalmode
 
CoordinateDefinitionHexane - Class in etomica.models.hexane
Implementation of CoordinateDefinitionMolecule that handles hexane.
CoordinateDefinitionHexane(ISimulation, IBox, Primitive, SpeciesHexane, ISpace) - Constructor for class etomica.models.hexane.CoordinateDefinitionHexane
 
CoordinateDefinitionHSDimer - Class in etomica.normalmode
CoordinateDefinition implementation for HS Dimer.
CoordinateDefinitionHSDimer(ISimulation, IBox, Primitive, Basis, ISpace) - Constructor for class etomica.normalmode.CoordinateDefinitionHSDimer
 
CoordinateDefinitionHSDimer.IntegerFunction - Interface in etomica.normalmode
 
CoordinateDefinitionLeaf - Class in etomica.normalmode
CoordinateDefinition implementation for monatomic molecules that are simply leaf atoms.
CoordinateDefinitionLeaf(IBox, Primitive, ISpace) - Constructor for class etomica.normalmode.CoordinateDefinitionLeaf
 
CoordinateDefinitionLeaf(IBox, Primitive, Basis, ISpace) - Constructor for class etomica.normalmode.CoordinateDefinitionLeaf
 
CoordinateDefinitionLeafSuperBox - Class in etomica.normalmode
 
CoordinateDefinitionLeafSuperBox(IBox, Primitive, Basis, ISpace) - Constructor for class etomica.normalmode.CoordinateDefinitionLeafSuperBox
 
CoordinateDefinitionMolecule - Class in etomica.normalmode
CoordinateDefinition implementation for molecules.
CoordinateDefinitionMolecule(ISimulation, IBox, Primitive, int, ISpace) - Constructor for class etomica.normalmode.CoordinateDefinitionMolecule
 
CoordinateDefinitionMolecule(ISimulation, IBox, Primitive, int, Basis, ISpace) - Constructor for class etomica.normalmode.CoordinateDefinitionMolecule
 
CoordinateDefinitionMolecule.MoleculeSiteSource - Class in etomica.normalmode
 
CoordinateDefinitionMoleculeVolumeFluctuation - Class in etomica.normalmode
CoordinateDefinition implementation for molecules.
CoordinateDefinitionMoleculeVolumeFluctuation(ISimulation, IBox, Primitive, int, ISpace) - Constructor for class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation
 
CoordinateDefinitionMoleculeVolumeFluctuation(ISimulation, IBox, Primitive, int, Basis, ISpace) - Constructor for class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation
 
CoordinateDefinitionMoleculeVolumeFluctuation.MoleculeSiteSource - Class in etomica.normalmode
 
CoordinateDefinitionParacetamol - Class in etomica.paracetamol
CoordinateDefinition implementation for paracetamol molecule.
CoordinateDefinitionParacetamol(ISimulation, IBox, Primitive, Basis, ISpace) - Constructor for class etomica.paracetamol.CoordinateDefinitionParacetamol
 
CoordinateDefinitionParacetamol.OrientationAgentSource - Class in etomica.paracetamol
 
coordinateDim - Variable in class etomica.normalmode.CalcJacobian
 
coordinateDim - Variable in class etomica.normalmode.CoordinateDefinition
 
CoordinatePairLeafSet - Class in etomica.virial
 
CoordinatePairLeafSet(IAtomList, ISpace) - Constructor for class etomica.virial.CoordinatePairLeafSet
Constructor for CoordinatePairLeafSet.
CoordinatePairMoleculeSet - Class in etomica.virial
 
CoordinatePairMoleculeSet(IMoleculeList, ISpace) - Constructor for class etomica.virial.CoordinatePairMoleculeSet
Constructor for CoordinatePairLeafSet.
CoordinatePairSet - Interface in etomica.virial
 
coordinteDefinition - Variable in class etomica.normalmode.MeterSolidDA
 
coordinteDefinition - Variable in class etomica.normalmode.MeterSolidDACut
 
copy() - Method in class etomica.models.hexane.PrimitiveHexane
Returns a new, identical instance of this primitive.
copy() - Method in class etomica.virial.IntSet
 
CopyOfOrthogonalPolynomial - Class in etomica.densityofstate
 
CopyOfOrthogonalPolynomial() - Constructor for class etomica.densityofstate.CopyOfOrthogonalPolynomial
 
copyTo(ClusterDiagram) - Method in class etomica.virial.cluster.ClusterDiagram
 
coreCluster - Variable in class etomica.virial.ClusterSumMultibodyShell
 
coreCluster - Variable in class etomica.virial.ClusterSumShell
 
cosDtheta - Variable in class etomica.dimer.IntegratorDimerMin
 
cosNominalTheta - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecularOriented
 
cosTheta - Variable in class etomica.normalmode.CoordinateDefinitionHSDimer
 
count - Variable in class etomica.normalmode.HSNPT.ActionSummer
 
count - Variable in class etomica.normalmode.MeterOverlapSwitch
 
count - Variable in class etomica.normalmode.WriteS
 
count - Static variable in class etomica.virial.MeterVirialIC
 
counter - Variable in class etomica.dimer.IntegratorDimerMin
 
counter - Variable in class etomica.dimer.IntegratorDimerRT
 
coupledMove - Variable in class etomica.models.hexane.TestHexane
 
coupledMove - Variable in class etomica.models.hexane.TestHexaneFileConfig
 
coupledMove - Variable in class etomica.models.hexane.TestSetToUHexane
 
cp - Variable in class etomica.normalmode.HSDimerNPT.HSMD3DParameters
 
cPairID - Variable in class etomica.virial.BoxCluster
 
cPairID - Variable in class etomica.virial.ClusterChainHS
 
cPairID - Variable in class etomica.virial.ClusterChainSoft
 
cPairID - Variable in class etomica.virial.ClusterCoupledFlipped
 
cPairID - Variable in class etomica.virial.ClusterCoupledFlippedPartial
 
cPairID - Variable in class etomica.virial.ClusterSinglyConnected
 
cPairID - Variable in class etomica.virial.ClusterSum
 
cPairID - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct
 
cPairID - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
 
cPairID - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
 
cPairID - Variable in class etomica.virial.ClusterWheatleyHS
 
cPairID - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
 
cPairID - Variable in class etomica.virial.ClusterWheatleySoft
 
cPairID - Variable in class etomica.virial.ClusterWheatleySoftBD
 
cPairSet - Variable in class etomica.virial.BoxCluster
 
cPairSetTmp - Variable in class etomica.virial.BoxCluster
 
cPairTrialSet - Variable in class etomica.virial.BoxCluster
 
crank - Variable in class etomica.models.hexane.TestHexane
 
crank - Variable in class etomica.models.hexane.TestHexaneFileConfig
 
createImageIcon(String) - Static method in class etomica.virial.GUI.models.ViewSpeciesSelection
 
createImageIcon(String) - Static method in class etomica.virial.GUI.views.ViewSpeciesSelection
 
createSpecies() - Method in interface etomica.virial.GUI.models.IMolecularModel_SpeciesFactory
 
createSpecies() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
 
createSpecies() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
 
createSpecies() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
 
createSpecies() - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
 
createSpecies() - Method in class etomica.virial.GUI.models.MolecularModelLJ_SpeciesLJ
 
createSpecies() - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
 
createSpecies() - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
 
createSpecies() - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
 
createSpecies() - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
 
createSpecies() - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
 
createSpeciesFactory() - Method in interface etomica.virial.GUI.models.IMolecularModel_SpeciesFactory
 
createSpeciesFactory() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
 
createSpeciesFactory() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
 
createSpeciesFactory() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
 
createSpeciesFactory() - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
 
createSpeciesFactory() - Method in class etomica.virial.GUI.models.MolecularModelLJ_SpeciesLJ
 
createSpeciesFactory() - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
 
createSpeciesFactory() - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
 
createSpeciesFactory() - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
 
createSpeciesFactory() - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
 
createSpeciesFactory() - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
 
createThreads() - Method in class etomica.threads.AtomDecompositionMD
 
CRINGS - Static variable in class etomica.virial.simulations.VirialHS.VirialHSParam
 
CRINGS - Static variable in class etomica.virial.simulations.VirialSWWE.VirialSWWEParam
 
criticalRho_LJ - Variable in class etomica.virial.simulations.VirialSF6LJAlkaneUAMix.VirialMixParam
 
criticalRho_SF6 - Variable in class etomica.virial.simulations.VirialSF6LJAlkaneUAMix.VirialMixParam
 
criticalT_LJ - Variable in class etomica.virial.simulations.VirialSF6LJAlkaneUAMix.VirialMixParam
 
criticalT_SF6 - Variable in class etomica.virial.simulations.VirialSF6LJAlkaneUAMix.VirialMixParam
 
crossVector - Variable in class etomica.virial.MCMoveClusterMoleculeLayerMove
 
cs - Variable in class etomica.dimer.P1LepsHarmonic
 
cType - Variable in class etomica.paracetamol.SpeciesParacetamol
 
cType - Variable in class etomica.virial.SpeciesAnthracene3site464
 
cType - Variable in class etomica.virial.SpeciesAnthracene3site545
 
cType - Variable in class etomica.virial.SpeciesMethane
 
cType - Variable in class etomica.virial.SpeciesPh3site464
 
cType - Variable in class etomica.virial.SpeciesPh3site545
 
cType - Variable in class etomica.virial.SpeciesTraPPEAnthracene
 
cType - Variable in class etomica.virial.SpeciesTraPPECO2
 
cType - Variable in class etomica.virial.SpeciesTraPPENaphthalene
 
cType - Variable in class etomica.virial.SpeciesTraPPEPhenanthrene
 
cu - Variable in class etomica.dimer.EnergyMap
 
cu - Variable in class etomica.meam.MEAM_MC
 
cu - Variable in class etomica.meam.MEAMMd3D
 
Cu - Static variable in class etomica.meam.ParameterSetMEAM
 
cu - Variable in class etomica.threaded.domain.MEAMMd3DThreaded
 
Cu3Sn - Static variable in class etomica.meam.ParameterSetMEAM
 
cuAdatom - Variable in class etomica.dimer.EnergyMap
 
cuB - Variable in class etomica.meam.MEAM_3DMDwithSnCuGB
 
cuFix - Variable in class etomica.dimer.EnergyMap
 
cuFixedB - Variable in class etomica.meam.MEAM_3DMDwithSnCuGB
 
curvature - Variable in class etomica.dimer.IntegratorDimerRT
 
cVec - Variable in class etomica.normalmode.MCMoveVolumeMonoclinicAngle
 

D

D - Variable in class etomica.conjugategradient.PreconditionedConjugateGradient
 
d - Variable in class etomica.dimer.SimDimerLJadatom
 
d - Variable in class etomica.dimer.SimDimerMEAMadatom
 
d - Variable in class etomica.dimer.SimDimerMEAMGB
 
D - Variable in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
 
D - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
 
D - Variable in class etomica.normalmode.SimBennet.SimBennetParam
 
D - Variable in class etomica.normalmode.SimHarmonicUmbrella.SimBennetParam
 
D - Variable in class etomica.normalmode.SimOverlap.SimOverlapParam
 
D - Variable in class etomica.normalmode.SimOverlapLJ.SimOverlapParam
 
D - Variable in class etomica.normalmode.SimOverlapLJModule.SimOverlapParam
 
D - Variable in class etomica.normalmode.SimOverlapSoftSphere.SimOverlapParam
 
D - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP.SimOverlapParam
 
D - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting.SimOverlapParam
 
D - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness.SimOverlapParam
 
D - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox.SimOverlapParam
 
D - Variable in class etomica.normalmode.SimOverlapSSnxy.SimOverlapParam
 
D - Variable in class etomica.normalmode.SimTargetUmbrella.SimBennetParam
 
D - Variable in class etomica.normalmode.SimUmbrella.SimBennetParam
 
D - Variable in class etomica.normalmode.SimUmbrellaSoftSphere.SimBennetParam
 
D() - Method in class etomica.paracetamol.ConfigurationMonoclinicLattice.MyLattice
 
D() - Method in class etomica.paracetamol.ConfigurationOrthorhombicLattice.MyLattice
 
d2f(int[], double[]) - Method in class etomica.conjugategradient.FiniteDifferenceDerivativeCG
 
d2sum - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
 
d2u(double) - Method in class etomica.virial.P1IntraLambda
 
d2u(double) - Method in class etomica.yukawa.P2HC2Yukawa
 
d2u(double) - Method in class etomica.yukawa.P2Yukawa
r^2 * d^2u/dr^2 method.
D4 - Static variable in class etomica.virial.cluster.Standard
 
D5 - Static variable in class etomica.virial.cluster.Standard
 
D6 - Static variable in class etomica.virial.cluster.Standard
 
dab - Variable in class etomica.dimer.P1LepsHarmonic
 
dac - Variable in class etomica.dimer.P1LepsHarmonic
 
dAcc - Variable in class etomica.spin.Heisenberg
 
dadbSum - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
 
dadbSum - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
 
daDef - Variable in class etomica.normalmode.SimHSMDVacancy.HSMDVParams
 
daDef - Variable in class etomica.normalmode.SimLJVacancy.LJParams
 
DampingParams() - Constructor for class etomica.virial.B3ForSphericallySymmetricU.DampingParams
 
data - Variable in class etomica.normalmode.DataProcessorBoltzmannFactor
 
data - Variable in class etomica.normalmode.DataSourceFE
 
data - Variable in class etomica.normalmode.DataSourceFEHistogram
 
data - Variable in class etomica.normalmode.DataSourceImposedFEFit
 
data - Variable in class etomica.normalmode.DataSourceImposedFEHistogram
 
data - Variable in class etomica.normalmode.DataSourcePMu
 
data - Variable in class etomica.normalmode.DataSourcePN
 
data - Variable in class etomica.normalmode.MeterBoltzmann
 
data - Variable in class etomica.normalmode.MeterBoltzmannHarmonic
 
data - Variable in class etomica.normalmode.MeterBoltzmannHTTP
 
data - Variable in class etomica.normalmode.MeterBoltzmannTarget
 
data - Variable in class etomica.normalmode.MeterDADB
 
data - Variable in class etomica.normalmode.MeterDDP
 
data - Variable in class etomica.normalmode.MeterDirectSamplingHarmonic
 
data - Variable in class etomica.normalmode.MeterDirectSamplingTarget
 
data - Variable in class etomica.normalmode.MeterDP
 
data - Variable in class etomica.normalmode.MeterHarmonicSingleEnergy
 
data - Variable in class etomica.normalmode.MeterOverlapSwitch
 
data - Variable in class etomica.normalmode.MeterPlaneSlip
 
data - Variable in class etomica.normalmode.MeterSamplingHarmonic
 
data - Variable in class etomica.normalmode.MeterSamplingTarget
 
data - Variable in class etomica.normalmode.MeterSolidDA
 
data - Variable in class etomica.normalmode.MeterSolidDACut
 
data - Variable in class etomica.normalmode.MeterSolidMirror
 
data - Variable in class etomica.normalmode.MeterSolidProps
 
data - Variable in class etomica.normalmode.MeterSolidPropsLJ
 
data - Variable in class etomica.normalmode.MeterTargetTP
 
data - Variable in class etomica.normalmode.MeterTilt
 
data - Variable in class etomica.normalmode.MeterTiltHistogram
 
data - Variable in class etomica.normalmode.MeterTiltRotation
 
data - Variable in class etomica.normalmode.MeterTiltRotationHistogram
 
data - Variable in class etomica.normalmode.MeterTiltRotationStdev
 
data - Variable in class etomica.normalmode.MeterWorkBennetHarmonic
 
data - Variable in class etomica.normalmode.MeterWorkBennetTarget
 
data - Variable in class etomica.normalmode.MeterWorkHarmonicBennet
 
data - Variable in class etomica.normalmode.MeterWorkHarmonicPhaseSpace
 
data - Variable in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
 
data - Variable in class etomica.normalmode.MeterWorkHarmonicUmbrella
 
data - Variable in class etomica.normalmode.MeterWorkTargetBennet
 
data - Variable in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
 
data - Variable in class etomica.normalmode.MeterWorkTargetPhaseSpace
 
data - Variable in class etomica.normalmode.MeterWorkTargetUmbrella
 
data - Variable in class etomica.normalmode.MeterWorkUmbrellaHarmonic
 
data - Variable in class etomica.normalmode.MeterWorkUmbrellaTarget
 
data - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1DGraphic
 
data - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2DGraphic
 
data - Variable in class etomica.virial.overlap.DataProcessorVirialOverlap
 
DataCutter - Class in etomica.zeolite
 
DataCutter(String, int) - Constructor for class etomica.zeolite.DataCutter
 
dataDistance - Variable in class etomica.virial.MeterSamplingWeight
 
dataEVec - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
 
dataGroup - Variable in class etomica.normalmode.MeterTiltRotationHistogram
 
dataInfo - Variable in class etomica.normalmode.DataProcessorBoltzmannFactor
 
dataInfo - Variable in class etomica.normalmode.DataSourceFE
 
dataInfo - Variable in class etomica.normalmode.DataSourceFEHistogram
 
dataInfo - Variable in class etomica.normalmode.DataSourceImposedFEFit
 
dataInfo - Variable in class etomica.normalmode.DataSourceImposedFEHistogram
 
dataInfo - Variable in class etomica.normalmode.DataSourcePMu
 
dataInfo - Variable in class etomica.normalmode.DataSourcePN
 
dataInfo - Variable in class etomica.normalmode.MeterBoltzmann
 
dataInfo - Variable in class etomica.normalmode.MeterBoltzmannHarmonic
 
dataInfo - Variable in class etomica.normalmode.MeterBoltzmannHTTP
 
dataInfo - Variable in class etomica.normalmode.MeterBoltzmannTarget
 
dataInfo - Variable in class etomica.normalmode.MeterDADB
 
dataInfo - Variable in class etomica.normalmode.MeterDDP
 
dataInfo - Variable in class etomica.normalmode.MeterDirectSamplingHarmonic
 
dataInfo - Variable in class etomica.normalmode.MeterDirectSamplingTarget
 
dataInfo - Variable in class etomica.normalmode.MeterDP
 
dataInfo - Variable in class etomica.normalmode.MeterHarmonicSingleEnergy
 
dataInfo - Variable in class etomica.normalmode.MeterOverlapSwitch
 
dataInfo - Variable in class etomica.normalmode.MeterPlaneSlip
 
dataInfo - Variable in class etomica.normalmode.MeterSamplingHarmonic
 
dataInfo - Variable in class etomica.normalmode.MeterSamplingTarget
 
dataInfo - Variable in class etomica.normalmode.MeterSolidDA
 
dataInfo - Variable in class etomica.normalmode.MeterSolidDACut
 
dataInfo - Variable in class etomica.normalmode.MeterSolidMirror
 
dataInfo - Variable in class etomica.normalmode.MeterSolidProps
 
dataInfo - Variable in class etomica.normalmode.MeterSolidPropsLJ
 
dataInfo - Variable in class etomica.normalmode.MeterTargetTP
 
dataInfo - Variable in class etomica.normalmode.MeterTilt
 
dataInfo - Variable in class etomica.normalmode.MeterTiltHistogram
 
dataInfo - Variable in class etomica.normalmode.MeterTiltRotation
 
dataInfo - Variable in class etomica.normalmode.MeterTiltRotationHistogram
 
dataInfo - Variable in class etomica.normalmode.MeterTiltRotationStdev
 
dataInfo - Variable in class etomica.normalmode.MeterWorkBennetHarmonic
 
dataInfo - Variable in class etomica.normalmode.MeterWorkBennetTarget
 
dataInfo - Variable in class etomica.normalmode.MeterWorkHarmonicBennet
 
dataInfo - Variable in class etomica.normalmode.MeterWorkHarmonicPhaseSpace
 
dataInfo - Variable in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
 
dataInfo - Variable in class etomica.normalmode.MeterWorkHarmonicUmbrella
 
dataInfo - Variable in class etomica.normalmode.MeterWorkTargetBennet
 
dataInfo - Variable in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
 
dataInfo - Variable in class etomica.normalmode.MeterWorkTargetPhaseSpace
 
dataInfo - Variable in class etomica.normalmode.MeterWorkTargetUmbrella
 
dataInfo - Variable in class etomica.normalmode.MeterWorkUmbrellaHarmonic
 
dataInfo - Variable in class etomica.normalmode.MeterWorkUmbrellaTarget
 
dataInfoA - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1DGraphic
 
dataInfoA - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2DGraphic
 
dataInfoA - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
 
dataInfoGroup - Variable in class etomica.normalmode.MeterTiltRotationHistogram
 
dataOverlap - Variable in class etomica.normalmode.SimOverlapModule
 
DataProcessorBoltzmannFactor - Class in etomica.normalmode
 
DataProcessorBoltzmannFactor() - Constructor for class etomica.normalmode.DataProcessorBoltzmannFactor
 
DataProcessorCvMD - Class in etomica.meam
 
DataProcessorCvMD() - Constructor for class etomica.meam.DataProcessorCvMD
 
DataProcessorFoo() - Constructor for class etomica.models.hexane.TestHexaneHarmonic.DataProcessorFoo
 
DataProcessorPhi - Class in etomica.densityofstate
 
DataProcessorPhi() - Constructor for class etomica.densityofstate.DataProcessorPhi
 
DataProcessorR2() - Constructor for class etomica.virial.simulations.VirialPolyhedra.DataProcessorR2
 
DataProcessorR2() - Constructor for class etomica.virial.simulations.VirialPolyhedra2.DataProcessorR2
 
DataProcessorSum - Class in etomica.normalmode
DataProcessor that sends on the sum of the incoming data values as a scalar.
DataProcessorSum() - Constructor for class etomica.normalmode.DataProcessorSum
 
DataProcessorVirialOverlap - Class in etomica.virial.overlap
DataProcessor which takes in values for v/pi and pi2/pi (from MeterVirial) and calculates the overlap values for various values of alpha.
DataProcessorVirialOverlap(int, boolean) - Constructor for class etomica.virial.overlap.DataProcessorVirialOverlap
 
dataSink - Variable in class etomica.virial.simulations.SimulationVirial
 
DataSourceAvgPressure - Class in etomica.normalmode
Averages the measured pressures for various N.
DataSourceAvgPressure(DataDistributer, MCMoveOverlapListener, double) - Constructor for class etomica.normalmode.DataSourceAvgPressure
 
DataSourceAvgPressure2 - Class in etomica.normalmode
Computes pressure from the grand canonical route based on measured free energy differences and simulation parameters.
DataSourceAvgPressure2(MCMoveOverlapListener, double, double, double, double) - Constructor for class etomica.normalmode.DataSourceAvgPressure2
 
DataSourceFE - Class in etomica.normalmode
Free energy data source that computes free energy differences based on overlap sampling performed by an MCMoveOverlapListener.
DataSourceFE(MCMoveOverlapListener) - Constructor for class etomica.normalmode.DataSourceFE
 
DataSourceFEHistogram - Class in etomica.normalmode
Returns a histogram of # of atoms based on free energy results and the given chemical potential.
DataSourceFEHistogram(MCMoveOverlapListener, double) - Constructor for class etomica.normalmode.DataSourceFEHistogram
 
DataSourceImposedFEFit - Class in etomica.normalmode
Like DataSourceFEHistogram, returns a probability histogram for N based on free energies.
DataSourceImposedFEFit(MCMoveOverlapListener, MCMoveInsertDeleteBiased, double) - Constructor for class etomica.normalmode.DataSourceImposedFEFit
 
DataSourceImposedFEHistogram - Class in etomica.normalmode
This is a strange creature...
DataSourceImposedFEHistogram(MCMoveOverlapListener, MCMoveInsertDeleteBiased, double) - Constructor for class etomica.normalmode.DataSourceImposedFEHistogram
 
DataSourceMuRoot - Class in etomica.normalmode
Datasource that returns an estimate of mu based on thermodynamic self-consistency of pressure measurements and defect free energies.
DataSourceMuRoot(MCMoveOverlapListener, double, DataDistributer, double, double, double) - Constructor for class etomica.normalmode.DataSourceMuRoot
 
DataSourceMuRoot.DataSourceMuRootPressure - Class in etomica.normalmode
 
DataSourceMuRoot.DataSourceMuRootVacancyConcentration - Class in etomica.normalmode
 
DataSourceMuRoot1 - Class in etomica.normalmode
Datasource that returns an estimate of mu based on thermodynamic self-consistency of pressure measurements and defect free energies.
DataSourceMuRoot1(MCMoveOverlapListener, double, DataDistributer, double, double, double) - Constructor for class etomica.normalmode.DataSourceMuRoot1
 
DataSourceMuRoot1.DataSourceMuRootPressure - Class in etomica.normalmode
 
DataSourceMuRoot1.DataSourceMuRootVacancyConcentration - Class in etomica.normalmode
 
DataSourceMuRootPMatch - Class in etomica.normalmode
Datasource that returns an estimate of mu based on thermodynamic self-consistency of pressure measurements and defect free energies.
DataSourceMuRootPMatch(MCMoveOverlapListener, double, DataDistributer, double, double, double) - Constructor for class etomica.normalmode.DataSourceMuRootPMatch
 
DataSourceMuRootPMatch.DataSourceMuRootPressure - Class in etomica.normalmode
 
DataSourceMuRootPMatch.DataSourceMuRootVacancyConcentration - Class in etomica.normalmode
 
DataSourceMuRootPressure() - Constructor for class etomica.normalmode.DataSourceMuRoot.DataSourceMuRootPressure
 
DataSourceMuRootPressure() - Constructor for class etomica.normalmode.DataSourceMuRoot1.DataSourceMuRootPressure
 
DataSourceMuRootPressure() - Constructor for class etomica.normalmode.DataSourceMuRootPMatch.DataSourceMuRootPressure
 
DataSourceMuRootVacancyConcentration() - Constructor for class etomica.normalmode.DataSourceMuRoot.DataSourceMuRootVacancyConcentration
 
DataSourceMuRootVacancyConcentration() - Constructor for class etomica.normalmode.DataSourceMuRoot1.DataSourceMuRootVacancyConcentration
 
DataSourceMuRootVacancyConcentration() - Constructor for class etomica.normalmode.DataSourceMuRootPMatch.DataSourceMuRootVacancyConcentration
 
DataSourcePMu - Class in etomica.normalmode
DataSource that returns P2-P1 or mu-mu* as a function of mu.
DataSourcePMu(MCMoveOverlapListener, double, int, double, DataDistributer, double, double, double, boolean) - Constructor for class etomica.normalmode.DataSourcePMu
 
DataSourcePN - Class in etomica.normalmode
DataSource that returns measured pressure as a function of N
DataSourcePN(DataDistributer, int) - Constructor for class etomica.normalmode.DataSourcePN
 
DataSourceVirialOverlap - Class in etomica.virial.overlap
Measures ratio of two cluster integrals using overlap sampling.
DataSourceVirialOverlap(AccumulatorVirialOverlapSingleAverage, AccumulatorVirialOverlapSingleAverage) - Constructor for class etomica.virial.overlap.DataSourceVirialOverlap
 
DataVirialOverlap - Class in etomica.virial.overlap
Convenience class that analyzes data from the reference and target system, providing average and error estimates on values and ratios.
DataVirialOverlap(AlphaSource, AccumulatorRatioAverageCovarianceFull, AccumulatorRatioAverageCovarianceFull) - Constructor for class etomica.virial.overlap.DataVirialOverlap
 
DataVirialOverlap.FullResult - Class in etomica.virial.overlap
 
dataWV - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
 
dbc - Variable in class etomica.dimer.P1LepsHarmonic
 
dc11 - Variable in class etomica.normalmode.MeterSolidPropsLJ
 
DCF - Class in etomica.virial.cluster
Main method that simply generates and displays the graphs in the direct correlation function.
DCF() - Constructor for class etomica.virial.cluster.DCF
 
dcom - Variable in class etomica.virial.MCMoveClusterRingPartialRegrow
 
ddP - Variable in class etomica.normalmode.MeterSolidProps
 
ddP - Variable in class etomica.normalmode.MeterSolidPropsLJ
 
debug - Static variable in class etomica.virial.ClusterSum
 
debug - Static variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
 
debug - Variable in class etomica.virial.ClusterWheatleySoft
 
debug - Static variable in class etomica.virial.MayerGeneral
 
defaultValue() - Method in enum etomica.virial.GUI.models.EnumPotentialParamDescription
 
degree - Variable in class etomica.virial.MCMoveClusterAtomHSTree
 
degree - Variable in class etomica.virial.MCMoveClusterPolyhedraTree
 
del_r - Variable in class etomica.virial.CalcFFT
 
deleteConnection(int, int) - Method in class etomica.virial.cluster.ClusterDiagram
Deletes a connection from one node1 to node2.
delta - Variable in class etomica.normalmode.MCMoveRotateMoleculePhiTheta
 
delta1 - Variable in class etomica.normalmode.MCMoveSingleMode
 
delta2 - Variable in class etomica.normalmode.MCMoveSingleMode
 
deltaBMu - Variable in class etomica.normalmode.DataSourcePMu
 
deltaCut2 - Variable in class etomica.virial.ClusterSumNonAdditiveTrimerEnergy
 
deltaCut2 - Variable in class etomica.virial.ClusterSumPolarizable
 
deltaCut2 - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct
 
deltaCut2 - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
 
deltaCut2 - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
 
deltaR - Variable in class etomica.dimer.IntegratorDimerMin
 
deltaR - Variable in class etomica.dimer.IntegratorDimerRT
 
deltaTheta - Variable in class etomica.dimer.IntegratorDimerMin
 
deltaTheta - Variable in class etomica.dimer.IntegratorDimerRT
 
deltaU - Variable in class etomica.normalmode.MCMoveSingleMode
 
deltaV - Variable in class etomica.dimer.IntegratorDimerRT
 
deltaV - Variable in class etomica.paracetamol.AnalyticalDerivativeEnergyParacetamol
 
deltaXl - Variable in class etomica.dimer.IntegratorDimerRT
 
deltaXmax - Variable in class etomica.dimer.IntegratorDimerRT
 
denomSum - Variable in class etomica.normalmode.MeterWorkHarmonicBennet
 
denomSum - Variable in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
 
denomSum - Variable in class etomica.normalmode.MeterWorkTargetBennet
 
denomSum - Variable in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
 
denomSum - Variable in class etomica.normalmode.MeterWorkUmbrellaHarmonic
 
denomSum - Variable in class etomica.normalmode.MeterWorkUmbrellaTarget
 
density - Variable in class etomica.meam.EFSTungsten.Params
 
density - Variable in class etomica.normalmode.LJVacancyMin.SimOverlapParam
 
density - Variable in class etomica.normalmode.MeterSolidProps
 
density - Variable in class etomica.normalmode.MeterSolidPropsLJ
 
density - Variable in class etomica.normalmode.MinimizeHCP
 
density - Variable in class etomica.normalmode.MinimizeHCP.SimOverlapParam
 
density - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1D
 
density - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3D
 
density - Variable in class etomica.normalmode.SimBennet.SimBennetParam
 
density - Variable in class etomica.normalmode.SimEinStep1.SimOverlapParam
 
density - Variable in class etomica.normalmode.SimEinStep1HCP.SimOverlapParam
 
density - Variable in class etomica.normalmode.SimEinStep2.SimOverlapParam
 
density - Variable in class etomica.normalmode.SimEinStep2HCP.SimOverlapParam
 
density - Variable in class etomica.normalmode.SimHarmonicUmbrella.SimBennetParam
 
density - Variable in class etomica.normalmode.SimHSMDVacancy.HSMDVParams
 
density - Variable in class etomica.normalmode.SimLJHTTISuper.SimOverlapParam
 
density - Variable in class etomica.normalmode.SimLJHTTISuperHCP.SimOverlapParam
 
density - Variable in class etomica.normalmode.SimLJVacancy.LJParams
 
density - Variable in class etomica.normalmode.SimOverlap.SimOverlapParam
 
density - Variable in class etomica.normalmode.SimOverlapLJ.SimOverlapParam
 
density - Variable in class etomica.normalmode.SimOverlapLJModule.SimOverlapParam
 
density - Variable in class etomica.normalmode.SimOverlapSoftSphere.SimOverlapParam
 
density - Variable in class etomica.normalmode.SimOverlapSoftSphereEin.SimOverlapParam
 
density - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm.SimOverlapParam
 
density - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP.SimOverlapParam
 
density - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting.SimOverlapParam
 
density - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness.SimOverlapParam
 
density - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox.SimOverlapParam
 
density - Variable in class etomica.normalmode.SimOverlapSoftSphereTP.SimOverlapParam
 
density - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP.SimOverlapParam
 
density - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox.SimOverlapParam
 
density - Variable in class etomica.normalmode.SimOverlapSSnxy.SimOverlapParam
 
density - Variable in class etomica.normalmode.SimTargetUmbrella.SimBennetParam
 
density - Variable in class etomica.normalmode.SimUmbrella.SimBennetParam
 
density - Variable in class etomica.normalmode.SimUmbrellaSoftSphere.SimBennetParam
 
density - Variable in class etomica.virial.simulations.TestLJAssociationMC3D_NPT.VirialAssociatingFluidParam
 
DensityOfState - Class in etomica.densityofstate
A Yukawa Monte-Carlo simulation in 3D
DensityOfState() - Constructor for class etomica.densityofstate.DensityOfState
 
DensityOfState(int) - Constructor for class etomica.densityofstate.DensityOfState
 
DensityOfStatesPolynomial - Class in etomica.densityofstate
A Yukawa Monte-Carlo simulation in 3D
DensityOfStatesPolynomial() - Constructor for class etomica.densityofstate.DensityOfStatesPolynomial
 
DensityOfStatesPolynomial(int) - Constructor for class etomica.densityofstate.DensityOfStatesPolynomial
 
derivative2nd(IVectorMutable, Potential2SoftSpherical) - Method in class etomica.normalmode.HessianDB
 
DerivativeEnergyFunction - Class in etomica.conjugategradient
 
DerivativeEnergyFunction(IBox, PotentialMaster, ISpace) - Constructor for class etomica.conjugategradient.DerivativeEnergyFunction
 
DerivativeEnergyFunction.MyAgentSource - Class in etomica.conjugategradient
 
derivativeFunction - Variable in class etomica.conjugategradient.FiniteDifferenceDerivativeCG
 
description() - Method in enum etomica.virial.GUI.models.EnumPotentialParamDescription
 
dest - Variable in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
 
dest - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
 
DeviceButtonSingle - Class in etomica.zeolite
Button that causes an action to be performed.
DeviceButtonSingle(IController) - Constructor for class etomica.zeolite.DeviceButtonSingle
Constructs button that is not connected to any action.
DeviceButtonSingle(IController, IAction) - Constructor for class etomica.zeolite.DeviceButtonSingle
Constructs a button connected to the given action.
DeviceCellNum3DSlider - Class in etomica.normalmode
 
DeviceCellNum3DSlider(IController) - Constructor for class etomica.normalmode.DeviceCellNum3DSlider
 
DeviceCellNumXYSlider - Class in etomica.normalmode
 
DeviceCellNumXYSlider(IController) - Constructor for class etomica.normalmode.DeviceCellNumXYSlider
 
DeviceEigenvaluesSlider - Class in etomica.normalmode
 
DeviceEigenvaluesSlider(IController) - Constructor for class etomica.normalmode.DeviceEigenvaluesSlider
 
DeviceWaveVectorSlider - Class in etomica.normalmode
 
DeviceWaveVectorSlider(IController) - Constructor for class etomica.normalmode.DeviceWaveVectorSlider
 
df(int[], double[]) - Method in class etomica.conjugategradient.DerivativeEnergyFunction
 
df(int[], double[]) - Method in class etomica.conjugategradient.FiniteDifferenceDerivativeCG
 
df(int[], double[]) - Method in class etomica.conjugategradient.TestNonLinearConjugateGradients
 
df(int[], double[]) - Method in class etomica.paracetamol.AnalyticalDerivativeEnergyParacetamol
 
df(int[], double[]) - Method in class etomica.paracetamol.NumericalDerivativeEnergyParacetamol
 
dForces - Variable in class etomica.dimer.SimDimerLJadatom
 
dForces - Variable in class etomica.dimer.SimDimerMEAMadatom
 
dForces - Variable in class etomica.dimer.SimDimerMEAMGB
 
dFrot - Variable in class etomica.dimer.IntegratorDimerMin
 
dFrot - Variable in class etomica.dimer.IntegratorDimerRT
 
dFsq - Variable in class etomica.dimer.IntegratorDimerRT
 
diagramIndex - Variable in class etomica.virial.ConfigurationClusterWertheimGCPM
 
diagramIndex - Variable in class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
 
diagramIndex - Variable in class etomica.virial.ConfigurationClusterWertheimGCPMDirectSampling
 
diagramIndex - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid4Pt.VirialAssociatingFluidParam
 
diagramIndex - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid.VirialAssociatingFluidParam
 
diagramIndex - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid2.VirialAssociatingFluidParam
 
diagramIndex - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid2Pt.VirialAssociatingFluidParam
 
diagramIndex - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid3Pt.VirialAssociatingFluidParam
 
diagramIndex - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid4Points.VirialAssociatingFluidParam
 
diagramIndex - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid4Pt.VirialAssociatingFluidParam
 
diagramIndex - Variable in class etomica.virial.simulations.VirialAssociatingFluid.VirialAssociatingFluidParam
 
diagramIndex - Variable in class etomica.virial.simulations.VirialAssociatingFluid4points.VirialAssociatingFluidParam
 
DiagramSource - Interface in etomica.virial.cluster
 
difference(ClusterDiagram[], ClusterDiagram[]) - Static method in class etomica.virial.cluster.ClusterOperations
Generates the set of diagrams obtained by subtracting the second set from the first set.
dim - Variable in class etomica.normalmode.MeterSolidDA
 
dim - Variable in class etomica.normalmode.MeterSolidDACut
 
dimer - Variable in class etomica.dimer.SimDimerMEAMGB
 
dimerAtomType - Variable in class etomica.normalmode.SpeciesHSDimer
 
dimerCurvature(IVectorMutable[], IVectorMutable[], IVectorMutable[]) - Method in class etomica.dimer.IntegratorDimerRT
Computes curvature value, C, for the energy surface.
dimerForceCenter(IVectorMutable[]) - Method in class etomica.dimer.IntegratorDimerRT
 
dimerForceEff(IVectorMutable[], IVectorMutable[], IVectorMutable[]) - Method in class etomica.dimer.IntegratorDimerRT
 
dimerForcePerp(IVectorMutable[], IVectorMutable[], IVectorMutable[]) - Method in class etomica.dimer.IntegratorDimerMin
Finds the component of the dimer's total force that is perpendicular to the normal vector.
dimerForcePerp(IVectorRandom[], IVectorMutable[], IVectorMutable[], IVectorMutable[]) - Method in class etomica.dimer.IntegratorDimerRT
 
dimerForces(IVectorMutable[], IVectorMutable[], IVectorMutable[]) - Method in class etomica.dimer.IntegratorDimerMin
Resets forces in boxes 0 and min, calls potential.calculate, and copies over the new forces to local arrays.
dimerForces(IVectorMutable[], IVectorMutable[], IVectorMutable[]) - Method in class etomica.dimer.IntegratorDimerRT
 
dimerForcesStar(IVectorMutable[], IVectorMutable[], IVectorMutable[]) - Method in class etomica.dimer.IntegratorDimerMin
Used in the middle of the rotateDimer method.
dimerForcesStar(IVectorMutable[], IVectorMutable[], IVectorMutable[]) - Method in class etomica.dimer.IntegratorDimerRT
 
dimerNormal() - Method in class etomica.dimer.IntegratorDimerMin
Computes an n-dimensional vector in potential energy hyperspace, pointing in the direction of the dimer (intersecting both simulation boxes).
dimerNormal() - Method in class etomica.dimer.IntegratorDimerRT
 
dimerSaddleTolerance() - Method in class etomica.dimer.IntegratorDimerRT
 
dimerUpdatePositions(double, IVectorMutable[]) - Method in class etomica.dimer.IntegratorDimerRT
 
dimx - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2D
 
dimy - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2D
 
DirectSamplingTargetQCArReferenceAzizAr - Class in etomica.virial.simulations
This class used the direct-sampling formulation of Mayer-Sampling Monte Carlo to compute the second virial coefficient of argon, as described with a quantum potential (via Q-Chem), at a particular temperature.
DirectSamplingTargetQCArReferenceAzizAr() - Constructor for class etomica.virial.simulations.DirectSamplingTargetQCArReferenceAzizAr
 
DirectSamplingTargetQCArReferenceAzizAr.VirialLJParam - Class in etomica.virial.simulations
Inner class for parameters
DiscardCriteria(char, int, char, int) - Constructor for class etomica.virial.cluster.VirialDiagramsPT.DiscardCriteria
 
disconnectedP - Variable in class etomica.virial.cluster.MayerIonicDiagram1qbond
 
disconnectedP - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
 
disconnectedP - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
 
disconnectedP - Variable in class etomica.virial.cluster.VirialDiagrams
 
disconnectedP - Variable in class etomica.virial.cluster.VirialDiagramsMix
 
disconnectedP - Variable in class etomica.virial.cluster.VirialDiagramsMix2
 
disconnectedP - Variable in class etomica.virial.cluster.VirialDiagramsPT
 
disconnectedP - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
 
disconnectedP - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
 
display - Variable in class etomica.meam.EFSTungsten
 
display - Variable in class etomica.meam.MEAM_3DMDwithSnAgGB
 
display - Variable in class etomica.meam.MEAM_3DMDwithSnCuGB
 
display - Variable in class etomica.meam.MEAMMd3D
 
display - Variable in class etomica.threaded.domain.MEAMMd3DThreaded
 
displayAHarmonic - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1DGraphic
 
displayAHarmonic - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2DGraphic
 
displayAHarmonic - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
 
DisplayBoxCanvas2DNpTScaling - Class in etomica.normalmode.nptdemo
 
DisplayBoxCanvas2DNpTScaling(DisplayBox, ISpace, Controller, CoordinateDefinition) - Constructor for class etomica.normalmode.nptdemo.DisplayBoxCanvas2DNpTScaling
 
displayBoxScaled - Variable in class etomica.normalmode.nptdemo.HSNPT2DGraphic
 
displayDensity - Variable in class etomica.normalmode.nptdemo.ColorSchemeScaledOverlap
 
displayDensity - Variable in class etomica.normalmode.nptdemo.DisplayBoxCanvas2DNpTScaling
 
displayList() - Method in class etomica.virial.GUI.components.ArrayMoleculeDisplayList
 
displayMoleculeList() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
 
displayMoleculeList() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
 
displaySelectedSpecies(int, int) - Method in class etomica.virial.GUI.controllers.ControllerSpeciesSelection
 
displayTable - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1DGraphic
 
displayTable - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2DGraphic
 
displayTableEigen - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
 
displayTableWV - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
 
distance - Variable in class etomica.paracetamol.AnalyticalDerivativeEnergyParacetamol
 
distance - Variable in class etomica.virial.ConfigurationClusterMove
 
doAvgDef - Variable in class etomica.normalmode.DataSourceFE
 
doBlockSum() - Method in class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage
 
doCaching - Variable in class etomica.virial.ClusterSum
 
doCaching - Variable in class etomica.virial.ClusterSumPolarizable
 
doCaching - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
 
doCaching - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
 
doCaching - Variable in class etomica.virial.ClusterWheatleySoft
 
doCaching - Variable in class etomica.virial.ClusterWheatleySoftBD
 
doCalculation(IAtomList, IPotential) - Method in class etomica.dimer.PotentialCalculationForcePressureSumGB
Adds forces due to given potential acting on the atoms produced by the iterator.
doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.normalmode.PotentialCalculationEFSSP
 
doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.normalmode.PotentialCalculationLJSP
 
doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.normalmode.PotentialCalculationSolidSuper
Adds forces due to given potential acting on the atoms produced by the iterator.
doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.normalmode.PotentialCalculationSolidSuperCut
Adds forces due to given potential acting on the atoms produced by the iterator.
doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.normalmode.PotentialCalculationSolidSuperCutLS
Adds forces due to given potential acting on the atoms produced by the iterator.
doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.threaded.PotentialCalculationForceSumThreaded
 
doCorrection - Variable in class etomica.virial.simulations.VirialLJOrC.VirialLJrParam
 
doCorti - Variable in class etomica.normalmode.MCMoveVolumeSolid
 
doCov - Variable in class etomica.virial.MeterVirialEBinMultiThreaded
 
doCov - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.SimulationWorker
 
doCov - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.VirialHSBinParam
 
doD2 - Variable in class etomica.normalmode.MeterSolidDA
 
doD2 - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
 
doDiff - Variable in class etomica.virial.simulations.VirialHePI.VirialHePIParam
 
doDisconnectedMatching - Variable in class etomica.virial.cluster.VirialDiagrams
 
doDisconnectedMatching - Variable in class etomica.virial.cluster.VirialDiagramsMix2
 
doDisconnectedMatching - Variable in class etomica.virial.cluster.VirialDiagramsPT
 
doExchange - Variable in class etomica.virial.cluster.VirialDiagrams.ArticulatedAt0
 
doExchange - Variable in class etomica.virial.cluster.VirialDiagrams
 
doExchange - Variable in class etomica.virial.cluster.VirialDiagramsPT.ArticulatedAt0
 
doExchange - Variable in class etomica.virial.cluster.VirialDiagramsPT
 
doExchangeCondensing - Variable in class etomica.virial.cluster.VirialDiagrams
 
doExchangeCondensing - Variable in class etomica.virial.cluster.VirialDiagramsPT
 
doExchangeF - Variable in class etomica.virial.cluster.VirialDiagrams
 
doExchangeF - Variable in class etomica.virial.cluster.VirialDiagramsPT
 
doExcludeNonNeighbors - Variable in class etomica.normalmode.MCMoveAtomCoupled
 
doExcludeNonNeighbors - Variable in class etomica.normalmode.MCMoveMoleculeCoupled
 
doExp - Variable in class etomica.virial.cluster.VirialDiagramsPT
 
doExp - Variable in class etomica.virial.simulations.VirialSwsPT.VirialSiepmannSpheresParam
 
doExpDensityprofile - Variable in class etomica.virial.cluster.ExternalVirialDiagrams
 
doFancyMonoclinic - Static variable in class etomica.normalmode.HSDimerNPT
 
doFancyOriented - Static variable in class etomica.normalmode.HSDimerNPT
 
doGraphics - Static variable in class etomica.normalmode.HSDimerNPT
 
doHB - Variable in class etomica.virial.cluster.VirialDiagrams
 
doHB - Variable in class etomica.virial.cluster.VirialDiagramsPT
 
doHist - Variable in class etomica.virial.simulations.VirialCO2H2OGCPM.VirialParam
 
doHist - Variable in class etomica.virial.simulations.VirialCO2H2OGCPMX.VirialParam
 
doHist - Variable in class etomica.virial.simulations.VirialCO2H2OSC.VirialCO2SCParam
 
doHist - Variable in class etomica.virial.simulations.VirialCO2PI.VirialH2PIParam
 
doHist - Variable in class etomica.virial.simulations.VirialEmulNonAdditive.VirialParam
 
doHist - Variable in class etomica.virial.simulations.VirialH2PI.VirialH2PIParam
 
doHist - Variable in class etomica.virial.simulations.VirialHeNonAdditive.VirialParam
 
doHist - Variable in class etomica.virial.simulations.VirialHeNonAdditiveWheatley.VirialParam
 
doHist - Variable in class etomica.virial.simulations.VirialHePI.VirialHePIParam
 
doHist - Variable in class etomica.virial.simulations.VirialHePI_PotentialCorrection.VirialHePIParam
 
doHist - Variable in class etomica.virial.simulations.VirialHePIXCOdd.VirialHePIParam
 
doHist - Variable in class etomica.virial.simulations.VirialLJ.VirialLJParam
 
doHist - Variable in class etomica.virial.simulations.VirialPolyhedra.VirialHSParam
 
doHist - Variable in class etomica.virial.simulations.VirialPolyhedra2.VirialHSParam
 
doHistory - Variable in class etomica.meam.EFSTungsten.Params
 
doIgnoreRefAvg - Variable in class etomica.virial.overlap.DataVirialOverlap
 
doIncludePair - Variable in class etomica.normalmode.MCMoveMoleculeCoupled
 
doit(NormalModes, int, double, int) - Static method in class etomica.normalmode.CalcHarmonicA
 
doit(String, int) - Static method in class etomica.normalmode.NormalModeEigenGetter
 
doit(String) - Static method in class etomica.paracetamol.NormalModeEigenGetter
 
doKeepEBonds - Variable in class etomica.virial.cluster.VirialDiagrams
 
doKeepEBonds - Variable in class etomica.virial.cluster.VirialDiagramsMix
 
doKeepEBonds - Variable in class etomica.virial.cluster.VirialDiagramsMix2
 
doKeepEBonds - Variable in class etomica.virial.cluster.VirialDiagramsPT
 
doMinimalBC - Variable in class etomica.virial.cluster.VirialDiagrams
 
doMinimalBC - Variable in class etomica.virial.cluster.VirialDiagramsMix
 
doMinimalBC - Variable in class etomica.virial.cluster.VirialDiagramsPT
 
doMinimalMulti - Variable in class etomica.virial.cluster.VirialDiagrams
 
doMinimalMulti - Variable in class etomica.virial.cluster.VirialDiagramsMix
 
doMinimalMulti - Variable in class etomica.virial.cluster.VirialDiagramsPT
 
doMulti - Variable in class etomica.virial.ClusterWheatleyMultibody
 
doMulti - Variable in class etomica.virial.ClusterWheatleyMultibodyBD
 
doMulti - Variable in class etomica.virial.ClusterWheatleyMultibodyMix
 
doMultiFromPair - Variable in class etomica.virial.cluster.VirialDiagrams
 
doMultiFromPair - Variable in class etomica.virial.cluster.VirialDiagramsPT
 
doNBodyStuff(IAtom, PotentialCalculation, int, IPotentialAtomic) - Method in class etomica.threaded.atom.PotentialMasterListWorker
 
doNBodyStuff(IAtom, PotentialCalculation, int, IPotentialAtomic) - Method in class etomica.threaded.domain.PotentialMasterListWorker
 
doNegativeExchange - Variable in class etomica.virial.cluster.VirialDiagrams
 
doNegativeExchange - Variable in class etomica.virial.cluster.VirialDiagramsPT
 
DooDad(int) - Constructor for class etomica.virial.simulations.VirialHSBinMultiThreaded.DooDad
 
doOverwrite - Variable in class etomica.normalmode.WriteS
 
doParse(String, ISpace) - Static method in class etomica.virial.simulations.ShapeParser
 
doReeHoover - Variable in class etomica.virial.cluster.MayerIonicDiagram1qbond
 
doReeHoover - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
 
doReeHoover - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
 
doReeHoover - Variable in class etomica.virial.cluster.VirialDiagrams
 
doReeHoover - Variable in class etomica.virial.cluster.VirialDiagramsMix
 
doReeHoover - Variable in class etomica.virial.cluster.VirialDiagramsMix2
 
doReeHoover - Variable in class etomica.virial.cluster.VirialDiagramsPT
 
doReeHoover - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
 
doReeHoover - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
 
doReeHoover - Variable in class etomica.virial.simulations.VirialLJ.VirialLJParam
 
doResize - Variable in class etomica.virial.simulations.VirialPolyhedra.VirialHSParam
 
doReweight - Variable in class etomica.normalmode.SimHSMDVacancy.HSMDVParams
 
doReweight - Variable in class etomica.normalmode.SimLJVacancy.LJParams
 
doReweight - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.SimulationWorker
 
doReweight - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.SimulationWorker
 
doRing - Variable in class etomica.virial.ClusterChainSoft
 
doRot - Static variable in class etomica.normalmode.HSDimerNPT
 
doRotationTransform(double, double) - Method in class etomica.normalmode.MCMoveRotateMoleculePhiTheta
 
doSearch(int, int) - Method in class etomica.virial.ClusterSumMultibody
 
doShape - Static variable in class etomica.normalmode.HSDimerNPT
 
doShortcut - Variable in class etomica.virial.cluster.MayerIonicDiagram1qbond
 
doShortcut - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
 
doShortcut - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
 
doShortcut - Variable in class etomica.virial.cluster.VirialDiagrams
 
doShortcut - Variable in class etomica.virial.cluster.VirialDiagramsMix
 
doShortcut - Variable in class etomica.virial.cluster.VirialDiagramsMix2
 
doShortcut - Variable in class etomica.virial.cluster.VirialDiagramsPT
 
doShortcut - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
 
doShortcut - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
 
doStatistics - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
 
doStepInternal() - Method in class etomica.dimer.IntegratorDimerMin
 
doStepInternal() - Method in class etomica.dimer.IntegratorDimerRT
 
doStepInternal() - Method in class etomica.dimer.IntegratorEnergyMap
 
doStepInternal() - Method in class etomica.normalmode.IntegratorHarmonic
 
doStepInternal() - Method in class etomica.tmmc.IntegratorTMMC
Method to select and perform an elementary Monte Carlo move.
doStepInternal() - Method in class etomica.virial.overlap.IntegratorOverlap
 
doSubtractComb - Variable in class etomica.normalmode.DataSourceFE
 
doSurfacetension - Variable in class etomica.virial.cluster.ExternalVirialDiagrams
 
doThermostat() - Method in class etomica.normalmode.IntegratorHardMDMC
 
doThermostat() - Method in class etomica.normalmode.IntegratorHarmonic
 
doTotal - Variable in class etomica.virial.simulations.VirialH2PI.VirialH2PIParam
 
doTotal - Variable in class etomica.virial.simulations.VirialHePI.VirialHePIParam
 
doTotal - Variable in class etomica.virial.simulations.VirialHePI_PotentialCorrection.VirialHePIParam
 
doTotal - Variable in class etomica.virial.simulations.VirialHePIXCEven.VirialHePIParam
 
doTotal - Variable in class etomica.virial.simulations.VirialHePIXCOdd.VirialHePIParam
 
doTransform() - Method in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
 
doTransform(double) - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
 
doTransform(double) - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecularOriented
 
doTransformPhi(IMolecule) - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecularOriented
 
doTransformTheta(IMolecule, double, double) - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecularOriented
 
doTrial() - Method in class etomica.models.hexane.MCMoveCBMC
 
doTrial(IMolecule) - Method in class etomica.models.hexane.MCMoveCBMC
 
doTrial() - Method in class etomica.models.hexane.MCMoveCombinedCbmcTranslation
 
doTrial() - Method in class etomica.models.hexane.MCMoveReptate
method to perform a trial move.
doTrial() - Method in class etomica.normalmode.MCMoveAtomCoupled
Method to perform trial move.
doTrial() - Method in class etomica.normalmode.MCMoveAtomCoupledBennet
Method to perform trial move.
doTrial() - Method in class etomica.normalmode.MCMoveAtomCoupledUmbrella
Method to perform trial move.
doTrial() - Method in class etomica.normalmode.MCMoveAtomSuperBox
Method to perform trial move.
doTrial() - Method in class etomica.normalmode.MCMoveEinsteinCrystal
 
doTrial() - Method in class etomica.normalmode.MCMoveHarmonic
 
doTrial() - Method in class etomica.normalmode.MCMoveHarmonicEin
 
doTrial() - Method in class etomica.normalmode.MCMoveHarmonicStep
 
doTrial() - Method in class etomica.normalmode.MCMoveMoleculeCoupled
 
doTrial() - Method in class etomica.normalmode.MCMovePhaseAngle
 
doTrial() - Method in class etomica.normalmode.MCMoveRotateMoleculePhiTheta
 
doTrial() - Method in class etomica.normalmode.MCMoveSingleMode
 
doTrial() - Method in class etomica.normalmode.MCMoveVolumeMonoclinic
 
doTrial() - Method in class etomica.normalmode.MCMoveVolumeMonoclinicAngle
 
doTrial() - Method in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
 
doTrial() - Method in class etomica.normalmode.MCMoveVolumeSolid
 
doTrial() - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
 
doTrial() - Method in class etomica.normalmode.MCMoveWV
 
doTrial() - Method in class etomica.paracetamol.MCMoveMoleculeCoupledDLPOLY
 
doTrial() - Method in class etomica.spin.MCMoveSpinFlip
 
doTrial() - Method in class etomica.virial.MCMoveChangeBondLength
 
doTrial() - Method in class etomica.virial.MCMoveClusterAngleBend
 
doTrial() - Method in class etomica.virial.MCMoveClusterAngleBendAceticAcid
 
doTrial() - Method in class etomica.virial.MCMoveClusterAtom
 
doTrial() - Method in class etomica.virial.MCMoveClusterAtomChainHSTail
 
doTrial() - Method in class etomica.virial.MCMoveClusterAtomDiscrete
 
doTrial() - Method in class etomica.virial.MCMoveClusterAtomHSChain
 
doTrial() - Method in class etomica.virial.MCMoveClusterAtomHSRing
 
doTrial() - Method in class etomica.virial.MCMoveClusterAtomHSTree
 
doTrial() - Method in class etomica.virial.MCMoveClusterAtomMulti
 
doTrial() - Method in class etomica.virial.MCMoveClusterAtomQ
 
doTrial() - Method in class etomica.virial.MCMoveClusterAtomRotateMulti
 
doTrial() - Method in class etomica.virial.MCMoveClusterDiagram
 
doTrial() - Method in class etomica.virial.MCMoveClusterMolecule
 
doTrial() - Method in class etomica.virial.MCMoveClusterMoleculeLayerMove
 
doTrial() - Method in class etomica.virial.MCMoveClusterMoleculeMulti
 
doTrial() - Method in class etomica.virial.MCMoveClusterPolyhedraChain
 
doTrial() - Method in class etomica.virial.MCMoveClusterPolyhedraTree
 
doTrial() - Method in class etomica.virial.MCMoveClusterReptateMulti
 
doTrial() - Method in class etomica.virial.MCMoveClusterRingPartialRegrow
 
doTrial() - Method in class etomica.virial.MCMoveClusterRingRegrow
 
doTrial() - Method in class etomica.virial.MCMoveClusterRingRegrowExchange
 
doTrial() - Method in class etomica.virial.MCMoveClusterRingRegrowOrientation
 
doTrial() - Method in class etomica.virial.MCMoveClusterRingScale
 
doTrial() - Method in class etomica.virial.MCMoveClusterRotateCH3
 
doTrial() - Method in class etomica.virial.MCMoveClusterRotateMolecule3D
 
doTrial() - Method in class etomica.virial.MCMoveClusterRotateMoleculeMulti
 
doTrial() - Method in class etomica.virial.MCMoveClusterTorsionAceticAcid
 
doTrial() - Method in class etomica.virial.MCMoveClusterTorsionAlkaneEH
 
doTrial() - Method in class etomica.virial.MCMoveClusterTorsionMulti
 
doTrial() - Method in class etomica.virial.MCMoveClusterWiggleAceticAcid
 
doTrial() - Method in class etomica.virial.MCMoveClusterWiggleAlkaneEH
 
doTrial() - Method in class etomica.virial.MCMoveClusterWiggleMulti
 
doTrial() - Method in class etomica.virial.paralleltempering.MCMoveSwapCluster
 
DoubleAssociationSitesFluid2Pt - Class in etomica.virial.simulations
 
DoubleAssociationSitesFluid2Pt() - Constructor for class etomica.virial.simulations.DoubleAssociationSitesFluid2Pt
 
DoubleAssociationSitesFluid2Pt.VirialAssociatingFluidParam - Class in etomica.virial.simulations
 
DoubleAssociationSitesFluid3Pt - Class in etomica.virial.simulations
 
DoubleAssociationSitesFluid3Pt() - Constructor for class etomica.virial.simulations.DoubleAssociationSitesFluid3Pt
 
DoubleAssociationSitesFluid3Pt.VirialAssociatingFluidParam - Class in etomica.virial.simulations
 
DoubleAssociationSitesFluid4Pt - Class in etomica.virial.simulations
repulsive potential: Lennard-Jones potential attractive potential: short-handed square well potential Wertheim's double attraction-site model, hyper-point diagram 4 point diagram calculation
DoubleAssociationSitesFluid4Pt() - Constructor for class etomica.virial.simulations.DoubleAssociationSitesFluid4Pt
 
DoubleAssociationSitesFluid4Pt.VirialAssociatingFluidParam - Class in etomica.virial.simulations
 
doUpdateFMulti(int, IMoleculeList, CoordinatePairSet) - Method in class etomica.virial.ClusterSumMultibody
 
doWheatley - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.SimulationWorker
 
doWheatley - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.VirialHSBinParam
 
doWheatley - Variable in class etomica.virial.simulations.VirialLJ.VirialLJParam
 
doWiggle - Variable in class etomica.virial.GUI.models.ModelSimulationEnvironment
 
doWiggle - Variable in class etomica.virial.simulations.SimulationVirial
 
doWiggle - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
 
dP - Variable in class etomica.normalmode.MeterSolidProps
 
dP - Variable in class etomica.normalmode.MeterSolidPropsLJ
 
dP - Variable in class etomica.normalmode.PotentialCalculationLJSP
 
dpVirialOverlap - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
 
dr - Variable in class etomica.meam.PotentialCuLREP
 
dr - Variable in class etomica.meam.PotentialEFS
 
dr - Variable in class etomica.meam.PotentialFeEAM
 
dr - Variable in class etomica.meam.PotentialFeEAM_LS
 
dR - Variable in class etomica.meam.PotentialFeEAM_LS
 
dr - Variable in class etomica.normalmode.MCMoveEinsteinCrystal
 
dr - Variable in class etomica.normalmode.MCMoveRotateMoleculePhiTheta
 
dr - Variable in class etomica.normalmode.MCMoveVolumeSolid
 
dr - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecularOriented
 
dr - Variable in class etomica.normalmode.MeterDADB
 
dr - Variable in class etomica.normalmode.MeterDisplacementMoleculeRMS
 
dr - Variable in class etomica.normalmode.MeterDisplacementRMS
 
dr - Variable in class etomica.normalmode.MeterMaxExpansion
 
dr - Variable in class etomica.normalmode.MeterPhiDeviation
 
dr - Variable in class etomica.normalmode.MeterSolidDA
 
dr - Variable in class etomica.normalmode.MeterSolidMirror
 
dr - Variable in class etomica.normalmode.MeterSolidProps
 
dr - Variable in class etomica.normalmode.MeterSolidPropsLJ
 
dr - Variable in class etomica.normalmode.MeterThetaDeviation
 
dr - Variable in class etomica.normalmode.MeterTilt
 
dr - Variable in class etomica.normalmode.MeterTiltHistogram
 
dr - Variable in class etomica.normalmode.MeterTiltRotation
 
dr - Variable in class etomica.normalmode.MeterTiltRotationHistogram
 
dr - Variable in class etomica.normalmode.MeterTiltRotationStdev
 
dr - Variable in class etomica.normalmode.nptdemo.ColorSchemeScaledOverlap
 
dr - Variable in class etomica.normalmode.P2XOrder
 
dr - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
 
dr - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
 
dr - Variable in class etomica.virial.CoordinatePairLeafSet
 
dr - Variable in class etomica.virial.CoordinatePairMoleculeSet
 
dr - Variable in class etomica.virial.MCMoveClusterAtomChainHSTail
 
dr - Variable in class etomica.virial.MCMoveClusterAtomDiscrete
 
dr - Variable in class etomica.virial.MCMoveClusterAtomHSChain
 
dr - Variable in class etomica.virial.MCMoveClusterPolyhedraChain
 
dr - Variable in class etomica.virial.simulations.VirialHSOrC.VirialLJrParam
 
dr - Variable in class etomica.virial.simulations.VirialLJOrC.VirialLJrParam
 
dr - Variable in class etomica.virial.simulations.VirialLJOrICPYC.VirialLJrParam
 
dr21 - Variable in class etomica.virial.MCMoveClusterTorsionAlkaneEH
 
dr21 - Variable in class etomica.virial.MCMoveClusterTorsionMulti
 
dr23 - Variable in class etomica.virial.MCMoveClusterTorsionAlkaneEH
 
dr23 - Variable in class etomica.virial.MCMoveClusterTorsionMulti
 
dr34 - Variable in class etomica.virial.MCMoveClusterTorsionAlkaneEH
 
dr34 - Variable in class etomica.virial.MCMoveClusterTorsionMulti
 
drA - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
 
drA - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
 
drawAtom(Graphics, int[], IAtom) - Method in class etomica.normalmode.nptdemo.DisplayBoxCanvas2DNpTScaling
 
drB - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
 
drB - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
 
dri - Variable in class etomica.normalmode.PotentialCalculationEFSSP
 
dri - Variable in class etomica.normalmode.PotentialCalculationLJSP
 
drij - Variable in class etomica.meam.PotentialCuLREP
 
drij - Variable in class etomica.meam.PotentialEFS
 
drij - Variable in class etomica.meam.PotentialFeEAM
 
drij - Variable in class etomica.normalmode.PotentialCalculationEFSSP
 
drij - Variable in class etomica.normalmode.PotentialCalculationLJSP
 
drik - Variable in class etomica.meam.PotentialCuLREP
 
drik - Variable in class etomica.meam.PotentialEFS
 
drik - Variable in class etomica.meam.PotentialFeEAM
 
drj - Variable in class etomica.normalmode.P1ConstraintNbr
 
drj - Variable in class etomica.normalmode.P1ConstraintNbrHcp
 
drj - Variable in class etomica.normalmode.PotentialCalculationEFSSP
 
drj - Variable in class etomica.normalmode.PotentialCalculationLJSP
 
drj_tmp - Variable in class etomica.normalmode.PotentialCalculationLJSP
 
drjk - Variable in class etomica.meam.PotentialCuLREP
 
drjk - Variable in class etomica.meam.PotentialEFS
 
drjk - Variable in class etomica.meam.PotentialFeEAM
 
drk - Variable in class etomica.normalmode.P1ConstraintNbr
 
drk - Variable in class etomica.normalmode.P1ConstraintNbrHcp
 
drSite0 - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
 
drSite0 - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
 
drSite1 - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
 
drSite1 - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
 
drSum - Variable in class etomica.normalmode.MCMoveRotateMoleculePhiTheta
 
drSum - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecularOriented
 
drSum - Variable in class etomica.normalmode.MeterPlaneSlip
 
drSum - Variable in class etomica.normalmode.MeterTilt
 
drSum - Variable in class etomica.normalmode.MeterTiltRotation
 
drSum - Variable in class etomica.normalmode.MeterTiltRotationHistogram
 
drSumPlane - Variable in class etomica.normalmode.MeterTiltRotation
 
drSumSave - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecularOriented
 
drtmp - Variable in class etomica.meam.PotentialFeEAM_LS
 
dRtmp - Variable in class etomica.meam.PotentialFeEAM_LS
 
ds - Variable in class etomica.normalmode.MeterSolidMirror
 
dSigma - Variable in class etomica.normalmode.MeterSolidPropsLJ
 
dst - Variable in class etomica.virial.CalcFFT
 
dsum - Variable in class etomica.virial.MeterVirialBDBinMultiThreaded.MyData
 
dsum2 - Variable in class etomica.virial.MeterVirialBDBinMultiThreaded.MyData
 
dsvo - Variable in class etomica.normalmode.SimOverlap
 
dsvo - Variable in class etomica.normalmode.SimOverlapLJ
 
dsvo - Variable in class etomica.normalmode.SimOverlapLJModule
 
dsvo - Variable in class etomica.normalmode.SimOverlapSoftSphere
 
dsvo - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
 
dsvo - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
 
dsvo - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting
 
dsvo - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
 
dsvo - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox
 
dsvo - Variable in class etomica.normalmode.SimOverlapSSnxy
 
dsvo - Variable in class etomica.virial.simulations.SimulationVirialMultiOverlap
 
dsvo - Variable in class etomica.virial.simulations.SimulationVirialOverlap
 
dTheta - Variable in class etomica.dimer.IntegratorDimerMin
 
dTheta - Variable in class etomica.dimer.IntegratorDimerRT
 
dTheta - Variable in class etomica.virial.MCMoveClusterAngleBend
 
dTheta - Variable in class etomica.virial.MCMoveClusterAngleBendAceticAcid
 
du(double) - Method in class etomica.virial.P1IntraLambda
 
du(double) - Method in class etomica.yukawa.P2HC2Yukawa
 
du(double) - Method in class etomica.yukawa.P2Yukawa
r * du/dr method.
dU_est - Variable in class etomica.normalmode.MeterSolidPropsLJ
 
dummyRefCluster - Static variable in class etomica.virial.simulations.VirialN2
 
dummyTarCluster - Static variable in class etomica.virial.simulations.VirialN2
 
dvo - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
 
dXl - Variable in class etomica.dimer.IntegratorDimerRT
 

E

E(CoordinatePairLeafSet) - Method in class etomica.virial.CoordinatePairLeafSet
 
E(CoordinatePairLeafSet) - Method in class etomica.virial.CoordinatePairMoleculeSet
 
e0 - Variable in class etomica.dimer.IntegratorDimerMin
 
e2 - Variable in class etomica.virial.ClusterWheatleyExtendSW
 
eBond - Variable in class etomica.virial.cluster.ExchangeSplit.ExchangeSplitParameters
 
eBond - Variable in class etomica.virial.cluster.MayerIonicDiagram1qbond
 
eBond - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
 
eBond - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
 
eBond - Variable in class etomica.virial.cluster.VirialDiagrams
 
eBond - Variable in class etomica.virial.cluster.VirialDiagramsMix
 
eBond - Variable in class etomica.virial.cluster.VirialDiagramsMix2
 
eBond - Variable in class etomica.virial.cluster.VirialDiagramsPT
 
eBond - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
 
eBond - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
 
eBond - Variable in class etomica.virial.PYGenerator.IteratorEF
 
Ec - Variable in class etomica.meam.ParameterSetMEAM
 
Echarge - Static variable in class etomica.paracetamol.SpeciesParacetamol
 
Echarge - Static variable in class etomica.virial.ConformationCO2
 
eCliqueCount - Variable in class etomica.virial.ClusterSumHS
 
eCliqueCount - Variable in class etomica.virial.ClusterWheatleyHS
 
eCliqueCount - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
 
eCliqueList - Variable in class etomica.virial.ClusterSumHS
 
eCliqueList - Variable in class etomica.virial.ClusterWheatleyHS
 
eCliqueList - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
 
edgeCount - Variable in class etomica.virial.ClusterSumHS
 
edgeCount - Variable in class etomica.virial.ClusterWheatleyHS
 
edgeCount - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
 
edgeCountCore - Variable in class etomica.virial.ClusterWheatleyExtendSW
 
edgeCountWell - Variable in class etomica.virial.ClusterWheatleyExtendSW
 
eExchange - Variable in class etomica.virial.cluster.CondenseExchange.CondenseExchangeParameters
 
efbcBond - Variable in class etomica.virial.cluster.VirialDiagrams
 
efbcBond - Variable in class etomica.virial.cluster.VirialDiagramsMix
 
efbcBond - Variable in class etomica.virial.cluster.VirialDiagramsMix2
 
efbcBond - Variable in class etomica.virial.cluster.VirialDiagramsPT
 
EFSTungsten - Class in etomica.meam
Molecular-Dynamics Simulation Using the extended Finnis-Sinclair Method (EFS) Potential.
EFSTungsten(int, double, double) - Constructor for class etomica.meam.EFSTungsten
 
EFSTungsten.Params - Class in etomica.meam
 
eigenTable - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
 
eigenvalues - Variable in class etomica.normalmode.NormalModes3D
 
eigenvectors - Variable in class etomica.normalmode.MeterHarmonicCoordinate
 
eigenvectors - Variable in class etomica.normalmode.MeterHarmonicEnergy
 
eigenvectors - Variable in class etomica.normalmode.MeterHarmonicSingleEnergy
 
eigenVectors - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
 
eigenvectors - Variable in class etomica.normalmode.NormalModes2D
 
eigenvectors - Variable in class etomica.normalmode.NormalModes3D
 
eigenVectors - Variable in class etomica.normalmode.NormalModesVariable
 
eMin - Variable in class etomica.dimer.IntegratorDimerMin
 
enableDimerSearch(String, long, Boolean, Boolean) - Method in class etomica.dimer.SimDimerLJadatom
 
enableDimerSearch(String, long, Boolean, Boolean) - Method in class etomica.dimer.SimDimerMEAMadatom
 
enableDimerSearch(String, long, Boolean, Boolean) - Method in class etomica.dimer.SimDimerMEAMGB
 
enableMinimumSearch(String, Boolean) - Method in class etomica.dimer.SimDimerLJadatom
 
enableMinimumSearch(String, Boolean) - Method in class etomica.dimer.SimDimerMEAMadatom
 
enableMinimumSearch(String, Boolean) - Method in class etomica.dimer.SimDimerMEAMGB
 
enableMolecularDynamics(long) - Method in class etomica.dimer.SimDimerLJadatom
 
enableMolecularDynamics(long) - Method in class etomica.dimer.SimDimerMEAMadatom
 
enableMolecularDynamics(long) - Method in class etomica.dimer.SimDimerMEAMGB
 
energy - Variable in class etomica.dimer.IntegratorDimerMin
 
energy - Variable in class etomica.dimer.IntegratorEnergyMap
 
energy(IAtomList) - Method in class etomica.dimer.P1LepsHarmonic
 
energy - Variable in class etomica.meam.EFSTungsten
 
energy - Variable in class etomica.meam.MEAM_3DMDwithGB
 
energy - Variable in class etomica.meam.MEAM_3DMDwithSnAgGB
 
energy - Variable in class etomica.meam.MEAM_3DMDwithSnCuGB
 
energy - Variable in class etomica.meam.MEAM_MC
 
energy - Variable in class etomica.meam.MEAMMd3D
 
energy(IAtomList) - Method in class etomica.meam.PotentialCuLREP
 
energy(IAtomList) - Method in class etomica.meam.PotentialEFS
 
energy(IAtomList) - Method in class etomica.meam.PotentialFeEAM
 
energy(IAtomList) - Method in class etomica.meam.PotentialFeEAM_LS
 
energy(IAtomList) - Method in class etomica.meam.PotentialMEAM
 
energy(IAtomList) - Method in class etomica.normalmode.P1Constraint
 
energy(IAtomList) - Method in class etomica.normalmode.P1ConstraintNbr
Returns sum of energy for all triplets containing the given atom
energy(IAtomList) - Method in class etomica.normalmode.P1ConstraintNbrHcp
Returns sum of energy for all triplets containing the given atom
energy(IAtomList) - Method in class etomica.normalmode.P2XOrder
Interaction energy of the pair.
energy(IAtomList) - Method in class etomica.paracetamol.P2ElectrostaticDreiding
 
energy(IAtomList) - Method in class etomica.spin.P1MagneticField
 
energy(IAtomList) - Method in class etomica.spin.P2Spin
Returns the energy for the given pair of atoms.
energy - Variable in class etomica.threaded.domain.MEAMMd3DThreaded
 
energy(IAtomList) - Method in class etomica.threaded.PotentialThreaded
 
energy(IMoleculeList, double[]) - Method in class etomica.virial.MayerFunctionMolecularThreeBody
 
energy(IMoleculeList, double[]) - Method in class etomica.virial.MayerFunctionSphericalThreeBody
 
energy(IMoleculeList, double[]) - Method in class etomica.virial.MayerFunctionThreeBody
 
energy(IAtomList) - Method in class etomica.virial.P1IntraLambda
 
energy(IAtomList) - Method in class etomica.virial.PotentialCommonAtomic
 
energy(IMoleculeList) - Method in class etomica.virial.PotentialEmulCached
 
energy(IMoleculeList) - Method in class etomica.virial.PotentialGroup3PI
 
energy(IMoleculeList) - Method in class etomica.virial.PotentialGroup3PI.PotentialGroup3PISkip
 
energy(IMoleculeList) - Method in class etomica.virial.PotentialGroupPI
 
energy(IMoleculeList) - Method in class etomica.virial.PotentialGroupPI.PotentialGroupPISkip
 
energy(IMoleculeList) - Method in class etomica.virial.PotentialNonAdditive
 
energy(int, IMoleculeList) - Method in class etomica.virial.PotentialNonAdditive
 
energy(IMoleculeList) - Method in class etomica.virial.PotentialNonAdditive.PotentialNonAdditiveNB
 
energy(IAtomList) - Method in class etomica.yukawa.P2HC2Yukawa
Energy of the pair as given by the u(double) method
energyBox0 - Variable in class etomica.dimer.IntegratorDimerMin
 
energyBox0 - Variable in class etomica.dimer.IntegratorDimerRT
 
energyBox1 - Variable in class etomica.dimer.IntegratorDimerRT
 
energyBox2 - Variable in class etomica.dimer.IntegratorDimerRT
 
energyBoxMin - Variable in class etomica.dimer.IntegratorDimerMin
 
energyChange() - Method in class etomica.models.hexane.CBMCGrowSolidHexane
 
energyChange() - Method in class etomica.models.hexane.CBMCGrowStraightAlkane
 
energyChange() - Method in class etomica.models.hexane.MCMoveCBMC
 
energyChange() - Method in class etomica.models.hexane.MCMoveCombinedCbmcTranslation
 
energyChange() - Method in class etomica.models.hexane.MCMoveReptate
 
energyChange() - Method in class etomica.normalmode.MCMoveAtomCoupled
 
energyChange() - Method in class etomica.normalmode.MCMoveAtomCoupledBennet
 
energyChange() - Method in class etomica.normalmode.MCMoveAtomCoupledUmbrella
 
energyChange() - Method in class etomica.normalmode.MCMoveAtomSuperBox
 
energyChange() - Method in class etomica.normalmode.MCMoveEinsteinCrystal
 
energyChange() - Method in class etomica.normalmode.MCMoveHarmonic
 
energyChange() - Method in class etomica.normalmode.MCMoveHarmonicStep
 
energyChange() - Method in class etomica.normalmode.MCMoveMoleculeCoupled
 
energyChange() - Method in class etomica.normalmode.MCMovePhaseAngle
 
energyChange() - Method in class etomica.normalmode.MCMoveSingleMode
 
energyChange() - Method in class etomica.normalmode.MCMoveVolumeMonoclinic
 
energyChange() - Method in class etomica.normalmode.MCMoveVolumeMonoclinicAngle
 
energyChange() - Method in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
 
energyChange() - Method in class etomica.normalmode.MCMoveVolumeSolid
 
energyChange() - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
 
energyChange() - Method in class etomica.normalmode.MCMoveWV
 
energyChange() - Method in class etomica.normalmode.P2XOrder
 
energyChange() - Method in class etomica.paracetamol.MCMoveMoleculeCoupledDLPOLY
 
energyChange() - Method in class etomica.spin.MCMoveSpinFlip
 
energyChange() - Method in class etomica.virial.MCMoveChangeBondLength
 
energyChange() - Method in class etomica.virial.MCMoveClusterAngleBend
 
energyChange() - Method in class etomica.virial.MCMoveClusterAngleBendAceticAcid
 
energyChange() - Method in class etomica.virial.MCMoveClusterAtomQ
 
energyChange(IBox) - Method in class etomica.virial.MCMoveClusterAtomQ
 
energyChange() - Method in class etomica.virial.MCMoveClusterDiagram
 
energyChange() - Method in class etomica.virial.MCMoveClusterReptateMulti
 
energyChange() - Method in class etomica.virial.MCMoveClusterRingPartialRegrow
 
energyChange() - Method in class etomica.virial.MCMoveClusterRingRegrow
 
energyChange() - Method in class etomica.virial.MCMoveClusterRingRegrowExchange
 
energyChange() - Method in class etomica.virial.MCMoveClusterRingRegrowOrientation
 
energyChange() - Method in class etomica.virial.MCMoveClusterRingScale
 
energyChange(IBox) - Method in class etomica.virial.paralleltempering.MCMoveSwapCluster
 
energyi(IAtom) - Method in class etomica.normalmode.P1ConstraintNbr
Returns the energy for atom i due to requirements for i and its neighbors (but not for i as a neighbor)
energyi(IAtom) - Method in class etomica.normalmode.P1ConstraintNbrHcp
Returns the energy for atom i due to requirements for i and its neighbors (but not for i as a neighbor)
energyij(IAtom, IAtom) - Method in class etomica.normalmode.P1ConstraintNbr
Return the energy for i due to requirement that it be between j and the atom opposite from j.
EnergyMap - Class in etomica.dimer
Simulation class using IntegratorEnergyMap.
EnergyMap(double, String) - Constructor for class etomica.dimer.EnergyMap
 
EnergyMapCluster - Class in etomica.dimer
Simulation using Henkelman's Dimer method to find a saddle point for an adatom of Sn on a surface, modeled with MEAM.
EnergyMapCluster(Space) - Constructor for class etomica.dimer.EnergyMapCluster
 
energyMeter - Variable in class etomica.models.hexane.MCMoveCombinedCbmcTranslation
 
energyMeter - Variable in class etomica.models.hexane.MCMoveReptate
 
energyMeter - Variable in class etomica.normalmode.MCMoveAtomCoupled
 
energyMeter - Variable in class etomica.normalmode.MCMoveAtomCoupledBennet
 
energyMeter - Variable in class etomica.normalmode.MCMoveAtomCoupledUmbrella
 
energyMeter - Variable in class etomica.normalmode.MCMoveAtomSuperBox
 
energyMeter - Variable in class etomica.normalmode.MCMoveHarmonicStep
 
energyMeter - Variable in class etomica.normalmode.MCMoveMoleculeCoupled
 
energyMeter - Variable in class etomica.normalmode.MCMoveSingleMode
 
energyMeter - Variable in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
 
energyMeter - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
 
energyMeter - Variable in class etomica.paracetamol.MCMoveMoleculeCoupledDLPOLY
 
energyMeter - Variable in class etomica.spin.MCMoveSpinFlip
 
energyMeter - Variable in class etomica.virial.MCMoveClusterAngleBend
 
energyMeter - Variable in class etomica.virial.MCMoveClusterAngleBendAceticAcid
 
energyMeter - Variable in class etomica.virial.MCMoveClusterRingPartialRegrow
 
energyMeter - Variable in class etomica.virial.MCMoveClusterRingScale
 
energyMeter - Variable in class etomica.virial.MCMoveClusterRotateCH3
 
energyMeter - Variable in class etomica.virial.MCMoveClusterTorsionAlkaneEH
 
energyMeter - Variable in class etomica.virial.MCMoveClusterTorsionMulti
 
energyMeter - Variable in class etomica.virial.MCMoveClusterWiggleAceticAcid
 
energyMeter - Variable in class etomica.virial.MCMoveClusterWiggleAlkaneEH
 
energyMeter - Variable in class etomica.virial.MCMoveClusterWiggleMulti
 
energyNew - Variable in class etomica.normalmode.MCMoveHarmonicStep
 
energyNew - Variable in class etomica.normalmode.MCMoveSingleMode
 
energyOld - Variable in class etomica.normalmode.MCMoveHarmonicStep
 
energyOld - Variable in class etomica.normalmode.MCMoveSingleMode
 
energySum - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
 
energySum - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
 
EnumPotentialParamDescription - Enum in etomica.virial.GUI.models
 
EnumSiteName - Enum in etomica.virial.GUI.models
 
ePlot - Variable in class etomica.zeolite.ZeoliteSimulation
 
eps - Variable in class etomica.meam.PotentialFeEAM
 
epsFe - Variable in class etomica.meam.PotentialFeEAM_LS
 
epsilon - Variable in class etomica.normalmode.SoftSphereSolidEOS
 
epsilon - Variable in class etomica.normalmode.SoftSphereSolidEOSCalculator
 
epsilon - Variable in class etomica.virial.simulations.Virial2CLJQ.Virial2CLJQParam
 
epsilon - Variable in class etomica.virial.simulations.VirialExternalFieldConfinedOverlap.VirialExternalFieldParam
 
epsilon - Variable in class etomica.virial.simulations.VirialExternalFieldConfinedOverlapRho.VirialExternalFieldParam
 
epsilon - Variable in class etomica.virial.simulations.VirialExternalFieldConfinedOverlapSW.VirialExternalFieldParam
 
epsilonCG - Variable in class etomica.conjugategradient.NonLinearConjugateGradients
 
epsilonN - Variable in class etomica.virial.simulations.VirialN2TraPPE.VirialN2Param
 
epsilonNR - Variable in class etomica.conjugategradient.NonLinearConjugateGradients
 
epsilonSF6 - Variable in class etomica.virial.simulations.VirialSF6LJAlkaneUAMix.VirialMixParam
 
epsilonWF - Variable in class etomica.virial.simulations.VirialExternalFieldConfinedOverlapRho.VirialExternalFieldParam
 
epsilonWF - Variable in class etomica.virial.simulations.VirialExternalFieldConfinedOverlapSW.VirialExternalFieldParam
 
eqSteps - Variable in class etomica.virial.simulations.VirialHePCKLJS.VirialParam
 
eqSteps - Variable in class etomica.virial.simulations.VirialHePCKLJSCHNCCorrection.VirialLJParam
 
eqSteps - Variable in class etomica.virial.simulations.VirialHePCKLJSPYCorrection.VirialLJParam
 
eqSteps - Variable in class etomica.virial.simulations.VirialLJCHNCCorrection.VirialLJParam
 
eqSteps - Variable in class etomica.virial.simulations.VirialLJPYCorrection.VirialLJParam
 
equals(Object) - Method in class etomica.virial.IntSet
 
equilibrate(String, long) - Method in class etomica.normalmode.SimOverlap
 
equilibrate(String, long) - Method in class etomica.normalmode.SimOverlapLJ
 
equilibrate(long) - Method in class etomica.normalmode.SimOverlapModule
 
equilibrate(String, long) - Method in class etomica.normalmode.SimOverlapSoftSphere
 
equilibrate(long) - Method in class etomica.normalmode.SimOverlapSoftSphereEinHarm
 
equilibrate(String, long) - Method in class etomica.normalmode.SimOverlapSoftSphereHCP
 
equilibrate(String, long) - Method in class etomica.normalmode.SimOverlapSoftSphereReweighting
 
equilibrate(long) - Method in class etomica.normalmode.SimOverlapSoftSphereSoftness
 
equilibrate(String, long) - Method in class etomica.normalmode.SimOverlapSoftSphereSuperBox
 
equilibrate(String, long) - Method in class etomica.normalmode.SimOverlapSSnxy
 
equilibrate(long) - Method in class etomica.virial.simulations.SimulationVirial
 
equilibrate(String, long) - Method in class etomica.virial.simulations.SimulationVirialMultiOverlap
 
equilibrate(String, long) - Method in class etomica.virial.simulations.SimulationVirialOverlap
 
equilibrate(String, long) - Method in class etomica.virial.simulations.SimulationVirialOverlap2
 
EQUILIBRATION - Static variable in class etomica.paracetamol.MCParacetamolMonoclinicDLMULTI
 
EQUILIBRATION - Static variable in class etomica.paracetamol.MCParacetamolOrthorhombicDLMULTI
 
eRBond - Variable in class etomica.virial.cluster.BondConnectedSubstitution.BondConnectedSubstitutionParameters2Site
 
eRBond - Variable in class etomica.virial.cluster.BondConnectedSubstitution3Site.BondConnectedSubstitutionParameters3Site
 
eRBond - Variable in class etomica.virial.cluster.BondConnectedSubstitutionNaphthalene.BondConnectedSubstitutionParameters2SiteNa
 
errorStat - Variable in class etomica.virial.overlap.DataVirialOverlap
 
ethanol - Static variable in class etomica.virial.simulations.VirialRowleyAlcohol
 
ethanol - Static variable in class etomica.virial.simulations.VirialTraPPEAlcohol
 
etomica.apps.junit.virial - package etomica.apps.junit.virial
 
etomica.conjugategradient - package etomica.conjugategradient
 
etomica.densityofstate - package etomica.densityofstate
 
etomica.dimer - package etomica.dimer
 
etomica.eigenstuff - package etomica.eigenstuff
 
etomica.meam - package etomica.meam
 
etomica.models.hexane - package etomica.models.hexane
Under development; subject to significant change or removal.
etomica.normalmode - package etomica.normalmode
 
etomica.normalmode.nptdemo - package etomica.normalmode.nptdemo
 
etomica.paracetamol - package etomica.paracetamol
 
etomica.spin - package etomica.spin
 
etomica.threaded - package etomica.threaded
 
etomica.threaded.atom - package etomica.threaded.atom
 
etomica.threaded.domain - package etomica.threaded.domain
 
etomica.threads - package etomica.threads
 
etomica.tmmc - package etomica.tmmc
 
etomica.virial - package etomica.virial
 
etomica.virial.cluster - package etomica.virial.cluster
 
etomica.virial.GUI - package etomica.virial.GUI
 
etomica.virial.GUI.components - package etomica.virial.GUI.components
 
etomica.virial.GUI.containers - package etomica.virial.GUI.containers
 
etomica.virial.GUI.controllers - package etomica.virial.GUI.controllers
 
etomica.virial.GUI.models - package etomica.virial.GUI.models
 
etomica.virial.GUI.views - package etomica.virial.GUI.views
 
etomica.virial.overlap - package etomica.virial.overlap
 
etomica.virial.paralleltempering - package etomica.virial.paralleltempering
 
etomica.virial.simulations - package etomica.virial.simulations
 
etomica.yukawa - package etomica.yukawa
 
etomica.zeolite - package etomica.zeolite
 
eValNum - Variable in class etomica.normalmode.IntegratorHarmonic
 
eValPostAction - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
 
eValSlider - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
 
eVec - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
 
ex - Variable in class etomica.normalmode.MeterSolidPropsLJ
 
excBond - Variable in class etomica.virial.cluster.ExchangeSplit.ExchangeSplitParameters
 
excBond - Variable in class etomica.virial.cluster.VirialDiagrams
 
excBond - Variable in class etomica.virial.cluster.VirialDiagramsMix
 
excBond - Variable in class etomica.virial.cluster.VirialDiagramsMix2
 
excBond - Variable in class etomica.virial.cluster.VirialDiagramsPT
 
ExceptionDoNotRemoveSpecies - Exception in etomica.virial.GUI.components
 
ExceptionDoNotRemoveSpecies(int) - Constructor for exception etomica.virial.GUI.components.ExceptionDoNotRemoveSpecies
 
ExceptionSameSpeciesSamePotential - Exception in etomica.virial.GUI.components
 
ExceptionSameSpeciesSamePotential() - Constructor for exception etomica.virial.GUI.components.ExceptionSameSpeciesSamePotential
 
ExceptionSingleSiteAtomicPotential - Exception in etomica.virial.GUI.components
 
ExceptionSingleSiteAtomicPotential() - Constructor for exception etomica.virial.GUI.components.ExceptionSingleSiteAtomicPotential
 
ExchangeSplit - Class in etomica.virial.cluster
This operation splits each e-bond component into a sum of permuted (exchanged) nodes.
ExchangeSplit() - Constructor for class etomica.virial.cluster.ExchangeSplit
 
ExchangeSplit.ExchangeSplitParameters - Class in etomica.virial.cluster
 
ExchangeSplitParameters(MulFlexibleParameters, byte, char, char, boolean) - Constructor for class etomica.virial.cluster.ExchangeSplit.ExchangeSplitParameters
 
excludeBogusConfigs - Variable in class etomica.virial.MeterVirialBDBinMultiThreaded
 
excludeBogusConfigs - Variable in class etomica.virial.MeterVirialBinMultiThreaded
 
exp6 - Variable in class etomica.virial.MayerSSSeries
 
exponentN - Variable in class etomica.normalmode.MinimizeHCP.SimOverlapParam
 
exponentN - Variable in class etomica.normalmode.SimBennet.SimBennetParam
 
exponentN - Variable in class etomica.normalmode.SimEinStep1.SimOverlapParam
 
exponentN - Variable in class etomica.normalmode.SimEinStep1HCP.SimOverlapParam
 
exponentN - Variable in class etomica.normalmode.SimEinStep2.SimOverlapParam
 
exponentN - Variable in class etomica.normalmode.SimEinStep2HCP.SimOverlapParam
 
exponentN - Variable in class etomica.normalmode.SimHarmonicUmbrella.SimBennetParam
 
exponentN - Variable in class etomica.normalmode.SimOverlapSoftSphere.SimOverlapParam
 
exponentN - Variable in class etomica.normalmode.SimOverlapSoftSphereDP.SimOverlapParam
 
exponentN - Variable in class etomica.normalmode.SimOverlapSoftSphereEin.SimOverlapParam
 
exponentN - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm.SimOverlapParam
 
exponentN - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP.SimOverlapParam
 
exponentN - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting.SimOverlapParam
 
exponentN - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness.SimOverlapParam
 
exponentN - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox.SimOverlapParam
 
exponentN - Variable in class etomica.normalmode.SimOverlapSoftSphereTP.SimOverlapParam
 
exponentN - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP.SimOverlapParam
 
exponentN - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox.SimOverlapParam
 
exponentN - Variable in class etomica.normalmode.SimOverlapSSnxy.SimOverlapParam
 
exponentN - Variable in class etomica.normalmode.SimTargetUmbrella.SimBennetParam
 
exponentN - Variable in class etomica.normalmode.SimUmbrella.SimBennetParam
 
exponentN - Variable in class etomica.normalmode.SimUmbrellaSoftSphere.SimBennetParam
 
externalMeter - Variable in class etomica.models.hexane.MCMoveCBMC
 
ExternalVirialDiagrams - Class in etomica.virial.cluster
 
ExternalVirialDiagrams(int, boolean, boolean, boolean) - Constructor for class etomica.virial.cluster.ExternalVirialDiagrams
 
extraFile - Variable in class etomica.virial.simulations.VirialSQWBinMultiRecalcW.VirialHSParam
 
extraTargetClusters - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
 

F

f(double[]) - Method in class etomica.conjugategradient.DerivativeEnergyFunction
 
f(double[]) - Method in class etomica.conjugategradient.FiniteDifferenceDerivativeCG
 
f(double[]) - Method in class etomica.conjugategradient.TestFiniteDifferenceDerivative
 
f(double[]) - Method in class etomica.conjugategradient.TestNonLinearConjugateGradients
 
F - Variable in class etomica.dimer.IntegratorDimerRT
 
f(int) - Method in interface etomica.normalmode.CoordinateDefinitionHSDimer.IntegerFunction
 
f - Variable in class etomica.normalmode.LJVacancyMin.VectorForce
 
f - Variable in class etomica.normalmode.SimEinStep1.SimOverlapParam
 
f - Variable in class etomica.normalmode.SimEinStep1HCP.SimOverlapParam
 
f - Variable in class etomica.normalmode.SimEinStep2.SimOverlapParam
 
f - Variable in class etomica.normalmode.SimEinStep2HCP.SimOverlapParam
 
f(double[]) - Method in class etomica.paracetamol.NumericalDerivativeEnergyParacetamol
 
f - Variable in class etomica.virial.cluster.CondenseExchange.CondenseExchangeParameters
 
f - Variable in class etomica.virial.ClusterChainHS
 
f - Variable in class etomica.virial.ClusterChainSoft
 
f - Variable in class etomica.virial.ClusterSinglyConnected
 
f - Variable in class etomica.virial.ClusterSum
 
f(IMoleculeList, double, double) - Method in class etomica.virial.ClusterSumIC.FR2
 
f - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct
 
f - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
 
f - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
 
f - Variable in class etomica.virial.ClusterTree
 
f - Variable in class etomica.virial.ClusterWheatleyHS
 
f - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
 
f - Variable in class etomica.virial.ClusterWheatleySoft
 
f - Variable in class etomica.virial.ClusterWheatleySoftBD
 
f - Variable in class etomica.virial.ConfigurationClusterAceticAcid
 
f(IMoleculeList, double, double) - Method in class etomica.virial.MayerD2FDT2Spherical
 
f(IMoleculeList, double, double) - Method in class etomica.virial.MayerDFDTSpherical
 
f(IMoleculeList, double, double) - Method in class etomica.virial.MayerDFQFHDTSpherical
 
f(IMoleculeList, double, double) - Method in class etomica.virial.MayerEGeneral
 
f(IMoleculeList, double, double) - Method in class etomica.virial.MayerEHardSphere
 
f(IMoleculeList, double, double) - Method in class etomica.virial.MayerENonGeneral
 
f(IMoleculeList, double, double) - Method in class etomica.virial.MayerESpherical
 
f(IMoleculeList, double, double) - Method in interface etomica.virial.MayerFunction
returns Mayer function between atoms in the pair at temperature 1/beta
f(IMoleculeList, double[], double) - Method in interface etomica.virial.MayerFunctionNonAdditive
returns exp(-beta*(U - Upair)) r2 is listed in the order (0,1),(0,2)...(0,n-1),(1,2),(1,3)...(1,n-1)...(n-2,n-1)
f(IMoleculeList, int, int[], double[], double) - Method in interface etomica.virial.MayerFunctionNonAdditive
returns exp(-beta*(U - Upair)) This method allows an implementation to operate on distances and indices instead of molecules.
f(IMoleculeList, double[], double) - Method in class etomica.virial.MayerFunctionNonAdditiveFull
returns exp(-beta*(U - Upair)) r2 is listed in the order (0,1),(0,2)...(0,n-1),(1,2),(1,3)...(1,n-1)...(n-2,n-1)
f(IMoleculeList, int, int[], double[], double) - Method in class etomica.virial.MayerFunctionNonAdditiveFull
returns exp(-beta*(U - Upair)) This method allows an implementation to operate on distances and indices instead of molecules.
f(IMoleculeList, double, double) - Method in class etomica.virial.MayerFunctionProductGeneral
 
f(IMoleculeList, double, double) - Method in class etomica.virial.MayerFunctionSum
 
f(IMoleculeList, double, double) - Method in class etomica.virial.MayerFunctionSumGeneral
 
f(IMoleculeList, double, double) - Method in class etomica.virial.MayerFunctionTemperature
 
f(IMoleculeList, double[], double) - Method in class etomica.virial.MayerFunctionThreeBody
 
f(IMoleculeList, int, int[], double[], double) - Method in class etomica.virial.MayerFunctionThreeBody
 
f(IMoleculeList, double, double) - Method in class etomica.virial.MayerGeneral
 
f(IMoleculeList, double, double) - Method in class etomica.virial.MayerGeneralAtomic
 
f(IMoleculeList, double, double) - Method in class etomica.virial.MayerGeneralSpherical
 
f(IMoleculeList, double, double) - Method in class etomica.virial.MayerHardSphere
 
f(IMoleculeList, double, double) - Method in class etomica.virial.MayerPTAtt
 
f(IMoleculeList, double, double) - Method in class etomica.virial.MayerPUGeneral
 
f(IMoleculeList, double, double) - Method in class etomica.virial.MayerSphericalPlus
 
f(IMoleculeList, double, double) - Method in class etomica.virial.MayerSphericalPTAtt
 
f(IMoleculeList, double, double) - Method in class etomica.virial.MayerSSSeries
 
f(IMoleculeList, double, double) - Method in class etomica.virial.MayerWell
 
f(IMoleculeList, double, double) - Method in class etomica.virial.MayerXSpherical
 
f(IMoleculeList, double, double) - Method in class etomica.virial.MuFGeneral
 
f(IMoleculeList, double, double) - Method in class etomica.virial.MuGeneral
 
F0 - Variable in class etomica.dimer.IntegratorDimerMin
 
F1 - Variable in class etomica.dimer.IntegratorDimerRT
 
f1 - Variable in class etomica.normalmode.MeterSolidProps
 
f1 - Variable in class etomica.normalmode.MeterSolidPropsLJ
 
f1 - Variable in class etomica.normalmode.PotentialCalculationEFSSP
 
f1 - Variable in class etomica.normalmode.PotentialCalculationLJSP
 
f1 - Variable in class etomica.virial.ClusterWheatleyExtendSW
 
f12 - Variable in class etomica.virial.ClusterSumIC
 
F1perp - Variable in class etomica.dimer.IntegratorDimerRT
 
F1star - Variable in class etomica.dimer.IntegratorDimerRT
 
F2 - Variable in class etomica.dimer.IntegratorDimerRT
 
f2 - Variable in class etomica.normalmode.MeterSolidProps
 
f2 - Variable in class etomica.normalmode.MeterSolidPropsLJ
 
f2 - Variable in class etomica.virial.ConfigurationClusterAceticAcid
 
F2perp - Variable in class etomica.dimer.IntegratorDimerRT
 
F2star - Variable in class etomica.dimer.IntegratorDimerRT
 
f3 - Variable in class etomica.virial.ConfigurationClusterAceticAcid
 
fA - Variable in class etomica.virial.ClusterSumHS
 
fA - Variable in class etomica.virial.ClusterWheatleyExtendSW
 
fA - Variable in class etomica.virial.ClusterWheatleyHS
 
fA - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
 
fA - Variable in class etomica.virial.ClusterWheatleySoft
 
fA - Variable in class etomica.virial.ClusterWheatleySoftBD
 
fAB - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
 
fABList - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
 
fABValues - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
 
fac - Variable in class etomica.virial.MCMoveClusterRingPartialRegrow
 
fac - Variable in class etomica.virial.MCMoveClusterRingRegrow
 
fac - Variable in class etomica.virial.MCMoveClusterRingRegrowExchange
 
fac - Variable in class etomica.virial.MCMoveClusterRingScale
 
fac1 - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
 
fac1 - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
 
fac10 - Static variable in class etomica.virial.MCMoveClusterAtomHSRing
 
fac2 - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
 
fac2 - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
 
fac3 - Static variable in class etomica.virial.MCMoveClusterAtomHSRing
 
fac4 - Static variable in class etomica.virial.MCMoveClusterAtomHSRing
 
fac5 - Static variable in class etomica.virial.MCMoveClusterAtomHSRing
 
fac6 - Static variable in class etomica.virial.MCMoveClusterAtomHSRing
 
fac7 - Static variable in class etomica.virial.MCMoveClusterAtomHSRing
 
fac8 - Static variable in class etomica.virial.MCMoveClusterAtomHSRing
 
fac9 - Static variable in class etomica.virial.MCMoveClusterAtomHSRing
 
factOrder - Variable in class etomica.virial.MayerPTAtt
 
factOrder - Variable in class etomica.virial.MayerSphericalPTAtt
 
FACTORY - Static variable in class etomica.virial.paralleltempering.MCMoveSwapCluster
 
fAList - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
 
fancyMove - Variable in class etomica.normalmode.HSDimerNPT.HSMD3DParameters
 
fancyMove - Variable in class etomica.normalmode.HSNPT.HSMD3DParameters
 
fAValues - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
 
fB - Variable in class etomica.virial.ClusterSumHS
 
fB - Variable in class etomica.virial.ClusterWheatleyExtendSW
 
fB - Variable in class etomica.virial.ClusterWheatleyHS
 
fB - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
 
fB - Variable in class etomica.virial.ClusterWheatleySoft
 
fB - Variable in class etomica.virial.ClusterWheatleySoftBD
 
fBond - Variable in class etomica.virial.cluster.MayerIonicDiagram1qbond
 
fBond - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
 
fBond - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
 
fBond - Variable in class etomica.virial.cluster.VirialDiagrams
 
fBond - Variable in class etomica.virial.cluster.VirialDiagramsMix
 
fBond - Variable in class etomica.virial.cluster.VirialDiagramsMix2
 
fBond - Variable in class etomica.virial.cluster.VirialDiagramsPT
 
fBond - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
 
fBond - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
 
fBond - Variable in class etomica.virial.PYGenerator.IteratorEF
 
fC - Variable in class etomica.virial.ClusterSumHS
 
fC - Variable in class etomica.virial.ClusterWheatleyExtendSW
 
fC - Variable in class etomica.virial.ClusterWheatleyHS
 
fC - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
 
fC - Variable in class etomica.virial.ClusterWheatleySoft
 
fC - Variable in class etomica.virial.ClusterWheatleySoftBD
 
FCC - Static variable in class etomica.normalmode.SoftSphereSolidEOS
 
FCC - Static variable in class etomica.normalmode.SoftSphereSolidEOSCalculator
 
fCList - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
 
fe - Variable in class etomica.normalmode.MeterSolidPropsLJ
 
fe - Variable in class etomica.normalmode.PotentialCalculationLJSP
 
fee - Variable in class etomica.normalmode.MeterSolidPropsLJ
 
fee - Variable in class etomica.normalmode.PotentialCalculationLJSP
 
Feff - Variable in class etomica.dimer.IntegratorDimerRT
 
Feffstar - Variable in class etomica.dimer.IntegratorDimerRT
 
FerrenbergSwendsen - Class in etomica.densityofstate
 
FerrenbergSwendsen() - Constructor for class etomica.densityofstate.FerrenbergSwendsen
 
fExchange - Variable in class etomica.virial.cluster.CondenseExchange.CondenseExchangeParameters
 
ffBond - Variable in class etomica.virial.cluster.VirialDiagrams
 
ffBond - Variable in class etomica.virial.cluster.VirialDiagramsPT
 
ffr - Variable in class etomica.virial.CalcFFT
 
fFunction - Variable in class etomica.conjugategradient.DerivativeEnergyFunction
 
field - Variable in class etomica.spin.Heisenberg
 
file - Variable in class etomica.dimer.IntegratorDimerMin
 
file - Variable in class etomica.dimer.IntegratorDimerRT
 
file - Variable in class etomica.virial.simulations.VirialHePI_PotentialCorrection.VirialHePIParam
 
filename - Variable in class etomica.normalmode.HarmonicCrystalSsFccNxy.Params
 
filename - Variable in class etomica.normalmode.SimBennet.SimBennetParam
 
filename - Static variable in class etomica.normalmode.SimFluidSoftSphere
 
filename - Variable in class etomica.normalmode.SimHarmonicUmbrella.SimBennetParam
 
filename - Variable in class etomica.normalmode.SimOverlap.SimOverlapParam
 
filename - Variable in class etomica.normalmode.SimOverlapLJ.SimOverlapParam
 
filename - Variable in class etomica.normalmode.SimOverlapLJModule.SimOverlapParam
 
filename - Variable in class etomica.normalmode.SimOverlapSoftSphere.SimOverlapParam
 
filename - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP.SimOverlapParam
 
filename - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting.SimOverlapParam
 
filename - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox.SimOverlapParam
 
filename - Variable in class etomica.normalmode.SimOverlapSSnxy.SimOverlapParam
 
filename - Variable in class etomica.normalmode.SimTargetUmbrella.SimBennetParam
 
filename - Variable in class etomica.normalmode.SimUmbrella.SimBennetParam
 
filename - Variable in class etomica.normalmode.SimUmbrellaSoftSphere.SimBennetParam
 
filename - Variable in class etomica.normalmode.WriteS
 
fileWriter - Variable in class etomica.dimer.IntegratorDimerMin
 
fileWriter - Variable in class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage
 
fillArrays() - Method in class etomica.zeolite.MSDProcessor
 
fillNeighborListArray(int, int, NeighborListManager, IBox) - Method in class etomica.threaded.atom.PotentialMasterListWorker
 
findcf(double, double, double) - Method in class etomica.normalmode.MinimizeHCP
 
findDensityatP(double, int, int, double) - Method in class etomica.normalmode.SoftSphereSolidEOS
 
findMaxScore(boolean, ClusterDiagram, int[]) - Static method in class etomica.virial.cluster.ClusterGenerator
Determines whether any cluster permuted from the given one by exchanging points from startPoint to stopPoint (inclusive) has a higher score than that passed in.
findOppositeAtomIndex(IAtom, IAtomList) - Method in class etomica.normalmode.P1ConstraintNbr
find atom in list that is opposite atomi from atomj (as defined by drj)
findTransP(int, int, int, double, int) - Method in class etomica.normalmode.SoftSphereSolidEOS
 
finished - Variable in class etomica.threaded.atom.PotentialMasterListWorker
 
finished - Variable in class etomica.threaded.domain.PotentialMasterListWorker
 
finiteDifferenceDerivative - Variable in class etomica.paracetamol.NumericalDerivativeEnergyParacetamol
 
FiniteDifferenceDerivativeCG - Class in etomica.conjugategradient
 
FiniteDifferenceDerivativeCG(IBox, PotentialMaster, AnalyticalDerivativeEnergyParacetamol, ISpace) - Constructor for class etomica.conjugategradient.FiniteDifferenceDerivativeCG
 
FiniteDifferenceDerivativeCG.MyAgentSource - Class in etomica.conjugategradient
 
firstDerivative - Variable in class etomica.virial.simulations.VirialHePCKLJSTempDeriv.VirialParam
 
fivea - Static variable in class etomica.virial.ConformationPhenanthreneTraPPE
 
fixed - Variable in class etomica.dimer.PotentialCalculationForcePressureSumGB
 
fixed - Variable in class etomica.dimer.SimDimerLJadatom
 
fixed - Variable in class etomica.dimer.SimDimerLJgb
 
fixed - Variable in class etomica.dimer.SimDimerMEAMadatom
 
fixed - Variable in class etomica.dimer.SimDimerMEAMGB
 
fixedCOM - Variable in class etomica.normalmode.MCMoveEinsteinCrystal
 
fixedDaDef - Variable in class etomica.normalmode.SimLJVacancy.LJParams
 
fixedLatticeVector - Variable in class etomica.models.hexane.PrimitiveHexane
 
fixedSizes - Variable in class etomica.models.hexane.PrimitiveHexane
 
fixOverlap - Variable in class etomica.models.hexane.MCMoveReptate
 
fk - Variable in class etomica.virial.CalcFFT
 
fL - Variable in class etomica.virial.ClusterSinglyConnected
 
flex - Variable in class etomica.normalmode.SimOverlapSoftSphereTP.SimOverlapParam
 
flex - Variable in class etomica.virial.cluster.MayerIonicDiagram1qbond
 
flex - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
 
flex - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
 
flex - Variable in class etomica.virial.cluster.VirialDiagrams
 
flex - Variable in class etomica.virial.cluster.VirialDiagramsMix
 
flex - Variable in class etomica.virial.cluster.VirialDiagramsMix2
 
flex - Variable in class etomica.virial.cluster.VirialDiagramsPT
 
flex - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
 
flex - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
 
flex - Variable in class etomica.virial.simulations.VirialAlkaneFlex.VirialSiepmannSpheresParam
 
flexApproach - Variable in class etomica.virial.simulations.VirialHePI.VirialHePIParam
 
flexCancelOnly - Variable in class etomica.virial.cluster.VirialDiagrams
 
flexCancelOnly - Variable in class etomica.virial.cluster.VirialDiagramsPT
 
flexColors - Variable in class etomica.virial.cluster.VirialDiagrams
 
flexColors - Variable in class etomica.virial.cluster.VirialDiagramsMix
 
flexColors - Variable in class etomica.virial.cluster.VirialDiagramsMix2
 
flexColors - Variable in class etomica.virial.cluster.VirialDiagramsPT
 
flexID - Variable in class etomica.virial.simulations.VirialCH4AlkaneEHMix.VirialMixParam
 
flexID - Variable in class etomica.virial.simulations.VirialCO2AlkaneEHMix.VirialMixParam
 
flexID - Variable in class etomica.virial.simulations.VirialCO2AlkaneUAMix.VirialMixParam
 
flexID - Variable in class etomica.virial.simulations.VirialN2AlkaneEHMix.VirialMixParam
 
flexID - Variable in class etomica.virial.simulations.VirialN2AlkaneUAMix.VirialMixParam
 
flexID - Variable in class etomica.virial.simulations.VirialSF6LJAlkaneUAMix.VirialMixParam
 
flexOnlyTerm - Variable in class etomica.virial.simulations.VirialAceticAcidFlex.VirialParam
 
flip(IMolecule) - Method in class etomica.virial.ClusterCoupledAtomFlipped
 
flip(IMolecule) - Method in class etomica.virial.ClusterCoupledFlipped
 
flipList - Variable in class etomica.virial.ClusterCoupledFlippedPartial
 
flippedAtoms - Variable in class etomica.virial.ClusterCoupledFlipped
 
flippedAtoms - Variable in class etomica.virial.ClusterCoupledFlippedPartial
 
fLN - Variable in class etomica.virial.ClusterSinglyConnected
 
fluctuationFactor - Variable in class etomica.normalmode.HSNPT.ColorSchemeDisplacement
 
fluctuationFromAvg - Variable in class etomica.normalmode.HSNPT.ColorSchemeDisplacement
 
fluid - Variable in class etomica.normalmode.SimHSMDVacancy.HSMDVParams
 
fMap - Variable in class etomica.virial.ClusterWheatleySoftBDMix
 
fMap - Variable in class etomica.virial.ClusterWheatleySoftMix
 
fMap3 - Variable in class etomica.virial.ClusterWheatleyMultibodyMix
 
fmBond - Variable in class etomica.virial.cluster.VirialDiagrams
 
fmBond - Variable in class etomica.virial.cluster.VirialDiagramsPT
 
Fmin - Variable in class etomica.dimer.IntegratorDimerMin
 
Fmin2 - Variable in class etomica.dimer.IntegratorDimerMin
 
Fmin2perp - Variable in class etomica.dimer.IntegratorDimerMin
 
Fmin2star - Variable in class etomica.dimer.IntegratorDimerMin
 
Fminperp - Variable in class etomica.dimer.IntegratorDimerMin
 
Fminstar - Variable in class etomica.dimer.IntegratorDimerMin
 
fMulti - Variable in class etomica.virial.ClusterWheatleyMultibody
 
fMulti - Variable in class etomica.virial.ClusterWheatleyMultibodyBD
 
fname - Variable in class etomica.normalmode.SimOverlapSoftSphere
 
fname - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
 
fname - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting
 
fname - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
 
fname - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox
 
fname - Variable in class etomica.normalmode.SimOverlapSSnxy
 
fNonAdditive - Variable in class etomica.virial.ClusterSumMultibody
 
fNonAdditive - Variable in class etomica.virial.ClusterWheatleyMultibody
 
fNonAdditive - Variable in class etomica.virial.ClusterWheatleyMultibodyBD
 
fNonAdditiveNeeded - Variable in class etomica.virial.ClusterSumMultibody
 
fNonAdditiveValues - Variable in class etomica.virial.ClusterSumMultibody
 
fOld - Variable in class etomica.virial.ClusterSum
 
fOld - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct
 
fOld - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
 
fOld - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
 
fOld - Variable in class etomica.virial.ClusterTree
 
foo - Static variable in class etomica.virial.MCMoveClusterDiagram
 
foo2 - Static variable in class etomica.virial.MCMoveClusterDiagram
 
force() - Method in class etomica.normalmode.LJVacancyMin.VectorForce
 
force0 - Variable in class etomica.dimer.IntegratorDimerMin
 
force0 - Variable in class etomica.dimer.IntegratorDimerRT
 
force1 - Variable in class etomica.dimer.IntegratorDimerRT
 
force2 - Variable in class etomica.dimer.IntegratorDimerRT
 
forceManager - Variable in class etomica.normalmode.MeterDADB
 
forceManager - Variable in class etomica.normalmode.MeterSolidProps
 
forceManager - Variable in class etomica.normalmode.MeterSolidPropsLJ
 
forceMin - Variable in class etomica.dimer.IntegratorDimerMin
 
forceSum - Variable in class etomica.conjugategradient.DerivativeEnergyFunction
 
forceSum - Variable in class etomica.conjugategradient.FiniteDifferenceDerivativeCG
 
foura - Static variable in class etomica.virial.ConformationPhenanthreneTraPPE
 
FourAssociationSitesFluid2Pt - Class in etomica.virial.simulations
Wertheim 2 point diagram simulation using Mayer sampling for four association sites model
FourAssociationSitesFluid2Pt() - Constructor for class etomica.virial.simulations.FourAssociationSitesFluid2Pt
 
FourAssociationSitesFluid2Pt.VirialAssociatingFluidParam - Class in etomica.virial.simulations
 
fourierMul(Graph, Graph, byte) - Static method in class etomica.virial.IEGenerator
 
foursqrt3a - Static variable in class etomica.virial.ConformationAnthraceneTraPPE
 
foursqrt3a - Static variable in class etomica.virial.ConformationPhenanthreneTraPPE
 
Fpara - Variable in class etomica.dimer.IntegratorDimerMin
 
Fpara - Variable in class etomica.dimer.IntegratorDimerRT
 
Fperp - Variable in class etomica.dimer.IntegratorDimerMin
 
Fperp - Variable in class etomica.dimer.IntegratorDimerRT
 
Fperplast - Variable in class etomica.dimer.IntegratorDimerRT
 
fPrime - Variable in class etomica.conjugategradient.DerivativeEnergyFunction
 
fPrime - Variable in class etomica.paracetamol.NumericalDerivativeEnergyParacetamol
 
Fprimerot - Variable in class etomica.dimer.IntegratorDimerMin
 
Fprimerot - Variable in class etomica.dimer.IntegratorDimerRT