a BenchNbrUpdates
a P1LepsHarmonic
a P2EAM
a PotentialEAM_LS
a PotentialEAM
a PadeApproximation
a CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
a CalcNumerical2ndDerivative
a CalcNumerical2ndDerivativeNitrogen
a FiniteDifferenceDerivativeCGNitrogenBeta
a MinimizeGammaNitrogenLatticeParameter
a P2Water4PSoft
a IntegratorPolymer
a P2HePCKLJS
a P2HSDipole
a P2LJDipole
a P2ReactionFieldDipole
a PotentialCalculationPhiSum
a HardSphereFluid
a Euler
a PartitionsP
The list of all partitions as a vector.
a ConformationAnthraceneTraPPE
a ConformationPhenanthreneTraPPE
a MCMoveClusterAtomHSTree
a MCMoveClusterPolyhedraTree
A P2CO2Hellmann.Parameters
A PotentialCuLREP
A PotentialEFS
A P2CO2Hellmann
A PNWaterGCPM
A PNWaterGCPMReactionField
A P2HePCKLJS
A P2NitrogenHellmann
A P3CPSNonAdditiveHe
A P3CPSNonAdditiveHeLessSimplified
A P3CPSNonAdditiveHeOrig
A P3CPSNonAdditiveHeSimplified
A P3HydrogenManzhos
A(double) EOSSWPatel
a_AD P2HePCJS
a_BO P2HePCJS
a_QED P2HePCJS
a_REL P2HePCJS
a0 PotentialEAM_LS
a0 Potential2SoftSphericalLSMulti
a0 Potential2SoftSphericalLSMultiLat
a0 ClathrateHarmonicFE.SimParams
a0 MinimizationTIP4P.SimParams
a0 ProtonDisorderGenerator.SimParams
a0 P2WaterPotentialsJankowski
a0 P4BondTorsion
a0 P4BondTorsionAlkaneXCCH
a0 Potential2SoftSphericalLS
A0 P2HeSimplified
A0 HardSphereSolid
a1 P2QChemInterpolated
a1 P2QChemInterpolated.DampingParams
a1 P3AdditiveQChem.DampingParams
a1 P3QChem.DampingParams
a1 P4BondTorsion
a1 P4BondTorsionAlkaneXCCH
a1 B3ForSphericallySymmetricU.DampingParams
A1 P1LepsHarmonic
A1 P2Nitrogen
A1 P2NitrogenAB
A1 P2NitrogenAnisotropic
A1 P2HeSimplified
A1(double) EOSSWPatel
a2 P2EAM
a2 P2QChemInterpolated
a2 P2QChemInterpolated.DampingParams
a2 P3AdditiveQChem.DampingParams
a2 P3QChem.DampingParams
a2 P4BondTorsion
a2 P4BondTorsionAlkaneXCCH
a2 B3ForSphericallySymmetricU.DampingParams
A2 P1LepsHarmonic
A2 P2Nitrogen
A2 P2NitrogenAB
A2 P2NitrogenAnisotropic
A2 P2HeSimplified
a3 P4BondTorsion
a3 P4BondTorsionAlkaneXCCH
A3 P2HeSimplified
AA P2CO2Hellmann
AA P2NitrogenHellmann
AAbonded ReactionEquilibrium
AAlphaFunction(int, double) FindTransitionTemperature
aam DisplayBoxCanvasG3DSys
aamOriented DisplayBoxCanvasG3DSys
AandPAlpha(double, double) FindTransitionTemperature
AandPBeta(double, double) FindTransitionTemperature
ab PrimitiveHexagonal
ab PrimitiveHexagonal2D
AB P2CO2Hellmann
AB P2NitrogenHellmann
ABbonded ChainEquilibriumSim
ABbonded ReactionEquilibrium
ABetaFunction(int, double) FindTransitionTemperature
abicipeso4(double, double, double, double) P2O2Bartolomei
AbnormalCompletionException etomica.exception
Exception that indicates a method is defined for a class (perhaps to adhere
to an interface), but its implementation is not yet completed.
AbnormalCompletionException() AbnormalCompletionException
Constructor for AbnormalCompletionException
AbnormalCompletionException(String) AbnormalCompletionException
Constructor for MethodNotImplementedException.
aBonds VirialDiagramsPT
AboutBoxWindow etomica.graphics
AboutBoxWindow(Component) AboutBoxWindow
AboutBoxWindow(Component, String) AboutBoxWindow
AboutBoxWindow(Component, String, String[], String[]) AboutBoxWindow
abParams MaxIsomorphWertheim.MaxIsomorphWertheimParameters
abs() BigSurd
Absolute value.
abs() Rational
Absolute value.
Abs() Function.Abs
AbstractBitmap etomica.graph.model.impl
AbstractBitmap() AbstractBitmap
AbstractLattice T > - Interface in etomica.lattice
Interface for a generic lattice, which is a collection of sites that can be
accessed individually via specification of a set of integers.
AbstractOptionHandler() Main.AbstractOptionHandler
AbstractSearchState etomica.graph.isomorphism
AbstractSearchState() AbstractSearchState
AbstractSearchState(Graph, Graph) AbstractSearchState
AbstractTraversal etomica.graph.traversal
AbstractTraversal() AbstractTraversal
ac DataProcessorBounds
ac DataProcessorVar
aC EnumSiteName
acc GlassGraphic.SFacButtonAction
acc MultiharmonicGraphicMC.DataSourceBias
acc DataAccDiffCorrectedPusher
acc DataAccDifficultyPusher
acc DataAccSamplesPusher
acc DataOverlap.DataSourceOverlapAvgSimple
accept(IAtomList) ApiFilteredCylinder.AtomFilterInCylinder
accept(IAtom, IAtom) ColloidSim.CriterionNone
accept(IAtom, IAtom) CriterionTether3
accept(IAtom, IAtom) CriterionAdapter
Implementation of this method should introduce new criterion and return
true if pair meets this criterion and that of the wrapped
NeighborCriterion.
accept(IAtom, IAtom) CriterionAll
Always returns true, indicating that all atoms pairs are neighbors.
accept(IAtom, IAtom) CriterionBondedSimple
accept(IAtom, IAtom) CriterionInterMolecular
accept(IAtom, IAtom) CriterionNone
Always returns false, indicating that no atoms pairs are neighbors.
accept(IAtom, IAtom) CriterionPositionWall
accept(IAtom, IAtom) CriterionSimple
accept(IAtom, IAtom) NeighborCriterion
accept(Graph) FieldNodeCount
accept(Graph) LocalFilter
accept(Graph) PropertyFilter
accept(Graph, Set<Graph>) GlobalFilter
accept(Graph, Set<Graph>) IdenticalGraphFilter
accept(Graph, Set<Graph>) IsomorphismFilter
accept(IMoleculeList) CriterionAdapterMolecular
Implementation of this method should introduce new criterion and return
true if pair meets this criterion and that of the wrapped
NeighborCriterion.
accept(IMoleculeList) CriterionAllMolecular
Always returns true, indicating that all atoms pairs are neighbors.
accept(IMoleculeList) CriterionSimpleMolecular
accept(IMoleculeList) CriterionSpecies
Returns true if the species of the molecule matches the Species given at
construction and if the wrapped criterion accept also returns true.
accept(IMoleculeList) CriterionSpeciesPair
Returns true if the Species for the pair of molecules match the Species
given at construction (without regard to the order of the pair), and if
the wrapped criterion also accepts the pair.
accept(IMoleculeList) NeighborCriterionMolecular
accept(File) SVGConverter.SVGFileFilter
acceptanceProbability() MCMoveTracker
Returns the average probability of accepting the move associated with
this tracker.
acceptanceRatio() MCMoveTracker
Returns the fraction of accepted trials of the move associated with
this tracker.
acceptanceTarget MCMoveStepTracker
acceptNotify() MCMoveBiasUB
acceptNotify() MCMoveBiasUBMolecule
acceptNotify() MCMoveDimer
Method called by IntegratorMC in the event that the most recent trial is accepted.
acceptNotify() MCMoveDimerRotate
Method called by IntegratorMC in the event that the most recent trial is accepted.
acceptNotify() MCMoveSmer
Method called by IntegratorMC in the event that the most recent trial is accepted.
acceptNotify() MCMoveSmerRotate
Method called by IntegratorMC in the event that the most recent trial is accepted.
acceptNotify() MCMoveVolumeAssociated
acceptNotify() MCMoveVolumeAssociatedMolecule
acceptNotify() MyMCMove
acceptNotify() MCMoveAtomCoupled
Method called by IntegratorMC in the event that the most recent trial is accepted.
acceptNotify() MCMoveAtomSwap
Method called by IntegratorMC in the event that the most recent trial is accepted.
acceptNotify() MCMove
Method called by IntegratorMC in the event that the most recent trial is
accepted.
acceptNotify() MCMoveAtom
acceptNotify() MCMoveBoxSize
acceptNotify() MCMoveDimer
Method called by IntegratorMC in the event that the most recent trial is accepted.
acceptNotify() MCMoveDimerRotate
Method called by IntegratorMC in the event that the most recent trial is accepted.
acceptNotify() MCMoveInsertDelete
acceptNotify() MCMoveInsertDeleteBiased
acceptNotify() MCMoveMolecule
Method called by IntegratorMC in the event that the most recent trial is accepted.
acceptNotify() MCMoveMoleculeExchange
acceptNotify() MCMoveSemigrand
acceptNotify() MCMoveSwapConfiguration
Swaps positions of molecules in two boxes.
acceptNotify() MCMoveVolume
acceptNotify() MCMoveVolumeExchange
acceptNotify() MCMoveMoleculeCoupledInitPert
acceptNotify() MCMoveMoleculeCoupledSuperBox
acceptNotify() MCMoveRotateMolecule3DN2AveCosThetaConstraint
acceptNotify() MCMoveVolumeN2
acceptNotify() MyMCMove
acceptNotify() MyMCMove
acceptNotify() MCMoveSwap
acceptNotify() MCMoveMultiHarmonic
acceptNotify() MCMoveAtomCoupled
Method called by IntegratorMC in the event that the most recent trial is accepted.
acceptNotify() MCMoveAtomCoupledBennet
Method called by IntegratorMC in the event that the most recent trial is accepted.
acceptNotify() MCMoveAtomCoupledUmbrella
Method called by IntegratorMC in the event that the most recent trial is accepted.
acceptNotify() MCMoveAtomSuperBox
Method called by IntegratorMC in the event that the most recent trial is accepted.
acceptNotify() MCMoveEinsteinCrystal
acceptNotify() MCMoveHarmonic
acceptNotify() MCMoveHarmonicStep
acceptNotify() MCMoveMoleculeCoupled
acceptNotify() MCMovePhaseAngle
acceptNotify() MCMoveRotateMoleculePhiTheta
acceptNotify() MCMoveSingleMode
acceptNotify() MCMoveVolumeMonoclinic
acceptNotify() MCMoveVolumeMonoclinicAngle
acceptNotify() MCMoveVolumeMonoclinicScaled
acceptNotify() MCMoveVolumeSolid
acceptNotify() MCMoveVolumeSolidNPTMolecular
acceptNotify() MCMoveVolumeSolidNPTMolecularOriented
acceptNotify() MCMoveWV
acceptNotify() MCMoveGeometricCluster
acceptNotify() MCMoveGeometricClusterRestrictedGE
acceptNotify() MCMoveSpinCluster
acceptNotify() MCMoveSpinFlip
acceptNotify() MCMoveBondLength
acceptNotify() MCMoveClusterBondLength
acceptNotify() MCMoveClusterConformationMDTest
acceptNotify() MCMoveClusterMoleculeHSChain
acceptNotify() MCMoveClusterMoleculeHSChainB3
acceptNotify() MCMoveClusterRotateArm
acceptNotify() MCMoveRotateArm
acceptNotify() BoxCluster
Informs the box that the trial was accepted so it will keep the new
coordinate pairs.
acceptNotify() MCMoveChangeBondLength
acceptNotify() MCMoveClusterAngleBend
acceptNotify() MCMoveClusterAngleBendAceticAcid
acceptNotify() MCMoveClusterAtom
acceptNotify() MCMoveClusterAtomChainHSTail
acceptNotify() MCMoveClusterAtomDiscrete
acceptNotify() MCMoveClusterAtomHSChain
acceptNotify() MCMoveClusterAtomHSRing
acceptNotify() MCMoveClusterAtomHSTree
acceptNotify() MCMoveClusterAtomInBox
acceptNotify() MCMoveClusterAtomMulti
acceptNotify() MCMoveClusterAtomQ
acceptNotify() MCMoveClusterAtomRotateMulti
acceptNotify() MCMoveClusterDiagram
acceptNotify() MCMoveClusterMolecule
acceptNotify() MCMoveClusterMoleculeHSChain
acceptNotify() MCMoveClusterMoleculeMulti
acceptNotify() MCMoveClusterPolyhedraChain
acceptNotify() MCMoveClusterPolyhedraTree
acceptNotify() MCMoveClusterReptateMulti
acceptNotify() MCMoveClusterRingPartialRegrow
acceptNotify() MCMoveClusterRingRegrow
acceptNotify() MCMoveClusterRingRegrowExchange
acceptNotify() MCMoveClusterRingRegrowOrientation
acceptNotify() MCMoveClusterRingScale
acceptNotify() MCMoveClusterRotateCH3
acceptNotify() MCMoveClusterRotateMolecule3D
acceptNotify() MCMoveClusterRotateMoleculeMulti
acceptNotify() MCMoveClusterTorsionAceticAcid
acceptNotify() MCMoveClusterTorsionAlkaneEH
acceptNotify() MCMoveClusterTorsionMulti
acceptNotify() MCMoveClusterWiggleAceticAcid
acceptNotify() MCMoveClusterWiggleAlkaneEH
acceptNotify() MCMoveClusterWiggleMulti
acceptNotify() MCMoveSwapCluster
Swaps positions of molecules in two boxes.
accRefUa2 MultiharmonicGraphicMC.DataSourceUa2
accTargetUa2 MultiharmonicGraphicMC.DataSourceUa2
accumulator SimOverlapAlphaN2TP
accumulator SimOverlapBetaN2RPScaling
accumulator SimOverlapBetaN2TP
accumulator SimOverlapDisorderedAlphaN2RPScaling
accumulator SimOverlapDisorderedAlphaN2TP
accumulator MultiharmonicMC
accumulator SimOverlapSoftSphereDP
accumulator SimOverlapSoftSphereEin
accumulator SimOverlapSoftSphereTP
accumulator SimOverlapSoftSphereTPHCP
accumulator SimOverlapSoftSphereTPSlantedBox
accumulator SimulationVirial
accumulator1 DCVGCMD
accumulator1 DCVGCMD
accumulator2 DCVGCMD
accumulator2 DCVGCMD
accumulatorAction SimulationRestart
AccumulatorAutocorrelationPTensor etomica.modules.glass
Accumulator designed to compute the unnormalized autocorrelation of the
pressure tensor components, assuming that off-diagonal components average to
0.
AccumulatorAutocorrelationPTensor(int, double) AccumulatorAutocorrelationPTensor
AccumulatorAutocorrelationShearStress etomica.modules.glass
Accumulator designed to compute the normalized autocorrelation of the
shear stress, assuming zero average.
AccumulatorAutocorrelationShearStress(int, double) AccumulatorAutocorrelationShearStress
accumulatorAverage DisplayTextBoxesCAE
AccumulatorAverage etomica.data
Accumulator that keeps statistics for averaging and error analysis.
AccumulatorAverage() AccumulatorAverage
Default constructor sets block size to 1000 and sets the
interval for pushing the output data (pushInterval) to 100.
AccumulatorAverage(long) AccumulatorAverage
Constructs with interval for pushing the output data set to 100.
AccumulatorAverage.StatType etomica.data
Enumerated type that can be used to indicate the statistic to be taken
from the accumulator (e.g., average, error, current value, etc.).
AccumulatorAverageBlockless etomica.data
AccumulatorAverage that does not use blocks (best used when each sample
is independent).
AccumulatorAverageBlockless() AccumulatorAverageBlockless
Default constructor sets block size to Default value, and sets the
interval for pushing the output data (pushInterval) to 100.
AccumulatorAverageBlockless.AllData etomica.data
AccumulatorAverageBlockless.StatType etomica.data
Enumerated type that can be used to indicated the statistic to be taken
from the accumulator (e.g., average, error, current value, etc.).
AccumulatorAverageBlocklessSlim etomica.data
AccumulatorAverage that does not use blocks (best used when each sample
is independent).
AccumulatorAverageBlocklessSlim() AccumulatorAverageBlocklessSlim
AccumulatorAverageBlocklessSlim.StatType etomica.data
Enumerated type that can be used to indicated the statistic to be taken
from the accumulator (e.g., average, error, current value, etc.).
AccumulatorAverageBootstrap etomica.data
AccumulatorAverage that keeps track of block averages and standard
deviations corresponding to all block sizes from 1 to the n where n is the
largest power of 2 less than the current number of samples.
AccumulatorAverageBootstrap() AccumulatorAverageBootstrap
AccumulatorAverageBootstrap(int) AccumulatorAverageBootstrap
With this constructor, the accumulator will use an internal RNG with a
set seed such that each resampling of the data will be identical (the
same set of samples will go into the averages and the standard
deviations, etc).
AccumulatorAverageBootstrap(IRandom) AccumulatorAverageBootstrap
AccumulatorAverageBootstrap(IRandom, int) AccumulatorAverageBootstrap
AccumulatorAverageBootstrap.HistogramFactory etomica.data
AccumulatorAverageCollapsing etomica.data
AccumulatorAverage that adjusts the block size during the simulation.
AccumulatorAverageCollapsing() AccumulatorAverageCollapsing
Default constructor sets the maximum number of blocks (maxBlocks) to a default value of 20,
the initial block size (blockSize) to 1 and the interval for pushing the output data (pushInterval)
to 100.
AccumulatorAverageCollapsing(int) AccumulatorAverageCollapsing
Constructor with default pushInterval of 100 and initial blockSize of 1.
AccumulatorAverageCollapsing(int, int) AccumulatorAverageCollapsing
Constructor with default pushInterval of 100.
AccumulatorAverageCollapsingLog etomica.data
AccumulatorAverage that keeps track of block averages and standard
deviations corresponding to all block sizes from 1 to the n where n is the
largest power of 2 less than the current number of samples.
AccumulatorAverageCollapsingLog() AccumulatorAverageCollapsingLog
AccumulatorAverageCollapsingLog(int) AccumulatorAverageCollapsingLog
With this constructor, the accumulator will use an internal RNG with a
set seed such that each resampling of the data will be identical (the
same set of samples will go into the averages and the standard
deviations, etc).
AccumulatorAverageCollapsingLog(IRandom) AccumulatorAverageCollapsingLog
AccumulatorAverageCollapsingLog(IRandom, int) AccumulatorAverageCollapsingLog
AccumulatorAverageCollapsingLogAB etomica.data
AccumulatorAverageCollapsingLogAB() AccumulatorAverageCollapsingLogAB
AccumulatorAverageCollapsingLogAB(IRandom) AccumulatorAverageCollapsingLogAB
AccumulatorAverageCovariance etomica.data
Class that does the work of AccumulatorAverageFixed and also calculates the
covariance of the incoming data values (the covariance of each value with
each other value, as well as itself (which is actually its standard
deviation)) as well as the covariance of the block averages of the different
data quantities.
AccumulatorAverageCovariance() AccumulatorAverageCovariance
AccumulatorAverageCovariance(boolean) AccumulatorAverageCovariance
AccumulatorAverageCovariance(long) AccumulatorAverageCovariance
AccumulatorAverageCovariance(long, boolean) AccumulatorAverageCovariance
AccumulatorAverageFixed etomica.data
AccumulatorAverage that maintains a fixed block size.
AccumulatorAverageFixed() AccumulatorAverageFixed
Default constructor sets block size to 1000 and sets the
interval for pushing the output data (pushInterval) to 100.
AccumulatorAverageFixed(long) AccumulatorAverageFixed
Constructs with interval for pushing the output data set to 100.
AccumulatorAverageFixedOutputFile etomica.data
AccumulatorAverage that maintains a fixed block size.
AccumulatorAverageFixedOutputFile() AccumulatorAverageFixedOutputFile
Default constructor sets block size to Default value, and sets the
interval for pushing the output data (pushInterval) to 100.
AccumulatorAverageFixedOutputFile(int) AccumulatorAverageFixedOutputFile
AccumulatorCounter etomica.data
Data processor that simply counts the number of times its
addData method is invoked.
AccumulatorCounter() AccumulatorCounter
AccumulatorFactory etomica.modules.statistics
AccumulatorHistogram etomica.data
Accumulator that keeps histogram of data.
AccumulatorHistogram() AccumulatorHistogram
Creates instance using HistogramSimple factory and specifying histograms
having 100 bins.
AccumulatorHistogram(Histogram) AccumulatorHistogram
Creates instance using given histogram factory with default nBins of 100.
AccumulatorHistogram(Histogram, int) AccumulatorHistogram
Creates instance using the given histogram factory making histograms having
the given number of bins.
accumulatorHistory ActionHistoryWindow
AccumulatorHistory etomica.data
Accumulator that keeps history of data.
AccumulatorHistory() AccumulatorHistory
Creates instance using HistorySimple factory and specifying historys
having 100 bins.
AccumulatorHistory(History) AccumulatorHistory
AccumulatorHistory.DataSourceCount etomica.data
Simple DataSource to use as a default time DataSource.
AccumulatorMimicMu etomica.modules.statistics
AccumulatorMimicMu(IntegratorBox) AccumulatorMimicMu
AccumulatorOverlapAverageUa2 etomica.modules.multiharmonic.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
AccumulatorOverlapAverageUa2(int, boolean) AccumulatorOverlapAverageUa2
AccumulatorPTensor etomica.modules.glass
AccumulatorPTensor(IntegratorMD, double) AccumulatorPTensor
AccumulatorPTensor.TemperatureSink etomica.modules.glass
accumulatorPump SimOverlapAlphaN2TP
accumulatorPump SimOverlapBetaN2RPScaling
accumulatorPump SimOverlapBetaN2TP
accumulatorPump SimOverlapDisorderedAlphaN2RPScaling
accumulatorPump SimOverlapDisorderedAlphaN2TP
accumulatorPump SimOverlapSoftSphereDP
accumulatorPump SimOverlapSoftSphereEin
accumulatorPump SimOverlapSoftSphereTP
accumulatorPump SimOverlapSoftSphereTPHCP
accumulatorPump SimOverlapSoftSphereTPSlantedBox
accumulatorPump SimulationVirial
accumulatorPumps SimOverlapBetaN2RP
accumulatorPumps SimOverlapNitrogenModel
accumulatorPumps SimOverlap
accumulatorPumps SimOverlapLJ
accumulatorPumps SimOverlapLJModule
accumulatorPumps SimOverlapModule
accumulatorPumps SimOverlapSoftSphere
accumulatorPumps SimOverlapSoftSphereEinHarm
accumulatorPumps SimOverlapSoftSphereHCP
accumulatorPumps SimOverlapSoftSphereReweighting
accumulatorPumps SimOverlapSoftSphereSoftness
accumulatorPumps SimOverlapSoftSphereSuperBox
accumulatorPumps SimOverlapSSnxy
accumulatorPumps SimulationVirialOverlap2
AccumulatorRatioAverageCovariance etomica.data
Accumulator for calculating ratio between sums.
AccumulatorRatioAverageCovariance() AccumulatorRatioAverageCovariance
AccumulatorRatioAverageCovariance(long) AccumulatorRatioAverageCovariance
AccumulatorRatioAverageCovarianceFull etomica.data
Accumulator for calculating ratio between sums.
AccumulatorRatioAverageCovarianceFull() AccumulatorRatioAverageCovarianceFull
AccumulatorRatioAverageCovarianceFull(long) AccumulatorRatioAverageCovarianceFull
accumulators SimOverlapBetaN2RP
accumulators SimOverlapNitrogenModel
accumulators SimOverlap
accumulators SimOverlapLJ
accumulators SimOverlapLJModule
accumulators SimOverlapSoftSphere
accumulators SimOverlapSoftSphereEinHarm
accumulators SimOverlapSoftSphereHCP
accumulators SimOverlapSoftSphereReweighting
accumulators SimOverlapSoftSphereSoftness
accumulators SimOverlapSoftSphereSuperBox
accumulators SimOverlapSSnxy
accumulators MeterVirialBDBin
accumulators SimulationVirialOverlap2
AccumulatorVirialOverlapSingleAverage 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) AccumulatorVirialOverlapSingleAverage
AccumulatorVirialOverlapSingleAverage(long, int, boolean) AccumulatorVirialOverlapSingleAverage
AceticAcidMCParam() TestAceticAcidMC3D_NPT.AceticAcidMCParam
AceticAcidModPotentialHelper etomica.models.OPLS
PotentialHelper class of acetic acid using improved OPLS (or TraPPE) united atom model
AceticAcidModPotentialHelper() AceticAcidModPotentialHelper
AceticAcidPotentialHelper etomica.models.OPLS
PotentialHelper class of acetic acid using OPLS united atom model
AceticAcidPotentialHelper() AceticAcidPotentialHelper
ACollectionBondedPotential etomica.virial.GUI.components
ACollectionBondedPotential() ACollectionBondedPotential
acos(BigDecimal) BigDecimalMath
The inverse trigonometric cosine.
acosh(BigDecimal) BigDecimalMath
The inverse hyperbolic cosine.
action Grabber.CornerSetListener
ActionConfigWindow etomica.graphics
Action that opens a new window and dumps the coordinates into the window.
ActionConfigWindow(Box) ActionConfigWindow
ActionCornerSetter(Grabber, int) Grabber.ActionCornerSetter
ActionGraphic etomica.graphics
Wrapper of an etomica Action that permits it to be used as a java.awt action listener.
ActionGraphic(IAction) ActionGraphic
ActionGroup etomica.action
An action formed from a set of other actions.
ActionGroupSeries etomica.action
A set of Action instances grouped and performed in series
as if a single action.
ActionGroupSeries() ActionGroupSeries
Constructs an action group that holds no actions.
ActionGroupSeries(IAction[]) ActionGroupSeries
Defines group via the given array of actions.
actionHash DeviceSelector
ActionHistoryWindow etomica.graphics
Action that opens a new window and dumps the coordinates into the window.
ActionHistoryWindow(AccumulatorHistory) ActionHistoryWindow
ActionIntegrate etomica.action
Action that repeatedly invokes an Integrator's doStep method.
ActionIntegrate(Integrator) ActionIntegrate
Constructs activity to generate configurations with
the given integrator.
ActionIntegrate(Integrator, boolean) ActionIntegrate
ActionMinimizeEnergy etomica.action
ActionMinimizeEnergy(Space, int, PotentialMaster, Box) ActionMinimizeEnergy
ActionMinimizeEnergy.MyForceTorque etomica.action
ActionMoveWall(DeviceSlider, Sam, IAction) SamGraphic.ActionMoveWall
actionPerformed() ActionGroupSeries
Invokes all actions in the group, in the order that they were added at construction and
in previous calls to addAction.
actionPerformed() ActionIntegrate
Main loop for conduct of integration.
actionPerformed() ActionMinimizeEnergy
actionPerformed() ActionToggle
Toggles the state of the target object (true to false, false to true).
actionPerformed() BoxDeleteMolecules
Performs the action of deleting test == false molecules, considering
all molecules in the box last given to setBox.
actionPerformed() BoxImposePbc
actionPerformed() BoxInflate
Performs boundary dimension change
actionPerformed() BoxInflateAnisotropic
Performs anisotropic inflation.
actionPerformed() BoxInflateDeformable
Performs isotropic inflation.
actionPerformed() BoxQuench
actionPerformed() BoxRandomizeMomenta
actionPerformed() BoxScaleMomenta
actionPerformed() CalcVibrationalModes
actionPerformed() IAction
Completes the action defined by the class implementing this interface.
actionPerformed() IntegratorReset
actionPerformed() PDBWriter
actionPerformed() SimulationDataAction
actionPerformed() SimulationRestart
Resets boxs, integrators, and accumulators.
actionPerformed() WriteConfiguration
Writes the leaf Atom coordinates to the file confName.pos_new.
actionPerformed() WriteConfigurationBinary
Writes the leaf Atom coordinates to the file confName.pos_new.
actionPerformed() WriteConfigurationDLPOLY
Writes the leaf Atom coordinates to the file confName.pos_new.
actionPerformed() WriteConfigurationP2DLPOLY
Writes the leaf Atom coordinates to the file CONFIG.
actionPerformed() XYZWriter
actionPerformed() MeterCavity
actionPerformed() DataPump
Transmits the data from the source to the sink.
actionPerformed() DataPumpListenerPow
actionPerformed() DataPumpListenerSmart
actionPerformed() DataStreamAction
actionPerformed() MeterDihedralAngle
Measures the dihedral angle's for the current configuration of the given box.
actionPerformed() MeterRDF
Takes the RDF for the current configuration of the given box.
actionPerformed() MeterRDFPC
Takes the RDF for the current configuration of the given box.
actionPerformed() ActionConfigWindow
actionPerformed() ActionGraphic
actionPerformed() ActionHistoryWindow
actionPerformed() ActionVelocityWindow
actionPerformed() Device.ActionSet
actionPerformed() DisplayPolytope
actionPerformed() IntegratorRigidMatrixIterative.BoxImposePbcMolecule
actionPerformed() MCMoveIDBiasAction
actionPerformed() MeterMeanForce
actionPerformed() AkimaSplineSmootherApp.PlotAction
actionPerformed() AkimaSplineSmootherDyApp.PlotAction
actionPerformed() MeterNormalizedCoord
Assigning the histogram to data
actionPerformed() MeterNormalizedCoordBeta
Assigning the histogram to data
actionPerformed() MeterOrientationDistribution
Assigning the histogram to data
actionPerformed() MeterRotationDistributionGroup
Assigning the histogram to data
actionPerformed() ModifyAction
Executes the setValue method of the wrapped modifier, using
the value given in the most recent call to this.setValue.
actionPerformed() ModifyBooleanAction
actionPerformed() ColloidGraphic.GraftAction
actionPerformed() GlassGraphic.SFacButtonAction
actionPerformed() ActionPistonUpdate
actionPerformed() SamGraphic.ActionMoveWall
actionPerformed() HSNPT.ActionSummer
actionPerformed() MeterAtomicDisplacement
actionPerformed() MeterNormalMode
Calculating things and adds terms to the sums
actionPerformed() MeterTiltHistogram
actionPerformed() MeterTiltRotationHistogram
actionPerformed() WriteS
actionPerformed() VelocityWriter
actionPerformed() MeterBondLength
Takes the RDF for the current configuration of the given box.
actionPerformed() ActionRecenter
actionPerformed() MeterVirialBDBin
actionPerformed() MeterVirialBDBinMultiThreaded
actionPerformed() MeterVirialBinMultiThreaded
actionPerformed() MeterVirialEBinMultiThreaded
actionPerformed() MSDCoordWriter
actionPerformed() MSDCoordWriter.AfterPBC
actionPerformed() ZeoliteSimStart
actionPerformed(E) IListener
actionPerformed(IAtom) AtomAction
Performs the defined action on the specified atom
actionPerformed(IAtom) AtomActionRandomizeVelocity
Assigns velocity to atom with components selected from a Maxwell-Boltzmann
distribution with temperature most recently set for the action.
actionPerformed(IAtom) AtomActionRotateBy
actionPerformed(IAtom) AtomActionTransformed
actionPerformed(IAtom) AtomActionTranslateBy
actionPerformed(IAtom) AtomActionTransformed
actionPerformed(IMolecule) MoleculeAction
actionPerformed(IMolecule) MoleculeActionTranslateTo
actionPerformed(IMolecule) MoleculeChildAtomAction
actionPerformed(IMolecule) MoleculeActionRelaxWater3P
actionPerformed(IEvent) AssociationManager
actionPerformed(IEvent) AssociationManagerMolecule
actionPerformed(IEvent) IntegratorPT.BoxTracker
Method called when two boxes are successfully exchanged.
actionPerformed(IEvent) MCMoveInsertDeleteLatticeVacancy
actionPerformed(IEvent) MCMoveInsertDeleteVacancy
actionPerformed(IEvent) MCMoveOverlapListener
actionPerformed(IEvent) MCMoveListenerRGE
actionPerformed(ActionEvent) ActionGraphic
actionPerformed(ActionEvent) DisplayPlot.DataWriter
actionPerformed(ActionEvent) DisplayPlot.RawDataWindowOpener
actionPerformed(ActionEvent) MyApplet.Starter
actionPerformed(ActionEvent) MyApplet.Stopper
actionPerformed(ActionEvent) Grabber.ActionCornerSetter
actionPerformed(ActionEvent) Wigner3jGUI
Interpreter parser loop.
actionPerformed(ActionEvent) ControllerAlertMsgBox.CloseWindowButtonListener
actionPerformed(ActionEvent) ControllerAlertMsgBoxSpeciesRemoval.NoDoNotRemoveSpeciesButtonListener
actionPerformed(ActionEvent) ControllerAlertMsgBoxSpeciesRemoval.YesRemoveSpeciesButtonListener
actionPerformed(ActionEvent) ViewConsoleOutputBox
actionPerformed(Object) DataStreamAction
ActionPistonUpdate etomica.modules.pistoncylinder
Action that informs the integrator that some property of the piston
has changed (pressure, mass, velocity)
ActionPistonUpdate(IntegratorHardPiston) ActionPistonUpdate
ActionRecenter etomica.surfacetension
ActionRecenter(LJMC) ActionRecenter
ActionSet() Device.ActionSet
ActionSummer(Box, Space) HSNPT.ActionSummer
ActionToggle etomica.action
Action that toggles a boolean value.
ActionToggle(ModifierBoolean) ActionToggle
ActionToggle(ModifierBoolean, String, String) ActionToggle
ActionVelocityWindow etomica.graphics
Action that opens a new window and dumps the velocities into the window.
ActionVelocityWindow(Box) ActionVelocityWindow
active DataAccumulator
Flag specifying whether the manager responds to integrator events
activeCornerSetter Grabber
activity Controller.ActivityHandle
Activity etomica.action.controller
A process conducted as part of a simulation.
Activity() Activity
ActivityHandle(A, CompletableFuture<Void>) Controller.ActivityHandle
activityIntegrate SelfAssemblySim
ActivityIntegrate etomica.action.activity
ActivityIntegrate(Integrator) ActivityIntegrate
ActivityIntegrate(Integrator, boolean) ActivityIntegrate
ActivityIntegrate(Integrator, long) ActivityIntegrate
ActivityIntegrate(Integrator, long, boolean) ActivityIntegrate
actualFlipList ClusterCoupledFlippedPartial
adAtomPos SimDimerLJadatom
adAtomPos SimKMCLJadatom
add(float) Quaternion
add(int) Rational
Add another integer.
add(int, IAtom) AtomPair
add(int, IAtom) AtomSetSinglet
add(int, IMolecule) MoleculePair
add(int, IMolecule) MoleculeSetSinglet
add(IAtom) AtomArrayList
add(IAtom) AtomPair
add(IAtom) AtomSetSinglet
add(Feature) FeatureSet
add(Requirement) RequirementSet
add(Coefficient) Coefficient
add(Coefficient) CoefficientImpl
add(Graph) GraphList
add(Device) SimulationGraphic
Adds displays graphic to the simulation display pane
add(Display) SimulationGraphic
add(IFunction) FunctionChain
Adds the given function to the chain of functions.
add(IMolecule) MoleculeArrayList
add(IMolecule) MoleculePair
add(IMolecule) MoleculeSetSinglet
add(P2HardBondedList.MyBond) P2HardBondedList.BondArrayList
add(TreeLinker) TreeList
add(BigIntegerPoly) BigIntegerPoly
Add another polynomial
add(BigSurd) BigSurd
Add two surds of compatible discriminant.
add(BigSurd) BigSurdVec
Add two vectors algebraically.
add(BigSurdVec) BigSurdVec
Add two vectors algebraically.
add(Rational) Rational
Add another fraction.
add(String, double) FeatureSet
add(String, String) FeatureSet
add(BigDecimal, BigInteger) BigDecimalMath
Add a BigDecimal and a BigInteger.
add(BigInteger) Ifactor
Summation with another positive integer
add(BigInteger) Rational
Add another integer.
add(Matrix3f) Matrix3f
Sets the value of this matrix to sum of itself and matrix m1.
add(Tuple3f) Tuple3f
Sets the value of this tuple to the vector sum of itself and tuple t1.
add(Tuple3i) Tuple3i
Sets the value of this tuple to the sum of itself and t1.
ADD_HYDROGEN_TITLE JmolConstants
add2(Tuple3f, Tuple3f) Tuple3f
Sets the value of this tuple to the vector sum of tuples t1 and t2.
addAccumulator(ConstructionParams, String, String) DataStreamResource
addAction(IAction) ActionGroup
Adds the given action to this group, placing it at the end of the list.
addAction(IAction) ActionGroupSeries
addActionSequential(IAction) Controller
addActivity(A) Controller
Adds an Activity to be executed by the Controller on a separate thread.
addActivity(ActivityIntegrate, long) Controller
addActivity(ActivityIntegrate, long, double) Controller
addAddSpecies1ButtonListener(ActionListener) ViewSpeciesSelection
addAddSpecies2ButtonListener(ActionListener) ViewSpeciesSelection
addAddSpecies3ButtonListener(ActionListener) ViewSpeciesSelection
addAlkaneLengthViewListener(int) ControllerAlkaneLengthSelection
addAll(int, Collection<? extends IAtom>) AtomPair
addAll(int, Collection<? extends IAtom>) AtomSetSinglet
addAll(int, Collection<? extends IMolecule>) MoleculePair
addAll(int, Collection<? extends IMolecule>) MoleculeSetSinglet
addAll(IAtomList) AtomArrayList
addAll(Collection<? extends IAtom>) AtomPair
addAll(Collection<? extends IAtom>) AtomSetSinglet
addAll(Collection<? extends Graph>) GraphList
addAll(Collection<? extends IMolecule>) MoleculeArrayList
addAll(Collection<? extends IMolecule>) MoleculePair
addAll(Collection<? extends IMolecule>) MoleculeSetSinglet
addAlterSimEnvButtonListener(ActionListener) ViewSpeciesSelection
addAlterSimEnvButtonListener(ActionListener) ViewSpeciesSelection
addAnotherSpeciesButtonListener(ActionListener) ViewSpeciesSelection
addAsTab(Component, String, boolean) SimulationGraphic
addAtom(AtomType, Vector...) SpeciesBuilder
addAtom(AtomType, Vector, String) SpeciesBuilder
addAtom(IAtom) Cell
addAtomNotify(IAtom) NeighborListManager
Constructs neighbor lists for the given atom
addAtomNotify(IAtom) NeighborListManagerSlanty
Constructs neighbor lists for the given atom
addAuthor(String) DefaultToolbar
addBDOne(BigDecimal) DataDoubleBDArray
addBDZero(BigDecimal) DataDoubleBDArray
addBondedPotentialSets(CollectionPotentialAtomicLike, Space, int) ACollectionBondedPotential
addBondedPotentialSets(CollectionPotentialAtomicLike, Space, int) CollectionBondedPotentialAlcohols
addBondedPotentialSets(CollectionPotentialAtomicLike, Space, int) CollectionBondedPotentialAlkanes
addBoundBoxPoint(Point3f) BoxInfo
addBox(Box) Simulation
Adds a Box to the simulation.
addButton(String, IAction) DeviceButtonGroup
Adds a radio button with the given label, which (when selected) performs
the given action.
addCellNumSliderListener(ChangeListener) DeviceCellNum3DSlider
Add the specified listener to the list of listeners that
will get invoked when the 'nCell #' slider value changes.
addChildAtom(IAtom) Molecule
Adds the given Atom as a child of this Atom.
addChooseOkayButtonListener(ActionListener) ViewSimEnvironmentSelection
addCloseWindowButtonListener(ActionListener) ViewAlertMsgBox
addCloseWindowButtonListener(ActionListener) ViewAlkaneLengthSelection
addCloseWindowButtonListener(ActionListener) ViewSimEnvironmentSelection
addCluster(ClusterDiagram) MyApplet.Starter
addClusterDiagram(ClusterDiagram) ClusterDiagramTree
Adds the given diagram to the tree, adding nodes as needed
addCollisionListener(IntegratorHard.CollisionListener) IntegratorHard
Registers an object that implements the CollisionListener interface.
addComparator(Comparator<Graph>) ComparatorChain
Add a comparator that will be used to sort sort graphs.
addComponent(Component, JPanel, int, int, int, int) MyApplet
Componet c is added to JPanel panel following the rule of GridBagLayout manager
addConnection(int, int) ClusterDiagram
Adds a connection between the node1 and node2.
addContributor(String) DefaultToolbar
addCount(AtomType, int) SpeciesBuilder
addCountOfSpeciesSLMListener(ChangeListener, int) ViewSpeciesSelection
addData(double) MeterVirialBinMultiThreaded.MyData
addData(double[]) MeterVirialEBinMultiThreaded.MyData
addData(double[]) MeterVirialEBinMultiThreaded.MyDataCov
addData(IData) AccumulatorAverageBlockless
Add the given values to the sums and block sums.
addData(IData) AccumulatorAverageBlocklessSlim
Add the given values to the sums and block sums.
addData(IData) AccumulatorAverageBootstrap
Add the given values to the sums and block sums.
addData(IData) AccumulatorAverageCollapsing
Add the given values to the sums and block sums.
addData(IData) AccumulatorAverageCollapsingLog
Add the given values to the sums and block sums.
addData(IData) AccumulatorAverageCollapsingLogAB
Add the given values to the sums and block sums.
addData(IData) AccumulatorAverageCovariance
addData(IData) AccumulatorAverageFixed
Add the given values to the sums and block sums.
addData(IData) AccumulatorAverageFixedOutputFile
Add the given values to the sums and block sums.
addData(IData) AccumulatorCounter
Increments the counter.
addData(IData) AccumulatorHistogram
Adds each value in the given Data to its own histogram.
addData(IData) AccumulatorHistory
Adds each value in the given array to its own history.
addData(IData) DataAccumulator
Defined by subclass to specify what this accumulator does when data is added to it.
addData(IData) AccumulatorAutocorrelationPTensor
addData(IData) AccumulatorAutocorrelationShearStress
addData(IData) AccumulatorVirialOverlapSingleAverage
Add the given values to the sums and block sums
addData(BigDecimal, MathContext) MeterVirialBDBinMultiThreaded.MyData
addDataListener(DataSetListener) DataSet
addDataSink(IDataSink) DataFork
addDataSink(IDataSink) DataPipeForked
Adds the given DataSink to those receiving the Data entering this DataFork,
keeping all previously entered DataSinks.
addDataSink(IDataSink) DataProcessorForked
Adds the given DataSink to those receiving the Data entering this DataFork,
keeping all previously entered DataSinks.
addDataSink(IDataSink, AccumulatorAverage.StatType[]) AccumulatorAverage
Adds a new DataSink that will receive a specific subset of the statistics
generated by this accumulator.
addDataSink(IDataSink, AccumulatorAverageBlockless.StatType[]) AccumulatorAverageBlockless
Adds a new DataSink that will receive a specific subset of the statistics
generated by this accumulator.
addDataSource(IDataSource) DataSourceGroup
Adds the given DataSource to those held by the group.
addDataSource(IDataSource) DataTableAverages
Adds the given data source to those feeding the table.
addDownNbr(IAtom, int) AtomNeighborLists
Adds the given atom as a "down" neighbor interacting via the potential
with the given index.
addDownNbr(IMolecule, int) MoleculeNeighborLists
Adds the given atom as a "down" neighbor interacting via the potential
with the given index.
addDrawable(Drawable) DisplayBox
addDrawable(Object) DisplayBox
addEditVariablesButtonListener(ActionListener) ViewSpeciesSelection
addEditVariablesButtonListener(ActionListener) ViewSpeciesSelection
addEquilibration(long) SimulationVirial
addEquivalents(ArrayList<ClusterDiagram>) ClusterOperations
Replaces all isomorphic clusters in the given list by a single cluster
with weight given by their sum.
addEValNumSliderListener(ChangeListener) DeviceEigenvaluesSlider
Add the specified listener to the list of listeners that
will get invoked when the 'eigenvalues #' slider value changes.
addFactors(int[]) Graph
addFactors(int[]) GraphImpl
addFig(Figure) G3DSys
Adds the Figure to the associated FigureManager
addFilter(String) ConstructorImpl
addFilter(String) Parser.Constructor
addIntegrator(Integrator) IntegratorGEMC
addIntegrator(Integrator) IntegratorManagerMC
addIntegrator(Integrator) IntegratorRGEMC
addIntegrator(IntegratorBox) IntegratorPT
Adds the given integrator to those managed by this integrator, and
includes integrator's box to the set among which configurations are
swapped.
addIntersectionVertex(Point3f, float, int, int, Map<String, Integer>, int, int) MeshSurface
additive VirialGCPM.VirialGCPMParam
addLine(LineSegment) DisplayBoxCanvasG3DSys
addListener(BoxEventListener) BoxEventManager
addListener(IntegratorListener) IntegratorEventManager
Adds the given listener to this event manager.
addListener(IntegratorListener) IntegratorListenerGroupSeries
Adds the given listener to the group.
addListener(ConfigurationStorage.ConfigurationStorageListener) ConfigurationStorage
addListener(INeighborListListener) NeighborListEventManager
addListener(INeighborListListenerMolecular) NeighborListEventManagerMolecular
addListener(SimulationListener) SimulationEventManager
addListener(BoundaryEventListener) BoundaryEventManager
Adds the given listener to this event manager.
addListener(IListener<E>) EventManager
Adds the given listener to this event manager.
addMCMove(MCMove) MCMoveManager
Adds the given MCMove to the set of moves performed by the integrator and
recalculates move frequencies.
addMolecule(IMolecule) Box
Adds the given molecule to the this Box.
addMolecule(IMolecule) CellMolecular
addMoleculeListDisplayLSMListener(ListSelectionListener) ViewSpeciesSelection
addMoleculeListDisplayLSMListener(ListSelectionListener) ViewSpeciesSelection
addMoleculeListDisplayTMListener(TableModelListener) ViewSpeciesSelection
addMoleculeListDisplayTMListener(TableModelListener) ViewSpeciesSelection
addMoleculeNotify(IMolecule) NeighborListManagerMolecular
Constructs neighbor lists for the given atom
addMoleculeNotify(IMolecule) NeighborListManagerSlantyMolecular
Constructs neighbor lists for the given molecule
addMSDSink(DataSourceMSD.MSDSink) DataSourceMSD
addNewMolecule(ISpecies) Box
Creates a molecule of the given species and adds it to the box
addNoDoNotRemoveSpeciesButtonListener(ActionListener) ViewAlertMsgBoxSpeciesRemoval
addObject(T[], T) Arrays
Returns an array formed from adding the newObject to the elements
in the given array.
addOption(String, IAction) DeviceSelector
addPair(NodePair) SearchState
addPair(NodePair) UllmanSearchState
addPair(NodePair) VF2SearchState
addPair(NodePair) VFSearchState
addParser(ParameterParser) ParameterBase
addPlane(Plane) DisplayBoxCanvasG3DSys
addPoint(Point3f, Point3f, Point3f, float) BoxInfo
addPointXYZ(float, float, float, Point3f, Point3f, float) BoxInfo
addPolygonC(int[], int, BitSet) MeshSurface
addPotential(IPotential) PotentialArray
Identifies the given potential to this type instance and returns
the index assigned to it.
addPotential(IPotentialAtomic) PotentialMasterLrc
addPotential(IPotentialAtomic, AtomType[]) PotentialGroup
Adds the given potential and sets it up to apply to the atoms in the basis
having the given types.
addPotential(IPotentialAtomic, AtomType[]) PotentialMaster
Indicates to the PotentialMaster that the given potential should apply to
the specified atom types.
addPotential(IPotentialAtomic, AtomType[]) PotentialMasterMonatomic
addPotential(IPotentialAtomic, AtomsetIteratorBasisDependent) PotentialGroup
Adds the given potential to this group, defining it to apply to the atoms
provided by the given basis-dependent iterator.
addPotential(IPotentialAtomic, AtomsetIteratorBasisDependent, AtomType[]) PotentialGroupNbr
addPotential(IPotentialAtomic, AtomsetIteratorBasisDependent, AtomType[]) PotentialGroup
addPotential(IPotentialMolecular) PotentialArrayMolecular
Identifies the given potential to this type instance and returns
the index assigned to it.
addPotential(IPotentialMolecular) PotentialMasterLrc
addPotential(IPotentialMolecular, MoleculesetIteratorPDT, ISpecies[]) PotentialMaster
addPotential(IPotentialMolecular, ISpecies[]) PotentialMasterNbrMolecular
addPotential(IPotentialMolecular, ISpecies[]) PotentialMasterHybrid
addPotential(IPotentialMolecular, ISpecies[]) PotentialMasterNbr
addPotential(IPotentialMolecular, ISpecies[]) PotentialMaster
Indicates to the PotentialMaster that the given potential should apply to
the specified species.
addPotential(IPotentialMolecular, ISpecies[]) PotentialMasterMonatomic
addPotential(IPotential, AtomType) PotentialArrayByType
Identifies the given potential to this type instance and returns
the index assigned to it.
addPotentialButtonListener(ActionListener) ViewSpeciesSelection
addPotentialButtonListener(ActionListener) ViewSpeciesSelection
addPotentialNbrList(IPotentialAtomic, AtomType[], NeighborCriterion) PotentialMasterList
Add the given potential to be used for the given atom types and the
given criterion.
addPotentialsJListListener(ListSelectionListener) ViewSpeciesSelection
addPotentialsJListListener(ListSelectionListener) ViewSpeciesSelection
addPotParamDisplayLSMListener(ListSelectionListener) ViewSpeciesSelection
addPotParamDisplayLSMListener(ListSelectionListener) ViewSpeciesSelection
addPotParamDisplayTMListener(TableModelListener) ViewSpeciesSelection
addPotParamDisplayTMListener(TableModelListener) ViewSpeciesSelection
addProgressListener(double, long) SimulationVirialOverlap2
Causes a progress report (coefficient value and uncertainty) 10 times
during the course of the simulation.
addProgressListener(double, long, boolean) SimulationVirialOverlap2
Causes a progress report (coefficient value and uncertainty) 10 times
during the course of the simulation.
addPropertyChangeListener(PropertyChangeListener) Display
addPropertyChangeListener(PropertyChangeListener) Grabber.ActionCornerSetter
addQuad(int, int, int, int) MeshSurface
addRadioGroupActionListener(ActionListener) DeviceThermoSliderGEMC
Add the specified listener to the list of listeners that
will get invoked when the isothermal or adiabatic radio button
is pushed.
addRadioGroupActionListener(ActionListener) 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) 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) 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.
addRangedPotential(IPotentialMolecular, ISpecies) PotentialMasterNbrMolecular
addRangedPotentialForSpecies(IPotentialMolecular, ISpecies[]) PotentialMasterListMolecular
Adds the potential as a ranged potential that applies to the given
AtomTypes.
addRangedPotentialForSpecies(IPotentialMolecular, ISpecies[]) PotentialMasterNbrMolecular
addRangedPotentialForTypes(IPotentialAtomic, AtomType[]) PotentialMasterCell
addRangedPotentialForTypes(IPotentialAtomic, AtomType[]) PotentialMasterList
Adds the potential as a ranged potential that applies to the given
AtomTypes.
addRangedPotentialForTypes(IPotentialAtomic, AtomType[]) PotentialMasterHybrid
addRangedPotentialForTypes(IPotentialAtomic, AtomType[]) PotentialMasterNbr
addRangedPotentialForTypes(IPotentialAtomic, AtomType[]) PotentialMasterSite
addRemoveButtonListener(ActionListener) ViewSpeciesSelection
addRemoveSpecies1ButtonListener(ActionListener) ViewSpeciesSelection
addRemoveSpecies2ButtonListener(ActionListener) ViewSpeciesSelection
addRemoveSpecies3ButtonListener(ActionListener) ViewSpeciesSelection
addResetButtonListener(ActionListener) ViewSpeciesSelection
addResetButtonListener(ActionListener) ViewSpeciesSelection
addReverseComparator(Comparator<Graph>) ComparatorChain
Add a comparator that will be used to sort sort graphs in reverse order.
addRound(BigComplex, BigComplex) BigDecimalMath
Add and round according to the larger of the two ulp's.
addRound(BigComplex, BigDecimal) BigDecimalMath
Add and round according to the larger of the two ulp's.
addRound(BigDecimal, BigDecimal) BigDecimalMath
Add and round according to the larger of the two ulp's.
addRunButtonListener(ActionListener) ViewSpeciesSelection
addRunButtonListener(ActionListener) ViewSpeciesSelection
addSameSpeciesButtonListener(ActionListener) ViewSpeciesSelection
addSaveValuesButtonListener(ActionListener) ViewAlkaneLengthSelection
addSaveValuesButtonListener(ActionListener) ViewSimEnvironmentSelection
addSink(DataSinkBlockAveragerSFac.Sink) DataSinkBlockAveragerSFac
addSpecies(ISpecies) ConfigurationLatticeWithPlane
addSpecies(ISpecies) Simulation
Adds species to the list of all ISpecies in the simulation, and
notifies all Boxes of the addition.
addSpecies(Object) ArrayMoleculeDisplayList
addSpeciesButtonListener(ActionListener) ViewSpeciesSelection
addSpeciesIndextoSites(String[], int) BuilderCollectionPotential
addSpeciesJListListener(ListSelectionListener) ViewSpeciesSelection
addSpeciesJListListener(ListSelectionListener) ViewSpeciesSelection
addSpeciesMolecule(int) ModelSelectedSpecies
addSpeciesNotify(ISpecies) Box
Notifies the Box that the given species has been added to the
simulation.
addStateChangedListener(ChangeListener) Osmosis.InitializeMolecules
addTag(DataTag) DataInfo
Adds the tag
addTag(DataTag) IDataInfo
Adds the tag to this IDataInfo object.
addTag(DataTag) DataGroup.DataInfoGroup
addTags(DataTag[]) DataInfo
Convenience method to add all of the given tags.
addTags(DataTag[]) IDataInfo
Convenience method to add all of the given tags.
addTags(DataTag[]) DataGroup.DataInfoGroup
addTemperatureSliderListener(ChangeListener) DeviceThermoSliderGEMC
Add the specified listener to the list of listeners that
will get invoked when the temperature slider value changes.
addTensor(int, Tensor) DataSourceTensorVirialHardProfile
Adds the given contribution to the virial sum for bin iBin.
addThermostatAction(IAction) IntegratorHardMDMC
addToHashMapPotentialNonBonded(String[], IPotential) CollectionPotentialAtomicLike
addToHashMapPotentialNonBonded(String[], IPotential) CollectionPotentialAtomicUnlike
addToken(String, Token) Token
addTriangle(int, int, int) MeshSurface
addTriangleCheck(int, int, int, int, int, int) MeshSurface
addUnrangedPotential(AtomType, AtomType, IPotentialAtomic) PotentialMasterCellMixed
Indicatest that the given potential describes the interactions between the
given atom types.
addUpNbr(IAtom, int) AtomNeighborLists
Adds the given atom as a "down" neighbor interacting via the potential
with the given index.
addUpNbr(IMolecule, int) MoleculeNeighborLists
Adds the given atom as a "down" neighbor interacting via the potential
with the given index.
addValue(double) Histogram
Adds the given value to the Histogram
addValue(double) HistogramCollapsing
addValue(double) HistogramDiscrete
addValue(double) HistogramExpanding
addValue(double) HistogramNotSoSimple
addValue(double) HistogramReweightedData
addValue(double) HistogramSimple
addValue(double, double) HistogramNotSoSimple
addValue(double, double) HistogramReweightedData
addValue(double, double) History
Adds the given x, y pair to the History.
addValue(double, double) HistoryCollapsingAverage
adds data to the history.
addValue(double, double) HistoryCollapsingDiscard
adds data to the history.
addValue(double, double) HistoryComplete
addValue(double, double) HistoryScrolling
addValueChangedListener(DeviceBoxValueChangedListener) DeviceBox
Add an object to be notified when the DeviceBox value to changes
addVertexCopy(Point3f) MeshSurface
addVertexCopy(Point3f, float, boolean, int) MeshSurface
addVertexCopyVal(Point3f, float) MeshSurface
addWaveVectorNumSliderListener(ChangeListener) DeviceWaveVectorSlider
Add the specified listener to the list of listeners that
will get invoked when the 'wave vectors #' slider value changes.
addXYCellNumSliderListener(ChangeListener) DeviceCellNumXYSlider
Add the specified listener to the list of listeners that
will get invoked when the 'xCell #' and 'yCell #' slider value changes.
addYesRemoveSpeciesButtonListener(ActionListener) ViewAlertMsgBoxSpeciesRemoval
aDim MinimizeBetaNitrogenLatticeParameter
aDim MinimizeBetaNitrogenLatticeParameterFromFile
aDim MinimizeBetaNitrogenTranslationDOF
adjustCountdown IntegratorOverlap
adjustInterval MCMoveStepTracker
adjustInterval IntegratorOverlap
adjustStep MCMoveStepTracker
adjustStepFreq VirialCPSHeliumNonAdditiveClassical_Correction.VirialParam
adjustStepFreq VirialCPSHeliumNonAdditiveClassical.VirialParam
adjustStepFreq() IntegratorOverlap
Deprecated.
Adjusts the frequency with which steps for each sub-integrator are
performed.
adjustStepFrequency VirialHePCKLJS.VirialParam
adjustStepFrequency VirialHePCKLJSCHNCCorrection.VirialLJParam
adjustStepFrequency VirialHePCKLJSPYCorrection.VirialLJParam
adjustStepSize SimGCPMWaterMCNPT.GCPMWaterMCParam
adjustStepSize SimGCPMWaterMCNVT.GCPMWaterMCParam
adjustStepSize() MCMoveStepTracker
adpmax Token
ADPMAX EnumVdw
adpmin Token
ADPMIN EnumVdw
Adsorption etomica.modules.adsorption
Simulation for Adsorption module.
Adsorption() Adsorption
AdsorptionGraphic etomica.modules.adsorption
Catalysis graphical app.
AdsorptionGraphic(Adsorption, Space) AdsorptionGraphic
AdsorptionGraphic.Applet etomica.modules.adsorption
advance() CartesianIterator
advance() CartesianPermutator
advance() ClusterGenerator
Advances the cluster to the next cluster matching the given criteria.
advanceAcrossTimeStep(double) IntegratorHard
Advances all atom coordinates by tStep, without any intervening collisions.
advanceAcrossTimeStep(double) IntegratorHardPiston
advanceAcrossTimeStep(double) P1HardMovingBoundary
aEE DLJ_NVT_1site.Param
aEE TIP4P_NVT.Param
aEE Heisenberg.Param
aEE Heisenberg3Pair.Param
aEE HeisenbergPair.Param
AEE PotentialCalculationPair
AEEJ0 PotentialCalculationHeisenberg
AEEJ0 PotentialCalculationMoleculeAgentSum
AEEJ0 PotentialCalculationMoleculeAgentSumPair
Aelement SimpleElementForSimilarSpecies
aErr P2HePCKLJS
affectedAtomIterator MCMoveDimer
affectedAtomIterator MCMoveDimerRotate
affectedAtomIterator MCMoveSmer
affectedAtomIterator MCMoveSmerRotate
affectedAtomIterator MCMoveVolumeAssociated
affectedAtomIterator MCMoveVolumeAssociatedMolecule
affectedAtomIterator MCMoveAtomCoupled
affectedAtomIterator MCMoveAtomSwap
affectedAtomIterator MCMoveAtom
affectedAtomIterator MCMoveBoxSize
affectedAtomIterator MCMoveDimer
affectedAtomIterator MCMoveDimerRotate
affectedAtomIterator MCMoveInsertDelete
affectedAtomIterator MCMoveMolecule
affectedAtomIterator MCMoveVolume
affectedAtomIterator MCMoveVolumeN2
affectedAtomIterator MCMoveAtomCoupled
affectedAtomIterator MCMoveAtomCoupledBennet
affectedAtomIterator MCMoveAtomCoupledUmbrella
affectedAtomIterator MCMoveAtomSuperBox
affectedAtomIterator MCMoveVolumeMonoclinic
affectedAtomIterator MCMoveVolumeMonoclinicAngle
affectedAtomIterator MCMoveVolumeMonoclinicScaled
affectedAtomIterator MCMoveVolumeSolid
affectedAtomIterator MCMoveVolumeSolidNPTMolecular
affectedAtomIterator MCMoveSpinFlip
affectedAtomIterator MCMoveClusterAngleBend
affectedAtomIterator MCMoveClusterAngleBendAceticAcid
affectedAtomList MCMoveAtomCoupled
affectedAtomList MCMoveAtomCoupledBennet
affectedAtomList MCMoveAtomCoupledUmbrella
affectedAtomList MCMoveAtomSuperBox
affectedAtoms MCMoveDimer
affectedAtoms MCMoveDimerRotate
affectedAtoms MCMoveDimer
affectedAtoms MCMoveDimerRotate
affectedAtoms() MCMoveBiasUB
affectedAtoms() MCMoveBiasUBMolecule
affectedAtoms() MCMoveDimer
affectedAtoms() MCMoveDimerRotate
affectedAtoms() MCMoveSmer
affectedAtoms() MCMoveSmerRotate
affectedAtoms() MCMoveVolumeAssociated
affectedAtoms() MCMoveVolumeAssociatedMolecule
affectedAtoms() MCMoveAtomCoupled
affectedAtoms() MCMoveAtomSwap
affectedAtoms() MCMoveAtom
affectedAtoms() MCMoveBox
affectedAtoms() MCMoveBoxSize
affectedAtoms() MCMoveDimer
affectedAtoms() MCMoveDimerRotate
affectedAtoms() MCMoveInsertDelete
Returns an iterator giving molecule that is being added or deleted
in the current or most recent trial.
affectedAtoms() MCMoveMolecule
affectedAtoms() MCMoveSemigrand
affectedAtoms() MCMoveVolume
affectedAtoms() MCMoveMoleculeCoupledInitPert
affectedAtoms() MCMoveMoleculeCoupledSuperBox
affectedAtoms() MCMoveVolumeN2
affectedAtoms() MCMoveSwap
affectedAtoms() MCMoveMultiHarmonic
affectedAtoms() MCMoveAtomCoupled
affectedAtoms() MCMoveAtomCoupledBennet
affectedAtoms() MCMoveAtomCoupledUmbrella
affectedAtoms() MCMoveAtomSuperBox
affectedAtoms() MCMoveEinsteinCrystal
affectedAtoms() MCMoveHarmonic
affectedAtoms() MCMoveHarmonicStep
affectedAtoms() MCMoveMoleculeCoupled
affectedAtoms() MCMovePhaseAngle
affectedAtoms() MCMoveSingleMode
affectedAtoms() MCMoveVolumeMonoclinic
affectedAtoms() MCMoveVolumeMonoclinicAngle
affectedAtoms() MCMoveVolumeMonoclinicScaled
affectedAtoms() MCMoveVolumeSolid
affectedAtoms() MCMoveVolumeSolidNPTMolecular
affectedAtoms() MCMoveWV
affectedAtoms() MCMoveGeometricCluster
affectedAtoms() MCMoveSpinCluster
affectedAtoms() MCMoveSpinFlip
affectedAtoms() MCMoveChangeBondLength
affectedAtoms() MCMoveClusterAngleBend
affectedAtoms() MCMoveClusterAngleBendAceticAcid
affectedAtoms() MCMoveClusterAtomQ
affectedAtoms() MCMoveClusterDiagram
affectedAtoms() MCMoveClusterReptateMulti
affectedAtoms() MCMoveClusterRingPartialRegrow
affectedAtoms() MCMoveClusterRingRegrow
affectedAtoms() MCMoveClusterRingRegrowExchange
affectedAtoms() MCMoveClusterRingRegrowOrientation
affectedAtoms() MCMoveClusterRingScale
affectedAtoms(Box) MCMove
Returns an iterator that yields the atoms that were affected by the trial
move the last time doTrial was invoked (regardless of whether the move
was accepted).
affectedAtoms(Box) MCMoveBox
affectedAtoms(Box) MCMoveMoleculeExchange
affectedAtoms(Box) MCMoveSwapConfiguration
affectedAtoms(Box) MCMoveVolumeExchange
affectedAtoms(Box) MCMoveGeometricClusterRestrictedGE
affectedAtoms(Box) MCMoveClusterAtomQ
affectedAtoms(Box) MCMoveSwapCluster
affectedMol MCMoveRotateMolecule3DSuperBox
affectedMoleculeIterator MCMoveBiasUBMolecule
affectedMoleculeIterator MCMoveMolecule
affectedMoleculeIterator MCMoveMoleculeCoupledInitPert
affectedMoleculeIterator MCMoveMoleculeCoupledSuperBox
affectedMoleculeIterator MCMoveRotateMolecule3DSuperBox
affectedMoleculeIterator MCMoveMoleculeCoupled
affectedMoleculeList MCMoveMoleculeCoupledInitPert
affectedMoleculeList MCMoveMoleculeCoupledSuperBox
affectedMoleculeList MCMoveRotateMolecule3DSuperBox
affectedMoleculeList MCMoveMoleculeCoupled
affectedMolecules(Box) MCMoveBiasUBMolecule
affectedMolecules(Box) MCMoveVolumeAssociatedMolecule
affectedMolecules(Box) MCMoveMolecular
affectedMolecules(Box) MCMoveMolecule
affectedMolecules(Box) MCMoveMoleculeCoupledSuperBox
affectedMolecules(Box) MCMoveRotateMolecule3DSuperBox
AfterPBC(Box, AtomIterator) MSDCoordWriter.AfterPBC
Agent() MCMoveVolumeAssociated.Agent
Agent() MCMoveVolumeAssociatedMolecule.Agent
Agent(IAtomKinetic, IntegratorHard) IntegratorHard.Agent
Agent(Space) IntegratorGear4.Agent
Agent(Space) IntegratorVerlet.Agent
agentManager ActionMinimizeEnergy
agentManager ColorSchemeCollectiveAgent
agentManager IntegratorGear4
agentManager IntegratorHard
agentManager IntegratorVelocityVerlet
agentManager IntegratorVelocityVerletShake
agentManager IntegratorVerlet
agentManager FixedWall
agentManager ColorSchemeRadical
agentManager ConfigurationCatalysis
agentManager InteractionTracker
agentManager P2SquareWellBonding
agentManager P2SquareWellBondingCO
agentManager P2SquareWellSurface
agentManager AtomTestChainLength
agentManager ChainEquilibriumSim
agentManager ColorSchemeRadical
agentManager FreeRadicalPolymerizationSim
agentManager MeterChainLength
agentManager MeterConversion
agentManager P2SquareWellBonded
agentManager P2SquareWellRadical
agentManager AtomTestLiquidAtomic
agentManager IntegratorDroplet
agentManager MeterDimerFraction
agentManager P2SquareWellBonded
agentManager MeterFlux
agentManager P1Tether
agentManager AtomTestChainLength
agentManager SelfAssemblySim
agentManager NeighborCellManagerMolecular
agentManager NeighborCellManager
agentManager CriterionPositionWall
agentManager CriterionSimple
agentManager CriterionSimpleMolecular
agentManager HSNPT.ActionSummer
agentManager HSNPT.ColorSchemeDisplacement
agentManager1Body NeighborListManagerMolecular
agentManager1Body NeighborListManager
agentManager2Body NeighborListManagerMolecular
agentManager2Body NeighborListManager
agents ReactionEquilibrium
agents P2SemiclassicalAtomic
agentStream() MoleculeAgentManager
aH EnumSiteName
AHarm NormalModeAnalysisDisplay1DGraphic
AHarm NormalModeAnalysisDisplay2DGraphic
AHarm NormalModeAnalysisDisplay3DGraphic
ai ZeoliteSimulation
Ai PotentialCalculationPhiSum
aiInner ApiInnerVariable
The iterators used to generate the sets of atoms.
aiInner ApiIntergroup
aiInner MpiInnerVariable
The iterators used to generate the sets of atoms.
aiInnerSize ApiIntergroupExchange
aiOuter ApiInnerVariable
aiOuter ApiIntergroup
aiOuter MpiInnerVariable
aiOuter MpiIntraspecies1A
aiOuterSize ApiIntergroupExchange
aj P2WaterSzalewicz
Aj PotentialCalculationPhiSum
aj3 P2WaterSzalewicz
akima MultiharmonicGraphicMC.DataSinkReweightedDeltaU
akima MultiharmonicGraphicMC.DataSourceAlphaFE
akima MultiharmonicGraphicMC.DataSourceBias
akima DataOverlap
akima DataOverlap.DataSourceOverlapAvgCollapsing
akimaSpline FindTransitionTemperature
akimaSpline SoftSphereSolidEOS
AkimaSpline etomica.math.numerical
DataProcessor that interpolates incoming data using an Akima spline
interpolation scheme.
AkimaSpline() AkimaSpline
AkimaSplineSmoother etomica.math.numerical
Optimization algorithm which attempts to smooth data without moving any
point far from its original location.
AkimaSplineSmoother(IRandom) AkimaSplineSmoother
AkimaSplineSmootherApp etomica.math.numerical
App to drive AkimaSplineSmoother
AkimaSplineSmootherApp(String) AkimaSplineSmootherApp
AkimaSplineSmootherApp.Applet etomica.math.numerical
AkimaSplineSmootherApp.IntegratorSmoother etomica.math.numerical
AkimaSplineSmootherApp.PlotAction etomica.math.numerical
AkimaSplineSmootherDy etomica.math.numerical
Optimization algorithm which attempts to smooth data without moving any
point far from its original location.
AkimaSplineSmootherDy(IRandom) AkimaSplineSmootherDy
AkimaSplineSmootherDyApp etomica.math.numerical
App to drive AkimaSplineSmoother
AkimaSplineSmootherDyApp(String) AkimaSplineSmootherDyApp
AkimaSplineSmootherDyApp.Applet etomica.math.numerical
AkimaSplineSmootherDyApp.IntegratorSmoother etomica.math.numerical
AkimaSplineSmootherDyApp.PlotAction etomica.math.numerical
AkimaSplineSmootherMain etomica.math.numerical
Main method to drive AkimaSplineSmoother
AkimaSplineSmootherMain() AkimaSplineSmootherMain
AL10 Gamma
al1l2l0(int, int, int, double, double, double) P2HydrogenPatkowski
al1l2l0(int, int, int, double, double, double) P2HydrogenPatkowskiAtomic
Alat SimHSMDVacancy.HSMDVParams
alfst P2WaterPotentialsJankowski
align DisplayBox
align DisplayPolytope
align_on_z_axis(Vector[], Vector[]) P2WaterPotentialsJankowski
alignedV1 P2WaterPotentialsJankowski
alignedV2 P2WaterPotentialsJankowski
alkaneSpherePanel ViewAlkaneLengthSelection
all MCMoveInsertDeleteLatticeVacancy.AtomIteratorBruteForce
all Token
ALL P2WaterSzalewicz.Component
allatoms IntegratorDimerMin
allatoms IntegratorDimerRT
allAtoms MeterRDFPC
allAtoms P1ImageHarmonic
allAtoms IntegratorVelocityVerlet
allAtoms IntegratorVelocityVerletShake
allAtoms MeterMappedRdf
allAtoms MeterMappedU
allAtoms MeterMappedVirial
allAtoms MeterMappedVirialV
allAtoms MeterMeanForce
allAtoms PotentialCalculationMappedEnergy
allAtoms PotentialCalculationMappedVirial
allAtoms PotentialCalculationMappedVirialV
allAtoms CalcGradientDifferentiable
allAtoms IntegratorDroplet
allAtoms MeterEnergyMeanField
allAtoms MeterMappedAveraging
allAtoms MeterMappedAveraging3Pair
allAtoms MeterMappedAveragingCorrelation
allAtoms MeterMappedAveragingFreeEnergy
allAtoms MeterMappedAveragingPair
allAtoms MeterMappedAveragingPairExcess
allAtoms MeterMappedAveragingSum
allAtoms MeterMappedAveragingVSum
allAtoms MeterMappedAveragingVSum3Pair
allAtoms MeterMappedAveragingVSumPair
allAtoms MeterMeanField
allAtoms MeterPairSum
allAtoms SurfaceTensionMapped
allAtoms(IAtomList) Debug
determines if all of the atoms in the given array are set to be debugged
(via ATOMx_NUM and setAtoms(box)).
allAtoms(IMoleculeList) Debug
determines if all of the atoms in the given array are set to be debugged
(via ATOMx_NUM and setAtoms(box)).
allCoords ConfigFromFileLAMMPS.ModifierConfiguration
allCriteria PotentialMasterListMolecular
allData DataClusterer
allData MultiharmonicGraphicMC.DataSourceAlphaFE
allData MultiharmonicGraphicMC.DataSourceBias
AllData(long, IData, IData) AccumulatorAverageBlockless.AllData
allDone() MyApplet.Starter
allEdges ConfigFromFileLAMMPS.ModifierConfiguration
allfloat Token
AllIsomorphs etomica.graph.operations
Returns all graphs that are isomorphs of the original graph(s).
AllIsomorphs() AllIsomorphs
AllIsomorphs.AllIsomorphsParameters etomica.graph.operations
AllIsomorphsParameters(boolean) AllIsomorphs.AllIsomorphsParameters
AllIsomorphsParameters(boolean, Property) AllIsomorphs.AllIsomorphsParameters
allLnAlpha MultiharmonicGraphicMC.DataSourceAlphaFE
allLnAlpha MultiharmonicGraphicMC.DataSourceBias
allMoleculeList Box
allMyData MeterVirialBDBinMultiThreaded
allMyData MeterVirialBinMultiThreaded
allMyData MeterVirialEBinMultiThreaded
allMyData VirialHSBinMultiThreaded.SimulationWorker
allMyData VirialSQWBinMultiThreaded.SimulationWorker
allocateBitmap() AbstractBitmap
Allocates the storage space for bitSize() bits.
allocateBitmap() BitmapOfLong
allocateBitmap() BitmapOfLongVector
allocateColix(int) Colix
allocateRgbImage(int, int, int[], int, boolean) ApiPlatform
allocateRgbImage(int, int, int[], int, boolean) Platform
allOr P2WaterSzalewicz
allOr0 P2CO2H2OWheatley
allOr0 P2CO2Hellmann.P2CO2SC
allOr0 P2NitrogenHellmann.P2N2QFH
allOr1 P2CO2H2OWheatley
allOr1 P2CO2Hellmann.P2CO2SC
allOr1 P2NitrogenHellmann.P2N2QFH
ALLOWED Prefix
Constant used when invoking constructor of SimpleUnit class to indicate
that the unit permits the use of a prefix.
allowedQuaternionFrames JmolConstants
allowedScriptTypes SVGConverter
Set of allowed script types.
allowembeddedscripts Token
allowgestures Token
allowkeystrokes Token
allowmodelkit Token
allowmoveatoms Token
allowmultitouch Token
allowrotateselected Token
allPermutations BiComponentSubst.BiComponentSubstParameters
allPermutations FactorOnce.FactorOnceParameters
allPermutations MyApplet
allPermutations VirialDiagrams
allPermutations VirialDiagramsMix2
allPermutations VirialDiagramsPT
allPermutations ClusterICPYC
allPermutationsCB MyApplet
allPotentials PotentialMasterNbrMolecular
allPotentials PotentialMasterMonatomic
AllSigs(int) ClusterWheatleyHS.AllSigs
allVal MayerHSMixture
allValue MinimizeBetaNitrogenLatticeParameter
allValue MinimizeBetaNitrogenLatticeParameterFromFile
allValue MinimizeBetaNitrogenLatticeParameterLSFromFile
allValue MinimizeBetaNitrogenTranslationDOF
allValueClusters SimulationVirial
allWrappers() SimulationModel
allZero ClusterWheatleyPartitionScreening
alpha P1LepsHarmonic
alpha SimLattice.LjMC3DParams
alpha P2CO2Hellmann
alpha FindBetaN2AngleFromParameter
alpha MeterTargetRPMolecule
alpha MeterTargetTPMolecule
alpha SimOverlapAlphaN2TP.SimOverlapParam
alpha SimOverlapBetaN2RP.SimOverlapParam
alpha SimOverlapBetaN2RPScaling.SimOverlapParam
alpha SimOverlapBetaN2TP.SimOverlapParam
alpha SimOverlapDisorderedAlphaN2RPScaling.SimOverlapParam
alpha SimOverlapDisorderedAlphaN2TP.SimOverlapParam
alpha EOSSWPatel
alpha MeterMBAR
alpha MultiharmonicGraphicMC.DataSourceAlphaFE
alpha MultiharmonicGraphicMC.DataSourceBias
alpha MeterUmbrella
alpha MCMoveEinsteinCrystal
alpha MCMoveHarmonicEin
alpha MeterOverlapSwitch
alpha MeterTargetTP
alpha SimLJHTTISuperHCP.SimOverlapParam
alpha SimLJHTTISuperHCP2.SimOverlapParam
alpha SimOverlapSoftSphereEin.SimOverlapParam
alpha SimOverlapSoftSphereSoftness.SimOverlapParam
alpha SimOverlapSoftSphereTP.SimOverlapParam
alpha SimOverlapSoftSphereTPHCP.SimOverlapParam
alpha SimOverlapSoftSphereTPSlantedBox.SimOverlapParam
alpha MeterOverlap
alpha EwaldSummation
alpha EwaldSumMolecules
alpha P1HydrogenMielke
alpha P2HePCKLJS
alpha P2NitrogenHellmann
alpha P3AxilrodTeller.MyAgent
alpha P3CPSNonAdditiveHe
alpha P3CPSNonAdditiveHeLessSimplified
alpha P3CPSNonAdditiveHeOrig
alpha P3CPSNonAdditiveHeSimplified
alpha P3Induction
alpha P3Induction.MyAgent
ALPHA_SHIFT Colix
alpha1 P2Nitrogen
alpha1 P2NitrogenAB
alpha1 P2NitrogenAnisotropic
alpha1 P2NitrogenShellModel
alpha2 P2Nitrogen
alpha2 P2NitrogenAB
alpha2 P2NitrogenAnisotropic
alpha2 P2NitrogenShellModel
alpha2 EwaldSummation
alpha3 EwaldSummation
alphaA P2CO2Hellmann
alphaA P2NitrogenHellmann
alphaB P2CO2Hellmann
alphaB P2NitrogenHellmann
alphaCenter MeterTargetRPMolecule
alphaCenter MeterTargetTPMolecule
alphaCenter MeterMBAR
alphaCenter AccumulatorOverlapAverageUa2
alphaCenter MeterOverlapSwitch
alphaCenter MeterTargetTP
alphaCenter SimOverlapSoftSphereEinHarm
alphaCenter SimOverlapSoftSphereEinHarm.SimOverlapParam
alphaCenter MeterOverlap
alphaCenter AccumulatorVirialOverlapSingleAverage
alphaCenter DataProcessorVirialOverlap
alphaChoice MultiharmonicGraphicMC
alphaCoeffs FindTransitionTemperature
alphaData MultiharmonicGraphicMC.DataSourceAlphaChi
alphaData MultiharmonicGraphicMC.DataSourceAlphaAlpha
alphaData MultiharmonicGraphicMC.DataSourceAlphaChi
alphaData MultiharmonicGraphicMC.DataSourceAlphaAlpha
alphaData MultiharmonicGraphicMC.DataSourceAlphaChi
alphaFac MeterUmbrella
alphaInfo MultiharmonicGraphicMC.DataSourceAlphaChi
alphaInfo MultiharmonicGraphicMC.DataSourceAlphaAlpha
alphaInfo MultiharmonicGraphicMC.DataSourceAlphaChi
alphaInfo MultiharmonicGraphicMC.DataSourceAlphaAlpha
alphaInfo MultiharmonicGraphicMC.DataSourceAlphaChi
alphaIso P3NitrogenHellmannNonAdditive
alphaIsoSim P3NitrogenHellmannNonAdditive
alphaPar PNCO2GCPM
alphaPar PNGCPM.GCPMAgent
alphaPerp PNCO2GCPM
alphaPerp PNGCPM.GCPMAgent
alphaPol PNWaterGCPM
alphaPol PNWaterGCPMReactionField
alphaSource MultiharmonicGraphicMC.DataSinkReweightedDeltaU
alphaSource MultiharmonicGraphicMC.DataSourceAlphaFE
alphaSource MultiharmonicGraphicMC.DataSourceBias
alphaSource DataOverlap
alphaSource DataVirialOverlap
AlphaSource etomica.overlap
Class that can return values of alpha.
alphaSpan MeterTargetRPMolecule
alphaSpan MeterTargetTPMolecule
alphaSpan SimOverlapAlphaN2TP.SimOverlapParam
alphaSpan SimOverlapBetaN2RP.SimOverlapParam
alphaSpan SimOverlapBetaN2RPScaling.SimOverlapParam
alphaSpan SimOverlapBetaN2TP.SimOverlapParam
alphaSpan SimOverlapDisorderedAlphaN2RPScaling.SimOverlapParam
alphaSpan SimOverlapDisorderedAlphaN2TP.SimOverlapParam
alphaSpan MeterMBAR
alphaSpan AccumulatorOverlapAverageUa2
alphaSpan MeterOverlapSwitch
alphaSpan MeterTargetTP
alphaSpan SimOverlapSoftSphereEin.SimOverlapParam
alphaSpan SimOverlapSoftSphereEinHarm
alphaSpan SimOverlapSoftSphereEinHarm.SimOverlapParam
alphaSpan SimOverlapSoftSphereSoftness.SimOverlapParam
alphaSpan SimOverlapSoftSphereTP.SimOverlapParam
alphaSpan SimOverlapSoftSphereTPHCP.SimOverlapParam
alphaSpan SimOverlapSoftSphereTPSlantedBox.SimOverlapParam
alphaSpan MeterOverlap
alphaSpan AccumulatorVirialOverlapSingleAverage
alphaSpan DataProcessorVirialOverlap
alphaTag MultiharmonicGraphicMC.DataSourceAlphaChi
alphaTag MultiharmonicGraphicMC.DataSourceAlphaAlpha
alphaTag MultiharmonicGraphicMC.DataSourceAlphaChi
alphaTag MultiharmonicGraphicMC.DataSourceAlphaAlpha
alphaTag MultiharmonicGraphicMC.DataSourceAlphaChi
ALPREC Gamma
altArgbsCpk JmolConstants
altElementIndexFromNumber(int) Elements
altElementMax Elements
length of the altElementSymbols, altElementNames, altElementNumbers arrays
altElementNameFromIndex(int) Elements
altElementNumberFromIndex(int) Elements
altElementSymbolFromIndex(int) Elements
alternateStylesheet SVGConverter
Alternate stylesheet for which should be applied to the SVG
altIsotopeSymbolFromIndex(int) Elements
altIsotopeSymbolFromIndex2(int) Elements
altloc Token
ALTLOC EnumPalette
altVertices MeshSurface
alwaysScaleMomenta IntegratorMD
ambientFraction Shader
ambientpercent Token
ambientPercent Shader
AMINO EnumPalette
Ampere etomica.units
The ampere unit of electrical current.
and(Bitmap) Bitmap
and: bitmap -> bitmap = (bitmap & other).
and(Bitmap) AbstractBitmap
and(Bitmap) BitmapOfLong
TIME = O(1) for a compatible instance of other.
and(Bitmap) BitmapOfLongVector
and(BitSet) BitSet
Performs a logical AND of this target bit set with the argument bit
set.
ANDERSEN IntegratorMD.ThermostatType
ANDERSEN_SCALING IntegratorMD.ThermostatType
ANDERSEN_SINGLE IntegratorMD.ThermostatType
andNot(BitSet) BitSet
Clears all of the bits in this BitSet whose corresponding bit is
set in the specified BitSet.
andNot(BitSet, BitSet) BitSetUtil
angle Primitive
angle MeterTargetRPMolecule
angle SimDirectBetaN2RP.SimOverlapParam
angle SimOverlapBetaN2RP.SimOverlapParam
angle SimOverlapBetaN2RPScaling.SimOverlapParam
angle SimOverlapDisorderedAlphaN2RPScaling.SimOverlapParam
angle P3BondAngle
angle P3CPSNonAdditiveHeOrig
angle Orientation2D
angle Token
angle AxisAngle4f
The angle.
angle() CGS
angle() LJ
angle() MKS
angle() UnitSystem
angle() UnitSystem.Sim
angle(Vector3f) Vector3f
Returns the angle in radians between this vector and the vector parameter;
the return value is constrained to the range [0,PI].
Angle etomica.units.dimensions
Base for all angular units.
angleCCC ConformationAlkaneEH
angleCCC_half ConformationAlkaneEH
angleCCH ConformationAlkaneEH
angleHCH ConformationAlkaneEH
angleHCH_half ConformationAlkaneEH
angleHOH ConformationWater3P
angleHOH ConformationWaterTIP4P
anglePanel LatticeEditor
angles P2WaterPotentialsJankowski
Angstrom etomica.units
ANGSTROMS_PER_BOHR JmolConstants
angularMomentum MoleculeOrientedDynamic
angularVelocity AtomOrientedDynamic
angularVelocity MeterKineticEnergyRigid
angularVelocity IntegratorVelocityVerletQuaternion
animationfps Token
ANIntergroupCoupled etomica.atom.iterator
Iterator that returns coupled iterates of any size; the first set contains
the first atom from each basis.
ANIntergroupCoupled(int) ANIntergroupCoupled
ANIntergroupExchange etomica.atom.iterator
ANIntergroupExchange(int) ANIntergroupExchange
anIntragroupExchange ANIntergroupExchange
ANIntragroupExchange etomica.atom.iterator
ANIntragroupExchange(int, int) ANIntragroupExchange
anoise P2WaterPotentialsJankowski
ans MeterMappedAveragingPairExcess
Ans MeterMappedAveraging
Ans MeterMappedAveraging3Pair
Ans MeterMappedAveragingPair
Ans MeterMappedAveragingSum
Ans MeterMappedAveragingVSum
Ans MeterMappedAveragingVSum3Pair
Ans MeterMappedAveragingVSumPair
Ans MeterPairSum
antialiasdisplay Token
antialiasEnabled GData
antialiasimages Token
antialiasThisFrame GData
antialiastranslucent Token
aNumber MeterElongation
aNumber MeterStrain
anx PNCO2GCPM.P3GCPMAxilrodTeller
anyAtom(IAtom...) Debug
anyAtom(List<IAtom>) Debug
determines whether any of the atoms in the given array are set to be debugged
(via ATOMx_NUM)
anyMolecule(IMoleculeList) Debug
determines whether any of the atoms in the given array are set to be debugged
(via ATOMx_NUM)
apacheErfc() ErfcBenchmark
apacheFactorial() FactorialBenchmark
apacheLnFactorial() LnFactorialBenchmark
aPair MayerGeneralAtomic
aPairSet BoxCluster
api MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbrCell
Api1ACell etomica.nbr.cell
Generates pairs that are cell-based neighbors of a specific Atom.
Api1ACell(double, Box, NeighborCellManager) Api1ACell
Constructor makes iterator that must have box specified and then be
reset() before iteration.
Api1ASite etomica.nbr.site
Iteration is performed using site lists.
Api1ASite(int, BoxAgentManager) Api1ASite
Constructor makes iterator that must have box specified and then be
reset() before iteration.
ApiBuilder etomica.atom.iterator
Provides static methods for construction of some useful pair iterators.
apiDown MpiIntraspecies1A
ApiFilteredCylinder etomica.modules.pistoncylinder
Our own ApiFiltered that's box-dependent
ApiFilteredCylinder(ApiFilteredCylinder.AtomFilterInCylinder) ApiFilteredCylinder
ApiFilteredCylinder.AtomFilterInCylinder etomica.modules.pistoncylinder
Filter to expclude any pair with an atom within some distance from a
wall.
ApiIndexList etomica.atom.iterator
Iterator that returns intramolecular pairs of atoms with specific indices.
ApiIndexList(int[][]) ApiIndexList
Constructs iterator without defining atoms in pair.
ApiInnerVariable etomica.atom.iterator
Pair iterator synthesized from two atom iterators, such that the inner-loop
iteration depends on the outer-loop atom.
ApiInnerVariable(AtomIterator, AtomIteratorAtomDependent) ApiInnerVariable
Construct a pair iterator using the given atom iterators.
ApiInnerVariable(AtomIterator, AtomIteratorAtomDependent, boolean) ApiInnerVariable
Construct a pair iterator using the given atom iterators, indicating
whether the atoms ordering in the AtomPair should be swapped from the
default behavior.
ApiInterArrayList etomica.atom.iterator
Returns all pairs formed from two different untabbed lists of atoms.
ApiInterArrayList() ApiInterArrayList
Construct iterator with an empty lists.
ApiInterArrayList(IAtomList, IAtomList) ApiInterArrayList
Constructs iterator to return pairs from the given lists.
ApiIntergroup etomica.atom.iterator
Iterator that returns pairs formed using two different basis atoms, so that
the iterates are taken from two different groups.
ApiIntergroup() ApiIntergroup
Default iterator is an ApiInnerFixed formed from two AtomIteratorBasis
instances.
ApiIntergroup(AtomIteratorBasisDependent, AtomIteratorBasisDependent) ApiIntergroup
Constructs a pair iterator that returns iterates from the given
pairIterator, which is expected to contain two basis-dependent
iterators.
ApiIntergroupCoupled etomica.atom.iterator
Iterator that returns coupled iterates; the first pair contains the first
atom from each basis.
ApiIntergroupCoupled() ApiIntergroupCoupled
ApiIntergroupCoupled(AtomIteratorBasis, AtomIteratorBasis) ApiIntergroupCoupled
ApiIntergroupExchange etomica.atom.iterator
ApiIntergroupExchange(int) ApiIntergroupExchange
ApiIntergroupIntraSpecies etomica.atom.iterator
Iterator that returns pairs formed using two different basis atoms, so that
the iterates are taken from two different groups.
ApiIntergroupIntraSpecies(AtomIteratorBasisDependent, AtomIteratorBasisDependent) ApiIntergroupIntraSpecies
Constructs a pair iterator that returns iterates from the given
pairIterator, which is expected to contain two basis-dependent
iterators.
ApiIntraArrayList etomica.atom.iterator
Returns all pairs formed from a single list of atoms.
ApiIntraArrayList() ApiIntraArrayList
Construct iterator with an empty list.
ApiIntraArrayList(IAtomList) ApiIntraArrayList
Constructs iterator to return pairs from the given list.
ApiIntragroup etomica.atom.iterator
Returns iterates from the childList of a single basis atom.
ApiIntragroup() ApiIntragroup
Constructor makes iterator that must have basis specified and then be
reset() before iteration.
ApiIntragroup(AtomIteratorAtomDependent, AtomIteratorAtomDependent) ApiIntragroup
ApiIntragroup(AtomsetIteratorBasisDependent, AtomIteratorAtomDependent, AtomIteratorAtomDependent) ApiIntragroup
ApiLeafAtoms etomica.atom.iterator
Iterator that returns all pairs that can be formed from all leaf atoms of a
given box.
ApiLeafAtoms() ApiLeafAtoms
Creates new pair iterator that requires reset() before beginning
iteration.
apiPlatform GData
ApiPlatform org.jmol.api
APIPotentialReference(MeterHarmonicEnergy[]) SimOverlapLJModule.APIPotentialReference
APIPotentialTarget(PotentialMaster) SimOverlapLJModule.APIPotentialTarget
apiUp MpiIntraspecies1A
AppControllerMixtureBuilder etomica.virial.GUI.controllers
AppControllerMixtureBuilder(AppViewMixtureBuilder, AppModelMixtureBuilder) AppControllerMixtureBuilder
append(double[], double[]) VirialAlkaneEHTest
append(double[], double[]) VirialAlkaneFlex
append(double[], double[]) VirialCO2PI
append(double[], double[]) VirialH2PI
append(double[], double[]) VirialH2PIBoltzmann
append(double[], double[]) VirialH2PIXC
append(double[], double[]) VirialHePI_PotentialCorrection
append(double[], double[]) VirialHePI
append(double[], double[]) VirialHePISysErr
append(double[], double[]) VirialHePIXC
append(double[], double[]) VirialHePIXCEven
append(double[], double[]) VirialHePIXCOdd
append(ClusterBonds[], ClusterBonds[]) VirialAlkaneEHTest
append(ClusterBonds[], ClusterBonds[]) VirialAlkaneFlex
append(ClusterBonds[], ClusterBonds[]) VirialCO2PI
append(ClusterBonds[], ClusterBonds[]) VirialH2PI
append(ClusterBonds[], ClusterBonds[]) VirialH2PIBoltzmann
append(ClusterBonds[], ClusterBonds[]) VirialH2PIXC
append(ClusterBonds[], ClusterBonds[]) VirialHePI_PotentialCorrection
append(ClusterBonds[], ClusterBonds[]) VirialHePI
append(ClusterBonds[], ClusterBonds[]) VirialHePISysErr
append(ClusterBonds[], ClusterBonds[]) VirialHePIXC
append(ClusterBonds[], ClusterBonds[]) VirialHePIXCEven
append(ClusterBonds[], ClusterBonds[]) VirialHePIXCOdd
append(String) StringXBuilder
appendB(boolean) StringXBuilder
appendC(char) StringXBuilder
appendCB(char[], int, int) StringXBuilder
appendD(double) StringXBuilder
appendF(float) StringXBuilder
note that JavaScript could drop off the ".0" in "1.0"
appendI(int) StringXBuilder
appendnew Token
appendO(Object) StringXBuilder
appendSB(StringXBuilder) StringXBuilder
AppFrameMixtureBuilder etomica.virial.GUI.containers
AppFrameMixtureBuilder(String) AppFrameMixtureBuilder
Applet() DisplayPolytope.Applet
Applet() AkimaSplineSmootherApp.Applet
Applet() AkimaSplineSmootherDyApp.Applet
Applet() AdsorptionGraphic.Applet
Applet() CatalysisGraphic.Applet
Applet() ChainEquilibriumGraphic.Applet
Applet() FreeRadicalPolymerizationGraphic.Applet
Applet() ColloidGraphic.Applet
Applet() CrystalViewer.Applet
Applet() DCVGCMDGraphic.Applet
Applet() DropletAtomicGraphic.Applet
Applet() DropletGraphic.Applet
Applet() LJMCGraphic.Applet
Applet() InsertionGraphic.Applet
Applet() InterfacialSWGraphic.Applet
Applet() LjmdGraphic.Applet
Applet() MaterialFractureGraphic.Applet
Applet() MuGraphic.Applet
Applet() MultiharmonicGraphicMC.Applet
Applet() MultiharmonicGraphic.Applet
Applet() MultiharmonicGraphicMC.Applet
Applet() MultiharmonicGraphicMC.Applet
Applet() MultiharmonicGraphicMC.Applet
Applet() PistonCylinderGraphic.Applet
Applet() ReactionEquilibriumGraphic.Applet
Applet() RheologyGraphic.Applet
Applet() ReverseOsmosisGraphic.Applet
Applet() ReverseOsmosisWaterGraphic.Applet
Applet() SamGraphic.Applet
Applet() SwmdGraphic.Applet
Applet() B2Fit.Applet
Applet() VLE.Applet
Applet() HTTPSoftSphereApplet.Applet
Applet() NormalModeAnalysisDisplay1D.Applet
Applet() NormalModeAnalysisDisplay1DGraphic.Applet
Applet() NormalModeAnalysisDisplay2DGraphic.Applet
Applet() NormalModeAnalysisDisplay3D.Applet
Applet() NormalModeAnalysisDisplay3DGraphic.Applet
Applet() SimLJVacancy.Applet
Applet() DipoleBox.Applet
Applet() DipoleBoxMatrix.Applet
Applet() SingleDipole.Applet
Applet() SingleDumbellRattle.Applet
Applet() SingleDumbellShake.Applet
Applet() SingleWater.Applet
Applet() SingleWaterMatrix.Applet
Applet() SingleWaterRattle.Applet
Applet() SingleWaterShake.Applet
Applet() WaterBox.Applet
Applet() WaterDroplet.Applet
Applet() WaterDropletMatrix.Applet
Applet() WaterDropletRattle.Applet
Applet() WaterDropletShake.Applet
Applet() WaterTrimer.Applet
Applet() WaterTrimerRattle.Applet
Applet() WaterTrimerShake.Applet
Applet() LJMD3D.Applet
Applet() LJMD3DNbr.Applet
appletproxy Token
ApplicationMixtureBuilder etomica.virial.GUI
ApplicationMixtureBuilder() ApplicationMixtureBuilder
apply(Graph) DropOrphanNodes
apply(Graph) GraphOp
apply(Graph) GraphOp.GraphOpNull
apply(Graph) GraphOpMaxRoot
apply(Graph) SplitGraph
apply(Graph, Graph) MulUnion
apply(Graph, Graph, ConvParameters) Conv
apply(Graph, Graph, Mul.MulParameters) Mul
apply(Graph, Graph, MulFlexible.MulFlexibleParameters) MulFlexible
apply(Graph, AllIsomorphs.AllIsomorphsParameters) AllIsomorphs
apply(Graph, BiComponentSubst.BiComponentSubstParameters) BiComponentSubst
apply(Graph, CombineABSite.CombineABSiteParameters) CombineABSite
apply(Graph, ComponentSubst.ComponentSubstParameters) ComponentSubst
apply(Graph, DeleteEdgeParameters) DeleteEdge
apply(Graph, DifByConstant.DifByConstantParameters) DifByConstant
apply(Graph, DifParameters) DifByEdge
apply(Graph, ExcludeParameters) Exclude
apply(Graph, FactorOnce.FactorOnceParameters) FactorOnce
apply(Graph, IntParameters) Int
apply(Graph, MaxIsomorph.MaxIsomorphParameters) MaxIsomorph
apply(Graph, MaxIsomorphWertheim.MaxIsomorphWertheimParameters) MaxIsomorphWertheim
apply(Graph, MulFlexible.MulFlexibleParameters) Factor
apply(Graph, MulFlexible.MulFlexibleParameters) Unfactor
apply(Graph, MulScalarParameters) MulScalar
apply(Graph, MulScalarParameters) UnaryChain
apply(Graph, RelabelParameters) Relabel
apply(Graph, RelabelParameters) RelabelWertheim
apply(Graph, SplitOne.SplitOneParameters) SplitOne
apply(Graph, SplitOneBiconnected.SplitOneParametersBC) SplitOneBiconnected
apply(Graph, SplitParameters) Split
apply(Graph, BondConnectedSubstitution.BondConnectedSubstitutionParameters2Site) BondConnectedSubstitution
apply(Graph, BondConnectedSubstitution3Site.BondConnectedSubstitutionParameters3Site) BondConnectedSubstitution3Site
apply(Graph, BondConnectedSubstitutionNaphthalene.BondConnectedSubstitutionParameters2SiteNa) BondConnectedSubstitutionNaphthalene
apply(Graph, CondenseExchange.CondenseExchangeParameters) CondenseExchange
apply(Graph, List<Byte>) GraphExtract
apply(Graph, List<Integer>, List<Integer>) FactorOnce
apply(Set<Graph>, Parameters) AllIsomorphs
apply(Set<Graph>, Parameters) BiComponentSubst
apply(Set<Graph>, Parameters) CombineABSite
apply(Set<Graph>, Parameters) ComponentSubst
apply(Set<Graph>, Parameters) DecorateWertheim2Site
apply(Set<Graph>, Parameters) DecorateWertheim2SiteRho
apply(Set<Graph>, Parameters) DecorateWertheim3SiteRho
apply(Set<Graph>, Parameters) DecorateWertheimNaphthalene2Rho
apply(Set<Graph>, Parameters) DeleteEdge
apply(Set<Graph>, Parameters) DifByConstant
apply(Set<Graph>, Parameters) DifByEdge
apply(Set<Graph>, Parameters) DifByNode
apply(Set<Graph>, Parameters) Exclude
apply(Set<Graph>, Parameters) Exp
apply(Set<Graph>, Parameters) Factor
apply(Set<Graph>, Parameters) FactorOnce
apply(Set<Graph>, Parameters) IdenticalFree
apply(Set<Graph>, Parameters) Int
apply(Set<Graph>, Parameters) IsoFree
apply(Set<Graph>, Parameters) MaxIsomorph
apply(Set<Graph>, Parameters) MaxIsomorphWertheim
apply(Set<Graph>, Parameters) MulScalar
apply(Set<Graph>, Parameters) NCopy
apply(Set<Graph>, Parameters) PCopy
apply(Set<Graph>, Parameters) Pow
apply(Set<Graph>, Parameters) ReeHoover
apply(Set<Graph>, Parameters) Relabel
apply(Set<Graph>, Parameters) RelabelWertheim
apply(Set<Graph>, Parameters) SetPropertyFilter
apply(Set<Graph>, Parameters) Split
apply(Set<Graph>, Parameters) SplitOne
apply(Set<Graph>, Parameters) SplitOneBiconnected
apply(Set<Graph>, Parameters) Unary
apply(Set<Graph>, Parameters) UnaryChain
apply(Set<Graph>, Parameters) Unfactor
apply(Set<Graph>, Parameters) BondConnectedSubstitution
apply(Set<Graph>, Parameters) BondConnectedSubstitution3Site
apply(Set<Graph>, Parameters) BondConnectedSubstitutionNaphthalene
apply(Set<Graph>, Parameters) CondenseExchange
apply(Set<Graph>, Parameters) ExchangeSplit
apply(Set<Graph>, Set<Graph>[], Parameters) MulFlexible
apply(Set<Graph>, Set<Graph>, Parameters) Binary
apply(Set<Graph>, Set<Graph>, Parameters) Conv
apply(Set<Graph>, Set<Graph>, Parameters) Decorate
apply(Set<Graph>, Set<Graph>, Parameters) Delete
apply(Set<Graph>, Set<Graph>, Parameters) Mul
apply(Set<Graph>, Set<Graph>, Parameters) MulFlexible
apply(Set<Graph>, Set<Graph>, Parameters) MulUnion
apply(Set<Graph>, Set<Graph>, Parameters) Sub
apply(Set<Graph>, Set<Graph>, Parameters) Sum
apply(Set<Graph>, Set<Graph>, Parameters) Union
applyAnaglygh(EnumStereoMode, int[]) Graphics3D
applyAnaglygh(EnumStereoMode, int[]) GData
applyBlueAnaglyph() Graphics3D
applyColorTranslucencyLevel(short, float) Colix
applyCustomAnaglyph(int[]) Graphics3D
applyCyanAnaglyph() Graphics3D
applyExponentPattern(String) ScientificFormat
applyGreenAnaglyph() Graphics3D
applyLocalizedPattern(String) ScientificFormat
applyMantissaPattern(String) ScientificFormat
applyPattern(String) ScientificFormat
apply this pattern
applysymmetrytobonds Token
applyTranslationRotation() Polytope
Calculate transformed vertices from current values of vertices, position,
and orientation.
AppModelMixtureBuilder etomica.virial.GUI.models
AppModelMixtureBuilder() AppModelMixtureBuilder
appName SimulationGraphic
approx VLESim.GEMCParams
approx(float, float) Parser
APPROX VirialHePI.PotentialChoice
AppViewMixtureBuilder etomica.virial.GUI.views
AppViewMixtureBuilder(AppFrameMixtureBuilder, AppModelMixtureBuilder) AppViewMixtureBuilder
area SVGConverter
Output AOI area.
area() CGS
area() LJ
area() MKS
area() UnitSystem
area() UnitSystem.Sim
Area etomica.units.dimensions
Base for all area units.
areBonded(IAtom, IAtom) P2SquareWellBonded
This function tells you if two atoms are bonded
This could probably be public, although a public version would
need to first re-retrieve agents
areBonded(IAtom, IAtom) P2SquareWellRadical
This function tells you if two atoms are bonded
areEqual(ScriptVariable, ScriptVariable) ScriptVariable
areEqual(BitSet, BitSet) BitSetUtil
aRef VirialH2PIBoltzmann.VirialHePIParam
aRef VirialH2PIXC.VirialHePIParam
aRef VirialHePIXC.VirialHePIParam
aRef VirialHePIXCEven.VirialHePIParam
arep P2HydrogenHinde
arep P2HydrogenHindeAtomic
aResidualFcc(double, double) LennardJones
Molar Helmholtz free energy for the fcc solid, in excess of an ideal gas at the
same temperature and density.
arg() Complex
Argument of this Complex number, the angle in radians with the x-axis in polar coordinates.
argbCurrent GData
argbsAmino JmolConstants
argbsChainAtom JmolConstants
some pastel colors
C0D0FF - pastel blue
B0FFB0 - pastel green
B0FFFF - pastel cyan
FFC0C8 - pink
FFC0FF - pastel magenta
FFFF80 - pastel yellow
FFDEAD - navajowhite
FFD070 - pastel gold
FF9898 - light coral
B4E444 - light yellow-green
C0C000 - light olive
FF8060 - light tomato
00FF7F - springgreen
cpk on; select atomno>100; label %i; color chain; select selected & hetero; cpk off
argbsChainHetero JmolConstants
argbsCpk EnumPalette
Default table of CPK atom colors.
argbsCpkRasmol EnumPalette
argbsFormalCharge JmolConstants
argbShapelyBackbone JmolConstants
argbShapelyDefault JmolConstants
argbShapelySpecial JmolConstants
argbsIsosurfaceNegative JmolConstants
argbsIsosurfacePositive JmolConstants
argbsRoygbScale JmolConstants
argbsRwbScale JmolConstants
argbsShapely JmolConstants
Argon etomica.chem.elements
Class for the Argon element.
Argon(String) Argon
Argon(String, double) Argon
args Main
List of arguments describing the conversion task to be
performed.
args EtomicaModuleInfo
armLength MCMoveBondLength
armLength MCMoveClusterBondLength
armLength MCMoveClusterRotateArm
armLength MCMoveRotateArm
armLength MCMoveWiggle
array HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
array HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
array HarmonicBetaNitrogenModelPairMoleculeSequentialLS
array Token
ArrayA2B etomica.normalmode
Reads a file containing n mxm matrices as ASCII and serializes them to
another file.
ArrayA2B() ArrayA2B
ArrayB2A etomica.normalmode
Reads a file containing n mxm matrices as (serialized) binary data and
writes them to another file as text (ASCII).
ArrayB2A() ArrayB2A
arrayCollect(String[], String[]) Strings
Takes the elements of two string arrays and collects them
into a new array containing both sets of strings.
arrayCopyBool(boolean[], int) ArrayUtil
arrayCopyByte(byte[], int) ArrayUtil
arrayCopyF(float[], int) ArrayUtil
arrayCopyI(int[], int) ArrayUtil
arrayCopyII(int[][], int) ArrayUtil
arrayCopyObject(Object, int) ArrayUtil
note -- cannot copy if array is null!
arrayCopyPt(Point3f[], int) ArrayUtil
arrayCopyRangeI(int[], int, int) ArrayUtil
a specialized method that allows copying from a starting point either
to the end or to the middle (color schemes, especially)
arrayCopyRangeRevI(int[], int, int) ArrayUtil
arrayCopyS(String[], int) ArrayUtil
arrayCopyShort(short[], int) ArrayUtil
arrayIndex(int[]) RectangularLattice
Returns the index in the 1-d array for the site corresponding
to the given lattice index.
ArrayMoleculeDisplayList etomica.virial.GUI.components
ArrayMoleculeDisplayList() ArrayMoleculeDisplayList
ArrayProperty etomica.meta.properties
Container class for mapping an instance to an array property.
ArrayProperty(Object, PropertyDescriptor) ArrayProperty
ArrayReader1D etomica.math.numerical
Reads in lots of 1D arrays from a file.
ArrayReader1D etomica.normalmode
Reads in lots of 1D arrays from a file.
ArrayReader1D() ArrayReader1D
ArrayReader1D() ArrayReader1D
ArrayReader2D etomica.normalmode
Reads in lots of 2D arrays from a file.
ArrayReader2D() ArrayReader2D
Arrays etomica.util
Non-instantiable class with static utility methods for working with arrays.
arrayShape DataDoubleArray.DataInfoDoubleArray
arrayShape DataDoubleBDArray.DataInfoDoubleBDArray
arraySize MeterMappedAveragingCorrelation
ArrayUtil org.jmol.util
ArrayUtil() ArrayUtil
ArticulatedAt0(boolean) VirialDiagrams.ArticulatedAt0
ArticulatedAt0(boolean) VirialDiagramsPT.ArticulatedAt0
ArticulatedAt0(boolean, char) VirialDiagrams.ArticulatedAt0
ArticulatedAt0(boolean, char) VirialDiagramsPT.ArticulatedAt0
articulationPair FFTDecomposition
articulationPoints HasSimpleArticulationPoint
aS_AD P2HePCJS
aS_BO P2HePCJS
aS_QED P2HePCJS
aS_REL P2HePCJS
asBoolean() ScriptVariable
asFloat() ScriptVariable
AshtonWildingLJ etomica.osmoticvirial
Extends Ashton and Wilding approach for calculation of gas virial coefficient
to Lennard-Jones model.
AshtonWildingLJ(int, double, boolean) AshtonWildingLJ
AshtonWildingLJ.simParams etomica.osmoticvirial
AshtonWildingOsmoticVirial etomica.osmoticvirial
Implements Ashton and Wilding method for calculation of osmotic virial coefficient (B2, B3)
for Hard-Sphere model as described in the paper DOI: 10.1063/1.4883718.
AshtonWildingOsmoticVirial(int, double, double, boolean, double, double, boolean) AshtonWildingOsmoticVirial
AshtonWildingOsmoticVirial.simParams etomica.osmoticvirial
AshtonWildingVirial etomica.osmoticvirial
Implements Ashton and Wilding method for calculation of gas virial coefficients (B2, B3)
for Hard-Sphere model as described in the paper DOI: 10.1063/1.4883718.
AshtonWildingVirial(int, double, boolean, boolean) AshtonWildingVirial
AshtonWildingVirial.simParams etomica.osmoticvirial
asin(BigDecimal) BigDecimalMath
The inverse trigonometric sine.
asinh(BigDecimal) BigDecimalMath
The inverse hyperbolic sine.
asInt() ScriptVariable
Asolid(double) HardSphereFluid
Returns the difference between absolute free energies between the given
densities for solid (FCC) hard spheres.
Asolid(double) HardSphereSolid
Returns the difference between absolute free energies between the given
densities for solid (FCC) hard spheres.
Asolid(double, int) HardSphereFluid
Returns the difference between absolute free energies between the given
densities for solid (FCC) hard spheres.
Asolid(double, int) HardSphereSolid
aspectRatio LJMC.LJMCParams
assignCell(IAtom) NeighborCellManager
Assigns the cell for the given atom.
assignCell(IMolecule) NeighborCellManagerMolecular
Assigns the cell for the given atom.
assignCellAll() BoxCellManager
Assigns cells to all molecules in the box.
assignCellAll() NeighborCellManagerMolecular
Assigns cells to all interacting atoms in the box.
assignCellAll() NeighborCellManager
Assigns cells to all interacting atoms in the box.
assignCellAll() NeighborSiteManager
Should not be called, because cell assignments are made as atoms are created.
assignColumnFrom(int, double[]) DataDoubleArray
Assigns values in given array to the i-th "hypercolumn" of this data array.
assignColumnFrom(int, BigDecimal[]) DataDoubleBDArray
Assigns values in given array to the i-th "hypercolumn" of this data array.
assignColumnTo(int, double[]) DataDoubleArray
Assigns values in the i=th "hypercolumn" of this array to the given array.
assignColumnTo(int, BigDecimal[]) DataDoubleBDArray
Assigns values in the i=th "hypercolumn" of this array to the given array.
AssignmentImpl etomica.graph.engine.impl
AssignmentImpl(Parser.Variable, Parser.StrictExpression) AssignmentImpl
assignSubsectionFrom(int[], double[]) DataDoubleArray
Assigns values in the given array to the subsection of this array
beginning at the specified index.
assignSubsectionFrom(int[], double[]) DataDoubleBDArray
Assigns values in the given array to the subsection of this array
beginning at the specified index.
assignTo(double[]) IData
Fills the given array with the values held by this Data instance.
assignTo(double[]) DataDouble
Returns a new one-element array formed from the current value of this
instance.
assignTo(double[]) DataDoubleArray
Returns the encapsulated array, implementing the Data interface.
assignTo(double[]) DataDoubleBDArray
Returns the encapsulated array, implementing the Data interface.
assignTo(double[]) DataGroup
assignTo(double[]) DataTable
Returns a new array formed from the values held by the data instance.
assignTo(double[]) DataTensor
Returns a new array formed by the elements of the wrapped tensor.
assignTo(double[]) DataVector
Assigns the elements of the wrapped vector to the given array.
assignTo(double[]) Tensor
Fills the given array with the elements of this tensor.
assignTo(double[]) Vector
Assigns the components of this vector to the elements of the given array.
assignTo(double[]) Tensor1D
assignTo(double[]) Vector1D
assignTo(double[]) Tensor2D
assignTo(double[]) Vector2D
assignTo(double[]) Tensor3D
assignTo(double[]) Vector3D
assignTo(double[]) TensorND
assignTo(double[]) VectorND
assignTo(double[][]) Tensor
Fills the given 2-dimensional array with the elements of this tensor.
assignTo(double[][]) Tensor1D
assignTo(double[][]) Tensor2D
assignTo(double[][]) Tensor3D
assignTo(double[][]) TensorND
assignTo(Vector[]) Tensor
Assigns the tensor elements column-wise to the given vectors.
assignTo(Vector[]) Tensor1D
assignTo(Vector[]) Tensor2D
assignTo(Vector[]) Tensor3D
assignTo(Vector[]) TensorND
association(MoleculePair, Box) ConfigurationClusterWertheimGCPM
association(MoleculePair, Box) ConfigurationClusterWertheimGCPM4Pt
association(MoleculePair, Box) ConfigurationClusterWertheimGCPMDirectSampling
association(MayerFunction, MoleculePair, Box) ConfigurationClusterAceticAcid
association2(MoleculePair, Box) ConfigurationClusterWertheimGCPM
association2(MoleculePair, Box) ConfigurationClusterWertheimGCPM4Pt
association2(MoleculePair, Box) ConfigurationClusterWertheimGCPMDirectSampling
association3(MoleculePair, Box) ConfigurationClusterWertheimGCPM
association3(MoleculePair, Box) ConfigurationClusterWertheimGCPM4Pt
association3(MoleculePair, Box) ConfigurationClusterWertheimGCPMDirectSampling
association4(MoleculePair, Box) ConfigurationClusterWertheimGCPMDirectSampling
association4(MoleculePair, MoleculePair, Box) ConfigurationClusterWertheimGCPM
association4(MoleculePair, MoleculePair, Box) ConfigurationClusterWertheimGCPM4Pt
association5(MoleculePair, MoleculePair, Box) ConfigurationClusterWertheimGCPM
association5(MoleculePair, MoleculePair, Box) ConfigurationClusterWertheimGCPM4Pt
association6(MoleculePair, MoleculePair, Box) ConfigurationClusterWertheimGCPM
AssociationDefinition etomica.association
Interface for a method that defines whether two atoms are considered associated.
AssociationDefinitionMolecule etomica.association
Interface for a method that defines whether two molecules are considered associated.
associationEnergy Wertheim2SiteAceticAcid.WertheimParam
associationEnergy WertheimGCPM3PtEBondDecomp.VirialAssociatingFluidParam
associationEnergy WertheimGCPM3PtThreeSite.VirialAssociatingFluidParam
associationEnergy WertheimGCPM4PtEBondDecomp.WertheimAssociatingFluidParam
associationEnergy WertheimGCPM4PtEBondDecompFinal.VirialAssociatingFluidParam
associationEnergy WertheimGCPM4PtThreeSite.VirialAssociatingFluidParam
associationEnergy WertheimGCPM4PtThreeSiteEDecompDirectSampling.VirialAssociatingFluidParam
associationHelper TestAceticAcidMC3D_NPT
associationHelper ColorSchemeSmer
associationHelper ColorSchemeSmerByLength
associationHelper MCMoveMoleculeMonomer
associationHelper MCMoveMoleculeRotateAssociated
associationHelper MCMoveMoleculeSmer
associationHelper MCMoveVolumeAssociatedMolecule
associationHelper TestIGAssociationMC3D_NPT_DoubleSites
associationHelper TestLJAssociationMC3D_NPT_DoubleSites
associationHelper TestLJAssociationMC3D_NPT
associationHelper TestLJAssociationMC3D_NVTOld
AssociationHelperBranched etomica.association
AssociationHelperBranched is capable of populating a list of atoms in an smer
within a simulation with multiple association sites per atom.
AssociationHelperBranched(Space, Box, AssociationManager) AssociationHelperBranched
AssociationHelperDouble etomica.association
AssociationHelperDouble is capable of populating a list of atoms in an smer
within a simulation with double-bonding (two bonding sites per atom).
AssociationHelperDouble(Space, Box, AssociationManager) AssociationHelperDouble
AssociationHelperMolecule etomica.association
AssociationHelperBranched is capable of populating a list of molecules in an smer
within a simulation with multiple association sites per molecule.
AssociationHelperMolecule(Space, Box, AssociationManagerMolecule) AssociationHelperMolecule
AssociationHelperSingle etomica.association
AssociationHelperSingle is capable of populating a list of atoms in an smer
within a simulation with single-bonding (one bonding site per atom).
AssociationHelperSingle(AssociationManager) AssociationHelperSingle
associationManager TestAceticAcidMC3D_NPT
associationManager AssociationHelperBranched
associationManager AssociationHelperDouble
associationManager AssociationHelperMolecule
associationManager AssociationHelperSingle
associationManager AtomSourceRandomDimer
associationManager AtomSourceRandomMonomer
associationManager AtomSourceRandomSmer
associationManager MCMoveAtomDimer
associationManager MCMoveAtomMonomer
associationManager MCMoveAtomNoSmer
associationManager MCMoveAtomSmer
associationManager MCMoveDimer
associationManager MCMoveDimerRotate
associationManager MCMoveMoleculeMonomer
associationManager MCMoveMoleculeRotateAssociated
associationManager MCMoveMoleculeSmer
associationManager MCMoveRotateAssociated
associationManager MCMoveRotateNoSmer
associationManager MCMoveSmer
associationManager MCMoveSmerRotate
associationManager MCMoveVolumeAssociated
associationManager MCMoveVolumeAssociatedMolecule
associationManager MoleculeSourceRandomDimer
associationManager MoleculeSourceRandomMonomer
AssociationManager etomica.association
Class to define and track atom associations.
AssociationManager(Box, PotentialMasterCell, AssociationDefinition) AssociationManager
AssociationManagerMolecule etomica.association
Class to define and track molecule associations.
AssociationManagerMolecule(Simulation, Box, BoxAgentManager<NeighborCellManagerMolecular>, AssociationDefinitionMolecule, double) AssociationManagerMolecule
associationManagerOriented TestIGAssociationMC3D_NPT_DoubleSites
associationManagerOriented TestLJAssociationMC3D_NPT_DoubleSites
associationManagerOriented TestLJAssociationMC3D_NPT
associationManagerOriented TestLJAssociationMC3D_NVTOld
associationPotential ConfigurationClusterWertheimGCPM
associationPotential ConfigurationClusterWertheimGCPM4Pt
associationPotential ConfigurationClusterWertheimGCPMDirectSampling
associationPotential2 ConfigurationClusterWertheimGCPM
associationPotential2 ConfigurationClusterWertheimGCPM4Pt
associationPotential2 ConfigurationClusterWertheimGCPMDirectSampling
associationPotential3 ConfigurationClusterWertheimGCPM
associationPotential3 ConfigurationClusterWertheimGCPM4Pt
associationPotential3 ConfigurationClusterWertheimGCPMDirectSampling
asString() ScriptVariable
asymp(double, double, double, double) P2HydrogenPatkowski
asymp(double, double, double, double) P2HydrogenPatkowskiAtomic
at(int) Bernoulli
The Bernoulli number at the index provided.
at(int) BigIntegerPoly
Retrieve a polynomial coefficient.
at(int) Euler
The Euler number at the index provided.
at(int) EulerPhi
Compute phi(n).
at(int) Factorial
Compute the factorial of the non-negative integer.
at(int) Harmonic
The Harmonic number at the index specified
at(int) PartitionsP
return the number of partitions of i
at(int) Prime
return the ithprime
at(BigInteger) EulerPhi
Compute phi(n).
atan(BigDecimal) BigDecimalMath
The inverse trigonometric tangent.
aTarget VirialH2PIBoltzmann.VirialHePIParam
aTarget VirialH2PIXC.VirialHePIParam
aTarget VirialHePIXC.VirialHePIParam
aTarget VirialHePIXCEven.VirialHePIParam
atom MCMoveDimer
atom MCMoveDimerRotate
atom MCMoveSmer
atom MCMoveSmerRotate
atom AtomSetSinglet
atom BoxAtomEvent
atom MCMoveAtomCoupled
atom MCMoveAtomSwap
atom IntegratorHard.Agent
atom MCMoveAtom
atom MCMoveDimer
atom MCMoveDimerRotate
atom MCMoveGeometricClusterRestrictedGE
atom PotentialReactive.BondChangeData
atom MCMoveSpinFlip
atom MeterVirialExternalFieldSW.Near
atom() IntegratorHard.Agent
Atom etomica.atom
Atom that represents a physical atom with a position.
Atom(Space) Atom
Makes a simple atom for the given space.
Atom(Space, AtomType) Atom
atom_aC_A IntegratorDimerApproach
atom_aC_B IntegratorDimerApproach
atom_aH_A IntegratorDimerApproach
atom_aH_B IntegratorDimerApproach
atom_H1_A IntegratorDimerApproach
ATOM_IN_FRAME JmolConstants
atom_O_A IntegratorDimerApproach
atom_O_B IntegratorDimerApproach
ATOM_SIZE Debug
The minimum allowable distance between Atoms.
ATOM_SLABBED JmolConstants
atom0 AtomPair
atom0 MCMoveAtomCoupled
atom0 MCMoveAtomCoupledBennet
atom0 MCMoveAtomCoupledUmbrella
atom0 MCMoveAtomSuperBox
atom1 MCMoveDimer
atom1 MCMoveDimerRotate
atom1 AtomPair
atom1 ApiIntergroupExchange
atom1 DataSourceAtomDistance
atom1 MCMoveDimer
atom1 MCMoveDimerRotate
atom1 MCMoveAtomCoupled
atom1 MCMoveAtomCoupledBennet
atom1 MCMoveAtomCoupledUmbrella
atom1 MCMoveAtomSuperBox
ATOM1_INDEX Debug
Atom index of first atom of interest.
atom2 ApiIntergroupExchange
atom2 DataSourceAtomDistance
atom2 MCMoveAtomCoupled
atom2 MCMoveAtomSwap
ATOM2_INDEX Debug
Atom index of second atom of interest.
atomA MCMoveSwap
AtomAction etomica.action
Performs an action on an atom.
atomActionRandomizeVelocity BoxRandomizeMomenta
atomActionRandomizeVelocity IntegratorMD
AtomActionRandomizeVelocity etomica.action
Action that sets the velocity vector of a given atom to a randomly
chosen value sampled from a Boltzmann distribution.
AtomActionRandomizeVelocity(double, IRandom) AtomActionRandomizeVelocity
Constructs class to assign velocities according to the given temperature.
atomActionRotateBy IntegratorDimerApproach
AtomActionRotateBy etomica.action
Performs RIGHT-HANDED rotations of an atom about the x-, y-, and z-axes by the specified angles (roll, pitch, and yaw angles, respectively) in radians.
AtomActionRotateBy(Space) AtomActionRotateBy
AtomActionTransformed etomica.action
Moves (translates) an atom by a specified vector amount.
AtomActionTransformed etomica.models.nitrogen
Moves (translates) an atom by a specified vector amount.
AtomActionTransformed(Space) AtomActionTransformed
AtomActionTransformed(Space) AtomActionTransformed
atomActionTranslateBy IntegratorDimerApproach
AtomActionTranslateBy etomica.action
Moves (translates) an atom by a specified vector amount.
AtomActionTranslateBy(Space) AtomActionTranslateBy
atomActionTranslateTo ConfigurationLattice
atomActionTranslateTo ConfigurationLatticeSimple
atomActionTranslateTo LatticeSumCrystalMolecular
atomActionTranslateTo CoordinateDefinition
atomAgent0 IntegratorDimerMin
atomAgent0 IntegratorDimerRT
atomAgent1 IntegratorDimerRT
atomAgent2 IntegratorDimerRT
atomAgentClass BoxAgentSourceAtomManager
atomAgentManager LatticeSumMolecularCrystal
atomAgentManager EwaldSummation
atomAgentManager EwaldSumMolecules
atomAgentManager P1HarmonicSite
atomAgentMin IntegratorDimerMin
atomAgentSource BoxAgentSourceAtomManager
AtomArrayList etomica.atom
AtomArrayList() AtomArrayList
AtomArrayList(int) AtomArrayList
AtomArrayList(IAtomList) AtomArrayList
atomB MCMoveSwap
atomColor ClipPlaneEditor
AtomFilterInCylinder(Boundary, P1HardMovingBoundary, double) ApiFilteredCylinder.AtomFilterInCylinder
AtomForceAgent(Space) IntegratorRigidIterative.AtomForceAgent
atomGroupAction CoordinateDefinitionNitrogen
atomGroupAction CoordinateDefinitionNitrogenSuperBox
atomGroupAction LatticeSumCrystalMolecular
atomGroupAction MCMoveRotateMolecule3DConstraint
atomGroupAction MCMoveRotateMolecule3DFixedAngle
atomGroupAction MinimizationBetaNitrogenModelLS
atomGroupAction CoordinateDefinitionHSDimer
atomGroupActionRotateBy IntegratorDimerApproach
atomGroupActionTranslate CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
atomGroupActionTranslate CalcNumerical2ndDerivativeNitrogen
atomGroupActionTranslate CoordinateDefinitionNitrogen
atomGroupActionTranslate HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
atomGroupActionTranslate HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
atomGroupActionTranslate HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
atomGroupActionTranslate HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
atomGroupActionTranslate HarmonicBetaNitrogenModelPairMoleculeSequentialLS
atomGroupActionTranslate HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
atomGroupActionTranslate HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
atomGroupActionTranslate LatticeSumCrystalMolecular
atomGroupActionTranslate MinimizationBetaNitrogenModelLS
atomGroupActionTranslateBy IntegratorDimerApproach
AtomGroupVelocityAverage etomica.atom
Calculates the mass average velocity over a set of atoms.
AtomGroupVelocityAverage(Space) AtomGroupVelocityAverage
AtomHardStressCollector etomica.modules.glass
AtomHardStressCollector(IntegratorHard) AtomHardStressCollector
AtomHydrogen etomica.atom
AtomHydrogen(Space, AtomTypeOriented, double) AtomHydrogen
atomicMass Elements
atomicNumber ElementChemical
atomicPotentials PotentialMasterLrc
atomicTensor(IAtom, IAtom) P2Water4PSoft.AtomicTensorAtomicPair
atomicTensor(IAtom, IAtom) LatticeSumMolecularCrystal.AtomicTensorAtomicPair
atomicTensorAtomicPair NormalModesMolecular
atomicToMolecularD(IMolecule, IMolecule) P2Water4PSoft
atomicToMolecularD(LatticeSumMolecularCrystal.AtomicTensorAtomicPair, IMolecule, IMolecule) LatticeSumMolecularCrystal
atomid Token
ATOMID_ALPHA_CARBON JmolConstants
ATOMID_ALPHA_ONLY_MASK JmolConstants
ATOMID_AMINO_NITROGEN JmolConstants
ATOMID_C1_PRIME JmolConstants
ATOMID_C2 JmolConstants
ATOMID_C3_PRIME JmolConstants
ATOMID_C4 JmolConstants
ATOMID_C4_PRIME JmolConstants
ATOMID_C5 JmolConstants
ATOMID_C5M JmolConstants
ATOMID_C6 JmolConstants
ATOMID_C7 JmolConstants
ATOMID_C8 JmolConstants
ATOMID_CARBONYL_CARBON JmolConstants
ATOMID_CARBONYL_OD1 JmolConstants
ATOMID_CARBONYL_OD2 JmolConstants
ATOMID_CARBONYL_OE1 JmolConstants
ATOMID_CARBONYL_OE2 JmolConstants
ATOMID_CARBONYL_OXYGEN JmolConstants
ATOMID_DISTINGUISHING_ATOM_MAX JmolConstants
ATOMID_H3T_TERMINUS JmolConstants
ATOMID_H5T_TERMINUS JmolConstants
ATOMID_HO3_PRIME JmolConstants
ATOMID_HO5_PRIME JmolConstants
ATOMID_MAX JmolConstants
ATOMID_N1 JmolConstants
ATOMID_N2 JmolConstants
ATOMID_N3 JmolConstants
ATOMID_N4 JmolConstants
ATOMID_N6 JmolConstants
ATOMID_N7 JmolConstants
ATOMID_N9 JmolConstants
ATOMID_NUCLEIC_MASK JmolConstants
ATOMID_NUCLEIC_PHOSPHORUS JmolConstants
ATOMID_O1 JmolConstants
ATOMID_O1P JmolConstants
ATOMID_O2 JmolConstants
ATOMID_O2_PRIME JmolConstants
ATOMID_O2P JmolConstants
ATOMID_O3_PRIME JmolConstants
ATOMID_O4 JmolConstants
ATOMID_O5_PRIME JmolConstants
ATOMID_O5T_TERMINUS JmolConstants
ATOMID_O6 JmolConstants
ATOMID_OP1 JmolConstants
ATOMID_OP2 JmolConstants
ATOMID_PHOSPHORUS_ONLY_MASK JmolConstants
ATOMID_PROTEIN_MASK JmolConstants
ATOMID_S4 JmolConstants
ATOMID_SG JmolConstants
ATOMID_TERMINATING_OXT JmolConstants
atomindex Token
atomIterator MCMoveAtomSwap
atomIterator MCMoveInsertDeleteLatticeVacancy
atomIterator MCMoveGeometricCluster
atomIterator MCMoveGeometricClusterRestrictedGE
atomIterator MCMoveSpinCluster
AtomIterator etomica.atom.iterator
Interface for classes that loop over a set of atoms.
AtomIterator0() PotentialMaster.AtomIterator0
AtomIteratorArrayList etomica.atom.iterator
An atom iterator of the elements from an AtomArrayList (in proper
sequence).
AtomIteratorArrayList(IteratorDirective.Direction) AtomIteratorArrayList
Constructs new iterator with an empty list.
AtomIteratorArrayList(IteratorDirective.Direction, int) AtomIteratorArrayList
Constructs new iterator set to iterate given list (upon reset).
AtomIteratorArrayList(IteratorDirective.Direction, int, AtomToIndex, AtomToAtomLeafList) AtomIteratorArrayList
AtomIteratorArrayListAdjacent etomica.atom.iterator
Returns one or both of the atoms adjacent to a specified atom in
its parent's child list.
AtomIteratorArrayListAdjacent(IteratorDirective.Direction) AtomIteratorArrayListAdjacent
Constructor gives iterator not ready for iteration.
AtomIteratorArrayListAdjacent(IteratorDirective.Direction, AtomToIndex, AtomToAtomLeafList) AtomIteratorArrayListAdjacent
AtomIteratorArrayListSimple etomica.atom.iterator
An atom iterator of the elements from an AtomArrayList (in proper
sequence).
AtomIteratorArrayListSimple() AtomIteratorArrayListSimple
Constructs new iterator with an empty list.
AtomIteratorArrayListSimple(IAtomList) AtomIteratorArrayListSimple
Constructs new iterator set to iterate given list (upon reset).
AtomIteratorAtomDependent etomica.atom.iterator
Interface for an atom iterator that can be altered by setting
of an atom.
AtomIteratorBasis etomica.atom.iterator
Elementary basis-dependent iterator that gives atoms meeting specification
of a basis and a target.
AtomIteratorBasis() AtomIteratorBasis
Constructor makes iterator in an unset condition; must set basis and call reset before
beginning iteration.
AtomIteratorBasisAdjustableStart etomica.atom.iterator
Elementary basis-dependent iterator that gives atoms meeting specification
of a basis and a target.
AtomIteratorBasisAdjustableStart() AtomIteratorBasisAdjustableStart
Constructor makes iterator in an unset condition; must set basis and call reset before
beginning iteration.
AtomIteratorBasisDependent etomica.atom.iterator
AtomIteratorBasisFilteredType etomica.atom.iterator
AtomIteratorBasisFilteredType(AtomType) AtomIteratorBasisFilteredType
AtomIteratorBasisFilteredType2 etomica.atom.iterator
This iterator returns atoms that are one of two types.
AtomIteratorBasisFilteredType2(AtomType, AtomType) AtomIteratorBasisFilteredType2
AtomIteratorBoxDependent etomica.atom.iterator
Interface indicating that an atom iterator can determine appropriate
atoms for iteration given an arbitrary box.
AtomIteratorBruteForce(Box) MCMoveInsertDeleteLatticeVacancy.AtomIteratorBruteForce
AtomIteratorLeafAtoms etomica.atom.iterator
Iterator that will loop over all leaf atoms in a box.
AtomIteratorLeafAtoms() AtomIteratorLeafAtoms
Creates iterator with no box specified.
AtomIteratorLeafAtoms(Box) AtomIteratorLeafAtoms
Creates iterator conditioned to give all leaf atoms of the specified
box.
AtomIteratorLeafFilteredType etomica.atom.iterator
AtomIteratorLeafFilteredType(Box, AtomType) AtomIteratorLeafFilteredType
AtomIteratorNbr(NeighborListManager) MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbr
AtomIteratorNbrCell(double, NeighborCellManager, Box) MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbrCell
AtomIteratorNull etomica.atom.iterator
Static iterator that returns no atoms.
AtomIteratorSinglet etomica.atom.iterator
Iterator that expires after returning a single atom, which is
specified by a call to the setAtom method, or via the constructor.
AtomIteratorSinglet() AtomIteratorSinglet
Constructs iterator without defining atom.
AtomIteratorSinglet(IAtom) AtomIteratorSinglet
Constructs iterator specifying that it return the given atom.
atomLeafAgentManager MCMoveVolumeAssociated
AtomLeafAgentManager E > - Class in etomica.atom
AtomAgentManager acts on behalf of client classes (an AgentSource) to
manage agents for every leaf Atom in a box.
AtomLeafAgentManager(AtomLeafAgentManager.AgentSource<E>, Box) AtomLeafAgentManager
AtomLeafAgentManager(Function<IAtom, ? extends E>, Box) AtomLeafAgentManager
AtomLeafAgentManager.AgentSource E > - Interface in etomica.atom
Interface for an object that wants an agent associated with each Atom in
a Box.
AtomLeafDynamic etomica.atom
AtomLeafDynamic(Space, AtomType) AtomLeafDynamic
atomLeafIndexChanged(IAtom, int) BoxEventManager
AtomLeafsetIterator etomica.atom.iterator
Interface for classes that loop over a set of atoms.
atomList ANIntragroupExchange
atomList MeterStructureFactor
AtomListFromArray etomica.atom
AtomSet formed by wrapping an Atom array.
AtomListFromArray(int) AtomListFromArray
Wraps a new atom array of the given length.
AtomListFromArray(IAtom[]) AtomListFromArray
Wraps the given atom array.
AtomListProperty etomica.meta.properties
Created by kofke on 7/24/17.
AtomListProperty(Object, PropertyDescriptor) AtomListProperty
atomLists ANIntergroupCoupled
atomMove SimEinStep1
atomMove SimEinStep1HCP
atomMove SimEinStep2
atomMove SimEinStep2HCP
atomMove SimLJHTTISuper
atomMove SimLJHTTISuperHCP
atomMove SimLJHTTISuperHCP2
atomMove SimOverlapSoftSphere
atomMove SimOverlapSoftSphereDP
atomMove SimOverlapSoftSphereEin
atomMove SimOverlapSoftSphereEinHarm
atomMove SimOverlapSoftSphereHCP
atomMove SimOverlapSoftSphereTP
atomMove SimOverlapSoftSphereTPHCP
atomMove SimOverlapSoftSphereTPSlantedBox
atomMove SimOverlapSSnxy
atomMoveRef SimOverlapSoftSphereSoftness
atomMoveTarg SimOverlapSoftSphereSoftness
atomname Token
AtomNbrClusterer etomica.modules.glass
AtomNbrClusterer(Box, AtomTest) AtomNbrClusterer
AtomNbrClusterer(Box, AtomTest, boolean) AtomNbrClusterer
AtomNeighborLists etomica.nbr.list
Class used to maintain neighbor lists.
AtomNeighborLists() AtomNeighborLists
Constructs sequencer for the given atom.
atomno Token
atomNumber StrainColorScheme
atomNumberMod StrainColorScheme
AtomOriented etomica.atom
AtomOriented(Space, AtomType) AtomOriented
AtomOriented(Space, AtomType, boolean) AtomOriented
AtomOrientedDynamic etomica.atom
AtomOrientedDynamic(Space, AtomType) AtomOrientedDynamic
AtomOrientedDynamic(Space, AtomType, boolean) AtomOrientedDynamic
AtomOrientedQuaternion etomica.atom
AtomOrientedQuaternion(Space, AtomType) AtomOrientedQuaternion
atomPair MCMoveGeometricCluster
atomPair MCMoveGeometricClusterRestrictedGE
atomPair PotentialMasterMonatomic
AtomPair etomica.atom
Data structure that contains two mutable atom instances.
AtomPair() AtomPair
AtomPair(IAtom, IAtom) AtomPair
atomPairs MCMoveGeometricCluster
atomPairs MCMoveGeometricClusterRestrictedGE
atomPairs MCMoveSpinCluster
AtomPairSet etomica.virial
Class that holds a set of atom pairs.
AtomPairSet(IMoleculeList) AtomPairSet
Constructor for AtomPairSet.
atompicking Token
atomPosDef LatticeSumMolecularCrystal
atomPositionCOM IntegratorRigidIterative
atomPositionCOM IntegratorRigidMatrixIterative
atomPositionCOM OrientationCalcWater3P
atomPositionCOM OrientationCalcWater4P
atomPositionCOM IntegratorVelocityVerletQuaternion
AtomPotential1ListSource(PotentialMasterList) NeighborListManager.AtomPotential1ListSource
AtomPotentialList etomica.nbr.list
Class used to maintain list of whether each 1-body potential that applies to an AtomType is currently in effect or
not for an Atom.
AtomPotentialList() AtomPotentialList
Constructs sequencer for the given atom.
atomproperty Token
atoms ANIntergroupCoupled
atoms ANIntergroupExchange
atoms ANIntragroupExchange
atoms MCMoveAtomCoupled
atoms MCMoveAtomSwap
atoms PotentialMolecularMonatomic
atoms ClusterSumNonAdditiveTrimerEnergy
atoms CoordinatePairMoleculeSet
atoms MCMoveClusterRingPartialRegrow
atoms MCMoveClusterRingScale
atoms Token
Atomset3IteratorIndexList etomica.atom.iterator
Atomset Iterator that iterates over set-of-three atoms
Atomset3IteratorIndexList(int[][]) Atomset3IteratorIndexList
Constructs iterator without defining set of atoms.
Atomset4IteratorIndexList etomica.atom.iterator
Atomset Iterator that iterates over set-of-four atoms
Atomset4IteratorIndexList(int[][]) Atomset4IteratorIndexList
Constructs iterator without defining set of atoms.
atomSetA IntegratorDimerApproach
AtomSetAllMolecules etomica.box
Creates a facade that makes a set of molecule lists look like a single list.
AtomSetAllMolecules() AtomSetAllMolecules
Constructs an empty list.
atomSetB IntegratorDimerApproach
AtomsetIterator etomica.atom.iterator
Interface for classes that loop over a set of atoms.
AtomsetIteratorAllLeafAtoms etomica.atom.iterator
Iterator for all the molecules of a set of species in a box.
AtomsetIteratorAllLeafAtoms() AtomsetIteratorAllLeafAtoms
AtomsetIteratorBasisDependent etomica.atom.iterator
Interface for an AtomIterator that can be conditioned with
target and basis atoms.
AtomsetIteratorBoxDependent etomica.atom.iterator
Interface indicating that an iterator can determine appropriate
atoms for iteration given an arbitrary box.
AtomsetIteratorCellular etomica.nbr.cell
Interface for atomset iterators that use cell-based neighbor
lists for iteration.
AtomsetIteratorDirectable etomica.atom.iterator
Interface for an iterator that can interpret specification of
direction UP or DOWN.
AtomsetIteratorPDT etomica.atom.iterator
This is an interface for iterators that are box dependent, directable,
and targetable.
AtomsetIteratorTargetable etomica.atom.iterator
Interface for an iterator that can be targeted at one or more atoms.
atomSetSinglet ApiIntergroup
atomSetSinglet AtomIteratorArrayListAdjacent
atomSetSinglet AtomIteratorArrayListSimple
atomSetSinglet AtomIteratorSinglet
atomSetSinglet IntegratorImageMultistepMD
atomSetSinglet IntegratorHard.Agent
atomSetSinglet IntegratorHardPiston
atomSetSinglet MoleculeIteratorArrayListSimple
atomSetSinglet MoleculeIteratorSinglet
atomSetSinglet PotentialGroupNbr
atomSetSinglet PotentialMasterMonatomic
AtomSetSinglet etomica.atom
Data structure that contains a single mutable atom instance.
AtomSetSinglet() AtomSetSinglet
AtomSetSinglet(IAtom) AtomSetSinglet
AtomSignalKineticEnergy etomica.modules.glass
AtomSignalKineticEnergy() AtomSignalKineticEnergy
AtomSignalMobility etomica.modules.glass
AtomSignalMobility(ConfigurationStorage) AtomSignalMobility
AtomSignalMotion etomica.modules.glass
AtomSignalMotion(ConfigurationStorage, int) AtomSignalMotion
AtomSignalSourceByType() MeterStructureFactor.AtomSignalSourceByType
AtomSignalStress etomica.modules.glass
AtomSignalStress(AtomStressSource, int[][]) AtomSignalStress
atomSinglet MCMoveAtomNPath
atomSinglet MCMoveAtomCoupled
AtomSite etomica.nbr.site
Site used to form array of cells for cell-based neighbor listing.
AtomSite(int) AtomSite
atomSource MCMoveDimer
atomSource MCMoveDimerRotate
atomSource MCMoveSmer
atomSource MCMoveSmerRotate
atomSource MCMoveAtomCoupled
atomSource MCMoveAtomSwap
atomSource MCMoveAtom
atomSource MCMoveDimer
atomSource MCMoveDimerRotate
atomSource MCMoveAtomCoupled
atomSource MCMoveAtomCoupledBennet
atomSource MCMoveAtomCoupledUmbrella
atomSource MCMoveGeometricCluster
atomSource MCMoveGeometricClusterRestrictedGE
AtomSource etomica.atom
Interface for objects when return atoms (meeting some specification)
from a box.
AtomSourceRandomDimer etomica.association
AtomSourceRandomDimer() AtomSourceRandomDimer
AtomSourceRandomLeaf etomica.atom
AtomSource that returns a completely random leaf atom.
AtomSourceRandomLeaf() AtomSourceRandomLeaf
AtomSourceRandomMonomer etomica.association
AtomSourceRandomMonomer() AtomSourceRandomMonomer
AtomSourceRandomSmer etomica.association
AtomSourceRandomSmer() AtomSourceRandomSmer
AtomSourceRandomSpecies etomica.atom
AtomSource that returns a completely random leaf atom.
AtomSourceRandomSpecies() AtomSourceRandomSpecies
AtomSourceRandomSpecies(IRandom, ISpecies) AtomSourceRandomSpecies
atomSpeciesA MCMoveAtomSuperBox
atomSpeciesB MCMoveAtomSuperBox
AtomStressSource etomica.modules.glass
AtomTag() MeterChainLength.AtomTag
atomTest DataSourcePercolation
atomTest DataSourcePercolation0
AtomTest etomica.atom
Interface for a class that determines if an atom satisfies a test.
AtomTestChainLength etomica.modules.chainequilibrium
AtomTestChainLength etomica.modules.selfassembly
AtomTestChainLength(AtomLeafAgentManager<IAtom[]>) AtomTestChainLength
AtomTestChainLength(AtomLeafAgentManager<IAtom[]>) AtomTestChainLength
AtomTestChainLength.LengthAgent etomica.modules.chainequilibrium
AtomTestChainLength.LengthAgent etomica.modules.selfassembly
AtomTestCollective etomica.atom
AtomTest that needs to be informed whenever something has changed and the
status of atoms should be redetermined.
atomTestDeviation AtomNbrClusterer
atomTestDeviation DataSourceStrings
AtomTestDeviation etomica.modules.glass
AtomTestDeviation(Box, ConfigurationStorage) AtomTestDeviation
AtomTestDeviation(ConfigFromFileLAMMPS.ColorSchemeDeviation) ConfigFromFileLAMMPS.AtomTestDeviation
atomTestDoDisplay DisplayBox
AtomTestLiquid etomica.modules.droplet
AtomTestLiquid(Space, IDataSource) AtomTestLiquid
AtomTestLiquidAtomic etomica.modules.droplet
AtomTestLiquidAtomic(PotentialMasterList, Box) AtomTestLiquidAtomic
AtomTestRandom etomica.modules.glass
This class accepts any atom with a random probability.
AtomTestRandom(IRandom) AtomTestRandom
AtomToAtomLeafList etomica.atom
Interface for class that determines an AtomArrayList given an atom.
atomToAtomSet MpiIntraspecies1A
AtomToAtomSetFixed etomica.atom
AtomToAtomSetFixed() AtomToAtomSetFixed
AtomToIndex etomica.atom
Interface for class that associates an integer with an atom.
AtomToIndexChild etomica.atom
Defines the index as the Atom's node's index.
AtomToIndexChild() AtomToIndexChild
AtomToParentChildList etomica.atom
AtomToParentChildList() AtomToParentChildList
atomToPosVec(IAtom) P2WaterPotentialsJankowski
atomTranslator DataSourcePositionedBoltzmannFactor
atomTranslator MCMoveInsertDelete
atomtype Token
atomType MeterWallForce.PotentialCalculationWallForce
AtomType etomica.atom
Identifies a set of atoms and defines properties of those atoms.
AtomType(IElement) AtomType
AtomType(IElement, String) AtomType
AtomTypeAgentManager E > - Class in etomica.atom
AtomTypeAgentManager acts on behalf of client classes (an AgentSource) to manage agents for every AtomType in a box.
AtomTypeAgentManager(AtomTypeAgentManager.AgentSource<E>, Simulation) AtomTypeAgentManager
AtomTypeAgentManager.AgentSource E > - Interface in etomica.atom
Interface for an object that wants an agent associated with each AtomType in a Simulation.
AtomTypeOriented etomica.atom
Atom type for a sphere that has some feature depending upon an orientation coordinate.
AtomTypeOriented(IElement, Space) AtomTypeOriented
Deprecated.
AtomTypeOriented(IElement, Vector) AtomTypeOriented
atomTypeOrientedManager DisplayBoxCanvasG3DSys
atomtypes Token
atomTypes P2PotentialGroupBuilder.ModelParams
atomTypes P2SquareWellRobust
atomTypes VirialTraPPE.TraPPEParams
AtomTypeSpheroPolyhedron etomica.atom
AtomTypeSpheroPolyhedron(IElement, Space, List<Vector>, double) AtomTypeSpheroPolyhedron
atomx Token
atomy Token
atomz Token
ATTO Prefix
auto Token
AUTO EnumVdw
AUTO_BABEL EnumVdw
AUTO_JMOL EnumVdw
AUTO_RASMOL EnumVdw
autobond Token
autofps Token
autoRowLabels DisplayTable
aveCosTheta MCMoveRotateMolecule3DN2AveCosThetaConstraint
average AccumulatorAverage
average AccumulatorAverageBlockless
average Token
AVERAGE AccumulatorAverage
AVERAGE AccumulatorAverageBlockless
AVERAGE AccumulatorAverageBlocklessSlim
averageBox DisplayTextBoxesCAE
averages AccumulatorAverageBootstrap
averages AccumulatorAverageCollapsingLog
avg AtomSignalKineticEnergy
avg AtomSignalStress
avg StatisticsMCGraphic.HistoryPlotBits
AVG MultiharmonicGraphicMC.DataSourceAlphaFE
AVG MultiharmonicGraphicMC.DataSourceBias
avgAbsCheck ClusterWheatleySoft
avgAbsCheck ClusterWheatleySoftDerivatives
avgAbsCheckBD ClusterWheatleySoft
avgAbsCheckBD ClusterWheatleySoftDerivatives
avgEnergy LJMD3D
avgEnergy LJMD3DNbr
avgEnergy TestLJMD3D
avgErrData AccumulatorAutocorrelationPTensor
avgErrDataInfo AccumulatorAutocorrelationPTensor
avgErrFork AccumulatorAutocorrelationPTensor
avgStat DataVirialOverlap
AVOGADRO Constants
Avogadro's number, 6.022140857(74)e23 molecules/mole.
Axc0 PotentialCalculationHeisenberg
Axc0 PotentialCalculationMoleculeAgentSum
Axc0 PotentialCalculationMoleculeAgentSumPair
Axc0 PotentialCalculationPair
Axc0 PotentialCalculationVSum
Axc1 PotentialCalculationHeisenberg
Axc1 PotentialCalculationMoleculeAgentSum
Axc1 PotentialCalculationMoleculeAgentSumPair
Axc1 PotentialCalculationPair
Axc1 PotentialCalculationVSum
axes CoordinateDefinitionHSDimer
axes Token
Axes g3dsys.images
Axes(G3DSys, short) Axes
AXES G3DSys
AXES_DEFAULT_FONTSIZE JmolConstants
axescolor Token
axesmode Token
axesmolecular Token
axesorientationrasmol Token
axesscale Token
axesTensor IntegratorRigidMatrixIterative
axesunitcell Token
axeswindow Token
axis CoordinateDefinitionNitrogen
axis CoordinateDefinitionNitrogenSuperBox
axis TestRotationVector
axis AtomTestLiquid
axis ConfigurationDroplet
axis ColorSchemeDirection
axis CoordinateDefinitionHSDimer
axis MCMoveClusterRotateArm
axis MCMoveRotateArm
axis ClusterCoupledAtomFlipped
axis MCMoveClusterRotateCH3
axis Token
axis0 MCMoveClusterAtomHSRing
axis1color Token
axis2color Token
axis3color Token
AxisAngle4f org.jmol.util
A 4 element axis angle represented by single precision floating point
x,y,z,angle components.
AxisAngle4f() AxisAngle4f
Constructs and initializes a AxisAngle4f to (0,0,1,0).
axisNX JmolConstants
axisNY JmolConstants
axisNZ JmolConstants
axisX JmolConstants
axisY JmolConstants
axisZ JmolConstants
Axs0 PotentialCalculationHeisenberg
Axs0 PotentialCalculationMoleculeAgentSum
Axs0 PotentialCalculationMoleculeAgentSumPair
Axs0 PotentialCalculationPair
Axs0 PotentialCalculationVSum
Axs1 PotentialCalculationHeisenberg
Axs1 PotentialCalculationMoleculeAgentSum
Axs1 PotentialCalculationMoleculeAgentSumPair
Axs1 PotentialCalculationPair
Axs1 PotentialCalculationVSum
Ayc0 PotentialCalculationHeisenberg
Ayc0 PotentialCalculationMoleculeAgentSum
Ayc0 PotentialCalculationMoleculeAgentSumPair
Ayc0 PotentialCalculationPair
Ayc0 PotentialCalculationVSum
Ayc1 PotentialCalculationHeisenberg
Ayc1 PotentialCalculationMoleculeAgentSum
Ayc1 PotentialCalculationMoleculeAgentSumPair
Ayc1 PotentialCalculationPair
Ayc1 PotentialCalculationVSum
Ays0 PotentialCalculationHeisenberg
Ays0 PotentialCalculationMoleculeAgentSum
Ays0 PotentialCalculationMoleculeAgentSumPair
Ays0 PotentialCalculationPair
Ays0 PotentialCalculationVSum
Ays1 PotentialCalculationHeisenberg
Ays1 PotentialCalculationMoleculeAgentSum
Ays1 PotentialCalculationMoleculeAgentSumPair
Ays1 PotentialCalculationPair
Ays1 PotentialCalculationVSum
b P1LepsHarmonic
b PadeApproximation
b P2CO2Hellmann
b IntegratorPolymer
b P2HePCKLJS
b P2NitrogenHellmann
b P2WaterPotentialsJankowski
b P3CPSNonAdditiveHeSimplified
b P3HydrogenManzhos
B P2CO2Hellmann.Parameters
B PotentialCuLREP
B PotentialEFS
B P2HePCKLJS
B P3CPSNonAdditiveHeSimplified
B1 P2Nitrogen
B1 P2NitrogenAB
B1 P2NitrogenAnisotropic
B10HS(double) Standard
B11HS(double) Standard
B12HS(double) Standard
B2 VEOS3SW
B2 Standard
B2 ShapeParser.ShapeData
B2(double) LennardJones
Returns the 2nd virial coefficient.
B2(double, double) LJQB2
Returns B2 for the LJ+quadrupole model.
B2Fit etomica.modules.vle
B2Fit() B2Fit
B2Fit.Applet etomica.modules.vle
B2Fit.FunctionB2LJQ etomica.modules.vle
Function using LJQB2 to evaluate B2 as a function of Q, epsilon, sigma
and T.
B2Fit.FunctionMayerB2LJQ etomica.modules.vle
Function using Mayer sampling to evaluate B2 as a function of Q,
epsilon, sigma and T.
B2ForSphericallySymmetricUByTrapezoidRule etomica.virial
B2ForSphericallySymmetricUByTrapezoidRule() B2ForSphericallySymmetricUByTrapezoidRule
B2Hash B2Fit.FunctionMayerB2LJQ
B2HS(double) Standard
B2Ionic 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() B2Ionic
B2SW(double, double, double) Standard
B3 VEOS3SW
B3ForSphericallySymmetricU 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() B3ForSphericallySymmetricU
B3ForSphericallySymmetricU.DampingParams etomica.virial
B3HS(double) Standard
B3LJ 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() B3LJ
B3NonAddForSphericallySymmetricU etomica.virial
Computes the classical, non-additive component of B3 for a spherically symmetric potential using quadrature.
B3NonAddForSphericallySymmetricU() B3NonAddForSphericallySymmetricU
B3SW(double, double, double) Standard
b45 P1Sinusoidal
B4FFTLJ etomica.virial
Computes four approximations of B4 by FFT: HNC(C), HNC(V), PY(C), and PY(V).
B4FFTLJ() B4FFTLJ
B4HS(double) Standard
B5FFTLJ etomica.virial
Computes four approximations of B5 by FFT: HNC(C), HNC(V), PY(C), and PY(V).
B5FFTLJ() B5FFTLJ
B5HS(double) Standard
B6FFTLJ etomica.virial
Modification of FFT Program of B4
B6FFTLJ() B6FFTLJ
B6HS(double) Standard
B7HS(double) Standard
B8HS(double) Standard
B9HS(double) Standard
bA P2CO2Hellmann
bA P2NitrogenHellmann
BABEL EnumVdw
BABEL21 EnumVdw
backbone Token
backgroundcolor Token
backgroundColor SVGConverter
Background color for the output images.
backgroundImage GData
backgroundmodel Token
backlit Token
backTrack() AbstractSearchState
backTrack() SearchState
backTrack() VF2SearchState
backTrack() VFSearchState
backwardDataMap DataSet
bALattice DataSourceMuRoot1
bALattice DataSourceMuRootPMatch
bALattice DataSourcePMu
Ball g3dsys.images
Class for drawing spheres (atoms)
Ball(G3DSys, short, float, float, float, float) Ball
Ball(G3DSys, short, Point3f, float) Ball
BALL G3DSys
implemented shapes
Bar etomica.units
The bar unit of pressure, equal to 10^5 N/m^2.
Barye etomica.units
The barye unit of pressure, equal to 1 dyn/cm^2.
baseline() BenchVector3D
basepair Token
baseUnits() UnitSystem
Base dimensions are {length, mass, time, current, temperature, quantity, luminous intensity}
BasicHealthCheck etomica.server.health
BasicHealthCheck() BasicHealthCheck
basis BravaisLatticeCrystal
basis MinimizationBetaNitrogenModelLS
basis MinimizeBetaNitrogenLatticeParameterLSFromFile
basis SimOverlapBetaN2RP
basis CoordinateDefinition
basis HessianDB
basis LJVacancyMin
basis NormalModeAnalysisDisplay1D
basis NormalModeAnalysisDisplay2D
basis NormalModeAnalysisDisplay3D
basis NormalModes2D
basis NormalModes3D
basis SimBennet
basis SimCalcSLJ
basis SimCalcSMorse
basis SimCalcSSoftSphere2D
basis SimCalcSSoftSphereFCC
basis SimCalcSSoftSphereFCCSuperBox
basis SimEinStep1
basis SimEinStep1HCP
basis SimEinStep2
basis SimEinStep2HCP
basis SimHarmonicUmbrella
basis SimLJHTTISuper
basis SimLJHTTISuperHCP
basis SimLJHTTISuperHCP2
basis SimLJHTTISuperSFMD
basis SimOverlap
basis SimOverlapLJ
basis SimOverlapLJModule
basis SimOverlapSoftSphere
basis SimOverlapSoftSphereDP
basis SimOverlapSoftSphereEin
basis SimOverlapSoftSphereEinHarm
basis SimOverlapSoftSphereHCP
basis SimOverlapSoftSphereReweighting
basis SimOverlapSoftSphereSoftness
basis SimOverlapSoftSphereSuperBox
basis SimOverlapSoftSphereTP
basis SimOverlapSoftSphereTPHCP
basis SimOverlapSoftSphereTPSlantedBox
basis SimOverlapSSnxy
basis SimTargetUmbrella
basis SimUmbrella
basis SimUmbrellaSoftSphere
basis EwaldSummation
basis P2QChemInterpolated
basis P2QChemInterpolated.DampingParams
basis P3AdditiveQChem.DampingParams
basis P3QChem.DampingParams
Basis etomica.lattice.crystal
General basis class that hold scaled coordinates of atoms within a unit cell.
Basis(Vector[]) Basis
BasisBetaSnA5 etomica.lattice.crystal
Basis that helps construct a beta-tin crystal.
BasisBetaSnA5() BasisBetaSnA5
BasisBigCell etomica.normalmode
BasisBigCell(Space, Basis, int[]) BasisBigCell
basisCell MCMoveMoleculeCoupledSuperBox
basisCell MCMoveRotateMolecule3DSuperBox
BasisCell(IMoleculeList, Vector) CoordinateDefinition.BasisCell
BasisCubicBcc etomica.lattice.crystal
A 2-atom basis for a bcc crystal
BasisCubicBcc() BasisCubicBcc
Makes a bcc 2-atom basis.
BasisCubicDiamond etomica.lattice.crystal
An 8-atom basis that for a diamond crystal.
BasisCubicDiamond() BasisCubicDiamond
Makes a diamond-on-fcc 8-atom basis.
BasisCubicFcc etomica.lattice.crystal
A 4-atom basis fot an fcc crystal.
BasisCubicFcc() BasisCubicFcc
Makes a fcc 4-atom basis.
BasisCubicFccDiamond etomica.lattice.crystal
A 2-atom basis that makes a diamond crystal using a BravaisLattice
having a Cubic primitive with an fcc basis.
BasisCubicFccDiamond() BasisCubicFccDiamond
Makes a diamond-on-fcc 2-atom basis using the given factory to make the atoms.
basisDim NormalModesMolecular
basisFCC HessianDB
BasisHcp etomica.lattice.crystal
A 2-atom basis for an hcp crystal.
BasisHcp() BasisHcp
BasisHcp4 etomica.lattice.crystal
A 4-atom basis for an hcp crystal.
BasisHcp4() BasisHcp4
BasisHcpBaseCentered etomica.lattice.crystal
A 2-atom basis for an hcp crystal
(base-centered or side-centered)
BasisHcpBaseCentered() BasisHcpBaseCentered
basisMolecules ConfigurationSAM
BasisMonatomic etomica.lattice.crystal
Single-atom basis with the coordinate at the origin.
BasisMonatomic(Space) BasisMonatomic
Creates a single-atom basis with the coordinate at the origin.
BasisOrthorhombicHexagonal etomica.lattice.crystal
A 2D hexagonal 2-atom basis
BasisOrthorhombicHexagonal() BasisOrthorhombicHexagonal
Makes a 2D hexagonal 2-atom basis
BasisOrthorhombicHexagonal3D(Space) ConfigurationCatalysis.BasisOrthorhombicHexagonal3D
Makes a fcc 4-atom basis.
basisSize() ANIntergroupCoupled
Returns 2, indicating that the setBasis method expects an array of two
atoms.
basisSize() ANIntergroupExchange
Returns 2, indicating that the setBasis method expects an array of two
atoms.
basisSize() ANIntragroupExchange
Returns 2, indicating that the setBasis method expects an array of two
atoms.
basisSize() ApiIndexList
basisSize() ApiIntergroup
Returns 2, indicating that the setBasis method expects an array of two
atoms.
basisSize() ApiIntragroup
Returns 1, indicating the the array given to the setBasis method
should have only one element.
basisSize() AtomIteratorBasis
Returns 1, indicating that only a single-atom basis is appropriate.
basisSize() AtomIteratorBasisAdjustableStart
Returns 1, indicating that only a single-atom basis is appropriate.
basisSize() Atomset3IteratorIndexList
basisSize() Atomset4IteratorIndexList
basisSize() AtomsetIteratorAllLeafAtoms
basisSize() AtomsetIteratorBasisDependent
Indicates the size of the basis needed to set the iterator.
basisSize() MoleculesetIteratorBasisDependent
Indicates the size of the basis needed to set the iterator.
basisSize() PotentialMaster.AtomIterator0
basisSurface ConfigurationSAM
bB P2CO2Hellmann
bB P2NitrogenHellmann
BBbonded ReactionEquilibrium
bbcageTickEdges BoxInfo
bBond VirialDiagrams
bBond VirialDiagramsPT
bCalc(int) QSeries
Computes the coefficient b_j based on the beta coefficients given by the BetaSource.
BCC SoftSphereSolidEOS
BCC SoftSphereSolidEOSCalculator
BCVisitor etomica.graph.traversal
This TraversalVisitor visits nodes and keeps track of biconnected
components.
BCVisitor(List<List<Byte>>) BCVisitor
BDAccFrac ClusterCoupledFlippedMultivalue
BDAccFrac ClusterWheatleySoft
BDAccFrac ClusterWheatleySoftDerivatives
BDAccFrac VirialLJD.VirialLJParam
BDAccFrac VirialLJDU.VirialLJParam
BDAccFrac VirialLJPT.VirialLJParam
BDbeta ClusterWheatleySoftDerivativesBD
BDcount ClusterCoupledFlippedMultivalue
BDexp(BigDecimal) ClusterWheatleySoftDerivativesBD
BDExpInternal(BigDecimal) ClusterWheatleySoftDerivativesBD
bdJdtheta0 MeterEnergyMeanField
BDlog(BigDecimal) ClusterWheatleySoftDerivativesBD
BDONE ClusterWheatleySoftBD
BDONE ClusterWheatleySoftDerivativesBD
BDONE MeterVirialBDBin
bdrij P2CO2H2OWheatley.P2CO2H2OSC
bdrij P2CO2H2OWheatley.P2CO2H2OSCTI
bdry SimCalcJ
bdry SimCalcS
bdry SimModesJ
BDtol VirialHeD.VirialParam
BDtol VirialHeNonAdditiveD.VirialParam
BDtol VirialLJDU.VirialLJParam
BDtol VirialTraPPE.VirialParam
BDZERO ClusterWheatleySoftBD
BDZERO ClusterWheatleySoftDerivativesBD
BDZERO MeterVirialBD
BDZERO MeterVirialBDBin
BDZERO MeterVirialBDBinMultiThreaded
BDZERO MeterVirialSWWE
beadFac VirialH2PI.VirialH2PIParam
beadFac VirialH2PISimple.VirialH2PISimpleParam
beadFac VirialHePIXCOdd.VirialHePIParam
beadFac VirialN2PI.VirialN2Param
beadFac VirialO2PI.VirialO2Param
beginRendering(Matrix3f) Graphics3D
beginRendering(Matrix3f) GData
BenchApiAACell etomica
BenchApiAACell() BenchApiAACell
BenchBox etomica
BenchBox() BenchBox
BenchBox.IVecSys etomica
BenchBox.VectorSystem etomica
benchCoords() BenchBox
benchCoords1d() BenchBox
benchCoords1dColMajor() BenchBox
benchCoordsNoLoopInvariant() BenchBox
benchCoordsParallel() BenchBox
benchCustomFJTask() BenchApiAACell
benchExecutorService() BenchApiAACell
benchNbrUpdates() BenchNbrUpdates
BenchNbrUpdates etomica
BenchNbrUpdates() BenchNbrUpdates
benchNbrUpdatesParallel() BenchNbrUpdates
benchNormalBox() BenchBox
benchPairIterator() BenchApiAACell
benchPairIteratorFast() BenchApiAACell
benchParallelStreams() BenchApiAACell
BenchSimCatalysis etomica.simulation
BenchSimCatalysis() BenchSimCatalysis
BenchSimDCVGCMD etomica.simulation
BenchSimDCVGCMD() BenchSimDCVGCMD
BenchSimHSMD3D etomica.simulation
BenchSimHSMD3D() BenchSimHSMD3D
BenchSimLammpsLJ etomica.simulation
BenchSimLammpsLJ() BenchSimLammpsLJ
BenchSimLJGCMC3D etomica.simulation
BenchSimLJGCMC3D() BenchSimLJGCMC3D
BenchSimLJMC3D etomica.simulation
BenchSimLJMC3D() BenchSimLJMC3D
BenchSimLJMD3D etomica.simulation
BenchSimLJMD3D() BenchSimLJMD3D
BenchSimSurfacetensionLJMC etomica.simulation
BenchSimSurfacetensionLJMC() BenchSimSurfacetensionLJMC
BenchSimSWChain etomica.simulation
BenchSimSWChain() BenchSimSWChain
BenchSimVirialH2OGCPMD etomica.virial.simulations
BenchSimVirialH2OGCPMD() BenchSimVirialH2OGCPMD
BenchSimVirialLJ etomica.simulation
BenchSimVirialLJ() BenchSimVirialLJ
benchVecSys() BenchBox
BenchVector etomica.space
BenchVector() BenchVector
BenchVector3D etomica.space
BenchVector3D() BenchVector3D
Bernoulli etomica.veos.bigdecimal
Bernoulli numbers.
Bernoulli() Bernoulli
berr PNWaterGCPM
BesselFunction etomica.util.numerical
BesselFunction() BesselFunction
besselI(double, double) SpecialFunctions
The modified Bessel function of the first kind, I
Reference: http://mathworld.wolfram.com/ModifiedBesselFunctionoftheFirstKind.html
besselJ(double, double) SpecialFunctions
The unmodified Bessel function of the first kind, J.
beta PotentialCalculationMappedRdf
beta PotentialCalculationMappedEnergy
beta PotentialCalculationMappedVirial
beta PotentialCalculationMappedVirialV
beta PotentialCalculationMappedVirialV.USine
beta FindBetaN2AngleFromParameter
beta P1HydrogenMielke
beta P4TorsionDreiding
beta MeterEnergyMeanField
beta MeterMappedAveragingCorrelation
beta ClusterChainSoft
beta ClusterExchange
beta ClusterSinglyConnected
beta ClusterSum
beta ClusterSumPolarizableWertheimProduct
beta ClusterSumPolarizableWertheimProduct4Pt
beta ClusterSumPolarizableWertheimProduct4PtFinal
beta ClusterTree
beta ClusterWheatleyExtendSW
beta ClusterWheatleyHS
beta ClusterWheatleyPartitionScreening
beta ClusterWheatleyPT
beta ClusterWheatleySoft
beta ClusterWheatleySoftBD
beta ClusterWheatleySoftDerivatives
beta ClusterWheatleySoftDerivativesBD
beta(int) BetaSource
beta(int) HardRods
beta(int) VanderWaals
beta3 P3CPSNonAdditiveHe
beta3 P3CPSNonAdditiveHeOrig
beta3_111 P3CPSNonAdditiveHe
beta3_111 P3CPSNonAdditiveHeLessSimplified
beta3_112 P3CPSNonAdditiveHe
beta3_113 P3CPSNonAdditiveHe
beta3_122 P3CPSNonAdditiveHe
beta3_222 P3CPSNonAdditiveHe
beta4211 P3CPSNonAdditiveHe
beta4211 P3CPSNonAdditiveHeLessSimplified
beta4211 P3CPSNonAdditiveHeOrig
beta4211_1112 P3CPSNonAdditiveHe
beta4211_1121 P3CPSNonAdditiveHe
beta4211_2111 P3CPSNonAdditiveHe
beta4220 P3CPSNonAdditiveHe
beta4220 P3CPSNonAdditiveHeLessSimplified
beta4220 P3CPSNonAdditiveHeOrig
beta4220_1111 P3CPSNonAdditiveHe
beta4220_1211 P3CPSNonAdditiveHe
beta4220_2111 P3CPSNonAdditiveHe
betaCoeffs FindTransitionTemperature
BetaPhaseLatticeParameter etomica.models.nitrogen
The parameters that are determined through conjugate gradient method to give the lowest lattice energy
for beta-N2 phase structure
BetaPhaseLatticeParameter() BetaPhaseLatticeParameter
BetaPhaseLatticeParameterLS etomica.models.nitrogen
The parameters that are determined through conjugate gradient method to give the lowest lattice energy
for beta-N2 phase structure
for lattice sum, rC = 250 A
BetaPhaseLatticeParameterLS() BetaPhaseLatticeParameterLS
BetaPhaseLatticeParameterNA etomica.models.nitrogen
The parameters that are determined through conjugate gradient method to give the lowest lattice energy
for beta-N2 phase structure
BetaPhaseLatticeParameterNA() BetaPhaseLatticeParameterNA
BetaSource etomica.veos
betaUAB MeterWorkHarmonicTargetandReweighting
betaUAW MeterWorkHarmonicTargetandReweighting
betaUAWf MeterWorkHarmonicTargetandReweighting
betaUBA MeterWorkTargetHarmonicandReweighting
betaUBW MeterWorkTargetHarmonicandReweighting
betaUBWf MeterWorkTargetHarmonicandReweighting
bgcolor GData
bGuess VirialOptimizer
BHS(int, double) Standard
Returns the nth virial coefficient for hard spheres of diameter sigma.
bias MCMoveClusterTorsionAlkaneEH
bias MCMoveClusterTorsionMulti
BIAS MultiharmonicGraphicMC.DataSourceAlphaFE
BIAS MultiharmonicGraphicMC.DataSourceBias
biasInsert(IAtom, IAtom) BiasVolume
biasInsert(IAtom, IAtom) BiasVolumeCube
biasInsert(IAtom, IAtom) BiasVolumeSphere
biasInsert(IAtom, IAtom) BiasVolumeSphereOriented
biasInsert(IAtom, IAtom) BiasVolumeSphereOrientedDoubleSites
biasInsert(IMolecule, IMolecule) BiasVolumeAceticAcid
biasInsert(IMolecule, IMolecule) BiasVolumeMolecule
biasOld MCMoveVolume
biasVolume() BiasVolume
biasVolume() BiasVolumeAceticAcid
biasVolume() BiasVolumeCube
biasVolume() BiasVolumeMolecule
biasVolume() BiasVolumeSphere
biasVolume() BiasVolumeSphereOriented
biasVolume() BiasVolumeSphereOrientedDoubleSites
BiasVolume etomica.association
BiasVolume(Space) BiasVolume
BiasVolume2SiteAceticAcid etomica.association
BiasVolume2SiteAceticAcid(Space, IRandom) BiasVolume2SiteAceticAcid
BiasVolumeAceticAcid etomica.association
BiasVolumeAceticAcid(Space, IRandom, Box) BiasVolumeAceticAcid
BiasVolumeCube etomica.association
BiasVolumeCube(Space, IRandom) BiasVolumeCube
BiasVolumeMolecule etomica.association
BiasVolumeMolecule(Space) BiasVolumeMolecule
BiasVolumeSphere etomica.association
BiasVolumeSphere(Space, IRandom) BiasVolumeSphere
BiasVolumeSphereOriented etomica.association
BiasVolumeSphereOriented(Space, IRandom) BiasVolumeSphereOriented
BiasVolumeSphereOrientedDoubleSites etomica.association
BiasVolumeSphereOrientedDoubleSites(Space, IRandom) BiasVolumeSphereOrientedDoubleSites
BiComponentSubst etomica.graph.operations
This class handles the substitution g = A where g is a Graph and A is a set
of Graph.
BiComponentSubst() BiComponentSubst
BiComponentSubst.BiComponentSubstParameters etomica.graph.operations
BiComponentSubstParameters(Graph, Set<Graph>, boolean, boolean) BiComponentSubst.BiComponentSubstParameters
BiconectedNodalPoint etomica.graph.traversal
BiconectedNodalPoint() BiconectedNodalPoint
Biconnected etomica.graph.traversal
Biconnected() Biconnected
bigAngle P3CPSNonAdditiveHe
bigAngle P3CPSNonAdditiveHeLessSimplified
bigAngle P3CPSNonAdditiveHeOrig
bigAngle P3CPSNonAdditiveHeSimplified
BigComplex etomica.veos.bigdecimal
Complex numbers with BigDecimal real and imaginary components
BigComplex() BigComplex
Default ctor equivalent to zero.
BigComplex(double, double) BigComplex
ctor with real and imaginary parts
BigComplex(BigDecimal) BigComplex
ctor with real part.
BigComplex(BigDecimal, BigDecimal) BigComplex
ctor with real and imaginary parts
BigDecimalMath etomica.veos.bigdecimal
BigDecimal special functions.
BigDecimalMath() BigDecimalMath
BigDecimalValue(MathContext) BigSurd
Return the approximate floating point representation.
BigDecimalValue(MathContext) BigSurdVec
Construct an approximate floating point representation
BigDecimalValue(MathContext) Rational
Return a representation as BigDecimal.
BigIntegerMath etomica.veos.bigdecimal
BigInteger special functions and Number theory.
BigIntegerMath() BigIntegerMath
BigIntegerPoly etomica.veos.bigdecimal
Polynomial with integer coefficients.
BigIntegerPoly() BigIntegerPoly
Default ctor.
BigIntegerPoly(String) BigIntegerPoly
Ctor with a comma-separated list as the list of coefficients.
BigIntegerPoly(BigInteger[]) BigIntegerPoly
Ctor with a list of coefficients.
BigIntegerPoly(Vector<BigInteger>) BigIntegerPoly
Ctor with a list of coefficients.
bigomega() Ifactor
The sum of the prime factor exponents, with multiplicity.
BigSurd etomica.veos.bigdecimal
Square roots on the real line.
BigSurd() BigSurd
Default ctor, which represents the zero.
BigSurd(int, int) BigSurd
ctor given the numerator and denominator of the root.
BigSurd(Rational, Rational) BigSurd
ctor given the prefactor and the basis of the root.
BigSurd(BigInteger) BigSurd
ctor given the value under the root.
BigSurdVec etomica.veos.bigdecimal
A BigSurdVec represents an algebraic sum or differences of values
which each term an instance of BigSurd.
BigSurdVec() BigSurdVec
Default ctor, which represents the zero.
BigSurdVec(BigSurd) BigSurdVec
ctor given the value of a BigSurd.
BigSurdVec(BigSurd, BigSurd) BigSurdVec
ctor given two values, which (when added) represent this number a+b.
BigValue etomica.veos
Data class to handle operations involving large numbers.
BigValue() BigValue
Default constructor sets value to 0.0
BigValue(double) BigValue
Constructs using the given value.
BigValue(double, boolean) BigValue
Constructs given ln(|value|) and sign of value.
BigValue(IBigValue) BigValue
Copy constructor.
Binary etomica.graph.operations
BINARY_OP_CONV Parser
BINARY_OP_DEL Parser
BINARY_OP_MUL Parser
BINARY_OP_SUB Parser
BINARY_OP_SUM Parser
BINARY_OP_UNION Parser
binaryComp PolydisperseHS.HSPolyParam
binaryExtensions JmolConstants
BinaryOpByteImpl etomica.graph.engine.impl
BinaryOpByteImpl(String, Parser.Expression, Parser.Expression, byte) BinaryOpByteImpl
BinaryOpImpl etomica.graph.engine.impl
BinaryOpImpl(String, Parser.Expression, Parser.Expression) BinaryOpImpl
binom P2O2Bartolomei
binomial ClusterWheatleySoftDerivatives
binomial ClusterWheatleySoftDerivativesBD
binomial(int, int) BigIntegerMath
Evaluate binomial(n,k).
binomial(Rational, int) Rational
binomial (n choose m).
binomial(Rational, BigInteger) Rational
binomial (n choose m).
binomial(BigInteger, BigInteger) BigIntegerMath
Evaluate binomial(n,k).
binomialTInv(int) BigIntegerPoly
Inverse Binomial transform.
binSize DataSourceTensorVirialHardProfile
binSize MCMoveClusterTorsionAlkaneEH
binSize MCMoveClusterTorsionMulti
bisectorVec P2WaterPotentialsJankowski
BishopPipin(double, double, double, double) P2HydrogenPatkowski
BishopPipin(double, double, double, double) P2HydrogenPatkowskiAtomic
bitCount() Bitmap
Returns the number of bits set in the bitmap.
bitCount() AbstractBitmap
bitCount(int) BitmapOfLongVector
Returns the number of valid bits in the long with the given index.
Bitmap etomica.graph.model
Abstracts away the form in which bitmaps implement their operations and store their
data.
BitmapFactory etomica.graph.model
BitmapFactory() BitmapFactory
BitmapOfLong etomica.graph.model.impl
This class encodes edges in a space efficient fashion, with the limitation that it can
only encode up to 64 bits.
BitmapOfLong() BitmapOfLong
BitmapOfLong(byte[]) BitmapOfLong
BitmapOfLong(int) BitmapOfLong
BitmapOfLong(int, boolean) BitmapOfLong
BitmapOfLong(Bitmap) BitmapOfLong
BitmapOfLong(String) BitmapOfLong
BitmapOfLongVector etomica.graph.model.impl
Transparent implementation of arbitrarily large bitmaps based on an array of long
values.
BitmapOfLongVector(byte[]) BitmapOfLongVector
BitmapOfLongVector(int) BitmapOfLongVector
BitmapOfLongVector(int, boolean) BitmapOfLongVector
BitmapOfLongVector(Bitmap) BitmapOfLongVector
BitmapOfLongVector(String) BitmapOfLongVector
BitmapUtils etomica.graph.traversal
BitmapUtils() BitmapUtils
bitMask(byte) BitmapUtils
bitOffMask(byte) BitmapUtils
bitOffset(int) BitmapOfLongVector
The highest order bit is at bit 0 of bitmap[0], and the lowest order bit is at bit
bitSize() - 1 of bitmap[size()-1].
bitOnMask(byte) BitmapUtils
bitset Token
BitSet org.jmol.util
a fast 64-bit BitSet optimized for Java2Script -- about 25 times faster than
java.util.BitSet in JavaScript
BitSet() BitSet
Creates a new bit set.
BitSetUtil org.jmol.util
BitSetUtil() BitSetUtil
bitSize() Bitmap
Returns the length in bits of the bitmap.
bitSize() BitmapOfLong
bitSize() BitmapOfLongVector
bJ MeterMappedAveragingCorrelation
bJ MeterMappedAveragingCV
bJ MeterMappedAveragingVSum
bJ PotentialCalculationFreeEnergy
bJ PotentialCalculationHeisenberg
bJ PotentialCalculationMoleculeAgentSum
bJ PotentialCalculationMoleculeAgentSumMinusIdeal
bJ PotentialCalculationMoleculeAgentSumMinusIdealPair
bJ PotentialCalculationMoleculeAgentSumPair
bJ PotentialCalculationPair
bJ PotentialCalculationVSum
bl P2WaterPotentialsJankowski
bl MCMoveBondLength
bl MCMoveClusterBondLength
BLACK Colix
blankPanel PistonCylinderGraphic
blMax P2HydrogenHindePatkowskiAtomic
blN2 P2NitrogenHellmann
blN2 P3NitrogenHellmannNonAdditive
blN2 VirialN2
blN2 VirialN2PI
blO2 VirialO2PI
BLOCK_CORRELATION AccumulatorAverage
BLOCK_COVARIANCE AccumulatorAverageCovariance
blockAccumulator SimulationVirialOverlap2
blockAvg DataSinkBlockAveragerSFac
blockAvgs AccumulatorAverageCollapsing
blockCorrelation AccumulatorAverage
blockCountDown AccumulatorAverage
blockCounter AccumulatorAverageFixedOutputFile
blockCounter AccumulatorOverlapAverageUa2
blockCounter AccumulatorVirialOverlapSingleAverage
blockCovariance AccumulatorAverageCovariance
blockCovSum AccumulatorAverageCovariance
blockDataSink AccumulatorAverageFixed
blockFilename AccumulatorAverageFixed
blocks VirialCPSHeliumNonAdditiveClassical_Correction.VirialParam
blocks VirialCPSHeliumNonAdditiveClassical.VirialParam
blocks VirialHePI_PotentialCorrection.VirialHePIParam
blocks VirialHePIXCOdd.VirialHePIParam
blocksEq VirialCPSHeliumNonAdditiveClassical_Correction.VirialParam
blocksEq VirialCPSHeliumNonAdditiveClassical.VirialParam
blocksEq VirialHePI_PotentialCorrection.VirialHePIParam
blocksEq VirialHePIXCOdd.VirialHePIParam
blockSize AccumulatorAverage
blockSize SimulationVirialOverlap2
blockSize VirialLJD.VirialLJParam
blockSize VirialLJDU.VirialLJParam
blockSize VirialLJPT.VirialLJParam
blockSums AccumulatorAverageBootstrap
blockSums AccumulatorAverageCollapsingLog
blockSumX AccumulatorPTensor
blockSumX DataSourceBlockAvgCor
blockSumX DataSourceHisogram
blockSumX DataSourceMSDcorP
blockSumX DataSourcePMSDHistory
blockVarSum AccumulatorAverageFixed
blOption VirialH2PI.VirialH2PIParam
blOption VirialH2PISimple.VirialH2PISimpleParam
BLUE Colix
bmu MCMoveIDBiasAction
bmu DataSourceAvgPressure
bmu DataSourceAvgPressure2
bmu DataSourceFEHistogram
bmu DataSourceImposedFEFit
bmu DataSourceImposedFEHistogram
bmu DataSourceMuRoot
bmu DataSourceMuRoot1
bmu DataSourceMuRootPMatch
bmu DataSourcePMu
bmu PotentialCalculationFreeEnergy
bmu PotentialCalculationHeisenberg
bmu PotentialCalculationMoleculeAgentSum
bmu PotentialCalculationMoleculeAgentSumMinusIdeal
bmu PotentialCalculationMoleculeAgentSumMinusIdealPair
bmu PotentialCalculationMoleculeAgentSumPair
bmu PotentialCalculationPair
bmu PotentialCalculationVSum
bmuLat DataSourceMuRoot
BnFlexibleContributionTraPPEUAMethanol 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() BnFlexibleContributionTraPPEUAMethanol
BnFlexibleContributionTraPPEUAMethanol.VirialParam etomica.virial.simulations
Inner class for parameters
BnHNCLJ etomica.virial
This is just a main method for HypernettedChain.java...
BnHNCLJ() BnHNCLJ
BnHSIonic 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() BnHSIonic
BnIETP2Spherical etomica.virial
This is just a main method for HypernettedChain.java or PercusYevick.java...
BnIETP2Spherical() BnIETP2Spherical
BnJHBVArgon_Analytic etomica.virial
Computes virial coefficients for argon using the analytical expressions
developed by Jaeger, Hellmann, Bich, and Vogel (2011), JCP, 135: 084308.
BnJHBVArgon_Analytic() BnJHBVArgon_Analytic
BnPCJSDHe etomica.virial
This is just a main method for PercusYevick.java.
BnPCJSDHe() BnPCJSDHe
BnPCJSDHe.BnPCJSDHeParams etomica.virial
BnPCJSDHeParams() BnPCJSDHe.BnPCJSDHeParams
BnPY_1QC_Helium 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() BnPY_1QC_Helium
BnPYCHe etomica.virial
This is just a main method for PercusYevick.java.
BnPYCHe() BnPYCHe
BnPYCHe.BnPYHeParams etomica.virial
BnPYHardSphere etomica.virial
This is just a main method for PercusYevick.java...
BnPYHardSphere() BnPYHardSphere
BnPYHeParams() BnPYCHe.BnPYHeParams
BnPYLJ etomica.virial
This is just a main method for PercusYevick.java.
BnPYLJ() BnPYLJ
BnSCALJ etomica.virial
Combines the Percus-Yevick and hypernetted-chain approximations to the virial coefficients to
generate a self-consistent (thermodynamically consistent) approximation.
BnSCALJ() BnSCALJ
bohrConv P2WaterSzalewicz
BohrRadius etomica.units
The Borh Radius unit of length, corresponding to the size of a Hydrogen
atom's electron cloud.
BOLTZMANN_K Constants
Boltzmann's constant, in (sim units)/kelvin.
boltzmannAverage SimDirectBetaN2RP
boltzmannAverage SimDirectBetaN2RPAngleToNoAngle
boltzmannAverage SimDirectBetaN2RPInitPert
boltzmannAverage SimDirectDisorderedAlphaN2RPInitPert
BoltzmannProcessor etomica.normalmode
DataProcessor that returns the Boltzmann factor of the incoming energy.
BoltzmannProcessor() BoltzmannProcessor
bond ConformationAnthraceneTraPPE
bond ConformationPhenanthreneTraPPE
bond(IAtom, IAtom) P2SquareWellBonded
this function will bond atoms a & b together
bond(IAtom, IAtom) P2SquareWellRadical
this function will bond atoms a & b together
Bond g3dsys.images
Bond(G3DSys, Ball, Ball) Bond
Bond(G3DSys, Ball, Ball, short) Bond
BOND_ORDER_MAP Metadata
BONDAC P2HardAssociationGCPMReference
BONDAC PNWaterGCPMThreeSite
BondArrayList() P2HardBondedList.BondArrayList
BONDBC P2HardAssociationGCPMReference
BONDBC PNWaterGCPMThreeSite
BONDCA P2HardAssociationGCPMReference
BONDCA PNWaterGCPMThreeSite
BONDCB P2HardAssociationGCPMReference
BONDCB PNWaterGCPMThreeSite
BondChangeData() PotentialReactive.BondChangeData
BondConnectedSubstitution etomica.virial.cluster
If Wertheim diagrams have bond connected network, fR bond is split into eR and -one bond.
BondConnectedSubstitution() BondConnectedSubstitution
BondConnectedSubstitution.BondConnectedSubstitutionParameters2Site etomica.virial.cluster
BondConnectedSubstitution3Site etomica.virial.cluster
If Wertheim diagrams have bond connected network, fR bond is split into eR and -one bond.
BondConnectedSubstitution3Site() BondConnectedSubstitution3Site
BondConnectedSubstitution3Site.BondConnectedSubstitutionParameters3Site etomica.virial.cluster
BondConnectedSubstitutionNaphthalene 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() BondConnectedSubstitutionNaphthalene
BondConnectedSubstitutionNaphthalene.BondConnectedSubstitutionParameters2SiteNa etomica.virial.cluster
BondConnectedSubstitutionParameters2Site(char, char) BondConnectedSubstitution.BondConnectedSubstitutionParameters2Site
BondConnectedSubstitutionParameters2SiteNa(char, char, List<Character>, List<Character>, List<Character>, List<Character>) BondConnectedSubstitutionNaphthalene.BondConnectedSubstitutionParameters2SiteNa
BondConnectedSubstitutionParameters3Site(char, char) BondConnectedSubstitution3Site.BondConnectedSubstitutionParameters3Site
BondConstraints(int[][], double[]) IntegratorVelocityVerletShake.BondConstraints
bondcount Token
bondCount P2SquareWellBonded.RingResult
bondDecomp MayerIonicDiagram1qbond
bondDecomp MayerIonicDiagram2qbonds
bondDecomp MayerIonicDiagram4qbonds
bondDecomp WertheimDiagrams2SiteRho
bondDecomp WertheimDiagrams3SiteRho
bondedAtom1 InteractionTracker.CatalysisAgent
bondedAtom2 InteractionTracker.CatalysisAgent
bondedAtoms IntegratorVelocityVerletShake.BondConstraints
bondedAtoms MCMoveWiggleAceticAcid
bondedAtoms MCMoveClusterWiggleAceticAcid
bondFac P2HardSphereMC
bondFac P2SquareWellMonomer
bondIndexArray ClusterBonds
bondingAgentManager ColorSchemeStepWise
bondingAngleRestriction WertheimGCPM4PtEBondDecomp.WertheimAssociatingFluidParam
bondingAngleRestriction WertheimGCPM4PtThreeSiteEDecompDirectSampling.VirialAssociatingFluidParam
bondingAngleRestriction PNWaterGCPMThreeSite
BondInteractionTypeToggler() MyApplet.BondInteractionTypeToggler
bondL P2CO2Hellmann.P2CO2SC
bondL Conformation7SiteRigidSF6
BONDL EnumPotentialParamDescription
bondL_CC Sam
bondlength ConformationCO2
bondlength ConformationAnthracene3site
bondlength ConformationNaphthaleneTraPPE
bondlength ConformationPh3site
bondLength AtomHydrogen
bondLength ConformationLinear
bondLength MCMoveClusterTorsionAlkaneEH
bondLength MCMoveClusterTorsionMulti
bondLengthOH ConformationWater3P
bondLengthOH ConformationWaterTIP4P
bondLengths IntegratorVelocityVerletShake.BondConstraints
bondList MCMoveAtomSmer
bondList MCMoveMoleculeSmer
bondList VirialLJSeries.VirialLJParam
bondManager P2HardSphereMC
bondManager P2SquareWellMonomer
bondManager CriterionTether3
bondMap ExcludeParameters
bondmodeor Token
bondOrigN ConformationNitrogen
bondOrigN ConformationNitrogenShellModel
bondOrigP ConformationNitrogenShellModel
bondOrigP1 ConformationNitrogen
bondOrigP2 ConformationNitrogen
bondpicking Token
bondradiusmilliangstroms Token
bonds DisplayBoxCanvas3DGlass
bonds MCMoveClusterAtomHSTree
bonds MCMoveClusterPolyhedraTree
bonds Token
bondsA CombineABSite.CombineABSiteParameters
bondsB CombineABSite.CombineABSiteParameters
bondsTree ClusterTree
bondTheta Sam
bondtolerance Token
bondType P2AceticAcidTwoSite
bondTypeToggler MyApplet
BondTypeToggler() MyApplet.BondTypeToggler
booleanparam Token
bootstrap() CartesianIterator
bootstrap() CartesianPermutator
BORDER DeviceBox.LabelType
BORDER DisplayTextBox.LabelType
BOT Gamma
BOTEXP Gamma
bothSides MyMCMove
BOTTOM DisplayBox
BOTTOM DisplayPolytope
boundaries MeterFlux
boundary AssociationHelperBranched
boundary AssociationHelperDouble
boundary AssociationHelperMolecule
boundary PotentialCalculationRDF
boundary P2EAM
boundary PotentialCuLREP
boundary PotentialEAM_LS
boundary PotentialEAM
boundary PotentialEFS
boundary IntegratorImageHarmonicMD
boundary IntegratorMDHarmonicMC
boundary P1ImageHarmonic
boundary ColorSchemeOverlap
boundary Potential2SoftSphericalLSMulti
boundary Potential2SoftSphericalLSMultiLat
boundary PotentialCalculationEnergySumCutoff
boundary PotentialCalculationSumCutoff
boundary PotentialCalculationMappedRdf
boundary PNCO2GCPM
boundary PNGCPM
boundary MinimizeBetaNitrogenLatticeParameter
boundary MinimizeBetaNitrogenLatticeParameterFromFile
boundary MinimizeBetaNitrogenTranslationDOF
boundary P2Nitrogen
boundary P2NitrogenAB
boundary P2NitrogenAnisotropic
boundary P2NitrogenShellModel
boundary P2Water3P
boundary P2Water4P
boundary P2WaterTIP4PHardCore
boundary PNWaterGCPM
boundary PNWaterGCPMReactionField
boundary P1Wall
boundary P2SquareWellBonding
boundary P1Wall
boundary MeterOrientation
boundary MoleculePositionGeometricCenterPBC
boundary CriterionSimple
boundary CriterionSimpleMolecular
boundary HessianDB
boundary LJVacancyMin
boundary NormalModeAnalysisDisplay1D
boundary NormalModeAnalysisDisplay2D
boundary NormalModeAnalysisDisplay3D
boundary NormalModes1DHR
boundary NormalModes2D
boundary P1ConstraintNbr
boundary P1ConstraintNbrHcp
boundary PotentialCalculationSolidSuper
boundary PotentialCalculationSolidSuperCut
boundary SimBennet
boundary SimCalcSLJ
boundary SimCalcSMorse
boundary SimCalcSSoftSphere2D
boundary SimCalcSSoftSphereFCC
boundary SimCalcSSoftSphereFCCSuperBox
boundary SimEinStep1
boundary SimEinStep1HCP
boundary SimEinStep2
boundary SimEinStep2HCP
boundary SimHarmonic
boundary SimHarmonicUmbrella
boundary SimLJHTTISuper
boundary SimLJHTTISuperHCP
boundary SimLJHTTISuperHCP2
boundary SimLJHTTISuperSFMD
boundary SimOverlapSoftSphereDP
boundary SimOverlapSoftSphereEin
boundary SimOverlapSoftSphereEinHarm
boundary SimOverlapSoftSphereTP
boundary SimOverlapSoftSphereTPHCP
boundary SimOverlapSoftSphereTPSlantedBox
boundary SimTarget
boundary SimTargetUmbrella
boundary SimUmbrella
boundary SimUmbrellaSoftSphere
boundary MeterRmin
boundary MeterRminSpecies
boundary PotentialDepletion
boundary P2HardSpherePoly
boundary P1HardBoundary
boundary P1HydrogenMielke
boundary P2CO2EMP
boundary P2DiscreteFeynmanHibbs
boundary P2EffectiveFeynmanHibbs
boundary P2HydrogenHinde
boundary P2HydrogenHindeAtomic
boundary P2HydrogenHindePatkowski
boundary P2HydrogenHindePatkowskiAtomic
boundary P2HydrogenPatkowski
boundary P2HydrogenPatkowskiAtomic
boundary P2MoleculeSoftTruncatedSwitched
boundary P2MoleculeTruncated
boundary P2NitrogenHellmann
boundary P2O2Bartolomei
boundary P2QChem
boundary P2ReactionFieldDipole
boundary P2ReactionFieldDipoleTruncated
boundary P2SoftSphericalTruncatedSwitched
boundary P2SoftTruncated
boundary P2SpheroPolyhedron
boundary P2WaterPotentialsJankowski
boundary P2WCAP
boundary P3AxilrodTeller
boundary P3BondAngle
boundary P3BondAngleDreiding
boundary P3CPSNonAdditiveHe
boundary P3CPSNonAdditiveHeLessSimplified
boundary P3CPSNonAdditiveHeOrig
boundary P3CPSNonAdditiveHeSimplified
boundary P3HydrogenATM
boundary P3HydrogenManzhos
boundary P3Induction
boundary P3NitrogenHellmannNonAdditive
boundary P4BondTorsion
boundary P4BondTorsionAlkaneXCCH
boundary P4TorsionDreiding
boundary Potential1
boundary Potential2HardSpherical
boundary Potential2SoftSpherical
boundary Potential2SoftSphericalLS
boundary PotentialEmul
boundary BoundaryEvent
boundary MayerHSMixture
boundary VirialB2WaterTIP4P_DHS_difference.P2WaterDHS
Boundary etomica.space
Parent class of boundary objects that describe the size and periodic nature
of the box boundaries.
Boundary(Space, Polytope) Boundary
Subclasses must invoke this constructor and provide a Space instance that
can be used to generate Vectors, and a Polytope that defines the shape
and volume of the boundary region.
boundaryCoefficients MeterFlux
BoundaryDeformableLattice etomica.space
Deformable boundary that takes the shape of a primitive with some number
of cells in each dimension.
BoundaryDeformableLattice(Primitive, double[]) BoundaryDeformableLattice
Creates boundary with the shape of the given primitive and the given
number of cells for each dimension.
BoundaryDeformableLattice(Primitive, int[]) BoundaryDeformableLattice
Creates boundary with the shape of the given primitive and the given
number of cells for each dimension.
BoundaryDeformablePeriodic etomica.space
Boundary shaped as an arbitrary parallelepiped.
BoundaryDeformablePeriodic(Space) BoundaryDeformablePeriodic
Make a cubic boundary with edges of length equal to the default boxSize and
periodic in every direction.
BoundaryDeformablePeriodic(Space, double) BoundaryDeformablePeriodic
Make a cubic boundary of specified edge length and periodicity.
BoundaryDeformablePeriodic(Space, Vector[]) BoundaryDeformablePeriodic
Make a parallelepiped boundary of specified shape and periodicity.
BoundaryDeformablePeriodicSwitch etomica.models.nitrogen
BoundaryDeformablePeriodicSwitch(Space, Vector[]) BoundaryDeformablePeriodicSwitch
BoundaryEvent etomica.space
Event that informs a listener about some change to a boundary.
BoundaryEvent(Boundary) BoundaryEvent
BoundaryEventListener etomica.space
Listener for boundary events.
BoundaryEventManager etomica.space
Manager of listeners for boundary events.
BoundaryEventManager() BoundaryEventManager
boundaryHardA OsmosisSim
boundaryHardB OsmosisSim
boundaryHarmonic SimOverlapNitrogenModel
boundaryHarmonic SimOverlap
boundaryHarmonic SimOverlapLJ
boundaryHarmonic SimOverlapLJModule
boundaryHarmonic SimOverlapSoftSphere
boundaryHarmonic SimOverlapSoftSphereHCP
boundaryHarmonic SimOverlapSoftSphereReweighting
boundaryHarmonic SimOverlapSoftSphereSuperBox
boundaryHarmonic SimOverlapSSnxy
boundaryInflate(BoundaryEvent) NeighborCellManagerMolecular
boundaryInflate(BoundaryEvent) NeighborCellManager
boundaryInflate(BoundaryEvent) BoundaryEventListener
Informs the listener that the boundary shape and/or size has changed.
boundaryPadding ConfigurationLattice
BoundaryPistonCylinder etomica.modules.pistoncylinder
Boundary class for PistonCylinder that accounts for the piston and collision
radius when calculating the (available) volume
BoundaryPistonCylinder(Space) BoundaryPistonCylinder
BoundaryRectangular etomica.space
Boundary that is in the shape of a rectangular parallelepiped.
BoundaryRectangular(Space) BoundaryRectangular
Constructs cubic boundary of the given periodicity, using the space and default box-size
given by the Simulation.
BoundaryRectangular(Space, double) BoundaryRectangular
Constructs cubic boundary of the given periodicity with each edge of length boxSize
BoundaryRectangular(Space, double[]) BoundaryRectangular
Constructs rectangular boundary of the given periodicity with edges given by the
values in the array boxSize.
BoundaryRectangularNonperiodic etomica.space
Boundary that is not periodic in any direction.
BoundaryRectangularNonperiodic(Space) BoundaryRectangularNonperiodic
Make a boundary with unit volume.
BoundaryRectangularPeriodic etomica.space
Rectangular boundary that is periodic in every dimension.
BoundaryRectangularPeriodic(Space) BoundaryRectangularPeriodic
Constructs cubic boundary with the default box-size given by the Simulation.
BoundaryRectangularPeriodic(Space, double) BoundaryRectangularPeriodic
Constructs cubic boundary for the given Space, with each edge of length boxSize.
BoundaryRectangularPeriodic(Space, double[]) BoundaryRectangularPeriodic
Constructs rectangular boundary for the given Space, with each edge of length boxSize.
BoundaryRectangularPeriodicSwitch etomica.models.nitrogen
BoundaryRectangularPeriodicSwitch(Space) BoundaryRectangularPeriodicSwitch
BoundaryRectangularPore etomica.space
Class for implementing pore periodic boundary conditions, in which
one dimension is periodic.
BoundaryRectangularPore(Space) BoundaryRectangularPore
Makes cubic volume with the x-dimension (index 0)
not periodic.
BoundaryRectangularPore(Space, int) BoundaryRectangularPore
Makes cubic volume with the indicated dimension not periodic.
BoundaryRectangularPore(Space, int, double) BoundaryRectangularPore
Constructor for periodic boundary conditions with a pore
in the given dimension.
BoundaryRectangularSlit etomica.space
Class for implementing slit periodic boundary conditions, in which
one dimension is not periodic.
BoundaryRectangularSlit(int, double, Space) BoundaryRectangularSlit
Constructor for periodic boundary conditions with a slit
in the given dimension.
BoundaryRectangularSlit(int, Space) BoundaryRectangularSlit
Makes cubic volume with the indicated dimension not periodic.
BoundaryRectangularSlit(Space) BoundaryRectangularSlit
Makes cubic volume with the x-dimension (index 0)
not periodic.
boundaryRef SimOverlapSoftSphereEinHarm
boundaryRef SimOverlapSoftSphereSoftness
boundarySemiB OsmosisSim
boundaryTarg SimOverlapSoftSphereSoftness
boundaryTarget SimOverlapNitrogenModel
boundaryTarget SimOverlap
boundaryTarget SimOverlapLJ
boundaryTarget SimOverlapLJModule
boundaryTarget SimOverlapSoftSphere
boundaryTarget SimOverlapSoftSphereHCP
boundaryTarget SimOverlapSoftSphereReweighting
boundaryTarget SimOverlapSoftSphereSuperBox
boundaryTarget SimOverlapSSnxy
BoundaryTruncatedOctahedron etomica.space3d
This class enables creation of a periodic truncated-octahedron boundary.
BoundaryTruncatedOctahedron(Space) BoundaryTruncatedOctahedron
BoundaryTruncatedOctahedron(Space, double) BoundaryTruncatedOctahedron
boundbox Token
boundboxcolor Token
box ActionMinimizeEnergy
box BoxActionAdapter
box BoxRandomizeMomenta
box BoxScaleMomenta
box WriteConfiguration
box CH4NVT
box DHS_NVT
box DLJ_NVT_1site
box TestAceticAcidMC3D_NPT
box SimGCPMWaterMCNPT
box SimGCPMWaterMCNVT
box TestIGAssociationMC3D_NPT_DoubleSites
box TestLJAssociationMC3D_NPT_DoubleSites
box TestLJAssociationMC3D_NPT
box TestLJAssociationMC3D_NVTOld
box AtomLeafAgentManager
box AtomSourceRandomSpecies
box BoxEvent
box RandomPositionSourceDeformable
box RandomPositionSourceRectangular
box DataProcessorGContactP
box DataProcessorPContactG
box HSMDCavity
The Box holding the atoms.
box HSMDWidom
The Box holding the atoms.
box MeterWidomCavity
box DataProcessorInterfacialTension
box MeterDihedralAngle
box MeterHyperVirial
box MeterKineticEnergyRigid
box MeterPotentialEnergy
box MeterPressure
box MeterPressureTensor
box MeterProfileByAtoms
box MeterProfileByVolume
box MeterRDF
box MeterRDFPC
box MeterRMSD
box MeterStructureFactor
box MeterTemperature
box MeterWidomInsertion
box DCVGCMD
box DHS_NVT
box DLJ_NVT_1site
box TIP4P_NVT
box PotentialCalculationForcePressureSumGB
box SimDimerLJadatom
box EFSTungsten
box ConfigurationOverlapException
box ConfigFromFileLAMMPS.ColorSchemeDeviation
box ConfigFromFileLAMMPS.ModifierConfiguration
box DataSourceEnergies
box SimFe
box SimIdealGas
box SimLattice
box SimLJ
box DeviceNSelector
box IntegratorBox
box IntegratorRigidMatrixIterative.BoxImposePbcMolecule
box MCMoveBox
box MCMoveInsertDeleteLatticeVacancy.AtomIteratorBruteForce
box FixedWall
box LJMC
box LJMD
box MeterWallForce
box MeterWallPosition
box SimKMCLJadatom
box DataProcessorReweight
box LjMC3D
box LjMd3D
box LjMd3D.DataProcessorReweight
box MeterPotentialEnergyCutoff
box MeterPU
box MeterPUCut
box MeterPUCutLS
box MeterWidomInsertionCorrection
box MeterWidomInsertionP
box PotentialCalculationEnergySumCutoff
box PotentialCalculationSumCutoff
box MeterMappedRdf
box SimMappedRdf
box MappedU
box MappedVirialLJ
box MappedVirialLJVGr
box MeterMappedU
box MeterMappedVirial
box MeterMappedVirialV
box MeterMeanForce
box PotentialCalculationMappedEnergy
box PotentialCalculationMappedVirial
box PotentialCalculationMappedVirialV
box CalcGradientDifferentiable
box LJmuVT
box LJNPT
box LJNVT
box MeterDensityDistribution
box ClathrateHarmonicFE
box MinimizationTIP4P
box ProtonDisorderGenerator
box CalcAnalytical2ndDerivativeNitrogen
box CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
box CalcNumerical2ndDerivative
box CalcNumerical2ndDerivativeNitrogen
box FiniteDifferenceDerivativeCGNitrogenBeta
box HarmonicAlphaNitrogenModel
box HarmonicAlphaNitrogenModelDecomposed
box HarmonicAlphaNitrogenModelPairMolecule
box HarmonicAlphaNitrogenModelPairMoleculeSequential
box HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2
box HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
box HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
box HarmonicBetaNitrogenModel
box HarmonicBetaNitrogenModelDecomposed
box HarmonicBetaNitrogenModelPairMoleculeSequential
box HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
box HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2
box HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
box HarmonicBetaNitrogenModelPairMoleculeSequentialLS
box HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
box HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
box MinimizationBetaNitrogenModel
box MinimizationBetaNitrogenModelLS
box MinimizeBetaNitrogenLatticeParameter
box MinimizeBetaNitrogenLatticeParameterFromFile
box MinimizeBetaNitrogenLatticeParameterLSFromFile
box MinimizeBetaNitrogenTranslationDOF
box MinimizeGammaNitrogenLatticeParameter
box SimDirectBetaN2RPInitPert
box SimDirectDisorderedAlphaN2RPInitPert
box SimOverlapAlphaN2TP
box SimOverlapBetaN2RPScaling
box SimOverlapBetaN2TP
box SimOverlapDisorderedAlphaN2RPScaling
box SimOverlapDisorderedAlphaN2TP
box SimulationAlphaNitrogenModel
box SimulationBetaNitrogenModel
box SimulationBetaNitrogenModelTest
box SimulationGammaNitrogenModel
box DimerApproach
box PNWaterGCPMReactionField
box TestEwaldTIP4PWater
box ModifierNMolecule
box Adsorption
box MeterExcessAdsorbed
box Catalysis
box MeterDensityCO
box MeterDensityCO2
box MeterDensityO2
box AtomTestChainLength
box ChainEquilibriumSim
box ColorSchemeRadical
box FreeRadicalPolymerizationSim
box MeterChainLength
box MeterConversion
box P2SquareWellBonded
box ColloidSim
box MeterEnd2End
box CrystalViewer
box LatticeEditor
box DCVGCMD
box Droplet
box DropletAtomic
box DropletGraphic.ModifierBoxSize
box MeterDeformation
box LJMC
box AtomNbrClusterer
box AtomTestDeviation
box ColorSchemeCluster
box ColorSchemeDeviation
box ColorSchemeDirection
box ConfigurationStorage
box DataClusterWriter
box DataSourcePercolation0
box DataSourceStrings
box SimGlass
box Insertion
box DataProcessorInterfacialTensionProfile
box InterfacialSW
box InterfacialSWGraphic.ModifierBoxSize
box Ljmd
box MaterialFracture
box MeterElongation
box MeterLoad
box MeterStrain
box MeterStress
box P1Tension
box StrainColorScheme
box MeterDensitySides
box Mu
box MuGraphic.DataSinkExcludeOverlap
box MultiharmonicMC
box ColorSchemeCluster
box MeterLargestCluster
box OsmosisSim
box PistonCylinder
box ReactionEquilibrium
box MeterEndToEnd
box MeterNormalStress
box MeterViscosity
box SimulationRheology
box MeterFlux
box MeterOsmoticPressure
box ReverseOsmosis
box ReverseOsmosisGraphic.DataSinkExcludeOverlap
box ReverseOsmosisWater
box ReverseOsmosisWaterGraphic.DataSinkExcludeOverlap
box CriterionTether3
box MeterTilt
box MeterWallPressure
box Sam
box AtomTestChainLength
box SelfAssemblySim
box Swmd
box MeterPressure2
box MoleculeIteratorAll
box MpiIntraspecies1A
box MoleculeSourceRandomMolecule
box NeighborCellManagerMolecular
box NeighborCellManager
box PotentialMasterCellMixed
box NeighborListManagerMolecular
box NeighborListManager
box CoordinateDefinition
box DeviceCellNum3DSlider
box DeviceCellNumXYSlider
box HessianDB
box HSDimerNPT
box HSNPT
box LatticeSumMolecularCrystal
box LJVacancyMin
box MeterAPIPotentialEnergy
box MeterMaxExpansion
box MeterPhiDeviation
box MeterPlaneSlip
box MeterSolidDA
box MeterSolidDACut
box MeterSolidMirror
box MeterThetaDeviation
box MeterTilt
box MeterTiltHistogram
box MeterTiltRotation
box MeterTiltRotationHistogram
box MeterTiltRotationStdev
box MinimizeHCP
box ModifierCells3D
box ModifierXCells2D
box ModifierYCells2D
box NormalModeAnalysisDisplay1D
box NormalModeAnalysisDisplay2D
box NormalModeAnalysisDisplay3D
box NormalModesMolecular
box HSNPT2DSim
box P2XOrder
box PotentialCalculationEFSSP
box PotentialCalculationLJSP
box PotentialCalculationSolidSuper
box PotentialCalculationSolidSuperCut
box SimBennet
box SimCalcJ
box SimCalcS
box SimCalcSLJ
box SimCalcSMorse
box SimCalcSSoftSphere2D
box SimCalcSSoftSphereFCC
box SimCalcSSoftSphereFCCSuperBox
box SimEinStep1
box SimEinStep1HCP
box SimEinStep2
box SimEinStep2HCP
box SimFluidSoftSphere
box SimHarmonic
box SimHarmonicUmbrella
box SimHSMDVacancy
box SimLJHTTISuper
box SimLJHTTISuperHCP
box SimLJHTTISuperHCP2
box SimLJHTTISuperSFMD
box SimLJVacancy
box SimModesJ
box SimOverlapSoftSphereDP
box SimOverlapSoftSphereEin
box SimOverlapSoftSphereEinHarm
box SimOverlapSoftSphereTP
box SimOverlapSoftSphereTPHCP
box SimOverlapSoftSphereTPSlantedBox
box SimTarget
box SimTargetUmbrella
box SimUmbrella
box SimUmbrellaSoftSphere
box AshtonWildingLJ
box AshtonWildingOsmoticVirial
box AshtonWildingVirial
box GCWidomInsertHS
box NVTWidomInsertLJ
box PolydisperseHS
The Box holding the atoms.
box EwaldSummation
box EwaldSumMolecules
box P2ReactionFieldDipoleTruncated.P0ReactionField
box Potential0Lrc
box PotentialGroup
box DipoleBox
box DipoleBoxMatrix
box ChainHSMD3D
box HSMC2D
box HSMD2D_noNbr
box HSMD2D
box HSMD3D
The Box holding the atoms.
box HSMD3DNoNbr
box LJMD2D
box LJMD3D
box LJMD3DNbr
box SoftSphere3d
box SWMD2D
box SWMD3D
box Boundary
box Heisenberg
box Heisenberg3Pair
box HeisenbergPair
box MeterDipoleMoment
box MeterEnergyMeanField
box MeterMeanField
box Ising
box MeterBondLength
box StarPolymerMC
box StarPolymerMD
box LJMC
box SurfaceTensionMapped
box TestHSMD3D
box TestLJGCMC3D
box TestLJMC3D
box TestLJMD3D
box TestSWChain
box MeterVirialBDBinMultiThreaded
box MeterVirialBinMultiThreaded
box MeterVirialEBinMultiThreaded
box SimulationVirial
box SimulationVirialOverlap2
box TestLJAssociationMC3D_NPT
box ZeoliteSimulation
The Box holding the atoms.
box() Simulation
Convenience method to retrieve the first (and typically only) Box in the simulation.
Box etomica.box
A Box collects all atoms that interact with one another; atoms in different
boxes do not interact.
Box g3dsys.images
Class for drawing a bounding box around the figures in molecule space
Box(Boundary, Space) Box
Constructs box with the given Boundary, which specifies the size and shape of the Box and specifies what
happens to atoms as they cross the box boundary e.g.
Box(Space) Box
Constructs box with default rectangular periodic boundary.
Box(G3DSys, short) Box
BOX G3DSys
BOX_INDEX Debug
index of box of interest.
box1 IntegratorDimerRT
box1 MCMoveMoleculeExchange
box1 GCRestrictedGibbsHS
box1 MCMoveGeometricClusterRestrictedGE
box1 GEMCWithRotation
box1 PotentialCommonAtomic
box2 IntegratorDimerRT
box2 MCMoveMoleculeExchange
box2 GCRestrictedGibbsHS
box2 MCMoveGeometricClusterRestrictedGE
box2 GEMCWithRotation
boxA MultiharmonicMC
boxA MultiharmonicMC
BoxAction etomica.action
Elementary action performed on a Box.
BoxActionAdapter etomica.action
Convenience class used to define a BoxAction.
BoxActionAdapter() BoxActionAdapter
boxAdded(Box) SimulationEventManager
boxAgentManager CriterionSimple
boxAgentManager CriterionSimpleMolecular
boxAgentManager PotentialMasterNbrMolecular
boxAgentManager P1HarmonicSite
BoxAgentManager E > - Class in etomica.box
Acts on behalf of client classes (a BoxAgentSource) to manage
agents for each Box in a simulation.
BoxAgentManager(BoxAgentManager.BoxAgentSource<E>, Simulation) BoxAgentManager
Constructs and sets the Simulation containing Boxes to be tracked.
BoxAgentManager(Simulation, Function<Box, ? extends E>) BoxAgentManager
BoxAgentManager(Simulation, Function<Box, ? extends E>, Consumer<? super E>) BoxAgentManager
BoxAgentManager.BoxAgentSource E > - Interface in etomica.box
Interface for an object that makes an agent to be associated with each box
upon construction.
boxAgentSource PotentialMasterNbrMolecular
BoxAgentSourceAtomManager E > - Class in etomica.box
BoxAgentSource that creates an AtomLeafAgentManager.
BoxAgentSourceAtomManager(AtomLeafAgentManager.AgentSource<E>, Class) BoxAgentSourceAtomManager
BoxAgentSourceCellManager etomica.nbr.cell
BoxAgentSource responsible for creating a NeighborCellManager.
BoxAgentSourceCellManager(IMoleculePositionDefinition, double) BoxAgentSourceCellManager
BoxAgentSourceCellManagerListMolecular etomica.nbr.list.molecule
BoxAgentSource responsible for creating a NeighborCellManagerMolecular.
BoxAgentSourceCellManagerListMolecular(Simulation, IMoleculePositionDefinition, Space) BoxAgentSourceCellManagerListMolecular
BoxAgentSourceCellManagerMolecular etomica.nbr.cell.molecule
BoxAgentSource responsible for creating a NeighborCellManagerMolecular.
BoxAgentSourceCellManagerMolecular(Simulation, IMoleculePositionDefinition, Space) BoxAgentSourceCellManagerMolecular
BoxAgentSourceMoleculeManager E > - Class in etomica.box
BoxAgentSource that creates an MoleculeAgentManager.
BoxAgentSourceMoleculeManager(MoleculeAgentManager.MoleculeAgentSource<E>, Simulation) BoxAgentSourceMoleculeManager
BoxAtomEvent etomica.box
A box event that is somehow related to an atom.
BoxAtomEvent(Box, IAtom) BoxAtomEvent
BoxAtomIndexEvent etomica.box
Box event that indicates that an atom's index has changed.
BoxAtomIndexEvent(Box, IAtom, int) BoxAtomIndexEvent
boxAtomLeafIndexChanged(BoxAtomIndexEvent) AtomLeafAgentManager
boxAtomLeafIndexChanged(BoxAtomIndexEvent) BoxEventListener
Called when an atom's global (leaf) index has changed.
boxAtomLeafIndexChanged(BoxAtomIndexEvent) BoxEventListenerAdapter
boxAtomLeafIndexChanged(BoxAtomIndexEvent) IntegratorMD
boxB MultiharmonicMC
boxB MultiharmonicMC
BoxCellManager etomica.box
Interface for class that handles assignment of atoms to cells in a box.
boxCells MCMoveAtomSuperBox
BoxCluster etomica.virial
BoxCluster(ClusterWeight, Space) BoxCluster
Constructor for BoxCluster.
BoxCluster(ClusterWeight, Space, double) BoxCluster
BoxDeleteMolecules etomica.action
Deletes molecules from a box as determined by an AtomTest.
BoxDeleteMolecules(Predicate<IMolecule>) BoxDeleteMolecules
boxDim MinimizeBetaNitrogenLatticeParameter
boxDim MinimizeBetaNitrogenLatticeParameterFromFile
boxDim MinimizeBetaNitrogenTranslationDOF
BoxEvent etomica.box
A box event fired by the box's event manager.
BoxEvent(Box) BoxEvent
BoxEventListener etomica.box
A box listener receives notifications for box events.
BoxEventListenerAdapter etomica.box
BoxEventListenerAdapter() BoxEventListenerAdapter
BoxEventManager etomica.box
BoxEventManager(Box) BoxEventManager
boxGlobalAtomLeafIndexChanged(BoxIndexEvent) AtomLeafAgentManager
boxGlobalAtomLeafIndexChanged(BoxIndexEvent) BoxEventListener
Called when the maximum leaf index in the box has changed.
boxGlobalAtomLeafIndexChanged(BoxIndexEvent) BoxEventListenerAdapter
boxGlobalAtomLeafIndexChanged(BoxIndexEvent) IntegratorMD
boxH ClipPlaneEditor
boxHarmonic SimOverlapNitrogenModel
boxHarmonic SimOverlap
boxHarmonic SimOverlapLJ
boxHarmonic SimOverlapLJModule
boxHarmonic SimOverlapSoftSphere
boxHarmonic SimOverlapSoftSphereHCP
boxHarmonic SimOverlapSoftSphereReweighting
boxHarmonic SimOverlapSoftSphereSuperBox
boxHarmonic SimOverlapSSnxy
BoxImposePbc etomica.action
Action that imposes the central-image effect of a box having periodic
boundaries.
BoxImposePbc(Box, Space) BoxImposePbc
Creates the action ready to perform on the given box.
BoxImposePbc(Space) BoxImposePbc
Creates the action without specifying a box.
BoxImposePbcMolecule(Box, Space) IntegratorRigidMatrixIterative.BoxImposePbcMolecule
boxIndex P1ConstraintNbr
BoxIndexEvent etomica.box
Event that conveys that the maximum leaf index in a Box has changed
(or is about to change).
BoxIndexEvent(Box, int) BoxIndexEvent
boxInflate MeterWidomInsertionP
BoxInflate etomica.action
Performs actions that cause volume of system to expand or contract, with
molecule positions scaled to keep them in the same relative positions.
BoxInflate(Box, Space) BoxInflate
Constructs BoxInflate action with the given box, but no directive to
actually change the box size.
BoxInflate(Box, Space, double) BoxInflate
Constructs BoxInflate action set to change the given box's density to
the given value.
BoxInflate(Space) BoxInflate
Constructs BoxInflate action without a box or directive to actually change
the box size.
BoxInflateAnisotropic etomica.action
Class that perform anisotropic angle fluctuation
BoxInflateAnisotropic(Box, Space) BoxInflateAnisotropic
BoxInflateAnisotropic(Space) BoxInflateAnisotropic
BoxInflateDeformable etomica.action
Performs actions that cause volume of a deformable system to expand, with molecule
positions scaled to keep them in the same relative positions.
BoxInflateDeformable(Box, Space) BoxInflateDeformable
BoxInflateDeformable(Space) BoxInflateDeformable
BoxInfo org.jmol.util
BoxInfo() BoxInfo
boxK ClipPlaneEditor
boxL ClipPlaneEditor
boxLength SimulationVirial
boxLengths SimulationVirialOverlap2
boxLiquid VLESim
boxLiquid SWVLESim
boxLiquid VLESim
boxMin IntegratorDimerMin
boxMoleculeAdded(BoxMoleculeEvent) AtomLeafAgentManager
boxMoleculeAdded(BoxMoleculeEvent) BoxEventListener
Called when a molecule is added to the box.
boxMoleculeAdded(BoxMoleculeEvent) BoxEventListenerAdapter
boxMoleculeAdded(BoxMoleculeEvent) IntegratorHard
boxMoleculeAdded(BoxMoleculeEvent) IntegratorMD
boxMoleculeAdded(BoxMoleculeEvent) MoleculeAgentManager
BoxMoleculeCountEvent etomica.box
Box event that indicates the number of molecules of a particular species has
changed.
BoxMoleculeCountEvent(Box, ISpecies, int) BoxMoleculeCountEvent
BoxMoleculeEvent etomica.box
A box event that is somehow related to a molecule.
BoxMoleculeEvent(Box, IMolecule) BoxMoleculeEvent
boxMoleculeIndexChanged(BoxMoleculeIndexEvent) BoxEventListener
Called when an molecule's index has changed.
boxMoleculeIndexChanged(BoxMoleculeIndexEvent) BoxEventListenerAdapter
boxMoleculeIndexChanged(BoxMoleculeIndexEvent) IntegratorMD
boxMoleculeIndexChanged(BoxMoleculeIndexEvent) MoleculeAgentManager
BoxMoleculeIndexEvent etomica.box
Box event that indicates that a molecule's index has changed.
BoxMoleculeIndexEvent(Box, IMolecule, int) BoxMoleculeIndexEvent
boxMoleculeRemoved(BoxMoleculeEvent) AtomLeafAgentManager
boxMoleculeRemoved(BoxMoleculeEvent) BoxEventListener
Called when a molecule is removed from the box.
boxMoleculeRemoved(BoxMoleculeEvent) BoxEventListenerAdapter
boxMoleculeRemoved(BoxMoleculeEvent) IntegratorMD
boxMoleculeRemoved(BoxMoleculeEvent) MoleculeAgentManager
boxNumberMolecules(BoxMoleculeCountEvent) BoxEventListener
Called when the number of molecules of a particular species has changed
in the box.
boxNumberMolecules(BoxMoleculeCountEvent) BoxEventListenerAdapter
boxNumberMolecules(BoxMoleculeCountEvent) IntegratorMD
boxO ProtonDisorderGenerator
boxPanel LatticeEditor
BoxQuench etomica.action
Scales all velocities of a box so that its kinetic temperature is equal to
a given value.
BoxQuench(double, int) BoxQuench
Constructs class without specifying box and using Default temperature.
BoxQuench(int) BoxQuench
BoxQuench(Box, double) BoxQuench
Constructs class ready to perform quench on given box to given temperature.
BoxRandomizeMomenta etomica.action
Randomizes the velocities of all the leaf atoms in a Box based on the
Maxwell-Boltzmann distribution.
BoxRandomizeMomenta(Box, IRandom) BoxRandomizeMomenta
boxRef SimOverlapBetaN2RP
boxRef SimOverlapSoftSphereEinHarm
boxRef SimOverlapSoftSphereSoftness
boxRemoved(Box) SimulationEventManager
boxScale MCMoveBoxSize
BoxScaleMomenta etomica.action
Scales the momenta of all the leaf atoms in a Box such that the kinetic
temperature matches some value.
BoxScaleMomenta(Box, Space) BoxScaleMomenta
boxSize MCMoveVolumeMonoclinicScaled
boxSize MCMoveVolumeSolidNPTMolecular
boxSize EwaldSummation
boxSize EwaldSumMolecules
boxSize0 MeterDisplacementRMS
boxTarg SimDirectBetaN2RP
boxTarg SimDirectBetaN2RPAngleToNoAngle
boxTarg SimOverlapBetaN2RP
boxTarg SimOverlapSoftSphereSoftness
boxTarget SimOverlapNitrogenModel
boxTarget SimOverlap
boxTarget SimOverlapLJ
boxTarget SimOverlapLJModule
boxTarget SimOverlapSoftSphere
boxTarget SimOverlapSoftSphereHCP
boxTarget SimOverlapSoftSphereReweighting
boxTarget SimOverlapSoftSphereSuperBox
boxTarget SimOverlapSSnxy
BoxTracker() IntegratorPT.BoxTracker
boxVapor VLESim
boxVapor SWVLESim
boxVapor VLESim
boxVec MinimizationBetaNitrogenModelLS
boxWellManager P2SquareWellRobust
bpharm SimLJHTTISuper.SimOverlapParam
bpharm SimLJHTTISuperHCP.SimOverlapParam
bpharm SimLJHTTISuperHCP2.SimOverlapParam
bpharm SimLJHTTISuperSFMD.SimOverlapParam
bpHarm MeterSolidDA
bpharmLJ SimLJHTTISuper.SimOverlapParam
bpharmLJ SimLJHTTISuperHCP.SimOverlapParam
bpharmLJ SimLJHTTISuperHCP2.SimOverlapParam
bpRes MeterSolidDACut
bpResDADv2 MeterSolidDACut
branch Token
BravaisLattice etomica.lattice
Arbitrary-dimension Bravais Lattice, in which the sites are instances of
etomica.space.Vector, with positions given as linear combinations of a set of
primitive vectors.
BravaisLattice(Primitive) BravaisLattice
BravaisLatticeCrystal etomica.lattice
A lattice with sites given by the "atom" sites of a crystal.
BravaisLatticeCrystal(Primitive, Basis) BravaisLatticeCrystal
Constructs a lattice having sites given by the "atom" sites of the given
crystal.
BreadthFirst etomica.graph.traversal
BreadthFirst() BreadthFirst
brillouin Token
broadhurstBBP(int, int, int[], MathContext) BigDecimalMath
Broadhurst ladder sequence.
broken MultiharmonicGraphicMC.DataSourceFE
broken3body P2WaterSzalewicz
bScaled Rgb16
bsDisplay MeshSurface
bsNull BitSetUtil
bsPolygons MeshSurface
bsSelectRange(Token, int) ScriptVariable
bsSelectToken(Token) ScriptVariable
bsSelectVar(ScriptVariable) ScriptVariable
bsSlabDisplay MeshSurface
bsSlabGhost MeshSurface
bSum ClusterSinglyConnected
bt PotentialCalculationFSum
bt MeterMappedAveraging
bt MeterMappedAveraging3Pair
bt MeterMappedAveragingCorrelation
bt MeterMappedAveragingCV
bt MeterMappedAveragingFreeEnergy
bt MeterMappedAveragingPair
bt MeterMappedAveragingPairExcess
bt MeterMappedAveragingSum
bt MeterMappedAveragingVSum
bt MeterMappedAveragingVSum3Pair
bt MeterMappedAveragingVSumPair
bt MeterPairSum
bt PotentialCalculationFreeEnergy
bt PotentialCalculationFSum
bt PotentialCalculationHeisenberg
bt PotentialCalculationMoleculeAgentSum
bt PotentialCalculationMoleculeAgentSumMinusIdeal
bt PotentialCalculationMoleculeAgentSumMinusIdealPair
bt PotentialCalculationMoleculeAgentSumPair
bt PotentialCalculationPair
bt PotentialCalculationVSum
bThetadot MeterEnergyMeanField
buf RandomNumberGeneratorUnix
bufferSize GData
build() SpeciesBuilder
BuilderCollectionPotential etomica.virial.GUI.components
BuilderCollectionPotential() BuilderCollectionPotential
BuildProperties etomica.util
BuildProperties() BuildProperties
bump(IAtomList, double) P2HardSphereCavity
Implements collision dynamics and updates lastCollisionVirial
bump(IAtomList, double) P1Wall
bump(IAtomList, double) P2SquareWellBonding
Implements collision dynamics between two square-well atoms.
bump(IAtomList, double) P2SquareWellBondingCO
Implements collision dynamics between two square-well atoms.
bump(IAtomList, double) P2SquareWellSurface
Implements collision dynamics between two square-well atoms.
bump(IAtomList, double) P2SquareWellBonded
bump(IAtomList, double) P2SquareWellRadical
bump(IAtomList, double) P1Wall
bump(IAtomList, double) P2SquareWellMonomer
bump(IAtomList, double) P1MagicWall
bump(IAtomList, double) P2SquareWellOneSide
Implements collision dynamics between two square-well atoms.
bump(IAtomList, double) P1HardWall
bump(IAtomList, double) P2SquareWellBonded
bump(IAtomList, double) P2XOrder
bump(IAtomList, double) P2HardSpherePoly
Implements collision dynamics and updates lastCollisionVirial
bump(IAtomList, double) P1HardBoundary
bump(IAtomList, double) P1HardMovingBoundary
bump(IAtomList, double) P1HardPeriodic
Performs no action.
bump(IAtomList, double) P2DoubleWell
Implements collision dynamics between two square-well atoms.
bump(IAtomList, double) P2HardAssociation
Implements the collision dynamics.
bump(IAtomList, double) P2HardBond
Implements collision dynamics for pair attempting to separate beyond
tether distance
bump(IAtomList, double) P2HardBondedList
bump(IAtomList, double) P2HardSphere
Implements collision dynamics and updates lastCollisionVirial
bump(IAtomList, double) P2HardWrapper
bump(IAtomList, double) P2Ideal
Does nothing.
bump(IAtomList, double) P2PenetrableBond
Implements collision dynamics between two square-well atoms.
bump(IAtomList, double) P2PenetrableSphere
Implements collision dynamics between two penetrable-sphere atoms.
bump(IAtomList, double) P2PenetrableSquareWell
Implements collision dynamics between two square-well atoms.
bump(IAtomList, double) P2RoughSphere
Implements collision dynamics and updates lastCollisionVirial
Assumes atoms have same size and mass
bump(IAtomList, double) P2SquareWell
Implements collision dynamics between two square-well atoms.
bump(IAtomList, double) P2SquareWellRobust
Implements collision dynamics between two square-well atoms.
bump(IAtomList, double) P2Tether
Implements collision dynamics for pair attempting to separate beyond tether distance
bump(IAtomList, double) PotentialHard
Implements the collision dynamics.
button DeviceButton
button DeviceButtonSingle
buttonActions DeviceButtonGroup
buttonCorner1 Grabber
buttonCorner2 Grabber
buttonGroup DeviceButtonGroup
buttonPanel DeviceButtonGroup
buttons DeviceButtonGroup
bv TestAceticAcidMC3D_NPT
bv P2AceticAcidTwoSite
bv P2HardAssociationRefAceticAcidTwoSite
bveci PNCO2GCPM.P3GCPMAxilrodTeller
bveci PNGCPM.P3GCPMAxilrodTeller
bvecj PNCO2GCPM.P3GCPMAxilrodTeller
bvecj PNGCPM.P3GCPMAxilrodTeller
bveck PNCO2GCPM.P3GCPMAxilrodTeller
bveck PNGCPM.P3GCPMAxilrodTeller
bVirial VirialOptimizer
bVirialFromFile VirialOptimizer
bvso TestIGAssociationMC3D_NPT_DoubleSites
bvso TestLJAssociationMC3D_NPT_DoubleSites
c P1LepsHarmonic
c PotentialEAM_LS
c LjMd3D.VolumeBias
c PotentialCalculationMappedVirialV.USine
c PadeApproximation
c PadeApproximation.VirialParam
c MinimizeGammaNitrogenLatticeParameter
c P2WaterSzalewicz
c StatisticsMCGraphic.DataProcessorUndo
c SoftSphereSolidEOS
c SoftSphereSolidEOSCalculator
c P2WaterPotentialsJankowski
c HardSphereSolid
c ClusterPY
C EnumSiteName
C PotentialEAM
C Gamma
C P2Nitrogen
C P2NitrogenAB
C P2NitrogenAnisotropic
C P2HePCKLJS
C_AD P2HePCJS
C_BO P2HePCJS
C_QED P2HePCJS
C_REL P2HePCJS
c0 PotentialCuLREP
c0 PotentialEFS
c0 DisplayTable
c1 PotentialCuLREP
c1 PotentialEFS
c1 PotentialCalculationMappedRdf
c1 PotentialCalculationMappedEnergy
c1 PotentialCalculationMappedVirial
c1 PotentialCalculationMappedVirialV
c1 EOSSWPatel
c10 P1HydrogenMielke
C10Data P2QChemInterpolated
C1CH31 BiasVolume2SiteAceticAcid
C1CH31 BiasVolumeAceticAcid
C1DBO1 BiasVolume2SiteAceticAcid
C1DBO1 BiasVolumeAceticAcid
C1SBO1 BiasVolume2SiteAceticAcid
C1SBO1 BiasVolumeAceticAcid
c2 PotentialCuLREP
c2 PotentialEFS
c2 EOSSWPatel
c2 BnJHBVArgon_Analytic
c2_sqrt BnJHBVArgon_Analytic
C2C1 BiasVolume2SiteAceticAcid
C2C1 BiasVolumeAceticAcid
C2CH32 BiasVolume2SiteAceticAcid
C2CH32 BiasVolumeAceticAcid
C2DBO2 BiasVolume2SiteAceticAcid
C2DBO2 BiasVolumeAceticAcid
C2SBO2 BiasVolume2SiteAceticAcid
C2SBO2 BiasVolumeAceticAcid
c3 PotentialCuLREP
c3 PotentialEFS
c3 P2WaterSzalewicz
c3 EOSSWPatel
c3 BnJHBVArgon_Analytic
C3 Standard
c3_sqrt BnJHBVArgon_Analytic
c3Add BnJHBVArgon_Analytic
c3Add_sqrt BnJHBVArgon_Analytic
c4 PotentialCuLREP
c4 PotentialEFS
c4 BnJHBVArgon_Analytic
c4_sqrt BnJHBVArgon_Analytic
c4Add BnJHBVArgon_Analytic
c4Add_sqrt BnJHBVArgon_Analytic
c5 P2HydrogenHinde
c5 P2HydrogenHindeAtomic
c5 BnJHBVArgon_Analytic
c5_sqrt BnJHBVArgon_Analytic
c5Add BnJHBVArgon_Analytic
c5Add_sqrt BnJHBVArgon_Analytic
c6 P1HydrogenMielke
c6 P2HydrogenHinde
c6 P2HydrogenHindeAtomic
c6 P2NitrogenHellmann
c6 P2O2Bartolomei
c6 BnJHBVArgon_Analytic
C6 P2CO2Hellmann
c6_sqrt BnJHBVArgon_Analytic
c6A P2NitrogenHellmann
C6A P2CO2Hellmann
c6Add BnJHBVArgon_Analytic
c6Add_sqrt BnJHBVArgon_Analytic
c6B P2NitrogenHellmann
C6B P2CO2Hellmann
C6BO P2HePCKLJS
C6Data P2QChemInterpolated
c7Add BnJHBVArgon_Analytic
c7Add_sqrt BnJHBVArgon_Analytic
c8 P1HydrogenMielke
c8 P2HydrogenHinde
c8 P2HydrogenHindeAtomic
c8 P2O2Bartolomei
C8 P2CO2Hellmann
C8A P2CO2Hellmann
C8B P2CO2Hellmann
C8Data P2QChemInterpolated
C9iso P3NitrogenHellmannNonAdditive
C9isoSim P3NitrogenHellmannNonAdditive
cA DecorateWertheim2Site.DecorateWertheimParameters2Site
cA2nD HarmonicAlphaNitrogenModelPairMoleculeSequential
cA2nD HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2
cA2nD HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
cA2nD HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
cA2nD HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
cAB DecorateWertheim2Site.DecorateWertheimParameters2Site
calc(double[][]) Eigen
Check for symmetry, then construct the eigenvalue decomposition
CalcAnalytical2ndDerivativeNitrogen etomica.models.nitrogen
Determine the second derivative of the atomic/ molecular potential energy w.r.t.
CalcAnalytical2ndDerivativeNitrogen(Space, Box, P2Nitrogen, CoordinateDefinitionNitrogen) CalcAnalytical2ndDerivativeNitrogen
CalcAnalytical2ndDerivativeNitrogen(Space, Box, P2Nitrogen, CoordinateDefinitionNitrogen, boolean, double) CalcAnalytical2ndDerivativeNitrogen
calcAngle(Vector, Vector) BiasVolume2SiteAceticAcid
calcAngle(Vector, Vector) BiasVolumeAceticAcid
calcApprox BnPCJSDHe.BnPCJSDHeParams
calcApprox VirialHeNonAdditive.VirialParam
calcApprox VirialHeNonAdditiveWheatley.VirialParam
calcApprox VirialHePISysErr.VirialHePIParam
calcApprox VirialHePIXCEven.VirialHePIParam
calcApprox VirialHePIXCOdd.VirialHePIParam
calcApprox VirialHePYCorrection.VirialHePYCParam
calcApprox VirialHeSC.VirialHePYCParam
calcAveCosThetaInitial() MCMoveRotateMolecule3DN2AveCosThetaConstraint
calcAveragePoint(Point3f, Point3f, Point3f) Measure
calcAveragePointN(Point3f[], int, Point3f) Measure
calcB2(double, double) VirialLJQB2
calcBestAxisThroughPoints(Point3f[], Point3f, Vector3f, Vector3f, int) Measure
calcBMu(double, double, double) LJmuVT
calcBoth(double, double) Gamma
calcConversion(IMoleculeList) MeterConversion
calcDiff VirialHeD.VirialParam
calcDiff VirialHeNonAdditiveD.VirialParam
calcdMudP(double, double) HardSphereSolid
calcdmudrho(double, double) HardSphereSolid
calcdPdrho(double, double) HardSphereSolid
calcer IntegratorVelocityVerletQuaternion.MyTypeAgent
calcErr(int, int) AkimaSplineSmoother
calcErr(int, int) AkimaSplineSmootherDy
calcF(double) MayerFunctionThreeBody
Returns exp(x)-1 computed directly or using a series expansion
calcfAB(int, boolean) ClusterWheatleyPartitionScreening
calcfAB0(boolean) ClusterWheatleyPartitionScreening
calcFacs() P2DiscreteFeynmanHibbs
calcfC(boolean) ClusterWheatleyPartitionScreening
CalcFFT etomica.virial
CalcFFT can calculate distribution functions using FFT.
CalcFFT(IFunction, double, int) CalcFFT
calcfQ(BoxCluster) ClusterWheatleyPartitionScreening
This calculates all fQ values given that the entries for pairs have
already been populated.
calcFullFQ() ClusterWheatleyPT
This calculates all FQ values given that the entries for pairs have
already been populated.
calcFullFQ(BoxCluster) ClusterSumHS
This calculates all FQ values given that the entries for pairs have
already been populated.
calcFullFQ(BoxCluster) ClusterWheatleyExtendSW
This calculates all FQ values given that the entries for pairs have
already been populated.
calcFullFQ(BoxCluster) ClusterWheatleyHS
This calculates all FQ values given that the entries for pairs have
already been populated.
calcFullFQ(BoxCluster) ClusterWheatleyMultibody
calcFullFQ(BoxCluster) ClusterWheatleyMultibodyBD
calcFullFQ(BoxCluster) ClusterWheatleyMultibodyDerivatives
calcFullFQ(BoxCluster) ClusterWheatleyMultibodyDerivativesBD
calcFullFQ(BoxCluster) ClusterWheatleyMultibodyMix
calcFullFQ(BoxCluster) ClusterWheatleySoft
This calculates all FQ values given that the entries for pairs have
already been populated.
calcFullFQ(BoxCluster) ClusterWheatleySoftBD
This calculates all FQ values given that the entries for pairs have
already been populated.
calcFullFQ(BoxCluster) ClusterWheatleySoftDerivatives
This calculates all FQ values given that the entries for pairs have
already been populated.
calcFullFQ(BoxCluster) ClusterWheatleySoftDerivativesBD
This calculates all FQ values given that the entries for pairs have
already been populated.
calcGageLength() MeterElongation
calcGageLength() MeterStrain
calcGamma(double, double) Gamma
Return the normalized complementary incomplete gamma function,
(integral from t=x to t=inf of exp(-t)*t^(a-1)) / gamma(a) if a>0
or
(integral from t=x to t=inf of exp(-t)*t^(a-1)) * exp(x)*x^(-a) if a<=0
calcGammaStar(double, double) Gamma
Return the normalized incomplete gamma function,
(integral from t=0 to t=x of exp(-t)*t^(a-1)) / x^a if a>0
If a=0 and x=0, gammaStar is indeterminate and an exception is thrown.
calcGradientDifferentiable SimDimerLJadatom
CalcGradientDifferentiable etomica.math.numerical
Uses finite difference methods to determine the second order differential of the potential (i.e.
CalcGradientDifferentiable(Box, PotentialMaster, IMoleculeList, Space) CalcGradientDifferentiable
calcGreyscaleRgbFromRgb(int) ColorUtil
Return a greyscale rgb value 0-FF using NTSC color luminance algorithm
CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen etomica.models.nitrogen
Determine the second derivative of the atomic/ molecular potential energy w.r.t.
CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen(Space, Box, P2Nitrogen, CoordinateDefinitionNitrogen, boolean) CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen(Space, Box, P2Nitrogen, CoordinateDefinitionNitrogen, boolean, double, boolean) CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
CalcHarmonicA 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() CalcHarmonicA
CalcJacobian etomica.normalmode
Class that calculates the dq/dx Jacobian.
CalcJacobian() CalcJacobian
calcLegendrePolynomial(int, double) SpecialFunctions
Calculates Pn(x), Legendre polynomial of order n for the given input value.
calcModes SimDimerLJadatom
calcMu LjMd3D.LjMd3DParams
calcNormalizedNormal(Point3f, Point3f, Point3f, Vector3f, Vector3f, Vector3f) Measure
CalcNumerical2ndDerivative etomica.models.nitrogen
Determine the second derivative of the atomic/ molecular potential energy w.r.t.
CalcNumerical2ndDerivative(Box, PotentialMaster, CoordinateDefinition) CalcNumerical2ndDerivative
CalcNumerical2ndDerivativeNitrogen etomica.models.nitrogen
Determine the second derivative of the atomic/ molecular potential energy w.r.t.
CalcNumerical2ndDerivativeNitrogen(Box, P2Nitrogen, CoordinateDefinitionNitrogen) CalcNumerical2ndDerivativeNitrogen
CalcNumerical2ndDerivativeNitrogen(Box, P2Nitrogen, CoordinateDefinitionNitrogen, boolean, double) CalcNumerical2ndDerivativeNitrogen
calcOrientation(IMolecule, double[]) OrientationCalcWater3P
calcOrientation(IMolecule, double[]) OrientationCalcWater4P
calcOrientation(IMolecule, double[]) OrientationCalcQuaternion
calcOrientation(IMolecule, IOrientationFull3D) OrientationCalcWater3P
calcOrientation(IMolecule, IOrientationFull3D) OrientationCalcWater4P
calcOrientation(IMolecule, IOrientationFull3D) OrientationCalc
Calculates the orientation of the given molecule and stores that
in the given orientation.
calcOrientation(IMolecule, IOrientationFull3D) OrientationCalcAtom
calcpPade(int, int, double) VirialOptimizer
calcRates() IntegratorKMC
calcRates() IntegratorKMCCluster
calcReeHoover() ClusterGenerator
Calculates the Ree-Hoover coefficient (coefficient for Ree-Hoover
diagram / coefficient for Mayer diagram) for mCluster and sets mCluster's
mReeHooverFactor to it.
calcReeHooverCoefficient(Graph, int, byte) ReeHoover
calcRotationRadius(Point3f) G3DSys
Finds the atom distance furthest from the given point; for rotation
calcScore(int[]) ClusterDiagram
compute a score for the cluster.
calcSignature(BoxCluster) ClusterWheatleyPartitionScreening
calcSignatures() ClusterWheatleyPartitionScreening
Compute signatures used for lookup tables of fA, fAB, fC
calcSphereShading() Shader
calcSupport(AtomTypeSpheroPolyhedron, Vector) P2SpheroPolyhedron
calcT(Vector, double[], double[]) CoordinateDefinition
Calculates the complex "T vector", which is collective coordinate given
by the Fourier sum (over atoms) of the generalized coordinate vector.
calcU(IMoleculeList) CoordinateDefinitionNitrogen
calcU(IMoleculeList) CoordinateDefinitionNitrogenSuperBox
calcU(IMoleculeList) CoordinateDefinition
Calculates the generalized coordinates for the given molecules in their
current position and orientation.
calcU(IMoleculeList) CoordinateDefinitionHSDimer
calcU(IMoleculeList) CoordinateDefinitionLeaf
Assigns the given array u to be the current position of the atom minus its lattice position
calcU(IMoleculeList) CoordinateDefinitionMolecule
calcU(IMoleculeList) CoordinateDefinitionMoleculeVolumeFluctuation
calcU(Vector) TestRotationVector
calculate(IAtom, IAtomList, int, PotentialArrayByType, IteratorDirective.Direction, PotentialCalculation) PotentialMasterMonatomic
calculate(IAtom, NeighborIterator, PotentialCalculation, IteratorDirective.Direction) PotentialMasterCell
calculate(IAtom, NeighborIterator, PotentialCalculation, IteratorDirective.Direction) PotentialMasterCellMixed
calculate(Box, IteratorDirective, PotentialCalculation) PotentialMasterCell
calculate(Box, IteratorDirective, PotentialCalculation) PotentialMasterCellMixed
calculate(Box, IteratorDirective, PotentialCalculation) PotentialMasterListMolecular
Overrides superclass method to enable direct neighbor-list iteration
instead of iteration via species/potential hierarchy.
calculate(Box, IteratorDirective, PotentialCalculation) PotentialMasterList
Overrides superclass method to enable direct neighbor-list iteration
instead of iteration via species/potential hierarchy.
calculate(Box, IteratorDirective, PotentialCalculation) PotentialMasterHybrid
Overrides superclass method to enable direct neighbor-list iteration
instead of iteration via species/potential hierarchy.
calculate(Box, IteratorDirective, PotentialCalculation) PotentialMasterSite
calculate(Box, IteratorDirective, PotentialCalculation) PotentialMaster
Performs the given PotentialCalculation on the atoms of the given Box.
calculate(Box, IteratorDirective, PotentialCalculation) PotentialMasterLrc
Performs given PotentialCalculation on all LRC potentials added to this group.
calculate(Box, IteratorDirective, PotentialCalculation) PotentialMasterMonatomic
calculate(Box, PotentialCalculation, boolean) PotentialMasterCell
calculate(Box, PotentialCalculation, boolean) PotentialMasterList
calculate(Box, PotentialCalculation, boolean) PotentialMasterSite
calculate(IMolecule, IteratorDirective.Direction, PotentialCalculation, NeighborListManagerMolecular) PotentialMasterListMolecular
calculate(MoleculesetIterator, IteratorDirective.Direction, IAtom, PotentialCalculation) PotentialGroup
Performs the specified calculation over the iterates given by the iterator,
using the directive to set up the iterators for the sub-potentials of this group.
calculateDU(double) P22CLJmuQ
calculateEnergy(double) P22CLJmuQ
calculateEnergy(double) P22CLJQ
calculateEnergy(Box) IAPIPotential
Returns the potential energy of the given box.
calculateEnergy(Box) SimOverlapLJModule.APIPotentialReference
calculateEnergy(Box) SimOverlapLJModule.APIPotentialTarget
calculateForces() IntegratorGear4
calculateLatticeDimensions(int, Vector) ConfigurationLattice
calculateLatticeDimensions(int, Vector) ConfigurationLatticeSimple
calculateModes() NormalModesMolecular
calculateModes() NormalModesPotential
calculateModes() NormalModesSoftSpherical
calculateQuaternionRotation(Point3f[][], float[]) Measure
calculateRangeIndependent(IMolecule, IteratorDirective.Direction, IAtom, PotentialCalculation) PotentialGroupNbr
Performs the specified calculation over the iterates given by the iterator,
using the directive to set up the iterators for the sub-potentials of this group.
calculateSum(FunctionData<Object>) LatticeSum
calculateSum(FunctionData<Object>) LatticeSumCrystal
calculateSum(FunctionData<Object>) LatticeSumCrystalMolecular
calculateSum(LatticeSumMolecularCrystal.AtomicTensorAtomicPair) LatticeSumMolecularCrystal
calculateSystemSigmaHSRef(IMolecularModel_SpeciesFactory[], int[]) ModelSimulationEnvironment
calculateSystemSigmaHSRef(ModelSelectedSpecies) ModelSimulationEnvironment
calcV(double, double) PotentialCalculationMappedRdf
calcV(double, double) PotentialCalculationMappedEnergy
calcValue() ClusterChainHS
calcValue() ClusterChainSoft
calcValue() ClusterSinglyConnected
calcValue() ClusterSum
calcValue() ClusterSumAssociation
calcValue() ClusterSumExternalField
calcValue() ClusterSumIC
calcValue() ClusterSumMultibody
calcValue() ClusterSumPolarizableWertheimProduct
calcValue() ClusterSumPolarizableWertheimProduct4Pt
calcValue() ClusterSumPolarizableWertheimProduct4PtFinal
calcValue() ClusterSumStickyEF
calcValue(BoxCluster) ClusterICPYC
calcValue(BoxCluster) ClusterPY
calcValue(BoxCluster) ClusterSumHS
Returns the cluster value for the given configuration.
calcValue(BoxCluster) ClusterWheatley
Calculates the value of the configuration.
calcValue(BoxCluster) ClusterWheatleyExtendSW
Returns the cluster value for the given configuration.
calcValue(BoxCluster) ClusterWheatleyHS
Returns the cluster value for the given configuration.
calcValue(BoxCluster) ClusterWheatleyMultibody
calcValue(BoxCluster) ClusterWheatleyMultibodyBD
calcValue(BoxCluster) ClusterWheatleyMultibodyDerivatives
calcValue(BoxCluster) ClusterWheatleyMultibodyDerivativesBD
calcValue(BoxCluster) ClusterWheatleyMultibodyMix
calcValue(BoxCluster) ClusterWheatleyPartitionScreening
Returns the cluster value for the given configuration.
calcValue(BoxCluster) ClusterWheatleyPT
Returns the cluster value for the given configuration.
calcValue(BoxCluster) ClusterWheatleySoft
Returns the cluster value for the given configuration.
calcValue(BoxCluster) ClusterWheatleySoftBD
Returns the cluster value for the given configuration.
calcValue(BoxCluster) ClusterWheatleySoftDerivatives
Returns the cluster value for the given configuration.
calcValue(BoxCluster) ClusterWheatleySoftDerivativesBD
Returns the cluster value for the given configuration.
calcValue(BoxCluster, boolean) ClusterWheatleyHS
calcValue(BoxCluster, boolean) ClusterWheatleyPartitionScreening
calcVibrationalModes SimDimerLJadatom
CalcVibrationalModes etomica.action
Calculates the eigenvalues of an NxN matrix.
CalcVibrationalModes() CalcVibrationalModes
calcWeight() MCMoveClusterRingPartialRegrow
calcXs(double) PotentialCalculationMappedVirialV
calcXs(double, double) PotentialCalculationMappedEnergy
calcXs(double, double) PotentialCalculationMappedVirial
calcZbufferLimits() G3DSys
callCount MeterRDF
callCount MeterRDFPC
callCount MeterMBAR
callCount MeterBondLength
called Match
Calorie etomica.units
The Joule unit of energy, equal to 1 N-m or 1 kg-m^2/s^2.
cameradepth Token
cAN2nD HarmonicAlphaNitrogenModelPairMoleculeSequential
cAN2nD HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2
cAN2nD HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
cAN2nD HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
cAN2nD HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
canAdd() ArrayProperty
canAdd() AtomListProperty
canAdd() InstanceProperty
canAdd() MoleculeListProperty
canAdd() Property
canAdd() VectorProperty
cancelMap MayerIonicDiagram1qbond
cancelMap MayerIonicDiagram2qbonds
cancelMap MayerIonicDiagram4qbonds
cancelMap VirialDiagrams
cancelMap VirialDiagramsMix
cancelMap VirialDiagramsMix2
cancelMap VirialDiagramsPT
cancelMap WertheimDiagrams2SiteRho
cancelMap WertheimDiagrams3SiteRho
cancelP MayerIonicDiagram1qbond
cancelP MayerIonicDiagram2qbonds
cancelP MayerIonicDiagram4qbonds
cancelP VirialDiagramsMix
cancelP VirialDiagramsMix2
cancelP WertheimDiagrams2SiteRho
cancelP WertheimDiagrams3SiteRho
canCount() ArrayProperty
canCount() AtomListProperty
canCount() InstanceProperty
canCount() MoleculeListProperty
canCount() Property
canCount() VectorProperty
Candela etomica.units
The candela is the luminous intensity, in a given direction, of a source that
emits monochromatic radiation of frequency 540 x 1012 hertz and that has a
radiant intensity in that direction of 1/683 watt per steradian.
canDoTriangles() Graphics3D
canIncrement() ScriptVariable
canMoveLeft() ConsoleUI
canMoveRight() ConsoleUI
canRead() ArrayProperty
canRead() AtomListProperty
canRead() InstanceProperty
canRead() MoleculeListProperty
canRead() Property
canRead() VectorProperty
canRemove() ArrayProperty
canRemove() AtomListProperty
canRemove() InstanceProperty
canRemove() MoleculeListProperty
canRemove() Property
canRemove() VectorProperty
canvas DisplayBox
canvas DisplayPolytope
canWrite() ArrayProperty
canWrite() AtomListProperty
canWrite() InstanceProperty
canWrite() MoleculeListProperty
canWrite() Property
canWrite() VectorProperty
cap Token
capAABond DecorateWertheimNaphthalene2Rho.DecorateNaphthalene2Site
capABBond DecorateWertheimNaphthalene2Rho.DecorateNaphthalene2Site
capBABond DecorateWertheimNaphthalene2Rho.DecorateNaphthalene2Site
capBBBond DecorateWertheimNaphthalene2Rho.DecorateNaphthalene2Site
capF1Bond WertheimDiagrams3SiteRho
capF2Bond WertheimDiagrams3SiteRho
capFABBond DecorateWertheim2Site.DecorateWertheimParameters2Site
capFABBond DecorateWertheim2SiteRho.DecorateWertheimParameters2Site
capFABBond WertheimDiagrams2SiteRho
capFACBond DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
capFACBond WertheimDiagrams3SiteRho
capFBABond DecorateWertheim2Site.DecorateWertheimParameters2Site
capFBABond DecorateWertheim2SiteRho.DecorateWertheimParameters2Site
capFBABond WertheimDiagrams2SiteRho
capFBCBond DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
capFBCBond WertheimDiagrams3SiteRho
capFBond WertheimDiagrams2SiteRho
capFBond WertheimDiagrams3SiteRho
capFCABond DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
capFCABond WertheimDiagrams3SiteRho
capFCBBond DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
capFCBBond WertheimDiagrams3SiteRho
capitalize(String) Strings
Capitalizes the first letter of the given string.
CAPTURE P2HardSphereCavity.CollisionType
carbohydrate Token
Carbon etomica.chem.elements
Class for the Carbon element.
Carbon(String) Carbon
Carbon(String, double) Carbon
cardinality() BitSet
Returns the number of bits set to true in this BitSet.
cardinalityN(int) BitSet
cardinalityOf(BitSet) BitSetUtil
cardinality = "total number of set bits"
cartA P2WaterPotentialsJankowski
cartB P2WaterPotentialsJankowski
CartesianIterator etomica.graph.iterators
CartesianIterator() CartesianIterator
CartesianPermutator etomica.graph.iterators
CartesianPermutator(int[], int[]) CartesianPermutator
cartoon Token
cartoonbaseedges Token
cartoonfancy Token
cartoonrockets Token
CastGroupOfTablesToDataTable etomica.data.types
A DataProcessor that converts a homogeneous DataGroup into a multidimensional DataDoubleArray.
CastGroupOfTablesToDataTable() CastGroupOfTablesToDataTable
Sole constructor.
CastGroupToDoubleArray etomica.data.types
A DataProcessor that converts a homogeneous DataGroup into a multidimensional DataDoubleArray.
CastGroupToDoubleArray() CastGroupToDoubleArray
Sole constructor.
CastToDouble etomica.data.types
A DataProcessor that converts a Data instance into a DataDouble.
CastToDouble() CastToDouble
Sole constructor.
CastToDoubleArray etomica.data.types
A DataProcessor that converts a Data instance into a DataDoubleArray.
CastToDoubleArray() CastToDoubleArray
Sole constructor.
CastToGroup etomica.data.types
A DataProcessor that effectively wraps a Data instance into a DataGroup.
CastToGroup() CastToGroup
CastToTable etomica.data.types
A DataProcessor that converts a Data instance into a DataTable.
CastToTable() CastToTable
Sole constructor.
Catalysis etomica.modules.catalysis
Simulation for Catalysis module.
Catalysis(Space, int) Catalysis
Catalysis(Space, int, IRandom) Catalysis
CatalysisAgent() InteractionTracker.CatalysisAgent
CatalysisGraphic etomica.modules.catalysis
Catalysis graphical app.
CatalysisGraphic(Catalysis, Space, boolean) CatalysisGraphic
CatalysisGraphic.Applet etomica.modules.catalysis
cavityDipole P2ReactionFieldDipole
cavityDipole P2ReactionFieldDipoleTruncated
CavityParam() HSMDCavity.CavityParam
cB DecorateWertheim2Site.DecorateWertheimParameters2Site
cbrt(BigDecimal) BigDecimalMath
The cube root.
cc HardSphereSolid
CCbondL ConformationAlkaneEH
cclec P2O2Bartolomei
ccpol2Angles P2WaterPotentialsJankowski
ccpol2BL P2WaterPotentialsJankowski
cdataIso P2HydrogenPatkowskiIso
cDim MinimizeBetaNitrogenLatticeParameter
cDim MinimizeBetaNitrogenLatticeParameterFromFile
cDim MinimizeBetaNitrogenTranslationDOF
cdum P2HydrogenPatkowski
cdum P2HydrogenPatkowskiAtomic
cdz HardSphereSolid
ceil() Rational
ceil(): the nearest integer not smaller than this.
cell Token
Cell etomica.nbr.cell
Site used to form array of cells for cell-based neighbor listing.
Cell(int) Cell
Cell.CellFactory etomica.nbr.cell
CellFactory() Cell.CellFactory
CellFactory() CellMolecular.CellFactory
CellLattice etomica.lattice
A lattice of arbitrarily-sized rectangular cells, such that a point in space can be
associated with one of the cells.
CellLattice(Space, Vector, SiteFactory) CellLattice
CellLattice.NeighborIterator etomica.lattice
Extends the SimpleLattice neighbor iterator to provide methods that
specify the neighbor range in terms of a distance, rather than an index range.
CellMolecular etomica.nbr.cell.molecule
Site used to form array of cells for cell-based neighbor listing.
CellMolecular(int) CellMolecular
CellMolecular.CellFactory etomica.nbr.cell.molecule
cellPosition CoordinateDefinition.BasisCell
cellRange NeighborCellManagerMolecular
cellRange NeighborCellManager
cells CoordinateDefinition
cells MCMoveAtomSuperBox
cellSizeX ConfigurationCatalysis
cellSizeX ConfigurationSAM
cellSizeZ ConfigurationCatalysis
cellSizeZ ConfigurationSAM
cellSpecies PotentialMasterCellMixed
center CrystalViewer
center ConfigurationDroplet
center IntegratorPolymer
center MoleculePositionGeometricCenterPBC
center Token
center JmolConstants
CENTER DisplayBox
CENTER DisplayPolytope
centerAtomColor StrainColorScheme
centerMass P2Water4PSoft
centers DataClusterer
CENTI Prefix
centralImage(Vector) BoundaryDeformablePeriodicSwitch
centralImage(Vector) BoundaryRectangularPeriodicSwitch
centralImage(Vector) Boundary
Determines the translation vector needed to apply a periodic-image
transformation that moves the given point to an image point within the
boundary (if it lies outside, in a direction subject to periodic
imaging).
centralImage(Vector) BoundaryDeformablePeriodic
centralImage(Vector) BoundaryRectangularNonperiodic
Returns a vector with all elements zero.
centralImage(Vector) BoundaryRectangularPeriodic
centralImage(Vector) BoundaryRectangularPore
centralImage(Vector) BoundaryRectangularSlit
centralImage(Vector) BoundaryTruncatedOctahedron
centralOrigin DisplayBox
Coordinate origin for central image
Explicit to 2D because drawing is done to 2D image
centralOrigin DisplayPolytope
Coordinate origin for central image
Explicit to 2D because drawing is done to 2D image
centrlFactNumt(int, int) BigIntegerMath
The central factorial number t(n,k) number at the indices provided.
centrlFactNumT(int, int) BigIntegerMath
The central factorial number T(n,k) number at the indices provided.
Ceps P2EAM
cErr P2HePCKLJS
cex P2HydrogenPatkowski
cex P2HydrogenPatkowskiAtomic
cexIso P2HydrogenPatkowskiIso
cff VirialHSMixture.VirialHSParam
cff VirialHSMixtureOverlap.VirialHSParam
cgc(int, int, int, int, int, int, int) P2HydrogenPatkowski
cgc(int, int, int, int, int, int, int) P2HydrogenPatkowskiAtomic
CGS etomica.units.systems
Centimeter-Gram-Second system of units.
CGS() CGS
CH EnumSiteName
CH_ONE Bitmap
CH_ZERO Bitmap
CH2 EnumSiteName
CH2element SimpleElementForSimilarSpecies
CH3 EnumSiteName
CH3element SimpleElementForSimilarSpecies
CH4NVT etomica.AlkaneEH
CH4(TraPPE-EH)
Canonical ensemble Monte Carlo simulation (NVT)
CH4NVT(Space, int, double, double, double) CH4NVT
CH4NVT.Param etomica.AlkaneEH
chain Token
chain(int) Standard
Returns a chain of bonds, {{0,1},{1,2},...{n-2,n-1}}
Chain etomica.virial.cluster
Chain(int) Chain
Constructor for Chain.
CHAIN EnumPalette
CHAIN_TAIL VirialHS.VirialHSParam
CHAIN_TAIL VirialHSMixture.VirialHSParam
CHAIN_TAIL VirialSWWE.VirialSWWEParam
CHAIN_TREE VirialHS.VirialHSParam
CHAIN_TREE VirialHSMixture.VirialHSParam
CHAIN_TREE VirialPolyhedra.VirialHSParam
CHAIN_TREE VirialPolyhedra2.VirialHSParam
CHAIN_TREE VirialSWWE.VirialSWWEParam
chaincasesensitive Token
ChainedIterator etomica.graph.iterators
ChainedIterator() ChainedIterator
ChainEquilibriumGraphic etomica.modules.chainequilibrium
Module for chain reaction (polymerization) using ChainEquilibriumSim as the
simulation class.
ChainEquilibriumGraphic(ChainEquilibriumSim, Space) ChainEquilibriumGraphic
ChainEquilibriumGraphic.Applet etomica.modules.chainequilibrium
ChainEquilibriumSim etomica.modules.chainequilibrium
ChainEquilibriumSim(Space) ChainEquilibriumSim
chainFrac VirialPolymerOverlapMC.VirialHSParam
chainFrac VirialPolymerOverlapWithMD.VirialHSParam
chainFrac VirialPolymerOverlapWithMDB3.VirialHSParam
chainFrac ClusterChainHS
chainFrac VirialHS.VirialHSParam
chainFrac VirialHSBinMultiThreaded.SimulationWorker
chainFrac VirialHSBinMultiThreaded.VirialHSBinParam
chainFrac VirialHSMixture.VirialHSParam
chainFrac VirialHSMixtureOverlap.VirialHSParam
chainFrac VirialPolyhedra.VirialHSParam
chainFrac VirialPolyhedra2.VirialHSParam
chainFrac VirialSQWBinMultiThreaded.SimulationWorker
chainFrac VirialSQWBinMultiThreaded.VirialHSBinParam
chainFrac VirialSWWE.VirialSWWEParam
ChainHSMD3D etomica.simulation.prototypes
Molecular dynamics of chains of hard spheres.
ChainHSMD3D() ChainHSMD3D
chainIterator(Iterator<Graph>) ChainedIterator
chainLength AtomTestChainLength.LengthAgent
chainLength ColloidSim
chainLength ConfigurationColloid
chainLength MeterEnd2End
chainLength NeighborListManagerColloid
chainLength P2HardSphereMC
chainLength P2SquareWellMonomer
chainLength Sam
chainLength AtomTestChainLength.LengthAgent
chainLengthManager AtomTestChainLength
chainLengthManager ColorSchemeRadical
chainLengthManager AtomTestChainLength
chainNumber ColorSchemeRadical.LengthAgent
ChainParameters(Parameters, Parameters) UnaryChain.ChainParameters
chainPhi Sam
chainPsi Sam
CHAINS VirialPolymerOverlapMC.VirialHSParam
CHAINS VirialPolymerOverlapWithMD.VirialHSParam
CHAINS VirialPolymerOverlapWithMDB3.VirialHSParam
CHAINS VirialHS.VirialHSParam
CHAINS VirialHSMixture.VirialHSParam
CHAINS VirialPolyhedra.VirialHSParam
CHAINS VirialPolyhedra2.VirialHSParam
CHAINS VirialSWWE.VirialSWWEParam
chainTheta Sam
CHANGEABLE_MASK Colix
changeableColixMap GData
changeBox() LatticeEditor
changeColixArgb(short, int) GData
changeSign() Complex
Negative of this complex number (changeSign stands for change sign).
characterEndA BondConnectedSubstitutionNaphthalene.BondConnectedSubstitutionParameters2SiteNa
characterEndB BondConnectedSubstitutionNaphthalene.BondConnectedSubstitutionParameters2SiteNa
characterStartA BondConnectedSubstitutionNaphthalene.BondConnectedSubstitutionParameters2SiteNa
characterStartB BondConnectedSubstitutionNaphthalene.BondConnectedSubstitutionParameters2SiteNa
charAt(int) StringXBuilder
charge PNGCPM.GCPMAgent
charge EwaldSummation.MyCharge
charge EwaldSumMolecules.MyCharge
charge P2PotentialGroupBuilder.ModelParams
charge VirialN2TraPPE.VirialN2Param
charge VirialTraPPE.TraPPEParams
charge() CGS
charge() LJ
charge() MKS
charge() UnitSystem
charge() UnitSystem.Sim
Charge etomica.chem.electrostatics
Charge etomica.units.dimensions
The dimension for electrical charge.
Charge() Charge
Charge(double) Charge
CHARGE EnumPotentialParamDescription
charge2 PNGCPM.GCPMAgent
ChargeAgentSourceRPM(SpeciesGeneral, boolean) MinimizationTIP4P.ChargeAgentSourceRPM
ChargeAgentSourceTIP4PWater etomica.models.water
ChargeAgentSourceTIP4PWater() ChargeAgentSourceTIP4PWater
chargeAll PNCO2GCPM
chargeC PNCO2GCPM
chargeC P2NitrogenShellModel
chargeCC P2NitrogenShellModel
chargeCC P2CO2EMP
chargeCN P2NitrogenShellModel
chargeCO P2CO2EMP
chargeCP P2NitrogenShellModel
chargeH TIP4P_NVT
chargeH P2Water3P
chargeH P2Water4P
chargeH P2WaterTIP4PHardCore
chargeH PNWaterGCPM
chargeH PNWaterGCPMReactionField
chargeHH P2Water3P
chargeHH P2Water4P
chargeHH P2WaterTIP4PHardCore
chargeM TIP4P_NVT
chargeM P2Water4P
chargeM P2WaterTIP4PHardCore
chargeM PNWaterGCPM
chargeM PNWaterGCPMReactionField
chargeMH P2Water4P
chargeMH P2WaterTIP4PHardCore
chargeMM P2Water4P
chargeMM P2WaterTIP4PHardCore
chargeN P2NitrogenShellModel
chargeNN P2NitrogenShellModel
chargeNP P2NitrogenShellModel
chargeO PNCO2GCPM
chargeO P2Water3P
chargeOH P2Water3P
chargeOO P2Water3P
chargeOO P2CO2EMP
chargeP P2NitrogenShellModel
chargeP1 P2Nitrogen
chargeP1 P2NitrogenAB
chargeP1 P2NitrogenAnisotropic
chargeP1P1 P2Nitrogen
chargeP1P1 P2NitrogenAB
chargeP1P1 P2NitrogenAnisotropic
chargeP1P2 P2Nitrogen
chargeP1P2 P2NitrogenAB
chargeP1P2 P2NitrogenAnisotropic
chargeP2 P2Nitrogen
chargeP2 P2NitrogenAB
chargeP2 P2NitrogenAnisotropic
chargeP2P2 P2Nitrogen
chargeP2P2 P2NitrogenAB
chargeP2P2 P2NitrogenAnisotropic
chargePP P2NitrogenShellModel
CHbondL ConformationAlkaneEH
check() BasicHealthCheck
check() TreeList
checks the tree for consistency of connections and ordering by sortKey.
check(Graph) FFTDecomposition
check(Graph) FieldNodeCountMax
check(Graph) HasArticulationPair
check(Graph) HasArticulationPoint
check(Graph) HasEdgeCount
check(Graph) HasNodalPoint
check(Graph) HasNoRootEdge
check(Graph) HasSimpleArticulationPoint
check(Graph) IsBiconnected
check(Graph) IsConnected
check(Graph) IsFFT
check(Graph) Property
check(Graph) VirialDiagrams.ArticulatedAt0
check(Graph) VirialDiagramsMix2.MaxIsomorphCriteriaMixture
check(Graph) VirialDiagramsPT.ArticulatedAt0
check(Graph) VirialDiagramsPT.DiscardCriteria
check(Graph) IsFFT
checkBox MyApplet
checkBox1 MyApplet
checkBox2 MyApplet
checkCarbohydrate(String) JmolConstants
checkConfig(BoxCluster) ClusterSumHS
checkConfig(BoxCluster) ClusterWheatley
Determines whether the configuration is zero-valued or not.
checkConfig(BoxCluster) ClusterWheatleyExtendSW
checkConfig(BoxCluster) ClusterWheatleyHS
checkConfig(BoxCluster) ClusterWheatleyPartitionScreening
checkCore P2CO2H2OWheatley
checkCoreCO P2CO2H2OWheatley
checkDimensions() CellLattice.NeighborIterator
Checks whether lattice dimensions have changed, and updates integer
neighbor range if they have.
checkDimensions() NeighborCellManagerMolecular
Checks the box's dimensions to make sure the number of cells is
appropriate.
checkDimensions() NeighborCellManager
Checks the box's dimensions to make sure the number of cells is
appropriate.
checkE P2ElectrostaticWithHardCore
checkFac ClusterWheatleySoftDerivatives
checkForSimilarSites(String[], String[], IMolecularModel_SpeciesFactory[]) BuilderCollectionPotential
checkGraph(Graph) DecorateWertheim3SiteRho
checkIfCompatible(ModelSelectedSpecies, ModelSimulationEnvironment) BuilderCollectionPotential
checkIfSameSpeciesWithSimilarPotentials(IMolecularModel_SpeciesFactory, IMolecularModel_SpeciesFactory, int, int) ControllerSpeciesSelection
checkIndexOfSpeciesSelected() ControllerSpeciesSelection
checkme ClusterWheatleyPartitionScreening
checkMemory() Logger
checkMin() IntegratorKMC
checkMin() IntegratorKMCCluster
checkOHBondLength() IntegratorDimerApproach
checkRing(IAtom, IAtom, int) P2SquareWellBonded
this function will bond atoms a & b together
checkSet(Set<Graph>) DecorateWertheim3SiteRho
checkString(String) UnitFilter
checkTimer(String, boolean) Logger
checkTranslucent(boolean) Graphics3D
checkUnitSystemString(String) UnitFilter
chemForm VirialTraPPE.VirialParam
chi4Data DataSourcePercolation
chi4Data DataSourceQ4
chi4DataInfo DataSourcePercolation
chi4DataInfo DataSourceQ4
Chi4Source() DataSourcePercolation.Chi4Source
chi4Tag DataSourcePercolation
chi4Tag DataSourceQ4
chiData MultiharmonicGraphicMC.DataSourceAlphaChi
chiData MultiharmonicGraphicMC.DataSourceAlphaAlpha
chiData MultiharmonicGraphicMC.DataSourceAlphaChi
chiData MultiharmonicGraphicMC.DataSourceAlphaAlpha
chiData MultiharmonicGraphicMC.DataSourceAlphaChi
chiInfo MultiharmonicGraphicMC.DataSourceAlphaChi
chiInfo MultiharmonicGraphicMC.DataSourceAlphaAlpha
chiInfo MultiharmonicGraphicMC.DataSourceAlphaChi
chiInfo MultiharmonicGraphicMC.DataSourceAlphaAlpha
chiInfo MultiharmonicGraphicMC.DataSourceAlphaChi
childList Molecule
childProps Wrapper
children ClusterTreeNode
chiSum IntegratorMDHarmonicMC
chiSum MCMoveTracker
chiTag MultiharmonicGraphicMC.DataSourceAlphaChi
chiTag MultiharmonicGraphicMC.DataSourceAlphaAlpha
chiTag MultiharmonicGraphicMC.DataSourceAlphaChi
chiTag MultiharmonicGraphicMC.DataSourceAlphaAlpha
chiTag MultiharmonicGraphicMC.DataSourceAlphaChi
Chlorine etomica.chem.elements
Class for the Chlorine element.
Chlorine(String) Chlorine
Chlorine(String, double) Chlorine
choices() AccumulatorRatioAverageCovariance
choices() AccumulatorRatioAverageCovarianceFull
chooseRate() IntegratorKMC
chooseRate() IntegratorKMCCluster
Chop() Function.Chop
Constructs with default cutoff value of 2 Double.MIN_VALUE.
Chop(double) Function.Chop
chopF(MayerFunction[]) ClusterSumStickyEF
chrg3 P2WaterSzalewicz
chs SimGlass
circle(double, double, double, double) Plot
Circle etomica.math.geometry
A circle in 2D.
Circle() Circle
Creates circle with unit radius
Circle(double) Circle
Creates circle of the given radius.
CL_OPTION_ALLOWED_SCRIPTS Main
Option to specify the set of allowed scripts
CL_OPTION_ALLOWED_SCRIPTS_DESCRIPTION Main
CL_OPTION_ALTERNATE_STYLESHEET Main
Option to specify the CSS alternate stylesheet when
converting the SVG images
CL_OPTION_ALTERNATE_STYLESHEET_DESCRIPTION Main
CL_OPTION_AOI Main
Option to specify the area of interest in the output
image.
CL_OPTION_AOI_DESCRIPTION Main
CL_OPTION_BACKGROUND_COLOR Main
Option to specify the output image's background color
CL_OPTION_BACKGROUND_COLOR_DESCRIPTION Main
CL_OPTION_CONSTRAIN_SCRIPT_ORIGIN Main
Option to determine whether scripts a constrained to the
same origin as the document referencing them.
CL_OPTION_CONSTRAIN_SCRIPT_ORIGIN_DESCRIPTION Main
CL_OPTION_DEFAULT_FONT_FAMILY Main
Option to specify the default value for the font-family
CSS property when converting the SVG image
CL_OPTION_DEFAULT_FONT_FAMILY_DESCRIPTION Main
CL_OPTION_DPI Main
Option to specify the resolution for the output image
CL_OPTION_DPI_DESCRIPTION Main
CL_OPTION_HEIGHT Main
Option to specify the output image's height
CL_OPTION_HEIGHT_DESCRIPTION Main
CL_OPTION_INDEXED Main
Option to specify if the PNG should be indexed.
CL_OPTION_INDEXED_DESCRIPTION Main
CL_OPTION_LANGUAGE Main
Option to specify the user language with which SVG
documents should be processed
CL_OPTION_LANGUAGE_DESCRIPTION Main
CL_OPTION_MAX_HEIGHT Main
Option to specify the output image's maximum height.
CL_OPTION_MAX_HEIGHT_DESCRIPTION Main
CL_OPTION_MAX_WIDTH Main
Option to specify the output image's maximum width.
CL_OPTION_MAX_WIDTH_DESCRIPTION Main
CL_OPTION_MEDIA_TYPE Main
Option to specify the CSS media type when converting
the SVG image
CL_OPTION_MEDIA_TYPE_DESCRIPTION Main
CL_OPTION_MIME_TYPE Main
Option to specify the output image's mime type
CL_OPTION_MIME_TYPE_DESCRIPTION Main
CL_OPTION_ONLOAD Main
Option to specify that the converted SVG files should
be after the dispatch of the 'onload' event.
CL_OPTION_ONLOAD_DESCRIPTION Main
CL_OPTION_OUTPUT Main
Option to specify the output directory or file
CL_OPTION_OUTPUT_DESCRIPTION Main
CL_OPTION_QUALITY Main
Option to specify the output JPEG quality
CL_OPTION_QUALITY_DESCRIPTION Main
CL_OPTION_SECURITY_OFF Main
Option to turn off secure execution of scripts
CL_OPTION_SECURITY_OFF_DESCRIPTION Main
CL_OPTION_SNAPSHOT_TIME Main
Option to specify that the document should be rasterized after
seeking to the specified document time.
CL_OPTION_SNAPSHOT_TIME_DESCRIPTION Main
CL_OPTION_USER_STYLESHEET Main
Option to specify an addition user stylesheet
CL_OPTION_USER_STYLESHEET_DESCRIPTION Main
CL_OPTION_VALIDATE Main
Option to specify that the converted SVG files should
be validated during the conversion process.
CL_OPTION_VALIDATE_DESCRIPTION Main
CL_OPTION_WIDTH Main
Option to specify the output image's width
CL_OPTION_WIDTH_DESCRIPTION Main
clash Token
CLASSBASE_OPTIONS JmolConstants
classical BnPYCHe.BnPYHeParams
classlist() Lister
className ConstructionParams
className SimulationConstructor
CLASSPATH_SCAN Common
ClassRequirement etomica.compatibility
ClathrateHarmonicFE etomica.models.clathrates
ClathrateHarmonicFE(Space, int[], double, double, double[], int, String, boolean, double, boolean) ClathrateHarmonicFE
ClathrateHarmonicFE.SimParams etomica.models.clathrates
cleanUp() DataLogger
clear() AtomArrayList
clear() AtomPair
clear() AtomSetSinglet
clear() DiameterHashByElement
clear() Console
clear() ConsoleUI
clear() GraphList
clear() Plot
Clears the plot.
clear() MoleculeArrayList
clear() MoleculePair
clear() MoleculeSetSinglet
clear() IteratorDirective
Puts directive in default state of no atoms specified, up direction, no
potential criteria applied, no LRC included.
clear() P2HardBondedList.BondArrayList
clear() IndexMap
clear() Graphics3D
clear() GData
clear(int) BitSet
Sets the bit specified by the index to false.
clear(Parser.Command) Interpreter
clearAll() BitSet
Sets all of the bits in this BitSet to false.
clearBit(int) Bitmap
clearBit(int) BitmapOfLong
The highest order bit is at bit 0 of bitmap, and the lowest order bit is at bit
bitSize() - 1 of bitmap.
clearBit(int) BitmapOfLongVector
The highest order bit is at bit 0 of bitmap[0], and the lowest order bit is at bit
bitSize() - 1 of bitmap[size()-1].
clearBits(int, int) BitSet
Sets the bits from the specified fromIndex (inclusive) to the
specified toIndex (exclusive) to false.
clearData() DisplayPlotXChart
clearFontCache() Graphics3D
clearFontCache() GData
clearNbrs() AtomNeighborLists
Clears neighbor lists, removing all listed neighbor atoms.
clearNbrs() AtomPotentialList
Clears neighbor lists, resetting all flags to false (not interacting).
clearNbrs() MoleculeNeighborLists
Clears neighbor lists, removing all listed neighbor molecules.
clearNbrs() MoleculePotentialList
Clears neighbor lists, resetting all flags to false (not interacting).
clearRatesandEnergies() IntegratorKMCCluster
clearTags() DataInfo
Removes all tags.
clearTags() IDataInfo
Removes all tags.
clipCode(int) GData
clipCode3(int, int, int) GData
clipPlaneEditor CrystalViewer
ClipPlaneEditor etomica.modules.crystalviewer
Class that produces a panel with controls that presence, orientation
and position of a plane that clips atoms from the display.
ClipPlaneEditor(Simulation, LatticePlane, DisplayBox) ClipPlaneEditor
cliqueCheck(int, int) ClusterSumHS
Checks to see if the set |clique| is a clique separator.
cliqueCheck(int, int) ClusterWheatleyHS
Checks to see if the set |clique| is a clique separator.
cliqueCheck(int, int) ClusterWheatleyPartitionScreening
Checks to see if the set |clique| is a clique separator.
cliqueCount ClusterSumHS
cliqueCount ClusterWheatleyHS
cliqueCount ClusterWheatleyPartitionScreening
cliqueCountE2 ClusterWheatleyExtendSW
cliqueCountEF ClusterWheatleyExtendSW
cliqueCountF1 ClusterWheatleyExtendSW
cliqueCountNone ClusterWheatleyExtendSW
cliqueList ClusterSumHS
cliqueList ClusterWheatleyHS
cliqueList ClusterWheatleyPartitionScreening
cliqueListE2 ClusterWheatleyExtendSW
cliqueListEF ClusterWheatleyExtendSW
cliqueListF1 ClusterWheatleyExtendSW
cliqueListNone ClusterWheatleyExtendSW
cliqueSet ClusterSumHS
cliqueSet ClusterWheatleyHS
cliqueSet ClusterWheatleyPartitionScreening
cliqueSetE2 ClusterWheatleyExtendSW
cliqueSetEF ClusterWheatleyExtendSW
cliqueSetF1 ClusterWheatleyExtendSW
cliqueSetNone ClusterWheatleyExtendSW
clone() Tensor
clone() Tensor1D
Support of implementation of Cloneable interface.
clone() Tensor2D
Support of implementation of Cloneable interface.
clone() Tensor3D
Support of implementation of Cloneable interface.
clone() TensorND
clone() ScientificFormat
clone() BigIntegerPoly
Create a copy of this.
clone() BigSurd
Create a deep copy.
clone() Ifactor
Deep copy.
clone() Rational
Create a copy.
clone() IMolecularModel_SpeciesFactory
clone() MolecularModel2CLJQ_SpeciesCO2
clone() MolecularModel2CLJQ_SpeciesEthane
clone() MolecularModel2CLJQ_SpeciesLJ
clone() MolecularModelEMP2_SpeciesCO2
clone() MolecularModelLJ_SpeciesLJ
clone() MolecularModelLJQ_SpeciesLJ
clone() MolecularModelSKS_SpeciesAlkane
clone() MolecularModelSPCE_SpeciesH2O
clone() MolecularModelTRAPPE_SpeciesAlkane
clone() MolecularModelTrappe_SpeciesCO2
clone() BitSet
Cloning this BitSet produces a new BitSet that is equal to
it.
close() Viewer
close() ClusterViewer
closeAlkaneView() ViewAlkaneLengthSelection
closeFile() AccumulatorAverageFixedOutputFile
closeFile() DataLogger
closeFile() DataClusterWriter
closeFile() VelocityWriter
closeFile() AccumulatorVirialOverlapSingleAverage
closeFile() MSDCoordWriter
closeFW() MeterTargetTPMolecule
Closes file with overlap data.
closeFW() MeterTargetTP
Closes file with overlap data.
closeSimEnvParamView() ViewSimEnvironmentSelection
closeWindow ViewAlkaneLengthSelection
CloseWindowButtonListener() ControllerAlertMsgBox.CloseWindowButtonListener
cluster MyApplet
cluster ClusterMultiToSingle
cluster ClusterWheatleyMultibodyDerivatives.ClusterRetrievePrimes
cluster ClusterWheatleyMultibodyDerivativesBD.ClusterRetrievePrimes
cluster ClusterWheatleyPT.ClusterRetrievePrimesBD
cluster ClusterWheatleySoftDerivatives.ClusterRetrievePrimes
cluster ClusterWheatleySoftDerivatives.ClusterRetrievePrimesBD
cluster ClusterWheatleySoftDerivativesBD.ClusterRetrievePrimes
cluster MeterVirialExternalField
cluster MeterVirialExternalFieldConfined
cluster MeterVirialExternalFieldSW
cluster VirialH2OGCPMD.Clusterfoo
ClusterAbstract etomica.virial
ClusterAbstractMultivalue etomica.virial
clusterAdd ClusterDifference
ClusterAssociation etomica.virial.cluster
ClusterAssociation() ClusterAssociation
clusterAtoms MCMoveGeometricCluster
clusterAtoms MCMoveSpinCluster
clusterAtoms1 MCMoveGeometricClusterRestrictedGE
clusterAtoms2 MCMoveGeometricClusterRestrictedGE
clusterAtomsList1 MCMoveGeometricClusterRestrictedGE
clusterAtomsList2 MCMoveGeometricClusterRestrictedGE
clusterBD ClusterWheatleySoft
clusterBD ClusterWheatleySoftDerivatives
clusterBDBD ClusterWheatleySoftDerivativesBD
ClusterBonds etomica.virial
ClusterBonds(int[][], boolean) ClusterBonds
ClusterBonds(int, int[][][]) ClusterBonds
Constructor for Cluster, with default to not using permutations (this can
be changed after construction if desired).
ClusterBonds(int, int[][][], boolean) ClusterBonds
Constructor for Cluster.
ClusterBondsNonAdditive etomica.virial
Subclass of ClusterBonds capable of handling non-additive Mayer functions.
ClusterBondsNonAdditive(int[][], int[][]) ClusterBondsNonAdditive
ClusterBondsNonAdditive(int, int[][][], int[][]) ClusterBondsNonAdditive
Construct a ClusterBondsNonAdditive of size n, using the given list of
pair and multibonds.
ClusterChainHS 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) ClusterChainHS
Constructs with default to perform chain-only calculation, with chainFrac = 1.0
ClusterChainHS(int, MayerFunction, boolean) ClusterChainHS
Constructs to perform either chain-only or ring-only calculation, as directed by doRing (true for ring-only)
ClusterChainHS(int, MayerFunction, double, double) 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 etomica.virial
This class calculates the sum of all chain clusters.
ClusterChainSoft(int, MayerFunction) ClusterChainSoft
ClusterChainSoft(int, MayerFunction, boolean) ClusterChainSoft
ClusterCollapsedTreeNode etomica.virial.cluster
ClusterCollapsedTreeNode(int, int) ClusterCollapsedTreeNode
ClusterCollapsedTreeNode(ClusterTreeNode, ClusterTreeNode) ClusterCollapsedTreeNode
ClusterConstant etomica.virial
This class returns a constant value needed when using random placement of atoms in a box to sample the target system.
ClusterConstant(int, double) ClusterConstant
ClusterCoupledAtomFlipped etomica.virial
ClusterCoupledAtomFlipped(ClusterAbstract, Space) ClusterCoupledAtomFlipped
ClusterCoupledAtomFlipped(ClusterAbstract, Space, double) ClusterCoupledAtomFlipped
ClusterCoupledFlipped etomica.virial
ClusterCoupledFlipped(ClusterAbstract, Space) ClusterCoupledFlipped
cluster must have caching disabled
ClusterCoupledFlipped(ClusterAbstract, Space, double) ClusterCoupledFlipped
cluster must have caching disabled
configurations will be flipped when the minimum distance between any two molecules
exceeds minFlipDistance.
ClusterCoupledFlippedMultivalue etomica.virial
ClusterCoupledFlippedMultivalue(ClusterAbstractMultivalue, ClusterAbstractMultivalue, Space, double, int, double) ClusterCoupledFlippedMultivalue
cluster must have caching disabled
configurations will be flipped when the minimum distance between any two molecules
exceeds minFlipDistance.
ClusterCoupledFlippedPartial etomica.virial
ClusterCoupledFlippedPartial(ClusterAbstract, Space, int[][]) ClusterCoupledFlippedPartial
clusterCriteria ClusterSumAssociation
ClusterDiagram etomica.virial.cluster
Holds information about a cluster diagram, including the bonds, root points,
and score.
ClusterDiagram(int, int) 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[][]) 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) ClusterDiagram
ClusterDiagram(ClusterDiagram) ClusterDiagram
Creates a copy of the given cluster
ClusterDiagramTree etomica.virial.cluster
Holds information about a cluster diagram, including the bonds, root points,
and score.
ClusterDiagramTree(int, int) ClusterDiagramTree
Constructs a cluster having numBody points and numRootPoints root points.
ClusterDifference etomica.virial
This class holds multiple clusters and returns the value from one minus the
average value from the others.
ClusterDifference(ClusterAbstract, ClusterAbstract[]) ClusterDifference
clusterer ColorSchemeCluster
clusterer DataSourcePercolation
clusterer DataSourcePercolation0
clusterer ColorSchemeCluster
clusterer MeterClusterSizes
clusterer MeterLargestCluster
ClusterExchange etomica.virial
ClusterExchange(IPotentialAtomic) ClusterExchange
clusterFileIn ReadCluster.ReadClusterParams
clusterFileOut ReadCluster.ReadClusterParams
Clusterfoo(ClusterAbstract, double, double) VirialH2OGCPMD.Clusterfoo
ClusterGenerator etomica.virial.cluster
Generates all clusters matching certain criteria.
ClusterGenerator(ClusterDiagram) ClusterGenerator
ClusterICPYC etomica.virial
Cluster class that computes the correction to the ICPY (incrementally
corrected Percus-Yevick) formulation.
ClusterICPYC(int, MayerFunction) ClusterICPYC
clusterMultiBD ClusterWheatleyMultibody
clusterMultiBD ClusterWheatleyMultibodyDerivatives
clusterMultiBDBD ClusterWheatleyMultibodyDerivativesBD
ClusterMultiToSingle etomica.virial
ClusterMultiToSingle(ClusterAbstractMultivalue, int) ClusterMultiToSingle
ClusterMultivalueUmbrella etomica.virial
Umbrella cluster wraps a ClusterAbstractMultivalue.
ClusterMultivalueUmbrella(ClusterAbstractMultivalue) ClusterMultivalueUmbrella
Contructs an umbrella cluster that wraps a multi-value cluster
ClusterOperations etomica.virial.cluster
ClusterOperations() ClusterOperations
clusterOutName DataClusterer
clusterP DataClusterer
ClusterPanel etomica.modules.clustergenerator
ClusterPanel(ClusterDiagram, boolean, boolean, boolean, boolean, boolean) ClusterPanel
clusterPop DataClusterer
ClusterPY etomica.virial
ClusterPY(int, MayerFunction) ClusterPY
ClusterRetrieveOrders(int) ClusterWheatleyPT.ClusterRetrieveOrders
ClusterRetrievePrimes(ClusterWheatleyMultibodyDerivativesBD, int) ClusterWheatleyMultibodyDerivativesBD.ClusterRetrievePrimes
ClusterRetrievePrimes(ClusterWheatleyMultibodyDerivatives, int) ClusterWheatleyMultibodyDerivatives.ClusterRetrievePrimes
ClusterRetrievePrimes(ClusterWheatleySoftDerivativesBD, int) ClusterWheatleySoftDerivativesBD.ClusterRetrievePrimes
ClusterRetrievePrimes(ClusterWheatleySoftDerivatives, int) ClusterWheatleySoftDerivatives.ClusterRetrievePrimes
ClusterRetrievePrimesBD(ClusterWheatleySoftDerivatives, int) ClusterWheatleyPT.ClusterRetrievePrimesBD
ClusterRetrievePrimesBD(ClusterWheatleySoftDerivatives, int) ClusterWheatleySoftDerivatives.ClusterRetrievePrimesBD
clusters AtomNbrClusterer
clusters DataClusterer
clusters ClusterSum
clusters ClusterSumPolarizableWertheimProduct
clusters ClusterSumPolarizableWertheimProduct4Pt
clusters ClusterSumPolarizableWertheimProduct4PtFinal
clusters MeterVirial
clusters MeterVirialBD
clusters MeterVirialExternalFieldOverlapConfined
clusters MeterVirialExternalFieldOverlapConfinedRho
clusters MeterVirialExternalFieldOverlapConfinedSW
clusters MeterVirialExternalFieldOverlapRho
clusters MeterVirialExternalFieldRho
clusters MeterVirialSWWE
ClusterSinglyConnected etomica.virial
This class calculates the sum of all tree clusters using an adaptation of Wheatley's
recursive formulation.
ClusterSinglyConnected(int, MayerFunction) ClusterSinglyConnected
clusterSize ColorSchemeCluster
clusterSize DataSourcePercolation
clusterSize DataSourcePercolation0
clusterSize ColorSchemeCluster
clusterSizeOrder ColorSchemeCluster
clusterStack DataSourcePercolation
clusterStack DataSourcePercolation0
clusterSubtract ClusterDifference
ClusterSum etomica.virial
ClusterSum(ClusterBonds[], double[], MayerFunction[]) ClusterSum
Constructor for ClusterSum.
ClusterSumAssociation 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) ClusterSumAssociation
Constructor for ClusterSum.
ClusterSumAssociation.ClusterCriteria etomica.virial
ClusterSumEF etomica.virial
ClusterSumEF(ClusterBonds[], double[], MayerFunction[]) ClusterSumEF
Constructs a Cluster sum of the given cluster and weights.
ClusterSumExternalField etomica.virial
ClusterSumExternalField(ClusterBonds[], double[], MayerFunction[]) ClusterSumExternalField
ClusterSumHS etomica.virial
This class calculates the sum of all biconnected clusters for hard spheres.
ClusterSumHS(ClusterBonds[], double[], MayerFunction) ClusterSumHS
ClusterSumIC etomica.virial
ClusterSumIC(ClusterBonds[], double[], MayerFunction[], MayerFunction[]) ClusterSumIC
ClusterSumIC.FR2 etomica.virial
ClusterSumMultibody etomica.virial
Cluster class capable of computing multibody (up to 6th order) contributions
to diagrams.
ClusterSumMultibody(ClusterBonds[], double[], MayerFunction[], MayerFunctionNonAdditive[]) ClusterSumMultibody
ClusterSumMultibodyShell etomica.virial
ClusterSumMultibodyShell(ClusterSumMultibody, ClusterBonds[], double[], MayerFunction[], MayerFunctionNonAdditive[]) 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 etomica.virial
ClusterSumNonAdditiveTrimerEnergy(ClusterBonds[], double[], MayerFunction[], Potential) ClusterSumNonAdditiveTrimerEnergy
Adapted by Kate from ClusterSumPolarizable (simplification for nonadditive trimer energy only).
ClusterSumPolarizable etomica.virial
ClusterSumPolarizable(ClusterBonds[], double[], MayerFunction[]) ClusterSumPolarizable
Constructor for ClusterSum.
ClusterSumPolarizableWertheimProduct etomica.virial
ClusterSumPolarizableWertheimProduct(ClusterBonds[], double[], MayerFunction[]) ClusterSumPolarizableWertheimProduct
Constructor for ClusterSum for Wertheim diagram including multi body term.
ClusterSumPolarizableWertheimProduct4Pt etomica.virial
ClusterSumPolarizableWertheimProduct4Pt(ClusterBonds[], double[], MayerFunction[]) ClusterSumPolarizableWertheimProduct4Pt
Constructor for ClusterSum for Wertheim diagram including multi body term.
ClusterSumPolarizableWertheimProduct4PtFinal etomica.virial
ClusterSumPolarizableWertheimProduct4PtFinal(ClusterBonds[], double[], MayerFunction[]) ClusterSumPolarizableWertheimProduct4PtFinal
Constructor for ClusterSum for Wertheim diagram including multi body term.
ClusterSumShell etomica.virial
ClusterSumShell(ClusterSum, ClusterBonds[], double[], MayerFunction[]) 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 etomica.virial
ClusterSumStickyEF(ClusterBonds[], double[], MayerFunction[], ClusterSumStickyEF[], IRandom) ClusterSumStickyEF
ClusterSumStickyEF(ClusterSumEF, ClusterSumStickyEF[], IRandom) ClusterSumStickyEF
ClusterTree etomica.virial
ClusterTree(ClusterDiagramTree, MayerFunction[]) ClusterTree
ClusterTreeBonds etomica.virial
ClusterTreeBonds() ClusterTreeBonds
ClusterTreeEF etomica.virial
ClusterTreeEF(ClusterDiagramTree, MayerFunction[]) ClusterTreeEF
ClusterTreeNode etomica.virial.cluster
ClusterTreeNode(int) ClusterTreeNode
ClusterViewer etomica.graph.viewer
ClusterWeight etomica.virial
ClusterWeight.Factory etomica.virial
ClusterWeightAbs etomica.virial
ClusterWeightAbs(ClusterAbstract) ClusterWeightAbs
clusterWeights ClusterSum
clusterWeights ClusterSumPolarizableWertheimProduct
clusterWeights ClusterSumPolarizableWertheimProduct4Pt
clusterWeights ClusterSumPolarizableWertheimProduct4PtFinal
ClusterWeightSumWall etomica.virial
ClusterWeightSumWall(ClusterWeightSumWall.DataSourceClusterWall, int) ClusterWeightSumWall
ClusterWeightSumWall.DataSourceClusterWall etomica.virial
ClusterWeightUmbrella etomica.virial
Umbrella cluster weight wrapper function.
ClusterWeightUmbrella(ClusterAbstract[]) ClusterWeightUmbrella
Contructs an umbrella cluster from the given clusters.
ClusterWheatley etomica.virial
clusterWheatleyBDBD ClusterWheatleyMultibodyBD
ClusterWheatleyExtendSW etomica.virial
ClusterWheatleyExtendSW(int, MayerFunction, MayerFunction) ClusterWheatleyExtendSW
ClusterWheatleyHS etomica.virial
This class calculates the sum of all biconnected clusters using Wheatley's
recursive formulation.
ClusterWheatleyHS(int, MayerFunction) ClusterWheatleyHS
ClusterWheatleyHS.AllSigs etomica.virial
ClusterWheatleyMultibody etomica.virial
This class uses Wheatley's recursion approach to calculating all biconnected
diagrams, but adds in non-additive contributions.
ClusterWheatleyMultibody(int, MayerFunction, MayerFunctionNonAdditive) ClusterWheatleyMultibody
ClusterWheatleyMultibody(int, MayerFunction, MayerFunctionNonAdditive[]) ClusterWheatleyMultibody
ClusterWheatleyMultibody(int, MayerFunction, MayerFunctionNonAdditive, MayerFunctionNonAdditive[], double) ClusterWheatleyMultibody
ClusterWheatleyMultibodyBD 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) ClusterWheatleyMultibodyBD
ClusterWheatleyMultibodyBD(int, MayerFunction, MayerFunctionNonAdditive, int) ClusterWheatleyMultibodyBD
ClusterWheatleyMultibodyBD(int, MayerFunction, MayerFunctionNonAdditive, MayerFunctionNonAdditive[], int) ClusterWheatleyMultibodyBD
ClusterWheatleyMultibodyDerivatives etomica.virial
This class uses Wheatley's recursion approach to calculating all biconnected
diagrams, but adds in non-additive contributions.
ClusterWheatleyMultibodyDerivatives(int, MayerFunction, MayerFunctionNonAdditive[], double, int, boolean) ClusterWheatleyMultibodyDerivatives
ClusterWheatleyMultibodyDerivatives(int, MayerFunction, MayerFunctionNonAdditive, double, int, boolean) ClusterWheatleyMultibodyDerivatives
ClusterWheatleyMultibodyDerivatives(int, MayerFunction, MayerFunctionNonAdditive, MayerFunctionNonAdditive[], double, int, boolean) ClusterWheatleyMultibodyDerivatives
ClusterWheatleyMultibodyDerivatives.ClusterRetrievePrimes etomica.virial
ClusterWheatleyMultibodyDerivativesBD etomica.virial
This class uses Wheatley's recursion approach to calculating all biconnected
diagrams, but adds in non-additive contributions.
ClusterWheatleyMultibodyDerivativesBD(int, MayerFunction, MayerFunctionNonAdditive, MayerFunctionNonAdditive[], int, int, boolean) ClusterWheatleyMultibodyDerivativesBD
ClusterWheatleyMultibodyDerivativesBD.ClusterRetrievePrimes etomica.virial
ClusterWheatleyMultibodyMix 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) ClusterWheatleyMultibodyMix
Constructs a cluster capable of handling mixtures of nonadditive
molecules.
ClusterWheatleyPartitionScreening etomica.virial
This class calculates the sum of all biconnected clusters using Wheatley's
recursive formulation.
ClusterWheatleyPartitionScreening(int, MayerFunction) ClusterWheatleyPartitionScreening
ClusterWheatleyPartitionScreening(int, MayerFunction, int) ClusterWheatleyPartitionScreening
ClusterWheatleyPartitionScreening.FrequencyCounter etomica.virial
ClusterWheatleyPT etomica.virial
Cluster that uses recursion to compute temperature perturbation coefficients.
ClusterWheatleyPT(int, int, MayerFunction, MayerFunction, double) ClusterWheatleyPT
ClusterWheatleyPT.ClusterRetrieveOrders etomica.virial
ClusterWheatleyPT.ClusterRetrievePrimesBD etomica.virial
Cluster returns only BD values.
ClusterWheatleySoft etomica.virial
This class calculates the sum of all biconnected clusters using Wheatley's
recursive formulation.
ClusterWheatleySoft(int, MayerFunction, double) ClusterWheatleySoft
ClusterWheatleySoftBD etomica.virial
This class calculates the sum of all biconnected clusters using Wheatley's
recursive formulation.
ClusterWheatleySoftBD(int, MayerFunction, int) ClusterWheatleySoftBD
ClusterWheatleySoftDerivatives etomica.virial
This class calculates the sum of all biconnected clusters using Wheatley's
recursive formulation.
ClusterWheatleySoftDerivatives(int, MayerFunction, double, int) ClusterWheatleySoftDerivatives
ClusterWheatleySoftDerivatives.ClusterRetrievePrimes etomica.virial
ClusterWheatleySoftDerivatives.ClusterRetrievePrimesBD etomica.virial
Cluster returns only BD values.
ClusterWheatleySoftDerivativesBD etomica.virial
This class calculates the sum of all biconnected clusters using Wheatley's
recursive formulation.
ClusterWheatleySoftDerivativesBD(int, MayerFunction, int, int) ClusterWheatleySoftDerivativesBD
ClusterWheatleySoftDerivativesBD.ClusterRetrievePrimes etomica.virial
ClusterWheatleySoftDerivativesMix etomica.virial
ClusterWheatleySoftDerivativesMix(int, int[], MayerFunction[][], double, int) ClusterWheatleySoftDerivativesMix
ClusterWheatleySoftDerivativesMixBD etomica.virial
ClusterWheatleySoftDerivativesMixBD(int, int[], MayerFunction[][], int, int) ClusterWheatleySoftDerivativesMixBD
ClusterWheatleySoftMix etomica.virial
Cluster class using Whealtey's recursion to handle mixtures.
ClusterWheatleySoftMix(int, int[], MayerFunction[][], double) ClusterWheatleySoftMix
ClusterWheatleySoftMixBD etomica.virial
Cluster class using Whealtey's recursion with BigDecimal to handle mixtures.
ClusterWheatleySoftMixBD(int, int[], MayerFunction[][], int) ClusterWheatleySoftMixBD
cm P2SemiclassicalMolecular.MoleculeInfoBrute
cm2ndD HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
cmtoau P2WaterPotentialsJankowski
cmzFix P2WaterSzalewicz
cn P3HydrogenManzhos
CO P2CO2H2OWheatley
coef P2HydrogenHinde
coef P2HydrogenHindeAtomic
coeff PolynomialFit.FitResult
coefficient ClusterTreeNode
coefficient() Graph
coefficient() GraphImpl
Coefficient etomica.graph.model
coefficient_fourier EwaldSumMolecules
CoefficientImpl etomica.graph.model.impl
CoefficientImpl(int) CoefficientImpl
CoefficientImpl(int, int) CoefficientImpl
CoefficientImpl(int, int, double) CoefficientImpl
coefficients WaveVectorFactory1D
coefficients WaveVectorFactory2D
coefficients WaveVectorFactoryFcc
coefficients WaveVectorFactorySimple
coefficients MayerFunctionProductGeneral
coefficients MayerFunctionSum
coefficients MayerFunctionSumGeneral
coeffQ(int) QSeries
Computes coefficients of the polynomial in volume for Q for the given N.
coeffs NormalModeAnalysisDisplay1DGraphic
coeffs NormalModeAnalysisDisplay2DGraphic
coeffs NormalModeAnalysisDisplay3DGraphic
colix MeshSurface
Colix org.jmol.util
Implements a color index model using a colix as a
COLor IndeX .
Colix() Colix
colixBack MeshSurface
colixCurrent GData
collapse() ClusterDiagramTree
collapse(int) CorrelationSelf2
Collapses data by 2.
collapseBlocks() AccumulatorAverageCollapsing
collapseData() HistoryCollapsing
collapseData() HistoryCollapsingAverage
collapseData() HistoryCollapsingDiscard
collapseData(double) HistogramCollapsing
Collapses existing data and expands x range sufficiently so that the
given x value is within the range of the histogram.
collecting(int) MCMoveClusterConformationMDTest
CollectionBondedPotentialAlcohols etomica.virial.GUI.components
CollectionBondedPotentialAlcohols() CollectionBondedPotentialAlcohols
CollectionBondedPotentialAlkanes etomica.virial.GUI.components
CollectionBondedPotentialAlkanes(int) CollectionBondedPotentialAlkanes
CollectionPotentialAtomicLike etomica.virial.GUI.components
CollectionPotentialAtomicLike(int) CollectionPotentialAtomicLike
CollectionPotentialAtomicUnlike etomica.virial.GUI.components
CollectionPotentialAtomicUnlike(int, int) CollectionPotentialAtomicUnlike
CollectionPotentialMolecularLike etomica.virial.GUI.components
CollectionPotentialMolecularLike(int) CollectionPotentialMolecularLike
CollectionPotentialMolecularUnlike etomica.virial.GUI.components
CollectionPotentialMolecularUnlike(int, int) CollectionPotentialMolecularUnlike
collector DataAccPusher
colliderColor ColorSchemeColliders
Color applied to the downList atom of the colliding pair
collisionAction(IntegratorHard.Agent) DataProcessorCavity
collisionAction(IntegratorHard.Agent) MeterCavityMapped
collisionAction(IntegratorHard.Agent) MeterContactRatio
collisionAction(IntegratorHard.Agent) MeterPairedFraction
collisionAction(IntegratorHard.Agent) MeterPressureCollisionCount
Implementation of CollisionListener interface
Adds collision virial (from potential) to accumulator
collisionAction(IntegratorHard.Agent) MeterRDFMapped
collisionAction(IntegratorHard.Agent) DataSourceTensorVirialHard
Sums contribution to virial for each collision.
collisionAction(IntegratorHard.Agent) MeterPressureHard
Implementation of CollisionListener interface
Adds collision virial (from potential) to accumulator
collisionAction(IntegratorHard.Agent) MeterPressureHardTensor
collisionAction(IntegratorHard.Agent) IntegratorHard.CollisionListener
collisionAction(IntegratorHard.Agent) DataSourceWallPressureCatalysis
Implementation of CollisionListener interface
Adds collision virial (from potential) to accumulator
collisionAction(IntegratorHard.Agent) InteractionTracker
collisionAction(IntegratorHard.Agent) AtomHardStressCollector
collisionAction(IntegratorHard.Agent) InsertionGraphic.MeterWidom
collisionAction(IntegratorHard.Agent) DataSourceTensorVirialHardProfile
Sums contribution to virial for each collision.
collisionAction(IntegratorHard.Agent) DataSourceWallPressureMu
Implementation of CollisionListener interface
Adds collision virial (from potential) to accumulator
collisionAction(IntegratorHard.Agent) MeterOsmoticPressure
collisionAction(IntegratorHard.Agent) DataSourceWallPressure
Implementation of CollisionListener interface
Adds collision virial (from potential) to accumulator
collisionCount MeterPressureCollisionCount
collisionDiameter P2HardSphere
Separation at which spheres first overlap
collisionPartner IntegratorHard.Agent
collisionPartner() IntegratorHard.Agent
collisionPotential IntegratorHard.Agent
collisionTime() IntegratorHard.Agent
Accessor method for the time to next collision of this atom
collisionTime(IAtomList, double) P2HardSphereCavity
collisionTime(IAtomList, double) P1Wall
collisionTime(IAtomList, double) P2SquareWellBonding
Computes next time of collision of two square-well atoms, assuming free-flight kinematics.
collisionTime(IAtomList, double) P2SquareWellBondingCO
Computes next time of collision of two square-well atoms, assuming free-flight kinematics.
collisionTime(IAtomList, double) P2SquareWellSurface
Computes next time of collision of two square-well atoms, assuming free-flight kinematics.
collisionTime(IAtomList, double) P2SquareWellBonded
Computes next time of collision of the two atoms, assuming free-flight
kinematics.
collisionTime(IAtomList, double) P2SquareWellRadical
Computes next time of collision of the two atoms, assuming free-flight
kinematics.
collisionTime(IAtomList, double) P1Wall
collisionTime(IAtomList, double) P2HardSphereMC
Computes next time of collision of two square-well atoms, assuming free-flight kinematics.
collisionTime(IAtomList, double) P2SquareWellMonomer
Computes next time of collision of two square-well atoms, assuming free-flight kinematics.
collisionTime(IAtomList, double) P1MagicWall
collisionTime(IAtomList, double) P2SquareWellOneSide
Computes next time of collision of two square-well atoms, assuming free-flight kinematics.
collisionTime(IAtomList, double) P1HardWall
collisionTime(IAtomList, double) P2SquareWellBonded
Computes next time of collision of the two atoms, assuming free-flight
kinematics.
collisionTime(IAtomList, double) P2XOrder
collisionTime(IAtomList, double) P2HardSpherePoly
Time to collision of pair, assuming free-flight kinematics
collisionTime(IAtomList, double) P1HardBoundary
collisionTime(IAtomList, double) P1HardMovingBoundary
collisionTime(IAtomList, double) P1HardPeriodic
collisionTime(IAtomList, double) P2DoubleWell
Computes next time of collision of two square-well atoms, assuming free-flight kinematics.
collisionTime(IAtomList, double) P2HardAssociation
Computes the next time of collision of the given atomPair assuming free flight.
collisionTime(IAtomList, double) P2HardBond
Time at which two atoms will reach the end of their tether, assuming
free-flight kinematics
collisionTime(IAtomList, double) P2HardBondedList
collisionTime(IAtomList, double) P2HardSphere
Time to collision of pair, assuming free-flight kinematics
collisionTime(IAtomList, double) P2HardWrapper
collisionTime(IAtomList, double) P2Ideal
Returns Double.POSITIVE_INFINITY.
collisionTime(IAtomList, double) P2PenetrableBond
collisionTime(IAtomList, double) P2PenetrableSphere
Computes next time of collision of two square-well atoms, assuming free-flight kinematics.
collisionTime(IAtomList, double) P2PenetrableSquareWell
Computes next time of collision of two square-well atoms, assuming free-flight kinematics.
collisionTime(IAtomList, double) P2SquareWell
Computes next time of collision of two square-well atoms, assuming free-flight kinematics.
collisionTime(IAtomList, double) P2SquareWellRobust
Computes next time of collision of two square-well atoms, assuming free-flight kinematics.
collisionTime(IAtomList, double) P2Tether
Time at which two atoms will reach the end of their tether, assuming free-flight kinematics
collisionTime(IAtomList, double) PotentialHard
Computes the time of collision of the given atom(s) with the hard
potential, assuming no intervening collisions.
collisionTimeStep IntegratorHard
collisionValue(IntegratorHard.Agent) DataSourceTensorVirialHard
Contribution to the virial from the most recent collision of the given pair/potential.
collisionValue(IntegratorHard.Agent) MeterPressureHard
Implementation of Meter.MeterCollisional interface.
colloidDensityProfileMeter ColloidGraphic
ColloidGraphic etomica.modules.colloid
Colloid module app.
ColloidGraphic(ColloidSim, Space) ColloidGraphic
ColloidGraphic.Applet etomica.modules.colloid
ColloidGraphic.GraftAction etomica.modules.colloid
ColloidGraphic.WallRangeModifier etomica.modules.colloid
colloidMonomerBondManager ColloidSim
colloidMonomerBondManager ConfigurationColloid
ColloidSim etomica.modules.colloid
Colloid simulation.
ColloidSim() ColloidSim
ColloidSim.CriterionNone etomica.modules.colloid
color ColorSchemeSmer.ColorAgent
color Decorate.DecorateParameters
color DisplayBoxCanvasG3DSys.OrientedSite
color Bond
color Token
color() DeleteEdgeParameters
color() DifByConstant.DifByConstantParameters
color() DifParameters
COLOR_0 Metadata
COLOR_1 Metadata
COLOR_10 Metadata
COLOR_11 Metadata
COLOR_12 Metadata
COLOR_2 Metadata
COLOR_3 Metadata
COLOR_4 Metadata
COLOR_5 Metadata
COLOR_6 Metadata
COLOR_7 Metadata
COLOR_8 Metadata
COLOR_9 Metadata
COLOR_CODE_0 Metadata
COLOR_CODE_1 Metadata
COLOR_CODE_2 Metadata
COLOR_CODE_3 Metadata
COLOR_CODE_4 Metadata
COLOR_CODE_5 Metadata
COLOR_CODE_6 Metadata
COLOR_CODE_7 Metadata
COLOR_CODE_8 Metadata
COLOR_CODE_9 Metadata
COLOR_CODE_DEFAULT Metadata
COLOR_CODES Metadata
COLOR_MAP Metadata
color1 CondenseExchange.CondenseExchangeParameters
ColorAgent() ColorSchemeSmer.ColorAgent
colorAllAtoms() ConfigFromFileLAMMPS.ColorSchemeDeviation
colorAllAtoms() ColorSchemeCollective
Determine color of all atoms.
colorAllAtoms() ColorSchemeCollectiveAgent
colorAllAtoms() ColorSchemeCoordination
colorAllAtoms() ColorSchemeNeighbor
colorAllAtoms() ColorSchemeNeighborCell
colorAllAtoms() ColorSchemeOverlap
colorAllAtoms() ColorSchemeRadical
colorAllAtoms() ColorSchemeDropletSurface
colorAllAtoms() ColorSchemeLiquidVapor
colorAllAtoms() ColorSchemeCluster
colorAllAtoms() ColorSchemeCluster
colorAllAtoms() ColorSchemeScaledOverlap
colorCounts ComparatorNodeColors
colorMaps ColorSchemeStepWise
colorNew() DifByConstant.DifByConstantParameters
ColorOptionHandler() Main.ColorOptionHandler
colorPointFromInt(int, Point3f) ColorUtil
colorPointFromInt2(int) ColorUtil
colorPointFromString(String, Point3f) ColorUtil
colorPtToInt(Point3f) ColorUtil
colorrasmol Token
colors ColorSchemeSmerByLength
colors ConfigFromFileLAMMPS.ColorSchemeDeviation
colors ComparatorNodeColors
colors ColorSchemeOverlap
colors ColorSchemeCluster
colors ColorSchemeDeviation
colors ColorSchemeDirection
colors ColorSchemeScaledOverlap
COLORS Metadata
colorScheme ConfigFromFileLAMMPS.AtomTestDeviation
colorScheme ConfigFromFileLAMMPS.ModifierConfiguration
colorScheme DisplayBox
colorScheme ClipPlaneEditor
ColorScheme etomica.graphics
Class that defines the algorithm used to determine atoms colors when drawn to DisplayBox.
ColorScheme() ColorScheme
ColorScheme(Color) ColorScheme
ColorScheme.Simple etomica.graphics
Colors all atoms with baseColor.
ColorSchemeByType etomica.graphics
Colors the atom according to the color given by its type field.
ColorSchemeByType() ColorSchemeByType
ColorSchemeCell etomica.graphics
ColorSchemeCell(PotentialMasterNbr, IRandom, Box) ColorSchemeCell
ColorSchemeCluster etomica.modules.glass
ColorSchemeCluster etomica.modules.nucleation
ColorSchemeCluster(Box, AtomTest) ColorSchemeCluster
ColorSchemeCluster(Box, AtomTest) ColorSchemeCluster
ColorSchemeCollective etomica.graphics
ColorSchemeCollectiveAgent etomica.graphics
Parent class for color schemes that are best implemented by attaching colors
to all atoms at once, rather than determining the color of each as it is drawn.
ColorSchemeCollectiveAgent(Box) ColorSchemeCollectiveAgent
ColorSchemeColliders etomica.graphics
This colorScheme acts to color differently the two atoms that are scheduled to collide next.
ColorSchemeColliders(IntegratorHard) ColorSchemeColliders
ColorSchemeCoordination etomica.graphics
ColorSchemeCoordination(Simulation, PotentialMasterList, Box) ColorSchemeCoordination
ColorSchemeDeviation etomica.modules.glass
ColorSchemeDeviation(Box, ConfigurationStorage) ColorSchemeDeviation
ColorSchemeDeviation(Box, Space) ConfigFromFileLAMMPS.ColorSchemeDeviation
ColorSchemeDirection etomica.modules.glass
ColorSchemeDirection(Box, ConfigurationStorage) ColorSchemeDirection
ColorSchemeDisplacement(CoordinateDefinition, Space, HSNPT.ActionSummer) HSNPT.ColorSchemeDisplacement
ColorSchemeDropletSurface etomica.modules.droplet
ColorSchemeDropletSurface(AtomTestCollective) ColorSchemeDropletSurface
ColorSchemeLiquidVapor etomica.modules.droplet
ColorSchemeLiquidVapor(AtomTestCollective) ColorSchemeLiquidVapor
ColorSchemeNeighbor etomica.graphics
Color atoms based on being neighbors of the reference atom
ColorSchemeNeighbor(PotentialMasterList, Box) ColorSchemeNeighbor
ColorSchemeNeighborCell etomica.graphics
Colors atoms based on being in a neighboring cell to a reference atom.
ColorSchemeNeighborCell(PotentialMasterNbr, Box, int) ColorSchemeNeighborCell
ColorSchemeNull etomica.graphics
Does nothing at any time to set atom's color, leaving color to be set to default value.
ColorSchemeNull() ColorSchemeNull
colorSchemeOverlap HSNPT2DGraphic
ColorSchemeOverlap etomica.graphics
Color atoms based on how many overlaps they have with their neighbors
ColorSchemeOverlap(Space, PotentialMasterList, Box) ColorSchemeOverlap
ColorSchemePaired etomica.cavity
ColorSchemePaired(P2HardSphereCavity) ColorSchemePaired
ColorSchemePlane etomica.modules.crystalviewer
Colors atoms according to whether or not they are in a plane,
as determined by the inPlane method of a Plane instance.
ColorSchemePlane(LatticePlane) ColorSchemePlane
ColorSchemePlane(LatticePlane, Color, Color) ColorSchemePlane
ColorSchemeRadical etomica.modules.catalysis
ColorSchemeRadical etomica.modules.chainequilibrium
ColorSchemeRadical(AtomLeafAgentManager<IAtom[]>) ColorSchemeRadical
ColorSchemeRadical(AtomLeafAgentManager<InteractionTracker.CatalysisAgent>) ColorSchemeRadical
ColorSchemeRadical.LengthAgent etomica.modules.chainequilibrium
ColorSchemeRandom etomica.graphics
ColorSchemeRandom(Box, IRandom) ColorSchemeRandom
ColorSchemeRandomByMolecule etomica.graphics
ColorSchemeRandomByMolecule(Simulation, Box, IRandom) ColorSchemeRandomByMolecule
colorSchemeScaled HSNPT2DGraphic
ColorSchemeScaledOverlap etomica.normalmode.nptdemo
Color atoms based on being neighbors of the reference atom
ColorSchemeScaledOverlap(Space, PotentialMasterList, CoordinateDefinition) ColorSchemeScaledOverlap
ColorSchemeSmer etomica.association
Color scheme for smer association.
ColorSchemeSmer(IAssociationHelper, Box, IRandom) ColorSchemeSmer
ColorSchemeSmer.ColorAgent etomica.association
ColorSchemeSmerByLength etomica.association
Color scheme for smer association.
ColorSchemeSmerByLength(IAssociationHelper, IRandom) ColorSchemeSmerByLength
ColorSchemeStepWise etomica.modules.chainequilibrium
Color scheme for stepwise growth, based on the AtomType (alcohol vs.
ColorSchemeStepWise(Simulation, AtomLeafAgentManager<IAtom[]>) ColorSchemeStepWise
ColorSchemeTemperature etomica.graphics
Colors atoms according to their kinetic energy.
ColorSchemeTemperature() ColorSchemeTemperature
Constructs with default low of 200K and high of 400K.
ColorSchemeTemperature(double, double) ColorSchemeTemperature
colorTriadToInt(float, float, float) ColorUtil
ColorUtil org.jmol.util
ColorUtil() ColorUtil
cols DeviceButtonGroup
columnHeaders DisplayTable
columnInfoFactories DataTable.DataInfoTableFactory
columnNames ModelMoleculeListDisplayTable_new
columnNames ModelMoleculeListDisplayTable
columnNames ModelPotParamDisplayTable
com MCMoveRotateMoleculePhiTheta
com MCMoveVolumeSolidNPTMolecularOriented
com MCMoveClusterRingRegrow
com MCMoveClusterRingRegrowExchange
com MCMoveClusterRingScale
com0 OrientationCalcWater3P
com0 OrientationCalcWater4P
com0 P2WaterSzalewicz
com0 LatticeSumMolecularCrystal
com0 P2HydrogenHinde
com0 P2HydrogenHindeAtomic
com0 P2HydrogenHindePatkowski
com0 P2HydrogenHindePatkowskiAtomic
com0 P2HydrogenPatkowski
com0 P2HydrogenPatkowskiAtomic
com0 MCMoveClusterRingRegrow
com0 MCMoveClusterRingRegrowExchange
com1 P2Nitrogen
com1 P2NitrogenAB
com1 P2NitrogenAnisotropic
com1 P2Water4P
com1 LatticeSumMolecularCrystal
com1 P2HydrogenHinde
com1 P2HydrogenHindeAtomic
com1 P2HydrogenHindePatkowski
com1 P2HydrogenHindePatkowskiAtomic
com1 P2HydrogenPatkowski
com1 P2HydrogenPatkowskiAtomic
com2 P2Nitrogen
com2 P2NitrogenAB
com2 P2NitrogenAnisotropic
com2 P2Water4P
com3 P2WaterSzalewicz
CombinationIterator etomica.math.discrete
Iterator that returns different combinations of n integers taken k at a time.
CombinationIterator(int, int) CombinationIterator
Constructor for CombinationIterator.
combinationProbability P2SquareWellRadical
combineAB MaxIsomorphWertheim
CombineABSite etomica.graph.operations
Operation that attempts to change bonds in a graph so that equivalent graphs
in a set can be combined.
CombineABSite() CombineABSite
CombineABSite.CombineABSiteParameters etomica.graph.operations
CombineABSiteParameters(List<Character>, List<Character>) CombineABSite.CombineABSiteParameters
combineGraphs(Graph, Graph) CartesianIterator
combineGraphs(Graph, Graph) PartitionedIterator
combineLonelyNodes BiComponentSubst.BiComponentSubstParameters
combinePermutations(byte[], byte[]) CartesianPermutator
comH11r PNWaterGCPMReactionField
comH12r PNWaterGCPMReactionField
comH21r PNWaterGCPMReactionField
comH22r PNWaterGCPMReactionField
comHack P2WaterPotentialsJankowski
comHackDist P2WaterPotentialsJankowski
comHi1r PNWaterGCPMReactionField
comHi2r PNWaterGCPMReactionField
comHj1r PNWaterGCPMReactionField
comHj2r PNWaterGCPMReactionField
comM1r PNWaterGCPMReactionField
comM2r PNWaterGCPMReactionField
COMMAND_CLEAR Parser
COMMAND_DISPLAY Parser
COMMAND_DROP Parser
COMMAND_LIST Parser
COMMAND_PRINT Parser
COMMAND_QUIT Parser
COMMAND_READ Parser
COMMAND_READDB Parser
COMMAND_RUN Parser
COMMAND_SAVE Parser
COMMAND_SET Parser
COMMAND_SUMMARY Parser
COMMAND_WRITE Parser
COMMAND_WRITEDB Parser
CommandImpl etomica.graph.engine.impl
CommandImpl(String) CommandImpl
CommandPropertyValueImpl etomica.graph.engine.impl
CommandPropertyValueImpl(String, Parser.Property, Parser.Value) CommandPropertyValueImpl
CommandValueImpl etomica.graph.engine.impl
CommandValueImpl(String, Parser.Value) CommandValueImpl
CommandVariableImpl etomica.graph.engine.impl
CommandVariableImpl(String, Parser.Variable) CommandVariableImpl
CommandVariableValueImpl etomica.graph.engine.impl
CommandVariableValueImpl(String, Parser.Variable, Parser.Value) CommandVariableValueImpl
comMir PNWaterGCPMReactionField
comMjr PNWaterGCPMReactionField
Common etomica.meta
Common() Common
comOld MCMoveVolumeMonoclinicScaled
comOld MCMoveVolumeSolidNPTMolecular
comparableInstance(Bitmap) Bitmap
Returns a bitmap instance with the same number of bits as this bitmap.
comparableInstance(Bitmap) AbstractBitmap
comparator GraphList
comparator FFTDecomposition
comparator MeterVirialExternalFieldOverlapConfined
ComparatorBiConnected etomica.graph.model.comparators
ComparatorBiConnected() ComparatorBiConnected
ComparatorChain etomica.graph.model.comparators
Comparator class that can chain together a list of comparators.
ComparatorChain() ComparatorChain
comparatorDirections ComparatorChain
ComparatorNodeColors etomica.graph.model.comparators
Compares based on graph factors (when available) or node colors.
ComparatorNodeColors() ComparatorNodeColors
ComparatorNodeColors(char[]) ComparatorNodeColors
ComparatorNumEdges etomica.graph.model.comparators
ComparatorNumEdges() ComparatorNumEdges
ComparatorNumFieldNodes etomica.graph.model.comparators
ComparatorNumFieldNodes() ComparatorNumFieldNodes
ComparatorNumFieldNodesExchange() VirialDiagrams.ComparatorNumFieldNodesExchange
ComparatorNumFieldNodesExchange() VirialDiagramsPT.ComparatorNumFieldNodesExchange
ComparatorNumNodes etomica.graph.model.comparators
ComparatorNumNodes() ComparatorNumNodes
ComparatorNumRootNodes etomica.graph.model.comparators
ComparatorNumRootNodes() ComparatorNumRootNodes
comparators ComparatorChain
ComparatorStrand() FFTDecomposition.ComparatorStrand
compare(Graph, Graph) ComparatorBiConnected
compare(Graph, Graph) ComparatorChain
compare(Graph, Graph) ComparatorNodeColors
compare(Graph, Graph) ComparatorNumEdges
compare(Graph, Graph) ComparatorNumFieldNodes
compare(Graph, Graph) ComparatorNumNodes
compare(Graph, Graph) ComparatorNumRootNodes
compare(Graph, Graph) VirialDiagrams.ComparatorNumFieldNodesExchange
compare(Graph, Graph) VirialDiagramsPT.ComparatorNumFieldNodesExchange
compare(DoubleRange, DoubleRange) MeterVirialExternalFieldOverlapConfined.RangeComparator
compare(Object[], Object[]) Eigen.EigenSort
compare(Object, Object) FFTDecomposition.ComparatorStrand
compare(ScriptVariable, ScriptVariable) ScriptVariable.Sort
compareTo(int, Feature) Feature
compareTo(int, Feature) NumericFeature
compareTo(int, Feature) StringFeature
compareTo(AtomType) AtomType
compareTo(Feature) Feature
compareTo(Feature) NumericFeature
compareTo(Feature) StringFeature
compareTo(Bitmap) AbstractBitmap
compareTo(Bitmap) BitmapOfLong
compareTo(Edge) EdgeImpl
compareTo(Graph) GraphImpl
compareTo(Metadata) MetadataImpl
compareTo(Node) NodeImpl
compareTo(BigSurd) BigSurd
Compares the value of this with another constant.
compareTo(BigSurdVec) BigSurdVec
Compare algebraic value with oth.
compareTo(Ifactor) Ifactor
Compare value against another Ifactor
compareTo(Rational) Rational
Compares the value of this with another constant.
compareTo(IntSet) IntSet
compareTo(MeterVirialExternalFieldSW.Near) MeterVirialExternalFieldSW.Near
compareTo(BigInteger) Rational
Compares the value of this with another constant.
completeActivities() Controller
completeCommand(Map<String, Token>, boolean, boolean, String, int) Token
Complex etomica.math
Class that represents a complex number.
Complex(double, double) Complex
Constructs the complex number z = u + i*v
component DeviceSlider
Object with property being modulated
component DeviceSpinner
Object with property being modulated
component PNCO2GCPM
component PNGCPM
component P2WaterSzalewicz
component PNWaterGCPM
component(int, int) Tensor
component(int, int) Tensor1D
component(int, int) Tensor2D
component(int, int) Tensor3D
component(int, int) TensorND
ComponentEventControllerButton() DeviceTrioControllerButton.ComponentEventControllerButton
ComponentEventMyPanel() MyApplet.ComponentEventMyPanel
componentHidden(ComponentEvent) DeviceTrioControllerButton.ComponentEventControllerButton
componentHidden(ComponentEvent) MyApplet.ComponentEventMyPanel
ComponentIndex T > - Class in etomica.meta
ComponentIndex(Class<T>) ComponentIndex
componentMoved(ComponentEvent) DeviceTrioControllerButton.ComponentEventControllerButton
componentMoved(ComponentEvent) MyApplet.ComponentEventMyPanel
componentResized(ComponentEvent) DeviceTrioControllerButton.ComponentEventControllerButton
componentResized(ComponentEvent) MyApplet.ComponentEventMyPanel
componentShown(ComponentEvent) DeviceTrioControllerButton.ComponentEventControllerButton
componentShown(ComponentEvent) MyApplet.ComponentEventMyPanel
ComponentSubst etomica.graph.operations
This class handles the substitution g = A where g is a Graph and A is a set
of Graph.
ComponentSubst() ComponentSubst
ComponentSubst.ComponentSubstParameters etomica.graph.operations
ComponentSubstParameters(Graph, Set<Graph>, MulFlexible.MulFlexibleParameters) ComponentSubst.ComponentSubstParameters
CompoundDimension etomica.units.dimensions
CompoundDimension(Dimension[], double[]) CompoundDimension
CompoundDimension(Dimension[], double[], String) CompoundDimension
CompoundUnit etomica.units
Unit formed from other units raised to specified powers.
CompoundUnit(Unit[], double[]) CompoundUnit
Constructs unit with default name and abbreviation constructed from given units and exponents
CompoundUnit(Unit[], double[], String, String) CompoundUnit
compressibility HypernettedChain
compressibility PercusYevick
compressibility VirialHePCKLJSCHNCCorrection.VirialLJParam
compressibility VirialHePCKLJSPYCorrection.VirialLJParam
compressibility VirialLJCHNCCorrection.VirialLJParam
compressibility VirialLJPYCorrection.VirialLJParam
comps AtomSignalStress
compute() Wigner3jGUI
computeA(int[], double[], double) CalcNumerical2ndDerivative
computeA(int[], double[], double) FiniteDifferenceDerivativeCGNitrogenBeta
computeA(int[], int[], double) CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
computeA(int[], int[], double[]) CalcNumerical2ndDerivativeNitrogen
computeAngle(Tuple3f, Tuple3f, Tuple3f, Vector3f, Vector3f, boolean) Measure
computeAngleABC(Tuple3f, Tuple3f, Tuple3f, boolean) Measure
computeAO GCRestrictedGibbsHS.simParams
computeAPartitions(int, int) ClusterWheatleyPartitionScreening
computeB(double[], int, double, boolean) B3ForSphericallySymmetricU
computeB(double[], int, int, double, boolean) HypernettedChain
computeB(double[], int, int, double, boolean) PercusYevick
computeB(double[], int, int, double, boolean) PercusYevick1QC
computeB(int, int, double, double, Potential2SoftSpherical) BnIETP2Spherical
computeB(int, int, double, double, Potential2SoftSpherical) BnPY_1QC_Helium
computeB2QM(Potential2SoftSpherical, double) B3ForSphericallySymmetricU
computeB3NonAdd(Potential2SoftSpherical, PotentialSoft, Space, double) B3NonAddForSphericallySymmetricU
computeDstFiles(List) SVGConverter
Populates a vector with destination files names
computed from the names of the files in the sources vector
and the value of the dst property
computeHelicalAxis(String, int, Point3f, Point3f, Quaternion) Measure
computeIdeal AshtonWildingLJ.simParams
computeIdeal AshtonWildingOsmoticVirial.simParams
computeIdeal AshtonWildingVirial.simParams
computeImageParameters() DisplayBox
computeImageParameters() DisplayPolytope
computeImageParameters2(int, int) DisplayBox
computeImageParameters2(int, int) DisplayPolytope
computeOrigin(int, int, int) DisplayPolytope
computeP MappedVirialLJ.LJMDParams
computeP MappedVirialLJVGr.LJMDParams
computePartitions(int, int) ClusterSinglyConnected
computePMA MappedVirialLJ.LJMDParams
computePMA MappedVirialLJVGr.LJMDParams
computePopulation() DataClusterer
computeR SimMappedRdf.LJMDParams
computeRMA SimMappedRdf.LJMDParams
computeScaledSysParams(double, double, double, double) EwaldSummation
computeShiftOrigin(IAtom, Boundary) DisplayBoxCanvas1D
computeSources() SVGConverter
Populates a vector with the set of SVG files from the
srcDir if it is not null and with the sources (files or URLs)
if any.
computeTdotDerivs(double, MeterMeanField, Vector[], Vector[]) MeterMappedAveragingCorrelation
computeTorsion(Tuple3f, Tuple3f, Tuple3f, Tuple3f, boolean) Measure
computeTranscodingHints() SVGConverter
Computes the set of transcoding hints to use for the operation
computeU MappedU.LJMDParams
computeUMA MappedU.LJMDParams
computez2 NVTWidomInsertLJ.simParams
computez2z1 GCWidomInsertHS.simParams
computez3z2 GCWidomInsertHS.simParams
comW1 PNWaterGCPMReactionField
comW2 PNWaterGCPMReactionField
comWi PNWaterGCPM
comWi PNWaterGCPMReactionField
comWj PNWaterGCPM
comWj PNWaterGCPMReactionField
concatList(ScriptVariable, ScriptVariable, boolean) ScriptVariable
concatTokens(String[], int, int) Parser
CondenseExchange etomica.virial.cluster
This operation replaces groups of points connected (internally) by
e-exchange bonds with a single point.
CondenseExchange() CondenseExchange
CondenseExchange.CondenseExchangeParameters etomica.virial.cluster
CondenseExchangeParameters(char, char, char, char) CondenseExchange.CondenseExchangeParameters
config LJMC
config LJMD
config Adsorption
config Catalysis
config ChainEquilibriumSim
config FreeRadicalPolymerizationSim
config DCVGCMD
config Droplet
config MaterialFracture
config PistonCylinder
config SimulationRheology
config Sam
config SelfAssemblySim
configButton PistonCylinderGraphic
configFile ClathrateHarmonicFE.SimParams
configFile MinimizationTIP4P.SimParams
configFile ProtonDisorderGenerator.SimParams
ConfigFromFileLAMMPS etomica.freeenergy.npath
This reads ATOM files from LAMMPS and creates a display of one of the
configurations.
ConfigFromFileLAMMPS() ConfigFromFileLAMMPS
ConfigFromFileLAMMPS.AtomTestDeviation etomica.freeenergy.npath
ConfigFromFileLAMMPS.ColorSchemeDeviation etomica.freeenergy.npath
ConfigFromFileLAMMPS.ConfigFromFileLAMMPSParam etomica.freeenergy.npath
ConfigFromFileLAMMPS.ModifierConfiguration etomica.freeenergy.npath
ConfigFromFileLAMMPSParam() ConfigFromFileLAMMPS.ConfigFromFileLAMMPSParam
configIndex ConfigFromFileLAMMPS.ModifierConfiguration
configIndex AtomTestDeviation
configIndex ColorSchemeDeviation
configIndex ColorSchemeDirection
configIndex DisplayBoxCanvas2DGlass
configIndex DisplayBoxCanvas3DGlass
configIndex MeterGs
configList ConfigurationStorage
configMembrane ReverseOsmosis
configMembrane ReverseOsmosisWater
configStorage AtomSignalMobility
configStorage AtomSignalMotion
configStorage AtomTestDeviation
configStorage ColorSchemeDeviation
configStorage ColorSchemeDirection
configStorage CorrelationSelf2
configStorage DataSinkBlockAveragerSFac
configStorage DataSourceAlpha2
configStorage DataSourceCorrelation
configStorage DataSourceF
configStorage DataSourceFOld
configStorage DataSourceFs
configStorage DataSourceMSD
configStorage DataSourcePercolation
configStorage DataSourcePrevTime
configStorage DataSourceQ4
configStorage DataSourceStrings
configStorage DataSourceVAC
configStorage DisplayBoxCanvas2DGlass
configStorage DisplayBoxCanvas3DGlass
configStorage MeterCorrelation
configStorage MeterCorrelationSelf
configStorage MeterGs
configStorage StructureFactorComponentCorrelation
configuration SimulationRestart
configuration CoordinateDefinitionNitrogen
configuration CoordinateDefinitionNitrogenSuperBox
configuration ColloidSim
configuration Mu
configuration CoordinateDefinitionHSDimer
configuration Token
Configuration etomica.config
General class for assignment of molecules to positions in a box.
ConfigurationAligned etomica.spin.ising
Configuration used to align all atoms in a spin system, so all
point in the same direction.
ConfigurationAligned() ConfigurationAligned
ConfigurationCatalysis etomica.modules.catalysis
Configuration for catalysis module.
ConfigurationCatalysis(Simulation, Space, ISpecies, ISpecies, ISpecies, AtomLeafAgentManager) ConfigurationCatalysis
ConfigurationCatalysis.BasisOrthorhombicHexagonal3D etomica.modules.catalysis
ConfigurationCluster etomica.virial
ConfigurationCluster(Space) ConfigurationCluster
ConfigurationClusterAceticAcid etomica.virial
ConfigurationClusterAceticAcid(Space, IRandom, MayerFunction) ConfigurationClusterAceticAcid
ConfigurationClusterAceticAcid(Space, IRandom, MayerFunction, MayerFunction) ConfigurationClusterAceticAcid
ConfigurationClusterAceticAcid(Space, IRandom, MayerFunction, MayerFunction, MayerFunction) ConfigurationClusterAceticAcid
ConfigurationClusterChain etomica.virial
ConfigurationClusterChain(Space) ConfigurationClusterChain
ConfigurationClusterChainFourSites etomica.virial
ConfigurationClusterChainFourSites(Space) ConfigurationClusterChainFourSites
ConfigurationClusterMove etomica.virial
ConfigurationClusterMove(Space, IRandom) ConfigurationClusterMove
ConfigurationClusterMove(Space, IRandom, double) ConfigurationClusterMove
ConfigurationClusterWertheimGCPM etomica.virial
ConfigurationClusterWertheimGCPM(Space, IRandom, PNWaterGCPMThreeSite) ConfigurationClusterWertheimGCPM
ConfigurationClusterWertheimGCPM(Space, IRandom, PNWaterGCPMThreeSite, PNWaterGCPMThreeSite) ConfigurationClusterWertheimGCPM
ConfigurationClusterWertheimGCPM(Space, IRandom, PNWaterGCPMThreeSite, PNWaterGCPMThreeSite, double) ConfigurationClusterWertheimGCPM
ConfigurationClusterWertheimGCPM(Space, IRandom, PNWaterGCPMThreeSite, PNWaterGCPMThreeSite, PNWaterGCPMThreeSite) ConfigurationClusterWertheimGCPM
ConfigurationClusterWertheimGCPM4Pt etomica.virial
ConfigurationClusterWertheimGCPM4Pt(Space, IRandom, PNWaterGCPMThreeSite) ConfigurationClusterWertheimGCPM4Pt
ConfigurationClusterWertheimGCPM4Pt(Space, IRandom, PNWaterGCPMThreeSite, PNWaterGCPMThreeSite) ConfigurationClusterWertheimGCPM4Pt
ConfigurationClusterWertheimGCPM4Pt(Space, IRandom, PNWaterGCPMThreeSite, PNWaterGCPMThreeSite, double) ConfigurationClusterWertheimGCPM4Pt
ConfigurationClusterWertheimGCPM4Pt(Space, IRandom, PNWaterGCPMThreeSite, PNWaterGCPMThreeSite, PNWaterGCPMThreeSite) ConfigurationClusterWertheimGCPM4Pt
ConfigurationClusterWertheimGCPMDirectSampling etomica.virial
ConfigurationClusterWertheimGCPMDirectSampling(Space, IRandom, PNWaterGCPMThreeSite) ConfigurationClusterWertheimGCPMDirectSampling
ConfigurationClusterWertheimGCPMDirectSampling(Space, IRandom, PNWaterGCPMThreeSite, PNWaterGCPMThreeSite) ConfigurationClusterWertheimGCPMDirectSampling
ConfigurationClusterWertheimGCPMDirectSampling(Space, IRandom, PNWaterGCPMThreeSite, PNWaterGCPMThreeSite, double) ConfigurationClusterWertheimGCPMDirectSampling
ConfigurationClusterWertheimGCPMDirectSampling(Space, IRandom, PNWaterGCPMThreeSite, PNWaterGCPMThreeSite, PNWaterGCPMThreeSite) ConfigurationClusterWertheimGCPMDirectSampling
ConfigurationColloid etomica.modules.colloid
ConfigurationColloid(Space, ISpecies, ISpecies, IRandom) ConfigurationColloid
ConfigurationDroplet etomica.modules.droplet
ConfigurationDroplet(IRandom, Space) ConfigurationDroplet
ConfigurationFile etomica.config
reads configuration coordinates from a file and assigns them to the leaf atoms in a box
ConfigurationFile(String) ConfigurationFile
ConfigurationFileBinary etomica.config
reads configuration coordinates from a binary file and assigns them to the
leaf atoms in a box.
ConfigurationFileBinary(String) ConfigurationFileBinary
ConfigurationFileTIP4P etomica.models.water
This reads from a configuration file containing only H, H and O.
ConfigurationFileTIP4P(String, Space, boolean) ConfigurationFileTIP4P
ConfigurationFileXYZ etomica.zeolite
ConfigurationFileXYZ(String, Space) ConfigurationFileXYZ
ConfigurationLammps etomica.interfacial
ConfigurationLammps(Space, String, ISpecies, ISpecies, ISpecies) ConfigurationLammps
ConfigurationLattice etomica.config
Constructs configuration that has the molecules placed on the sites of a
lattice.
ConfigurationLattice(SpaceLattice, IndexIteratorSizable, Space) ConfigurationLattice
Construct class that will place atoms on sites of the given lattice,
proceeding in the order resulting from iteration through the given index
iterator.
ConfigurationLattice(SpaceLattice, Space) ConfigurationLattice
Constructs class using instance of IndexIteratorRectangular as the default
index iterator.
ConfigurationLattice.MyLattice etomica.config
Used to store the state of a lattice.
ConfigurationLatticeFreeRadical etomica.modules.chainequilibrium
Configuration that puts atoms randomly on a lattice and groups pairs of
initiator atoms together as though they are a single molecule.
ConfigurationLatticeFreeRadical(SpaceLattice, Space, IRandom) ConfigurationLatticeFreeRadical
ConfigurationLatticeRandom etomica.config
Configuration that puts atoms randomly on a lattice.
ConfigurationLatticeRandom(SpaceLattice, Space, IRandom) ConfigurationLatticeRandom
ConfigurationLatticeSimple etomica.config
Constructs configuration that has the molecules placed on the sites of a
lattice.
ConfigurationLatticeSimple(SpaceLattice, IndexIteratorSizable, Space) ConfigurationLatticeSimple
Construct class that will place atoms on sites of the given lattice,
proceeding in the order resulting from iteration through the given index
iterator.
ConfigurationLatticeSimple(SpaceLattice, Space) ConfigurationLatticeSimple
Constructs class using instance of IndexIteratorRectangular as the default
index iterator.
ConfigurationLatticeTube etomica.modules.dcvgcmd
Creates a configuration using a CubicLattice to specify positions.
ConfigurationLatticeTube(BravaisLatticeCrystal, double, IndexIteratorSizable, Space) ConfigurationLatticeTube
Constructor for ConfigurationLatticeTube.
ConfigurationLatticeTube(BravaisLatticeCrystal, double, Space) ConfigurationLatticeTube
ConfigurationLatticeWithPlane etomica.config
Constructs configuration that has the molecules placed on the sites of a
lattice.
ConfigurationLatticeWithPlane(SpaceLattice, Plane, Space) ConfigurationLatticeWithPlane
Constructs class using instance of IndexIteratorRectangular as the default
index iterator.
ConfigurationMembrane etomica.modules.rosmosis
ConfigurationMembrane(Simulation, Space) ConfigurationMembrane
ConfigurationMembraneWater etomica.modules.rosmosis
ConfigurationMembraneWater(Simulation, Space) ConfigurationMembraneWater
ConfigurationOrientedFile etomica.config
ConfigurationFile subclass capable of handling oriented atoms.
ConfigurationOrientedFile(String, Space) ConfigurationOrientedFile
ConfigurationOverlapException etomica.exception
Exception thrown when an overlap is detected in the configuration of
a box, subject to the status of an ignoreOverlap flag.
ConfigurationOverlapException(Box) ConfigurationOverlapException
Constructor for ConfigurationOverlapException
ConfigurationPolymer etomica.modules.rheology
Places polymer in a blob near the origin.
ConfigurationPolymer(Space, IRandom) ConfigurationPolymer
ConfigurationReplicate etomica.config
ConfigurationReplicate() ConfigurationReplicate
ConfigurationResourceFile etomica.config
ConfigurationResourceFile(String, Class) ConfigurationResourceFile
Configurations etomica.config
ConfigurationSAM etomica.modules.sam
ConfigurationSAM(Simulation, Space, ISpecies, ISpecies, PotentialMasterList) ConfigurationSAM
ConfigurationStorage etomica.modules.glass
Listener that can store configurations.
ConfigurationStorage(Box, ConfigurationStorage.StorageType) ConfigurationStorage
ConfigurationStorage(Box, ConfigurationStorage.StorageType, int, int) ConfigurationStorage
ConfigurationStorage.ConfigurationStorageListener etomica.modules.glass
ConfigurationStorage.StorageType etomica.modules.glass
ConfigurationStoragePumper etomica.modules.glass
Class that invokes the a pump only when an appropriate new configuration is available.
ConfigurationStoragePumper(DataPump, ConfigurationStorage) ConfigurationStoragePumper
ConfigurationUpdate etomica.server.representations
ConfigurationUpdate(double[][][], Boundary[]) ConfigurationUpdate
ConfigurationUpdateEncoder() ConfigurationWebsocket.ConfigurationUpdateEncoder
ConfigurationWater108 etomica.rotation
reads configuration coordinates from a file and assigns them to the leaf atoms in a box
ConfigurationWater108() ConfigurationWater108
ConfigurationWater108TIP4P etomica.rotation
reads configuration coordinates from a file and assigns them to the leaf atoms in a box
ConfigurationWater108TIP4P() ConfigurationWater108TIP4P
ConfigurationWater256 etomica.rotation
reads configuration coordinates from a file and assigns them to the leaf atoms in a box
ConfigurationWater256() ConfigurationWater256
ConfigurationWater3 etomica.rotation
reads configuration coordinates from a file and assigns them to the leaf atoms in a box
ConfigurationWater3() ConfigurationWater3
ConfigurationWater3_3P etomica.rotation
reads configuration coordinates from a file and assigns them to the leaf atoms in a box
ConfigurationWater3_3P() ConfigurationWater3_3P
ConfigurationWebsocket etomica.server.resources
ConfigurationWebsocket(SimulationStore, ObjectMapper, ScheduledThreadPoolExecutor) ConfigurationWebsocket
ConfigurationWebsocket.ConfigurationUpdateEncoder etomica.server.resources
ConfigurationZincblende etomica.config
Sets the configuration to the zincblende structure, which consists
of two fcc lattices, with one shifted in each direction by one-quarter
of the lattice constant.
ConfigurationZincblende(double, Space) ConfigurationZincblende
configVelList ConfigurationStorage
confluentHypergeometric1F1(double, double, double) SpecialFunctions
The confluent hypergeometric function, usually given the symbol 1F1.
confName WriteConfiguration
confName ConfigurationFile
confName ConfigurationFileBinary
conformation ConfigurationCatalysis
conformation ConfigurationSAM
Conformation7SiteRigidSF6 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(Space) Conformation7SiteRigidSF6
ConformationAceticAcid etomica.models.OPLS
Conformation for acetic acid
ConformationAceticAcid(Space) ConformationAceticAcid
ConformationAlkaneEH etomica.AlkaneEH
Conformation for normal alkanes, explicit hydrogen
Siepmann, TraPPE-EH
ConformationAlkaneEH(Space, int) ConformationAlkaneEH
ConformationAnthracene3site etomica.virial
Conformation for Anthracene
Reference paper: Iwai
3 site linear, group H to the two side benzene rings
ConformationAnthracene3site(Space) ConformationAnthracene3site
ConformationAnthraceneTraPPE 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(Space) ConformationAnthraceneTraPPE
ConformationChain etomica.config
General class for a collection of linearly linked atoms.
ConformationChain(Space) ConformationChain
ConformationChain2D etomica.config
ConformationChain2D(Space, Vector[]) ConformationChain2D
ConformationChain3D etomica.config
ConformationChain3D(Space, Vector[]) ConformationChain3D
ConformationChainLinear etomica.config
Places atoms in a straight line.
ConformationChainLinear(Space) ConformationChainLinear
ConformationChainLinear(Space, double) ConformationChainLinear
ConformationChainLinear(Space, double, double[]) ConformationChainLinear
ConformationChainZigZag etomica.config
Takes two vectors, and returns them in repeating order to form a zig-zag chain
molecule.
ConformationChainZigZag(Space) ConformationChainZigZag
ConformationChainZigZag(Space, Vector, Vector) ConformationChainZigZag
ConformationChainZigZag2 etomica.config
ConformationChainZigZag2(Space) ConformationChainZigZag2
ConformationChainZigZag2(Space, Vector, Vector) ConformationChainZigZag2
ConformationCO2 etomica.models.co2
Conformation for CO2
Reference paper: Partial molar ~~, Stubbs Darke-Wilhelm, Siepmann, JCP
ConformationCO2(Space) ConformationCO2
ConformationEthanol etomica.models.rowley
Conformation for ethanol (positioned in standard orientation) as published in Rowley et al (2006)
K.R.
ConformationEthanol(Space, boolean) ConformationEthanol
ConformationGeneric etomica.config
ConformationGeneric(Vector[]) ConformationGeneric
ConformationHSDimer etomica.normalmode
Conformation for HS Dimer
ConformationHSDimer(Space, double) ConformationHSDimer
ConformationLinear etomica.config
Places atoms in a straight line.
ConformationLinear(Space) ConformationLinear
ConformationLinear(Space, double) ConformationLinear
ConformationLinear(Space, double, double[]) ConformationLinear
ConformationMethane etomica.AlkaneEH
Conformation for TraPPE-Explicit hydrogen methane
C site and H site, NOTE the H is located in the middle of C-H bond
ConformationMethane(Space) ConformationMethane
ConformationMethanol etomica.models.rowley
Conformation for methanol in standard orientation as published in Rowley et al (2006)
OpenOffice Spreadsheet file, Methanol coordinates, used to calculate coordinates from bond lengths and angles:
K.R.
ConformationMethanol(Space, boolean) ConformationMethanol
ConformationNaphthaleneTraPPE etomica.virial
Conformation for Naphthalene
Reference paper: TraPPE: 4 UA description of linear and branched alkanes and alkylbenzenes, Siepmann et al
ConformationNaphthaleneTraPPE(Space) ConformationNaphthaleneTraPPE
ConformationNitrogen etomica.models.nitrogen
Conformation for Nitrogen
Reference paper: Etters RD.
ConformationNitrogen(Space) ConformationNitrogen
ConformationNitrogenShellModel etomica.models.nitrogen
Conformation for Nitrogen (Shell Model)
Reference: Fabianski R.
ConformationNitrogenShellModel(Space) ConformationNitrogenShellModel
ConformationPh3site 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(Space) ConformationPh3site
ConformationPhenanthreneTraPPE 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(Space) ConformationPhenanthreneTraPPE
ConformationStarPolymerGraft etomica.starpolymer
General Class for the conformation of Star polymers
ConformationStarPolymerGraft(Space, int, int) ConformationStarPolymerGraft
ConformationTube etomica.modules.dcvgcmd
ConformationTube(Space, int) ConformationTube
ConformationWater etomica.config
ConformationWater(Space) ConformationWater
ConformationWater3P etomica.models.water
Conformation for 3-point water molecule.
ConformationWater3P(Space) ConformationWater3P
ConformationWaterGCPM etomica.models.water
ConformationWaterGCPM(Space) ConformationWaterGCPM
ConformationWaterGCPMCOM etomica.models.water
Conformation for 4-point water molecule (plus 1 site at the COM).
ConformationWaterGCPMCOM(Space) ConformationWaterGCPMCOM
ConformationWaterTIP4P etomica.models.water
Conformation for 4-point water molecule.
ConformationWaterTIP4P(Space) ConformationWaterTIP4P
conjugate() Complex
Complex conjugate of this Complex number
(the conjugate of x+i*y is x-i*y).
conjugate() Quaternion
Returns the complex conjugate of the Quaternion q.
connect Token
connected Token
ConnectedToggler() MyApplet.ConnectedToggler
Console etomica.graph.engine
ConsoleContainer etomica.graph.engine
ConsoleReader etomica.graph.engine
ConsoleUI etomica.graph.engine
ConsoleUI() ConsoleUI
ConsoleWindow(ConsoleUI) Launcher.ConsoleWindow
ConsoleWindowRunnable(Launcher.ConsoleWindow) Launcher.ConsoleWindowRunnable
Constant() Function.Constant
Constant(double) Function.Constant
Constants etomica.util
Collection of assorted physical constants.
Constants.CompassDirection etomica.util
Enumerated type for the compass directions NORTH, SOUTH, EAST, WEST.
constMu LJMCGraphic
constMu StatisticsMCGraphic
constrainScriptOrigin SVGConverter
Controls whether scripts can only have the same origin as
the document which references them.
constraint P1ConstraintNbr
constraintAngle MCMoveRotateMolecule3DConstraint
constraintAngle MCMoveRotateMolecule3DFixedAngle
constraintAngle MeterDirectInitPert
constraintAngle PRotConstraint
constraintAngle SimOverlapAlphaN2TP.SimOverlapParam
constraintEnergy(Box) MeterBoltzmannHTTP
Returns true if all atoms in the given box satisfy p1's constraint
constraintEnergy(Box) MeterDDP
Returns true if all atoms in the given box satisfy p1's constraint
constraintEnergy(Box) MeterDP
Returns true if all atoms in the given box satisfy p1's constraint
constraintEnergy(Box) MeterTargetTP
Returns true if all atoms in the given box satisfy p1's constraint
constraintMap MCMoveClusterMoleculeMulti
constraintMap MCMoveClusterRotateMoleculeMulti
constraintPotential MCMoveAtomCoupled
constructHessianMatrix(int) HarmonicAlphaNitrogenModelPairMoleculeSequential
constructHessianMatrix(int) HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2
constructHessianMatrix(int) HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
constructHessianMatrix(int) HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
constructHessianMatrix(int) HarmonicBetaNitrogenModelPairMoleculeSequential
constructHessianMatrix(int) HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
constructHessianMatrix(int) HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2
constructHessianMatrix(int) HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
constructHessianMatrix(int) HarmonicBetaNitrogenModelPairMoleculeSequentialLS
constructHessianMatrix(int) HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
constructHessianMatrix(int) HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
constructHessianMatrix(String, int) HarmonicAlphaNitrogenModelPairMoleculeSequential
constructHessianMatrix(String, int) HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
constructHessianMatrix(String, int) HarmonicBetaNitrogenModelPairMoleculeSequential
constructHessianMatrix(String, int) HarmonicBetaNitrogenModelPairMoleculeSequentialLS
Construction etomica.server.core.construction
Construction() Construction
ConstructionInfo etomica.server.representations
ConstructionInfo(String, List<String>, Map<String, List<Long>>, Map<String, String>) ConstructionInfo
ConstructionParams etomica.server.representations
ConstructionParams() ConstructionParams
CONSTRUCTOR_COLORED Parser
CONSTRUCTOR_ISOCOLORED Parser
CONSTRUCTOR_ISOMONO Parser
CONSTRUCTOR_MONO Parser
ConstructorColoredImpl etomica.graph.engine.impl
ConstructorColoredImpl(Map<Character, Byte>, Map<Character, Byte>, boolean) ConstructorColoredImpl
ConstructorImpl etomica.graph.engine.impl
ConstructorImpl() ConstructorImpl
ConstructorMonoImpl etomica.graph.engine.impl
ConstructorMonoImpl(byte, byte, boolean) ConstructorMonoImpl
constructorParams ConstructionParams
constructorParams SimulationConstructor
cont VirialH2PISimple.VirialH2PISimpleParam
contact Token
contactData DataProcessorWidomContact
contains(double) DoubleRange
Indicates if a value falls within the range of this instance.
contains(IAtom) AtomArrayList
Returns true if the given atom is in the list, false otherwise
contains(IAtom) P2HardBondedList.BondArrayList
contains(IPotentialAtomic) PotentialGroup
Indicates if a given potential is a sub-potential of this group.
contains(Vector) Cube
Returns true if the given vector lies inside (or on the surface of)
this cell, false otherwise.
contains(Vector) Cuboid
Returns true if the given vector lies inside (or on the
surface of) this cell, false otherwise.
contains(Vector) Hypersphere
Returns true if the given point lies on or in the sphere.
contains(Vector) LineSegment
Returns true if the given vector lies between the ends of the segment, on
the line joining them.
contains(Vector) Parallelepiped
Returns true if the given vector lies inside (or on the
surface of) this cell, false otherwise.
contains(Vector) Parallelogram
Returns true if the given vector lies inside (or on the
surface of) this cell, false otherwise.
contains(Vector) Point
Returns true if this point is at exactly the same location as the point
defined by the given vector.
contains(Vector) PolygonGeneral
Returns true if the given point lies inside or on an edge of the polygon
contains(Vector) PolyhedronGeneral
Returns true if the given point lies inside or on an edge of the polyhedron
contains(Vector) Polytope
Returns true if the given vector lies inside the polytope,
false otherwise.
contains(Vector) Rectangle
Returns true if the given vector lies inside (or on the surface of)
this cell, false otherwise.
contains(Vector) Shape
Returns true if the point described by the vector lies in or on the
enclosed region.
contains(Vector) Square
Returns true if the given vector lies inside (or on the surface of)
this cell, false otherwise.
contains(Vector) TruncatedOctahedron
contains(Object) AtomPair
contains(Object) AtomSetSinglet
contains(Object) GraphList
contains(Object) MoleculePair
contains(Object) MoleculeSetSinglet
contains(BigInteger) Prime
Test if a number is a prime.
CONTAINS Feature
containsAll(Collection<?>) GraphList
containsKey(int) IndexMap
containsKey(Object) IndexMap
containsValue(Object) IndexMap
continuous VirialCO2PI.VirialH2PIParam
continuous VirialH2PI.VirialH2PIParam
contourlines Token
controlGraphic() DevicePlotPoints
Returns the top level panel that the points table and (if parameters are
vertically-oriented) function parameter slider components sit on.
controller SVGConverter
Controls some aspects of the converter's operation,
such as whether or not it should proceed in some
error situations.
controller Device
controller DisplayBox
controller DisplayCanvas
controller SimulationGraphic
controller SimOverlapModule
Controller etomica.action.controller
The Controller organizes and executes all actions and activities during a running simulation.
Controller() Controller
Controller.ActivityHandle A extends Activity > - Class in etomica.action.controller
Controller.ControllerHandle etomica.action.controller
ControllerAlertMsgBox etomica.virial.GUI.controllers
ControllerAlertMsgBox(String, ModelSpeciesSelection) ControllerAlertMsgBox
ControllerAlertMsgBox.CloseWindowButtonListener etomica.virial.GUI.controllers
ControllerAlertMsgBoxSpeciesRemoval etomica.virial.GUI.controllers
ControllerAlertMsgBoxSpeciesRemoval(String, ModelSpeciesSelection, int) ControllerAlertMsgBoxSpeciesRemoval
ControllerAlertMsgBoxSpeciesRemoval.NoDoNotRemoveSpeciesButtonListener etomica.virial.GUI.controllers
ControllerAlertMsgBoxSpeciesRemoval.YesRemoveSpeciesButtonListener etomica.virial.GUI.controllers
ControllerAlkaneLengthSelection etomica.virial.GUI.controllers
ControllerAlkaneLengthSelection(ModelSelectedSpecies) ControllerAlkaneLengthSelection
ControllerHandle() Controller.ControllerHandle
ControllerSimEnvironmentSelection etomica.virial.GUI.controllers
ControllerSimEnvironmentSelection(ModelSimulationEnvironment) ControllerSimEnvironmentSelection
controllerSpeciesSelection AppControllerMixtureBuilder
ControllerSpeciesSelection etomica.virial.GUI.controllers
controlPanel SimulationPanel
ControlResource etomica.server.resources
ControlResource(SimulationStore) ControlResource
contructFullMatrix(CoordinateDefinition, String) HarmonicAlphaNitrogenModelDecomposed
contructFullMatrix(CoordinateDefinition, String) HarmonicBetaNitrogenModelDecomposed
Conv etomica.graph.operations
Conv() Conv
Converter(String) Zeolite
Converter(String) ZeoliteSimulation
convertPointFromScreen(Object, Point3f) ApiPlatform
convertPointFromScreen(Object, Point3f) Platform
convolution(ClusterDiagram[], ClusterDiagram[]) 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.
convolution(ClusterDiagram, ClusterDiagram) 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.
ConvParameters etomica.graph.operations
ConvParameters(byte, Mul.MulParameters) ConvParameters
coord DisplayBoxCanvasG3DSys.OrientedSite
coord2 DisplayBoxCanvasG3DSys.OrientedFullSite
coord3 DisplayBoxCanvasG3DSys.OrientedFullSite
CoordComboList MCMoveClusterConformationMDTest
CoordinateConverter etomica.math.geometry.coordinate
CoordinateConverter() CoordinateConverter
coordinateDef FindPairMoleculeIndex
coordinateDef FindPairMoleculeIndexBetaN2
coordinateDef HarmonicAlphaNitrogenModel
coordinateDef HarmonicAlphaNitrogenModelDecomposed
coordinateDef HarmonicAlphaNitrogenModelPairMolecule
coordinateDef HarmonicAlphaNitrogenModelPairMoleculeSequential
coordinateDef HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2
coordinateDef HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
coordinateDef HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
coordinateDef HarmonicBetaNitrogenModel
coordinateDef HarmonicBetaNitrogenModelDecomposed
coordinateDef HarmonicBetaNitrogenModelPairMoleculeSequential
coordinateDef HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
coordinateDef HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2
coordinateDef HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
coordinateDef HarmonicBetaNitrogenModelPairMoleculeSequentialLS
coordinateDef HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
coordinateDef HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
coordinateDef LatticeSumCrystalMolecular
coordinateDef MCMoveMoleculeCoupledInitPert
coordinateDef MCMoveRotateMolecule3DConstraint
coordinateDef MCMoveRotateMolecule3DFixedAngle
coordinateDef MCMoveRotateMolecule3DN2AveCosThetaConstraint
coordinateDef MCMoveRotateMolecule3DSuperBox
coordinateDef MeterDirectInitPert
coordinateDef MinimizationBetaNitrogenModel
coordinateDef MinimizationBetaNitrogenModelLS
coordinateDef MinimizeBetaNitrogenLatticeParameterLSFromFile
coordinateDef MinimizeGammaNitrogenLatticeParameter
coordinateDef SimOverlapAlphaN2TP
coordinateDef SimOverlapBetaN2RPScaling
coordinateDef SimOverlapBetaN2TP
coordinateDef SimOverlapDisorderedAlphaN2RPScaling
coordinateDef SimOverlapDisorderedAlphaN2TP
coordinateDef SimulationAlphaNitrogenModel
coordinateDef SimulationBetaNitrogenModel
coordinateDef SimulationBetaNitrogenModelTest
coordinateDef SimulationGammaNitrogenModel
coordinateDefinition EFSTungsten
coordinateDefinition PotentialEAM_LS
coordinateDefinition Potential2SoftSphericalLSMultiLat
coordinateDefinition CalcAnalytical2ndDerivativeNitrogen
coordinateDefinition CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
coordinateDefinition CalcNumerical2ndDerivative
coordinateDefinition CalcNumerical2ndDerivativeNitrogen
coordinateDefinition FiniteDifferenceDerivativeCGNitrogenBeta
coordinateDefinition MeterNormalizedCoord
coordinateDefinition MeterNormalizedCoordBeta
coordinateDefinition MeterOrientationDistribution
coordinateDefinition MeterOrientationOrderParameter
coordinateDefinition MeterRotationDistributionGroup
coordinateDefinition MeterTargetRPMolecule
coordinateDefinition MeterTargetTPMolecule
coordinateDefinition MinimizeBetaNitrogenLatticeParameter
coordinateDefinition MinimizeBetaNitrogenLatticeParameterFromFile
coordinateDefinition MinimizeBetaNitrogenTranslationDOF
coordinateDefinition CalcJacobian
coordinateDefinition HessianDB
coordinateDefinition HSDimerNPT
coordinateDefinition HSNPT.ColorSchemeDisplacement
coordinateDefinition HSNPT
coordinateDefinition HTTPSoftSphereSim
coordinateDefinition LJVacancyMin
coordinateDefinition MCMoveAtomCoupledBennet
coordinateDefinition MCMoveAtomCoupledUmbrella
coordinateDefinition MCMoveAtomSuperBox
coordinateDefinition MCMoveEinsteinCrystal
coordinateDefinition MCMoveHarmonic
coordinateDefinition MCMoveHarmonicStep
coordinateDefinition MCMovePhaseAngle
coordinateDefinition MCMoveSingleMode
coordinateDefinition MCMoveVolumeSolid
coordinateDefinition MCMoveWV
coordinateDefinition MeterAtomicDisplacement
coordinateDefinition MeterBoltzmannHTTP
coordinateDefinition MeterDADB
coordinateDefinition MeterDDP
coordinateDefinition MeterDisplacementMoleculeRMS
coordinateDefinition MeterDisplacementRMS
coordinateDefinition MeterDP
coordinateDefinition MeterHarmonicCoordinate
coordinateDefinition MeterHarmonicEnergy
coordinateDefinition MeterHarmonicSingleEnergy
coordinateDefinition MeterJacobian
coordinateDefinition MeterNormalMode
coordinateDefinition MeterSolidMirror
coordinateDefinition MeterSolidProps
coordinateDefinition MeterSolidPropsLJ
coordinateDefinition MeterTargetTP
coordinateDefinition NormalModeAnalysisDisplay1D
coordinateDefinition NormalModeAnalysisDisplay2D
coordinateDefinition NormalModeAnalysisDisplay3D
coordinateDefinition ColorSchemeScaledOverlap
coordinateDefinition DisplayBoxCanvas2DNpTScaling
coordinateDefinition HSNPT2DSim
coordinateDefinition PotentialCalculationEFSSP
coordinateDefinition PotentialCalculationLJSP
coordinateDefinition PotentialCalculationSolidSuper
coordinateDefinition PotentialCalculationSolidSuperCut
coordinateDefinition SimBennet
coordinateDefinition SimCalcJ
coordinateDefinition SimCalcS
coordinateDefinition SimCalcSLJ
coordinateDefinition SimCalcSMorse
coordinateDefinition SimCalcSSoftSphere2D
coordinateDefinition SimCalcSSoftSphereFCC
coordinateDefinition SimCalcSSoftSphereFCCSuperBox
coordinateDefinition SimHarmonic
coordinateDefinition SimHarmonicUmbrella
coordinateDefinition SimLJHTTISuper
coordinateDefinition SimLJHTTISuperHCP
coordinateDefinition SimLJHTTISuperHCP2
coordinateDefinition SimLJHTTISuperSFMD
coordinateDefinition SimModesJ
coordinateDefinition SimOverlapSoftSphereTP
coordinateDefinition SimTarget
coordinateDefinition SimTargetUmbrella
coordinateDefinition SimUmbrella
coordinateDefinition SimUmbrellaSoftSphere
CoordinateDefinition 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(Box, int, Primitive, Basis, Space) CoordinateDefinition
CoordinateDefinition(Box, int, Primitive, Space) CoordinateDefinition
CoordinateDefinition.BasisCell etomica.normalmode
CoordinateDefinition.SiteSource etomica.normalmode
CoordinateDefinitionHSDimer etomica.normalmode
CoordinateDefinition implementation for HS Dimer.
CoordinateDefinitionHSDimer(Simulation, Box, Primitive, Basis, Space) CoordinateDefinitionHSDimer
CoordinateDefinitionHSDimer.IntegerFunction etomica.normalmode
CoordinateDefinitionLeaf etomica.normalmode
CoordinateDefinition implementation for monatomic molecules that are simply
leaf atoms.
CoordinateDefinitionLeaf(Box, Primitive, Basis, Space) CoordinateDefinitionLeaf
CoordinateDefinitionLeaf(Box, Primitive, Space) CoordinateDefinitionLeaf
CoordinateDefinitionLeafSuperBox etomica.normalmode
CoordinateDefinitionLeafSuperBox(Box, Primitive, Basis, Space) CoordinateDefinitionLeafSuperBox
CoordinateDefinitionMolecule etomica.normalmode
CoordinateDefinition implementation for molecules.
CoordinateDefinitionMolecule(Simulation, Box, Primitive, int, Basis, Space) CoordinateDefinitionMolecule
CoordinateDefinitionMolecule(Simulation, Box, Primitive, int, Space) CoordinateDefinitionMolecule
CoordinateDefinitionMolecule.MoleculeSiteSource etomica.normalmode
CoordinateDefinitionMoleculeVolumeFluctuation etomica.normalmode
CoordinateDefinition implementation for molecules.
CoordinateDefinitionMoleculeVolumeFluctuation(Simulation, Box, Primitive, int, Basis, Space) CoordinateDefinitionMoleculeVolumeFluctuation
CoordinateDefinitionMoleculeVolumeFluctuation(Simulation, Box, Primitive, int, Space) CoordinateDefinitionMoleculeVolumeFluctuation
CoordinateDefinitionMoleculeVolumeFluctuation.MoleculeSiteSource etomica.normalmode
CoordinateDefinitionNitrogen etomica.models.nitrogen
CoordinateDefinition implementation for nitrogen molecule.
CoordinateDefinitionNitrogen(Simulation, Box, Primitive, Basis, Space) CoordinateDefinitionNitrogen
CoordinateDefinitionNitrogen(Simulation, Box, Primitive, Basis, Space, int) CoordinateDefinitionNitrogen
CoordinateDefinitionNitrogen.OrientationAgentSource etomica.models.nitrogen
CoordinateDefinitionNitrogenSuperBox etomica.models.nitrogen
CoordinateDefinition implementation for nitrogen molecule.
CoordinateDefinitionNitrogenSuperBox(Simulation, Box, Primitive, Basis, Space) CoordinateDefinitionNitrogenSuperBox
CoordinateDefinitionNitrogenSuperBox.OrientationAgentSource etomica.models.nitrogen
coordinateDefTarg SimDirectBetaN2RP
coordinateDim CalcJacobian
coordinateDim CoordinateDefinition
CoordinatePairLeafSet etomica.virial
CoordinatePairLeafSet(IAtomList, Space) CoordinatePairLeafSet
Constructor for CoordinatePairLeafSet.
CoordinatePairMoleculeSet etomica.virial
CoordinatePairMoleculeSet(IMoleculeList, Space) CoordinatePairMoleculeSet
Constructor for CoordinatePairLeafSet.
CoordinatePairSet etomica.virial
coordinteDefinition MeterSolidDA
coordinteDefinition MeterSolidDACut
coords ConformationGeneric
Copper etomica.chem.elements
Class for the Copper element.
Copper(String) Copper
Copper(String, double) Copper
copy() SearchState
copy() UllmanSearchState
copy() VF2SearchState
copy() VFSearchState
copy() Bitmap
Creates an instance-compatible copy of this bitmap.
copy() Coefficient
copy() Edge
copy() Graph
copy() AbstractBitmap
copy() CoefficientImpl
copy() EdgeImpl
copy() GraphImpl
copy() NodeImpl
copy() Node
copy() Primitive
Returns a new, identical instance of this primitive.
copy() PrimitiveBcc
Returns a new PrimitiveCubic with the same size as this one.
copy() PrimitiveCubic
Returns a new PrimitiveCubic with the same size as this one.
copy() PrimitiveFcc
Returns a new PrimitiveCubic with the same size as this one.
copy() PrimitiveGeneral
copy() PrimitiveHexagonal
Returns a new PrimitiveHexagonal with the same size as this one.
copy() PrimitiveHexagonal2D
Returns a new PrimitiveHexagonal with the same size as this one.
copy() PrimitiveMonoclinic
Returns a new, identical instance of this primitive.
copy() PrimitiveOrthorhombic
Returns a new, identical instance of this primitive.
copy() PrimitiveOrthorhombicHexagonal
Returns a new, identical instance of this primitive.
copy() PrimitiveTetragonal
Returns a new PrimitiveTetragonal with the same size as this one.
copy() PrimitiveTriclinic
Returns a new, identical instance of this primitive.
copy() PrimitiveTrigonal
Returns a new, identical instance of this primitive.
copy() IntSet
copy(SearchState) SearchState
copy(SearchState) UllmanSearchState
copy(SearchState) VF2SearchState
copy(SearchState) VFSearchState
copy(BitSet) BitSetUtil
copy2(BitSet, BitSet) BitSetUtil
copyColixTranslucency(short, short) Colix
copyFrom(byte[]) AbstractBitmap
copyFrom(Bitmap) AbstractBitmap
copyFrom(Bitmap) BitmapOfLong
TIME = O(1).
copyFrom(Bitmap) BitmapOfLongVector
copyFrom(String) AbstractBitmap
copyHighest(int) Bitmap
Creates an instance-compatible copy of highest numBits bits of this bitmap.
copyHighest(int) AbstractBitmap
copyInvert(BitSet, int) BitSetUtil
copyLowest(int) Bitmap
Creates an instance-compatible copy of lowest numBits bits of this bitmap.
copyLowest(int) AbstractBitmap
copyright JmolConstants
copyTo(ClusterDiagram) ClusterDiagram
corBox DisplayTextBoxesCAE
core P2CO2H2OWheatley
core P2WaterSzalewicz
core PNWaterGCPM
core PNWaterGCPMReactionField
core() Ifactor
The square-free part.
core(BigInteger) BigIntegerMath
Evaluate core(n).
core_1 AbstractSearchState
core_2 AbstractSearchState
core_len AbstractSearchState
coreCluster ClusterSumMultibodyShell
coreCluster ClusterSumShell
coreCO P2CO2H2OWheatley
coreDiameter P2SquareWellBonding
coreDiameter P2SquareWellBondingCO
coreDiameter P2SquareWellSurface
coreDiameter P2SquareWellOneSide
coreDiameter P2DoubleWell
coreDiameter P2PenetrableSphere
coreDiameter P2SquareWell
coreDiameter P2SquareWellRobust
coreDiameterSquared P2SquareWellBonding
coreDiameterSquared P2SquareWellBondingCO
coreDiameterSquared P2SquareWellSurface
coreDiameterSquared P2SquareWellOneSide
coreDiameterSquared P2DoubleWell
coreDiameterSquared P2PenetrableSphere
coreDiameterSquared P2PenetrableSquareWell
coreDiameterSquared P2SquareWell
coreDiameterSquared P2SquareWellRobust
coreFac PNCO2GCPM
coreFac PNGCPM
cornerData Grabber
CornerData() Grabber.CornerData
CornerSetListener(Grabber, Grabber.ActionCornerSetter, int) Grabber.CornerSetListener
corPData DataSourceBlockAvgCor
corPDataInfo DataSourceBlockAvgCor
corPTag DataSourceBlockAvgCor
corrector() IntegratorGear4
CorrelationAgent(Space) MeterMappedAveragingCorrelation.CorrelationAgent
CorrelationSelf2 etomica.modules.glass
CorrelationSelf2(ConfigurationStorage, CorrelationSelf2.CorrelationType, double, int) CorrelationSelf2
CorrelationSelf2.CorrelationType etomica.modules.glass
CorrelationSelf2.MeterCorrelationSelf2 etomica.modules.glass
correlationSum AccumulatorAverageCollapsing
correlationSum AccumulatorAverageFixed
correlationSum AccumulatorAverageFixedOutputFile
correlationType CorrelationSelf2
correlationType MeterCorrelation
correlationType MeterCorrelationSelf
corrugationButton SamGraphic
corSum CorrelationSelf2
corSum MeterCorrelation
corSum MeterCorrelationSelf
corSum StructureFactorComponentCorrelation
corSumX DataSourceBlockAvgCor
cos() Complex
Cosine of this Complex number (doesn't change this Complex number).
cos(BigDecimal) BigDecimalMath
Trigonometric cosine.
cos1m2ThetaDiff P3CPSNonAdditiveHe
cos1m2ThetaDiff P3CPSNonAdditiveHeLessSimplified
cos2cosInt(double, double) FunctionCosIntegral
Integral of cos(t)^2 Exp(b cos(t)) for t from 0 to x.
cos2ThetaDiff P3CPSNonAdditiveHe
cos2ThetaDiff P3CPSNonAdditiveHeLessSimplified
coscosInt(double, double) FunctionCosIntegral
Integral of cos(t) Exp(b cos(t)) for t from 0 to x, accurate to within 0.01% for all b > 0 and -2Pi < x < 2Pi.
cosdtheta MeterMeanField
cosDtheta IntegratorDimerMin
cosg PNCO2GCPM.P3GCPMAxilrodTeller
cosg PNGCPM.P3GCPMAxilrodTeller
cosGamma PrimitiveHexagonal
cosGamma PrimitiveHexagonal2D
cosh() Complex
Hyperbolic cosine of this Complex number
(doesn't change this Complex number).
cosh(BigDecimal) BigDecimalMath
The hyperbolic cosine.
cosInt(double, double) FunctionCosIntegral
Integral of Exp(b cos(t)) for t from 0 to x, accurate to within 0.01% for all b > 0 and -2Pi < x < 2Pi.
coskrj EwaldSummation
cosNominalTheta MCMoveVolumeSolidNPTMolecularOriented
cosNTheta P3CPSNonAdditiveHe
cosNTheta P3CPSNonAdditiveHeLessSimplified
cost0 MeterMeanField
cosTheta CoordinateDefinitionHSDimer
cosThetaConstraint MCMoveRotateMolecule3DN2AveCosThetaConstraint
cosThetaDiff P3CPSNonAdditiveHe
cosThetaDiff P3CPSNonAdditiveHeLessSimplified
cosThetaSum P3CPSNonAdditiveHe
cosThetaSum P3CPSNonAdditiveHeLessSimplified
costiMtj1 MeterMappedAveragingCV
cot(double) BigDecimalMath
trigonometric cot.
cot(BigDecimal) BigDecimalMath
The trigonometric co-tangent.
Coulomb etomica.units
The Coulomb unit of electrical charge.
count BoxMoleculeCountEvent
count AccumulatorAverage
count AccumulatorAverageBlockless.AllData
count AccumulatorAverageBlockless
count AccumulatorAverageBlocklessSlim
count AccumulatorAverageBootstrap
count AccumulatorAverageCollapsingLog
count HistogramNotSoSimple
count MCMoveRotateMolecule3DSuperBox
count AccumulatorOverlapAverageUa2
count HSNPT.ActionSummer
count MeterOverlapSwitch
count WriteS
count PotentialCalculationHeisenberg
count PotentialCalculationMoleculeAgentSum
count PotentialCalculationMoleculeAgentSumMinusIdealPair
count PotentialCalculationMoleculeAgentSumPair
count PotentialCalculationPair
count ClusterWheatleySoftDerivatives
count MeterVirialIC
Count etomica.units
Unit class for the number, or quantity, of something.
count1 MCMoveRotateMolecule3DSuperBox
countBD ClusterWheatleySoft
countEdgeColor(Graph, char) DecorateWertheim2Site
countEdgeColor(Graph, char) DecorateWertheim2SiteRho
countEdgeColor(Graph, char) DecorateWertheimNaphthalene2Rho
counter ANIntergroupCoupled
counter ANIntergroupExchange
counter ANIntragroupExchange
counter IntegratorDimerMin
counter IntegratorDimerRT
counter PRotConstraint
countflips ClusterCoupledFlippedMultivalue
countMolecules(String) PotentialEmul
counts HistogramDiscrete
counts HistogramNotSoSimple
counts HistogramSimple
counts MeterDensityDistribution
covalent Token
covalentMars Elements
Default table of covalent Radii
stored as a short mar ...
covariance AccumulatorAverageCovariance
COVARIANCE AccumulatorAverageCovariance
covData DataSourceMSDcorP
covDataInfo DataSourceMSDcorP
covSum AccumulatorAverageCovariance
covTag DataSourceMSDcorP
cp HSDimerNPT.HSMD3DParameters
cPairID BoxCluster
cPairID ClusterChainHS
cPairID ClusterChainSoft
cPairID ClusterCoupledFlipped
cPairID ClusterCoupledFlippedMultivalue
cPairID ClusterCoupledFlippedPartial
cPairID ClusterSinglyConnected
cPairID ClusterSum
cPairID ClusterSumPolarizableWertheimProduct
cPairID ClusterSumPolarizableWertheimProduct4Pt
cPairID ClusterSumPolarizableWertheimProduct4PtFinal
cPairID ClusterWheatleyHS
cPairID ClusterWheatleyPartitionScreening
cPairID ClusterWheatleyPT
cPairID ClusterWheatleySoft
cPairID ClusterWheatleySoftBD
cPairID ClusterWheatleySoftDerivatives
cPairID ClusterWheatleySoftDerivativesBD
cPairSet BoxCluster
cPairSetTmp BoxCluster
cPairTrialSet BoxCluster
CPK EnumPalette
create Token
create() SpeciesAceticAcid
create() SpeciesMethanol
create() SpeciesWater3P
create() SpeciesWater4P
create(boolean) SpeciesMethane
create(boolean) SpeciesN2
create(boolean) SpeciesN2ShellModel
create(boolean) SpeciesEthanol
create(boolean) SpeciesMethanol
create(boolean) SpeciesMethanol
create(boolean) SpeciesWater3P
create(boolean) SpeciesWater4PCOM
create(boolean) Species7SiteRigidSF6
create(boolean) SpeciesPh3site464
create(boolean) SpeciesPh3site545
create(boolean) SpeciesTraPPEAnthracene
create(boolean) SpeciesTraPPENaphthalene
create(boolean) SpeciesTraPPEPhenanthrene
create(boolean, boolean) SpeciesWater3P
create(boolean, IConformation) SpeciesWater4P
create(boolean, IConformation, boolean) SpeciesWater4P
create(int) SpeciesAlkaneEH
create(int) SpeciesAlkane
create(int, AtomType, AtomType) SpeciesAlkane
create(int, AtomType, AtomType, double, double) SpeciesAlkane
create(IConformation) SpeciesWater4P
create(Space) SpeciesTraPPECO2
create(Space) SpeciesAnthracene3site464
create(Space) SpeciesAnthracene3site545
create(Space, boolean) SpeciesTraPPECO2
create(Space, boolean, double) SpeciesHSDimer
create(Space, AtomType, int, int) SpeciesPolymerMono
create(Space, AtomType, Vector, boolean) SpeciesSpheresRotatingMolecule
create(Space, IElement) SpeciesSpheresRotating
create(Space, IElement, boolean) SpeciesSpheresRotating
create(Space, IElement, boolean, boolean) SpeciesSpheresRotating
create(Space, List<Vector>, double, IElement) SpeciesPolyhedron
createAndShowGUI() UnitGraphics
createArrayOfArrayList(int) ArrayUtil
Helper method for creating a List<T>[]without warnings.
createArrayOfHashtable(int) ArrayUtil
Helper method for creating a Map<K, V>[] without warnings.
createBitmap(byte[]) BitmapFactory
createBitmap(byte, boolean) BitmapFactory
createBitmap(String) BitmapFactory
createCoefficient() GraphFactory
createDataStream(ConstructionParams, String) DataStreamResource
createDecimalSliderStandardLabels(double) DecimalSlider
createDisplayBoxPaintAction(Box) SimulationGraphic
createEdge(byte) GraphFactory
createEdge(byte, char) EdgeImpl
createEdges() GraphImpl
createEllipsoidShades() Shader
createFieldNode(byte, char) NodeImpl
createFont3D(int, int, float, float, ApiPlatform, Object) JmolFont
createGeodesic(int) Geodesic
createGraph(byte) GraphFactory
createGraph(byte, byte, Bitmap) GraphFactory
createGraph(byte, Bitmap) GraphFactory
createGraph(Node[]) GraphFactory
createHistograms(DataFork, Dimension, IRandom, IntegratorEventManager, boolean) StatisticsMCGraphic
createImage(Object) ApiPlatform
can be ignored (return null) if platform cannot save images
createImage(Object) Platform
could be byte[] (from ZIP file) or String (local file name) or URL
createImageIcon(String) ViewSpeciesSelection
createImageIcon(String) ViewSpeciesSelection
createInnerIterator() CartesianIterator
createInnerIterator() PartitionedIterator
createInnerPermutator() CartesianPermutator
createInstance(int) AbstractBitmap
createInstance(int) BitmapOfLong
createInstance(int) BitmapOfLongVector
createInstance(Bitmap) AbstractBitmap
Creates an instance of the implementing class based on the given parameters.
createInstance(Bitmap) BitmapOfLong
createInstance(Bitmap) BitmapOfLongVector
createInstance(ConstructionParams, SimulationModel) Construction
createIntegrators() IntegratorKMC
createIntegrators() IntegratorKMCCluster
createNode(byte) GraphFactory
createNode(byte, boolean) GraphFactory
createNode(byte, char, char) GraphFactory
createNode(byte, char, char) NodeImpl
createOffScreen(int, int) DisplayCanvas
createOuterIterator() CartesianIterator
createOuterIterator() IsomorphismPrefilteredPartitionedIterator
createOuterIterator() PartitionedIterator
createOuterPermutator() CartesianPermutator
createOutputDir(File) SVGConverter
Creates directories for output files if needed.
createReverseEdge(byte) GraphImpl
createReverseEdges() Graph
createReverseEdges() GraphImpl
createRootNode(byte, char) NodeImpl
createSimulation(SimulationConstructor) SimulationResource
createSpecies() IMolecularModel_SpeciesFactory
createSpecies() MolecularModel2CLJQ_SpeciesCO2
createSpecies() MolecularModel2CLJQ_SpeciesEthane
createSpecies() MolecularModel2CLJQ_SpeciesLJ
createSpecies() MolecularModelEMP2_SpeciesCO2
createSpecies() MolecularModelLJ_SpeciesLJ
createSpecies() MolecularModelLJQ_SpeciesLJ
createSpecies() MolecularModelSKS_SpeciesAlkane
createSpecies() MolecularModelSPCE_SpeciesH2O
createSpecies() MolecularModelTRAPPE_SpeciesAlkane
createSpecies() MolecularModelTrappe_SpeciesCO2
createStatPanel(DataFork, Dimension, AccumulatorFactory, boolean) StatisticsMCGraphic
createView(String, Set<Graph>) ClusterViewer
crep P2HydrogenHinde
crep P2HydrogenHindeAtomic
CRINGS VirialHS.VirialHSParam
CRINGS VirialHSMixture.VirialHSParam
CRINGS VirialSWWE.VirialSWWEParam
criteria PotentialMasterNbr
criteria1Body PotentialMasterNbr
criterion ColloidGraphic.WallRangeModifier
criterion PotentialGroup
criterion3 Sam
CriterionAdapter etomica.nbr
Wraps another criterion while adding additional criteria to the acceptance
decision.
CriterionAdapter(NeighborCriterion) CriterionAdapter
Constructs criterion that wraps the given criterion.
CriterionAdapterMolecular etomica.nbr.molecule
Wraps another criterion while adding additional criteria to the acceptance
decision.
CriterionAdapterMolecular(NeighborCriterionMolecular) CriterionAdapterMolecular
Constructs criterion that wraps the given criterion.
CriterionAll etomica.nbr
Specifies that all atoms pairs are to be considered neighbors.
CriterionAll() CriterionAll
CriterionAllMolecular etomica.nbr.molecule
Specifies that all atoms pairs are to be considered neighbors.
CriterionAllMolecular() CriterionAllMolecular
CriterionBondedSimple etomica.nbr
CriterionBondedSimple(NeighborCriterion) CriterionBondedSimple
CriterionInterMolecular etomica.nbr
Pair criterion that judges whether two atoms are or are not in the same
molecule.
CriterionInterMolecular(NeighborCriterion) CriterionInterMolecular
Constructs criterion in default state such that intramolecular pairs are rejected,
and intermolecular pairs are accepted.
CriterionNone etomica.nbr
CriterionNone() ColloidSim.CriterionNone
CriterionNone() CriterionNone
CriterionPositionWall etomica.nbr
Simple neighbor criterion based on distance moved by a leaf atom since
the last update.
CriterionPositionWall(Simulation) CriterionPositionWall
CriterionPositionWall.DoubleWrapper etomica.nbr
CriterionSimple etomica.nbr
Simple neighbor criterion based on distance moved by a leaf atom since
the last update.
CriterionSimple(Simulation, Space, double, double) CriterionSimple
CriterionSimpleMolecular etomica.nbr.molecule
Simple neighbor criterion based on distance between the two molecules
If the molecule moves further than r^2; the update method will kick in
to update the neighborlist.
CriterionSimpleMolecular(Simulation, Space, double, double) CriterionSimpleMolecular
CriterionSpecies etomica.nbr.molecule
Filters molecule to match a given species.
CriterionSpecies(NeighborCriterionMolecular, ISpecies) CriterionSpecies
CriterionSpeciesPair etomica.nbr.molecule
Filters molecule pairs to match a given pair of Species.
CriterionSpeciesPair(NeighborCriterionMolecular, ISpecies, ISpecies) CriterionSpeciesPair
CriterionTether3 etomica.modules.sam
Returns first leaf atom of each polymer molecule and the atom its bonded to.
CriterionTether3(Simulation, ISpecies, AtomType) CriterionTether3
criterionWallMonomer ColloidSim
criticalRho_LJ VirialSF6LJAlkaneUAMix.VirialMixParam
criticalRho_SF6 VirialSF6LJAlkaneUAMix.VirialMixParam
criticalT_LJ VirialSF6LJAlkaneUAMix.VirialMixParam
criticalT_SF6 VirialSF6LJAlkaneUAMix.VirialMixParam
cross Token
cross(Vector3f, Vector3f) Vector3f
Sets this vector to be the vector cross product of vectors v1 and v2.
crossPotentials ReverseOsmosisWaterGraphic.ModifierAtomDiameter
crossVector MCMoveClusterMoleculeLayerMove
crystal SimFe.LjMC3DParams
CrystalViewer etomica.modules.crystalviewer
CrystalViewer() CrystalViewer
CrystalViewer.Applet etomica.modules.crystalviewer
cs P1LepsHarmonic
csp P2HydrogenPatkowski
csp P2HydrogenPatkowskiAtomic
cspIso P2HydrogenPatkowskiIso
cSum DataSourceF
cSum DataSourceFOld
cten P2HydrogenHinde
cten P2HydrogenHindeAtomic
Cube etomica.math.geometry
A geometric cube.
Cube(Space) Cube
Constructs a cube of unit size.
Cube(Space, double) Cube
Constructs a cube with edge length having the given value.
cubeRoot(double) Vector3D
cubeVertexOffsets BoxInfo
cubeVertexOffsets TriangleData
CubicCentimeter etomica.units
The cubic centimeter unit of volume, cm^3.
CubicLattice etomica.lattice
Lattice or crystal with cubic symmetry, such that its spatial size can be
characterized by a single value, the lattice constant.
CubicMeter etomica.units
The cubic meter unit of volume, m^3.
Cuboid etomica.math.geometry
A polyhedron composed of three pairs of rectangular faces placed opposite
each other and joined at right angles, also known as a
rectangular parallelepiped.
Cuboid(Space) Cuboid
Constructs a cuboid with equal faces of unit size (a cube).
Cuboid(Space, double, double, double) Cuboid
Constructs a cuboid with edges of lengths having the given values.
cumint PotentialCalculationMappedRdf
cumint PotentialCalculationMappedEnergy
cumint PotentialCalculationMappedVirial
cumint PotentialCalculationMappedVirialV
cumint(double) PotentialCalculationMappedEnergy
cumint(double) PotentialCalculationMappedVirial
cumint(double) PotentialCalculationMappedVirialV
current() CGS
current() LJ
current() MKS
current() UnitSystem
current() UnitSystem.Sim
Current etomica.units.dimensions
The dimension for electrical current.
currentBlockAvg AccumulatorAverageCollapsing
currentBlockAvg AccumulatorAverageFixed
currentBlockSum AccumulatorAverageFixedOutputFile
currentBox DisplayTextBoxesCAE
currentCores InsertionGraphic.MeterWidom
currentKineticEnergy IntegratorMD
currentLattice LatticeEditor
currentlocalpath Token
currentlyRendering() Graphics3D
currentPotentialEnergy IntegratorBox
currentTime IntegratorMD
currentWells InsertionGraphic.MeterWidom
cursor ApiIndexList
cursor AtomIteratorArrayListSimple
Index of element to be returned by subsequent call to next.
cursor HistoryCollapsing
cursor HistoryScrolling
cursor MCMoveInsertDeleteLatticeVacancy.AtomIteratorBruteForce
cursor MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbr
cursor RectangularLatticeNbrIterator
cursor CriterionTether3
cursor MoleculeIteratorArrayListSimple
Index of element to be returned by subsequent call to next.
CURSOR_CROSSHAIR JmolConstants
CURSOR_DEFAULT JmolConstants
CURSOR_HAND JmolConstants
CURSOR_MOVE JmolConstants
CURSOR_WAIT JmolConstants
CURSOR_ZOOM JmolConstants
curvature IntegratorDimerRT
CUSTOM EnumStereoMode
customVF PotentialCalculationMappedVirialV
cut GlassClustering.SimParams
cutoff MeterStructureFactor
cutoff P1WCAWall
cutoff P1WCAWall
cutoff AtomTestLiquid
cutoff P1WCAWall
cutoff P2ReactionFieldDipole
cutoff P2ReactionFieldDipoleTruncated
cutoff2 P1WCAWall
cutoff2 P2ReactionFieldDipole
cutoff2 P2ReactionFieldDipoleTruncated
cutoff2 P2LJDipole
cutoffRatio P2MoleculeTruncated
cutoffRatio P2ReactionFieldDipoleTruncated
cutoffSq AtomTestLiquid
cutS ConfigFromFileLAMMPS.ConfigFromFileLAMMPSParam
cVec MCMoveVolumeMonoclinicAngle
cVector BoxInflateAnisotropic
cVectorOld BoxInflateAnisotropic
cvij MeterEnergyMeanField
CVisitor etomica.graph.traversal
This TraversalVisitor visits nodes and keeps track of biconnected
components.
CVisitor(List<List<Byte>>) CVisitor
cvSumExtra MeterEnergyMeanField
CYAN Colix
cycleDrawBoundaryType() ImageShell
Cycles to the next boundary drawing style
CYLINDER G3DSys
CYLINDER Bond
d SimDimerLJadatom
d RectangularLattice
d PadeApproximation.VirialParam
d MeterNormalStress
d P3HydrogenManzhos
d(int) Vector
Creates a Vector of the given dimension.
d(int, double, double) P2HydrogenPatkowski
d(int, double, double) P2HydrogenPatkowskiAtomic
d(int, double, double) P2HydrogenPatkowskiIso
d(int, double, double) P2WaterPotentialsJankowski
D MCMoveVolume
D Primitive
D RectangularLatticeNbrIterator
D Polytope
D SimDirectBetaN2RP.SimOverlapParam
D SimOverlapBetaN2RP.SimOverlapParam
D SimGlass.GlassParams
D StatisticsMCGraphic.StatsParams
D MCMoveVolumeMonoclinicScaled
D MCMoveVolumeSolidNPTMolecular
D SimBennet.SimBennetParam
D SimHarmonicUmbrella.SimBennetParam
D SimOverlap.SimOverlapParam
D SimOverlapLJ.SimOverlapParam
D SimOverlapLJModule.SimOverlapParam
D SimOverlapSoftSphere.SimOverlapParam
D SimOverlapSoftSphereHCP.SimOverlapParam
D SimOverlapSoftSphereReweighting.SimOverlapParam
D SimOverlapSoftSphereSoftness.SimOverlapParam
D SimOverlapSoftSphereSuperBox.SimOverlapParam
D SimOverlapSSnxy.SimOverlapParam
D SimTargetUmbrella.SimBennetParam
D SimUmbrella.SimBennetParam
D SimUmbrellaSoftSphere.SimBennetParam
D P3HydrogenManzhos
D VirialHSMixture.VirialHSParam
D VirialHSMixtureOverlap.VirialHSParam
D() ConfigurationLattice.MyLattice
D() AbstractLattice
Dimension of the lattice.
D() BravaisLattice
D() BravaisLatticeCrystal
Returns the spatial dimension + 1.
D() RectangularLattice
D() RectangularLatticeNbrIterator
D() Hypersphere
D() Polytope
The dimension of this polytope, which is not necessarily the dimension
of the space it is embedded in.
D() Shape
Returns the spatial dimension of the shape.
D() Space
D() Tensor
D() Space1D
D() Tensor1D
D() Space2D
D() Tensor2D
D() Space3D
D() Tensor3D
D() TensorND
d0 P3HydrogenManzhos
d2 P2CO2H2OWheatley.P2CO2H2OSC
d2Axc0 PotentialCalculationHeisenberg
d2Axc0 PotentialCalculationMoleculeAgentSum
d2Axc0 PotentialCalculationMoleculeAgentSumPair
d2Axc0 PotentialCalculationPair
d2Axc0 PotentialCalculationVSum
d2Axc1 PotentialCalculationHeisenberg
d2Axc1 PotentialCalculationMoleculeAgentSum
d2Axc1 PotentialCalculationMoleculeAgentSumPair
d2Axc1 PotentialCalculationPair
d2Axc1 PotentialCalculationVSum
d2Axs0 PotentialCalculationHeisenberg
d2Axs0 PotentialCalculationMoleculeAgentSum
d2Axs0 PotentialCalculationMoleculeAgentSumPair
d2Axs0 PotentialCalculationPair
d2Axs0 PotentialCalculationVSum
d2Axs1 PotentialCalculationHeisenberg
d2Axs1 PotentialCalculationMoleculeAgentSum
d2Axs1 PotentialCalculationMoleculeAgentSumPair
d2Axs1 PotentialCalculationPair
d2Axs1 PotentialCalculationVSum
d2Ayc0 PotentialCalculationHeisenberg
d2Ayc0 PotentialCalculationMoleculeAgentSum
d2Ayc0 PotentialCalculationMoleculeAgentSumPair
d2Ayc0 PotentialCalculationPair
d2Ayc0 PotentialCalculationVSum
d2Ayc1 PotentialCalculationHeisenberg
d2Ayc1 PotentialCalculationMoleculeAgentSum
d2Ayc1 PotentialCalculationMoleculeAgentSumPair
d2Ayc1 PotentialCalculationPair
d2Ayc1 PotentialCalculationVSum
d2Ays0 PotentialCalculationHeisenberg
d2Ays0 PotentialCalculationMoleculeAgentSum
d2Ays0 PotentialCalculationMoleculeAgentSumPair
d2Ays0 PotentialCalculationPair
d2Ays0 PotentialCalculationVSum
d2Ays1 PotentialCalculationHeisenberg
d2Ays1 PotentialCalculationMoleculeAgentSum
d2Ays1 PotentialCalculationMoleculeAgentSumPair
d2Ays1 PotentialCalculationPair
d2Ays1 PotentialCalculationVSum
d2dfac AkimaSplineSmoother
d2fac AkimaSplineSmoother
d2Max DataClusterer
d2phi_du2(int[]) CalcAnalytical2ndDerivativeNitrogen
d2phi_du2(int[], double[]) CalcNumerical2ndDerivative
d2phi_du2(int[], int[]) CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
d2phi_du2(int[], int[]) CalcNumerical2ndDerivativeNitrogen
d2pvx10dt1dt1 PotentialCalculationMoleculeAgentSum
d2pvx10dt1dt1 PotentialCalculationPair
d2pvx10dt1dt2 PotentialCalculationMoleculeAgentSum
d2pvx10dt1dt2 PotentialCalculationPair
d2pvx10dt1t1 PotentialCalculationPair
d2pvx20dt1dt2 PotentialCalculationMoleculeAgentSum
d2pvx20dt1dt2 PotentialCalculationPair
d2pvx20dt2dt2 PotentialCalculationMoleculeAgentSum
d2pvx20dt2dt2 PotentialCalculationPair
d2pvy10dt1dt1 PotentialCalculationMoleculeAgentSum
d2pvy10dt1dt1 PotentialCalculationPair
d2pvy10dt1dt2 PotentialCalculationMoleculeAgentSum
d2pvy10dt1dt2 PotentialCalculationPair
d2pvy10dt1t1 PotentialCalculationPair
d2pvy20dt1dt2 PotentialCalculationMoleculeAgentSum
d2pvy20dt1dt2 PotentialCalculationPair
d2pvy20dt2dt2 PotentialCalculationMoleculeAgentSum
d2pvy20dt2dt2 PotentialCalculationPair
d2r CalcAnalytical2ndDerivativeNitrogen
d2sum PotentialCalculationSolidSuper
d2tot P2CO2H2OWheatley.P2CO2H2OSC
d2tot P2CO2Hellmann.P2CO2SC
d2tot P2WaterSzalewicz.P2H2OSC
d2tot P2NitrogenHellmann.P2N2QFH
d2u(double) P2RepRowley
The second derivative of the pair energy, times the square of the
separation: r^2 d^2u/dr^2.
d2u(double) P2Cohesion
d2u(double) P1HydrogenMielke
d2u(double) P1IntraMolecular
d2u(double) P2Anharmonic
The second derivative of the pair energy, times the square of the
separation: r^2 d^2u/dr^2.
d2u(double) P2ArgonAziz1993
The second derivative of the pair energy, times the square of the
separation: r^2 d^2u/dr^2.
d2u(double) P2ArgonSlavicekEtAl2003
The second derivative of the pair energy, times the square of the
separation: r^2 d^2u/dr^2.
d2u(double) P2ArgonTangAndToennies2003
The second derivative of the pair energy, times the square of the
separation: r^2 d^2u/dr^2.
d2u(double) P2DiscreteFeynmanHibbs.P2HeEmpericalQuantum
d2u(double) P2Dreiding
The second derivative of the pair energy, times the square of the
separation: r^2 d^2u/dr^2.
d2u(double) P2Electrostatic
d2u(double) P2ElectrostaticWithHardCore
d2u(double) P2Exp6
The second derivative of the pair energy, times the square of the
separation: r^2 d^2u/dr^2.
d2u(double) P2Exp6Buckingham
The second derivative of the pair energy, times the square of the
separation: r^2 d^2u/dr^2.
d2u(double) P2Fene
The second derivative of the pair energy, times the square of the
separation: r^2 d^2u/dr^2.
d2u(double) P2Harmonic
The second derivative of the pair energy, times the square of the
separation: r^2 d^2u/dr^2.
d2u(double) P2HC2Yukawa
d2u(double) P2HePCJS
The second derivative of the pair energy, times the square of the
separation: r^2 d^2u/dr^2.
d2u(double) P2HePCKLJS
The second derivative of the pair energy, times the square of the
separation: r^2 d^2u/dr^2.
d2u(double) P2HeSimplified
The second derivative of the pair energy, times the square of the
separation: r^2 d^2u/dr^2.
d2u(double) P2HydrogenPatkowskiIso
d2u(double) P2LennardJones
The second derivative of the pair energy, times the square of the
separation: r^2 d^2u/dr^2.
d2u(double) P2LennardJonesDreiding
The second derivative of the pair energy, times the square of the
separation: r^2 d^2u/dr^2.
d2u(double) P2LJQQ
d2u(double) P2ModifiedMorse
The second derivative of the pair energy, times the square of the
separation: r^2 d^2u/dr^2.
d2u(double) P2Morse
The second derivative of the pair energy, times the square of the
separation: r^2 d^2u/dr^2.
d2u(double) P2QChemInterpolated
The second derivative of the pair energy, times the square of the
separation: r^2 d^2u/dr^2.
d2u(double) P2SoftSphere
The second derivative of the pair energy, times the square of the
separation: r^2 d^2u/dr^2.
d2u(double) P2SoftSphericalTruncated
Returns the 2nd derivative (r^2 d^2u/dr^2) of the wrapped potential if the separation
is less than the cutoff value
d2u(double) P2WCA
The second derivative of the pair energy, times the square of the
separation: r^2 d^2u/dr^2.
d2u(double) P2Yukawa
r^2 * d^2u/dr^2 method.
d2u(double) Potential2SoftSpherical
The second derivative of the pair energy, times the square of the
separation: r^2 d^2u/dr^2.
d2u(double) P1IntraLambda
d2uCorrection(double) P2SoftSphericalTruncated.P0Lrc
Uses result from integration-by-parts to evaluate integral of
r2 d2u/dr2 using integral of u.
d2vEx MoleculeAgent
d2vEx PotentialCalculationMoleculeAgentSum
d2vEx PotentialCalculationPair
d2vEx() MoleculeAgent
d2vEy MoleculeAgent
d2vEy PotentialCalculationMoleculeAgentSum
d2vEy PotentialCalculationPair
d2vEy() MoleculeAgent
d3Axc0 PotentialCalculationHeisenberg
d3Axc0 PotentialCalculationMoleculeAgentSum
d3Axc0 PotentialCalculationMoleculeAgentSumPair
d3Axc0 PotentialCalculationPair
d3Axc0 PotentialCalculationVSum
d3Axs0 PotentialCalculationHeisenberg
d3Axs0 PotentialCalculationMoleculeAgentSum
d3Axs0 PotentialCalculationMoleculeAgentSumPair
d3Axs0 PotentialCalculationPair
d3Axs0 PotentialCalculationVSum
d3Ayc0 PotentialCalculationHeisenberg
d3Ayc0 PotentialCalculationMoleculeAgentSum
d3Ayc0 PotentialCalculationMoleculeAgentSumPair
d3Ayc0 PotentialCalculationPair
d3Ayc0 PotentialCalculationVSum
d3Ays0 PotentialCalculationHeisenberg
d3Ays0 PotentialCalculationMoleculeAgentSum
d3Ays0 PotentialCalculationMoleculeAgentSumPair
d3Ays0 PotentialCalculationPair
d3Ays0 PotentialCalculationVSum
d3dfac AkimaSplineSmoother
d3fac AkimaSplineSmoother
D4 Standard
D5 Standard
D6 Standard
dab P1LepsHarmonic
dac P1LepsHarmonic
dAcc Ising
dadbSum Potential2SoftSphericalLSMultiLat.ReturnValue
dadbSum PotentialCalculationSolidSuper
dadbSum PotentialCalculationSolidSuperCut
daDef MCMoveOverlapListener
daDef SimHSMDVacancy.HSMDVParams
daDef SimLJVacancy.LJParams
Dalton etomica.units
damp(int, double, double) P2WaterSzalewicz
DampingParams() P2QChemInterpolated.DampingParams
DampingParams() P3AdditiveQChem.DampingParams
DampingParams() P3QChem.DampingParams
DampingParams() B3ForSphericallySymmetricU.DampingParams
DASH_MAP Metadata
daSpan MCMoveOverlapListener
data MeterEnthalpyVolume
data DataProcessorCavity
data DataProcessorErrorBar
data DataProcessorGContactP
data DataProcessorPContactG
data DataProcessorWidomContact
data MeterCavityMapped
data MeterRDFMapped
data MeterWidomCavity
data AccumulatorCounter
data DataDump
data DataProcessorChemicalPotential
data DataProcessorFunction
data DataProcessorInterfacialTension
data DataSourcePositionedBoltzmannFactor
data DataSourceScalar
data DataSourceTensorVirialHard
data MeterDihedralAngle
data MeterDipoleSumSquaredMappedAverage
data MeterHyperVirial
data MeterPressureByVolumeChange.DataSourceExp
data MeterPressureTensor
data MeterPressureTensorFromIntegrator
data MeterProfileByAtoms
data MeterProfileByVolume
data MeterRDF
data MeterRDFPC
data MeterStructureFactor
data DataGroup
data DataSourceEnergies
data DataProcessorReweight
data DataProcessorReweightRatio
data LjMd3D.DataProcessorCorrection
data LjMd3D.DataProcessorReweight
data MeterPotentialEnergyCutoff
data MeterPU
data MeterPUCut
data MeterPUCutLS
data MeterWidomInsertionCorrection
data MeterMappedRdf
data MeterMeanForce
data DataProcessorXY
data MeterBoltzmann
data MeterBoltzmannRotPerturb
data MeterTargetRPMolecule
data MeterTargetTPMolecule
data DataSourceDensityFunction
data DataSourceWallPressureCatalysis
data MeterChainLength
data MolecularWeightAvg
data MolecularWeightAvg2
data DropletGraphic.DataProcessorTensorSplitter
data MeterDeformation
data AccumulatorAutocorrelationPTensor
data AccumulatorAutocorrelationShearStress
data AccumulatorPTensor
data CorrelationSelf2
data DataSourceAlpha2
data DataSourceCorrelation
data DataSourceF
data DataSourceFOld
data DataSourceFs
data DataSourceHisogram
data DataSourceHistogramMSD
data DataSourceMSD
data DataSourceMSDcorP
data DataSourcePercolation
data DataSourcePercolation0
data DataSourcePMSDHistory
data DataSourceQ4
data DataSourceStrings
data DataSourceVAC
data GlassGraphic.DataProcessorTensorTrace
data MeterCorrelation
data MeterCorrelationSelf
data MeterGs
data StructureFactorComponentCorrelation
data DataProcessorInterfacialTensionProfile
data InterfacialSWGraphic.DataProcessorTensorSplitter
data MeterOrientation
data LjmdGraphic.DataProcessorTensorTrace
data DataSourceWallPressureMu
data MuGraphic.DataProcessorMu
data DataProcessorBias
data DataProcessorBounds
data DataProcessorDyDLnx
data MeterMBAR
data MultiharmonicGraphicMC.DataProcessAHT
data MultiharmonicGraphicMC.DataSourceAlphaFE
data MultiharmonicGraphicMC.DataSourceFunctionRaw
data MeterFlux
data MeterOsmoticPressure
data MeterTilt
data SamGraphic.DataPipeStressStrain
data AccumulatorMimicMu
data DataCollector
data DataProcessorMu
data StatisticsMCGraphic.DataProcessorUndo
data DataProcessorBoltzmannFactor
data DataSourceFE
data DataSourceFEHistogram
data DataSourceImposedFEFit
data DataSourceImposedFEHistogram
data DataSourcePMu
data DataSourcePN
data MeterBoltzmann
data MeterBoltzmannHarmonic
data MeterBoltzmannHTTP
data MeterBoltzmannTarget
data MeterDADB
data MeterDDP
data MeterDirectSamplingHarmonic
data MeterDirectSamplingTarget
data MeterDP
data MeterHarmonicSingleEnergy
data MeterOverlapSwitch
data MeterPlaneSlip
data MeterSamplingHarmonic
data MeterSamplingTarget
data MeterSolidDA
data MeterSolidDACut
data MeterSolidMirror
data MeterSolidProps
data MeterSolidPropsLJ
data MeterTargetTP
data MeterTilt
data MeterTiltHistogram
data MeterTiltRotation
data MeterTiltRotationHistogram
data MeterTiltRotationStdev
data MeterWorkBennetHarmonic
data MeterWorkBennetTarget
data MeterWorkHarmonicBennet
data MeterWorkHarmonicPhaseSpace
data MeterWorkHarmonicTargetandReweighting
data MeterWorkHarmonicUmbrella
data MeterWorkTargetBennet
data MeterWorkTargetHarmonicandReweighting
data MeterWorkTargetPhaseSpace
data MeterWorkTargetUmbrella
data MeterWorkUmbrellaHarmonic
data MeterWorkUmbrellaTarget
data NormalModeAnalysisDisplay1DGraphic
data NormalModeAnalysisDisplay2DGraphic
data MeterOverlap
data MeterDipoleMoment
data MeterEnergyMeanField
data MeterMappedAveraging
data MeterMappedAveraging3Pair
data MeterMappedAveragingCorrelation
data MeterMappedAveragingCV
data MeterMappedAveragingFreeEnergy
data MeterMappedAveragingPair
data MeterMappedAveragingPairExcess
data MeterMappedAveragingSum
data MeterMappedAveragingVSum
data MeterMappedAveragingVSum3Pair
data MeterMappedAveragingVSumPair
data MeterMeanField
data MeterBondLength
data DataProcessorSurfaceTension
data SurfaceTensionMapped
data DataProcessorVirialOverlap
data Token
DataAccCorrectedPusher etomica.modules.statistics
DataAccCorrectedPusher(int, DataCollector) DataAccCorrectedPusher
DataAccDiffCorrectedPusher etomica.modules.statistics
DataAccDiffCorrectedPusher(int, DataCollector, AccumulatorAverage) DataAccDiffCorrectedPusher
DataAccDifficultyPusher etomica.modules.statistics
DataAccDifficultyPusher(int, DataCollector, AccumulatorAverage) DataAccDifficultyPusher
DataAccPusher etomica.modules.statistics
DataAccPusher(int, DataCollector) DataAccPusher
DataAccSamplesPusher etomica.modules.statistics
DataAccSamplesPusher(int, DataCollector, AccumulatorAverage) DataAccSamplesPusher
DataAccumulator etomica.data
DataProcessor that accumulates and transforms given data and intermittently transmits
processed data to other DataSink(s).
DataAccumulator() DataAccumulator
Constructs accumulator with no initial DataSink.
DataAndInfo etomica.server.representations
DataAndInfo() DataAndInfo
DataAndInfoEncoder() DataStreamWebsocket.DataAndInfoEncoder
DataArrayWriter etomica.data
A DataWriter that writes out data as a table with optional column headings
DataArrayWriter() DataArrayWriter
databases JmolConstants
dataChanged(DataSet) DataSetListener
Method called when one or more pieces of data have changed.
dataChanged(DataSet) DisplayPlot
Causes the display of the plot to be updated.
dataChanged(DataSet) DisplayPlotXChart
dataChanged(DataSet) DisplayTable
Causes the display of the plot to be updated.
dataChanged(DataSet.DataSetSink) DataSet
Notifies the DataSet that new Data has arrived for the given psuedo
DataSink.
dataChanged(DataSet.DataSetSink) DataSinkTable
DataClusterer etomica.modules.glass
DataClusterer(int, IRandom) DataClusterer
DataClusterer.PressureSink etomica.modules.glass
DataClusterReader etomica.modules.glass
DataClusterReader() DataClusterReader
DataClusterWriter etomica.modules.glass
DataClusterWriter(Box, String) DataClusterWriter
DataClusterWriter.PressureSink etomica.modules.glass
DataCollector etomica.modules.statistics
DataCollector() DataCollector
dataCountChanged(DataSet) DataSetListener
Method called when a Data object is added.
dataCountChanged(DataSet) DisplayPlot
Updates the units array for the new column, using the default units.
dataCountChanged(DataSet) DisplayPlotXChart
dataCountChanged(DataSet) DisplayTable
Updates the units array for any new or deleted columns,
using the default units for new columns.
DataCutter etomica.zeolite
DataCutter(String, int) DataCutter
dataDistance MeterSamplingWeight
DataDistributer etomica.data
DataSink that takes a Data object and pushes it to a dataSink chosen
by an indexer.
DataDistributer(DataDistributer.Indexer, DataSplitter.IDataSinkFactory) DataDistributer
DataDistributer.Indexer etomica.data
DataDouble etomica.data.types
Data object wrapping a single mutable value of type double .
DataDouble() DataDouble
Constructs a new instance with given descriptors.
DataDouble.DataInfoDouble etomica.data.types
DataDouble.DataInfoDoubleFactory etomica.data.types
DataDoubleArray etomica.data.types
Data object that wraps a mutable array of doubles.
DataDoubleArray(int) DataDoubleArray
Constructs a new one-dimensional array of the given length.
DataDoubleArray(int[]) DataDoubleArray
Constructs a new multidimensional array of the given shape.
DataDoubleArray(int[], double[]) DataDoubleArray
Wraps the given array, xData in a DataDoubleArray of the given shape.
DataDoubleArray.DataInfoDoubleArray etomica.data.types
DataDoubleArray.DataInfoDoubleArrayFactory etomica.data.types
DataDoubleBDArray etomica.data.types
Data object that wraps a array of BigDecimals.
DataDoubleBDArray(int[], int) DataDoubleBDArray
Constructs a new multidimensional array of the given shape.
DataDoubleBDArray(int, int) DataDoubleBDArray
Constructs a new one-dimensional array of the given length.
DataDoubleBDArray.DataInfoDoubleBDArray etomica.data.types
DataDoubleBDArray.DataInfoDoubleBDArrayFactory etomica.data.types
DataDump etomica.data
DataDump acts both as a DataSink and a DataSource.
DataDump() DataDump
dataDy AkimaSplineSmootherApp
dataDy AkimaSplineSmootherDyApp
dataDy2 AkimaSplineSmootherApp
dataDy2 AkimaSplineSmootherDyApp
dataDy3 AkimaSplineSmootherDyApp
dataEVec NormalModeAnalysisDisplay3DGraphic
dataEy AkimaSplineSmootherApp
dataEy AkimaSplineSmootherDyApp
DataFork etomica.data
DataSink that takes a data stream and forwards it across multiple sinks.
DataFork() DataFork
Constructs with no initial DataSinks.
DataFork(IDataSink[]) DataFork
Constructs to forward data to the given sinks.
DataFunction etomica.data.types
Collects two or more DataDoubleArray instances, and organizes them into
"dependent" and "independent" subgroups.
DataFunction(int[]) DataFunction
Forms a DataFunction with the given array shape.
DataFunction(int[], double[]) DataFunction
Forms a DataFunction using the given independent and dependent data
instances.
DataFunction.DataInfoFunction etomica.data.types
DataFunction.DataInfoFunctionFactory etomica.data.types
dataGroup AccumulatorAverage
dataGroup AccumulatorAverageBlockless
dataGroup MeterTiltRotationHistogram
DataGroup etomica.data.types
Gathers one or more Data instances into a single Data object.
DataGroup(IData[]) DataGroup
Forms a data group from the given array of data objects.
DataGroup.DataInfoGroup etomica.data.types
DataGroup.DataInfoGroupFactory etomica.data.types
DataGroupFilter etomica.data
Extracts one or more of the Data instances wrapped in a DataGroup.
DataGroupFilter(int) DataGroupFilter
Creates a filter that will take the DataGroup element indicated
by the index, counting from 0.
DataGroupFilter(int[]) DataGroupFilter
Creates a filter that will take the set of elements from the DataGroup
corresponding to the given index values (with indexes counting from 0).
DataGroupSplitter etomica.data
DataSink that takes a DataGroup object and pushes each sub-Data object from
the incoming DataGroup to a different stream.
DataGroupSplitter() DataGroupSplitter
dataInfo MeterEnthalpyVolume
dataInfo MeterCavityMapped
dataInfo MeterRDFMapped
dataInfo MeterWidomCavity
dataInfo DataDistributer
dataInfo DataDump
dataInfo DataFork
dataInfo DataProcessor
dataInfo DataSourcePositionedBoltzmannFactor
dataInfo DataSourceScalar
dataInfo DataSourceTensorVirialHard
dataInfo DataSplitter
dataInfo MeterDipoleSumSquaredMappedAverage
dataInfo MeterHyperVirial
dataInfo MeterPressureByVolumeChange.DataSourceExp
dataInfo MeterPressureTensor
dataInfo MeterPressureTensorFromIntegrator
dataInfo MeterProfileByAtoms
dataInfo MeterProfileByVolume
dataInfo MeterStructureFactor
dataInfo DataSourceEnergies
dataInfo MeterPotentialEnergyCutoff
dataInfo MeterPU
dataInfo MeterPUCut
dataInfo MeterPUCutLS
dataInfo MeterWidomInsertionCorrection
Number of insertions attempted in each call to currentValue Default is
100
dataInfo MeterMeanForce
dataInfo MeterBoltzmann
dataInfo MeterBoltzmannRotPerturb
dataInfo MeterTargetRPMolecule
dataInfo MeterTargetTPMolecule
dataInfo DataSourceDensityFunction
dataInfo DataSourceWallPressureCatalysis
dataInfo MeterChainLength
dataInfo MolecularWeightAvg
dataInfo MolecularWeightAvg2
dataInfo MeterDeformation
dataInfo AccumulatorPTensor
dataInfo CorrelationSelf2
dataInfo DataSourceAlpha2
dataInfo DataSourceCorrelation
dataInfo DataSourceF
dataInfo DataSourceFOld
dataInfo DataSourceFs
dataInfo DataSourceHisogram
dataInfo DataSourceHistogramMSD
dataInfo DataSourceMSD
dataInfo DataSourceMSDcorP
dataInfo DataSourcePercolation
dataInfo DataSourcePercolation0
dataInfo DataSourcePMSDHistory
dataInfo DataSourceQ4
dataInfo DataSourceStrings
dataInfo DataSourceVAC
dataInfo MeterGs
dataInfo StructureFactorComponentCorrelation
dataInfo MeterOrientation
dataInfo DataSourceWallPressureMu
dataInfo MuGraphic.DataProcessorMu
dataInfo DataProcessorBias
dataInfo DataProcessorBounds
dataInfo DataProcessorDyDLnx
dataInfo MeterMBAR
dataInfo MultiharmonicGraphicMC.DataSourceAlphaFE
dataInfo MultiharmonicGraphicMC.DataSourceFunctionRaw
dataInfo MeterUmbrella
dataInfo MeterFlux
dataInfo MeterOsmoticPressure
dataInfo MeterTilt
dataInfo SamGraphic.DataPipeStressStrain
dataInfo DataCollector
dataInfo DataProcessorBoltzmannFactor
dataInfo DataSourceFE
dataInfo DataSourceFEHistogram
dataInfo DataSourceImposedFEFit
dataInfo DataSourceImposedFEHistogram
dataInfo DataSourcePMu
dataInfo DataSourcePN
dataInfo MeterBoltzmann
dataInfo MeterBoltzmannHarmonic
dataInfo MeterBoltzmannHTTP
dataInfo MeterBoltzmannTarget
dataInfo MeterDADB
dataInfo MeterDDP
dataInfo MeterDirectSamplingHarmonic
dataInfo MeterDirectSamplingTarget
dataInfo MeterDP
dataInfo MeterHarmonicSingleEnergy
dataInfo MeterOverlapSwitch
dataInfo MeterPlaneSlip
dataInfo MeterSamplingHarmonic
dataInfo MeterSamplingTarget
dataInfo MeterSolidDA
dataInfo MeterSolidDACut
dataInfo MeterSolidMirror
dataInfo MeterSolidProps
dataInfo MeterSolidPropsLJ
dataInfo MeterTargetTP
dataInfo MeterTilt
dataInfo MeterTiltHistogram
dataInfo MeterTiltRotation
dataInfo MeterTiltRotationHistogram
dataInfo MeterTiltRotationStdev
dataInfo MeterWorkBennetHarmonic
dataInfo MeterWorkBennetTarget
dataInfo MeterWorkHarmonicBennet
dataInfo MeterWorkHarmonicPhaseSpace
dataInfo MeterWorkHarmonicTargetandReweighting
dataInfo MeterWorkHarmonicUmbrella
dataInfo MeterWorkTargetBennet
dataInfo MeterWorkTargetHarmonicandReweighting
dataInfo MeterWorkTargetPhaseSpace
dataInfo MeterWorkTargetUmbrella
dataInfo MeterWorkUmbrellaHarmonic
dataInfo MeterWorkUmbrellaTarget
dataInfo MeterOverlap
dataInfo MeterDipoleMoment
dataInfo MeterEnergyMeanField
dataInfo MeterMappedAveraging
dataInfo MeterMappedAveraging3Pair
dataInfo MeterMappedAveragingCorrelation
dataInfo MeterMappedAveragingCV
dataInfo MeterMappedAveragingFreeEnergy
dataInfo MeterMappedAveragingPair
dataInfo MeterMappedAveragingPairExcess
dataInfo MeterMappedAveragingSum
dataInfo MeterMappedAveragingVSum
dataInfo MeterMappedAveragingVSum3Pair
dataInfo MeterMappedAveragingVSumPair
dataInfo MeterMeanField
dataInfo DataProcessorSurfaceTension
DataInfo etomica.data
Object associated with a Data instance and which provides descriptive
information about the data encapsulated in it.
DataInfo(String, Dimension) DataInfo
Constructs new instance with descriptive label and dimension.
dataInfoA NormalModeAnalysisDisplay1DGraphic
dataInfoA NormalModeAnalysisDisplay2DGraphic
dataInfoA NormalModeAnalysisDisplay3DGraphic
dataInfoChanged(DataSet.DataSetSink) DataSet
Notifies the DataSet that new DataInfo has arrived for the given
psuedo DataSink.
dataInfoChanged(DataSet.DataSetSink) DataSinkTable
DataInfoDouble(String, Dimension) DataDouble.DataInfoDouble
DataInfoDoubleArray(String, Dimension, int[]) DataDoubleArray.DataInfoDoubleArray
DataInfoDoubleArrayFactory(DataDoubleArray.DataInfoDoubleArray) DataDoubleArray.DataInfoDoubleArrayFactory
DataInfoDoubleBDArray(String, Dimension, int[], int) DataDoubleBDArray.DataInfoDoubleBDArray
DataInfoDoubleBDArrayFactory(DataDoubleBDArray.DataInfoDoubleBDArray) DataDoubleBDArray.DataInfoDoubleBDArrayFactory
DataInfoDoubleFactory(DataDouble.DataInfoDouble) DataDouble.DataInfoDoubleFactory
DataInfoFactory etomica.data
Interface for a mutable DataInfo factory.
DataInfoFactory(IDataInfo) DataInfoFactory
Creates a new instance using the info held by the template.
DataInfoFunction(String, Dimension, DataSourceIndependent) DataFunction.DataInfoFunction
DataInfoFunctionFactory(DataFunction.DataInfoFunction) DataFunction.DataInfoFunctionFactory
dataInfoGroup DataGroupSplitter
dataInfoGroup MeterTiltRotationHistogram
DataInfoGroup(String, Dimension, IDataInfo[]) DataGroup.DataInfoGroup
DataInfoGroupFactory(DataGroup.DataInfoGroup) DataGroup.DataInfoGroupFactory
DataInfoTable(String, IDataInfo[], int, String[]) DataTable.DataInfoTable
DataInfoTableFactory(DataTable.DataInfoTable) DataTable.DataInfoTableFactory
DataInfoTensor(String, Dimension, Space) DataTensor.DataInfoTensor
DataInfoTensorFactory(DataTensor.DataInfoTensor) DataTensor.DataInfoTensorFactory
DataInfoVector(String, Dimension, Space) DataVector.DataInfoVector
DataInfoVectorFactory(DataVector.DataInfoVector) DataVector.DataInfoVectorFactory
dataInterval LJMD.LJMDParams
dataInterval PistonCylinderGraphic
DataLogger etomica.data
DataSink that manages a FileWriter and also listens to non-interval
integrator events and sends appropriate data to a DataWriter.
DataLogger() DataLogger
DataLogger.DataWriter etomica.data
Interface for a DataSink that actually writes data to a file
dataOverlap SimOverlapModule
DataOverlap etomica.overlap
Utility class for overlap sampling.
DataOverlap(DataOverlap.DataSourceOverlapAvg, DataOverlap.DataSourceOverlapAvg, AlphaSource) DataOverlap
DataOverlap.DataSourceOverlapAvg etomica.overlap
Interface for a class capable of return the average and uncertainty for
a particular value of alpha.
DataOverlap.DataSourceOverlapAvgCollapsing etomica.overlap
Implementation of DataSourceOverlapLogAvg that retrieves data from a
splitter whose data is dumped into different
AccumulatorAverageCollapsingLog instances.
DataOverlap.DataSourceOverlapAvgCollapsingSplit etomica.overlap
DataOverlap.DataSourceOverlapAvgSimple etomica.overlap
Implementation of DataSourceOverlapAvg that retrieves data from a single
AccumulatorAverage
DataOverlap.DataSourceOverlapLogAvg etomica.overlap
Interface for a class capable of return the average and uncertainty as
well as the log of the average and the uncertainty in the log, for
a particular value of alpha.
DataOverlapCaching etomica.modules.multiharmonic.overlap
DataOverlap subclass that caches return values.
DataOverlapCaching(DataOverlap.DataSourceOverlapAvg, DataOverlap.DataSourceOverlapAvg, AlphaSource, IntegratorOverlap) DataOverlapCaching
DataPipe etomica.data
Interface for an object through which data can flow.
DataPipeForked etomica.data
DataPipeStressStrain(Sam) SamGraphic.DataPipeStressStrain
DataPlumbing(DataPumpListener, DataDump, UUID) DataStreamStore.DataPlumbing
DataProcessAHT(MultiharmonicGraphicMC.DataSourceUa, HistoryCollapsingDiscard) MultiharmonicGraphicMC.DataProcessAHT
DataProcessor etomica.data
An object that receives Data, processes it, and pushes the result on to a
DataSink.
DataProcessor() DataProcessor
DataProcessorBias etomica.modules.multiharmonic
Data Processor which calculates the bias in the incoming data based on the
true value of the free energy calculated from the
DataProcessorBias(DataSourceScalar) DataProcessorBias
DataProcessorBoltzmannFactor etomica.normalmode
DataProcessorBoltzmannFactor() DataProcessorBoltzmannFactor
DataProcessorBounds etomica.modules.multiharmonic
Calculates upper or lower bound of the incoming data based on the standard
deviation obtained from the accumulator.
DataProcessorBounds etomica.modules.statistics
DataProcessorBounds() DataProcessorBounds
DataProcessorBounds(IDataSink[]) DataProcessorBounds
DataProcessorCavity etomica.cavity
This processor scales up the measured cavity function so that its contact
value is equal to the RDF contact value.
DataProcessorCavity(IntegratorHard) DataProcessorCavity
DataProcessorChemicalPotential etomica.data
DataProcessor that takes as input the average density and average Boltzmann
factor profiles and calculates the chemical potential profile as the sum of
the ideal gas contribution (kT ln()) and the excess chemical
potential, (-kT ln()).
DataProcessorChemicalPotential() DataProcessorChemicalPotential
DataProcessorCorrection(int) LjMd3D.DataProcessorCorrection
DataProcessorCvMD etomica.eam
DataProcessorCvMD() DataProcessorCvMD
DataProcessorDyDLnx etomica.modules.multiharmonic
Calculates dy/dlnx vs.
DataProcessorDyDLnx() DataProcessorDyDLnx
DataProcessorErrorBar etomica.cavity
DataProcessorErrorBar(String) DataProcessorErrorBar
DataProcessorForked etomica.data
A DataProcessor that can handle multiple sinks, passing the same Data to each.
DataProcessorForked() DataProcessorForked
DataProcessorFunction etomica.data
Applies a simple scalar function to all elements of the Data
that passes through.
DataProcessorFunction(IFunction) DataProcessorFunction
DataProcessorGContactP etomica.cavity
DataProcessor that determines g(sigma) from P (measured with the virial)
DataProcessorGContactP(Box) DataProcessorGContactP
DataProcessorInterfacialTension etomica.data
Data Processor that takes the virial components as input data and returns
the interfacial tension.
DataProcessorInterfacialTension(Space) DataProcessorInterfacialTension
DataProcessorInterfacialTensionProfile etomica.modules.interfacial
DataProcessorInterfacialTensionProfile(Space) DataProcessorInterfacialTensionProfile
DataProcessorMu etomica.modules.statistics
DataProcessor that takes in and spits out
mu = -T*ln
DataProcessorMu(AccumulatorHistory, IntegratorBox) MuGraphic.DataProcessorMu
DataProcessorMu(IntegratorBox) DataProcessorMu
DataProcessorPContactG etomica.cavity
DataProcessor that determines g(sigma) from P (measured with the virial)
DataProcessorPContactG(Box) DataProcessorPContactG
DataProcessorR2() VirialPolyhedra.DataProcessorR2
DataProcessorR2() VirialPolyhedra2.DataProcessorR2
DataProcessorReweight etomica.liquidLJ
Takes incoming data, computes weight for configuration based on various
cutoffs, multiplies each incoming data by the weight and also adds
weights as extra data.
DataProcessorReweight(double, LjMd3D.ValueCache, LjMd3D.ValueCache, double, double, double, Box, IFunction) LjMd3D.DataProcessorReweight
DataProcessorReweight(double, ValueCache, double[], Box, int) DataProcessorReweight
DataProcessorReweightRatio etomica.liquidLJ
Takes incoming data sums including a weight sum for each cutoff,
computes averages as sum/(weight sum)
DataProcessorReweightRatio(int) DataProcessorReweightRatio
DataProcessorReweightRatio(int, int) DataProcessorReweightRatio
DataProcessorSum etomica.normalmode
DataProcessor that sends on the sum of the incoming data values as a scalar.
DataProcessorSum() DataProcessorSum
DataProcessorSurfaceTension etomica.surfacetension
DataProcessorSurfaceTension() DataProcessorSurfaceTension
DataProcessorTensorSplitter() DropletGraphic.DataProcessorTensorSplitter
DataProcessorTensorSplitter() InterfacialSWGraphic.DataProcessorTensorSplitter
DataProcessorTensorTrace() GlassGraphic.DataProcessorTensorTrace
DataProcessorTensorTrace() LjmdGraphic.DataProcessorTensorTrace
DataProcessorUndo(double) StatisticsMCGraphic.DataProcessorUndo
DataProcessorVar etomica.modules.multiharmonic
Data Processor whose sole purpose in life is to discard the incoming data
and push on the standard deviation from the accumulator.
DataProcessorVar() DataProcessorVar
DataProcessorVirialOverlap 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) DataProcessorVirialOverlap
DataProcessorWidomContact etomica.cavity
DataProcessorWidomContact() DataProcessorWidomContact
DataProcessorWidomContact.GContactSink etomica.cavity
DataProcessorXY etomica.metastable
DataProcessorXY(DataDump) DataProcessorXY
dataPump DisplayTimer
DataPump etomica.data
A DataProcessor whose action is to actively take Data from a DataSource and send it to
DataSinks.
DataPump(IDataSource, IDataSink) DataPump
Constructs DataPump with the given DataSource and
DataSink.
dataPumpA MultiharmonicMC
DataPumpListener etomica.data
DataPumpListener(IDataSource, IDataSink) DataPumpListener
DataPumpListener(IDataSource, IDataSink, int) DataPumpListener
DataPumpListenerPow etomica.data
DataPump class that takes data at steps 2^i, i=0,1,2,3...
DataPumpListenerPow(IDataSource, IDataSink) DataPumpListenerPow
DataPumpListenerPow(IDataSource, IDataSink, long, int, int) DataPumpListenerPow
DataPumpListenerPowStrict etomica.data
DataPump class that takes data at steps pow^i, i=0,1,2,3...
DataPumpListenerPowStrict(IDataSource, IDataSink) DataPumpListenerPowStrict
DataPumpListenerPowStrict(IDataSource, IDataSink, int) DataPumpListenerPowStrict
DataPumpListenerSmart etomica.data
Works with an instance of HistoryCollapsingDiscard to only retrieve new data
from the datasource when the history will actually use the data.
DataPumpListenerSmart(IDataSource, IDataSink, int, HistoryCollapsingDiscard) DataPumpListenerSmart
DataPumpListenerSmart(IDataSource, IDataSink, HistoryCollapsingDiscard) DataPumpListenerSmart
dataPumps DataTableAverages
dataseparator Token
DataSerializer etomica.server.serializers
DataSerializer() DataSerializer
dataSet DisplayPlot
DataSet etomica.data
Receives and organizes data from multiple streams.
DataSet() DataSet
DataSet.DataSetSink etomica.data
A special DataSink used by the DataSet to receive Data and DataInfo
from a single stream.
DataSetListener etomica.data
Interface for a class that performs some action in response to
a change in a DataSet instance.
DataSetSink(DataSet) DataSet.DataSetSink
DataSetSink(DataSet, String) DataSet.DataSetSink
dataSink DataProcessor
dataSink SimulationVirial
DataSinkBlockAveragerSFac etomica.modules.glass
DataSinkBlockAveragerSFac(ConfigurationStorage, int, MeterStructureFactor) DataSinkBlockAveragerSFac
DataSinkBlockAveragerSFac.Sink etomica.modules.glass
DataSinkConsole etomica.data
Writes data to console or another print stream.
DataSinkConsole() DataSinkConsole
Makes class using System.out as the default output stream.
DataSinkConsole(PrintStream) DataSinkConsole
Constructor that permits specification of the output printstream.
DataSinkExcludeOverlap() NucleationGraphic.DataSinkExcludeOverlap
DataSinkExcludeOverlap() SwmdGraphic.DataSinkExcludeOverlap
DataSinkExcludeOverlap(Box) MuGraphic.DataSinkExcludeOverlap
DataSinkExcludeOverlap(Box) ReverseOsmosisGraphic.DataSinkExcludeOverlap
DataSinkExcludeOverlap(Box) ReverseOsmosisWaterGraphic.DataSinkExcludeOverlap
dataSinkFactory DataDistributer
dataSinkFactory DataSplitter
dataSinkList DataFork
DataSinkReweightedDeltaU(AlphaSource) MultiharmonicGraphicMC.DataSinkReweightedDeltaU
dataSinks DataDistributer
dataSinks DataGroupSplitter
dataSinks DataSplitter
DataSinkTable etomica.data
Receives data from multiple streams and organizes it in the form of a table,
with each stream of data forming a column of the table.
DataSinkTable() DataSinkTable
dataSource DataPump
dataSourceA MeterUmbrella
DataSourceAcceptanceProbability etomica.data
Data source giving the average acceptance probability of MCMove type moves.
DataSourceAcceptanceProbability() DataSourceAcceptanceProbability
Constructs with no MCMove specified.
DataSourceAcceptanceProbability(MCMove) DataSourceAcceptanceProbability
DataSourceAcceptanceRatio etomica.data
Data source giving the acceptance rate of MCMove type moves.
DataSourceAcceptanceRatio() DataSourceAcceptanceRatio
Constructs with no MCMove specified.
DataSourceAcceptanceRatio(MCMove) DataSourceAcceptanceRatio
DataSourceAlpha2 etomica.modules.glass
Computes the excess kurtosis (alpha2) for the distribution of displacements
DataSourceAlpha2(ConfigurationStorage) DataSourceAlpha2
DataSourceAlphaAlpha(DataOverlap) MultiharmonicGraphicMC.DataSourceAlphaAlpha
DataSourceAlphaAlpha(DataSourceVirialOverlap) MultiharmonicGraphicMC.DataSourceAlphaAlpha
DataSourceAlphaChi(MeterMBAR, MeterMBAR, boolean) MultiharmonicGraphicMC.DataSourceAlphaChi
DataSourceAlphaChi(DataOverlap, double) MultiharmonicGraphicMC.DataSourceAlphaChi
DataSourceAlphaChi(DataSourceVirialOverlap, double) MultiharmonicGraphicMC.DataSourceAlphaChi
DataSourceAlphaFE(AlphaSource, int) MultiharmonicGraphicMC.DataSourceAlphaFE
DataSourceAtomDistance etomica.data
DataSourceAtomDistance(Space) DataSourceAtomDistance
DataSourceAtomic etomica.data
Interface for a DataSource that can return a value given an arbitrary atom.
DataSourceAvgPressure etomica.normalmode
Averages the measured pressures for various N.
DataSourceAvgPressure(DataDistributer, MCMoveOverlapListener, double) DataSourceAvgPressure
DataSourceAvgPressure2 etomica.normalmode
Computes pressure from the grand canonical route based on measured free
energy differences and simulation parameters.
DataSourceAvgPressure2(DataDistributer, MCMoveOverlapListener, double, double) DataSourceAvgPressure2
dataSourceB MeterUmbrella
DataSourceBias(AlphaSource) MultiharmonicGraphicMC.DataSourceBias
DataSourceBlockAvgCor etomica.modules.glass
Measures correlation of blocks of increasing size.
DataSourceBlockAvgCor(IntegratorMD) DataSourceBlockAvgCor
DataSourceChiSlope(DataOverlap) MultiharmonicGraphicMC.DataSourceChiSlope
DataSourceCorMSD etomica.modules.glass
DataSourceCorMSD(IntegratorMD) DataSourceCorMSD
DataSourceCorrelation etomica.modules.glass
Computes correlation of two input data streams, expected to each be 2 values.
DataSourceCorrelation(ConfigurationStorage, int) DataSourceCorrelation
DataSourceCorrelation.Meter etomica.modules.glass
DataSourceCorrelation.Receiver etomica.modules.glass
DataSourceCount() AccumulatorHistory.DataSourceCount
DataSourceCountCollisions etomica.data
This is a data source to count the number of collisions processed by a
hard-potential integrator.
DataSourceCountCollisions() DataSourceCountCollisions
Sets up data source with no integrator specified.
DataSourceCountCollisions(IntegratorHard) DataSourceCountCollisions
DataSourceCountSteps etomica.data
Data source that fronts the Integrator's step count as a piece of Data.
DataSourceCountSteps() DataSourceCountSteps
Sets up data source to count integrator steps.
DataSourceCountSteps(Integrator) DataSourceCountSteps
DataSourceCountTime etomica.data
Data source that returns the elapsed simulation time of an MD integrator.
DataSourceCountTime(IntegratorMD) DataSourceCountTime
DataSourceDensityFunction etomica.modules.adsorption
DataSourceDensityFunction(EOSSW, double, double) DataSourceDensityFunction
DataSourceDensityFunction(EOSSW, double, double, boolean) DataSourceDensityFunction
DataSourceEnergies etomica.freeenergy.npath
Created by andrew on 4/12/17.
DataSourceEnergies(PotentialMaster) DataSourceEnergies
DataSourceEnergies.PotentialCalculationEnergies etomica.freeenergy.npath
DataSourceEnergies.PotentialCalculationEnergiesEAM etomica.freeenergy.npath
DataSourceExp(DataSourceUniform) MeterPressureByVolumeChange.DataSourceExp
DataSourceF etomica.modules.glass
Computes the excess kurtosis (alpha2) for the distribution of displacements
DataSourceF(ConfigurationStorage) DataSourceF
DataSourceFE etomica.normalmode
Free energy data source that computes free energy differences based on
overlap sampling performed by an MCMoveOverlapListener.
DataSourceFE(MCMoveOverlapListener) DataSourceFE
DataSourceFE(String, MeterMBAR, MeterMBAR, int) MultiharmonicGraphicMC.DataSourceFE
DataSourceFEHistogram etomica.normalmode
Returns a histogram of # of atoms based on free energy results and the given
chemical potential.
DataSourceFEHistogram(MCMoveOverlapListener, double) DataSourceFEHistogram
DataSourceFOld etomica.modules.glass
Computes the excess kurtosis (alpha2) for the distribution of displacements
DataSourceFOld(ConfigurationStorage) DataSourceFOld
DataSourceFs etomica.modules.glass
Computes the excess kurtosis (alpha2) for the distribution of displacements
DataSourceFs(ConfigurationStorage) DataSourceFs
DataSourceFunction etomica.data
Datasource formed as a wrapper around a function.
DataSourceFunction() DataSourceFunction
DataSourceFunction(IFunction) DataSourceFunction
DataSourceFunction(String, Dimension, IFunction, int) DataSourceFunction
DataSourceFunction(String, Dimension, IFunction, int, String, Dimension) DataSourceFunction
DataSourceFunctionRaw(double[], double[]) MultiharmonicGraphicMC.DataSourceFunctionRaw
DataSourceGroup etomica.data
Collects one or more data sources into a single DataSource.
DataSourceGroup() DataSourceGroup
Forms a DataSourceGroup that contains no data sources, and which will give
an empty DataGroup for getData.
DataSourceGroup(IDataSource[]) DataSourceGroup
Forms a DataGroup containing the given data sources.
DataSourceHisogram etomica.modules.glass
DataSourceHisogram(IntegratorMD) DataSourceHisogram
DataSourceHisogram(IntegratorMD, int) DataSourceHisogram
DataSourceHistogramMSD etomica.modules.glass
DataSourceHistogramMSD(IntegratorMD) DataSourceHistogramMSD
DataSourceImposedFEFit etomica.normalmode
Like DataSourceFEHistogram, returns a probability histogram for N based on
free energies.
DataSourceImposedFEFit(MCMoveOverlapListener, MCMoveInsertDeleteBiased, double) DataSourceImposedFEFit
DataSourceImposedFEHistogram etomica.normalmode
This is a strange creature...
DataSourceImposedFEHistogram(MCMoveOverlapListener, MCMoveInsertDeleteBiased, double) DataSourceImposedFEHistogram
DataSourceIndependent etomica.data
Interface for an object that can provide X Data objects on request.
DataSourceIndependentSimple etomica.data
A simple implementation of DataSourceIndependent objects can use if they
cannot act as the DataSourceIndependent themselves (if perhaps they make
multiple DataFunctions)
DataSourceIndependentSimple(double[][], DataDoubleArray.DataInfoDoubleArray[]) DataSourceIndependentSimple
DataSourceIndependentSimple(double[], DataDoubleArray.DataInfoDoubleArray) DataSourceIndependentSimple
DataSourceIndex etomica.meta
DataSourceIndex(Class<IDataSource>) DataSourceIndex
dataSourceInfo DataPump
DataSourceMolecular etomica.data
Interface for a DataSource that can return a value given an arbitrary atom.
DataSourceMSD etomica.modules.glass
DataSourceMSD(ConfigurationStorage) DataSourceMSD
DataSourceMSD(ConfigurationStorage, AtomType) DataSourceMSD
DataSourceMSD.MSDSink etomica.modules.glass
DataSourceMSDcorP etomica.modules.glass
DataSourceMSDcorP(IntegratorMD) DataSourceMSDcorP
DataSourceMSDcorP(IntegratorMD, int) DataSourceMSDcorP
DataSourceMSDcorP.DataSourceMSDcovP etomica.modules.glass
Returns the covariance of the MSD with P, divided by t
DataSourceMSDcovP() DataSourceMSDcorP.DataSourceMSDcovP
DataSourceMuRoot 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) DataSourceMuRoot
DataSourceMuRoot.DataSourceMuRootDPressure etomica.normalmode
DataSourceMuRoot.DataSourceMuRootDU etomica.normalmode
DataSourceMuRoot.DataSourceMuRootPressure etomica.normalmode
DataSourceMuRoot.DataSourceMuRootVacancyConcentration etomica.normalmode
DataSourceMuRoot1 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) DataSourceMuRoot1
DataSourceMuRoot1.DataSourceMuRootPressure etomica.normalmode
DataSourceMuRoot1.DataSourceMuRootVacancyConcentration etomica.normalmode
DataSourceMuRootDPressure() DataSourceMuRoot.DataSourceMuRootDPressure
DataSourceMuRootDU() DataSourceMuRoot.DataSourceMuRootDU
DataSourceMuRootPMatch 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) DataSourceMuRootPMatch
DataSourceMuRootPMatch.DataSourceMuRootPressure etomica.normalmode
DataSourceMuRootPMatch.DataSourceMuRootVacancyConcentration etomica.normalmode
DataSourceMuRootPressure() DataSourceMuRoot.DataSourceMuRootPressure
DataSourceMuRootPressure() DataSourceMuRoot1.DataSourceMuRootPressure
DataSourceMuRootPressure() DataSourceMuRootPMatch.DataSourceMuRootPressure
DataSourceMuRootVacancyConcentration() DataSourceMuRoot.DataSourceMuRootVacancyConcentration
DataSourceMuRootVacancyConcentration() DataSourceMuRoot1.DataSourceMuRootVacancyConcentration
DataSourceMuRootVacancyConcentration() DataSourceMuRootPMatch.DataSourceMuRootVacancyConcentration
DataSourceOverlapAvgCollapsing() DataOverlap.DataSourceOverlapAvgCollapsing
DataSourceOverlapAvgCollapsingSplit(DataSplitter) DataOverlap.DataSourceOverlapAvgCollapsingSplit
DataSourceOverlapAvgSimple(AccumulatorAverage) DataOverlap.DataSourceOverlapAvgSimple
DataSourcePercolation etomica.modules.glass
DataSourcePercolation(ConfigurationStorage, AtomTestDeviation, int) DataSourcePercolation
DataSourcePercolation(ConfigurationStorage, AtomTestDeviation, int, HistogramNotSoSimple) DataSourcePercolation
DataSourcePercolation.Chi4Source etomica.modules.glass
DataSourcePercolation.ImmFractionByTypeSource etomica.modules.glass
DataSourcePercolation.ImmFractionSource etomica.modules.glass
DataSourcePercolation.PercolationByImmFrac etomica.modules.glass
DataSourcePercolation0 etomica.modules.glass
This class checks for percolation of neighbors from a random set of particles.
DataSourcePercolation0(Box, IRandom) DataSourcePercolation0
DataSourcePMSDHistory etomica.modules.glass
DataSourcePMSDHistory(IntegratorMD) DataSourcePMSDHistory
DataSourcePMSDHistory(IntegratorMD, int) DataSourcePMSDHistory
DataSourcePMu 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) DataSourcePMu
DataSourcePN etomica.normalmode
DataSource that returns measured pressure as a function of N
DataSourcePN(DataDistributer, int) DataSourcePN
DataSourcePoints etomica.data
DataSourcePoints(String, Dimension, Dimension) DataSourcePoints
DataSourcePositioned etomica.data
Interface for a DataSource that can return a value given an arbitrary
position.
DataSourcePositionedBoltzmannFactor etomica.data
Calculates the Boltzmann factor at a position within a box a molecule of a
particular species would have if it existed at that point.
DataSourcePositionedBoltzmannFactor(Space) DataSourcePositionedBoltzmannFactor
DataSourcePrevTime etomica.modules.glass
DataSourcePrevTime(ConfigurationStorage) DataSourcePrevTime
DataSourceQ4 etomica.modules.glass
DataSourceQ4(ConfigurationStorage, int) DataSourceQ4
DataSourceQ4.MeterChi4 etomica.modules.glass
dataSourceRef MeterOverlap
dataSourceRefBias MultiharmonicGraphicMC
dataSourceRefFE MultiharmonicGraphicMC
dataSourceRefStdev MultiharmonicGraphicMC
DataSourceRmsVelocity etomica.data
Meter for the root-mean-square velocity of a set of atoms.
DataSourceRmsVelocity() DataSourceRmsVelocity
DataSourceRmsVelocity(Histogram) DataSourceRmsVelocity
DataSourceScalar etomica.data
Particular data source for which the data is a simple scalar of type double.
DataSourceScalar(String, Dimension) DataSourceScalar
DataSourceStrings etomica.modules.glass
DataSourceStrings(ConfigurationStorage, int) DataSourceStrings
dataSourceTarget MeterOverlap
dataSourceTargetBias MultiharmonicGraphicMC
dataSourceTargetFE MultiharmonicGraphicMC
dataSourceTargetStdev MultiharmonicGraphicMC
DataSourceTensorVirialHard etomica.data
A MeterTensor that returns the virial component of the pressure tensor for a hard potential.
DataSourceTensorVirialHard(Space) DataSourceTensorVirialHard
DataSourceTensorVirialHard(Space, IntegratorHard) DataSourceTensorVirialHard
DataSourceTensorVirialHardProfile etomica.modules.interfacial
A DataSource that collects the average virial tensor as a function of
position for one dimension.
DataSourceTensorVirialHardProfile(Space) DataSourceTensorVirialHardProfile
DataSourceTensorVirialHardProfile.DataSourceVirialProfile etomica.modules.interfacial
DataSourceUa(DataOverlap) MultiharmonicGraphicMC.DataSourceUa
DataSourceUa2(IntegratorOverlap, DataOverlap, AccumulatorAverage, AccumulatorAverage) MultiharmonicGraphicMC.DataSourceUa2
DataSourceUniform etomica.data
A DataSource object that provides a set of uniformly spaced values between
two limits.
DataSourceUniform() DataSourceUniform
Default constructor.
DataSourceUniform(String, Dimension) DataSourceUniform
DataSourceUniform(String, Dimension, int, double, double) DataSourceUniform
Constructs a DataSourceUniform using the indicated number of values
and x range, and INCLUSIVE limits.
DataSourceUniform(String, Dimension, int, double, double, DataSourceUniform.LimitType, DataSourceUniform.LimitType) DataSourceUniform
Constructs a DataSourceUniform using the indicated number of values,
x range, and limit types, with dataInfo indicating that the data have
the given dimension.
DataSourceUniform.LimitType etomica.data
Typed constant that indicates the way limits of the range are interpreted.
DataSourceVAC etomica.modules.glass
Computes the excess kurtosis (alpha2) for the distribution of displacements
DataSourceVAC(ConfigurationStorage) DataSourceVAC
DataSourceVaporDensity(String, Dimension) DropletAtomicGraphic.DataSourceVaporDensity
DataSourceVirialOverlap etomica.virial.overlap
Measures ratio of two cluster integrals using overlap sampling.
DataSourceVirialOverlap(AccumulatorVirialOverlapSingleAverage, AccumulatorVirialOverlapSingleAverage) DataSourceVirialOverlap
DataSourceVirialProfile(DataSourceTensorVirialHardProfile) DataSourceTensorVirialHardProfile.DataSourceVirialProfile
DataSourceWallPressure etomica.modules.pistoncylinder
data source front for virial sum from P1HardMovingBoundary
returns pressure exerted on the wall by atoms
DataSourceWallPressure(P1HardMovingBoundary, IntegratorHard) DataSourceWallPressure
DataSourceWallPressureCatalysis etomica.modules.catalysis
DataSourceWallPressureCatalysis(Space, ISpecies, ISpecies, AtomLeafAgentManager) DataSourceWallPressureCatalysis
DataSourceWallPressureMu etomica.modules.mu
DataSourceWallPressureMu(Space) DataSourceWallPressureMu
DataSplitter etomica.data
DataSink that takes a Data object and pushes each numerical value from the
incoming Data to a different stream.
DataSplitter() DataSplitter
DataSplitter.IDataSinkFactory etomica.data
DataStreamAction etomica.data
DataStreamAction() DataStreamAction
DataStreamResource etomica.server.resources.data
DataStreamResource(SimulationStore, DataStreamStore, DataSourceIndex) DataStreamResource
DataStreamStore etomica.server.dao
DataStreamStore() DataStreamStore
DataStreamStore.DataPlumbing etomica.server.dao
DataStreamWebsocket etomica.server.resources.data
DataStreamWebsocket(SimulationStore, DataStreamStore, ObjectMapper, ScheduledThreadPoolExecutor) DataStreamWebsocket
DataStreamWebsocket.DataAndInfoEncoder etomica.server.resources.data
dataTable DisplayTable
DataTable etomica.data.types
Data object that holds double[] arrays as if they are columns in a
table.
DataTable(int, int) DataTable
Creates a new table with a specified number of columns all of a given
length.
DataTable(DataDoubleArray[]) DataTable
DataTable.DataInfoTable etomica.data.types
DataTable.DataInfoTableFactory etomica.data.types
DataTableAverages etomica.data
Convenience class for a data table that collects the AccumulatorAverage
statistics for a collection of DataSource instances.
DataTableAverages(Integrator) DataTableAverages
Sets up table with default types that give the current value, the
average, and the error bars.
DataTableAverages(Integrator, int, ArrayList<DataPump>) DataTableAverages
DataTableAverages(Integrator, AccumulatorAverage.StatType[], int, IDataSource[], ArrayList<DataPump>) DataTableAverages
Sets up table with no sources.
DataTableListener etomica.data
Interface for a class that performs some action in response to
a change in a DataSinkTable instance.
DataTableWriter etomica.data
A DataWriter that writes out data as a table with optional column headings
DataTableWriter() DataTableWriter
DataTag etomica.data
Data stream identifier.
DataTag() DataTag
DataTagBag etomica.graphics
Simple class that associates a set of tags with an object (unit, label, etc)
DataTagBag(DataTag[], Object) DataTagBag
DataTensor etomica.data.types
Data object wrapping a single mutable value of type (Space) Tensor.
DataTensor(Space) DataTensor
Constructs a new instance with the given DataInfo, wrapping a new Tensor
instance from the given space.
DataTensor.DataInfoTensor etomica.data.types
DataTensor.DataInfoTensorFactory etomica.data.types
dataTrueEy AkimaSplineSmootherDyApp
dataVar DataProcessorVar
DataVector etomica.data.types
Data object wrapping a single mutable value of type (Space) Vector.
DataVector(Space) DataVector
Constructs a new instance with the given DataInfo, wrapping a new Vector
instance from the given space.
DataVector.DataInfoVector etomica.data.types
DataVector.DataInfoVectorFactory etomica.data.types
DataVirialOverlap 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) DataVirialOverlap
DataVirialOverlap.FullResult etomica.virial.overlap
dataWalkerAction(Object) ResetAccumulators
dataWalkerAction(Object) ResetAccumulatorsAveraged
dataWalkerAction(Object) DataStreamAction
DataWriter(int, DisplayPlot) DisplayPlot.DataWriter
dataWV NormalModeAnalysisDisplay3DGraphic
date JmolConstants
davg DataProcessorWidomContact
dAxc0 PotentialCalculationHeisenberg
dAxc0 PotentialCalculationMoleculeAgentSum
dAxc0 PotentialCalculationMoleculeAgentSumPair
dAxc0 PotentialCalculationPair
dAxc0 PotentialCalculationVSum
dAxc1 PotentialCalculationHeisenberg
dAxc1 PotentialCalculationMoleculeAgentSum
dAxc1 PotentialCalculationMoleculeAgentSumPair
dAxc1 PotentialCalculationPair
dAxc1 PotentialCalculationVSum
dAxs0 PotentialCalculationHeisenberg
dAxs0 PotentialCalculationMoleculeAgentSum
dAxs0 PotentialCalculationMoleculeAgentSumPair
dAxs0 PotentialCalculationPair
dAxs0 PotentialCalculationVSum
dAxs1 PotentialCalculationHeisenberg
dAxs1 PotentialCalculationMoleculeAgentSum
dAxs1 PotentialCalculationMoleculeAgentSumPair
dAxs1 PotentialCalculationPair
dAxs1 PotentialCalculationVSum
dAyc0 PotentialCalculationHeisenberg
dAyc0 PotentialCalculationMoleculeAgentSum
dAyc0 PotentialCalculationMoleculeAgentSumPair
dAyc0 PotentialCalculationPair
dAyc0 PotentialCalculationVSum
dAyc1 PotentialCalculationHeisenberg
dAyc1 PotentialCalculationMoleculeAgentSum
dAyc1 PotentialCalculationMoleculeAgentSumPair
dAyc1 PotentialCalculationPair
dAyc1 PotentialCalculationVSum
dAys0 PotentialCalculationHeisenberg
dAys0 PotentialCalculationMoleculeAgentSum
dAys0 PotentialCalculationMoleculeAgentSumPair
dAys0 PotentialCalculationPair
dAys0 PotentialCalculationVSum
dAys1 PotentialCalculationHeisenberg
dAys1 PotentialCalculationMoleculeAgentSum
dAys1 PotentialCalculationMoleculeAgentSumPair
dAys1 PotentialCalculationPair
dAys1 PotentialCalculationVSum
dbc P1LepsHarmonic
DBDEN Gamma
DBNUM Gamma
DBO2C2 BiasVolume2SiteAceticAcid
DBO2H1 BiasVolume2SiteAceticAcid
DC Gamma
dc11 MeterSolidPropsLJ
DCF etomica.virial.cluster
Main method that simply generates and displays the graphs in the direct
correlation function.
DCF() DCF
dcom MCMoveClusterRingPartialRegrow
DCVGCMD etomica.dcvgcmd
Dual-control-volume grand-canonical molecular dynamics simulation.
DCVGCMD etomica.modules.dcvgcmd
Dual-control-volume grand-canonical molecular dynamics simulation.
DCVGCMD() DCVGCMD
DCVGCMD() DCVGCMD
DCVGCMDGraphic etomica.dcvgcmd
DCVGCMDGraphic etomica.modules.dcvgcmd
DCVGCMDGraphic(DCVGCMD, Space) DCVGCMDGraphic
DCVGCMDGraphic(DCVGCMD, Space) DCVGCMDGraphic
DCVGCMDGraphic.Applet etomica.modules.dcvgcmd
dd AkimaSplineSmootherApp.PlotAction
dd AkimaSplineSmootherDyApp.PlotAction
dd(int, double, double) P2HydrogenPatkowski
dd(int, double, double) P2HydrogenPatkowskiAtomic
dda MeterUmbrella
ddamp(int, double, double) P2WaterSzalewicz.P2H2OSC
dDimension() DimensionRatio
ddP MeterSolidProps
ddP MeterSolidPropsLJ
DE(double) IData
Divide-equals (*=) operation, dividing all values in data by given
value.
DE(double) DataDouble
Divide-equals (/=) operation.
DE(double) DataDoubleArray
Divide-equals (*=) operation.
DE(double) DataDoubleBDArray
Times-equals (*=) operation.
DE(double) DataGroup
DE(double) DataTensor
Divide-equals (*=) operation.
DE(double) DataVector
Divide-equals (*=) operation.
DE(IData) IData
Divide-equals (/=) operation.
DE(IData) DataDouble
Divide-equals (/=) operation.
DE(IData) DataDoubleArray
Divide-equals (/=) operation.
DE(IData) DataDoubleBDArray
Divide-equals (/=) operation.
DE(IData) DataGroup
DE(IData) DataTensor
Divide-equals (/=) operation.
DE(IData) DataVector
Divide-equals (/=) operation.
DE(Tensor) Tensor
"Divide equals" (/=) operation, element-by-element.
DE(Tensor) Tensor1D
DE(Tensor) Tensor2D
DE(Tensor) Tensor3D
DE(Tensor) TensorND
DE(Vector) Vector
Divide-equals (/=) operation.
DE(Vector) Vector1D
DE(Vector) Vector2D
DE(Vector) Vector3D
DE(Vector) VectorND
DE(IBigValue) BigValue
Divide-equals (/=) operation.
DE(IBigValue) IBigValue
Divide-equals (/=) operation.
DE(IBigValue) MyBigDecimal
Divide-equals (/=) operation.
deactivate() Grabber.ActionCornerSetter
debug MCMoveMoleculeRotateAssociated
debug P2CO2Hellmann
debug P2WaterSzalewicz
debug PotentialCalculationEnergySum
debug ClusterSum
debug ClusterSumPolarizableWertheimProduct4Pt
debug ClusterWheatleySoft
debug ClusterWheatleySoftDerivatives
debug ClusterWheatleySoftDerivativesBD
debug MayerGeneral
debug Token
debug(String) DefaultLogger
debug(String) Logger
Writes a log at DEBUG level.
debug(String) LoggerInterface
Writes a log at DEBUG level.
Debug etomica.util
Class holding static fields that determine whether debugging is on, how
much, what types and what (if anything) should be looked at specifically.
Debug() Debug
DEBUG_MODE ParserImpl
DEBUG_MODE IsomorphismFilter
DEBUG_NOW Debug
true if debugging is currently enabled (when the integrator reaches step START)
debugging P2CO2H2OWheatley
debugging Logger
debuggingHigh Logger
debugme PNCO2GCPM
debugme PNGCPM
debugMoleculePair Debug
debugPair Debug
debugscript Token
Debye etomica.units
The debye unit of electrical dipole moment, equal to 10^-18 statC-cm,
or 3.33564e-30 C-m.
dec() Bitmap
Decrements the integer value of this bitmap by one: bitmap--.
dec() AbstractBitmap
decapitalize(String) Strings
Converts the first letter of the given string to lower case.
DECI Prefix
decimal Token
Decimal etomica.units
Decimal representation of something that represents the fractional
amount of a whole (e.g., mole fraction) as a decimal value typically
between 0 and 1.
DecimalSlider etomica.graphics
Slider that permits variation of decimal (non-integer) values.
DecimalSlider() DecimalSlider
DecimalSlider(int) DecimalSlider
Decorate etomica.graph.operations
Performs decoration of diagrams by points.
Decorate() Decorate
Decorate.DecorateParameters etomica.graph.operations
DecorateNaphthalene2Site(MulFlexible.MulFlexibleParameters, char, char, char, char, Set<Graph>, Set<Graph>, Set<Graph>) DecorateWertheimNaphthalene2Rho.DecorateNaphthalene2Site
DecorateParameters(char, MulFlexible.MulFlexibleParameters) Decorate.DecorateParameters
DecorateParameters(int, MulFlexible.MulFlexibleParameters) Decorate.DecorateParameters
DecorateWertheim2Site etomica.graph.operations
Performs decoration of diagrams by various density points.
DecorateWertheim2Site() DecorateWertheim2Site
DecorateWertheim2Site.DecorateWertheimParameters2Site etomica.graph.operations
DecorateWertheim2SiteRho etomica.graph.operations
Performs decoration of diagrams by various density points.
DecorateWertheim2SiteRho() DecorateWertheim2SiteRho
DecorateWertheim2SiteRho.DecorateWertheimParameters2Site etomica.graph.operations
DecorateWertheim3SiteRho etomica.graph.operations
Performs decoration of diagrams by various density points.
DecorateWertheim3SiteRho() DecorateWertheim3SiteRho
DecorateWertheim3SiteRho.DecorateWertheimParameters3Site etomica.graph.operations
DecorateWertheimNaphthalene2Rho etomica.graph.operations
modified from Hye Min's DecorateWertheim2SiteRho class
Performs decoration of diagrams by various density points.
DecorateWertheimNaphthalene2Rho() DecorateWertheimNaphthalene2Rho
DecorateWertheimNaphthalene2Rho.DecorateNaphthalene2Site etomica.graph.operations
DecorateWertheimParameters2Site(int, MulFlexible.MulFlexibleParameters, char, char, Set<Graph>, Set<Graph>, Set<Graph>) DecorateWertheim2Site.DecorateWertheimParameters2Site
DecorateWertheimParameters2Site(MulFlexible.MulFlexibleParameters, char, char, Set<Graph>, Set<Graph>, Set<Graph>) DecorateWertheim2SiteRho.DecorateWertheimParameters2Site
DecorateWertheimParameters3Site(MulFlexible.MulFlexibleParameters, char, char, char, char, char, char, char, char, Set<Graph>, Set<Graph>, Set<Graph>, Set<Graph>, Set<Graph>, Set<Graph>, Set<Graph>) DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
decrementCollisionTime(double) IntegratorHard.Agent
Decreases the recorded time to collision of this atom
This action is performed when the atom is advanced without a collision
def EllipseDisplayAction
DEF_ISOMORPHISM_ALGO Match
DEFAULT_ATOM_COLOR ColorScheme
DEFAULT_BOND_MILLIANGSTROM_RADIUS JmolConstants
DEFAULT_BOND_RADIUS JmolConstants
DEFAULT_BOND_TOLERANCE JmolConstants
DEFAULT_FONTFACE JmolConstants
DEFAULT_FONTSTYLE JmolConstants
DEFAULT_HEIGHT SVGConverter
Default height
DEFAULT_HELP_PATH JmolConstants
DEFAULT_MAX_CONNECT_DISTANCE JmolConstants
DEFAULT_MAX_TEMPERATURE DeviceThermoSlider
DEFAULT_MIN_BOND_DISTANCE JmolConstants
DEFAULT_MIN_CONNECT_DISTANCE JmolConstants
DEFAULT_MIN_TEMPERATURE DeviceThermoSlider
DEFAULT_PERCENT_VDW_ATOM JmolConstants
DEFAULT_QUALITY SVGConverter
Default quality value.
DEFAULT_RESULT_TYPE SVGConverter
Default result type
DEFAULT_SIZE LatticeEditor
DEFAULT_STEREO_DEGREES EnumStereoMode
DEFAULT_STRUT_RADIUS JmolConstants
DEFAULT_WIDTH SVGConverter
Default width
defaultAdjustInterval MCMoveStepTracker
defaultAdjustStep MCMoveStepTracker
defaultanglelabel Token
defaultAtomFactory(Space, boolean) SpeciesGeneral
defaultColor ColorScheme
defaultcolorscheme Token
defaultColorsUsed ColorSchemeByType
defaultdirectory Token
defaultdistancelabel Token
defaultdrawarrowscale Token
defaultdropscript Token
defaultFileName() DataLogger
defaultFontFamily SVGConverter
Default value for the font-family when it is unspecified
defaultIOUnit() DataSourceAcceptanceProbability
defaultIOUnit() DataSourceAcceptanceRatio
DefaultIterator etomica.graph.iterators
DefaultIterator(byte) DefaultIterator
DefaultIterator(byte, byte) DefaultIterator
defaultlabelpdb Token
defaultlabelxyz Token
defaultlattice Token
defaultloadfilter Token
defaultloadscript Token
DefaultLogger org.jmol.util
Default implementation of the logger.
DefaultLogger() DefaultLogger
defaultMouseListener Grabber
DefaultMouseListener(Grabber) Grabber.DefaultMouseListener
DefaultPermutator etomica.graph.iterators
DefaultPermutator(int[]) DefaultPermutator
defaults Token
defaultstructuredssp Token
DefaultSVGConverterController etomica.graph.view.rasterizer
Default controller for the
SVGConverter operation.
DefaultSVGConverterController() DefaultSVGConverterController
DefaultToolbar etomica.graphics
DefaultToolbar() DefaultToolbar
DefaultToolbar(JPanel, String) DefaultToolbar
defaulttorsionlabel Token
defaulttranslucent Token
defaultValue() EnumPotentialParamDescription
defaultvdw Token
defBit(int, boolean) Bitmap
defBit(int, boolean) AbstractBitmap
defdfmt ScientificFormat
defefmt ScientificFormat
define Token
deform(Tensor) BoundaryDeformablePeriodic
Applies the given deformation tensor to the boundary in its current
shape.
deformation ConfigurationDroplet
degree MCMoveClusterAtomHSTree
degree MCMoveClusterPolyhedraTree
degree() BigIntegerPoly
Polynomial degree.
Degree etomica.units
Standard degree angular unit, such that for example a right angle is 90 degrees.
DEKA Prefix
del_r CalcFFT
delayExponent DeviceDelaySlider
delaymaximumms Token
delete Token
Delete etomica.graph.operations
Delete() Delete
deleteBits(BitSet, BitSet) BitSetUtil
this one slides deleted bits out of a pattern.
deleteCandidates MCMoveInsertDeleteLatticeVacancy
deleteCandidates MCMoveInsertDeleteVacancy
deleteCandidateSet MCMoveInsertDeleteVacancy
deleteCandidateTimes MCMoveInsertDeleteLatticeVacancy
deleteCandidateTimes MCMoveInsertDeleteVacancy
deleteConnection(int, int) ClusterDiagram
Deletes a connection from one node1 to node2.
deleteEdge(byte) Graph
deleteEdge(byte) GraphImpl
deleteEdge(byte, byte) Graph
deleteEdge(byte, byte) GraphImpl
DeleteEdge etomica.graph.operations
Deletes all edges of a given color.
DeleteEdge() DeleteEdge
DeleteEdgeParameters etomica.graph.operations
DeleteEdgeParameters(char) DeleteEdgeParameters
deleteElements(Object, int, int) ArrayUtil
deleteInstance(String) SimulationResource
deleteRow(int) DeviceTableModelGeneric
Delete an entire row from the table
delta IntegratorDimerApproach
delta MCMoveRotateMoleculePhiTheta
delta1 P2NitrogenShellModel
delta1 MCMoveSingleMode
delta2 P2NitrogenShellModel
delta2 MCMoveSingleMode
deltaA(double, double, int) HardSphere
Returns the difference between absolute free energies between the given
densities for solid (FCC) hard spheres.
deltaBMu DataSourcePMu
deltaCut2 ClusterSumNonAdditiveTrimerEnergy
deltaCut2 ClusterSumPolarizable
deltaCut2 ClusterSumPolarizableWertheimProduct
deltaCut2 ClusterSumPolarizableWertheimProduct4Pt
deltaCut2 ClusterSumPolarizableWertheimProduct4PtFinal
deltaEps P2PenetrableSquareWell
deltaMomentum MeterCavityMapped
deltaMomentum MeterRDFMapped
deltaMu LjMd3D.DataProcessorReweight
deltaP LjMd3D.DataProcessorReweight
deltaR IntegratorDimerMin
deltaR IntegratorDimerRT
deltaTheta IntegratorDimerMin
deltaTheta IntegratorDimerRT
deltaU CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
deltaU CalcNumerical2ndDerivative
deltaU CalcNumerical2ndDerivativeNitrogen
deltaU FiniteDifferenceDerivativeCGNitrogenBeta
deltaU MCMoveSingleMode
deltaV IntegratorDimerRT
deltaX BoxInflateAnisotropic
deltaX HistogramNotSoSimple
deltaX HistogramReweightedData
deltaX HistogramSimple
deltaXl IntegratorDimerRT
deltaXmax IntegratorDimerRT
denom() Rational
Get the denominator.
denominator Rational
denominator() Rational
Returns the denominator.
denomSum MeterWorkHarmonicBennet
denomSum MeterWorkHarmonicTargetandReweighting
denomSum MeterWorkTargetBennet
denomSum MeterWorkTargetHarmonicandReweighting
denomSum MeterWorkUmbrellaHarmonic
denomSum MeterWorkUmbrellaTarget
dense P2QChemInterpolated
density CH4NVT.Param
density DHS_NVT.Param
density DLJ_NVT_1site.Param
density TestAceticAcidMC3D_NPT.AceticAcidMCParam
density SimGCPMWaterMCNPT.GCPMWaterMCParam
density SimGCPMWaterMCNVT.GCPMWaterMCParam
density TestIGAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
density TestLJAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
density TestLJAssociationMC3D_NPT.VirialAssociatingFluidParam
density TestLJAssociationMC3D_NVTOld.VirialAssociatingFluidParam
density HSMDCavity.CavityParam
density HSMDWidom.HSMDParam
density DHS_NVT.Param
density DLJ_NVT_1site.Param
density TIP4P_NVT.Param
density EFSTungsten.Params
density SimFe.LjMC3DParams
density SimIdealGas.LjMC3DParams
density SimLattice.LjMC3DParams
density SimLJ.LjMC3DParams
density VLESim
density VLESim.GEMCParams
density LjMC3D.LjMC3DParams
density LjMd3D.LjMd3DParams
density LjMd3Dv2y.LjMd3DParams
density MeterMappedRdf
density SimMappedRdf.LJMDParams
density MappedU.LJMDParams
density MappedVirialLJ.LJMDParams
density MappedVirialLJVGr.LJMDParams
density LJNPT.LJMCParams
density LJNVT.LJMCParams
density FindTransitionTemperature
density MinimizationBetaNitrogenModelLS
density MinimizeBetaNitrogenLatticeParameter
density MinimizeBetaNitrogenLatticeParameterFromFile
density MinimizeBetaNitrogenLatticeParameterLSFromFile
density MinimizeBetaNitrogenTranslationDOF
density MinimizeGammaNitrogenLatticeParameter
density SimDirectBetaN2RP.SimOverlapParam
density SimOverlapAlphaN2TP.SimOverlapParam
density SimOverlapBetaN2RP.SimOverlapParam
density SimOverlapBetaN2RPScaling.SimOverlapParam
density SimOverlapBetaN2TP.SimOverlapParam
density SimOverlapDisorderedAlphaN2RPScaling.SimOverlapParam
density SimOverlapDisorderedAlphaN2TP.SimOverlapParam
density DropletAtomic
density SimGlass.GlassParams
density SWVLESim
density VLESim
density LJVacancyMin.SimOverlapParam
density MeterSolidProps
density MeterSolidPropsLJ
density MinimizeHCP
density MinimizeHCP.SimOverlapParam
density NormalModeAnalysisDisplay1D
density NormalModeAnalysisDisplay3D
density SimBennet.SimBennetParam
density SimEinStep1.SimOverlapParam
density SimEinStep1HCP.SimOverlapParam
density SimEinStep2.SimOverlapParam
density SimEinStep2HCP.SimOverlapParam
density SimHarmonicUmbrella.SimBennetParam
density SimHSMDVacancy.HSMDVParams
density SimLJHTTISuper.SimOverlapParam
density SimLJHTTISuperHCP.SimOverlapParam
density SimLJHTTISuperHCP2.SimOverlapParam
density SimLJHTTISuperSFMD.SimOverlapParam
density SimLJVacancy.LJParams
density SimOverlap.SimOverlapParam
density SimOverlapLJ.SimOverlapParam
density SimOverlapLJModule.SimOverlapParam
density SimOverlapSoftSphere.SimOverlapParam
density SimOverlapSoftSphereEin.SimOverlapParam
density SimOverlapSoftSphereEinHarm.SimOverlapParam
density SimOverlapSoftSphereHCP.SimOverlapParam
density SimOverlapSoftSphereReweighting.SimOverlapParam
density SimOverlapSoftSphereSoftness.SimOverlapParam
density SimOverlapSoftSphereSuperBox.SimOverlapParam
density SimOverlapSoftSphereTP.SimOverlapParam
density SimOverlapSoftSphereTPHCP.SimOverlapParam
density SimOverlapSoftSphereTPSlantedBox.SimOverlapParam
density SimOverlapSSnxy.SimOverlapParam
density SimTargetUmbrella.SimBennetParam
density SimUmbrella.SimBennetParam
density SimUmbrellaSoftSphere.SimBennetParam
density AshtonWildingLJ.simParams
density AshtonWildingVirial.simParams
density NVTWidomInsertLJ.simParams
density LJMC3D.SimParams
density LJMC3DDimer.SimParams
density HardSphereSolid.EOSParams
density TestLJAssociationMC3D_NPT.VirialAssociatingFluidParam
density1 DCVGCMD
density1 DCVGCMD
density2 DCVGCMD
density2 DCVGCMD
densityAccum ReactionEquilibriumGraphic
densityBox PistonCylinderGraphic
densityDisplay ReactionEquilibriumGraphic
densityDisplayTextBox PistonCylinderGraphic
densityForMu(double) HardSphereSolid
densityForPressure(double) HardSphereSolid
densityMeter PistonCylinderGraphic
densityProfileMeter ColloidGraphic
densityProfileMeter InterfacialSWGraphic
densityProfileMeter SurfaceTensionMapped
densityProfileMeterA AdsorptionGraphic
densityProfileMeterB AdsorptionGraphic
densityProfileSource DataProcessorChemicalPotential
depth Token
depth GData
DepthFirst etomica.graph.traversal
DepthFirst() DepthFirst
depthValue TransformManager
derivative2nd(Vector, Potential2SoftSpherical) HessianDB
derive() BigIntegerPoly
First derivative.
derr DataProcessorWidomContact
description EtomicaModuleInfo
description() EnumPotentialParamDescription
desiredPressure FindTransitionTemperature
dest MCMoveInsertDeleteLatticeVacancy
dest MCMoveInsertDeleteVacancy
dest MCMoveVolumeMonoclinicScaled
dest MCMoveVolumeSolidNPTMolecular
destination CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
destination CalcNumerical2ndDerivativeNitrogen
destinationType SVGConverter
Result type
DestinationType etomica.graph.view.rasterizer
Describes the type of destination for an SVGConverter operation.
destroy() ConfigurationWebsocket.ConfigurationUpdateEncoder
destroy() DataStreamWebsocket.DataAndInfoEncoder
destroy() Graphics3D
destroy() GData
det(BigInteger[][]) BigIntegerMath
Determinant of an integer square matrix.
determinant() Tensor
Computes the determinant of the matrix represented by this tensor
determinant() Tensor1D
determinant() Tensor2D
determinant() Tensor3D
determinant() TensorND
determinant() Matrix3f
Computes the determinant of this matrix.
determinant() Matrix4f
Computes the determinant of this matrix.
deviationVector FindBetaN2AngleFromParameter
Device etomica.graphics
Base class for all Devices.
Device() Device
Device(Controller) Device
Device.ActionSet etomica.graphics
DeviceBox etomica.graphics
A simple device the permits editing of a single value via a textbox
with an associated label.
DeviceBox() DeviceBox
DeviceBox(Controller) DeviceBox
DeviceBox.LabelType etomica.graphics
Typed constant used to indicate the type of label to be used with the display.
deviceBoxValueChanged(DeviceBoxValueChangedEvent) DeviceBox
deviceBoxValueChanged(DeviceBoxValueChangedEvent) DeviceBoxValueChangedListener
DeviceBoxValueChangedEvent etomica.graphics
DeviceBoxValueChangedEvent(DeviceBox, int) DeviceBoxValueChangedEvent
DeviceBoxValueChangedListener etomica.graphics
Interface that should be implemented to receive a value changed event
when a DeviceBox updateValue method is called.
DeviceButton etomica.graphics
Button that causes an action to be performed.
DeviceButton(Controller) DeviceButton
Constructs button that is not connected to any action.
DeviceButton(Controller, IAction) DeviceButton
Constructs a button connected to the given action.
DeviceButtonGroup etomica.graphics
Add etomica device for a group of radio buttons.
DeviceButtonGroup(Controller, int) DeviceButtonGroup
DeviceButtonSingle etomica.zeolite
Button that causes an action to be performed.
DeviceButtonSingle(Controller) DeviceButtonSingle
Constructs button that is not connected to any action.
DeviceButtonSingle(Controller, IAction) DeviceButtonSingle
Constructs a button connected to the given action.
DeviceCellNum3DSlider etomica.normalmode
DeviceCellNum3DSlider(Controller) DeviceCellNum3DSlider
DeviceCellNumXYSlider etomica.normalmode
DeviceCellNumXYSlider(Controller) DeviceCellNumXYSlider
DeviceCheckBox etomica.graphics
Button that toggles a boolean value via a check box.
DeviceCheckBox(ModifierBoolean) DeviceCheckBox
DeviceCheckBox(String, ModifierBoolean) DeviceCheckBox
DeviceDelaySlider etomica.graphics
DeviceDelaySlider(Controller) DeviceDelaySlider
DeviceEigenvaluesSlider etomica.normalmode
DeviceEigenvaluesSlider(Controller, IntegratorHarmonic) DeviceEigenvaluesSlider
deviceList() SimulationGraphic
DeviceNSelector etomica.graphics
Slider that selects the number of atoms of a given species in a box.
DeviceNSelector() DeviceNSelector
DeviceNSelector(Controller) DeviceNSelector
DevicePlotPoints etomica.graphics
DevicePlotPoints(Controller, String[], IFunction[], String[], boolean) DevicePlotPoints
DeviceRunControls etomica.graphics
DeviceRunControls(Controller) DeviceRunControls
DeviceSelector etomica.graphics
Generic Device that has a combo box.
DeviceSelector(Controller) DeviceSelector
DeviceSlider etomica.graphics
Device the changes a property using a graphical slider, via a Modifier.
DeviceSlider(Controller) DeviceSlider
DeviceSlider(Controller, int) DeviceSlider
DeviceSlider(Controller, Modifier) DeviceSlider
Constructs a slider connected to the get/set Value methods of the given Modifier
DeviceSlider(Controller, Modifier, int) DeviceSlider
DeviceSlider(Controller, Object, String) DeviceSlider
Constructs a slider connected to the given property of the given object
DeviceSlider(Controller, Object, String, int) DeviceSlider
DeviceSpinner etomica.graphics
Device the changes a property using a graphical spinner, via a Modifier.
DeviceSpinner(Controller) DeviceSpinner
DeviceSpinner(Controller, Modifier) DeviceSpinner
Constructs a spinner connected to the get/set Value methods of the given Modifier
DeviceSpinner(Controller, Object, String) DeviceSpinner
Constructs a spinner connected to the given property of the given object
DeviceSpinner.SpinnerListener etomica.graphics
Spinner listener, which relays the spinner change events to the modifier
DeviceTable etomica.graphics
Presents a table of numeric properties that can be edited by typing in values.
DeviceTable(String[]) DeviceTable
DeviceTable(TableModel) DeviceTable
DeviceTableModelGeneric etomica.graphics
DeviceTableModelGeneric(Object[][], String[]) DeviceTableModelGeneric
DeviceThermoSelector etomica.graphics
Permits selection of temperature from a discrete set of values.
DeviceThermoSelector(Controller, Unit, boolean) DeviceThermoSelector
DeviceThermoSelector(Simulation, IntegratorBox) DeviceThermoSelector
Constructor that specifies Kelvin as temperature units.
DeviceThermoSlider etomica.graphics
DeviceThermoSlider(Controller, IntegratorBox) DeviceThermoSlider
DeviceThermoSliderGEMC etomica.heVLE
Custom temperature slider for GEMC simulations.
DeviceThermoSliderGEMC(Controller, IntegratorBox, IntegratorBox, IntegratorManagerMC) DeviceThermoSliderGEMC
DeviceToggleButton etomica.graphics
Button that toggles a boolean value.
DeviceToggleButton(Controller) DeviceToggleButton
DeviceToggleButton(Controller, ModifierBoolean) DeviceToggleButton
DeviceToggleButton(Controller, ModifierBoolean, String, String) DeviceToggleButton
DeviceToggleRadioButtons etomica.graphics
Button that toggles a boolean value using a pair of radio buttons.
DeviceToggleRadioButtons(ModifierBoolean) DeviceToggleRadioButtons
Constructor with default labels of a blank title and "True" and "False" for
the true/false labels.
DeviceToggleRadioButtons(ModifierBoolean, String, String, String) DeviceToggleRadioButtons
DeviceTrioControllerButton etomica.graphics
Device comprising three buttons: (1) attaches to a controller to toggle its pause/resume state;
(2)causes a reset (restart) action of simulation to be performed; (3) causes reset of meter averages
only.
DeviceTrioControllerButton(Simulation, Space, Controller) DeviceTrioControllerButton
Contructs device with buttons that affect the given simulation.
DeviceTrioControllerButton.ComponentEventControllerButton etomica.graphics
Inner class that catches action of simulation panel
DeviceWaveVectorSlider etomica.normalmode
DeviceWaveVectorSlider(Controller) DeviceWaveVectorSlider
df IntegratorImageHarmonicMD
df(int[], double[]) FunctionMultiDimensionalDifferentiable
Returns the derivative indicated by the array d evaluated at the given point x.
df(int[], double[]) CalcGradientDifferentiable
df(int[], double[]) FiniteDifferenceDerivative
df(int[], int, double[]) CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
df(int, double) Function.Abs
df(int, double) Function.Constant
df(int, double) Function.Exp
df(int, double) Function.Identity
df(int, double) Function.Linear
df(int, double) Function.Log
df(int, double) Function.Reciprocal
df(int, double) Function.Sqrt
df(int, double) FunctionChain
Evaluates derivative via the chain rule.
df(int, double) FunctionDifferentiable
df(int, double) StatisticsMCGraphic.MyFunctionInvertible
df(int, double[], double) FittingFunctionNonLinear
df2(int[], double[]) CalcGradientDifferentiable
Uses the potential's force calculation at different displacements of a molecule in X, Y and Z
to determine the second derivative of the potential.
dfdx(double) MaxwellBoltzmann.Distribution
dfmt ScientificFormat
dForces SimDimerLJadatom
dFrot IntegratorDimerMin
dFrot IntegratorDimerRT
dFsq IntegratorDimerRT
DHS_NVT etomica.AlkaneEH
Canonical ensemble Monte Carlo simulation (NVT)
calculate dielectric constant for dipolar HS model
DHS_NVT etomica.dielectric
Canonical ensemble Monte Carlo simulation (NVT)
calculate dielectric constant for dipolar HS model
Electric field mapped average for dielectric constant
DHS_NVT(Space, int, double, double, double, double, double, double) DHS_NVT
DHS_NVT(Space, int, double, double, double, double, double, double) DHS_NVT
DHS_NVT.DipoleSourceDHS etomica.AlkaneEH
DHS_NVT.DipoleSourceDHS etomica.dielectric
DHS_NVT.Param etomica.AlkaneEH
DHS_NVT.Param etomica.dielectric
dHSCore P2NitrogenHellmann
diagE(Vector) Tensor
Makes this a diagonal tensor with elements set by the given vector.
diagE(Vector) Tensor1D
diagE(Vector) Tensor2D
diagE(Vector) Tensor3D
diagE(Vector) TensorND
diagramIndex WertheimGCPM3PtEBondDecomp.VirialAssociatingFluidParam
diagramIndex WertheimGCPM3PtThreeSite.VirialAssociatingFluidParam
diagramIndex WertheimGCPM4PtEBondDecomp.WertheimAssociatingFluidParam
diagramIndex WertheimGCPM4PtEBondDecompFinal.VirialAssociatingFluidParam
diagramIndex WertheimGCPM4PtThreeSite.VirialAssociatingFluidParam
diagramIndex WertheimGCPM4PtThreeSiteEDecompDirectSampling.VirialAssociatingFluidParam
diagramIndex ConfigurationClusterWertheimGCPM
diagramIndex ConfigurationClusterWertheimGCPM4Pt
diagramIndex ConfigurationClusterWertheimGCPMDirectSampling
diagramIndex DoubleAssociationSitesFluid4Pt.VirialAssociatingFluidParam
diagramIndex SingleAssociationSiteFluid.VirialAssociatingFluidParam
diagramIndex SingleAssociationSiteFluid2.VirialAssociatingFluidParam
diagramIndex SingleAssociationSiteFluid2Pt.VirialAssociatingFluidParam
diagramIndex SingleAssociationSiteFluid3Pt.VirialAssociatingFluidParam
diagramIndex SingleAssociationSiteFluid4Points.VirialAssociatingFluidParam
diagramIndex SingleAssociationSiteFluid4Pt.VirialAssociatingFluidParam
diagramIndex VirialAssociatingFluid.VirialAssociatingFluidParam
diagramIndex VirialAssociatingFluid4points.VirialAssociatingFluidParam
DiagramSource etomica.virial.cluster
diameter DisplayBoxCanvasG3DSys.OrientedSite
diameterHash DisplayBox
diameterHash ReverseOsmosisGraphic.ModifierAtomDiameter
diameterHash ReverseOsmosisWaterGraphic.ModifierAtomDiameter
DiameterHash etomica.atom
This provides an interface for a class that acts like a hashmap for atomic
diameters.
DiameterHashByElement etomica.atom
This class hashes atomic diameters based on the element.
DiameterHashByElement() DiameterHashByElement
DiameterHashByElementType etomica.atom
This class hashes atomic diameters based on both element and atom type.
DiameterHashByElementType() DiameterHashByElementType
DiameterHashByType etomica.atom
This class hashes atomic diameters based on the atom type.
DiameterHashByType() DiameterHashByType
DiameterHashGlass etomica.modules.glass
DiameterHashGlass() DiameterHashGlass
dielectricOutside DHS_NVT.Param
dielectricOutside DLJ_NVT_1site.Param
dielectricOutside DHS_NVT.Param
dielectricOutside DLJ_NVT_1site.Param
dielectricOutside TIP4P_NVT.Param
DifByConstant etomica.graph.operations
DifByConstant() DifByConstant
DifByConstant.DifByConstantParameters etomica.graph.operations
DifByConstantParameters(char, char) DifByConstant.DifByConstantParameters
DifByEdge etomica.graph.operations
DifByEdge() DifByEdge
DifByNode etomica.graph.operations
DifByNode() DifByNode
diff VirialOptimizer
diff(int, int) BenchBox.IVecSys
diff(int, int) BenchBox.VectorSystem
diffDiv(Rgb16, Rgb16, int) Rgb16
difference(ClusterDiagram[], ClusterDiagram[]) ClusterOperations
Generates the set of diagrams obtained by subtracting the second set from the first set.
diffuseFactor Shader
diffusepercent Token
diffusePercent Shader
difInterval TIP4P_NVT.Param
DifParameters etomica.graph.operations
DifParameters(char) DifParameters
digits DisplayTable
dihedralAngle(Plane) Plane
Dihedral angle between this plane and the given plane.
dim BoxQuench
dim MeterPressureCollisionCount
dim MeterPressureHard
dim IndexIteratorIncreasing
dim MeterExcessAdsorbed
dim MyMCMove
dim DropletGraphic.ModifierBoxSize
dim AccumulatorAutocorrelationPTensor
dim AccumulatorAutocorrelationShearStress
dim AccumulatorPTensor
dim InterfacialSWGraphic.ModifierBoxSize
dim MeterFlux
dim MeterSolidDA
dim MeterSolidDACut
dim TensorND
dimension DataInfoFactory
dimension() CompoundUnit
dimension() PrefixedUnit
Returns the dimension of this baseUnit.
dimension() SimpleUnit
Returns the dimension of this base unit.
dimension() LJ.LJUnit
dimension() Unit
Returns the dimension of the unit.
dimension(int) Pressure
Returns the Dimension instance for the "pressure" appropriate to the given
dimension.
dimension(int) Volume
Returns the Dimension instance for the "volume" appropriate to the given
dimension.
Dimension etomica.units.dimensions
Parent of all Dimension classes, which describe the physical dimensions
(e.g., mass, length, force) of a quantity.
Dimension(String, double[]) Dimension
Dimension(String, double, double, double) Dimension
Dimension(String, double, double, double, double, double, double, double) Dimension
DIMENSION Angle
DIMENSION Area
DIMENSION Charge
Singleton instance of this class.
DIMENSION Current
Singleton instance of this class.
DIMENSION Dipole
DIMENSION ElectricPotential
Singleton instance of this class.
DIMENSION Energy
Singleton instance of this class.
DIMENSION Force
DIMENSION Fraction
Singleton instance of this class.
DIMENSION Frequency
Singleton instance of this class.
DIMENSION Length
Singleton instance of this class.
DIMENSION LuminousIntensity
Singleton instance of this class.
DIMENSION Mass
Singleton instance of this class.
DIMENSION Momentum
Singleton instance of this class.
DIMENSION Null
Singleton instance of this class.
DIMENSION Power
Singleton instance of this class.
DIMENSION Pressure
Singleton instance of this class.
DIMENSION Pressure2D
DIMENSION Quantity
Singleton instance of this class.
DIMENSION Temperature
Singleton instance of this class.
DIMENSION Time
Singleton instance of this class.
DIMENSION Undefined
Singleton instance of this class.
DIMENSION Velocity
Singleton instance of this class.
DIMENSION Viscosity
Singleton instance of this class.
DIMENSION Volume
Singleton instance of this class.
DIMENSION Wavenumber
Singleton instance of this class.
Dimensioned etomica.units.dimensions
DimensionedDoubleEditor etomica.graphics
Editor to set the value of a double-type property having units associated with it.
DimensionedDoubleEditor(Dimension) DimensionedDoubleEditor
DimensionRatio etomica.units.dimensions
Class to form a dimension from ratio of two dimensions.
DimensionRatio(Dimension, Dimension) DimensionRatio
DimensionRatio(String, Dimension, Dimension) DimensionRatio
dimensions BoundaryRectangular
dimensions BoundaryTruncatedOctahedron
dimensions() DisplayPolytope
returns dimensions of polytope as the (max - min) value in
each dimension for all the vertices.
dimensionsHalf BoundaryRectangularPore
dimensionsHalf BoundaryRectangularSlit
dimensionsHalf BoundaryTruncatedOctahedron
dimensionString() Lister
dimerApproach DimerApproach
DimerApproach etomica.models.rowley
DimerApproach() DimerApproach
dimerColorManager ColorSchemeSmer
dimerCurvature(Vector[], Vector[], Vector[]) IntegratorDimerRT
Computes curvature value, C, for the energy surface.
dimerForceCenter(Vector[]) IntegratorDimerRT
dimerForceEff(Vector[], Vector[], Vector[]) IntegratorDimerRT
dimerForcePerp(Vector[], Vector[], Vector[]) IntegratorDimerMin
Finds the component of the dimer's total force that is perpendicular to the normal vector.
dimerForcePerp(Vector[], Vector[], Vector[], Vector[]) IntegratorDimerRT
dimerForces(Vector[], Vector[], Vector[]) IntegratorDimerMin
Resets forces in boxes 0 and min, calls potential.calculate, and copies over
the new forces to local arrays.
dimerForces(Vector[], Vector[], Vector[]) IntegratorDimerRT
dimerForcesStar(Vector[], Vector[], Vector[]) IntegratorDimerMin
Used in the middle of the rotateDimer method.
dimerForcesStar(Vector[], Vector[], Vector[]) IntegratorDimerRT
dimerNormal() IntegratorDimerMin
Computes an n-dimensional vector in potential energy hyperspace, pointing
in the direction of the dimer (intersecting both simulation boxes).
dimerNormal() IntegratorDimerRT
dimerPotential MCMoveDimer
dimerPotential MCMoveDimerRotate
dimerPotential MCMoveDimer
dimerPotential MCMoveDimerRotate
dimerPump ReactionEquilibriumGraphic
dimerSaddleTolerance() IntegratorDimerRT
dimerUpdatePositions(double, Vector[]) IntegratorDimerRT
dimVector BoxInflate
dimx NormalModeAnalysisDisplay2D
dimy NormalModeAnalysisDisplay2D
dipind(int, int, int[], int[]) P2WaterPotentialsJankowski
dipole TIP4P_NVT.DipoleSourceTIP4PWater
dipole DipoleSourceAceticAcid
dipole DipoleSourceWater
dipole Token
dipole() CGS
dipole() LJ
dipole() MKS
dipole() UnitSystem
dipole() UnitSystem.Sim
Dipole etomica.units.dimensions
Base unit for electrical dipole moment.
DipoleBox etomica.rotation
DipoleBox(Space, int, double) DipoleBox
DipoleBox.Applet etomica.rotation
DipoleBoxMatrix etomica.rotation
DipoleBoxMatrix(Space, int, double) DipoleBoxMatrix
DipoleBoxMatrix.Applet etomica.rotation
dipoleconv PotentialCalculationHeisenberg
dipoleconv PotentialCalculationMoleculeAgentSum
dipoleconv PotentialCalculationMoleculeAgentSumPair
dipoleFShift P2LJDipole
dipoleMagnitude Heisenberg.Param
dipoleMagnitude Heisenberg3Pair.Param
dipoleMagnitude HeisenbergPair.Param
dipoleMoment1 PNWaterGCPMReactionField
dipoleMoment2 PNWaterGCPMReactionField
dipolescale Token
dipoleSource MeterDipoleSumSquaredMappedAverage
dipoleSource P1ExternalField
dipoleSource P2ReactionFieldDipole
dipoleSource P2ReactionFieldDipoleTruncated
dipoleSource PotentialCalculationFSum
dipoleSource PotentialCalculationPhiSum
dipoleSource PotentialCalculationPhiSumHeisenberg
dipoleSource PotentialCalculationFSum
DipoleSource etomica.molecule
Interface for something that can calculate the dipole of a molecule.
DipoleSourceAceticAcid etomica.models.OPLS
calculates dipole for acetic acid
DipoleSourceAceticAcid(Space) DipoleSourceAceticAcid
DipoleSourceDHS(Space, double) DHS_NVT.DipoleSourceDHS
DipoleSourceDHS(Space, double) DHS_NVT.DipoleSourceDHS
DipoleSourceDLJ(Space, double) DLJ_NVT_1site.DipoleSourceDLJ
DipoleSourceDLJ(Space, double) DLJ_NVT_1site.DipoleSourceDLJ
DipoleSourceTIP4PWater(Space) TIP4P_NVT.DipoleSourceTIP4PWater
DipoleSourceWater etomica.models.water
Implementation of DipoleSource that can handle water molecules that are
MoleculeOriented.
DipoleSourceWater(Space) DipoleSourceWater
dipoleStrength DHS_NVT.DipoleSourceDHS
dipoleStrength DLJ_NVT_1site.DipoleSourceDLJ
dipoleStrength DHS_NVT.DipoleSourceDHS
dipoleStrength DLJ_NVT_1site.DipoleSourceDLJ
dipoleStrength DipoleSourceWater
dipoleStrength2 DHS_NVT.Param
dipoleStrength2 DLJ_NVT_1site.Param
dipoleStrength2 DHS_NVT.Param
dipoleStrength2 DLJ_NVT_1site.Param
dipoleUShift P2LJDipole
dipoleVector DHS_NVT.DipoleSourceDHS
dipoleVector DLJ_NVT_1site.DipoleSourceDLJ
dipoleVector DHS_NVT.DipoleSourceDHS
dipoleVector DLJ_NVT_1site.DipoleSourceDLJ
dipolex PotentialCalculationHeisenberg
dipolex PotentialCalculationMoleculeAgentSum
dipolex PotentialCalculationMoleculeAgentSumPair
dipoley PotentialCalculationHeisenberg
dipoley PotentialCalculationMoleculeAgentSum
dipoley PotentialCalculationMoleculeAgentSumPair
dir0 P2SpheroPolyhedron
dir1 P2SpheroPolyhedron
dir2 P2SpheroPolyhedron
direction ConfigurationOrientedFile
direction MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbr
direction MpiIntraspecies1A
direction PotentialMasterCellMixed
direction Orientation2D
direction Orientation3D
direction OrientationFull3D
direction() IteratorDirective
DirectSamplingTargetQCArReferenceAzizAr 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() DirectSamplingTargetQCArReferenceAzizAr
DirectSamplingTargetQCArReferenceAzizAr.VirialLJParam etomica.virial.simulations
Inner class for parameters
dirty MCMoveInsertDeleteLatticeVacancy
dirty MCMoveInsertDeleteVacancy
dirty AkimaSpline
disableEnergy() P2EAM
disablepopupmenu Token
DiscardCriteria(char, int, char, int) VirialDiagramsPT.DiscardCriteria
disconnectedP MayerIonicDiagram1qbond
disconnectedP MayerIonicDiagram2qbonds
disconnectedP MayerIonicDiagram4qbonds
disconnectedP VirialDiagrams
disconnectedP VirialDiagramsMix
disconnectedP VirialDiagramsMix2
disconnectedP VirialDiagramsPT
disconnectedP WertheimDiagrams2SiteRho
disconnectedP WertheimDiagrams3SiteRho
disp P2QChemInterpolated
disp P3AdditiveQChem.DampingParams
disp P3QChem.DampingParams
displacementLimit2 CriterionSimple
displacementLimit2 CriterionSimpleMolecular
display EFSTungsten
display ChainEquilibriumSim
display FreeRadicalPolymerizationSim
display ClipPlaneEditor
display ReactionEquilibrium
display SelfAssemblySim
display LJMD2D
display SWMD2D
display SWMD3D
display Token
display(Parser.CommandVariable) Interpreter
Display etomica.graphics
Superclass of all classes that display something from the simulation.
Display() Display
displayAHarmonic NormalModeAnalysisDisplay1DGraphic
displayAHarmonic NormalModeAnalysisDisplay2DGraphic
displayAHarmonic NormalModeAnalysisDisplay3DGraphic
displayBoundary DisplayBox
displayBox DisplayCanvas
displayBox CrystalViewer
displayBox PistonCylinderGraphic
DisplayBox etomica.graphics
Displays a picture of a box, with configurations of molecules, boundaries, and other objects as appropriate, assuming 2-dimensional system.
DisplayBox(Simulation, Box) DisplayBox
Warning: after instantiation, clients using G3DSys may need to toggle
display.canvas.setVisible false and then true to fix the 'sometimes
gray' bug.
DisplayBoxCanvas1D etomica.graphics
DisplayBoxCanvas1D(Space, DisplayBox, Controller) DisplayBoxCanvas1D
DisplayBoxCanvas2D etomica.graphics
DisplayBoxCanvas2D(DisplayBox, Space, Controller) DisplayBoxCanvas2D
DisplayBoxCanvas2DGlass etomica.modules.glass
DisplayBoxCanvas2DGlass(DisplayBox, Space, Controller, ConfigurationStorage) DisplayBoxCanvas2DGlass
DisplayBoxCanvas2DNpTScaling etomica.normalmode.nptdemo
DisplayBoxCanvas2DNpTScaling(DisplayBox, Space, Controller, CoordinateDefinition) DisplayBoxCanvas2DNpTScaling
DisplayBoxCanvas3DGlass etomica.modules.glass
DisplayBoxCanvas3DGlass(DisplayBox, Space, Controller, ConfigurationStorage) DisplayBoxCanvas3DGlass
DisplayBoxCanvasG3DSys etomica.graphics
DisplayBoxCanvasG3DSys(Simulation, DisplayBox, Space, Controller) DisplayBoxCanvasG3DSys
DisplayBoxCanvasG3DSys.OrientedAgentSource etomica.graphics
DisplayBoxCanvasG3DSys.OrientedFullSite etomica.graphics
DisplayBoxCanvasG3DSys.OrientedSite etomica.graphics
DisplayBoxCanvasGlass etomica.modules.glass
displayBoxScaled HSNPT2DGraphic
DisplayBoxSpin2D etomica.graphics
DisplayBoxSpin2D(DisplayBox, NeighborSiteManager, Space, Controller) DisplayBoxSpin2D
DisplayCanvas etomica.graphics
Superclass for classes that display information from simulation by painting to a canvas.
DisplayCanvas(Controller) DisplayCanvas
Construct a DisplayCanvas using the given controller (which may be null).
displaycellparameters Token
displayCycles Osmosis
displayCycles PistonCylinderGraphic
displayDensity ColorSchemeScaledOverlap
displayDensity DisplayBoxCanvas2DNpTScaling
displayed EllipseDisplayAction
displayEllipse(double) EllipseDisplayAction
displayList() SimulationGraphic
displayList() ArrayMoleculeDisplayList
displayMaxX GData
displayMaxY GData
displayMinX GData
displayMinY GData
displayMoleculeList() ViewSpeciesSelection
displayMoleculeList() ViewSpeciesSelection
displayPanel MyApplet
displayPlot EtomicaPlot
DisplayPlot etomica.graphics
Class for creating a plot of simulation data.
DisplayPlot() DisplayPlot
Creates a plot with a new, empty, DataSinkTable.
DisplayPlot(DataSet) DisplayPlot
Creates a plot using data from the given table.
DisplayPlot.DataWriter etomica.graphics
Writes a file with the raw data from a plot.
DisplayPlot.PopupListener etomica.graphics
DisplayPlot.RawDataWindowOpener etomica.graphics
Opens a window with the raw data from a plot.
DisplayPlotXChart etomica.graphics
DisplayPlotXChart() DisplayPlotXChart
DisplayPlotXChart(DataSet) DisplayPlotXChart
DisplayPolytope etomica.graphics
Displays a picture of a polytope.
DisplayPolytope(Polytope) DisplayPolytope
DisplayPolytope.Applet etomica.graphics
DisplayPolytopeCanvas2D etomica.graphics
DisplayPolytopeCanvas2D(DisplayPolytope) DisplayPolytopeCanvas2D
DisplayPolytopeCanvasG3DSys etomica.graphics
DisplayPolytopeCanvasG3DSys(DisplayPolytope) DisplayPolytopeCanvasG3DSys
displaySelectedSpecies(int, int) ControllerSpeciesSelection
displayTable NormalModeAnalysisDisplay1DGraphic
displayTable NormalModeAnalysisDisplay2DGraphic
DisplayTable etomica.graphics
Presents data in a tabular form.
DisplayTable() DisplayTable
DisplayTable(DataSinkTable) DisplayTable
displayTableEigen NormalModeAnalysisDisplay3DGraphic
displayTableWV NormalModeAnalysisDisplay3DGraphic
DisplayTextBox etomica.graphics
A simple display of a single value in a textbox with an associated label.
DisplayTextBox() DisplayTextBox
DisplayTextBox.LabelType etomica.graphics
Typed constant used to indicate the type of label to be used with the display.
DisplayTextBoxesCAE etomica.graphics
Display that presents three boxes with the current value, average,
and error, respectively, given by an AccumulatorAverage.
DisplayTextBoxesCAE() DisplayTextBoxesCAE
DisplayTimer etomica.graphics
DisplayBox to present the elapsed time in a
molecular dynamics simulation.
DisplayTimer(IntegratorMD) DisplayTimer
dispose() AtomLeafAgentManager
Notifies the AtomAgentManager it should disconnect itself as a listener and release all of its agents.
dispose() AtomTypeAgentManager
Releases its agents.
dispose() BoxAgentManager
Notifies the BoxAgentManager that it should release all agents and
stop listening for events from the simulation.
dispose() DisplayCanvas
dispose() DisplayTimer
Unhooks the DisplayTimer from the integrator
dispose() MoleculeAgentManager
Notifies the AtomAgentManager it should disconnect itself as a listener.
dispose() NeighborListManagerMolecular
dispose() NeighborListManager
dispose() SpeciesAgentManager
Unregisters this class as a listener for AtomType-related events and
releases its agents.
dispose() RandomNumberGeneratorUnix
Cleanup, close the file.
disposeGraphics(Object) ApiPlatform
disposeGraphics(Object) Platform
disproportionate(IAtom, IAtom) P2SquareWellRadical
this function will makes a and b unreactive by setting both to be bonded
to themselves (a-a, b-b).
distance ConfigurationClusterMove
distance Token
distance(Point3f) Point3f
Returns the distance between this point and point p1.
distance(Point4f) Point4f
Returns the distance between this point and point p1.
distanceSquared(Point3f) Point3f
Computes the square of the distance between this point and point p1.
distanceTo(Vector) Plane
Perpendicular distance from the plane to the given point.
distanceTo(Vector) Polyhedron
Returns the perpendicular distance to the nearest face of the
polyhedron.
distanceTo(Vector) PistonPlane
distanceTo(Vector) WallPlane
distanceToPlane(Point4f, Point3f) Measure
distanceToPlane(Vector3f, float, Point3f) Measure
distanceToPlaneD(Point4f, float, Point3f) Measure
distPol P2WaterSzalewicz
Distribution(Space, double, double) MaxwellBoltzmann.Distribution
div(Complex) Complex
Division of Complex numbers (doesn't change this Complex number).
div(Quaternion) Quaternion
div(Quaternion[], Quaternion[], int, boolean) Quaternion
divide(int) BigSurd
Divide by an integer.
divide(int) Rational
Divide by an integer.
divide(Coefficient) Coefficient
divide(Coefficient) CoefficientImpl
divide(BigSurd) BigSurd
Divide by another square root.
divide(Ifactor) Ifactor
Integer division through another positive integer.
divide(Rational) Rational
Divide by another fraction.
divide(BigInteger) BigSurd
Divide by an integer.
divide(BigInteger) Rational
Divide by an integer.
divideAndRemainder(BigIntegerPoly) BigIntegerPoly
Divide by another polynomial.
divideRound(int, BigDecimal) BigDecimalMath
Divide and round.
divideRound(BigComplex, BigComplex) BigDecimalMath
Divide and round.
divideRound(BigDecimal, int) BigDecimalMath
Divide and round.
divideRound(BigDecimal, BigDecimal) BigDecimalMath
Divide and round.
divideRound(BigDecimal, BigInteger) BigDecimalMath
Divide and round.
divideRound(BigInteger, BigComplex) BigDecimalMath
Divide and round.
divideRound(BigInteger, BigDecimal) BigDecimalMath
Divide and round.
divisor Potential0Lrc
divisors() Ifactor
The set of positive divisors.
divisors(BigInteger) BigIntegerMath
Compute the list of positive divisors.
divLeft(Quaternion) Quaternion
dJdeta MeterEnergyMeanField
DLGA(double) Gamma
DLJ_NVT_1site etomica.AlkaneEH
Canonical ensemble Monte Carlo simulation (NVT)
calculate dielectric constant epsilon for dipolar LJ model
DLJ_NVT_1site etomica.dielectric
Canonical ensemble Monte Carlo simulation (NVT)
calculate dielectric constant epsilon for dipolar LJ model
DLJ_NVT_1site(Space, int, double, double, double, double, double, double, double) DLJ_NVT_1site
DLJ_NVT_1site(Space, int, double, double, double, double, double, double, double) DLJ_NVT_1site
DLJ_NVT_1site.DipoleSourceDLJ etomica.AlkaneEH
DLJ_NVT_1site.DipoleSourceDLJ etomica.dielectric
DLJ_NVT_1site.Param etomica.AlkaneEH
DLJ_NVT_1site.Param etomica.dielectric
dmptab P2WaterSzalewicz
dn P3HydrogenManzhos
dna Token
do21 P1ImageHarmonic
doAbs ClusterWeightAbs
doAction() ActivityIntegrate
doAction(IAction) Device
Method called by subclasses to execute the action of the device.
doAction(IAction) DeviceSlider
doAdjustStepFrac IntegratorOverlap
doAdjustStepsOnTime IntegratorOverlap
doAEEMF Heisenberg.Param
doAEEMF MeterMappedAveragingVSum
doAggressiveAdjustStepFrac IntegratorOverlap
doApplyPBC WriteConfiguration
doApplyPBC NeighborCellManagerMolecular
doApplyPBC NeighborCellManager
doApplyPBC NeighborListManagerMolecular
doAveraging HistogramNotSoSimple
doAvgDef DataSourceFE
doBlockSum() AccumulatorAverageCollapsing
Performs the block sum after blockSize calls to addData.
doBlockSum() AccumulatorAverageCovariance
doBlockSum() AccumulatorAverageFixed
Performs the block sum after blockSize calls to addData.
doBlockSum() AccumulatorAverageFixedOutputFile
Performs the block sum after blockSize calls to addData.
doBlockSum() AccumulatorVirialOverlapSingleAverage
doCaching ClusterSum
doCaching ClusterSumPolarizable
doCaching ClusterSumPolarizableWertheimProduct4Pt
doCaching ClusterSumPolarizableWertheimProduct4PtFinal
doCaching ClusterWheatleyPT
doCaching ClusterWheatleySoft
doCaching ClusterWheatleySoftBD
doCaching ClusterWheatleySoftDerivatives
doCaching ClusterWheatleySoftDerivativesBD
doCalc(boolean, int, double) BesselFunction
doCalculation(IAtomList, IPotential) PotentialCalculationForcePressureSumGB
Adds forces due to given potential acting on the atoms produced by the iterator.
doCalculation(IAtomList, IPotentialAtomic) PotentialCalculationRDF
doCalculation(IAtomList, IPotentialAtomic) PotentialCalculationEnergySumEAM
Adds to the energy sum the energy values obtained from application of the given potential to the
atoms.
doCalculation(IAtomList, IPotentialAtomic) DataSourceEnergies.PotentialCalculationEnergies
doCalculation(IAtomList, IPotentialAtomic) PotentialCalculationDUDW
doCalculation(IAtomList, IPotentialAtomic) IntegratorHard.CollisionHandlerUp
doCalculation(IAtomList, IPotentialAtomic) MeterWallForce.PotentialCalculationWallForce
Adds forces due to given potential acting on the atoms produced by the iterator.
doCalculation(IAtomList, IPotentialAtomic) PotentialCalculationEnergySumCutoff
Adds to the energy sum the energy values obtained from application of the given potential to the
atoms produced by the given iterator.
doCalculation(IAtomList, IPotentialAtomic) PotentialCalculationSumCutoff
Adds to the energy sum the energy values obtained from application of the given potential to the
atoms produced by the given iterator.
doCalculation(IAtomList, IPotentialAtomic) PotentialCalculationSumCutoffLS
Adds to the energy sum the energy values obtained from application of the given potential to the
atoms produced by the given iterator.
doCalculation(IAtomList, IPotentialAtomic) PotentialCalculationMappedRdf
doCalculation(IAtomList, IPotentialAtomic) PotentialCalculationMappedEnergy
doCalculation(IAtomList, IPotentialAtomic) PotentialCalculationMappedVirial
doCalculation(IAtomList, IPotentialAtomic) PotentialCalculationMappedVirialV
doCalculation(IAtomList, IPotentialAtomic) PotentialCalculationForceSumGlass
Adds forces due to given potential acting on the atoms produced by the iterator.
doCalculation(IAtomList, IPotentialAtomic) PotentialCalculationForceStress
Adds forces due to given potential acting on the atoms produced by the iterator.
doCalculation(IAtomList, IPotentialAtomic) PotentialCalculationForceSumWallForce
Adds forces and torques due to given potential acting on the atoms produced by the iterator.
doCalculation(IAtomList, IPotentialAtomic) PotentialCalculationTorqueSumWallForce
doCalculation(IAtomList, IPotentialAtomic) PotentialCalculationForceSumWall
doCalculation(IAtomList, IPotentialAtomic) PotentialCalculationEFSSP
doCalculation(IAtomList, IPotentialAtomic) PotentialCalculationLJSP
doCalculation(IAtomList, IPotentialAtomic) PotentialCalculationSolidSuper
Adds forces due to given potential acting on the atoms produced by the iterator.
doCalculation(IAtomList, IPotentialAtomic) PotentialCalculationSolidSuperCut
Adds forces due to given potential acting on the atoms produced by the iterator.
doCalculation(IAtomList, IPotentialAtomic) PotentialCalculationSolidSuperCutLS
Adds forces due to given potential acting on the atoms produced by the iterator.
doCalculation(IAtomList, IPotentialAtomic) PotentialCalculation
Method giving the specific calculation performed by this class.
doCalculation(IAtomList, IPotentialAtomic) PotentialCalculationEnergySum
Adds to the energy sum the energy values obtained from application of the given potential to the
atoms.
doCalculation(IAtomList, IPotentialAtomic) PotentialCalculationEnergySumBigDecimal
Adds to the energy sum the energy values obtained from application of the given potential to the
atoms produced by the given iterator.
doCalculation(IAtomList, IPotentialAtomic) PotentialCalculationForcePressureSum
Adds forces due to given potential acting on the atoms produced by the iterator.
doCalculation(IAtomList, IPotentialAtomic) PotentialCalculationForceSum
Adds forces due to given potential acting on the atoms produced by the iterator.
doCalculation(IAtomList, IPotentialAtomic) PotentialCalculationFSum
doCalculation(IAtomList, IPotentialAtomic) PotentialCalculationHyperVirialSum
Adds to the virial sum the energy values obtained from application of the given potential to the
atoms produced by the given iterator.
doCalculation(IAtomList, IPotentialAtomic) PotentialCalculationMolecularVirialSum
doCalculation(IAtomList, IPotentialAtomic) PotentialCalculationPhiSum
doCalculation(IAtomList, IPotentialAtomic) PotentialCalculationPhiSumHeisenberg
doCalculation(IAtomList, IPotentialAtomic) PotentialCalculationPressureTensor
Adds the pressure tensor contribution based on the forces acting on each
pair of atoms produced by the iterator.
doCalculation(IAtomList, IPotentialAtomic) PotentialCalculationTorqueSum
Adds forces and torques due to given potential acting on the atoms produced by the iterator.
doCalculation(IAtomList, IPotentialAtomic) PotentialCalculationVirialSum
Adds to the virial sum the energy values obtained from application of the given potential to the
atoms produced by the given iterator.
doCalculation(IAtomList, IPotentialAtomic) MeterEnergyMeanField.PotentialCalculationCSsum
doCalculation(IAtomList, IPotentialAtomic) PotentialCalculationFreeEnergy
doCalculation(IAtomList, IPotentialAtomic) PotentialCalculationFSum
doCalculation(IAtomList, IPotentialAtomic) PotentialCalculationHeisenberg
doCalculation(IAtomList, IPotentialAtomic) PotentialCalculationMeanField
doCalculation(IAtomList, IPotentialAtomic) PotentialCalculationMoleculeAgentSum
doCalculation(IAtomList, IPotentialAtomic) PotentialCalculationMoleculeAgentSumMinusIdeal
doCalculation(IAtomList, IPotentialAtomic) PotentialCalculationMoleculeAgentSumMinusIdealPair
doCalculation(IAtomList, IPotentialAtomic) PotentialCalculationMoleculeAgentSumPair
doCalculation(IAtomList, IPotentialAtomic) PotentialCalculationPair
doCalculation(IAtomList, IPotentialAtomic) PotentialCalculationPhiSum
doCalculation(IAtomList, IPotentialAtomic) PotentialCalculationSumquare
doCalculation(IAtomList, IPotentialAtomic) PotentialCalculationVSum
doCalculation(IMoleculeList, IPotentialMolecular) PotentialCalculationTorqueSumWallForce
Adds forces and torques due to given potential acting on the atoms produced by the iterator.
doCalculation(IMoleculeList, IPotentialMolecular) PotentialCalculationEnergySum
Adds to the energy sum the energy values obtained from application of the given potential to the
molecules.
doCalculation(IMoleculeList, IPotentialMolecular) PotentialCalculationEnergySumBigDecimal
Adds to the energy sum the energy values obtained from application of the given potential to the
atoms produced by the given iterator.
doCalculation(IMoleculeList, IPotentialMolecular) PotentialCalculationFSum
doCalculation(IMoleculeList, IPotentialMolecular) PotentialCalculationMolecular
Method giving the specific calculation performed by this class.
doCalculation(IMoleculeList, IPotentialMolecular) PotentialCalculationMolecularVirialSum
doCalculation(IMoleculeList, IPotentialMolecular) PotentialCalculationPhiSum
doCalculation(IMoleculeList, IPotentialMolecular) PotentialCalculationPhiSumHeisenberg
doCalculation(IMoleculeList, IPotentialMolecular) PotentialCalculationTorqueSum
Adds forces and torques due to given potential acting on the atoms produced by the iterator.
doCalculation(IMoleculeList, IPotentialMolecular) PotentialCalculationFSum
doChainRef VirialHeD.VirialParam
doChainRef VirialHeNonAdditiveD.VirialParam
doChainRef VirialLJ.VirialLJParam
doChainRef VirialLJD.VirialLJParam
doChainRef VirialLJDU.VirialLJParam
doChainRef VirialLJPT.VirialLJParam
doChainRef VirialTraPPE.VirialParam
doClear DisplayPlot
doCommand(String, StatusAction) ControlResource
doConfigButton PistonCylinderGraphic
doConv HSMDCavity.CavityParam
doConventionalE Heisenberg.Param
doCopy IteratorWrapper
doCorrection VirialLJOrC.VirialLJrParam
doCorrelation Heisenberg.Param
doCorti MCMoveVolumeSolid
doCov MeterVirialEBinMultiThreaded
doCov VirialSQWBinMultiThreaded.SimulationWorker
doCov VirialSQWBinMultiThreaded.VirialHSBinParam
doCV Heisenberg.Param
doD2 MeterSolidDA
doD2 PotentialCalculationSolidSuper
doD2 SimLJHTTISuperSFMD.SimOverlapParam
dodebug MCMoveAtomSmer
dodebug MCMoveMoleculeSmer
dodebug MCMoveVolumeAssociated
dodebug MCMoveVolumeAssociatedMolecule
dodebug IntegratorMC
dodebug PNWaterGCPMReactionField
doDensityInput PistonCylinderGraphic
doDiff VirialHePI.VirialHePIParam
doDiff VirialHePISysErr.VirialHePIParam
doDipole Heisenberg.Param
doDisconnectedMatching VirialDiagrams
doDisconnectedMatching VirialDiagramsMix2
doDisconnectedMatching VirialDiagramsPT
doDouble MeterNormalStress
doDown RectangularLatticeNbrIterator
doEigenDecompose(double[][], String) HarmonicAlphaNitrogenModelDecomposed
doEigenDecompose(double[][], String) HarmonicBetaNitrogenModelDecomposed
doEigenDecomposeAndFile(double[][], String) HarmonicBetaNitrogenModel
doEnergyMF Heisenberg.Param
doEnforceBounds DataSourceUniform
doExchange VirialDiagrams.ArticulatedAt0
doExchange VirialDiagrams
doExchange VirialDiagramsPT.ArticulatedAt0
doExchange VirialDiagramsPT
doExchangeCondensing VirialDiagrams
doExchangeCondensing VirialDiagramsPT
doExchangeF VirialDiagrams
doExchangeF VirialDiagramsPT
doExcludeNonNeighbors MCMoveMoleculeCoupledInitPert
doExcludeNonNeighbors MCMoveAtomCoupled
doExcludeNonNeighbors MCMoveMoleculeCoupled
doExp VirialDiagramsPT
doExp VirialSwsPT.VirialSiepmannSpheresParam
doExpDensityprofile ExternalVirialDiagrams
doFancyMonoclinic HSDimerNPT
doFancyOriented HSDimerNPT
doFastButton PistonCylinderGraphic
doFindMinimum(double[]) MinimizeBetaNitrogenTranslationDOF
doFindMinimum(double[], double[], double[]) MinimizeBetaNitrogenLatticeParameter
doFindMinimum(double[], double[], double[]) MinimizeBetaNitrogenLatticeParameterFromFile
doFindMinimum(double[], double[], double[]) MinimizeBetaNitrogenLatticeParameterLSFromFile
doFit(double[], double[]) LinearFit
doFit(double[], double[]) FitTanh
doFit(double[], double[]) FitTanh
doFit(double[], double[], double[]) LinearFit
doFit(int, double[], double[]) PolynomialFit
Perform polynomial fit of the given order.
doFit(int, double[], double[], double[]) PolynomialFit
Perform polynomial fit of the given order with the given weights (w).
doFit(int, double[], double[], double[], boolean) PolynomialFit
doFlip(IMolecule) BiasVolume2SiteAceticAcid
doFlip(IMolecule) BiasVolumeAceticAcid
doGlobalMoves() IntegratorManagerMC
Method to select and perform an elementary Monte Carlo move.
doGoDown MpiIntraspecies1A
doGradientNoShift(Vector, Vector, double) P2Nitrogen
doGradientShift(Vector, Vector, double) P2Nitrogen
doGraphic Heisenberg.Param
doGraphics HSMDCavity.CavityParam
doGraphics HSMDWidom.HSMDParam
doGraphics HSDimerNPT
doHarmonic SimFe.LjMC3DParams
doHB VirialDiagrams
doHB VirialDiagramsPT
doHist VirialCO2H2OGCPM.VirialParam
doHist VirialCO2H2OGCPMX.VirialParam
doHist VirialCO2H2OSC.VirialCO2SCParam
doHist VirialCO2PI.VirialH2PIParam
doHist VirialEmulNonAdditive.VirialParam
doHist VirialH2OGCPMD.VirialParam
doHist VirialH2PI.VirialH2PIParam
doHist VirialHeD.VirialParam
doHist VirialHeNonAdditive.VirialParam
doHist VirialHeNonAdditiveD.VirialParam
doHist VirialHeNonAdditiveWheatley.VirialParam
doHist VirialHePI_PotentialCorrection.VirialHePIParam
doHist VirialHePI.VirialHePIParam
doHist VirialHePISysErr.VirialHePIParam
doHist VirialHePIXCOdd.VirialHePIParam
doHist VirialLJ.VirialLJParam
doHist VirialLJD.VirialLJParam
doHist VirialLJDU.VirialLJParam
doHist VirialLJPT.VirialLJParam
doHist VirialPolyhedra.VirialHSParam
doHist VirialPolyhedra2.VirialHSParam
doHistory EFSTungsten.Params
doIdeal Heisenberg.Param
doIdeal MeterMappedAveragingVSum
doIgnoreRefAvg DataVirialOverlap
doIncludeACInError AccumulatorAverage
doIncludeACInError() AccumulatorAverage
doIncludePair MCMoveMoleculeCoupledInitPert
doIncludePair MCMoveMoleculeCoupled
doInterpolateHole() AkimaSplineSmoother
doInterpolateHole2() AkimaSplineSmoother
doInterpolation(double[]) AkimaSpline
doInterpolationDy(double[]) AkimaSpline
doit(NormalModes, int, double, int) CalcHarmonicA
doit(String, int) NormalModeEigenGetter
doJustTilt AkimaSplineSmootherDyApp.PlotAction
doKeepEBonds VirialDiagrams
doKeepEBonds VirialDiagramsMix
doKeepEBonds VirialDiagramsMix2
doKeepEBonds VirialDiagramsPT
doLatticeSum CalcAnalytical2ndDerivativeNitrogen
doLatticeSum CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
doLatticeSum CalcNumerical2ndDerivativeNitrogen
doLogLevel(boolean) Logger
Indicates if the level is logged.
doMapping HSMDCavity.CavityParam
doMappingE Heisenberg.Param
doMappingFoobar HSMDWidom.HSMDParam
doMappingRDF HSMDCavity.CavityParam
doMappingRDF HSMDWidom.HSMDParam
doMinimalBC VirialDiagrams
doMinimalBC VirialDiagramsMix
doMinimalBC VirialDiagramsPT
doMinimalMulti VirialDiagrams
doMinimalMulti VirialDiagramsMix
doMinimalMulti VirialDiagramsPT
doMobileOnly AtomTestDeviation
doMulti ClusterWheatleyMultibody
doMulti ClusterWheatleyMultibodyBD
doMulti ClusterWheatleyMultibodyDerivatives
doMulti ClusterWheatleyMultibodyDerivativesBD
doMulti ClusterWheatleyMultibodyMix
doMultiFromPair VirialDiagrams
doMultiFromPair VirialDiagramsPT
doNBodyStuff(IMolecule, PotentialCalculation, int, IPotentialMolecular, NeighborListManagerMolecular) PotentialMasterListMolecular
Invokes the PotentialCalculationMolecular for the given Molecule with its up and down
neighbors as a single MoleculeSet.
doNbrs AtomNbrClusterer
done ANIntragroupExchange
doNegativeExchange VirialDiagrams
doNegativeExchange VirialDiagramsPT
doNMoleculeSlider PistonCylinderGraphic
doNonEquilibrium PotentialCalculationPressureTensor
DooDad(int) VirialHSBinMultiThreaded.DooDad
doOverwrite WriteS
dop3Aprox VirialHeNonAdditiveD.VirialParam
dop3AproxDiff VirialHeNonAdditiveD.VirialParam
doPaint(Graphics) DisplayBoxCanvas1D
doPaint is the method that handles the drawing of the box to the screen.
doPaint(Graphics) DisplayBoxCanvas2D
Method that handles the drawing of the box to the screen.
doPaint(Graphics) DisplayBoxCanvasG3DSys
doPaint(Graphics) DisplayCanvas
doPaint(Graphics) DisplayPolytopeCanvas2D
doPaint is the method that handles the drawing of the box to the screen.
doPaint(Graphics) DisplayPolytopeCanvasG3DSys
doPaint(Graphics) DisplayBoxCanvas3DGlass
doPair Heisenberg.Param
doPair MeterMappedAveragingVSum
doParse(String, Space) ShapeParser
doParseArgs(ParameterBase, String[]) ParseArgs
doPBC BoundaryDeformablePeriodicSwitch
doPBC BoundaryRectangularPeriodicSwitch
doPrevious ConfigFromFileLAMMPS.ModifierConfiguration
doPrint ClusterCoupledFlippedMultivalue
doPxyAutocor GlassProd.SimParams
doq2 SimLattice.LjMC3DParams
doRandStep() AkimaSplineSmoother
doRDF HSMDWidom.HSMDParam
doRDF PistonCylinderGraphic
doRealSum EwaldSummation
doReeHoover MayerIonicDiagram1qbond
doReeHoover MayerIonicDiagram2qbonds
doReeHoover MayerIonicDiagram4qbonds
doReeHoover VirialDiagrams
doReeHoover VirialDiagramsMix
doReeHoover VirialDiagramsMix2
doReeHoover VirialDiagramsPT
doReeHoover WertheimDiagrams2SiteRho
doReeHoover WertheimDiagrams3SiteRho
dorefpref VirialH2OGCPMD.VirialParam
dorefpref VirialHeD.VirialParam
dorefpref VirialHeNonAdditiveD.VirialParam
dorefpref VirialTraPPE.VirialParam
doResetFilter ColorSchemeLiquidVapor
doResize VirialPolyhedra.VirialHSParam
doReweight SimHSMDVacancy.HSMDVParams
doReweight SimLJVacancy.LJParams
doReweight VirialHSBinMultiThreaded.SimulationWorker
doReweight VirialSQWBinMultiThreaded.SimulationWorker
doRing ClusterChainSoft
doRot HSDimerNPT
doRotation(int, IMolecule, double, double) P2Water4PSoft
doRotationTransform(double, double) MCMoveRotateMoleculePhiTheta
doScaling MeterTargetRPMolecule
doScaling SimOverlapBetaN2RPScaling.SimOverlapParam
doScaling SimOverlapDisorderedAlphaN2RPScaling.SimOverlapParam
doSearch(int, int) ClusterSumMultibody
doSecDerXrNoShift(Vector, Vector, double) P2Nitrogen
doSecDerXrRotRotNoShift(Vector, Vector, double) P2Nitrogen
doSecDerXrRotRotWShift(Vector, Vector, double) P2Nitrogen
doSecDerXrWShift(Vector, Vector, double) P2Nitrogen
doSerialize Wrapper
doSerialize() Wrapper
doSfac ConfigFromFileLAMMPS.ConfigFromFileLAMMPSParam
doShape HSDimerNPT
doShiftInitY() AkimaSplineSmootherDy
doShortcut MayerIonicDiagram1qbond
doShortcut MayerIonicDiagram2qbonds
doShortcut MayerIonicDiagram4qbonds
doShortcut VirialDiagrams
doShortcut VirialDiagramsMix
doShortcut VirialDiagramsMix2
doShortcut VirialDiagramsPT
doShortcut WertheimDiagrams2SiteRho
doShortcut WertheimDiagrams3SiteRho
doShowCorrelation DisplayTextBoxesCAE
doShowCurrent DisplayTextBoxesCAE
doStatistics ClusterWheatleyPartitionScreening
doStep() Integrator
Performs the elementary integration step, such as a molecular dynamics
time step, or a Monte Carlo trial.
doStep() AkimaSplineSmoother
doStep() AkimaSplineSmootherDy
doStepInternal() IntegratorDimerApproach
doStepInternal() IntegratorDCVGCMD
doStepInternal() IntegratorDimerMin
doStepInternal() IntegratorDimerRT
doStepInternal() IntegratorEnergyMap
doStepInternal() IntegratorImageHarmonicMD
doStepInternal() IntegratorImageMultistepMD
doStepInternal() IntegratorMDHarmonicMC
doStepInternal() Integrator
Performs the elementary integration step, such as a molecular dynamics
time step, or a Monte Carlo trial.
doStepInternal() IntegratorGear4
doStepInternal() IntegratorHard
Steps all atoms across time interval timeStep, handling all intervening collisions.
doStepInternal() IntegratorManagerMC
Performs a Monte Carlo trial that attempts to swap the configurations
between two "adjacent" boxes, or instructs all integrators to perform
a single doStep.
doStepInternal() IntegratorMC
Method to select and perform an elementary Monte Carlo move and decide acceptance.
doStepInternal() IntegratorMD
doStepInternal() IntegratorRigidIterative
doStepInternal() IntegratorRigidMatrixIterative
doStepInternal() IntegratorVelocityVerlet
doStepInternal() IntegratorVelocityVerletRattle
doStepInternal() IntegratorVelocityVerletShake
doStepInternal() IntegratorVerlet
doStepInternal() IntegratorKMC
doStepInternal() IntegratorKMCCluster
doStepInternal() AkimaSplineSmootherApp.IntegratorSmoother
doStepInternal() AkimaSplineSmootherDyApp.IntegratorSmoother
doStepInternal() IntegratorHybrid
doStepInternal() IntegratorDCVGCMD
doStepInternal() IntegratorDroplet
doStepInternal() IntegratorHardPiston
doStepInternal() IntegratorPolymer
doStepInternal() IntegratorVelocityVerletSAM
doStepInternal() IntegratorHarmonic
doStepInternal() IntegratorOverlap
doStepInternal() IntegratorVelocityVerletQuaternion
doStepInternal() IntegratorTMMC
Method to select and perform an elementary Monte Carlo move.
doStepInternal() IntegratorOverlap
Deprecated.
doSubtractComb DataSourceFE
doSum112(double[], double[], double[], double[], double) P3CPSNonAdditiveHe
doSum113(double[], double[], double[], double[], double) P3CPSNonAdditiveHe
doSum122(double[], double[], double[], double[], double, double) P3CPSNonAdditiveHe
doSum644(double[], double[], double[], double[], double, double, double, double) P3CPSNonAdditiveHe
doSum660(double[], double[], double) P3CPSNonAdditiveHe
doSum734(double[], double[], double[], double[], double, double, double, double) P3CPSNonAdditiveHe
doSum770(double[], double[], double[]) P3CPSNonAdditiveHe
doSum833(double[], double[], double[], double, double, double) P3CPSNonAdditiveHe
doSum860(double[], double[], double) P3CPSNonAdditiveHe
doSums(double[], double) AccumulatorAverageBootstrap
Performs the block sum after
doSums(double[], double) AccumulatorAverageCollapsingLog
Performs the block sum after
doSurfacetension ExternalVirialDiagrams
doSwap ApiInnerVariable
doSwap SimGlass.GlassParams
doSwap MpiInnerVariable
dot(Vector) Vector
Returns the dot product of this vector with the given one.
dot(Vector) Vector1D
dot(Vector) Vector2D
dot(Vector) Vector3D
dot(Vector) VectorND
dot(Quaternion) Quaternion
dot(Vector3f) Vector3f
Computes the dot product of the this vector and vector v.
dotdensity Token
doThermostat() IntegratorMD
Invokes thermostat, modifying velocities according to specified temperature and
algorithm of thermostat specified via setThermostat.
doThermostat() IntegratorHardMDMC
doThermostat() IntegratorHarmonic
doThermostatInternal() IntegratorMD
Fires the thermostat if the appropriate interval has been reached.
doThermostatInternal() IntegratorPolymer
doTotal ClusterWheatleyMultibody
doTotal ClusterWheatleyMultibodyBD
doTotal ClusterWheatleyMultibodyDerivatives
doTotal ClusterWheatleyMultibodyDerivativesBD
doTotal VirialH2PI.VirialH2PIParam
doTotal VirialHeNonAdditiveD.VirialParam
doTotal VirialHeNonAdditiveWheatley.VirialParam
doTotal VirialHePI_PotentialCorrection.VirialHePIParam
doTotal VirialHePI.VirialHePIParam
doTotal VirialHePISysErr.VirialHePIParam
doTotal VirialHePIXCEven.VirialHePIParam
doTotal VirialHePIXCOdd.VirialHePIParam
doTransform() MCMoveRotateMolecule3D
doTransform() MCMoveRotateMolecule3DConstraint
doTransform() MCMoveRotateMolecule3DN2AveCosThetaConstraint
doTransform() MCMoveVolumeMonoclinicScaled
doTransform() MCMoveBondLength
doTransform() MCMoveClusterBondLength
doTransform() MCMoveClusterConformationMDTest
doTransform() MCMoveClusterRotateArm
doTransform() MCMoveRotateArm
doTransform(double) MCMoveVolumeSolidNPTMolecular
doTransform(double) MCMoveVolumeSolidNPTMolecularOriented
doTransform(IAtom) MCMoveDimerRotate
doTransform(IAtom) MCMoveDimerRotate
doTransform(IAtomOriented) MCMoveSmerRotate
doTransform(IMolecule) P2Water4PSoft
doTransform(IMolecule, IMoleculePositionDefinition, Tensor) MinimizationBetaNitrogenModel
doTransform(IMolecule, IMoleculePositionDefinition, Tensor) MinimizationBetaNitrogenModelLS
doTransform(IMolecule, Boundary, Tensor) MinimizationTIP4P
doTransform(IMolecule, Vector) MCMoveBiasUBMolecule
doTransform(IMolecule, Vector) MCMoveRotateMolecule3DSuperBox
doTransform(IMolecule, Vector, RotationTensor) OrientationCalcWater3P
doTransform(IMolecule, Vector, RotationTensor) OrientationCalcWater4P
doTransform(IMolecule, Vector, Vector, double) BiasVolume2SiteAceticAcid
doTransform(IMolecule, Vector, Vector, double) BiasVolumeAceticAcid
doTransformMolec(int, double) MCMoveRotateMolecule3DConstraint
doTransformPhi(IMolecule) MCMoveVolumeSolidNPTMolecularOriented
doTransformTheta(IMolecule, double, double) MCMoveVolumeSolidNPTMolecularOriented
doTransformToInitial(int, double) MCMoveRotateMolecule3DConstraint
doTrial() MCMoveAtomSmer
doTrial() MCMoveBiasUB
doTrial() MCMoveBiasUBMolecule
doTrial() MCMoveDimer
Method to perform trial move.
doTrial() MCMoveDimerRotate
Method to perform trial move.
doTrial() MCMoveMoleculeRotateAssociated
doTrial() MCMoveMoleculeSmer
doTrial() MCMoveRotateAssociated
doTrial() MCMoveSmer
Method to perform trial move.
doTrial() MCMoveSmerRotate
Method to perform trial move.
doTrial() MCMoveVolumeAssociated
doTrial() MCMoveVolumeAssociatedMolecule
doTrial() MyMCMove
Chooses and performs with equal probability an elementary molecule insertion
or deletion.
doTrial() MCMoveAtomCoupled
Method to perform trial move.
doTrial() MCMoveAtomNPath
Method to perform trial move.
doTrial() MCMoveAtomSwap
Method to perform trial move.
doTrial() MCMove
Method to perform trial move.
doTrial() MCMoveAtom
doTrial() MCMoveAtomInRegion
doTrial() MCMoveBoxSize
doTrial() MCMoveDimer
Method to perform trial move.
doTrial() MCMoveDimerRotate
Method to perform trial move.
doTrial() MCMoveInsertDelete
Chooses and performs with equal probability an elementary molecule insertion
or deletion.
doTrial() MCMoveInsertDeleteLatticeVacancy
doTrial() MCMoveInsertDeleteVacancy
doTrial() MCMoveMolecule
doTrial() MCMoveMoleculeExchange
doTrial() MCMoveMoleculeExchangeVLE
doTrial() MCMoveRotate
doTrial() MCMoveRotateMolecule3D
doTrial() MCMoveSemigrand
doTrial() MCMoveSwapConfiguration
doTrial() MCMoveTorsionAceticAcid
doTrial() MCMoveVolume
doTrial() MCMoveVolumeExchange
doTrial() MCMoveVolumeExchangeVLE
doTrial() MCMoveWiggleAceticAcid
doTrial() MCMoveAtomNbr
doTrial() MCMoveMoleculeCoupledInitPert
doTrial() MCMoveMoleculeCoupledSuperBox
doTrial() MCMoveRotateMolecule3DConstraint
doTrial() MCMoveRotateMolecule3DFixedAngle
doTrial() MCMoveRotateMolecule3DN2AveCosThetaConstraint
doTrial() MCMoveRotateMolecule3DSuperBox
doTrial() MCMoveVolumeN2
doTrial() MyMCMove
Chooses and performs with equal probability an elementary molecule insertion
or deletion.
doTrial() MyMCMove
Chooses and performs with equal probability an elementary molecule insertion
or deletion.
doTrial() MCMoveSwap
doTrial() MCMoveMultiHarmonic
doTrial() MCMoveAtomCoupled
Method to perform trial move.
doTrial() MCMoveAtomCoupledBennet
Method to perform trial move.
doTrial() MCMoveAtomCoupledUmbrella
Method to perform trial move.
doTrial() MCMoveAtomSuperBox
Method to perform trial move.
doTrial() MCMoveEinsteinCrystal
doTrial() MCMoveHarmonic
doTrial() MCMoveHarmonicEin
doTrial() MCMoveHarmonicStep
doTrial() MCMoveMoleculeCoupled
doTrial() MCMovePhaseAngle
doTrial() MCMoveRotateMoleculePhiTheta
doTrial() MCMoveSingleMode
doTrial() MCMoveVolumeMonoclinic
doTrial() MCMoveVolumeMonoclinicAngle
doTrial() MCMoveVolumeMonoclinicScaled
doTrial() MCMoveVolumeSolid
doTrial() MCMoveVolumeSolidNPTMolecular
doTrial() MCMoveWV
doTrial() MCMoveGeometricCluster
doTrial() MCMoveGeometricClusterRestrictedGE
doTrial() MCMoveRotate3Pair
doTrial() MCMoveRotatePair
doTrial() MCMoveSpinCluster
doTrial() MCMoveSpinFlip
doTrial() MCMoveBondLength
doTrial() MCMoveClusterBondLength
doTrial() MCMoveClusterConformationMDTest
doTrial() MCMoveClusterMoleculeHSChain
doTrial() MCMoveClusterMoleculeHSChainB3
doTrial() MCMoveClusterRotateArm
doTrial() MCMoveRotateArm
doTrial() MCMoveWiggle
doTrial() MCMoveChangeBondLength
doTrial() MCMoveClusterAngleBend
doTrial() MCMoveClusterAngleBendAceticAcid
doTrial() MCMoveClusterAtom
doTrial() MCMoveClusterAtomChainHSTail
doTrial() MCMoveClusterAtomDiscrete
doTrial() MCMoveClusterAtomHSChain
doTrial() MCMoveClusterAtomHSRing
doTrial() MCMoveClusterAtomHSTree
doTrial() MCMoveClusterAtomInBox
doTrial() MCMoveClusterAtomMulti
doTrial() MCMoveClusterAtomQ
doTrial() MCMoveClusterAtomRotateMulti
doTrial() MCMoveClusterDiagram
doTrial() MCMoveClusterMolecule
doTrial() MCMoveClusterMoleculeHSChain
doTrial() MCMoveClusterMoleculeLayerMove
doTrial() MCMoveClusterMoleculeMulti
doTrial() MCMoveClusterPolyhedraChain
doTrial() MCMoveClusterPolyhedraTree
doTrial() MCMoveClusterReptateMulti
doTrial() MCMoveClusterRingPartialRegrow
doTrial() MCMoveClusterRingRegrow
doTrial() MCMoveClusterRingRegrowExchange
doTrial() MCMoveClusterRingRegrowOrientation
doTrial() MCMoveClusterRingScale
doTrial() MCMoveClusterRotateCH3
doTrial() MCMoveClusterRotateMolecule3D
doTrial() MCMoveClusterRotateMoleculeMulti
doTrial() MCMoveClusterTorsionAceticAcid
doTrial() MCMoveClusterTorsionAlkaneEH
doTrial() MCMoveClusterTorsionMulti
doTrial() MCMoveClusterWiggleAceticAcid
doTrial() MCMoveClusterWiggleAlkaneEH
doTrial() MCMoveClusterWiggleMulti
doTrial() MCMoveSwapCluster
dots Token
dotscale Token
dotsselectedonly Token
dotsurface Token
DOUBLE EnumStereoMode
DoubleAssociationSitesFluid2Pt etomica.virial.simulations
DoubleAssociationSitesFluid2Pt() DoubleAssociationSitesFluid2Pt
DoubleAssociationSitesFluid2Pt.VirialAssociatingFluidParam etomica.virial.simulations
DoubleAssociationSitesFluid3Pt etomica.virial.simulations
DoubleAssociationSitesFluid3Pt() DoubleAssociationSitesFluid3Pt
DoubleAssociationSitesFluid3Pt.VirialAssociatingFluidParam etomica.virial.simulations
DoubleAssociationSitesFluid4Pt 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() DoubleAssociationSitesFluid4Pt
DoubleAssociationSitesFluid4Pt.VirialAssociatingFluidParam etomica.virial.simulations
doubleLength(Object) ArrayUtil
Very important that this not be used with Int32Array or Float32Array,
because it is not initialized to all zeros in MSIE 9.
doubleLengthBool(boolean[]) ArrayUtil
doubleLengthByte(byte[]) ArrayUtil
doubleLengthF(float[]) ArrayUtil
doubleLengthI(int[]) ArrayUtil
doubleLengthS(String[]) ArrayUtil
doubleLengthShort(short[]) ArrayUtil
DoubleRange etomica.math
DoubleRange(double, double) DoubleRange
Constructs the range defined by given values.
doubleValue() BigSurd
Return a double value representation.
doubleValue() BigSurdVec
Construct an approximate floating point representation
doubleValue() Rational
Return a double value representation.
DoubleWrapper() CriterionPositionWall.DoubleWrapper
doUntransform AccumulatorAverageBootstrap
doUp RectangularLatticeNbrIterator
doUpdate() DeviceBox
Updates the display of the box with the current value given by the modifier.
doUpdate() DeviceSlider
doUpdate() DeviceSpinner
doUpdate() DisplayPlot
Redraws the plot.
doUpdate() DisplayPlotXChart
doUpdate() DisplayPolytope
doUpdate() DeviceThermoSliderGEMC
doUpdateFMulti(int, IMoleculeList, CoordinatePairSet) ClusterSumMultibody
doVel ConfigurationStorage
doVSum Heisenberg.Param
doVSum MeterMappedAveragingVSum
doVSumMI Heisenberg.Param
doVSumMI MeterMappedAveragingVSum
doWheatley VirialHSBinMultiThreaded.SimulationWorker
doWheatley VirialHSBinMultiThreaded.VirialHSBinParam
doWidom HSMDWidom.HSMDParam
doWidomCavity HSMDWidom.HSMDParam
doWiggle ModelSimulationEnvironment
doWiggle SimulationVirial
doWiggle SimulationVirialOverlap2
DOWN IteratorDirective.Direction
downList IntegratorHard
downList AtomNeighborLists
downList MoleculeNeighborLists
dP MeterSolidProps
dP MeterSolidPropsLJ
dP PotentialCalculationLJSP
dPdRho(double) EOSSWPatel
dPdRho(double) VEOS3SW
dphi_du(int[], double[]) CalcNumerical2ndDerivative
dphi_du(int[], double[]) FiniteDifferenceDerivativeCGNitrogenBeta
dPlot B2Fit
dPlot B2Fit.FunctionB2LJQ
dPlot B2Fit.FunctionMayerB2LJQ
dpolx PNCO2GCPM.P3GCPMAxilrodTeller
dpVirialOverlap SimulationVirialOverlap2
dpvx10dt1 PotentialCalculationMoleculeAgentSum
dpvx10dt1 PotentialCalculationPair
dpvx10dt2 PotentialCalculationMoleculeAgentSum
dpvx10dt2 PotentialCalculationPair
dpvx11dt1 PotentialCalculationMoleculeAgentSum
dpvx11dt1 PotentialCalculationPair
dpvx11dt2 PotentialCalculationMoleculeAgentSum
dpvx11dt2 PotentialCalculationPair
dpvx20dt1 PotentialCalculationMoleculeAgentSum
dpvx20dt1 PotentialCalculationPair
dpvx20dt2 PotentialCalculationMoleculeAgentSum
dpvx20dt2 PotentialCalculationPair
dpvx21dt1 PotentialCalculationMoleculeAgentSum
dpvx21dt1 PotentialCalculationPair
dpvx21dt2 PotentialCalculationMoleculeAgentSum
dpvx21dt2 PotentialCalculationPair
dpvy10dt1 PotentialCalculationMoleculeAgentSum
dpvy10dt1 PotentialCalculationPair
dpvy10dt2 PotentialCalculationMoleculeAgentSum
dpvy10dt2 PotentialCalculationPair
dpvy11dt1 PotentialCalculationMoleculeAgentSum
dpvy11dt1 PotentialCalculationPair
dpvy11dt2 PotentialCalculationMoleculeAgentSum
dpvy11dt2 PotentialCalculationPair
dpvy20dt1 PotentialCalculationMoleculeAgentSum
dpvy20dt1 PotentialCalculationPair
dpvy20dt2 PotentialCalculationMoleculeAgentSum
dpvy20dt2 PotentialCalculationPair
dpvy21dt1 PotentialCalculationMoleculeAgentSum
dpvy21dt1 PotentialCalculationPair
dpvy21dt2 PotentialCalculationMoleculeAgentSum
dpvy21dt2 PotentialCalculationPair
dqdVCalc(double, int) Ushcats
dr AssociationHelperBranched
dr AssociationHelperDouble
dr AssociationHelperMolecule
dr MCMoveAtomMonomer
dr MCMoveAtomSmer
dr MCMoveBiasUB
dr MCMoveDimer
dr MCMoveDimerRotate
dr MCMoveMoleculeMonomer
dr MCMoveMoleculeSmer
dr MCMoveRotateAssociated
dr MCMoveSmer
dr MCMoveSmerRotate
dr MCMoveVolumeAssociated
dr MCMoveVolumeAssociatedMolecule
dr MeterCavityMapped
dr MeterRDFMapped
dr MeterWidomCavity
dr MeterDipoleSumSquaredMappedAverage
dr MeterRDF
dr MeterRMSD
dr PotentialCalculationRDF
dr P2EAM
dr PotentialCuLREP
dr PotentialEAM_LS
dr PotentialEAM
dr PotentialEFS
dr ConfigFromFileLAMMPS.ColorSchemeDeviation
dr IntegratorImageHarmonicMD
dr IntegratorMDHarmonicMC
dr MCMoveAtomSwap
dr P1ImageHarmonic
dr ColorSchemeOverlap
dr IntegratorVelocityVerletShake
dr MCMoveDimer
dr MCMoveDimerRotate
dr MCMoveInsertDeleteLatticeVacancy
dr MCMoveInsertDeleteVacancy
dr Potential2SoftSphericalLSMulti
dr Potential2SoftSphericalLSMultiLat
dr PotentialCalculationEnergySumCutoff
dr PotentialCalculationSumCutoff
dr PotentialCalculationMappedRdf
dr MeterMeanForce
dr PotentialCalculationMappedEnergy
dr PotentialCalculationMappedVirial
dr PotentialCalculationMappedVirialV
dr P2Water4PSoft
dr P2SquareWellBonding
dr MeterEnd2End
dr IntegratorDroplet
dr AtomNbrClusterer
dr AtomSignalMobility
dr AtomTestDeviation
dr ColorSchemeDeviation
dr ColorSchemeDirection
dr ConfigurationStorage
dr DataSourceF
dr DataSourceFOld
dr DataSourceFs
dr DataSourceQ4
dr DataSourceStrings
dr DisplayBoxCanvas2DGlass
dr DisplayBoxCanvas3DGlass
dr MeterCorrelation
dr MeterGs
dr InsertionGraphic.MeterWidom
dr MeterOrientation
dr P1MagicWall
dr IntegratorPolymer
dr MeterEndToEnd
dr MeterNormalStress
dr MeterViscosity
dr MeterTilt
dr MoleculePositionGeometricCenterPBC
dr CriterionPositionWall
dr CriterionSimple
dr CriterionSimpleMolecular
dr MCMoveEinsteinCrystal
dr MCMoveRotateMoleculePhiTheta
dr MCMoveVolumeSolid
dr MCMoveVolumeSolidNPTMolecularOriented
dr MeterDADB
dr MeterDisplacementMoleculeRMS
dr MeterDisplacementRMS
dr MeterMaxExpansion
dr MeterPhiDeviation
dr MeterSolidDA
dr MeterSolidMirror
dr MeterSolidProps
dr MeterSolidPropsLJ
dr MeterThetaDeviation
dr MeterTilt
dr MeterTiltHistogram
dr MeterTiltRotation
dr MeterTiltRotationHistogram
dr MeterTiltRotationStdev
dr ColorSchemeScaledOverlap
dr P2XOrder
dr PotentialCalculationSolidSuper
dr PotentialCalculationSolidSuperCut
dr MeterRmin
dr MeterRminSpecies
dr PotentialDepletion
dr P2HardSpherePoly
dr P2DiscreteFeynmanHibbs
dr P2EffectiveFeynmanHibbs
dr P2HydrogenHinde
dr P2HydrogenHindeAtomic
dr P2HydrogenHindePatkowski
dr P2HydrogenHindePatkowskiAtomic
dr P2HydrogenPatkowski
dr P2HydrogenPatkowskiAtomic
dr P2MoleculeSoftTruncatedSwitched
dr P2MoleculeTruncated
dr P2O2Bartolomei.P2O2TI
dr P2ReactionFieldDipole
dr P2ReactionFieldDipoleTruncated
dr P2SoftSphericalTruncatedSwitched
dr P2SoftTruncated
dr P2SpheroPolyhedron
dr P2WCAP
dr P3HydrogenATM
dr Potential2HardSpherical
dr Potential2SoftSpherical
dr Potential2SoftSphericalLS
dr PotentialCalculationFSum
dr PotentialCalculationPhiSum
dr PotentialCalculationPhiSumHeisenberg
dr MeterMappedAveraging
dr MeterMappedAveraging3Pair
dr MeterMappedAveragingFreeEnergy
dr MeterMappedAveragingPair
dr MeterMappedAveragingPairExcess
dr MeterMappedAveragingSum
dr MeterMappedAveragingVSum
dr MeterMappedAveragingVSum3Pair
dr MeterMappedAveragingVSumPair
dr MeterPairSum
dr P2Spin
dr PotentialCalculationFSum
dr PotentialCalculationSumquare
dr MCMoveBondLength
dr MCMoveClusterBondLength
dr MeterBondLength
dr CoordinatePairLeafSet
dr CoordinatePairMoleculeSet
dr MayerHSMixture
dr MCMoveClusterAtomChainHSTail
dr MCMoveClusterAtomDiscrete
dr MCMoveClusterPolyhedraChain
dr VirialHSOrC.VirialLJrParam
dr VirialLJOrC.VirialLJrParam
dr VirialLJOrICPYC.VirialLJrParam
dR PotentialEAM_LS
dR P3HydrogenGarberoglioMolecular
dr0 Potential2SoftSphericalLSMultiLat
dr0 P2Water4PSoft
dr0 CorrelationSelf2
dr0 PotentialCalculationSolidSuper
dr0 PotentialCalculationSolidSuperCut
dr01 CorrelationSelf2
dr01 MeterCorrelationSelf
dr01 P2Exp6
dr01 P2LennardJonesDreiding
dr1 IntegratorGear4.Agent
dr1 P2Nitrogen
dr1 P2Water4PSoft
dr1 P3AxilrodTeller
dr1 P3Induction
dr12 CorrelationSelf2
dr12 MeterCorrelationSelf
dr12 P3BondAngle
dr12 P3BondAngleDreiding
dr12 P4TorsionDreiding
dr1Sum MeterCorrelationSelf
dr1SumA MeterCorrelation
dr1SumB MeterCorrelation
dr2 MCMoveSmerRotate
dr2 MCMoveVolumeAssociated
dr2 MCMoveVolumeAssociatedMolecule
dr2 IntegratorGear4.Agent
dr2 P2Nitrogen
dr2 DataSourceStrings
dr2 P3AxilrodTeller
dr2 P3Induction
dr2 P2Spin
dr21 P4BondTorsion
dr21 P4BondTorsionAlkaneXCCH
dr21 MCMoveClusterTorsionAlkaneEH
dr21 MCMoveClusterTorsionMulti
dr23 P3BondAngle
dr23 P3BondAngleDreiding
dr23 P4BondTorsion
dr23 P4BondTorsionAlkaneXCCH
dr23 P4TorsionDreiding
dr23 MCMoveClusterTorsionAlkaneEH
dr23 MCMoveClusterTorsionMulti
dr2CountA MeterCorrelation
dr2CountB MeterCorrelation
dr2StringMax ColorSchemeDeviation
dr2Sum CorrelationSelf2
dr2Sum MeterCorrelationSelf
dr2SumA MeterCorrelation
dr2SumB MeterCorrelation
dr3 IntegratorGear4.Agent
dr34 P4BondTorsion
dr34 P4BondTorsionAlkaneXCCH
dr34 P4TorsionDreiding
dr34 MCMoveClusterTorsionAlkaneEH
dr34 MCMoveClusterTorsionMulti
dr3Sum MeterCorrelationSelf
dr4 IntegratorGear4.Agent
dra P4TorsionDreiding
drA Potential2SoftSphericalLSMultiLat
drA PotentialCalculationSolidSuper
drA PotentialCalculationSolidSuperCut
drAB P3CPSNonAdditiveHe
drAB P3CPSNonAdditiveHeLessSimplified
drAB P3CPSNonAdditiveHeOrig
drAB P3CPSNonAdditiveHeSimplified
drAC P3CPSNonAdditiveHe
drAC P3CPSNonAdditiveHeLessSimplified
drAC P3CPSNonAdditiveHeOrig
drAC P3CPSNonAdditiveHeSimplified
dragselected Token
drAll IntegratorMDHarmonicMC
draw Token
draw() GraphMap
draw() G3DSys
draw() Axes
draw() Ball
draw() Bond
draw() Box
draw() Ellipse
draw() Figure
All Figures know how to draw themselves via override.
draw() ImageShell
draw() Line
draw() Triangle
draw(Graphics, int[], double) Drawable
draw(Graphics, int[], double) Osmosis.MyWall
draw(Graphics, int[], double) P1HardBoundary
draw(Graphics, int[], double) P1HardMovingBoundary
draw(String, String, Point3f, float) Quaternion
DRAW_BOUNDARY_ALL DisplayCanvas
DRAW_BOUNDARY_MAX DisplayCanvas
DRAW_BOUNDARY_NONE DisplayCanvas
DRAW_BOUNDARY_OUTLINE DisplayCanvas
DRAW_BOUNDARY_SHELL DisplayCanvas
DRAW_EVERY_BOX ImageShell
DRAW_INNER_BOX ImageShell
DRAW_LARGE_BOX ImageShell
Drawable etomica.graphics
drawAtom(Graphics, int[], IAtom) DisplayBoxCanvas2D
drawAtom(Graphics, int[], IAtom) DisplayBoxSpin2D
drawAtom(Graphics, int[], IAtom) DisplayBoxCanvas2DGlass
drawAtom(Graphics, int[], IAtom) DisplayBoxCanvas2DNpTScaling
drawBond(Point3f, Point3f, short, short, byte, short, int) Graphics3D
drawDashedLine(int, int, Point3i, Point3i) Graphics3D
drawDisplacement DisplayBoxCanvas2DGlass
drawDisplacement DisplayBoxCanvas3DGlass
drawDottedLine(Point3i, Point3i) Graphics3D
drawEllipse(Point3f, Point3f, Point3f, boolean, boolean) Graphics3D
drawFilledCircle(short, short, int, int, int, int) Graphics3D
drawHermite4(int, Point3i, Point3i, Point3i, Point3i) Graphics3D
drawHermite7(boolean, boolean, int, Point3i, Point3i, Point3i, Point3i, Point3i, Point3i, Point3i, Point3i, int, short) Graphics3D
drawhover Token
drawImage(Object, int, int, int, int, short, int, int) Graphics3D
drawImage(Object, Object, int, int, int, int) ApiPlatform
drawImage(Object, Object, int, int, int, int) Platform
drawImageToBuffer(Object, Object, Object, int, int, int) ApiPlatform
drawImageToBuffer(Object, Object, Object, int, int, int) Platform
drawLine(short, short, int, int, int, int, int, int) Graphics3D
drawLineAB(Point3i, Point3i) Graphics3D
drawLineList DisplayPlot
drawLineXYZ(int, int, int, int, int, int) Graphics3D
drawpicking Token
drawPixel(int, int, int) Graphics3D
drawPoints(int, int[], int) Graphics3D
drawQuadrilateral(short, Point3i, Point3i, Point3i, Point3i) Graphics3D
drawRect(int, int, int, int, int, int) Graphics3D
draws a rectangle
drawSize DisplayBox
Size of drawing region of central image, in pixels
drawSize DisplayPolytope
Size of drawing region of central image, in pixels
drawString(String, JmolFont, int, int, int, int, short) Graphics3D
draws the specified string in the current font.
drawStringNoSlab(String, JmolFont, int, int, int, short) Graphics3D
draws the specified string in the current font.
drawSurface(MeshSurface, short) Graphics3D
drawTriangle3C(Point3i, short, Point3i, short, Point3i, short, int) Graphics3D
drawTriangle3I(Point3i, Point3i, Point3i, int) Graphics3D
drb P4TorsionDreiding
drB PotentialCalculationSolidSuper
drB PotentialCalculationSolidSuperCut
drBC P3CPSNonAdditiveHe
drBC P3CPSNonAdditiveHeLessSimplified
drBC P3CPSNonAdditiveHeOrig
drBC P3CPSNonAdditiveHeSimplified
drbxa P4TorsionDreiding
drho HardSphereSolid.EOSParams
dri ConfigurationStorage
dri MeterCorrelation
dri MeterGs
dri PotentialCalculationEFSSP
dri PotentialCalculationLJSP
drij PotentialCuLREP
drij PotentialEAM
drij PotentialEFS
drij P2CO2H2OWheatley
drij P2CO2Hellmann
drij P2WaterSzalewicz.P2H2OSC
drij PotentialCalculationEFSSP
drij PotentialCalculationLJSP
drijRot P2CO2H2OWheatley.P2CO2H2OSC
drijRot P2CO2H2OWheatley.P2CO2H2OSCTI
drijRot P2CO2Hellmann.P2CO2SC
drijRot P2WaterSzalewicz.P2H2OSC
drijRot P2NitrogenHellmann.P2N2QFH
drik PotentialCuLREP
drik PotentialEAM
drik PotentialEFS
drj MeterGs
drj P1ConstraintNbr
drj P1ConstraintNbrHcp
drj PotentialCalculationEFSSP
drj PotentialCalculationLJSP
drj_tmp PotentialCalculationLJSP
drjk PotentialCuLREP
drjk PotentialEAM
drjk PotentialEFS
drk MeterCorrelation
drk P1ConstraintNbr
drk P1ConstraintNbrHcp
drLat Potential2SoftSphericalLSMultiLat
drLatTmp Potential2SoftSphericalLSMultiLat
drOld IntegratorVelocityVerletShake
drOO P2SquareWellBondingCO
drop(Parser.CommandVariable) Interpreter
Droplet etomica.modules.droplet
Mesoscale simulation for Droplet module.
Droplet() Droplet
DropletAtomic etomica.modules.droplet
Atomic simulation for Droplet module.
DropletAtomic() DropletAtomic
DropletAtomicGraphic etomica.modules.droplet
Graphic UI for Droplet module.
DropletAtomicGraphic(DropletAtomic, Space) DropletAtomicGraphic
DropletAtomicGraphic.Applet etomica.modules.droplet
DropletAtomicGraphic.DataSourceVaporDensity etomica.modules.droplet
DropletGraphic etomica.modules.droplet
Graphic UI for Droplet module.
DropletGraphic(Droplet, Space) DropletGraphic
DropletGraphic.Applet etomica.modules.droplet
DropletGraphic.DataProcessorTensorSplitter etomica.modules.droplet
Inner class to find the total pressure of the system from the pressure
tensor.
DropletGraphic.ModifierBoxSize etomica.modules.droplet
DropOrphanNodes etomica.graph.operations
DropOrphanNodes() DropOrphanNodes
dropPrime() Ifactor
Divide through the highest possible power of the highest prime.
dropRadius DropletAtomic
drPrev IntegratorPolymer
drSite0 PotentialCalculationSolidSuper
drSite0 PotentialCalculationSolidSuperCut
drSite1 PotentialCalculationSolidSuper
drSite1 PotentialCalculationSolidSuperCut
drSum MeterTilt
drSum MCMoveRotateMoleculePhiTheta
drSum MCMoveVolumeSolidNPTMolecularOriented
drSum MeterPlaneSlip
drSum MeterTilt
drSum MeterTiltRotation
drSum MeterTiltRotationHistogram
drSumPlane MeterTiltRotation
drSumSave MCMoveVolumeSolidNPTMolecularOriented
drtmp PotentialEAM_LS
drtmp Potential2SoftSphericalLSMulti
drtmp Potential2SoftSphericalLS
drTmp MeterRMSD
drTmp IntegratorImageHarmonicMD
drTmp IntegratorMDHarmonicMC
drTmp Potential2SoftSphericalLSMultiLat
drTmp EwaldSummation
dRtmp PotentialEAM_LS
drTot MeterEnd2End
drvDamp P2WaterSzalewicz.P2H2OSC
ds IntegratorPolymer
ds MeterSolidMirror
dSigma MeterSolidPropsLJ
dsmr DataSourceAvgPressure2
dss LjMd3D.ValueCache
dss ValueCache
dsspcalchydrogen Token
dst SVGConverter
Destination image path.
dst CalcFFT
dsum MeterVirialBDBinMultiThreaded.MyData
dsum2 MeterVirialBDBinMultiThreaded.MyData
dsvo SimOverlapBetaN2RP
dsvo SimOverlapNitrogenModel
dsvo MultiharmonicGraphicMC.DataSourceAlphaAlpha
dsvo MultiharmonicGraphicMC.DataSourceAlphaChi
dsvo MultiharmonicGraphicMC.DataSourceChiSlope
dsvo MultiharmonicGraphicMC.DataSourceUa
dsvo MultiharmonicGraphicMC.DataSourceUa2
dsvo MultiharmonicGraphicMC.DataSourceAlphaAlpha
dsvo MultiharmonicGraphicMC.DataSourceAlphaChi
dsvo SimOverlap
dsvo SimOverlapLJ
dsvo SimOverlapLJModule
dsvo SimOverlapSoftSphere
dsvo SimOverlapSoftSphereEinHarm
dsvo SimOverlapSoftSphereHCP
dsvo SimOverlapSoftSphereReweighting
dsvo SimOverlapSoftSphereSoftness
dsvo SimOverlapSoftSphereSuperBox
dsvo SimOverlapSSnxy
dt AccumulatorAutocorrelationPTensor
dt AccumulatorAutocorrelationShearStress
dt AccumulatorPTensor
dtdotkdetak MeterMappedAveragingCorrelation
dtdotkdetak MeterMappedAveragingVSum
dtdotkdt0k MeterMappedAveragingCorrelation
dtdotkdt0k MeterMappedAveragingVSum
dtheta MeterMeanField
dTheta IntegratorDimerMin
dTheta IntegratorDimerRT
dTheta MCMoveClusterAngleBend
dTheta MCMoveClusterAngleBendAceticAcid
du(double) P2RepRowley
The derivative r*du/dr.
du(double) P2Cohesion
du(double) P1HydrogenMielke
du(double) P1IntraMolecular
du(double) P2Anharmonic
The derivative r*du/dr.
du(double) P2ArgonAziz1993
The derivative r*du/dr.
du(double) P2ArgonSlavicekEtAl2003
The derivative r*du/dr.
du(double) P2ArgonTangAndToennies2003
The derivative r*du/dr.
du(double) P2DiscreteFeynmanHibbs.P2HeEmpericalQuantum
du(double) P2Dreiding
The derivative r*du/dr.
du(double) P2Electrostatic
du(double) P2ElectrostaticWithHardCore
du(double) P2Exp6
The derivative r*du/dr.
du(double) P2Exp6Buckingham
The derivative r*du/dr.
du(double) P2Fene
The derivative r*du/dr.
du(double) P2HardAssociationConeDoubleSites
du(double) P2HardAssociationConeFourSites
du(double) P2HardAssociationConeOneSite
du(double) P2Harmonic
The derivative r*du/dr.
du(double) P2HC2Yukawa
du(double) P2HePCJS
The derivative r*du/dr.
du(double) P2HePCKLJS
The derivative r*du/dr.
du(double) P2HeSimplified
The derivative r*du/dr.
du(double) P2HydrogenPatkowskiIso
du(double) P2Ideal
Returns zero.
du(double) P2LennardJones
The derivative r*du/dr.
du(double) P2LennardJonesDreiding
The derivative r*du/dr.
du(double) P2LJQ
du(double) P2LJQQ
du(double) P2ModifiedMorse
The derivative r*du/dr.
du(double) P2Morse
The derivative r*du/dr.
du(double) P2QChemInterpolated
The derivative r*du/dr.
du(double) P2SoftSphere
The derivative r*du/dr.
du(double) P2SoftSphericalTruncated
Returns the derivative (r du/dr) of the wrapped potential if the separation
is less than the cutoff value
du(double) P2SoftSphericalTruncated.P0Lrc
du(double) P2SoftSphericalTruncatedForceShifted
du(double) P2SoftTruncated
du(double) P2WCA
The derivative r*du/dr.
du(double) P2Yukawa
r * du/dr method.
du(double) Potential2Soft
The derivative of the pair energy, times the separation r: r du/dr.
du(double) Potential2SoftSpherical
The derivative of the pair energy, times the separation r: r du/dr.
du(double) P1IntraLambda
du(IAtomList) P4TorsionDreiding
dU_est MeterSolidPropsLJ
duCorrection(double) P2SoftSphericalTruncated.P0Lrc
Uses result from integration-by-parts to evaluate integral of
r du/dr using integral of u.
dUdcosphi(double) P4BondTorsion
dudkT(double) P2EffectiveFeynmanHibbs
dudphi(int, double, double) P4TorsionDreiding
dUdphi(double) P4BondTorsionOPLS
dUdRotA CalcAnalytical2ndDerivativeNitrogen
dUdRotB CalcAnalytical2ndDerivativeNitrogen
dummyRefCluster VirialN2
dummyTarCluster VirialN2
dumpArray(String, float[][], int, int, int, int) ArrayUtil
dumpIntArray(int[], int) ArrayUtil
dumpit DataOverlap
dumpX DataProcessorXY
dUnit NucleationGraphic
dUnit PistonCylinderGraphic
dUnit ReverseOsmosisGraphic
dUnit ReverseOsmosisWaterGraphic
dUnit SwmdGraphic
duWork P2Nitrogen
dv BiasVolume2SiteAceticAcid
dv BiasVolumeAceticAcid
dv IntegratorImageHarmonicMD
dv IntegratorMDHarmonicMC
dv IntegratorVelocityVerletRattle
dv P2SquareWellBonding
dv P2SquareWellBondingCO
dv P2SquareWellSurface
dv P2Cohesion
dv InsertionGraphic.MeterWidom
dv P1MagicWall
dv P2SquareWellOneSide
dv P2HardSpherePoly
dv P2DoubleWell
dv P2HardSphere
dv P2PenetrableSphere
dv P2PenetrableSquareWell
dv P2SquareWell
dv P2SquareWellRobust
dV MeterProfileByVolume
dv1 IntegratorGear4.Agent
dv2 IntegratorGear4.Agent
dv3 IntegratorGear4.Agent
dv4 IntegratorGear4.Agent
dvEEx MoleculeAgent
dvEEx PotentialCalculationMoleculeAgentSum
dvEEx PotentialCalculationPair
dvEEx() MoleculeAgent
dvEEy MoleculeAgent
dvEEy PotentialCalculationMoleculeAgentSum
dvEEy PotentialCalculationPair
dvEEy() MoleculeAgent
dvEx MoleculeAgent
dvEx PotentialCalculationMoleculeAgentSum
dvEx PotentialCalculationPair
dvEx() MoleculeAgent
dvEy MoleculeAgent
dvEy PotentialCalculationMoleculeAgentSum
dvEy PotentialCalculationPair
dvEy() MoleculeAgent
dvo SimulationVirialOverlap2
dvOO P2SquareWellBondingCO
dvTmp IntegratorImageHarmonicMD
dvTmp IntegratorMDHarmonicMC
dXl IntegratorDimerRT
dy AkimaSplineSmootherApp
dy AkimaSplineSmootherDyApp
dy12 AkimaSplineSmoother
dynamicmeasurements Token
Dyne etomica.units
The dyne unit of force, equal to 1 g-cm/s^2.
g P1Smash
g ClusterWheatleyExtendSW
G Gamma
G Constants
The gravitational constant, in simulation units.
G_EARTH Constants
The standard acceleration of gravity on Earth.
g1Bond MayerIonicDiagram1qbond
g1Bond MayerIonicDiagram2qbonds
g1Bond MayerIonicDiagram4qbonds
G1Bond MayerIonicDiagram2qbonds
G1Bond MayerIonicDiagram4qbonds
g2Bond MayerIonicDiagram2qbonds
g2Bond MayerIonicDiagram4qbonds
G2Bond MayerIonicDiagram2qbonds
G2Bond MayerIonicDiagram4qbonds
G2pBond MayerIonicDiagram4qbonds
g3Bond MayerIonicDiagram4qbonds
G3Bond MayerIonicDiagram4qbonds
G3DSys g3dsys.control
Abstraction and delegation container class to facilitate communication
between the CoordMapper, FigureManager, and G3DPanel without deeply
coupling them in their own definitions.
G3DSys(Container) G3DSys
g3dsys.control - package g3dsys.control
g3dsys.images - package g3dsys.images
G3pBond MayerIonicDiagram4qbonds
g4Bond MayerIonicDiagram4qbonds
G4Bond MayerIonicDiagram4qbonds
ga P2CO2H2OWheatley.P2CO2H2OSC
ga P2CO2H2OWheatley.P2CO2H2OSCTI
gamma PrimitiveHexagonal
gamma PrimitiveHexagonal2D
gamma PNCO2GCPM
gamma PNGCPM.GCPMAgent
gamma P2WaterSzalewicz
gamma PNWaterGCPM
gamma PNWaterGCPMReactionField
gamma MeterSolidPropsLJ
gamma(double) SpecialFunctions
Returns the value of the gamma function of x.
gamma(MathContext) BigDecimalMath
Euler-Mascheroni constant.
Gamma etomica.math
This class calculates the incomplete gamma function and complementary
incomplete gamma function.
Gamma() Gamma
Gamma(Rational, MathContext) BigDecimalMath
The Gamma function.
Gamma(BigDecimal) BigDecimalMath
The Gamma function.
gamma_New MCMoveAtomCoupledBennet
gamma_New MCMoveAtomCoupledUmbrella
gamma_Old MCMoveAtomCoupledBennet
gamma_Old MCMoveAtomCoupledUmbrella
gammai IntegratorDimerRT
gb P2CO2H2OWheatley.P2CO2H2OSC
gb P2CO2H2OWheatley.P2CO2H2OSCTI
gbConst MyApplet
gbLayout MyApplet
GBond MayerIonicDiagram1qbond
GBond MayerIonicDiagram2qbonds
GBond MayerIonicDiagram4qbonds
gcd(Ifactor) Ifactor
Greatest common divisor of this and oth.
GCfreq AshtonWildingOsmoticVirial.simParams
gComp BiComponentSubst.BiComponentSubstParameters
gComp ComponentSubst.ComponentSubstParameters
GContactSink() DataProcessorWidomContact.GContactSink
GCPMAgent(double, double, double, double, double, double, double, double) PNGCPM.GCPMAgent
GCPMAgent(double, double, double, double, double, double, double, double, double) PNGCPM.GCPMAgent
GCPMWaterMCParam() SimGCPMWaterMCNPT.GCPMWaterMCParam
GCPMWaterMCParam() SimGCPMWaterMCNVT.GCPMWaterMCParam
GCRestrictedGibbsHS etomica.osmoticvirial
Calculate osmotic virial coefficients for Hard-Sphere potential in Grand Canonical ensemble for solvent
from Free-Energy Perturbation Approach in restricted grand canonical ensemble
GCRestrictedGibbsHS(double, double, int, boolean, double, double) GCRestrictedGibbsHS
GCRestrictedGibbsHS.simParams etomica.osmoticvirial
GCWidomInsertHS etomica.osmoticvirial
Calculate osmotic virial coefficients for Hard-Sphere potential in Grand Canonical ensemble for solvent
from Free-Energy Perturbation Approach utilizing Widom's Insertion.
GCWidomInsertHS(double, double, boolean, boolean) GCWidomInsertHS
GCWidomInsertHS.simParams etomica.osmoticvirial
GData org.jmol.util
GData() GData
geAtomPositionDefinition() MCMoveSemigrand
GEMCParams() VLESim.GEMCParams
GEMCWithRotation etomica.simulation.prototypes
Simple Gibbs-ensemble Monte Carlo simulation of rotating molecules.
GEMCWithRotation() GEMCWithRotation
GEMCWithRotation(Space) GEMCWithRotation
generalizedCoord CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
generalizedCoord CalcNumerical2ndDerivativeNitrogen
generateConfigs(String, double) SimDimerLJadatom
generateGraphicsCB MyApplet
generateNewU(double[]) FiniteDifferenceDerivativeCGNitrogenBeta
generator MyApplet
Geodesic org.jmol.util
Consolidated Geodesic from dotsRenderer 3/19/07 Bob Hanson
Constructs a canonical geodesic sphere of unit radius.
Geodesic() Geodesic
geosurface Token
gestureswipefactor Token
get(int) AtomArrayList
get(int) AtomListFromArray
Part of implementation of AtomSet interface.
get(int) AtomPair
get(int) AtomSetSinglet
get(int) IAtomList
Returns the i-th atom, with numbering beginning from 0.
get(int) AtomSetAllMolecules
get(int) IMoleculeList
Returns the i-th molecule, with numbering beginning from 0.
get(int) MoleculeArrayList
get(int) MoleculePair
get(int) MoleculeSetSinglet
get(int) IndexMap
get(int) BitSet
Returns the value of the bit with the specified index.
get(int) Int2IntHash
get(Object) DataStreamStore
get(Object) SimulationStore
get(Object) IndexMap
get(String) FeatureSet
get(String) Messages
get(String, String) Messages
get(Vector3f) Matrix4f
Retrieves the translational components of this matrix.
get2ndDerivative() HarmonicAlphaNitrogenModel
get2ndDerivative() HarmonicAlphaNitrogenModelPairMolecule
get2ndDerivative() HarmonicBetaNitrogenModel
get2ndDerivative(int) HarmonicAlphaNitrogenModelPairMoleculeSequential
get2ndDerivative(int) HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2
get2ndDerivative(int) HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
get2ndDerivative(int) HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
get2ndDerivative(int) HarmonicBetaNitrogenModelPairMoleculeSequential
get2ndDerivative(int) HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
get2ndDerivative(int) HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2
get2ndDerivative(int) HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
get2ndDerivative(int) HarmonicBetaNitrogenModelPairMoleculeSequentialLS
get2ndDerivative(int) HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
get2ndDerivative(int) HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
get2ndDerivativeFile(double[][], String) HarmonicBetaNitrogenModel
get2ndDerivativeMoleculei(CoordinateDefinition, int) HarmonicAlphaNitrogenModelDecomposed
get2ndDerivativeMoleculei(CoordinateDefinition, int) HarmonicBetaNitrogenModelDecomposed
get2SidedNormix(Vector3f, BitSet) Normix
get3dProjection(Vector3f) Quaternion
getA() MCMoveMoleculeSmer
getA() Plane
getA() PadeApproximation
getA() MinimizeGammaNitrogenLatticeParameter
getA() PistonPlane
getA() IntegratorPolymer
getA() WallPlane
getA() P2Exp6
getA() P2ModifiedMorse
getA() P2Morse
getA() MCMoveClusterAtomDiscrete
getA(int) P2HeSimplified
Returns the ith parameter value
u = A0 * exp(-A1*r) - A2/r^6 - A3/r^X
where X = 10 if useC10 is true, X=8 otherwise
getAcceptanceProbability() IntegratorMDHarmonicMC
getAcceptanceTarget() MCMoveStepTracker
getAccumulator() DisplayTextBoxesCAE
Accessor method for the data source that generates the displayed value.
getAccumulators() DataTableAverages
Returns a clone of the accumulator array.
getAccumulators() MeterVirialBDBin
getAccumulators() DataSourceVirialOverlap
getAccumulators() DataVirialOverlap
getAccumulatorUpdateInterval() DataTableAverages
getAcQuantity(int, int, double, double) SoftSphereSolidEOS
getAcQuantity(int, int, double, double) SoftSphereSolidEOSCalculator
getAction() DeviceButton
Returns the currently defined action associated with the button.
getAction() IntegratorListenerAction
getAction() DeviceButtonSingle
Returns the currently defined action associated with the button.
getActionQueue() Controller.ControllerHandle
getActualDiameter(IAtom) DiameterHashGlass
getActualStepFreq0() IntegratorOverlap
Deprecated.
getAddAnotherSpecies() ViewSpeciesSelection
getAddPotential() ViewSpeciesSelection
getAddPotential() ViewSpeciesSelection
getAddSameSpecies() ViewSpeciesSelection
getAddSpecies() ViewSpeciesSelection
getAddSpecies1() ViewSpeciesSelection
getAddSpecies2() ViewSpeciesSelection
getAddSpecies3() ViewSpeciesSelection
getADimension() P2Exp6
getADimension() P2Exp6Buckingham
getAdjustInterval() MCMoveStepTracker
getAdjustInterval() IntegratorOverlap
getAdjustStepSize() MCMoveStepTracker
getAEEJ0() PotentialCalculationHeisenberg
getAelement() SimpleElementForSimilarSpecies
getAfterPBC() MSDCoordWriter
getAgent(AtomType) AtomTypeAgentManager
Convenience method to return the agent the given AtomType.
getAgent(IAtom) AtomLeafAgentManager
Returns the agent associated with the given IAtom.
getAgent(Box) BoxAgentManager
getAgent(IMolecule) MoleculeAgentManager
Returns the agent associated with the given IAtom.
getAgent(ISpecies) SpeciesAgentManager
Convenience method to return the agent the given AtomType.
getAgentClass() ColorSchemeCollectiveAgent
getAgentClass() ColorSchemeRandom
getAgentManager() IntegratorVelocityVerlet
getAgentManager() InteractionTracker
getAgentManager() ChainEquilibriumSim
getAgentManager() FreeRadicalPolymerizationSim
getAgentManager() ReactionEquilibrium
getAgentManager() HSNPT.ActionSummer
getAgentManager() PotentialCalculationMeanField
getAgents() AtomLeafAgentManager
Get the agents map.
getAgents() AtomTypeAgentManager
getAgents() BoxAgentManager
getAgents() MoleculeAgentManager
getAgents() SpeciesAgentManager
getAlertMessage() ModelAlertMsgDialog
getAlertMsgBoxController() ControllerSpeciesSelection
getAlertMsgBoxSpeciesRemoval() ViewSpeciesSelection
getAlign(int) DisplayBox
getAlign(int) DisplayPolytope
getAlkaneIndex() MolecularModelSKS_SpeciesAlkane
getAlkaneIndex() MolecularModelTRAPPE_SpeciesAlkane
getAlkaneLength(int) ModelAlkaneLengthSelection
getAlkaneLengthSelectionDM() ControllerAlkaneLengthSelection
getAlkaneLengthSelectionView(int) ControllerAlkaneLengthSelection
getAlkaneSpheresSpecies(IMolecularModel_SpeciesFactory) ModelSimulationEnvironment
getAllActions() ActionGroup
Returns all actions from this group.
getAllActions() ActionGroupSeries
getAllCoordinates() SimulationWrapper
Array of coordinates of all atoms in all boxes in the wrapped Simulation.
getAllIdsOfType(Class) SimulationModel
getAllLastValues(BoxCluster) ClusterAbstractMultivalue
getAllLastValues(BoxCluster) ClusterCoupledFlippedMultivalue
getAllLastValues(BoxCluster) ClusterWheatleyMultibodyDerivatives
getAllLastValues(BoxCluster) ClusterWheatleyMultibodyDerivativesBD
getAllLastValues(BoxCluster) ClusterWheatleyPT
getAllLastValues(BoxCluster) ClusterWheatleySoftDerivatives
getAllLastValues(BoxCluster) ClusterWheatleySoftDerivativesBD
getAllMyData() MeterVirialBDBinMultiThreaded
getAllMyData() MeterVirialBinMultiThreaded
getAllMyData() MeterVirialEBinMultiThreaded
getAllowedScriptTypes() SVGConverter
Returns the list of allowed script types.
getAllQuantity(int, int, double, double) SoftSphereSolidEOS
getAllQuantity(int, int, double, double) SoftSphereSolidEOSCalculator
getAllredRochowElectroNeg(int) Elements
getAlpha() PrimitiveTrigonal
getAlpha() FindBetaN2AngleFromParameter
getAlpha() MeterUmbrella
getAlpha() MCMoveEinsteinCrystal
getAlpha() MCMoveHarmonicEin
getAlpha() P2Dreiding
getAlpha() P2Exp6Buckingham
getAlpha(int) MeterTargetRPMolecule
getAlpha(int) MeterTargetTPMolecule
getAlpha(int) MeterMBAR
getAlpha(int) MeterOverlapSwitch
getAlpha(int) MeterTargetTP
getAlpha(int) AlphaSource
Returns the ith alpha value (i=0..(n-1))
getAlpha(int) MeterOverlap
getAlpha(int) DataProcessorVirialOverlap
Returns ith factor used in the overlap value.
getAlphaCenter() MeterMBAR
getAlphaCenter() AccumulatorOverlapAverageUa2
getAlphaCenter() SimOverlapModule
getAlphaCenter() MeterOverlap
getAlphaCenter() AccumulatorVirialOverlapSingleAverage
getAlphaCenter() DataProcessorVirialOverlap
getAlphaFac() MeterUmbrella
getAlphaSource() DataOverlap
Returns an object capable of returning the different alpha values being
used.
getAlphaSource() DataVirialOverlap
getAlphaSpan() MeterMBAR
getAlphaSpan() AccumulatorOverlapAverageUa2
getAlphaSpan() MeterOverlap
getAlphaSpan() AccumulatorVirialOverlapSingleAverage
getAlphaSpan() DataProcessorVirialOverlap
getAlternateStylesheet() SVGConverter
getAlterSimEnv() ViewSpeciesSelection
getAlterSimEnv() ViewSpeciesSelection
getAlwaysScaleRandomizedMomenta() IntegratorMD
Returns true if the thermostat is set to always scale randomized momenta
to match the set temperature
getAmbientPercent() GData
getAminoAcidValenceAndCharge(String, String, int[]) JmolConstants
returns an array if we have special hybridization or charge
getAmplitude() P2Fene
getAmplitudeDimension() P2Fene
Not implemented correctly.
getAngle() Quaternion
Returns the angle associated with the quaternion
getAngle() MeterTargetRPMolecule
getAngle() P3BondAngle
Returns the nominal bond angle (in radians)
getAngle() P3BondAngleDreiding
Returns the nominal bond angle (in radians)
getAngle() P3CPSNonAdditiveHeOrig
Returns the nominal bond angle (in radians)
getAngle(int) ConformationChainLinear
getAngle(int) ConformationLinear
getAngleAlpha() PrimitiveCubic
getAngleAlpha() PrimitiveHexagonal
getAngleAlpha() PrimitiveMonoclinic
getAngleAlpha() PrimitiveOrthorhombic
getAngleAlpha() PrimitiveTetragonal
getAngleAlpha() PrimitiveTriclinic
getAngleBeta() PrimitiveCubic
getAngleBeta() PrimitiveHexagonal
getAngleBeta() PrimitiveMonoclinic
getAngleBeta() PrimitiveOrthorhombic
getAngleBeta() PrimitiveTetragonal
getAngleBeta() PrimitiveTriclinic
getAngleDimension() P3BondAngle
getAngleDimension() P3CPSNonAdditiveHeOrig
getAngleGamma() PrimitiveCubic
getAngleGamma() PrimitiveHexagonal
getAngleGamma() PrimitiveMonoclinic
getAngleGamma() PrimitiveOrthorhombic
getAngleGamma() PrimitiveTetragonal
getAngleGamma() PrimitiveTriclinic
getAngles() P2WaterPotentialsJankowski
getAngstromDepth() G3DSys
Gets the Angstrom depth of the model
getAngstromHeight() G3DSys
Gets the Angstrom height of the model
getAngstromWidth() G3DSys
Gets the Angstrom width of the model
getAngularVelocity() AtomOrientedDynamic
getAngularVelocity() IAtomOrientedKinetic
getAngularVelocity() IMoleculeOrientedKinetic
getAngularVelocity() MoleculeOrientedDynamic
getAnharmonicConstant() P2Anharmonic
getAnharmonicConstantDimension() P2Anharmonic
getAns(IAtom) MeterMappedAveragingVSum
getAPair(int, int) AtomPairSet
Returns atom pair for ith and jth atoms in set.
getAPairSet() BoxCluster
getApi1A() MpiMolecule
Returns the 1A iterator set at construction.
getApiAA() MpiMolecule
Returns the AA iterator set at construction.
getApproximation() ClusterOperations
getArea() SVGConverter
getArea() Parallelogram
getArea() Polygon
getArea() PolygonGeneral
Returns the value of the area enclosed by the polygon
getArea() Rectangle
Returns the area enclosed by the rectangle.
getArea() Square
Returns edgeLength^2.
getArgb() Rgb16
getArgb(short) Colix
getArgbFromString(String) ColorUtil
accepts [xRRGGBB] or [0xRRGGBB] or [0xFFRRGGBB] or #RRGGBB or
[red,green,blue] or a valid JavaScript color
getArgbGreyscale(short) Colix
getArray() AtomListFromArray
getArrayDimension() DataDoubleArray
Returns the dimension of the array, which is the number of integer
indices needed to access one of its elements.
getArrayDimension() DataDoubleBDArray
Returns the dimension of the array, which is the number of integer
indices needed to access one of its elements.
getArrayListPotentialCollection() ModelSimulationConstructor
getArrayShape() DataDoubleArray.DataInfoDoubleArray
Returns the size of each dimension in the constructed DataDoubleArray.
getArrayShape() DataDoubleArray.DataInfoDoubleArrayFactory
Returns a copy of the array shape array.
getArrayShape() DataDoubleBDArray.DataInfoDoubleBDArray
Returns the size of each dimension in the constructed DataDoubleArray.
getArrayShape() DataDoubleBDArray.DataInfoDoubleBDArrayFactory
Returns a copy of the array shape array.
getArrayShape(int) DataDoubleArray
Returns the length of the array in the i-th dimension.
getArrayShape(int) DataDoubleBDArray
Returns the length of the array in the i-th dimension.
getArticulationPair() FFTDecomposition
getArticulationPair() IsFFT
getArticulationPoints() HasSimpleArticulationPoint
getAscent() JmolFont
getAspect() Ellipse
set the aspect ratio (y/x) of the figure
getAssociatedAtoms() AssociationManager
getAssociatedAtoms(IAtom) AssociationManager
Returns the number of atoms on the list of associations of the given atom.
getAssociatedMolecules() AssociationManagerMolecule
getAssociatedMolecules(IMolecule) AssociationManagerMolecule
Returns the number of atoms on the list of associations of the given atom.
getAssociationDefinition() AssociationManager
getAssociationDefinition() AssociationManagerMolecule
getAsText() DimensionedDoubleEditor
Returns the value in the editor's units, formatted as a text string.
getAtom() AtomSourceRandomDimer
getAtom() AtomSourceRandomMonomer
getAtom() AtomSourceRandomSmer
getAtom() AtomSource
Returns an atom.
getAtom() AtomSourceRandomLeaf
returns a random atom from the box's leaf atom list
getAtom() AtomSourceRandomSpecies
returns a random atom from the box's leaf atom list
getAtom() AtomIteratorSinglet
getAtom() BoxAtomEvent
getAtom() ColorSchemeNeighbor
getAtom() ColorSchemeNeighborCell
getAtom() AtomSite
getAtom() PotentialReactive.BondChangeData
getAtom_aC_A() IntegratorDimerApproach
getAtom_aC_B() IntegratorDimerApproach
getAtom_aH_A() IntegratorDimerApproach
getAtom_aH_B() IntegratorDimerApproach
getAtom_H1_A() IntegratorDimerApproach
getAtom_O_A() IntegratorDimerApproach
getAtom_O_B() IntegratorDimerApproach
getAtomAction() MoleculeChildAtomAction
getAtomByTypeName(String) ISpecies
Get the index within the molecule of the first atom of a given AtomType name.
getAtomByTypeName(String) SpeciesGeneral
getAtomByTypeName(String) SpeciesGeneralMutable
getAtomByTypeName(String, int) ISpecies
Get the index within the molecule of the nth atom of given AtomType name.
getAtomByTypeName(String, int) SpeciesGeneral
getAtomByTypeName(String, int) SpeciesGeneralMutable
getAtomColor(IAtom) ColorSchemeSmer
getAtomColor(IAtom) ColorSchemeSmerByLength
getAtomColor(IAtom) ColorSchemePaired
getAtomColor(IAtom) ConfigFromFileLAMMPS.ColorSchemeDeviation
getAtomColor(IAtom) ColorScheme
getAtomColor(IAtom) ColorScheme.Simple
getAtomColor(IAtom) ColorSchemeByType
getAtomColor(IAtom) ColorSchemeCell
getAtomColor(IAtom) ColorSchemeCollectiveAgent
getAtomColor(IAtom) ColorSchemeColliders
Applies the special colors to the colliding pair while coloring all other atoms with baseColor.
getAtomColor(IAtom) ColorSchemeNull
Return without changing atom's color.
getAtomColor(IAtom) ColorSchemeRandom
getAtomColor(IAtom) ColorSchemeRandomByMolecule
getAtomColor(IAtom) ColorSchemeTemperature
getAtomColor(IAtom) ColorSchemeRadical
getAtomColor(IAtom) ColorSchemeRadical
getAtomColor(IAtom) ColorSchemeStepWise
getAtomColor(IAtom) ColorSchemePlane
getAtomColor(IAtom) ColorSchemeDropletSurface
getAtomColor(IAtom) ColorSchemeLiquidVapor
getAtomColor(IAtom) ColorSchemeCluster
getAtomColor(IAtom) ColorSchemeDeviation
getAtomColor(IAtom) ColorSchemeDirection
getAtomColor(IAtom) StrainColorScheme
getAtomColor(IAtom) ColorSchemeCluster
getAtomColor(IAtom) HSNPT.ColorSchemeDisplacement
getAtomDataInfo() DataSourceAtomic
getAtomDataInfo() DataSourceRmsVelocity
getAtomDataInfo() MeterTensorVelocity
getAtomicAndIsotopeNumber(int, int) Elements
getAtomicMass(int) Elements
getAtomicNumber() ElementChemical
getAtomicNumberDimension() ElementChemical
getAtomLeaf1(Box) Debug
Returns an AtomPair containing the two atoms with global indices
ATOM1_INDEX and ATOM2_INDEX within the given box.
getAtomList(IAtom) AtomToAtomLeafList
Returns the ArrayList that this instance associates with the given atom.
getAtomList(IAtom) AtomToAtomSetFixed
getAtomList(IAtom) AtomToParentChildList
getAtomPBIarray() MSDCoordWriter.AfterPBC
getAtomPositionDefinition() MoleculeActionTranslateTo
getAtomPositionDefinition() MCMoveMoleculeExchange
getAtomPropertiesLike(String) Token
getAtoms() IAtomList
getAtoms(Box) Debug
Returns an AtomPair containing the two atoms with global indices
ATOM1_INDEX and ATOM2_INDEX within the given box.
getAtomSource() MCMoveDimer
getAtomSource() MCMoveDimerRotate
getAtomSource() MCMoveSmer
getAtomSource() MCMoveSmerRotate
getAtomSource() MCMoveAtomCoupled
getAtomSource() MCMoveAtomSwap
getAtomSource() MCMoveAtom
The AtomSource is used to select the atom at the beginning of the trial
getAtomSource() MCMoveDimer
getAtomSource() MCMoveDimerRotate
getAtomSource() MCMoveMolecule
getAtomSource() MCMoveAtomCoupled
getAtomSource() MCMoveAtomCoupledBennet
getAtomSource() MCMoveAtomCoupledUmbrella
getAtomSource() MCMoveClusterAngleBend
getAtomSource() MCMoveClusterAngleBendAceticAcid
getAtomSource() MCMoveClusterAtomQ
getAtomTestDoDisplay() DisplayBox
Accessor method for the atom filter that determines which atoms
are displayed.
getAtomType(int) ISpecies
Returns the child type of this Species for the specified index.
getAtomType(int) SpeciesGeneral
getAtomType(int) SpeciesGeneralMutable
getAtomTypeCount() ISpecies
Returns the number of unique AtomTypes that make up this Species.
getAtomTypeCount() SpeciesGeneral
getAtomTypeCount() SpeciesGeneralMutable
getAtomTypes() ISpecies
Get the list of AtomTypes that make up this Species.
getAtomTypes() SpeciesGeneral
getAtomTypes() SpeciesGeneralMutable
getAtomTypes(IPotential) PotentialGroup
Returns the AtomTypes that the given potential applies to if the given
potential is within this potential group.
getAverage(int) DataOverlap.DataSourceOverlapAvg
getAverage(int) DataOverlap.DataSourceOverlapAvgCollapsing
getAverage(int) DataOverlap.DataSourceOverlapAvgSimple
getAverage(int) DataOverlap
Returns the ratio of the reference to target overlap ratio
reference/target for the given value alpha.
getAverage(int) DataSourceVirialOverlap
Returns the ratio of the reference to target overlap-to-virial ratios
(which reduces to target/reference) for the given value of the Bennet
parameter.
getAverageAndError() DataVirialOverlap
Returns the total result (appropriate ratio of target, reference and
overlap averages) and the uncertainty on that value.
getAverageAndError(boolean, double) DataOverlap
Returns the average from the reference or target system (as specified)
and its uncertainty for the given value of alpha
getAverageAndError(double) DataOverlap
Returns the average ratio and its uncertainty for the given value of
alpha
getAverageAndError(int) DataVirialOverlap
getAverageAndError(int, double, boolean) DataOverlapCaching
getAverageAndError(int, double, boolean) DataOverlap
getAverageAntibiasedLogs() AccumulatorAverageCollapsingLogAB
Returns the average natural logs of the block averages, for all block
sizes.
getAverageAtomPoint() G3DSys
getAverageCheck() ClusterWheatleySoft
getAverageCheck() ClusterWheatleySoftDerivatives
getAverageCheckBD() ClusterWheatleySoft
getAverageCheckBD() ClusterWheatleySoftDerivatives
getAverageLogs() AccumulatorAverageBootstrap
Returns the average natural logs of the block averages, for all block
sizes.
getAverageLogs() AccumulatorAverageCollapsingLog
Returns the average natural logs of the block averages, for all block
sizes.
getAverages() AccumulatorAverageBootstrap
Returns the averages for all block sizes
getAverages() AccumulatorAverageCollapsingLog
Returns the averages for all block sizes
getAvg() MeterVirialBinMultiThreaded.MyData
getAvg(int) MeterVirialEBinMultiThreaded.MyData
getAvgBondLength(double) AtomHydrogen
getAvgDouble() MeterVirialBDBinMultiThreaded.MyData
getAvgErrFork() AccumulatorAutocorrelationPTensor
getAxesForEllipsoid(double[], Vector3f[], float[]) Quadric
getAxis() Quaternion
Returns the axis associated with the Quaternion.
getAxis() ColorSchemeDirection
getB() MCMoveBiasUB
getB() Plane
getB() PadeApproximation
getB() PistonPlane
getB() IntegratorPolymer
getB() P1Sinusoidal
getB() WallPlane
getB() P2Exp6
getB() MCMoveClusterReptateMulti
getB(int) ClusterOperations
getBackgroundColor() SVGConverter
getBackgroundColor() DisplayBoxCanvasG3DSys
Gets the background color of the display box canvas.
getBackgroundColor() DisplayPolytopeCanvasG3DSys
Gets the background color of the display box canvas.
getBall1() Bond
getBall2() Bond
getBarrier() P2SquareWellBonding
getBarrier() P2SquareWellBondingCO
getBarrier() P2SquareWellBonded
getBarrierDimension() P2SquareWellBonded
getBasis() BravaisLatticeCrystal
getBasis() CoordinateDefinition
getBasisCells() CoordinateDefinition
getBasisMolecules() ConfigurationSAM
getBasisSize() LatticeCubicSimple
Returns 1.
getBasisSurface() ConfigurationSAM
getBboxVertices() BoxInfo
getBDcount() ClusterCoupledFlippedMultivalue
getBDfrac() ClusterCoupledFlippedMultivalue
getBDimension() P2Exp6
getBDimension() P2Exp6Buckingham
getBDtotcount() ClusterCoupledFlippedMultivalue
getBennetAverage(int) AccumulatorVirialOverlapSingleAverage
Returns average value of expression used to determine optimal
Bennet parameter (value[1]/(value[1]+expX[iParam]).
getBennetBias(int) AccumulatorOverlapAverageUa2
Returns iParam'th factor used in the Bennet sum.
getBennetBias(int) AccumulatorVirialOverlapSingleAverage
Returns iParam'th factor used in the Bennet sum.
getBeta() PrimitiveTrigonal
getBeta() FindBetaN2AngleFromParameter
getBeta() P4TorsionDreiding
getBetaUAWf() MeterWorkHarmonicTargetandReweighting
getBetaUAWr() MeterWorkHarmonicTargetandReweighting
getBetaUBWf() MeterWorkTargetHarmonicandReweighting
getBetaUBWr() MeterWorkTargetHarmonicandReweighting
getBgColixes(short[]) GData
getBiasCubeDimensions() BiasVolumeCube
getBiasSphereRadius() BiasVolume2SiteAceticAcid
getBiasSphereRadius() BiasVolumeAceticAcid
getBiasSphereRadius() BiasVolumeSphere
getBiasSphereRadius() BiasVolumeSphereOriented
getBiasSphereRadius() BiasVolumeSphereOrientedDoubleSites
getBiComponents(Graph) BCVisitor
Returns the biconnected components of the given graph.
getBinCounts() HistogramSimple
getBinSize() DataSourceTensorVirialHardProfile
getBisectingPlane(Point3f, Vector3f, Point3f, Vector3f, Point4f) Measure
getBitSet(ScriptVariable, boolean) ScriptVariable
getBlockCount() AccumulatorAverage
getBlockDataSink() AccumulatorAverageFixed
getBlockingSet(Graph) GlobalFilter
getBlockSize() AccumulatorAverage
getBn(double, double[], double[]) BnJHBVArgon_Analytic
getBond(int) ClusterCollapsedTreeNode
getBond(int) ClusterTreeNode
getBond(IAtom) P2HardBondedList.BondArrayList
getBondChangeData() PotentialReactive
getBondConstratins(ISpecies) IntegratorVelocityVerletShake
getBondDelta() P2HardBond
Accessor method for the bond extension factor
getBondDelta() P2PenetrableBond
Accessor method for the bond extension factor
getBondedList(IAtom) P2HardBondedList
Returns the list containing the bonds for the given atom.
getBondFac() P2HardSphereMC
getBondFac() P2SquareWellMonomer
getBondIndexArray() ClusterBonds
getBondingRadFromTable(int, int, short[]) Elements
getBondingRadiusFloat(short, int) Elements
getBondL() MolecularModelEMP2_SpeciesCO2
getBondL() MolecularModelSKS_SpeciesAlkane
getBondL() MolecularModelSPCE_SpeciesH2O
getBondL() MolecularModelTRAPPE_SpeciesAlkane
getBondL() MolecularModelTrappe_SpeciesCO2
getBondLength() AtomHydrogen
getBondLength() ConformationChainLinear
getBondLength() ConformationLinear
getBondLength() P2Dreiding
getBondLength() P2HardBond
Accessor method for the bond length
getBondLength() P2PenetrableBond
Accessor method for the bond length
getBondLength() MolecularModel2CLJQ_SpeciesCO2
getBondLength() MolecularModel2CLJQ_SpeciesEthane
getBondLength() MolecularModel2CLJQ_SpeciesLJ
getBondLengthDimension() ConformationChainLinear
getBondLengthDimension() ConformationLinear
getBondLengthDimension() P2HardBond
getBondLengthDimension() P2PenetrableBond
getBondLengths() P2WaterPotentialsJankowski
getBondsTree() ClusterTree
getBondType() Bond
getBoolean() ModifierBoolean
Returns the current state of the modified value.
getBoolean(boolean) ScriptVariable
getBoundaries() MeterFlux
getBoundary() Box
getBoundary() BoundaryEvent
getBoundaryFrameColor() DisplayBoxCanvasG3DSys
Gets the color of box boundary.
getBoundaryFrameColor() DisplayPolytopeCanvasG3DSys
Gets the color of box boundary.
getBoundaryPadding() ConfigurationLattice
getBoundaryTensor() BoundaryDeformablePeriodic
Returns the boundary tensor that fully describes the shape of the boundary.
getBoundaryVectors() G3DSys
Gets the boundary vectors used for calculating image shells
getBoundaryVectors() ImageShell
getBoundaryVectorsIterator() G3DSys
Gets the index iterator used for calculating image shells
getBoundaryVectorsIterator() ImageShell
getBoundBoxCenter() BoxInfo
getBoundBoxCornerVector() BoxInfo
getBoundBoxInfo() BoxInfo
getBoundBoxPoints(boolean) BoxInfo
getBoundingBoxCenter() G3DSys
getBox() ActionMinimizeEnergy
getBox() BoxAction
getBox() BoxActionAdapter
getBox() BoxRandomizeMomenta
getBox() BoxScaleMomenta
getBox() WriteConfiguration
Returns the box whose atom coordinates get written to the file.
getBox() WriteConfigurationBinary
Returns the box whose atom coordinates get written to the file.
getBox() WriteConfigurationDLPOLY
Returns the box whose atom coordinates get written to the file.
getBox() WriteConfigurationP2DLPOLY
Returns the box whose atom coordinates get written to the file.
getBox() MeterDimerMoleFraction
getBox() AtomLeafAgentManager
Convenience method to return the box the Manager is tracking.
getBox() BoxEvent
getBox() DataProcessorInterfacialTension
getBox() MeterAvgBondLength
getBox() MeterDensity
getBox() MeterDihedralAngle
getBox() MeterDipoleSumSquared1site
getBox() MeterDipoleSumSquaredMappedAverage
getBox() MeterDipoleSumSquaredTIP4PWater
getBox() MeterKineticEnergy
getBox() MeterKineticEnergyRigid
getBox() MeterLocalMoleFraction
getBox() MeterMoleculeTemperature
getBox() MeterMoleFraction
getBox() MeterMomentumCOM
getBox() MeterNMolecules
getBox() MeterPositionCOM
getBox() MeterPotentialEnergy
getBox() MeterPressureTensor
Returns the integrator associated with this instance.
getBox() MeterProfile
getBox() MeterProfileByAtoms
getBox() MeterProfileByVolume
getBox() MeterRadiusGyration
getBox() MeterRDF
getBox() MeterRDFPC
getBox() MeterTensorVelocity
getBox() MeterVolume
getBox() MeterFlux
getBox() DeviceNSelector
getBox() DisplayBox
getBox() IntegratorBox
getBox() MCMoveBox
getBox() MCMoveManager
getBox() MeterPotentialEnergyCutoff
getBox() MeterMappedRdf
getBox() AtomTestChainLength
getBox() ColorSchemeRadical
getBox() MeterChainLength
getBox() MeterFlux
getBox() MeterDeformation
getBox() ConfigurationStorage
getBox() DataProcessorInterfacialTensionProfile
getBox() MeterElongation
getBox() MeterStrain
getBox() MeterStress
getBox() StrainColorScheme
getBox() MeterFreeEnergy
getBox() MeterDimerFraction
getBox() MeterFlux
getBox() AtomTestChainLength
getBox() MeterPressure2
getBox() MoleculeAgentManager
Convenience method to return the box the Manager is tracking.
getBox() CoordinateDefinition
getBox() DeviceCellNum3DSlider
getBox() DeviceCellNumXYSlider
getBox() MeterAPIPotentialEnergy
getBox() MeterAtomicDisplacement
getBox() MeterHarmonicEnergy
getBox() MeterHarmonicSingleEnergy
getBox() MeterNormalMode
getBox() SimEinStep2.MeterPotentialEnergyComposite
getBox() SimEinStep2HCP.MeterPotentialEnergyComposite
getBox() SimOverlapSoftSphereEin.MeterPotentialEnergyComposite
getBox() SimOverlapSoftSphereEinHarm.MeterPotentialEnergyComposite
getBox() ParmedStructure
Gets the (single, rectangular) box found in this Structure.
getBox() Boundary
getBox() MeterSpinMSquare
getBox() MeterSpin
getBox() MCMoveClusterAtomQ
getBox() MeterSamplingWeight
getBox() MeterVirial
getBox() MeterVirialBD
getBox() MeterVirialBDBin
getBox() MeterVirialBDBinMultiThreaded
getBox() MeterVirialBinMultiThreaded
getBox() MeterVirialEBinMultiThreaded
getBox() MeterVirialExternalField
getBox() MeterVirialExternalFieldConfined
getBox() MeterVirialExternalFieldOverlapConfined
getBox() MeterVirialExternalFieldOverlapConfinedRho
getBox() MeterVirialExternalFieldOverlapConfinedSW
getBox() MeterVirialExternalFieldOverlapRho
getBox() MeterVirialExternalFieldRho
getBox() MeterVirialExternalFieldSW
getBox() MeterVirialIC
getBox() MeterVirialSWWE
getBox(int) Simulation
Returns one of the simulation Boxes.
getBoxBoundaries() ConfigurationUpdate
getBoxCellManager(Box) PotentialMasterCell
getBoxCellManager(Box) PotentialMasterList
getBoxCellManager(Box) PotentialMasterHybrid
getBoxCellManager(Box) PotentialMasterNbr
getBoxCellManager(Box) PotentialMasterSite
getBoxCount() Simulation
getBoxes() Simulation
Get all boxes in the simulation.
getBoxIndex() MeterMBAR
getBoxSize() Boundary
Returns the length of the sides of a rectangular box oriented in the lab
frame and in which the boundary is inscribed.
getBoxSize() BoundaryDeformablePeriodic
Returns the length of the sides of a rectangular box oriented in the lab
frame and in which the boundary is inscribed.
getBoxSize() BoundaryRectangular
Returns a vector with elements equal to the lengths of the edges of
the boundary.
getBoxSize() BoundaryTruncatedOctahedron
getButton() DeviceButton
getBXX() P2RepRowley
getBXXDimension() P2RepRowley
getByName(String) ISpecies
Get the index within a molecule instance of a named atom for this Species.
getByName(String) SpeciesGeneral
getByName(String) SpeciesGeneralMutable
getByte1() BinaryOpByteImpl
getByte1() UnaryOpByteImpl
getByte1() UnaryOpTwoByteImpl
getByte1() Parser.BinaryOpByte
getByte1() Parser.UnaryOpByte
getByte1() Parser.UnaryOpTwoByte
getByte2() UnaryOpTwoByteImpl
getByte2() Parser.UnaryOpTwoByte
getC() Plane
getC() MinimizeGammaNitrogenLatticeParameter
getC() PistonPlane
getC() WallPlane
getC() P2Exp6
getC(int) ClusterOperations
getCallCount() MeterMBAR
getCallCount() MeterNormalMode
getCancelMap() MayerIonicDiagram1qbond
getCancelMap() MayerIonicDiagram2qbonds
getCancelMap() MayerIonicDiagram4qbonds
getCancelMap() VirialDiagrams
getCancelMap() VirialDiagramsMix2
getCancelMap() VirialDiagramsPT
getCancelMap() WertheimDiagrams2SiteRho
getCancelMap() WertheimDiagrams3SiteRho
getCanonicalCopy(float) BoxInfo
getCanonicalCopy(Point3f[], float) BoxInfo
getCapSlabObject(String, boolean) MeshSurface
legacy -- for some scripts with early isosurface slabbing
getCDimension() P2Exp6
getCDimension() P2Exp6Buckingham
getCell(IAtom) NeighborCellManager
getCell(IMolecule) NeighborCellManagerMolecular
getCellAgentManager() PotentialMasterNbrMolecular
getCellRange() NeighborCellManagerMolecular
Returns the cellRange.
getCellRange() NeighborCellManager
Returns the cellRange.
getCellRange() PotentialMasterListMolecular
getCellRange() PotentialMasterList
getCellRange() PotentialMasterHybrid
getCellRange() PotentialMasterSite
getCellSize() CellLattice
Returns the spatial dimensions of all cells in the lattice, such that a cell in the
lattice will have a size in each direction as given by the corresponding value
in the returned array.
getCellSizeX() ConfigurationCatalysis
getCellSizeX() ConfigurationSAM
getCellSizeZ() ConfigurationCatalysis
getCellSizeZ() ConfigurationSAM
getCenter() Boundary
getCenterAndPoints(List<Point3f>) Measure
getCenterOfRotation() G3DSys
getCH2element() SimpleElementForSimilarSpecies
getCH3element() SimpleElementForSimilarSpecies
getChainLength() ColloidSim
getChainLength() ConfigurationColloid
getChainLength() SimulationRheology
getChainPhi(int) Sam
getChainPsi() Sam
getChainTheta() Sam
getChangeableColix(short, int) GData
getChangeableColixIndex(short) Colix
getCharge(int) MolecularModelEMP2_SpeciesCO2
getCharge(int) MolecularModelSPCE_SpeciesH2O
getCharge(int) MolecularModelTrappe_SpeciesCO2
getCharge1() P2Electrostatic
Returns the charge on the first type of atom.
getCharge1() P2ElectrostaticWithHardCore
Returns the charge on the first type of atom.
getCharge2() P2Electrostatic
Returns the charge on the second type of atom.
getCharge2() P2ElectrostaticWithHardCore
Returns the charge on the second type of atom.
getChargeH() P2Water4PSoft
getChargeH() P2WaterTIP4P
getChargeM() P2Water4PSoft
getChargeM() P2WaterTIP4P
getChart() DisplayPlotXChart
getCheckBox() DeviceCheckBox
getChi(double) MCMoveAtomDimer
getChi(double) MCMoveAtomMonomer
getChi(double) MCMoveAtomNoSmer
getChi(double) MCMoveAtomSmer
getChi(double) MCMoveBiasUB
getChi(double) MCMoveBiasUBMolecule
getChi(double) MCMoveDimer
getChi(double) MCMoveDimerRotate
getChi(double) MCMoveMoleculeMonomer
getChi(double) MCMoveMoleculeRotateAssociated
getChi(double) MCMoveRotateAssociated
getChi(double) MCMoveRotateNoSmer
getChi(double) MCMoveSmer
getChi(double) MCMoveSmerRotate
getChi(double) MCMoveVolumeAssociated
getChi(double) MCMoveVolumeAssociatedMolecule
getChi(double) MyMCMove
getChi(double) MCMoveAtomCoupled
getChi(double) MCMoveAtomNPath
getChi(double) MCMoveAtomSwap
getChi(double) MCMove
Chi is the parameter within standard Metropolis Monte Carlo.
getChi(double) MCMoveAtom
getChi(double) MCMoveBoxSize
getChi(double) MCMoveDimer
getChi(double) MCMoveDimerRotate
getChi(double) MCMoveInsertDelete
getChi(double) MCMoveInsertDeleteBiased
getChi(double) MCMoveInsertDeleteLatticeVacancy
getChi(double) MCMoveInsertDeleteVacancy
getChi(double) MCMoveMolecule
getChi(double) MCMoveMoleculeExchange
getChi(double) MCMoveSemigrand
getChi(double) MCMoveSwapConfiguration
getChi(double) MCMoveTorsionAceticAcid
getChi(double) MCMoveVolume
getChi(double) MCMoveVolumeExchange
getChi(double) MCMoveWiggleAceticAcid
getChi(double) MCMoveMoleculeCoupledInitPert
getChi(double) MCMoveMoleculeCoupledSuperBox
getChi(double) MCMoveRotateMolecule3DConstraint
getChi(double) MCMoveRotateMolecule3DFixedAngle
getChi(double) MCMoveRotateMolecule3DN2AveCosThetaConstraint
getChi(double) MCMoveVolumeN2
getChi(double) MyMCMove
getChi(double) MyMCMove
getChi(double) MCMoveSwap
getChi(double) MCMoveMultiHarmonic
getChi(double) MCMoveAtomCoupled
getChi(double) MCMoveAtomCoupledBennet
getChi(double) MCMoveAtomCoupledUmbrella
getChi(double) MCMoveAtomSuperBox
getChi(double) MCMoveEinsteinCrystal
getChi(double) MCMoveHarmonic
getChi(double) MCMoveHarmonicStep
getChi(double) MCMoveMoleculeCoupled
getChi(double) MCMovePhaseAngle
getChi(double) MCMoveRotateMoleculePhiTheta
getChi(double) MCMoveSingleMode
getChi(double) MCMoveVolumeMonoclinic
getChi(double) MCMoveVolumeMonoclinicAngle
getChi(double) MCMoveVolumeMonoclinicScaled
getChi(double) MCMoveVolumeSolid
getChi(double) MCMoveVolumeSolidNPTMolecular
getChi(double) MCMoveVolumeSolidNPTMolecularOriented
getChi(double) MCMoveWV
getChi(double) MCMoveGeometricCluster
Returns 1 because move is always accepted.
getChi(double) MCMoveGeometricClusterRestrictedGE
getChi(double) MCMoveRotate3Pair
getChi(double) MCMoveRotatePair
getChi(double) MCMoveSpinCluster
getChi(double) MCMoveSpinFlip
getChi(double) MCMoveBondLength
getChi(double) MCMoveClusterBondLength
getChi(double) MCMoveClusterMoleculeHSChain
getChi(double) MCMoveClusterMoleculeHSChainB3
getChi(double) MCMoveClusterRotateArm
getChi(double) MCMoveRotateArm
getChi(double) MCMoveWiggle
getChi(double) MCMoveChangeBondLength
getChi(double) MCMoveClusterAngleBend
getChi(double) MCMoveClusterAngleBendAceticAcid
getChi(double) MCMoveClusterAtom
getChi(double) MCMoveClusterAtomChainHSTail
getChi(double) MCMoveClusterAtomDiscrete
getChi(double) MCMoveClusterAtomHSChain
getChi(double) MCMoveClusterAtomHSRing
getChi(double) MCMoveClusterAtomHSTree
getChi(double) MCMoveClusterAtomInBox
getChi(double) MCMoveClusterAtomMulti
getChi(double) MCMoveClusterAtomQ
getChi(double) MCMoveClusterAtomRotateMulti
getChi(double) MCMoveClusterDiagram
getChi(double) MCMoveClusterMolecule
getChi(double) MCMoveClusterMoleculeHSChain
getChi(double) MCMoveClusterMoleculeMulti
getChi(double) MCMoveClusterPolyhedraChain
getChi(double) MCMoveClusterPolyhedraTree
getChi(double) MCMoveClusterReptateMulti
getChi(double) MCMoveClusterRingPartialRegrow
getChi(double) MCMoveClusterRingRegrow
getChi(double) MCMoveClusterRingRegrowExchange
getChi(double) MCMoveClusterRingRegrowOrientation
getChi(double) MCMoveClusterRingScale
getChi(double) MCMoveClusterRotateCH3
getChi(double) MCMoveClusterRotateMolecule3D
getChi(double) MCMoveClusterRotateMoleculeMulti
getChi(double) MCMoveClusterTorsionAceticAcid
getChi(double) MCMoveClusterTorsionAlkaneEH
getChi(double) MCMoveClusterTorsionMulti
getChi(double) MCMoveClusterWiggleAceticAcid
getChi(double) MCMoveClusterWiggleAlkaneEH
getChi(double) MCMoveClusterWiggleMulti
getChi(double) MCMoveSwapCluster
getChi(double[], double[], double[], double[]) PolynomialFit
Returns average relative deviation (relative to the uncertainty) of the
given fit from the given data.
getChildList() IMolecule
Returns the atoms in the molecule as an IAtomList.
getChildList() Molecule
getChildProperties() Wrapper
getClasses() SimulationModel
getCliqueCount() ClusterSumHS
getCliqueCount() ClusterWheatley
Returns number of cliques for the configuration passed to
checkConfig
getCliqueCount() ClusterWheatleyHS
getCliqueCount() ClusterWheatleyPartitionScreening
getCliques() ClusterSumHS
getCliques() ClusterWheatley
Returns an array containing the clique sets for the configuration passed
to checkConfig.
getCliques() ClusterWheatleyHS
getCliques() ClusterWheatleyPartitionScreening
getCloseWindow() ViewAlertMsgBox
getCloseWindow() ViewAlkaneLengthSelection
getCloseWindow() ViewSimEnvironmentSelection
getCluster() ClusterPanel
getCluster() ClusterMultivalueUmbrella
getCluster() MeterVirialExternalField
getCluster() MeterVirialExternalFieldConfined
getCluster() MeterVirialExternalFieldSW
getClusterer() MeterLargestCluster
getClusterNeighborDistance() DataClusterer
getClusters() AtomNbrClusterer
getClusters() ClusterSum
getClusters() ClusterSumNonAdditiveTrimerEnergy
getClusters() ClusterSumPolarizable
getClusters() ClusterSumPolarizableWertheimProduct
getClusters() ClusterSumPolarizableWertheimProduct4Pt
getClusters() ClusterSumPolarizableWertheimProduct4PtFinal
getClusters() ClusterWeightUmbrella
getClusters() MeterVirial
getClusters() MeterVirialBD
getClusters() MeterVirialSWWE
getCoeffAc(int, int) SoftSphereSolidEOS
getCoeffAc(int, int) SoftSphereSolidEOSCalculator
getCoefficients() WaveVectorFactory
Returns the coefficients for the wave vectors returned by
getWaveVectors.
getCoefficients() WaveVectorFactory1D
getCoefficients() WaveVectorFactory2D
getCoefficients() WaveVectorFactoryFcc
getCoefficients() WaveVectorFactoryFromFile
getCoefficients() WaveVectorFactorySimple
getColix(int) G3DSys
Converts the given argb int to a G3D Colix
getColix(int) Colix
getColix(Color) G3DSys
Converts the given AWT color to a G3D Colix
getColixArray(String) Colix
getColixInherited(short, short) Colix
getColixO(Object) Colix
getColixS(String) Colix
getColixTranslucencyFractional(short) Colix
getColixTranslucencyLevel(short) Colix
getColixTranslucent(int) Colix
getColixTranslucent3(short, boolean, float) Colix
getCollisionCount() IntegratorHard
getCollisionDiameter() P2HardSpherePoly
Accessor method for collision diameter
getCollisionDiameter() P2HardSphere
Accessor method for collision diameter
getCollisionDiameterDimension() P2HardSphere
getCollisionRadius() MeterOsmoticPressure
Returns the collision radius used to calculate the accessible "area".
getCollisionRadius() P1HardWall
Distance from the center of the sphere to the boundary at collision.
getCollisionRadius() P1HardBoundary
Distance from the center of the sphere to the boundary at collision.
getCollisionRadius() P1HardMovingBoundary
Distance from the center of the sphere to the boundary at collision.
getCollisionRadiusDimension() P1HardWall
Indicates collision radius has dimensions of Length.
getCollisionRadiusDimension() P1HardBoundary
Indicates collision radius has dimensions of Length.
getCollisionRadiusDimension() P1HardMovingBoundary
Indicates collision radius has dimensions of Length.
getColloidSigma() ColloidSim
getColor() Edge
getColor() EdgeImpl
getColor() MetadataImpl
getColor() NodeImpl
getColor() Metadata
getColor() Node
getColor() Axes
getColor() Ball
getColor() Box
getColor() Ellipse
getColor() Line
getColor() Triangle
getColor(AtomType) ColorSchemeByType
getColor1() UnaryOpColorImpl
getColor1() UnaryOpThreeColorImpl
getColor1() Parser.UnaryOpColor
getColor1() Parser.UnaryOpThreeColor
getColor1() Bond
getColor2() UnaryOpThreeColorImpl
getColor2() Parser.UnaryOpThreeColor
getColor2() Bond
getColor3() UnaryOpThreeColorImpl
getColor3() Parser.UnaryOpThreeColor
getColorArgbOrGray(short) GData
getColorIn() ColorSchemePlane
getColorMap() UnaryOpByteMapImpl
getColorMap() Parser.UnaryOpByteMap
getColorOut() ColorSchemePlane
getColorScheme() DisplayBox
Accessor method for the color scheme used for this display
getColumn(int, float[]) Matrix3f
Copies the matrix values in the specified column into the array parameter.
getColumn(int, float[]) Matrix4f
Copies the matrix values in the specified column into the array parameter.
getColumnClass(int) DeviceTableModelGeneric
getColumnCount() DeviceTableModelGeneric
Get the number of columns in the table
getColumnCount() ModelMoleculeListDisplayTable_new
getColumnCount() ModelMoleculeListDisplayTable
getColumnCount() ModelPotParamDisplayTable
getColumnInfoFactories() DataTable.DataInfoTableFactory
Returns a copy of the array of DataInfoFactories for the columns
getColumnName(int) DeviceTableModelGeneric
getColumnV(int, Vector3f) Matrix3f
Copies the matrix values in the specified column into the vector parameter.
getCombinationProbability() P2SquareWellRadical
Returns the probability that two radicals will bond instead of becoming
unreactive.
getCommand() CommandImpl
getCommand() Parser.Command
getCommandSet(String) Token
retrieves an unsorted list of viable commands that could be
completed by this initial set of characters.
getComponent() DeviceSlider
getComponent() DeviceSpinner
getComponents(Graph) CVisitor
Returns the biconnected components of the given graph.
getComponentSet() ComponentIndex
getComponentValues() MolecularModelLJQ_SpeciesLJ
getConfigDLPOLY() PotentialDLPOLY
getConfigIndex() ColorSchemeDeviation
getConfigIndex() ColorSchemeDirection
getConfigIndex() DisplayBoxCanvas2DGlass
getConfigIndex() DisplayBoxCanvas3DGlass
getConfigIndex() DisplayBoxCanvasGlass
getConfigIndex() MeterGs
getConfigP2DLPOLY() P2DLPOLY
getConfigStorage() AtomTestDeviation
getConfigStorage() ColorSchemeDeviation
getConfigStorage() ColorSchemeDirection
getConfigStorage() DataSourcePrevTime
getConfigStorage() DisplayBoxCanvas2DGlass
getConfigStorage() DisplayBoxCanvas3DGlass
getConfigStorage() DisplayBoxCanvasGlass
getConfiguration() SimulationRestart
getConfName() WriteConfiguration
Returns the configuration name.
getConfName() WriteConfigurationBinary
Returns the configuration name.
getConfName() WriteConfigurationDLPOLY
Returns the configuration name.
getConfName() WriteConfigurationP2DLPOLY
Returns the configuration name.
getConformation() ISpecies
getConformation() SpeciesGeneral
getConformation() SpeciesGeneralMutable
getConformation(int) ConfigurationSAM
getConformationsList() MCMoveClusterConformationMDTest
getConsole() ConsoleContainer
getConsole() Launcher.ConsoleWindow
getConstrainScriptOrigin() SVGConverter
Returns whether scripts can only be loaded from the same
origin as the documents referencing them.
getConstraint() MCMoveRotateMoleculePhiTheta
getConstraintAngle() MeterDirectInitPert
getConstructionInfo(Class, SimulationModel) Construction
getConstructorObject() ModelSpeciesSelection
getContainingCubeEdgeLength() TruncatedOctahedron
Returns the length of an edge of a cube in which the truncated octahedron
is inscribed.
getController() Device
getController() SimulationGraphic
getController() Simulation
getConvergence(Potential2SoftSpherical, int, double, double, boolean, boolean) B3ForSphericallySymmetricU
getConvergence(Potential2SoftSpherical, int, int, double, double, boolean) BnIETP2Spherical
getConvergence(Potential2SoftSpherical, int, int, double, double, boolean) BnPY_1QC_Helium
getConvergence(Potential2Spherical, int, double, double, double, boolean, double) BnPCJSDHe
getConvergence(Potential2Spherical, int, double, double, double, boolean, double) BnPYCHe
getCoordinateDefinition() MeterTargetTPMolecule
getCoordinateDefinition() IntegratorHarmonic
getCoordinateDefinition() MCMoveAtomCoupledBennet
getCoordinateDefinition() MCMoveAtomCoupledUmbrella
getCoordinateDefinition() MCMoveHarmonic
getCoordinateDefinition() MCMoveHarmonicStep
getCoordinateDefinition() MCMoveSingleMode
getCoordinateDefinition() MeterBoltzmannHTTP
getCoordinateDefinition() MeterDDP
getCoordinateDefinition() MeterDP
getCoordinateDefinition() MeterHarmonicCoordinate
getCoordinateDefinition() MeterHarmonicEnergy
getCoordinateDefinition() MeterHarmonicSingleEnergy
getCoordinateDefinition() MeterNormalMode
getCoordinateDefinition() MeterTargetTP
getCoordinateDim() CoordinateDefinition
Returns the number of generalized coordinates associated with each
molecule.
getCoordinates() ConfigurationUpdate
getCoreDiameter() P2SquareWellBonding
Accessor method for core diameter.
getCoreDiameter() P2SquareWellBondingCO
Accessor method for core diameter.
getCoreDiameter() P2SquareWellSurface
Accessor method for core diameter.
getCoreDiameter() P2SquareWellOneSide
Accessor method for core diameter.
getCoreDiameter() P2DoubleWell
Accessor method for core diameter.
getCoreDiameter() P2PenetrableSphere
Accessor method for core diameter.
getCoreDiameter() P2PenetrableSquareWell
Accessor method for core diameter.
getCoreDiameter() P2SquareWell
Accessor method for core diameter.
getCoreDiameter() P2SquareWellRobust
Accessor method for core diameter.
getCoreDiameter() P2TriangleWell
getCoreDiameterDimension() P2SquareWellBonding
getCoreDiameterDimension() P2SquareWellBondingCO
getCoreDiameterDimension() P2SquareWellSurface
getCoreDiameterDimension() P2SquareWellOneSide
getCoreDiameterDimension() P2DoubleWell
getCoreDiameterDimension() P2PenetrableSphere
getCoreDiameterDimension() P2PenetrableSquareWell
getCoreDiameterDimension() P2SquareWell
getCoreDiameterDimension() P2SquareWellRobust
getCoreDiameterDimension() P2TriangleWell
getCoreEdgeCount() ClusterWheatleyExtendSW
getCoreIterator() IndexIteratorTriangularPermutations
getCoreLen() AbstractSearchState
getCoreLen() SearchState
getCoreSet() AbstractSearchState
getCoreSet() SearchState
getCosdtheta() MeterMeanField
getCost0() MeterMeanField
getCount() BoxMoleculeCountEvent
getCount() AccumulatorAverageBootstrap
getCount() AccumulatorAverageCollapsingLog
getCount() Histogram
Returns the number of times the Histogram's addValue method was called.
getCount() HistogramDiscrete
getCount() HistogramNotSoSimple
getCount() HistogramReweightedData
getCount() HistogramSimple
getCount() HSNPT.ActionSummer
getCountOfMoleculesStrings() ModelSpeciesSelection
getCountOfSpeciesSLM(int) ViewSpeciesSelection
getCountOfSpeciesSLMListener() ViewSpeciesSelection
getCountSpecies(int) ModelSimulationEnvironment
getCoupling() P2Spin
* @return J the coupling parameter
getCoupling() P2Spin
getCov(int, int) MeterVirialEBinMultiThreaded.MyDataCov
getCPairID() BoxCluster
getCPairID() ClusterWheatleyPartitionScreening
getCPairSet() BoxCluster
returns the current coordinate pair set
getCriteria() PotentialArray
getCriteria() PotentialArrayMolecular
getCriteria(AtomType) PotentialMasterNbr
getCriteria1Body(AtomType) PotentialMasterNbr
getCriterion() Potential0
getCriterion(AtomType, AtomType) PotentialMasterNbr
getCriterion(IPotentialMolecular) PotentialMasterListMolecular
Returns the criterion used by to determine what atoms interact with the
given potential.
getCriterion(ISpecies) NeighborListManagerMolecular
getCriticalPoints(Point3f[], Tuple3f) BoxInfo
getCubicSize() PrimitiveBcc
Returns the common length of all primitive vectors.
getCubicSize() PrimitiveFcc
Returns the common length of all primitive vectors.
getCurrentLattice() LatticeEditor
Returns the currently selected crystal.
getCurrentStep() ActionIntegrate
getCurrentTime() IntegratorDCVGCMD
getCurrentTime() IntegratorMD
getCurrentTime() IntegratorHybrid
getCurrentTime() IntegratorDCVGCMD
getCutoff() MeterStructureFactor
getCutoff() AtomTestLiquid
getCutoffFactorLJ() P2HardAssociationCone
Accessor method for Lennard-Jones cutoff distance; divided by sigma
getCutoffFactorLJ() P2HardAssociationConeDoubleSites
Accessor method for Lennard-Jones cutoff distance; divided by sigma
getCutoffFactorLJ() P2HardAssociationConeFourSites
Accessor method for Lennard-Jones cutoff distance; divided by sigma
getCutoffFactorLJ() P2HardAssociationConeFourSitesSW
Accessor method for Lennard-Jones cutoff distance; divided by sigma
getCutoffFactorLJ() P2HardAssociationConeOneSite
Accessor method for Lennard-Jones cutoff distance; divided by sigma
getCutoffFactorLJ() P2HardAssociationConeSW
Accessor method for Lennard-Jones cutoff distance; divided by sigma
getCutoffFactorLJDimension() P2HardAssociationCone
getCutoffFactorLJDimension() P2HardAssociationConeDoubleSites
getCutoffFactorLJDimension() P2HardAssociationConeFourSites
getCutoffFactorLJDimension() P2HardAssociationConeFourSitesSW
getCutoffFactorLJDimension() P2HardAssociationConeOneSite
getCutoffFactorLJDimension() P2HardAssociationConeSW
getCXX() P2RepRowley
getD() MyEigenvalueDecomposition
Return the block diagonal eigenvalue matrix
getD() IndexIterator
getD() IndexIteratorRectangular
Returns the length of the integer array that is returned as an iterate.
getD() IndexIteratorReflecting
getD() IndexIteratorTriangular
Returns the length of the int array that is returned as each iterate.
getD() IndexIteratorTriangularPermutations
getD() CombinationIterator
getD() PermutationDegenerateIterator
getD() PermutationIterator
getD() Plane
getD() PistonPlane
getD() WallPlane
getD() Space
getD() Vector
Dimension of the space occupied by the vector.
getD() Vector1D
getD() Vector2D
getD() Vector3D
getD() VectorND
getD() IndexIterator
Get the number of dimensions
getD() Axes
getD() Ball
getD() Bond
getD() Box
getD() Ellipse
getD() ImageShell
getD() Line
getD(double, double, double) P3CPSNonAdditiveHeOrig
getD(double, double, int) P3CPSNonAdditiveHe
getD(double, double, int) P3CPSNonAdditiveHeLessSimplified
getD2dfac() AkimaSplineSmoother
getD2fac() AkimaSplineSmoother
getd2fdT2(int, double, double) B3LJ
Returns a discretized df/dT function containing N points with a
separation interval of del_r
getD2Sum() PotentialCalculationSolidSuper
getD3dfac() AkimaSplineSmoother
sets weight given to minimizing discontinuities in the 3nd derivative
(at data points)
getD3fac() AkimaSplineSmoother
getDADBSum() PotentialCalculationSolidSuper
Returns sum of Fi dot ri
getDADBSum() PotentialCalculationSolidSuperCut
Returns sum of Fi dot ri
getData() MeterEnthalpyVolume
getData() MeterCavityMapped
getData() MeterRDFMapped
getData() MeterWidomCavity
getData() AccumulatorAverageBlockless
Returns a DataGroup with Data instances holding the statistics kept by
this accumulator (as described in general comments for this class).
getData() AccumulatorAverageBlocklessSlim
Returns a DataGroup with Data instances holding the statistics kept by
this accumulator (as described in general comments for this class).
getData() AccumulatorAverageBootstrap
getData() AccumulatorAverageCollapsing
getData() AccumulatorAverageCollapsingLog
getData() AccumulatorAverageCovariance
getData() AccumulatorAverageFixed
getData() AccumulatorAverageFixedOutputFile
Returns a DataGroup with Data instances holding the statistics kept by
this accumulator (as described in general comments for this class).
getData() AccumulatorCounter
Returns the DataInteger with the count.
getData() AccumulatorHistogram
Returns the set of histograms.
getData() AccumulatorHistory
Returns the set of histories.
getData() AccumulatorRatioAverageCovariance
getData() AccumulatorRatioAverageCovarianceFull
getData() DataAccumulator
getData() DataDump
getData() DataSet.DataSetSink
getData() DataSourceFunction
Returns the DataFunction made by this source.
getData() DataSourceGroup
Returns a DataGroup that is formed from the Data objects returned by
the data sources in this instance.
getData() DataSourcePoints
getData() DataSourceRmsVelocity
Returns the rms velocity of the atoms given by the iterator.
getData() DataSourceScalar
getData() DataSourceTensorVirialHard
Current value of the meter, obtained by dividing sum of collision virial contributions by time elapsed since last call.
getData() DataSourceUniform
Returns the uniformly spaced values.
getData() HistogramDataSource
Returns the set of histograms.
getData() IDataSource
getData() MeterDihedralAngle
Returns the Dihedral distribution, averaged over the calls to actionPerformed since the
meter was reset or had some parameter changed (# of bins).
getData() MeterDipoleSumSquaredMappedAverage
getData() MeterHyperVirial
Computes total pressure in box by summing virial over all pairs, and adding
ideal-gas contribution.
getData() MeterMomentumCOM
Returns the instantaneous total center-of-mass momentum over all atoms in the box.
getData() MeterPositionCOM
Returns the position of the center of mass of all atoms in the box.
getData() MeterPressureByVolumeChange.DataSourceExp
getData() MeterPressureByVolumeChange
getData() MeterPressureHardTensor
getData() MeterPressureTensor
Computes total pressure in box by summing virial over all pairs, and adding
ideal-gas contribution.
getData() MeterPressureTensorFromIntegrator
getData() MeterProfile
Returns the profile for the current configuration.
getData() MeterProfileByAtoms
Returns the profile for the current configuration.
getData() MeterProfileByVolume
Returns the profile for the current configuration.
getData() MeterRDF
Returns the RDF, averaged over the calls to actionPerformed since the
meter was reset or had some parameter changed (xMax or # of bins).
getData() MeterRDFPC
Returns the RDF, averaged over the calls to actionPerformed since the
meter was reset or had some parameter changed (xMax or # of bins).
getData() MeterStructureFactor
getData() MeterTensorVelocity
Returns the velocity dyad (mass*vv) summed over all atoms, and divided by N
getData() DataDoubleArray
Returns the encapsulated array.
getData() DataDoubleBDArray
Returns the encapsulated array.
getData() DataSourceEnergies
getData() IntegratorPT.BoxTracker
Returns array y such that y[i] is the current
box of the configuration that began in box i.
getData() MeterPotentialEnergyCutoff
Computes total potential energy for box.
getData() MeterPU
Computes total pressure in box by summing virial over all pairs, and adding
ideal-gas contribution.
getData() MeterPUCut
Computes total pressure in box by summing virial over all pairs, and adding
ideal-gas contribution.
getData() MeterPUCutLS
getData() MeterWidomInsertionCorrection
Performs a Widom insertion average, doing nInsert insertion attempts
Temperature used to get exp(-uTest/kT) is that of the integrator for the
box
getData() MeterMappedRdf
Returns the RDF, averaged over the calls to actionPerformed since the
meter was reset or had some parameter changed (xMax or # of bins).
getData() MeterMeanForce
getData() MeterDensityDistribution
getData() MeterBoltzmann
getData() MeterBoltzmannRotPerturb
getData() MeterNormalizedCoord
Returns the DataGroup of uDistribtion[i]
getData() MeterNormalizedCoordBeta
Returns the DataGroup of uDistribtion[i]
getData() MeterOrientationDistribution
Returns the DataGroup of uDistribtion[i]
getData() MeterRotationDistributionGroup
Returns the DataGroup of uDistribtion[i]
getData() MeterTargetRPMolecule
getData() MeterTargetTPMolecule
getData() DataSourceDensityFunction
getData() DataSourceWallPressureCatalysis
getData() MeterChainLength
getData() MeterDeformation
getData() AccumulatorAutocorrelationPTensor
getData() AccumulatorAutocorrelationShearStress
getData() AccumulatorPTensor
getData() CorrelationSelf2.MeterCorrelationSelf2
getData() DataSourceAlpha2
getData() DataSourceBlockAvgCor
getData() DataSourceCorrelation.Meter
getData() DataSourceF
getData() DataSourceFOld
getData() DataSourceFs
getData() DataSourceHisogram
getData() DataSourceHistogramMSD
getData() DataSourceMSD
getData() DataSourceMSDcorP.DataSourceMSDcovP
getData() DataSourceMSDcorP
getData() DataSourcePercolation.Chi4Source
getData() DataSourcePercolation
getData() DataSourcePercolation.ImmFractionByTypeSource
getData() DataSourcePercolation.ImmFractionSource
getData() DataSourcePercolation.PercolationByImmFrac
getData() DataSourcePercolation0
getData() DataSourcePMSDHistory
getData() DataSourceQ4
getData() DataSourceQ4.MeterChi4
getData() DataSourceStrings
getData() DataSourceVAC
getData() GlassGraphic.MeterFromDumps
getData() MeterCorrelation
Returns the RDF, averaged over the calls to actionPerformed since the
meter was reset or had some parameter changed (xMax or # of bins).
getData() MeterCorrelationSelf
Returns the RDF, averaged over the calls to actionPerformed since the
meter was reset or had some parameter changed (xMax or # of bins).
getData() MeterGs
Returns the RDF, averaged over the calls to actionPerformed since the
meter was reset or had some parameter changed (xMax or # of bins).
getData() MeterStructureFactorStress3
getData() StructureFactorComponentCorrelation.Meter
getData() DataSourceTensorVirialHardProfile.DataSourceVirialProfile
getData() DataSourceWallPressureMu
getData() MeterMBAR
getData() MultiharmonicGraphicMC.DataSourceAlphaChi
getData() AccumulatorOverlapAverageUa2
Implements DataSource interface, but you probably want to
getData for a specific Bennet parameter.
getData() MultiharmonicGraphicMC.DataSourceAlphaAlpha
getData() MultiharmonicGraphicMC.DataSourceAlphaChi
getData() MultiharmonicGraphicMC.DataSourceAlphaFE
getData() MultiharmonicGraphicMC.DataSourceFunctionRaw
getData() MeterUmbrella
getData() MultiharmonicGraphicMC.DataSourceAlphaAlpha
getData() MultiharmonicGraphicMC.DataSourceAlphaChi
getData() MeterClusterSizes
getData() MeterRDFCylinder
getData() MeterDimerFraction
getData() MeterFlux
getData() MeterOsmoticPressure
getData() MeterTilt
getData() DataCollector
getData() DataSourceFE
getData() DataSourceFEHistogram
getData() DataSourceImposedFEFit
getData() DataSourceImposedFEHistogram
getData() DataSourcePMu
getData() DataSourcePN
getData() MeterAtomicDisplacement
getData() MeterBoltzmann
getData() MeterBoltzmannHarmonic
getData() MeterBoltzmannHTTP
getData() MeterBoltzmannTarget
Sets the fraction that the system is coupled to measured energy.
getData() MeterDADB
getData() MeterDDP
getData() MeterDirectSamplingHarmonic
getData() MeterDirectSamplingTarget
getData() MeterDP
getData() MeterHarmonicSingleEnergy
getData() MeterNormalMode
Returns the DataGroup of S(k) Tensors corresponding to the sum of
T(k)*transpose(T(-k)).
getData() MeterOverlapSwitch
getData() MeterPlaneSlip
getData() MeterSamplingHarmonic
getData() MeterSamplingTarget
getData() MeterSolidDA
Computes total pressure in box by summing virial over all pairs, and adding
ideal-gas contribution.
getData() MeterSolidDACut
Computes total pressure in box by summing virial over all pairs, and adding
ideal-gas contribution.
getData() MeterSolidMirror
Computes total pressure in box by summing virial over all pairs, and adding
ideal-gas contribution.
getData() MeterSolidProps
getData() MeterSolidPropsLJ
getData() MeterTargetTP
getData() MeterTilt
getData() MeterTiltHistogram
getData() MeterTiltRotation
getData() MeterTiltRotationHistogram
getData() MeterTiltRotationStdev
getData() MeterWorkBennetHarmonic
getData() MeterWorkBennetTarget
getData() MeterWorkHarmonicBennet
getData() MeterWorkHarmonicPhaseSpace
getData() MeterWorkHarmonicTargetandReweighting
getData() MeterWorkHarmonicUmbrella
getData() MeterWorkTargetBennet
getData() MeterWorkTargetHarmonicandReweighting
getData() MeterWorkTargetPhaseSpace
getData() MeterWorkTargetUmbrella
getData() MeterWorkUmbrellaHarmonic
getData() MeterWorkUmbrellaTarget
getData() MeterOverlap
getData() P2QChemInterpolated
getData() P3HydrogenManzhos
getData() DataAndInfo
getData() MeterDipoleMoment
getData() MeterEnergyMeanField
getData() MeterMappedAveraging
getData() MeterMappedAveraging3Pair
getData() MeterMappedAveragingCorrelation
getData() MeterMappedAveragingCV
getData() MeterMappedAveragingFreeEnergy
getData() MeterMappedAveragingPair
getData() MeterMappedAveragingPairExcess
getData() MeterMappedAveragingSum
getData() MeterMappedAveragingVSum
getData() MeterMappedAveragingVSum3Pair
getData() MeterMappedAveragingVSumPair
getData() MeterMeanField
getData() MeterBondLength
Returns the RDF, averaged over the calls to actionPerformed since the
meter was reset or had some parameter changed (xMax or # of bins).
getData() ModelMoleculeListDisplayTable_new
getData() ModelMoleculeListDisplayTable
getData() ModelPotParamDisplayTable
getData() MeterSamplingWeight
getData() MeterVirial
getData() MeterVirialBD
getData() MeterVirialExternalField
getData() MeterVirialExternalFieldConfined
getData() MeterVirialExternalFieldOverlapConfined
getData() MeterVirialExternalFieldOverlapConfinedRho
getData() MeterVirialExternalFieldOverlapConfinedSW
getData() MeterVirialExternalFieldOverlapRho
getData() MeterVirialExternalFieldRho
getData() MeterVirialExternalFieldSW
getData() MeterVirialIC
getData() MeterVirialSWWE
getData() AccumulatorVirialOverlapSingleAverage
Implements DataSource interface, but you probably want to
getData for a specific Bennet parameter.
getData(int) DataSet
Returns the ith Data from the set.
getData(int) DataGroup
Returns the i-th data element in the group, counting from 0.
getData(int) AccumulatorVirialOverlapSingleAverage
Return all standard data corresponding to the given Bennet parameter.
getData(IAtom) DataSourceAtomic
getData(IAtom) DataSourceRmsVelocity
getData(IAtom) MeterTensorVelocity
Returns the velocity dyad (mass*vv) for the given atom.
getData(AccumulatorAverage.StatType) AccumulatorAverage
Returns a specific element from the DataGroup returned
by getData().
getData(IMolecule) DataSourceMolecular
getData(IMolecule) MeterMoleculeTemperature
getData(IMolecule) MeterNMolecules
getData(IMolecule) MeterOrientation
getData(Vector) DataSourcePositioned
getData(Vector) DataSourcePositionedBoltzmannFactor
getDataAsArray() MeterMeanSquareDisplacement
getDataAsScalar() MeterDimerMoleFraction
getDataAsScalar() MeterContactRatio
getDataAsScalar() MeterPairedFraction
getDataAsScalar() MeterPressureCollisionCount
Returns P = (NT - (virial sum)/((elapsed time)*T*(space dimension)))/V
Virial sum and elapsed time apply to period since last call to this method.
getDataAsScalar() AccumulatorHistory.DataSourceCount
getDataAsScalar() DataSourceAcceptanceProbability
Returns the value of the acceptance ratios as currently kept by
the MCMove classes identified with setMove.
getDataAsScalar() DataSourceAcceptanceRatio
Returns the value of the acceptance ratio as currently kept by
the MCMove class identified with setMove.
getDataAsScalar() DataSourceAtomDistance
getDataAsScalar() DataSourceCountCollisions
Returns the simulation time elapsed by the integrator tracked
by this class since the last reset.
getDataAsScalar() DataSourceCountSteps
Returns the number of steps performed by the integrator
getDataAsScalar() DataSourceCountTime
Returns the simulation time elapsed by the integrator tracked
by this class since the last reset.
getDataAsScalar() DataSourceScalar
Returns a single scalar value as the measurement for the given box.
getDataAsScalar() MeterAvgBondLength
getDataAsScalar() MeterDensity
getDataAsScalar() MeterDipoleSumSquared1site
getDataAsScalar() MeterDipoleSumSquaredTIP4PWater
getDataAsScalar() MeterEnergy
Current value of the total energy (kinetic + potential)
getDataAsScalar() MeterKineticEnergy
Returns the total kinetic energy summed over all atoms produced by the iterator when applied to the given box.
getDataAsScalar() MeterKineticEnergyFromIntegrator
getDataAsScalar() MeterKineticEnergyRigid
Returns the total kinetic energy summed over all atoms produced by
the iterator when applied to the given box.
getDataAsScalar() MeterLocalDensity
getDataAsScalar() MeterLocalMoleFraction
getDataAsScalar() MeterMeanSquareDisplacement
getDataAsScalar() MeterMoleculeTemperature
getDataAsScalar() MeterMoleFraction
getDataAsScalar() MeterNMolecules
getDataAsScalar() MeterPotentialEnergy
Computes total potential energy for box.
getDataAsScalar() MeterPotentialEnergyFromIntegrator
getDataAsScalar() MeterPressure
Computes total pressure in box by summing virial over all pairs, and adding
ideal-gas contribution.
getDataAsScalar() MeterPressureHard
Returns P = (NT - (virial sum)/((elapsed time)*T*(space dimension)))/V
Virial sum and elapsed time apply to period since last call to this method.
getDataAsScalar() MeterPressureMolecular
Computes total pressure in box by summing virial over all pairs, and adding
ideal-gas contribution.
getDataAsScalar() MeterRadiusGyration
getDataAsScalar() MeterRMSD
getDataAsScalar() MeterTemperature
getDataAsScalar() MeterVolume
getDataAsScalar() MeterWidomInsertion
Performs a Widom insertion average, doing nInsert insertion attempts
Temperature used to get exp(-uTest/kT) is that of the integrator for the
box
getDataAsScalar() MeterFlux
getDataAsScalar() MeterWallForce
getDataAsScalar() MeterWallPosition
getDataAsScalar() MeterWidomInsertionP
Performs a Widom insertion average, doing nInsert insertion attempts
Temperature used to get exp(-uTest/kT) is that of the integrator for the
box
getDataAsScalar() MeterMappedU
getDataAsScalar() MeterMappedVirial
getDataAsScalar() MeterMappedVirialV
getDataAsScalar() MeterBoltzmannDirect
getDataAsScalar() MeterDirectInitPert
getDataAsScalar() MeterOrientationOrderParameter
getDataAsScalar() MeterRotPerturbMolecule
getDataAsScalar() MeterExcessAdsorbed
getDataAsScalar() MeterDensityCO
getDataAsScalar() MeterDensityCO2
getDataAsScalar() MeterDensityO2
getDataAsScalar() MeterConversion
getDataAsScalar() MeterEnd2End
getDataAsScalar() MeterFlux
getDataAsScalar() DropletAtomicGraphic.DataSourceVaporDensity
getDataAsScalar() DataSourcePrevTime
getDataAsScalar() InsertionGraphic.MeterWidom
getDataAsScalar() MeterElongation
getDataAsScalar() MeterLoad
getDataAsScalar() MeterStrain
getDataAsScalar() MeterStress
getDataAsScalar() MeterDensitySides
getDataAsScalar() MultiharmonicGraphicMC.DataSourceFE
getDataAsScalar() MeterFreeEnergy
getDataAsScalar() MultiharmonicGraphicMC.DataSourceBias
getDataAsScalar() MultiharmonicGraphicMC.DataSourceChiSlope
getDataAsScalar() MultiharmonicGraphicMC.DataSourceUa
getDataAsScalar() MultiharmonicGraphicMC.DataSourceUa2
getDataAsScalar() MeterLargestCluster
getDataAsScalar() MeterOsmoticPressure
getDataAsScalar() DataSourceWallPressure
getDataAsScalar() MeterEndToEnd
getDataAsScalar() MeterNormalStress
getDataAsScalar() MeterViscosity
getDataAsScalar() MeterWallPressure
getDataAsScalar() MeterPressure2
Computes total pressure in box by summing virial over all pairs, and adding
ideal-gas contribution.
getDataAsScalar() DataSourceAvgPressure
getDataAsScalar() DataSourceAvgPressure2
getDataAsScalar() DataSourceMuRoot.DataSourceMuRootDPressure
getDataAsScalar() DataSourceMuRoot.DataSourceMuRootDU
getDataAsScalar() DataSourceMuRoot.DataSourceMuRootPressure
getDataAsScalar() DataSourceMuRoot.DataSourceMuRootVacancyConcentration
getDataAsScalar() DataSourceMuRoot
getDataAsScalar() DataSourceMuRoot1.DataSourceMuRootPressure
getDataAsScalar() DataSourceMuRoot1.DataSourceMuRootVacancyConcentration
getDataAsScalar() DataSourceMuRoot1
getDataAsScalar() DataSourceMuRootPMatch.DataSourceMuRootPressure
getDataAsScalar() DataSourceMuRootPMatch.DataSourceMuRootVacancyConcentration
getDataAsScalar() DataSourceMuRootPMatch
getDataAsScalar() MeterAPIPotentialEnergy
getDataAsScalar() MeterDisplacementMoleculeRMS
getDataAsScalar() MeterDisplacementRMS
getDataAsScalar() MeterHarmonicCoordinate
getDataAsScalar() MeterHarmonicEnergy
getDataAsScalar() MeterHarmonicEnergyFromMove
getDataAsScalar() MeterJacobian
getDataAsScalar() MeterMaxExpansion
getDataAsScalar() MeterPhiDeviation
getDataAsScalar() MeterPressureSuperBox
Computes total pressure in box by summing virial over all pairs, and adding
ideal-gas contribution.
getDataAsScalar() MeterThetaDeviation
getDataAsScalar() SimEinStep2.MeterPotentialEnergyComposite
getDataAsScalar() SimEinStep2HCP.MeterPotentialEnergyComposite
getDataAsScalar() SimOverlapLJModule.MeterPotentialEnergyDifference
getDataAsScalar() SimOverlapSoftSphereEin.MeterPotentialEnergyComposite
getDataAsScalar() SimOverlapSoftSphereEinHarm.MeterPotentialEnergyComposite
getDataAsScalar() MeterRmin
getDataAsScalar() MeterRminSpecies
getDataAsScalar() MeterPairSum
getDataAsScalar() MeterSpinMSquare
getDataAsScalar() MeterSpin
getDataCount() DataSet
getDataDouble() DataSourceScalar
Causes the single getDataAsScalar(Box) value to be computed and
returned for the given box.
getDataFromSet(DataTag[]) DisplayPlot
getDataHistogramBetaUAWf() MeterWorkHarmonicTargetandReweighting
getDataHistogramBetaUAWr() MeterWorkHarmonicTargetandReweighting
getDataHistogramBetaUBWf() MeterWorkTargetHarmonicandReweighting
getDataHistogramBetaUBWr() MeterWorkTargetHarmonicandReweighting
getDataImaginary(int, int) LatticeSumCrystal.DataGroupLSC
Returns imaginary part of complex data.
getDataImaginary(int, int) LatticeSumCrystalMolecular.DataGroupLSC
Returns imaginary part of complex data.
getDataInfo() MeterEnthalpyVolume
getDataInfo() MeterCavityMapped
getDataInfo() MeterRDFMapped
getDataInfo() MeterWidomCavity
getDataInfo() AccumulatorHistogram
Returns the DataInfo for the output Data.
getDataInfo() AccumulatorHistory
getDataInfo() DataDump
getDataInfo() DataProcessor
getDataInfo() DataSet.DataSetSink
getDataInfo() DataSourceFunction
getDataInfo() DataSourceGroup
getDataInfo() DataSourcePoints
getDataInfo() DataSourceRmsVelocity
getDataInfo() DataSourceScalar
getDataInfo() DataSourceTensorVirialHard
getDataInfo() DataSourceUniform
getDataInfo() FunctionData
Returns a DataInfo that describes the Data object that is returned by this function's f method.
getDataInfo() HistogramDataSource
Returns the DataInfo for the output Data.
getDataInfo() IDataSource
getDataInfo() MeterDihedralAngle
getDataInfo() MeterDipoleSumSquaredMappedAverage
getDataInfo() MeterHyperVirial
getDataInfo() MeterMomentumCOM
getDataInfo() MeterPositionCOM
getDataInfo() MeterPressureByVolumeChange.DataSourceExp
getDataInfo() MeterPressureByVolumeChange
getDataInfo() MeterPressureHardTensor
getDataInfo() MeterPressureTensor
getDataInfo() MeterPressureTensorFromIntegrator
getDataInfo() MeterProfile
getDataInfo() MeterProfileByAtoms
getDataInfo() MeterProfileByVolume
getDataInfo() MeterRDF
getDataInfo() MeterRDFPC
getDataInfo() MeterStructureFactor
getDataInfo() MeterTensorVelocity
getDataInfo() DataSourceEnergies
getDataInfo() IntegratorPT.BoxTracker
getDataInfo() MeterPotentialEnergyCutoff
getDataInfo() MeterPU
getDataInfo() MeterPUCut
getDataInfo() MeterPUCutLS
getDataInfo() MeterWidomInsertionCorrection
getDataInfo() MeterMappedRdf
getDataInfo() MeterMeanForce
getDataInfo() MeterDensityDistribution
getDataInfo() MeterBoltzmann
getDataInfo() MeterBoltzmannRotPerturb
getDataInfo() MeterNormalizedCoord
getDataInfo() MeterNormalizedCoordBeta
getDataInfo() MeterOrientationDistribution
getDataInfo() MeterRotationDistributionGroup
getDataInfo() MeterTargetRPMolecule
getDataInfo() MeterTargetTPMolecule
getDataInfo() DataSourceDensityFunction
getDataInfo() DataSourceWallPressureCatalysis
getDataInfo() MeterChainLength
getDataInfo() MeterDeformation
getDataInfo() AccumulatorPTensor
getDataInfo() CorrelationSelf2.MeterCorrelationSelf2
getDataInfo() DataSourceAlpha2
getDataInfo() DataSourceBlockAvgCor
getDataInfo() DataSourceCorrelation.Meter
getDataInfo() DataSourceF
getDataInfo() DataSourceFOld
getDataInfo() DataSourceFs
getDataInfo() DataSourceHisogram
getDataInfo() DataSourceHistogramMSD
getDataInfo() DataSourceMSD
getDataInfo() DataSourceMSDcorP.DataSourceMSDcovP
getDataInfo() DataSourceMSDcorP
getDataInfo() DataSourcePercolation.Chi4Source
getDataInfo() DataSourcePercolation
getDataInfo() DataSourcePercolation.ImmFractionByTypeSource
getDataInfo() DataSourcePercolation.ImmFractionSource
getDataInfo() DataSourcePercolation.PercolationByImmFrac
getDataInfo() DataSourcePercolation0
getDataInfo() DataSourcePMSDHistory
getDataInfo() DataSourceQ4
getDataInfo() DataSourceQ4.MeterChi4
getDataInfo() DataSourceStrings
getDataInfo() DataSourceVAC
getDataInfo() GlassGraphic.MeterFromDumps
getDataInfo() MeterCorrelation
getDataInfo() MeterCorrelationSelf
getDataInfo() MeterGs
getDataInfo() MeterStructureFactorStress3
getDataInfo() StructureFactorComponentCorrelation.Meter
getDataInfo() DataSourceTensorVirialHardProfile.DataSourceVirialProfile
getDataInfo() DataSourceWallPressureMu
getDataInfo() MeterMBAR
getDataInfo() MultiharmonicGraphicMC.DataSourceAlphaChi
getDataInfo() MultiharmonicGraphicMC.DataSourceAlphaAlpha
getDataInfo() MultiharmonicGraphicMC.DataSourceAlphaChi
getDataInfo() MultiharmonicGraphicMC.DataSourceAlphaFE
getDataInfo() MultiharmonicGraphicMC.DataSourceFunctionRaw
getDataInfo() MeterUmbrella
getDataInfo() MultiharmonicGraphicMC.DataSourceAlphaAlpha
getDataInfo() MultiharmonicGraphicMC.DataSourceAlphaChi
getDataInfo() MeterClusterSizes
getDataInfo() MeterDimerFraction
getDataInfo() MeterFlux
getDataInfo() MeterOsmoticPressure
getDataInfo() MeterTilt
getDataInfo() DataCollector
getDataInfo() DataSourceFE
getDataInfo() DataSourceFEHistogram
getDataInfo() DataSourceImposedFEFit
getDataInfo() DataSourceImposedFEHistogram
getDataInfo() DataSourcePMu
getDataInfo() DataSourcePN
getDataInfo() MeterAtomicDisplacement
getDataInfo() MeterBoltzmann
getDataInfo() MeterBoltzmannHarmonic
getDataInfo() MeterBoltzmannHTTP
getDataInfo() MeterBoltzmannTarget
getDataInfo() MeterDADB
getDataInfo() MeterDDP
getDataInfo() MeterDirectSamplingHarmonic
getDataInfo() MeterDirectSamplingTarget
getDataInfo() MeterDP
getDataInfo() MeterHarmonicCoordinate
getDataInfo() MeterHarmonicSingleEnergy
getDataInfo() MeterNormalMode
getDataInfo() MeterOverlapSwitch
getDataInfo() MeterPlaneSlip
getDataInfo() MeterSamplingHarmonic
getDataInfo() MeterSamplingTarget
getDataInfo() MeterSolidDA
getDataInfo() MeterSolidDACut
getDataInfo() MeterSolidMirror
getDataInfo() MeterSolidProps
getDataInfo() MeterSolidPropsLJ
getDataInfo() MeterTargetTP
getDataInfo() MeterTilt
getDataInfo() MeterTiltHistogram
getDataInfo() MeterTiltRotation
getDataInfo() MeterTiltRotationHistogram
getDataInfo() MeterTiltRotationStdev
getDataInfo() MeterWorkBennetHarmonic
getDataInfo() MeterWorkBennetTarget
getDataInfo() MeterWorkHarmonicBennet
getDataInfo() MeterWorkHarmonicPhaseSpace
getDataInfo() MeterWorkHarmonicTargetandReweighting
getDataInfo() MeterWorkHarmonicUmbrella
getDataInfo() MeterWorkTargetBennet
getDataInfo() MeterWorkTargetHarmonicandReweighting
getDataInfo() MeterWorkTargetPhaseSpace
getDataInfo() MeterWorkTargetUmbrella
getDataInfo() MeterWorkUmbrellaHarmonic
getDataInfo() MeterWorkUmbrellaTarget
getDataInfo() MeterOverlap
getDataInfo() DataAndInfo
getDataInfo() MeterDipoleMoment
getDataInfo() MeterEnergyMeanField
getDataInfo() MeterMappedAveraging
getDataInfo() MeterMappedAveraging3Pair
getDataInfo() MeterMappedAveragingCorrelation
getDataInfo() MeterMappedAveragingCV
getDataInfo() MeterMappedAveragingFreeEnergy
getDataInfo() MeterMappedAveragingPair
getDataInfo() MeterMappedAveragingPairExcess
getDataInfo() MeterMappedAveragingSum
getDataInfo() MeterMappedAveragingVSum
getDataInfo() MeterMappedAveragingVSum3Pair
getDataInfo() MeterMappedAveragingVSumPair
getDataInfo() MeterMeanField
getDataInfo() MeterBondLength
getDataInfo() MeterSamplingWeight
getDataInfo() MeterVirial
getDataInfo() MeterVirialBD
getDataInfo() MeterVirialBDBin
getDataInfo() MeterVirialExternalField
getDataInfo() MeterVirialExternalFieldConfined
getDataInfo() MeterVirialExternalFieldOverlapConfined
getDataInfo() MeterVirialExternalFieldOverlapConfinedRho
getDataInfo() MeterVirialExternalFieldOverlapConfinedSW
getDataInfo() MeterVirialExternalFieldOverlapRho
getDataInfo() MeterVirialExternalFieldRho
getDataInfo() MeterVirialExternalFieldSW
getDataInfo() MeterVirialIC
getDataInfo() MeterVirialSWWE
getDataInfo(int) DataSet
Returns the ith DataInfo from the set.
getDataInfo(String, String) DataStreamResource
getDataInfoHistogramBetaUAWf() MeterWorkHarmonicTargetandReweighting
getDataInfoHistogramBetaUAWr() MeterWorkHarmonicTargetandReweighting
getDataInfoHistogramBetaUBWf() MeterWorkTargetHarmonicandReweighting
getDataInfoHistogramBetaUBWr() MeterWorkTargetHarmonicandReweighting
getDataLength() IntegratorPT.BoxTracker
getDataOverlap() SimOverlapModule
getDataReal(int, int) LatticeSumCrystal.DataGroupLSC
Returns real part of complex data.
getDataReal(int, int) LatticeSumCrystalMolecular.DataGroupLSC
Returns real part of complex data.
getDataResetAction() SimulationRestart
getDataReweighted() MeterWorkHarmonicBennet
getDataReweighted() MeterWorkTargetBennet
getDataReweighted() MeterWorkUmbrellaHarmonic
getDataReweighted() MeterWorkUmbrellaTarget
getDataSet() DisplayPlot
Returns the DataSinkTable instance that specifies the plot data.
getDataSet() DisplayPlotXChart
getDataSink() DataProcessor
getDataSink() DataProcessorForked
getDataSink(int) DataDistributer
Returns the DataSink for the ith output stream (corresponding to the ith
numerical value coming in).
getDataSink(int) DataGroupSplitter
Returns the DataSink for the ith output stream (corresponding to the ith
numerical value coming in).
getDataSink(int) DataSplitter
Returns the DataSink for the ith output stream (corresponding to the ith
numerical value coming in).
getDataSink(int) DataOverlap.DataSourceOverlapAvgCollapsing
getDataSink(int) DataOverlap.DataSourceOverlapAvgCollapsingSplit
getDataSinks() DataFork
getDataSinks() DataPipeForked
getDataSinks() DataProcessorForked
getDataSource() DataPump
getDataSource() MeterProfile
The meter that defines the profiled quantity
getDataSource() MeterProfileByAtoms
The meter that defines the profiled quantity
getDataSource() MeterProfileByVolume
The meter that defines the profiled quantity
getDataStreamPumps() SimulationDataAction
getDataStreamPumps() DeviceTrioControllerButton
Returns an ArrayList of DataPumps that are headers for the data streams.
getDataTable() DisplayTable
getDataTagBag(List<DataTagBag>, DataTag[]) DataTagBag
Returns the first DataTagBag from the given list that has no non-matching
tags with the given desiredTags
getDataTagBagExact(LinkedList<DataTagBag>, DataTag[]) DataTagBag
Return the DataTagBag with the given set of tags (exactly) if it exists,
or null of no such DataTagBag exists.
getDataXMax() DisplayPlotXChart
getDataXMin() DisplayPlotXChart
getDataYMax() DisplayPlotXChart
getDataYMin() DisplayPlotXChart
getDateFormat() ApiPlatform
getDateFormat() Platform
getDecimalSliderMajorTickSpacing() DecimalSlider
getDecimalSliderMaximum() DecimalSlider
getDecimalSliderMinimum() DecimalSlider
getDecimalSliderMinorTickSpacing() DecimalSlider
getDecimalSliderValue() DecimalSlider
getDefaultColor() ColorScheme
getDefaultFontFamily() SVGConverter
getDeformation() ConfigurationDroplet
getDegeneracy() PermutationDegenerateIterator
getDelayExponent() DeviceDelaySlider
getDeltaCut() ClusterSumNonAdditiveTrimerEnergy
getDeltaCut() ClusterSumPolarizable
getDeltaCut() ClusterSumPolarizableWertheimProduct
getDeltaCut() ClusterSumPolarizableWertheimProduct4Pt
getDeltaCut() ClusterSumPolarizableWertheimProduct4PtFinal
getDeltaN() MyMCMove
getDeltaN() MyMCMove
getDeltaU(double) MultiharmonicGraphicMC.DataSinkReweightedDeltaU
getDeltaU(IAtomKinetic, double, boolean, boolean) P1MagicWall
getDeltaX() HistogramExpanding
getDenominator() Coefficient
getDenominator() CoefficientImpl
getDenstiyProfileDump() DataProcessorChemicalPotential
getDepth() DisplayBoxCanvasG3DSys
Get depth percentage
getDepth() DisplayPolytopeCanvasG3DSys
Get depth percentage
getDepth() GData
gets g3d depth
getDepthPercent() G3DSys
getDescent() JmolFont
getDescription() ViewSpeciesSelection
getDescription() ViewSpeciesSelection
getDescription(String) IMolecularModel_SpeciesFactory
getDescription(String) MolecularModel2CLJQ_SpeciesCO2
getDescription(String) MolecularModel2CLJQ_SpeciesEthane
getDescription(String) MolecularModel2CLJQ_SpeciesLJ
getDescription(String) MolecularModelEMP2_SpeciesCO2
getDescription(String) MolecularModelLJ_SpeciesLJ
getDescription(String) MolecularModelLJQ_SpeciesLJ
getDescription(String) MolecularModelSKS_SpeciesAlkane
getDescription(String) MolecularModelSPCE_SpeciesH2O
getDescription(String) MolecularModelTRAPPE_SpeciesAlkane
getDescription(String) MolecularModelTrappe_SpeciesCO2
getDestination() MoleculeActionTranslateTo
getDestinationFile(String) SVGConverter
Get the name of the result image file.
getDestinationType() SVGConverter
getDeviationVector() FindBetaN2AngleFromParameter
getdFdr(double) P2MoleculeSoftTruncatedSwitched
getdFdr(double) P2SoftSphericalTruncatedSwitched
getdfdT(int, double, double) B3LJ
Returns a discretized df/dT function containing N points with a
separation interval of del_r
getDiameter(AtomType) DiameterHashByType
getDiameter(IAtom) DiameterHash
Returns an appropriate diameter for the given atom.
getDiameter(IAtom) DiameterHashByElement
getDiameter(IAtom) DiameterHashByElementType
getDiameter(IAtom) DiameterHashByType
getDiameter(IAtom) DiameterHashGlass
getDiameter(IElement) DiameterHashByElement
getDiameterHash() DisplayBox
Returns the DiameterHash used by this DisplayBox.
getDiameterHashByElement() DiameterHashByElementType
getDielectric() P2ReactionFieldDipole
getDielectric() P2ReactionFieldDipoleTruncated
Returns the dielectric constant of the fluid surrounding the cavity.
getDiffusePercent() GData
getDim() MeterFlux
getDimension() DataInfo
getDimension() DataInfoFactory
Returns the dimension
getDimension() IDataInfo
getDimension() IDataInfoFactory
Returns the dimension
getDimension() MeterTemperature
getDimension() ConfigFromFileLAMMPS.ModifierConfiguration
getDimension() Device
getDimension() FunctionMultiDimensional
The dimension of the space of independent variables.
getDimension() CalcGradientDifferentiable
getDimension() FiniteDifferenceDerivative
getDimension() Modifier
Returns the dimension of the property being modified.
getDimension() ModifierGeneral
getDimension() ModifierNMolecule
getDimension() ModifyAction
getDimension() ModifierPMu
getDimension() ColloidGraphic.WallRangeModifier
getDimension() LatticeEditor.NModifier
getDimension() IntegratorDCVGCMD.Mu1Modulator
getDimension() IntegratorDCVGCMD.Mu2Modulator
getDimension() DropletGraphic.ModifierBoxSize
getDimension() InterfacialSWGraphic.ModifierBoxSize
getDimension() MuGraphic.ModifierAtomDiameter
getDimension() MuGraphic.ModifierEpsilon
getDimension() MuGraphic.ModifierLambda
getDimension() NucleationGraphic.ModifierDensity
getDimension() ModifierPistonPressure
getDimension() PistonCylinderGraphic.ModifierAtomDiameter
getDimension() PistonCylinderGraphic.ModifierPistonDensity
getDimension() ReverseOsmosisGraphic.ModifierAtomDiameter
getDimension() ReverseOsmosisGraphic.ModifierEpsilon
getDimension() ReverseOsmosisWaterGraphic.ModifierAtomDiameter
getDimension() ReverseOsmosisWaterGraphic.ModifierEpsilon
getDimension() ReverseOsmosisWaterGraphic.ModifierSoluteCharge
getDimension() SamGraphic.ModifierWallPosition
getDimension() SwmdGraphic.ModifierAtomDiameter
getDimension() ModifierCells3D
getDimension() ModifierXCells2D
getDimension() ModifierYCells2D
getDimension() ModifierTPI
getDimension(double, double) Plot
Computes the separation in pixels of two points in the world window.
getDimensions() CellLattice
Returns the array that specifies the spatial dimensions of the lattice of cells.
getDimx() NormalModeAnalysisDisplay2D
getDimy() NormalModeAnalysisDisplay2D
getDipole(IMolecule) DHS_NVT.DipoleSourceDHS
getDipole(IMolecule) DLJ_NVT_1site.DipoleSourceDLJ
getDipole(IMolecule) DHS_NVT.DipoleSourceDHS
getDipole(IMolecule) DLJ_NVT_1site.DipoleSourceDLJ
getDipole(IMolecule) TIP4P_NVT.DipoleSourceTIP4PWater
getDipole(IMolecule) DipoleSourceAceticAcid
getDipole(IMolecule) DipoleSourceWater
getDipole(IMolecule) DipoleSource
Returns the dipole of the given molecule.
getDipole1() P2WaterTIP4PHardCore
getDipole1() VirialB2WaterTIP4P_DHS_difference.P2WaterDHS
getDipole2() P2WaterTIP4PHardCore
getDipole2() VirialB2WaterTIP4P_DHS_difference.P2WaterDHS
getdipoleconv() PotentialCalculationHeisenberg
getDipoleMomentSquare() P2LJDipole
getDipoleSource() P2ReactionFieldDipole
The DipoleSource returns the dipole vector of a given molecule.
getDipoleSource() P2ReactionFieldDipoleTruncated
Returns the dipole source used by this object.
getDipoleStrength() DipoleSourceWater
Returns the dipole strength.
getdipolex() PotentialCalculationHeisenberg
getdipoley() PotentialCalculationHeisenberg
getDirectedNormalThroughPoints(Point3f, Point3f, Point3f, Point3f, Vector3f, Vector3f, Vector3f) Measure
getDirection() RectangularLatticeNbrIterator
Gets the direction (up or down list) of the neighbors given by the iterator.
getDirection() IOrientation
getDirection() Orientation1D
getDirection() Orientation2D
getDirection() Orientation3D
getDirection() OrientationFull3D
getDirection() P1MagneticField
getDiscardProperty() SplitParameters
getDisplacement(IAtom) ConfigFromFileLAMMPS.ColorSchemeDeviation
getDisplacement(IAtom) ColorSchemeDirection
getDisplacementSq(IAtom) AtomTestDeviation
getDisplacementSq(IAtom) ColorSchemeDeviation
getDisplayBox(Box) SimulationGraphic
getDisplayDensity() ColorSchemeScaledOverlap
getDisplayDensity() DisplayBoxCanvas2DNpTScaling
getDisplayDensity() HSNPT2DGraphic
getDisplayPlot() DevicePlotPoints
Returns the top level panel that the function plot components sit on.
getDistanceToOrigin() Plane
Perpendicular distance from the plane to the origin.
getDitheredNoisyShadeIndex(float, float, float, float) Shader
getDoApplyPBC() WriteConfiguration
Returns true if PBC are applied to coordinates written to the file.
getDoApplyPBC() WriteConfigurationBinary
Returns true if PBC are applied to coordinates written to the file.
getDoApplyPBC() WriteConfigurationDLPOLY
Returns true if PBC are applied to coordinates written to the file.
getDoApplyPBC() WriteConfigurationP2DLPOLY
Returns true if PBC are applied to coordinates written to the file.
getDoApplyPBC() NeighborCellManagerMolecular
getDoApplyPBC() NeighborCellManager
getDoApplyPBC() NeighborListManagerMolecular
getDoApplyPBC() NeighborListManager
getDoAveraging() HistogramNotSoSimple
getDoCov() MeterVirialEBinMultiThreaded
getDoEnforceBounds() DataSourceUniform
getDoExcludeNonNeighbors() MCMoveMoleculeCoupledInitPert
Returns true if the move does not explicitly calculate the potential for
atom pairs that are not neighbors (as determined by the potentialMaster).
getDoExcludeNonNeighbors() MCMoveAtomCoupled
Returns true if the move does not explicitly calculate the potential for
atom pairs that are not neighbors (as determined by the potentialMaster).
getDoExcludeNonNeighbors() MCMoveMoleculeCoupled
Returns true if the move does not explicitly calculate the potential for
atom pairs that are not neighbors (as determined by the potentialMaster).
getDoMobileOnly() AtomTestDeviation
getDoPrevious() ConfigFromFileLAMMPS.ModifierConfiguration
getDoShowCurrent() DisplayTextBoxesCAE
getDoStrictBlockData() AccumulatorAverageFixed
getDoubleArray() Quaternion
Returns the Quaternion as a double array
getDoubleAvg() MeterVirialBDBinMultiThreaded.MyData
getDoubleDefaultParameters(String) IMolecularModel_SpeciesFactory
getDoubleDefaultParameters(String) MolecularModel2CLJQ_SpeciesCO2
getDoubleDefaultParameters(String) MolecularModel2CLJQ_SpeciesEthane
getDoubleDefaultParameters(String) MolecularModel2CLJQ_SpeciesLJ
getDoubleDefaultParameters(String) MolecularModelEMP2_SpeciesCO2
getDoubleDefaultParameters(String) MolecularModelLJ_SpeciesLJ
getDoubleDefaultParameters(String) MolecularModelLJQ_SpeciesLJ
getDoubleDefaultParameters(String) MolecularModelSKS_SpeciesAlkane
getDoubleDefaultParameters(String) MolecularModelSPCE_SpeciesH2O
getDoubleDefaultParameters(String) MolecularModelTRAPPE_SpeciesAlkane
getDoubleDefaultParameters(String) MolecularModelTrappe_SpeciesCO2
getDoubleVar() MeterVirialBDBinMultiThreaded.MyData
getDoWiggle() SimulationVirialOverlap2
getDownList() AtomNeighborLists
Returns an array of downlist-neighbor-atom lists.
getDownList() MoleculeNeighborLists
Returns an array of downlist-neighbor-molecule lists.
getDownList(IAtom) NeighborListManager
getDownList(IMolecule) NeighborListManagerMolecular
getDownNeighbors() RectangularLattice
getDrawables() DisplayBox
getDrawBoundary() DisplayCanvas
getDrawBoundaryType() ImageShell
Gets the boundary drawing style
getDrawDisplacement() DisplayBoxCanvas2DGlass
getDrawDisplacement() DisplayBoxCanvas3DGlass
getDrawDisplacement() DisplayBoxCanvasGlass
getDrawingHeight() DisplayBox
return int : height of the drawing area (only relevant for 1D)
getDrawOverflow() DisplayBox
getDrawSize() DisplayBox
getDrawSize() DisplayPolytope
getDrString() ColorSchemeDeviation
getDst() SVGConverter
getDtheta() MeterMeanField
getDUDW(IAtomList) P1ImageHarmonic
getDump() DataStreamStore.DataPlumbing
getDumpIndex() GlassGraphic.MeterFromDumps
getDv() P2Cohesion
getDy12(int) AkimaSplineSmoother
getE1() AbstractSearchState
getE1(byte, byte) AbstractSearchState
getE2() AbstractSearchState
getE2(byte, byte) AbstractSearchState
getE2CliqueCount() ClusterWheatleyExtendSW
getE2Cliques() ClusterWheatleyExtendSW
getECliqueCount() ClusterSumHS
getECliqueCount() ClusterWheatley
Returns number of e-bond cliques for the configuration passed to
checkConfig
getECliqueCount() ClusterWheatleyHS
getECliqueCount() ClusterWheatleyPartitionScreening
getECliques() ClusterSumHS
getECliques() ClusterWheatley
Returns an array containing the clique sets (based on e-bonds) for the
configuration passed to checkConfig.
getECliques() ClusterWheatleyHS
getECliques() ClusterWheatleyPartitionScreening
getEdge(byte) Graph
getEdge(byte) GraphImpl
getEdge(byte, byte) Graph
getEdge(byte, byte) GraphImpl
getEdgeCount() ClusterSumHS
Returns edgeCount (number of overlaps) of configuration passed to
checkConfig
getEdgeCount() ClusterWheatley
Returns edgeCount (number of overlaps) of configuration passed to
checkConfig
getEdgeCount() ClusterWheatleyHS
Returns edgeCount (number of overlaps) of configuration passed to
checkConfig
getEdgeCount() ClusterWheatleyPartitionScreening
Returns edgeCount (number of overlaps) of configuration passed to
checkConfig
getEdgeId(byte, byte) Graph
getEdgeId(byte, byte) GraphImpl
getEdgeLength() Cube
getEdgeLength() Square
getEdgeLength() TruncatedOctahedron
getEdgeLengths() Cuboid
Returns a vector with elements equal to the
edge lengths of the cuboid.
getEdgeLengths() LineSegment
Returns the length of the line segment as the element of a 1D vector.
getEdgeLengths() Rectangle
Returns a vector with elements equal to the
edge lengths of the rectangle.
getEdgeLengths() Rectangular
getEdges() LineSegment
getEdges() Point
getEdges() Polygon
Returns all edges defined by the polygon.
getEdges() Polyhedron
Returns all edges defined by the polyhedron.
getEdges() Polytope
getEdgeVector(int) Boundary
Returns the vector that defines the edge of this boundary for the given
dimension.
getEdgeVector(int) BoundaryDeformablePeriodic
getEdgeVector(int) BoundaryRectangular
getEdgeVector(int) BoundaryTruncatedOctahedron
getEditValues() DeviceSlider
getEditVariables() ViewSpeciesSelection
getEditVariables() ViewSpeciesSelection
getEFCliqueCount() ClusterWheatleyExtendSW
getEFCliques() ClusterWheatleyExtendSW
getEigenvalues() Eigen
getEigenvectors() NormalModes
First index corresponds to the wave vector; second index gives the eigenvector, and
third index gives the elements of the vector.
getEigenvectors() NormalModes1DHR
getEigenvectors() NormalModes2D
getEigenvectors() NormalModes3D
getEigenvectors() NormalModesFromFile
getEigenvectors() NormalModesMolecular
getEigenvectors() NormalModesPotential
getEigenvectors() NormalModesSoftSpherical
getEigenVectors() NormalModesVariable
getEigenVectors3() Eigen
getEigenvectorsFloatTransposed() Eigen
transpose V and turn into floats
getElectrostatic() BuilderCollectionPotential
getElement() AtomType
getElement(int, int) Matrix3f
Retrieves the value at the specified row and column of this matrix.
getElement(int, int) Matrix4f
Retrieves the value at the specified row and column of this matrix.
getElementHash() WriteConfigurationDLPOLY
getElementHash() WriteConfigurationP2DLPOLY
getElementNumber(short) Elements
getEligibleConstructor(Class) Construction
getEllipsoid(Vector3f[], float[], boolean) Eigen
getEllipsoidDD(double[][]) Eigen
getEllipsoidShade(float, float, float, int, Matrix4f) Shader
getEmbeddedSpace() Polytope
The space defining the vectors used to represent the vertices.
getEnabled() AccumulatorPTensor
getEnabled() ConfigurationStorage
getEnabled() DataSourceBlockAvgCor
getEnabled() DataSourceHisogram
getEnabled() DataSourceHistogramMSD
getEnabled() DataSourceMSDcorP
getEnabled() DataSourcePMSDHistory
getEnabled() Grabber.DefaultMouseListener
getEnd() Line
getEndpoint1() Bond
getEndpoint2() Bond
getEnergy() PotentialCalculationMappedEnergy
getEnergy(double[]) MinimizationBetaNitrogenModelLS
getEnergy(double[]) MinimizeBetaNitrogenLatticeParameter
getEnergy(double[]) MinimizeBetaNitrogenLatticeParameterFromFile
getEnergy(double[]) MinimizeBetaNitrogenLatticeParameterLSFromFile
getEnergy(double[]) MinimizeBetaNitrogenTranslationDOF
getEnergy(Vector[], Vector[]) P2WaterPotentialsJankowski
getEnergySum() PotentialCalculationSolidSuper
getEnergySum() PotentialCalculationSolidSuperCut
getEntries() ClusterWheatleyPartitionScreening.FrequencyCounter
getEpsilon() P1WCAWall
getEpsilon() P2Water3P
getEpsilon() P2Water3PSoft
getEpsilon() P2Water4P
getEpsilon() P2Water4PSoft
getEpsilon() P2WaterTIP4P
getEpsilon() P2WaterTIP4PHardCore
getEpsilon() P1Wall
getEpsilon() P2SquareWellBonding
Accessor method for depth of well
getEpsilon() P2SquareWellBondingCO
Accessor method for depth of well
getEpsilon() P2SquareWellSurface
Accessor method for depth of well
getEpsilon() P1Wall
getEpsilon() P1WCAPorousWall
getEpsilon() P1WCAWall
getEpsilon() P2Cohesion
getEpsilon() P2SquareWellOneSide
Accessor method for depth of well
getEpsilon() P1Tether
getEpsilon() P1WCAWall
getEpsilon() VLESim
getEpsilon() P22CLJQ
getEpsilon() P2Exp6Buckingham
getEpsilon() P2HardAssociation
Accessor method for depth of well.
getEpsilon() P2HardAssociationCone
Accessor method for Lennard-Jones energy parameter
getEpsilon() P2HardAssociationConeDoubleSites
Accessor method for Lennard-Jones energy parameter
getEpsilon() P2HardAssociationConeFourSites
Accessor method for Lennard-Jones energy parameter
getEpsilon() P2HardAssociationConeFourSitesSW
Accessor method for Lennard-Jones energy parameter
getEpsilon() P2HardAssociationConeOneSite
Accessor method for Lennard-Jones energy parameter
getEpsilon() P2HardAssociationConeSW
Accessor method for Lennard-Jones energy parameter
getEpsilon() P2HC2Yukawa
getEpsilon() P2LennardJones
Accessor method for Lennard-Jones energy parameter
getEpsilon() P2LennardJonesDreiding
Accessor method for Lennard-Jones energy parameter
getEpsilon() P2LJDipole
getEpsilon() P2LJQ
getEpsilon() P2LJQQ
getEpsilon() P2ModifiedMorse
getEpsilon() P2Morse
getEpsilon() P2PenetrableSphere
Mutator method for height of core.
getEpsilon() P2PenetrableSquareWell
Accessor method for depth of well
getEpsilon() P2SoftSphere
Accessor method for soft-sphere energy parameter
getEpsilon() P2SquareWell
Accessor method for depth of well
getEpsilon() P2SquareWellRobust
Accessor method for depth of well
getEpsilon() P2TriangleWell
getEpsilon() P2WCA
Accessor method for the energy parameter
getEpsilon() P2WCAP
Accessor method for the energy parameter
getEpsilon() P3BondAngle
Returns the characteristic energy of the potential
getEpsilon() P3CPSNonAdditiveHeOrig
Returns the characteristic energy of the potential
getEpsilon() P2LJDipole
getEpsilon() LJ
getEpsilon(int) MolecularModel2CLJQ_SpeciesCO2
getEpsilon(int) MolecularModel2CLJQ_SpeciesEthane
getEpsilon(int) MolecularModel2CLJQ_SpeciesLJ
getEpsilon(int) MolecularModelEMP2_SpeciesCO2
getEpsilon(int) MolecularModelLJ_SpeciesLJ
getEpsilon(int) MolecularModelLJQ_SpeciesLJ
getEpsilon(int) MolecularModelSKS_SpeciesAlkane
getEpsilon(int) MolecularModelSPCE_SpeciesH2O
getEpsilon(int) MolecularModelTRAPPE_SpeciesAlkane
getEpsilon(int) MolecularModelTrappe_SpeciesCO2
getEpsilonBonding() P2SquareWellBonding
getEpsilonBonding() P2SquareWellBondingCO
getEpsilonC() P2CO2EMP
getEpsilonCO() P2CO2EMP
getEpsilonCore() P2DoubleWell
Accessor method for depth of well
getEpsilonCore() P2PenetrableSquareWell
getEpsilonCoreDimension() P2PenetrableSquareWell
getEpsilonDimension() P2SquareWellBonding
getEpsilonDimension() P2SquareWellBondingCO
getEpsilonDimension() P2SquareWellSurface
getEpsilonDimension() P2SquareWellOneSide
getEpsilonDimension() P2DoubleWell
getEpsilonDimension() P2HardAssociation
getEpsilonDimension() P2HardAssociationCone
getEpsilonDimension() P2HardAssociationConeDoubleSites
getEpsilonDimension() P2HardAssociationConeFourSites
getEpsilonDimension() P2HardAssociationConeFourSitesSW
getEpsilonDimension() P2HardAssociationConeOneSite
getEpsilonDimension() P2HardAssociationConeSW
getEpsilonDimension() P2LennardJones
getEpsilonDimension() P2LennardJonesDreiding
getEpsilonDimension() P2ModifiedMorse
getEpsilonDimension() P2Morse
getEpsilonDimension() P2PenetrableSphere
getEpsilonDimension() P2PenetrableSquareWell
getEpsilonDimension() P2SoftSphere
getEpsilonDimension() P2SquareWell
getEpsilonDimension() P2SquareWellRobust
getEpsilonDimension() P2TriangleWell
getEpsilonDimension() P2WCA
getEpsilonDimension() P2WCAP
getEpsilonDimension() P3BondAngle
getEpsilonDimension() P3CPSNonAdditiveHeOrig
getEpsilonO() P2CO2EMP
getEpsilonWell() P2DoubleWell
getEpsInner() P2PenetrableBond
getEpsInnerDimension() P2PenetrableBond
getEpsOuter() P2PenetrableBond
getEpsOuterDimension() P2PenetrableBond
getEquationForQuadricWithCenter(float, float, float, Matrix3f, Vector3f, Matrix3f, double[], Matrix4f) Quadric
getError() DataSourceVirialOverlap
Returns the error in the ratio of the reference to target
overlap-to-virial ratios (which reduces to target/reference)
for the optimal value of the Bennet parameter.
getError(int) DataOverlap.DataSourceOverlapAvg
getError(int) DataOverlap.DataSourceOverlapAvgCollapsing
getError(int) DataOverlap.DataSourceOverlapAvgSimple
getError(int) DataOverlap
Returns the error in the ratio of the reference to target
overlap-to-virial ratios (which reduces to target/reference)
for the given value of the Bennet parameter.
getError(int) DataSourceVirialOverlap
Returns the error in the ratio of the reference to target
overlap-to-virial ratios (which reduces to target/reference)
for the given value of the Bennet parameter.
getErrorCode() SVGConverterException
getEta() MeterMeanField
getEta(int) ClusterOperations
Returns all diagrams of order n in the expansion for the indirect correlation function eta(r) = h(r) - c(r),
in the presence of any approximations currently in effect.
getEValNum() DeviceEigenvaluesSlider
getEValNum() IntegratorHarmonic
getEventInterval() Integrator
getEventManager() Box
getEventManager() Integrator
getEventManager() NeighborListManagerMolecular
getEventManager() NeighborListManager
getEventManager() Simulation
getEventManager() Boundary
getExecuteOnload() SVGConverter
Returns true if the scripts attached to the DOM using 'onload'
event attribute is going to be executed before rasterizing,
false otherwise.
getExp() MayerSSSeries
Returns the HS diameter.
getExpGroupingSize() ScientificFormat
getExpMaximumIntegerDigits() ScientificFormat
getExpMinimumIntegerDigits() ScientificFormat
getExpNegativePrefix() ScientificFormat
getExpNegativeSuffix() ScientificFormat
getExponent() P2SoftSphere
Accessor method for soft-sphere softness parameter
getExportName() Graphics3D
getExportType() Graphics3D
getExpPositivePrefix() ScientificFormat
getExpPositiveSuffix() ScientificFormat
getExpression() AssignmentImpl
getExpression() UnaryOpImpl
getExpression() Parser.Assignment
getExpression() Parser.UnaryOp
getExpression1() BinaryOpImpl
getExpression1() Parser.BinaryOp
getExpression2() BinaryOpImpl
getExpression2() Parser.BinaryOp
getExtension() DestinationType
getExtraDisconnectedVirialGraphs() MayerIonicDiagram1qbond
getExtraDisconnectedVirialGraphs() MayerIonicDiagram2qbonds
getExtraDisconnectedVirialGraphs() MayerIonicDiagram4qbonds
getExtraDisconnectedVirialGraphs() VirialDiagrams
getExtraDisconnectedVirialGraphs() WertheimDiagrams2SiteRho
getExtraDisconnectedVirialGraphs() WertheimDiagrams3SiteRho
getExtraDisconnectedVirialGraphs(int) VirialDiagramsPT
getExtraDisconnectedVirialGraphs(int[]) VirialDiagramsMix2
getExtrapolatedLogError(int, int) DataOverlap.DataSourceOverlapAvgCollapsing
getExtraTargetClusters() SimulationVirialOverlap2
getF(double) P2MoleculeSoftTruncatedSwitched
getF(double) P2SoftSphericalTruncatedSwitched
getF1CliqueCount() ClusterWheatleyExtendSW
getF1Cliques() ClusterWheatleyExtendSW
getFac() DiameterHashGlass
getFaces() Polyhedron
Returns all faces defined by the polyhedron.
getFaces() MeshSurface
getFacesFromCriticalPoints(Point3f[]) BoxInfo
getFaceVertexes(int) Geodesic
getFactory() IDataInfo
Returns a mutable factory that can make copies of this instance of
DataInfo.
getFactory() DataDouble.DataInfoDouble
getFactory() DataDoubleArray.DataInfoDoubleArray
getFactory() DataDoubleBDArray.DataInfoDoubleBDArray
getFactory() DataFunction.DataInfoFunction
getFactory() DataGroup.DataInfoGroup
getFactory() DataTable.DataInfoTable
getFactory() DataTensor.DataInfoTensor
getFactory() DataVector.DataInfoVector
getFactory() ModelSimulationConstructor
getFalseLabel() ActionToggle
getFalseLabel() DeviceToggleButton
getFalseLabel() DeviceToggleRadioButtons
getFieldColorMap() ConstructorColoredImpl
getFieldColorMap() Parser.ConstructorColored
getFieldNodes() ConstructorMonoImpl
getFieldNodes() Parser.ConstructorMono
getFigs() G3DSys
For use only by ImageShell class for iteration
getFile() SVGConverterFileSource
getFileName() DataLogger
getFileName() NormalModesMolecular
getFileName() NormalModesPotential
getFileNRef(String) SVGConverter
getFilter() MeterDeformation
getFirstAtom() AtomNbrClusterer
getFirstVector() ConformationChainZigZag
getFirstVector() ConformationChainZigZag2
getFit(double[], PolynomialFit.FitResult) PolynomialFit
getFixedCOM() MCMoveEinsteinCrystal
getFixedDeltaU() CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
getFixedDeltaU() CalcNumerical2ndDerivative
getFixedDeltaU() CalcNumerical2ndDerivativeNitrogen
getFixedDeltaU() FiniteDifferenceDerivativeCGNitrogenBeta
getFixedSpecies() GrainBoundaryTiltConfiguration
getflipcount() ClusterCoupledFlippedMultivalue
getFlipDisplacement() DisplayBoxCanvas2DGlass
getFlipDisplacement() DisplayBoxCanvas3DGlass
getFlipDisplacement() DisplayBoxCanvasGlass
getflipfrac() ClusterCoupledFlippedMultivalue
getFlipped() DiameterHashGlass
getFluctuationFactor() HSNPT.ColorSchemeDisplacement
getFM() G3DSys
Only to be used internally to escape endless delegation
getFNonAdditiveValues() ClusterSumMultibody
getFont3D(byte) JmolFont
getFont3D(float) GData
getFont3DCurrent() Graphics3D
getFont3DCurrent() GData
getFont3DFS(String, float) GData
getFont3DFSS(String, String, float) GData
getFont3DScaled(JmolFont, float) GData
getFontAscent(Object) ApiPlatform
getFontAscent(Object) Platform
getFontDescent(Object) ApiPlatform
getFontDescent(Object) Platform
getFontFaceID(String) JmolFont
getFontFid(float) GData
getFontFidFS(String, float) GData
getFontMetrics(JmolFont, Object) ApiPlatform
getFontMetrics(JmolFont, Object) Platform
getFontStyleID(String) GData
getFontStyleID(String) JmolFont
getForce() P1HardMovingBoundary
getForceconstant() MolecularModelSKS_SpeciesAlkane
getForceconstant() MolecularModelTRAPPE_SpeciesAlkane
getForceDimension() P1HardMovingBoundary
getForceSum() IntegratorVelocityVerlet
getFp8ShadeIndex(float, float, float) Shader
getfr(int, double, double) B3LJ
Returns a discretized f function containing N points with a
separation interval of del_r
getfr(int, double, double) B4FFTLJ
getfr(int, double, double) B5FFTLJ
getfr(int, double, double) B6FFTLJ
getfr(int, double, double) BnHNCLJ
getfr(int, double, double) BnPYLJ
getfr(int, double, double) BnSCALJ
getfr(int, double, double, double, int, boolean) B2Ionic
getfr(int, double, double, Potential2SoftSpherical) BnPY_1QC_Helium
getfr(int, double, double, Potential2Spherical) BnIETP2Spherical
getfr(IFunction) CalcFFT
getfr(Potential2SoftSpherical, int, double, double) B2ForSphericallySymmetricUByTrapezoidRule
getfr(Potential2SoftSpherical, int, double, double) B3ForSphericallySymmetricU
getfr(Potential2Spherical, int, double, double, double) BnPCJSDHe
getfr(Potential2Spherical, int, double, double, double) BnPYCHe
getFrac() MCMoveHarmonicEin
getFrac() SimOverlapSoftSphereEin.MeterPotentialEnergyComposite
getFrac() SimOverlapSoftSphereEinHarm.MeterPotentialEnergyComposite
getFraction() AtomTestRandom
getFrequencies() CalcVibrationalModes
Calculates the frequencies (omegas) of wave vectors described by the eigenvalues (lambdas) of
our system.
getFrequency(MCMove) MCMoveManager
Returns the trial frequency set for the given move, over and above the
move's nominal frequency.
getFromBinFile(String) ArrayReader2D
Deserializes a 3D array from the given file.
getFromFile(String) ArrayReader1D
getFromFile(String) ArrayReader1D
getFromFile(String) ArrayReader2D
Returns 2D arrays from the given file.
getFromFile(String, boolean) ArrayReader1D
getFromFile(String, boolean) ArrayReader1D
getFromFile(String, int) ReaderIn
getFromFile(String, int) ArrayReader2D
Returns 2D arrays from the given file.
getFromNode(byte) Graph
getFromNode(byte) GraphImpl
getFugacityFraction() MCMoveSemigrand
Accessor method for the set of fugacity fractions.
getFugacityFraction(int) MCMoveSemigrand
getFullBondMask() ClusterSumHS
getFullBondMask() ClusterWheatley
Returns number bond mask for all points for the configuration passed to
checkConfig
getFullBondMask() ClusterWheatleyHS
getFullBondMask() ClusterWheatleyPartitionScreening
getFullOverlapResultForAlpha(double) DataVirialOverlap
Returns the full set of overlap results (averages and uncertainties for
target and reference overlap averages).
getFullRatioResultForAlpha(double) DataVirialOverlap
Returns the full set of ratio results (reference and target ratios and
errors on those ratios).
getFullRatioResultForAlpha(double, int) DataVirialOverlap
getFullScreenDimensions(Object, int[]) ApiPlatform
getFullScreenDimensions(Object, int[]) Platform
getFullSystemResult() DataVirialOverlap
Simply return the reference and target averages and uncertainties.
getFullSystemResult(int) DataVirialOverlap
getFunction() DataSourceFunction
getFunction() ModifierFunctionWrapper
getFValues() ClusterSum
getFValues() ClusterSumPolarizableWertheimProduct
getFValues() ClusterSumPolarizableWertheimProduct4Pt
getFValues() ClusterSumPolarizableWertheimProduct4PtFinal
getG() P1Smash
getG1() AbstractSearchState
getG1() SearchState
getG2() AbstractSearchState
getG2() SearchState
getG3D() G3DSys
Get G3D
getG3DSys() DisplayBoxCanvasG3DSys
getGamma() PrimitiveTrigonal
getGamma() P3BondAngleDreiding
Returns the characteristic energy of the potential
getGData() Graphics3D
underlying GData object handles all general graphics setup.
getGlobalMoveInterval() IntegratorManagerMC
Accessor method for the average interval between box-swap trials.
getGoal() AbstractTraversal
getGraphics() EtomicaPlot
getGraphics(Object) ApiPlatform
getGraphics(Object) Platform
getGroup3Count() JmolConstants
getGroup3List() JmolConstants
getGroupID(int[], int) VirialDiagrams
getGroupID(int[], int) VirialDiagramsPT
getGroupingSize() ScientificFormat
getGSum() PotentialCalculationRDF
getGSum() PotentialCalculationMappedRdf
getH() FiniteDifferenceDerivative
getH() P1MagneticField
getH(int) ClusterOperations
Returns all diagrams of order n in the expansion for the total correlation function h(r), in the presence
of any approximations currently in effect.
getHarmonicEnergy() MCMoveAtomCoupledUmbrella
getHashmapAtomsetIterator() CollectionPotentialAtomicLike
getHashMapAtomTypeLikePairs() CollectionPotentialAtomicLike
getHashMapAtomTypesUnlikePairs() CollectionPotentialAtomicUnlike
getHashMapPotentialIntraBonded() CollectionPotentialAtomicLike
getHashMapPotentialNonBonded() CollectionPotentialAtomicLike
getHashMapPotentialNonBonded() CollectionPotentialAtomicUnlike
getHashMapPotentialNonBonded() HashMapPotentialNonBonded
getHeight() SVGConverter
getHeight() JmolFont
getHello() EtomicaServerConfig
getHelmholtzFreeEnergy(double) HarmonicCrystal
getHelmholtzFreeEnergy(double) HarmonicCrystalSsFccNxy
getHermiteList(int, Tuple3f, Tuple3f, Tuple3f, Tuple3f, Tuple3f, Tuple3f[], int, int, boolean) Hermite
getHexCode(short) Colix
getHexCodes(short[]) Colix
getHexColorFromRGB(int) Escape
getHexitValue(char) Escape
getHistogram() Histogram
Returns the histogram as an array of doubles
getHistogram() HistogramCollapsing
getHistogram() HistogramDiscrete
getHistogram() HistogramNotSoSimple
getHistogram() HistogramReweightedData
getHistogram() HistogramSimple
getHistogram() MCMoveOverlapListener
getHistogram() MeterMeanForce
getHistogram() DataSourcePercolation
getHistogram2() MeterMeanForce
getHistograms() AccumulatorHistogram
getHistory() AccumulatorHistory
getHistory() History
Returns an array containing the y values that have been added to the
History.
getHistory() HistoryCollapsing
Returns the history
getHistory() HistoryComplete
Returns an the history
getHistory() HistoryScrolling
Returns an array with the most recent history at the end.
getHistoryLength() History
Returns the number of data points tracked by the History.
getHistoryLength() HistoryCollapsing
getHistoryLength() HistoryComplete
getHistoryLength() HistoryScrolling
getHorizGBC() SimulationPanel
getHybridAcceptance() IntegratorMD
getHydrophobicity(int) Elements
getI1I0() MeterMeanField
getI2etc() MeterMeanField
getICPYCorrection(byte, boolean) PYGenerator
getId() Edge
getId() EdgeImpl
getId() NodeImpl
getId() Node
getId() PropertyUpdate
getId() ArrayMoleculeDisplayList
getId() MolecularModel2CLJQ_SpeciesCO2
getId() MolecularModel2CLJQ_SpeciesEthane
getId() MolecularModel2CLJQ_SpeciesLJ
getId() MolecularModelEMP2_SpeciesCO2
getId() MolecularModelLJ_SpeciesLJ
getId() MolecularModelLJQ_SpeciesLJ
getId() MolecularModelSKS_SpeciesAlkane
getId() MolecularModelSPCE_SpeciesH2O
getId() MolecularModelTRAPPE_SpeciesAlkane
getId() MolecularModelTrappe_SpeciesCO2
getId(Object) SimulationModel
getID() CoordinatePairLeafSet
getID() CoordinatePairMoleculeSet
getID() CoordinatePairSet
getID() Figure
Get the ID of the figure
getIDataInfo(int) MeterTiltRotationHistogram
getIdealRefFraction(double) DataOverlap
Returns the ideal fraction of time (or steps) spent in the reference
system under the assumption that the current data while spending
oldFrac amount of the calculation on the reference system.
getIdealRefFraction(double) IntegratorOverlap.ReferenceFracSource
getIdealRefFraction(double) DataSourceVirialOverlap
getIdealRefFraction(double) DataVirialOverlap
getIdealRefStepFraction() IntegratorOverlap
getIgnoredAtomType() MeterChainLength
getImageHeight(Object) ApiPlatform
getImageHeight(Object) Platform
getImagEigenvalues() MyEigenvalueDecomposition
Return the imaginary parts of the eigenvalues
getImagEigenvalues() Eigen
Return the imaginary parts of the eigenvalues
getImageShells() DisplayBox
getImageWidth(Object) ApiPlatform
getImageWidth(Object) Platform
getImaginary() FastFourierTransform
getIncludeHeader() DataArrayWriter
Returns whether the writer includes column headers or not
getIncludeHeader() DataTableWriter
Returns whether the writer includes column headers or not
getIndependentArrayDimension() MeterCavityMapped
getIndependentArrayDimension() MeterRDFMapped
getIndependentArrayDimension() MeterWidomCavity
getIndependentArrayDimension() AccumulatorAverageBootstrap
getIndependentArrayDimension() AccumulatorAverageCollapsingLog
getIndependentArrayDimension() DataSourceFunction
getIndependentArrayDimension() DataSourceIndependent
Returns the number of independent data dimensions
getIndependentArrayDimension() DataSourceIndependentSimple
getIndependentArrayDimension() DataSourcePoints
getIndependentArrayDimension() DataSourceRmsVelocity
getIndependentArrayDimension() MeterDihedralAngle
getIndependentArrayDimension() MeterProfile
getIndependentArrayDimension() MeterProfileByAtoms
getIndependentArrayDimension() MeterProfileByVolume
getIndependentArrayDimension() MeterRDF
getIndependentArrayDimension() MeterRDFPC
getIndependentArrayDimension() MeterStructureFactor
getIndependentArrayDimension() MeterMappedRdf
getIndependentArrayDimension() MeterMeanForce
getIndependentArrayDimension() DataProcessorXY
getIndependentArrayDimension() MeterChainLength
getIndependentArrayDimension() AccumulatorAutocorrelationPTensor
getIndependentArrayDimension() AccumulatorAutocorrelationShearStress
getIndependentArrayDimension() AccumulatorPTensor
getIndependentArrayDimension() DataSourceAlpha2
getIndependentArrayDimension() DataSourceBlockAvgCor
getIndependentArrayDimension() DataSourceCorrelation
getIndependentArrayDimension() DataSourceF
getIndependentArrayDimension() DataSourceFOld
getIndependentArrayDimension() DataSourceFs
getIndependentArrayDimension() DataSourceHisogram
getIndependentArrayDimension() DataSourceHistogramMSD
getIndependentArrayDimension() DataSourceMSD
getIndependentArrayDimension() DataSourceMSDcorP
getIndependentArrayDimension() DataSourcePercolation
getIndependentArrayDimension() DataSourcePercolation0
getIndependentArrayDimension() DataSourcePMSDHistory
getIndependentArrayDimension() DataSourceQ4
getIndependentArrayDimension() DataSourceStrings
getIndependentArrayDimension() DataSourceVAC
getIndependentArrayDimension() MeterCorrelation
getIndependentArrayDimension() MeterCorrelationSelf
getIndependentArrayDimension() MeterGs
getIndependentArrayDimension() StructureFactorComponentCorrelation
getIndependentArrayDimension() DataSourceTensorVirialHardProfile
getIndependentArrayDimension() DataProcessorDyDLnx
getIndependentArrayDimension() MultiharmonicGraphicMC.DataSourceAlphaChi
getIndependentArrayDimension() MultiharmonicGraphicMC.DataSourceAlphaAlpha
getIndependentArrayDimension() MultiharmonicGraphicMC.DataSourceAlphaChi
getIndependentArrayDimension() MultiharmonicGraphicMC.DataSourceAlphaFE
getIndependentArrayDimension() MultiharmonicGraphicMC.DataSourceFunctionRaw
getIndependentArrayDimension() MultiharmonicGraphicMC.DataSourceAlphaAlpha
getIndependentArrayDimension() MultiharmonicGraphicMC.DataSourceAlphaChi
getIndependentArrayDimension() StatisticsMCGraphic.DataProcessorUndo
getIndependentArrayDimension() DataSourceFE
getIndependentArrayDimension() DataSourceFEHistogram
getIndependentArrayDimension() DataSourceImposedFEFit
getIndependentArrayDimension() DataSourceImposedFEHistogram
getIndependentArrayDimension() DataSourcePMu
getIndependentArrayDimension() DataSourcePN
getIndependentArrayDimension() MeterAtomicDisplacement
getIndependentArrayDimension() MeterTiltHistogram
getIndependentArrayDimension() MeterBondLength
getIndependentData(int) MeterCavityMapped
getIndependentData(int) MeterRDFMapped
getIndependentData(int) MeterWidomCavity
getIndependentData(int) AccumulatorAverageBootstrap
getIndependentData(int) AccumulatorAverageCollapsingLog
getIndependentData(int) DataSourceFunction
getIndependentData(int) DataSourceIndependent
Returns the X data for the given dimension
getIndependentData(int) DataSourceIndependentSimple
getIndependentData(int) DataSourcePoints
getIndependentData(int) DataSourceRmsVelocity
getIndependentData(int) MeterDihedralAngle
getIndependentData(int) MeterProfile
getIndependentData(int) MeterProfileByAtoms
getIndependentData(int) MeterProfileByVolume
getIndependentData(int) MeterRDF
getIndependentData(int) MeterRDFPC
getIndependentData(int) MeterStructureFactor
getIndependentData(int) MeterMappedRdf
getIndependentData(int) MeterMeanForce
getIndependentData(int) DataProcessorXY
getIndependentData(int) MeterChainLength
getIndependentData(int) AccumulatorAutocorrelationPTensor
getIndependentData(int) AccumulatorAutocorrelationShearStress
getIndependentData(int) AccumulatorPTensor
getIndependentData(int) DataSourceAlpha2
getIndependentData(int) DataSourceBlockAvgCor
getIndependentData(int) DataSourceCorrelation
getIndependentData(int) DataSourceF
getIndependentData(int) DataSourceFOld
getIndependentData(int) DataSourceFs
getIndependentData(int) DataSourceHisogram
getIndependentData(int) DataSourceHistogramMSD
getIndependentData(int) DataSourceMSD
getIndependentData(int) DataSourceMSDcorP
getIndependentData(int) DataSourcePercolation
getIndependentData(int) DataSourcePercolation0
getIndependentData(int) DataSourcePMSDHistory
getIndependentData(int) DataSourceQ4
getIndependentData(int) DataSourceStrings
getIndependentData(int) DataSourceVAC
getIndependentData(int) MeterCorrelation
getIndependentData(int) MeterCorrelationSelf
getIndependentData(int) MeterGs
getIndependentData(int) StructureFactorComponentCorrelation
getIndependentData(int) DataSourceTensorVirialHardProfile
getIndependentData(int) DataProcessorDyDLnx
getIndependentData(int) MultiharmonicGraphicMC.DataSourceAlphaChi
getIndependentData(int) MultiharmonicGraphicMC.DataSourceAlphaAlpha
getIndependentData(int) MultiharmonicGraphicMC.DataSourceAlphaChi
getIndependentData(int) MultiharmonicGraphicMC.DataSourceAlphaFE
getIndependentData(int) MultiharmonicGraphicMC.DataSourceFunctionRaw
getIndependentData(int) MultiharmonicGraphicMC.DataSourceAlphaAlpha
getIndependentData(int) MultiharmonicGraphicMC.DataSourceAlphaChi
getIndependentData(int) StatisticsMCGraphic.DataProcessorUndo
getIndependentData(int) DataSourceFE
getIndependentData(int) DataSourceFEHistogram
getIndependentData(int) DataSourceImposedFEFit
getIndependentData(int) DataSourceImposedFEHistogram
getIndependentData(int) DataSourcePMu
getIndependentData(int) DataSourcePN
getIndependentData(int) MeterAtomicDisplacement
getIndependentData(int) MeterTiltHistogram
getIndependentData(int) MeterBondLength
getIndependentDataInfo(int) MeterCavityMapped
getIndependentDataInfo(int) MeterRDFMapped
getIndependentDataInfo(int) MeterWidomCavity
getIndependentDataInfo(int) AccumulatorAverageBootstrap
getIndependentDataInfo(int) AccumulatorAverageCollapsingLog
getIndependentDataInfo(int) DataSourceFunction
getIndependentDataInfo(int) DataSourceIndependent
Returns the DataInfo for the given dimension
getIndependentDataInfo(int) DataSourceIndependentSimple
getIndependentDataInfo(int) DataSourcePoints
getIndependentDataInfo(int) DataSourceRmsVelocity
getIndependentDataInfo(int) MeterDihedralAngle
getIndependentDataInfo(int) MeterProfile
getIndependentDataInfo(int) MeterProfileByAtoms
getIndependentDataInfo(int) MeterProfileByVolume
getIndependentDataInfo(int) MeterRDF
getIndependentDataInfo(int) MeterRDFPC
getIndependentDataInfo(int) MeterStructureFactor
getIndependentDataInfo(int) MeterMappedRdf
getIndependentDataInfo(int) MeterMeanForce
getIndependentDataInfo(int) DataProcessorXY
getIndependentDataInfo(int) MeterChainLength
getIndependentDataInfo(int) AccumulatorAutocorrelationPTensor
getIndependentDataInfo(int) AccumulatorAutocorrelationShearStress
getIndependentDataInfo(int) AccumulatorPTensor
getIndependentDataInfo(int) DataSourceAlpha2
getIndependentDataInfo(int) DataSourceBlockAvgCor
getIndependentDataInfo(int) DataSourceCorrelation
getIndependentDataInfo(int) DataSourceF
getIndependentDataInfo(int) DataSourceFOld
getIndependentDataInfo(int) DataSourceFs
getIndependentDataInfo(int) DataSourceHisogram
getIndependentDataInfo(int) DataSourceHistogramMSD
getIndependentDataInfo(int) DataSourceMSD
getIndependentDataInfo(int) DataSourceMSDcorP
getIndependentDataInfo(int) DataSourcePercolation
getIndependentDataInfo(int) DataSourcePercolation0
getIndependentDataInfo(int) DataSourcePMSDHistory
getIndependentDataInfo(int) DataSourceQ4
getIndependentDataInfo(int) DataSourceStrings
getIndependentDataInfo(int) DataSourceVAC
getIndependentDataInfo(int) MeterCorrelation
getIndependentDataInfo(int) MeterCorrelationSelf
getIndependentDataInfo(int) MeterGs
getIndependentDataInfo(int) StructureFactorComponentCorrelation
getIndependentDataInfo(int) DataSourceTensorVirialHardProfile
getIndependentDataInfo(int) DataProcessorDyDLnx
getIndependentDataInfo(int) MultiharmonicGraphicMC.DataSourceAlphaChi
getIndependentDataInfo(int) MultiharmonicGraphicMC.DataSourceAlphaAlpha
getIndependentDataInfo(int) MultiharmonicGraphicMC.DataSourceAlphaChi
getIndependentDataInfo(int) MultiharmonicGraphicMC.DataSourceAlphaFE
getIndependentDataInfo(int) MultiharmonicGraphicMC.DataSourceFunctionRaw
getIndependentDataInfo(int) MultiharmonicGraphicMC.DataSourceAlphaAlpha
getIndependentDataInfo(int) MultiharmonicGraphicMC.DataSourceAlphaChi
getIndependentDataInfo(int) StatisticsMCGraphic.DataProcessorUndo
getIndependentDataInfo(int) DataSourceFE
getIndependentDataInfo(int) DataSourceFEHistogram
getIndependentDataInfo(int) DataSourceImposedFEFit
getIndependentDataInfo(int) DataSourceImposedFEHistogram
getIndependentDataInfo(int) DataSourcePMu
getIndependentDataInfo(int) DataSourcePN
getIndependentDataInfo(int) MeterAtomicDisplacement
getIndependentDataInfo(int) MeterTiltHistogram
getIndependentDataInfo(int) MeterBondLength
getIndependentTag() MeterCavityMapped
getIndependentTag() MeterRDFMapped
getIndependentTag() MeterWidomCavity
getIndependentTag() AccumulatorAverageBootstrap
getIndependentTag() AccumulatorAverageCollapsingLog
getIndependentTag() DataSourceFunction
getIndependentTag() DataSourceIndependent
Returns the tag associated with this DataSource.
getIndependentTag() DataSourceIndependentSimple
getIndependentTag() DataSourcePoints
getIndependentTag() DataSourceRmsVelocity
getIndependentTag() MeterDihedralAngle
getIndependentTag() MeterProfile
getIndependentTag() MeterProfileByAtoms
getIndependentTag() MeterProfileByVolume
getIndependentTag() MeterRDF
getIndependentTag() MeterRDFPC
getIndependentTag() MeterStructureFactor
getIndependentTag() MeterMappedRdf
getIndependentTag() MeterMeanForce
getIndependentTag() DataProcessorXY
getIndependentTag() MeterChainLength
getIndependentTag() AccumulatorAutocorrelationPTensor
getIndependentTag() AccumulatorAutocorrelationShearStress
getIndependentTag() AccumulatorPTensor
getIndependentTag() DataSourceAlpha2
getIndependentTag() DataSourceBlockAvgCor
getIndependentTag() DataSourceCorrelation
getIndependentTag() DataSourceF
getIndependentTag() DataSourceFOld
getIndependentTag() DataSourceFs
getIndependentTag() DataSourceHisogram
getIndependentTag() DataSourceHistogramMSD
getIndependentTag() DataSourceMSD
getIndependentTag() DataSourceMSDcorP
getIndependentTag() DataSourcePercolation
getIndependentTag() DataSourcePercolation0
getIndependentTag() DataSourcePMSDHistory
getIndependentTag() DataSourceQ4
getIndependentTag() DataSourceStrings
getIndependentTag() DataSourceVAC
getIndependentTag() MeterCorrelation
getIndependentTag() MeterCorrelationSelf
getIndependentTag() MeterGs
getIndependentTag() StructureFactorComponentCorrelation
getIndependentTag() DataSourceTensorVirialHardProfile
getIndependentTag() DataProcessorDyDLnx
getIndependentTag() MultiharmonicGraphicMC.DataSourceAlphaChi
getIndependentTag() MultiharmonicGraphicMC.DataSourceAlphaAlpha
getIndependentTag() MultiharmonicGraphicMC.DataSourceAlphaChi
getIndependentTag() MultiharmonicGraphicMC.DataSourceAlphaFE
getIndependentTag() MultiharmonicGraphicMC.DataSourceFunctionRaw
getIndependentTag() MultiharmonicGraphicMC.DataSourceAlphaAlpha
getIndependentTag() MultiharmonicGraphicMC.DataSourceAlphaChi
getIndependentTag() StatisticsMCGraphic.DataProcessorUndo
getIndependentTag() DataSourceFE
getIndependentTag() DataSourceFEHistogram
getIndependentTag() DataSourceImposedFEFit
getIndependentTag() DataSourceImposedFEHistogram
getIndependentTag() DataSourcePMu
getIndependentTag() DataSourcePN
getIndependentTag() MeterAtomicDisplacement
getIndependentTag() MeterTiltHistogram
getIndependentTag() MeterBondLength
getIndex() Atom
getIndex() AtomType
getIndex() IAtom
getIndex() Box
getIndex() BoxAtomIndexEvent
getIndex() BoxIndexEvent
getIndex() BoxMoleculeIndexEvent
getIndex() DataDistributer.Indexer
getIndex() IMolecule
Returns this IMolecule's index, which is its place in the list of
molecules of its ISpecies in its Box.
getIndex() Molecule
getIndex() ISpecies
Returns the index for this ISpecies, within the context of an Simulation.
getIndex() SpeciesGeneral
getIndex() SpeciesGeneralMutable
getIndex(double) DataSourceUniform
Returns the index of the x value closest to the argument.
getIndex(IAtom) AtomToAtomSetFixed
getIndex(IAtom) AtomToIndex
Returns an integer that this instance associates with the given atom.
getIndex(IAtom) AtomToIndexChild
getIndex(IMolecule) MoleculeToIndex
Returns an integer that this instance associates with the given atom.
getIndex(IMolecule) MoleculeToMoleculeListSpecies
getIndex(IMolecule) MoleculeToMoleculeSetFixed
getIndexed() SVGConverter
getIndexIterator() Boundary
getIndexIterator() BoundaryDeformablePeriodic
getIndexIterator() BoundaryRectangularNonperiodic
getIndexIterator() BoundaryRectangularPeriodic
getIndexIterator() BoundaryRectangularPore
getIndexIterator() BoundaryRectangularSlit
getIndexIterator() BoundaryTruncatedOctahedron
getIndexSelectedSpecies() ExceptionDoNotRemoveSpecies
getInflateDimensions() MeterPressureByVolumeChange
Accessor method for setInflateDimension.
getInfo() Quaternion
getInnerIterator() ApiInnerVariable
Accessor method for the inner-loop atom iterator.
getInnerIterator() ApiIntergroup
Accessor method for the inner-loop atom iterator.
getInnerIterator() CartesianIterator
getInnerIterator() MpiInnerFixed
Accessor method for the inner-loop atom iterator.
getInnerIterator() MpiInnerVariable
Accessor method for the inner-loop atom iterator.
getInnerList() ApiInterArrayList
Returns the inner list used to generate the pairs.
getInnerList() MpiInterArrayList
Returns the inner list used to generate the pairs.
getInnerPermutator() CartesianPermutator
getInnerRadius() AtomTypeSpheroPolyhedron
getInnerRadius() P1Constraint
getInnerSpecies() SpeciesGeneralMutable
getInputFileName() ReadParameters
Returns the fileName parameters are read from.
getInputFileName() WriteParameters
Returns the fileName parameters are read from.
getInstance() Space1D
getInstance() Space2D
getInstance() Space3D
getInstance() HashMapPotentialNonBonded
getInstance() SimpleElementForSimilarSpecies
getInstance() ModelTemperatureAndSteps
getInstance(int) Space
getInstances() SimulationsIndexResource
getIntegrator() ActionIntegrate
getIntegrator() ActivityIntegrate
getIntegrator() Controller
getIntegrator() IntegratorAction
getIntegrator() IntegratorActionAdapter
getIntegrator() MeterPressureCollisionCount
getIntegrator() DataSourceTensorVirialHard
getIntegrator() MeterKineticEnergyFromIntegrator
getIntegrator() MeterPotentialEnergyFromIntegrator
getIntegrator() MeterPressure
Returns the integrator associated with this instance.
getIntegrator() MeterPressureByVolumeChange
Returns the integrator associated with this instance.
getIntegrator() MeterPressureHard
getIntegrator() MeterPressureHardTensor
getIntegrator() MeterPressureMolecular
Returns the integrator associated with this instance.
getIntegrator() MeterPressureTensorFromIntegrator
getIntegrator() MeterWidomInsertion
Returns the integrator associated with this class.
getIntegrator() IntegratorEvent
getIntegrator() MeterWidomInsertionP
Returns the integrator associated with this class.
getIntegrator() DataSourceWallPressureCatalysis
getIntegrator() Droplet
getIntegrator() SimGlass
getIntegrator() DataSourceWallPressureMu
getIntegrator() MeterPressureSuperBox
Returns the integrator associated with this instance.
getIntegrator() HSMD3D
getIntegrator() Simulation
getIntegrator() SimulationVirial
getIntegrator() SimulationVirialOverlap2
getIntegratorMC() IntegratorMD
getIntegratorOverlap() SimOverlapModule
getIntegrators() IntegratorManagerMC
getInteractingList() AtomPotentialList
Returns booleans indicating whether the Atom interacts with each potential or not.
getInteractingList() MoleculePotentialList
Returns booleans indicating whether the Atom interacts with each
potential or not.
getInteractionRange() CriterionPositionWall
Returns the interaction range of the wall potential.
getInteractionRange() CriterionSimple
getInteractionRange() CriterionSimpleMolecular
getInteractionRangeDimension() CriterionPositionWall
getInteractionRangeDimension() CriterionSimple
getInteractionRangeDimension() CriterionSimpleMolecular
getInteriorColor() ColorSchemeDropletSurface
getIntermolecularPotential() ParmedStructure
Gets the intermolecular
PotentialGroup for the atom types found in this Structure.
getIntersection(float, Point4f, Point3f[], List<Point3f[]>, float[], BitSet, MeshSurface, boolean, boolean, int, boolean) MeshSurface
getIntersection(Point3f, Vector3f, Point4f, Point3f, Vector3f, Vector3f) Measure
getIntersectionPP(Point4f, Point4f) Measure
getInterval() DataPumpListener
getInterval() DataPumpListenerPow
getInterval() DataPumpListenerPowStrict
getInterval() IntegratorListenerAction
getInterval() DataSourceHisogram
getIntialdisplaylist() ModelSpeciesSelection
getIntialpotentialdisplaylist() ModelSpeciesSelection
getIntraMolecularCriterion() CriterionInterMolecular
Returns the intramolecular criterion, or null if none is in use.
getIntraPotentials(ISpecies) PotentialMasterNbrMolecular
getIntraPotentials(ISpecies) PotentialMasterNbr
getInverseNormix(short) Normix
getIsFluctuationFromAvg() HSNPT.ColorSchemeDisplacement
getIsNewPair(int[]) FindPairMoleculeIndex
getIsNewPair(int[]) FindPairMoleculeIndexBetaN2
getIsothermalButtonsVisibility() DeviceThermoSlider
getIsothermalButtonsVisibility() DeviceThermoSliderGEMC
getIsotopeNumber(short) Elements
getIsRunningActivityStep() Controller.ControllerHandle
getIsString() ColorSchemeDeviation
getIterator() DataSourceRmsVelocity
getIterator() MeterKineticEnergy
Returns the iterator that defines the atoms summed for their kinetic energy.
getIterator() MeterLocalDensity
getIterator() MeterLocalMoleFraction
getIterator() MeterRadiusGyration
Accessor method for the iterator that generates the atom pairs used to
tabulate the ROG
getIterator() LatticeSum
getIterator() LatticeSumCrystal
getIterator() LatticeSumCrystalMolecular
getIy() AkimaSplineSmootherDy
calculate the cumulative integral of y, interpolating dy/dx with a
spline curve
getJacobian() CalcJacobian
getJavaInitializationString() DimensionedDoubleEditor
Returns value in simulation units.
getJSpinnerCountOfSpecies(int) ViewSpeciesSelection
getK() LatticeSum
getK() LatticeSumCrystal
getK() LatticeSumCrystalMolecular
getKappa() P2Yukawa
Accessor methods for size and energy parameters.
getKinetic() MeterEnergy
getKineticEnergy() MeterEnergy
getKineticEnergy() IntegratorMD
getLabel() ActionToggle
Returns the true or false label, depending on the current state of the
toggle.
getLabel() DataInfo
getLabel() DataInfoFactory
Returns the label
getLabel() IDataInfo
getLabel() IDataInfoFactory
Returns the label
getLabel() ConfigFromFileLAMMPS.ModifierConfiguration
getLabel() DeviceBox
getLabel() DeviceButton
getLabel() DeviceSelector
getLabel() DeviceSlider
getLabel() DeviceSpinner
getLabel() DeviceThermoSelector
getLabel() Display
Accessor method of the label describing the display.
getLabel() DisplayTextBox
getLabel() DisplayTextBoxesCAE
getLabel() Modifier
Returns a descriptive label of the property being modified.
getLabel() ModifierGeneral
getLabel() ModifierNMolecule
getLabel() ModifierPMu
getLabel() ColloidGraphic.WallRangeModifier
getLabel() LatticeEditor.NModifier
getLabel() IntegratorDCVGCMD.Mu1Modulator
getLabel() IntegratorDCVGCMD.Mu2Modulator
getLabel() DropletGraphic.ModifierBoxSize
getLabel() InterfacialSWGraphic.ModifierBoxSize
getLabel() MuGraphic.ModifierAtomDiameter
getLabel() MuGraphic.ModifierEpsilon
getLabel() MuGraphic.ModifierLambda
getLabel() NucleationGraphic.ModifierDensity
getLabel() ActionPistonUpdate
getLabel() ModifierPistonPressure
getLabel() PistonCylinderGraphic.ModifierAtomDiameter
getLabel() PistonCylinderGraphic.ModifierPistonDensity
getLabel() ReverseOsmosisGraphic.ModifierAtomDiameter
getLabel() ReverseOsmosisGraphic.ModifierEpsilon
getLabel() ReverseOsmosisWaterGraphic.ModifierAtomDiameter
getLabel() ReverseOsmosisWaterGraphic.ModifierEpsilon
getLabel() ReverseOsmosisWaterGraphic.ModifierSoluteCharge
getLabel() SamGraphic.ModifierWallPosition
getLabel() SwmdGraphic.ModifierAtomDiameter
getLabel() ModifierCells3D
getLabel() ModifierXCells2D
getLabel() ModifierYCells2D
getLabel() ModifierTPI
getLabel() DeviceButtonSingle
getLabelPosition() DeviceBox
getLabelPosition() DisplayTextBox
getLabelType() DeviceBox
getLabelType() DisplayTextBox
getLambda() P2SquareWellBonding
Accessor method for well-diameter multiplier.
getLambda() P2SquareWellBondingCO
Accessor method for well-diameter multiplier.
getLambda() P2SquareWellSurface
Accessor method for well-diameter multiplier.
getLambda() P2SquareWellOneSide
Accessor method for well-diameter multiplier.
getLambda() SimEinStep2.MeterPotentialEnergyComposite
getLambda() SimEinStep2HCP.MeterPotentialEnergyComposite
getLambda() P2DoubleWell
Accessor method for well-diameter multiplier.
getLambda() P2PenetrableSquareWell
Accessor method for well-diameter multiplier.
getLambda() P2SquareWell
Accessor method for well-diameter multiplier.
getLambda() P2SquareWellRobust
Accessor method for well-diameter multiplier.
getLambda() P2TriangleWell
getLambdaDimension() P2SquareWellBonding
getLambdaDimension() P2SquareWellBondingCO
getLambdaDimension() P2SquareWellSurface
getLambdaDimension() P2SquareWellOneSide
getLambdaDimension() P2DoubleWell
getLambdaDimension() P2PenetrableSquareWell
getLambdaDimension() P2SquareWell
getLambdaDimension() P2SquareWellRobust
getLambdaDimension() P2TriangleWell
getLambdas() CalcVibrationalModes
Performs an eigenvalue decomposition of the NxN matrix, fC.
getLanguage() SVGConverter
getLastA() WriteS
getLastBestParam() FitTanh
getLastBestParam() FitTanh
getLastColliderAgent() IntegratorHard
getLastCollisionType() P2HardSphereCavity
getLastConfigIndex() ConfigurationStorage
getLastCPairID() ClusterWheatleyPartitionScreening
getLastDMu() DataSourceMuRoot
getLastDPressure() DataSourceMuRoot
getLastDPressure() DataSourceMuRootPMatch
getLastDU() DataSourceMuRoot
getLastGamma() Gamma
Return the normalized complementary incomplete gamma function from the
last calculation.
getLastGammaStar() Gamma
Return the normalized incomplete gamma function from the last
calculation.
getLastLine() ConsoleUI
getLastLnTot() DataSourceMuRoot
getLastLnTot() DataSourceMuRootPMatch
getLastPolarizationEnergy() PNCO2GCPM
getLastPolarizationEnergy() PNGCPM
getLastPolarizationEnergy() PNWaterGCPM
getLastPolarizationEnergy() PNWaterGCPMReactionField
getLastPolarizationEnergy() PotentialPolarizable
Returns the polarization energy from the last call to energy(AtomSet).
getLastPressure() DataSourceMuRoot
getLastPressure() DataSourceMuRoot1
getLastPressure() DataSourceMuRootPMatch
getLastTotalEnergy() MCMoveHarmonic
Returns the harmonic energy of the configuration based on the last
harmonic move made by this MC Move.
getLastVacancyConcentration() DataSourceMuRoot
getLastVacancyConcentration() DataSourceMuRoot1
getLastVacancyConcentration() DataSourceMuRootPMatch
getLastValue() ClusterWheatleyPartitionScreening
getLastValues() ClusterDiagramTree
getLattice() BoxCellManager
Returns the lattice that defines the cell arrangement.
getLattice() LatticeSum
getLattice() LatticeSumCrystal
getLattice() RectangularLatticeNbrIterator
Returns the lattice from which the iterates are given.
getLattice() LatticeSumCrystalMolecular
getLattice() NeighborCellManagerMolecular
getLattice() NeighborCellManager
getLattice() NeighborSiteManager
Returns the lattice used to define the neighbor structure.
getLatticeAMemento() GrainBoundaryConfiguration
Returns a lattice with positions the same as those used in the
most recent use of initializeCoordinates.
getLatticeArrayIndex() Cell
getLatticeArrayIndex() CellMolecular
getLatticeArrayIndex() AtomSite
getLatticeBMemento() GrainBoundaryConfiguration
getLatticeConstant() CubicLattice
Accesses the size of the unit cell, the length of each edge of a single cell.
getLatticeConstant() LatticeCubicBcc
getLatticeConstant() LatticeCubicDiamond
getLatticeConstant() LatticeCubicFcc
getLatticeConstant() LatticeCubicSimple
getLatticeConstants() ConfigurationLattice.MyLattice
getLatticeConstants() BravaisLattice
getLatticeConstants() SpaceLattice
getLatticeCorrec() MCMoveVolumeN2
getLatticeEnergy() MeterTargetRPMolecule
getLatticeEnergy() MeterTargetTPMolecule
getLatticeEnergy() MinimizeBetaNitrogenLatticeParameter
getLatticeEnergy() MinimizeBetaNitrogenLatticeParameterFromFile
getLatticeEnergy() MinimizeBetaNitrogenLatticeParameterLSFromFile
getLatticeEnergy() MinimizeBetaNitrogenTranslationDOF
getLatticeEnergy() MinimizeGammaNitrogenLatticeParameter
getLatticeEnergy() HarmonicCrystal
getLatticeEnergy() HarmonicCrystalSsFccNxy
getLatticeEnergy() MCMoveAtomCoupledBennet
getLatticeEnergy() MCMoveAtomCoupledUmbrella
getLatticeEnergy() MeterBoltzmannHTTP
getLatticeEnergy() MeterOverlapSwitch
getLatticeEnergy() MeterTargetTP
getLatticeEnergy() SimOverlapLJModule.APIPotentialTarget
getLatticeMemento() ConfigurationLattice
Returns a lattice with positions the same as those used in the
most recent use of initializeCoordinates.
getLatticePosition(IAtom) CoordinateDefinition
getLatticePosition(IMolecule) CoordinateDefinitionMolecule
getLatticePosition(IMolecule) CoordinateDefinitionMoleculeVolumeFluctuation
getLayers() ImageShell
Gets the number of image shell layers
getLeafAtomCount() ISpecies
getLeafAtomCount() SpeciesGeneral
getLeafAtomCount() SpeciesGeneralMutable
getLeafIndex() Atom
getLeafIndex() IAtom
Returns the global index (within the Box) of this Atom.
getLeafList() Box
getLeafType() ISpecies
getLeafType() SpeciesGeneral
getLeafType() SpeciesGeneralMutable
getLength() IData
Returns the number of values held by the data instance.
getLength() IDataInfo
Returns the number of numerical values held by the IData object.
getLength() DataDouble.DataInfoDouble
getLength() DataDouble
Returns 1, indicating that this data object holds one value.
getLength() DataDoubleArray.DataInfoDoubleArray
Returns the total number of elements in the constructed DataDoubleArray.
getLength() DataDoubleArray
Returns the total length of the wrapped array.
getLength() DataDoubleBDArray.DataInfoDoubleBDArray
Returns the total number of elements in the constructed DataDoubleArray.
getLength() DataDoubleBDArray
Returns the total length of the wrapped array.
getLength() DataGroup.DataInfoGroup
getLength() DataGroup
getLength() DataTable
Returns the number of values held by the data instance.
getLength() DataTensor.DataInfoTensor
getLength() DataTensor
Returns the number of elements in the wrapped tensor.
getLength() DataVector.DataInfoVector
getLength() DataVector
Returns the number of elements in the wrapped vector.
getLength() LineSegment
getLengthAlkaneChain(int) ModelSimulationEnvironment
getLevel(int) Logger
Returns the text corresponding to a level.
getLightSource() GData
getLiquidColor() ColorSchemeLiquidVapor
getLiquidFilter() P2Cohesion
getList() ApiIntraArrayList
Returns the list used to generate the pairs.
getList() AtomIteratorArrayListSimple
getList() MpiIntraArrayList
Returns the list used to generate the pairs.
getList() ScriptVariable
getListeners() IntegratorEventManager
getListeners() IntegratorListenerGroupSeries
getLnBias(int) MCMoveInsertDeleteBiased
getLnBiasDiff() MCMoveInsertDeleteBiased
getLoad() PotentialCalculationForceStress
getLocale() Messages
Implements Localizable.getLocale().
getLocalVisitor() AbstractTraversal
getLog2StepStart() DataSourcePercolation
getLogAverage(int) DataOverlap.DataSourceOverlapAvgCollapsing
getLogAverage(int) DataOverlap.DataSourceOverlapLogAvg
getLogAverageAndError(boolean, double) DataOverlap
Returns the natural log of the average value from the reference or target
system (as specified) and its uncertainty for the given value of alpha
getLogAverageAndError(double) DataOverlap
Returns the natural log of the average ratio and its uncertainty for the
given value of alpha
getLogError(int) DataOverlap.DataSourceOverlapAvgCollapsing
getLogError(int) DataOverlap.DataSourceOverlapLogAvg
getLogError(int) DataOverlap
Returns the uncertainty in the log of the average corresponding to the
iAlpha value of alpha.
getLogLevel() Logger
getLxy() ConfigurationLammps
getMakeLrc() P2SoftSphericalTruncated
getMass() AtomType
getMass() Element
getMass() ElementChemical
getMass() ElementSimple
getMass() IElement
getMass() P1HardMovingBoundary
getMass() ISpecies
getMass() SpeciesGeneral
getMass() SpeciesGeneralMutable
getMass() MaxwellBoltzmann.Distribution
getMass() LJ
getMass(IMolecule) P2SemiclassicalMolecular.MoleculeInfo
Returns the mass of the molecule.
getMass(IMolecule) P2SemiclassicalMolecular.MoleculeInfoBrute
getMassDimension() AtomType
getMassDimension() Element
getMassDimension() P1HardMovingBoundary
getMassDimension() MaxwellBoltzmann.Distribution
getMathContext() MeterVirialBDBin
getMathContext() MeterVirialBDBinMultiThreaded
getMathContext() MeterVirialEBinMultiThreaded
getMatrix() Quaternion
getMatrixFromFile(String, int) HarmonicAlphaNitrogenModelDecomposed
getMatrixFromFile(String, int) HarmonicBetaNitrogenModelDecomposed
getMaxBlocks() AccumulatorAverageCollapsing
getMaxBonds() AssociationHelperBranched
getMaxBonds() AssociationHelperMolecule
getMaxClusterDistance() DataClusterer
getMaxDistance() MCMoveInsertDeleteLatticeVacancy
getMaxDistance() MCMoveInsertDeleteVacancy
getMaxDr() DataSourceQ4
getMaxElement() IndexIteratorTriangular
getMaxElement() LatticeSum
getMaxElementMin() IndexIteratorTriangular
getMaxHeight() SVGConverter
getMaximum() DeviceSlider
getMaximum() DeviceSpinner
getMaximumFractionDigits() ScientificFormat
getMaximumIntegerDigits() ScientificFormat
getMaximumSeparation() P2Fene
Accessor method for harmonic energy parameter
getMaximumSeparationDimension() P2Fene
getMaxIterations() IntegratorVelocityVerletShake
getMaxIterations() DataClusterer
getMaxLatticeShell() LatticeSumCrystal
getMaxLatticeShell() LatticeSumCrystalMolecular
getMaxLatticeShell() HarmonicCrystal
getMaxLatticeShell() HarmonicCrystalSsFccNxy
getMaxLatticeShell() NormalModesPotential
getMaxNbrsVapor() AtomTestLiquidAtomic
getMaxPotentialRange() PotentialMasterListMolecular
Returns the maximum range of any potential held by this potential master
getMaxPotentialRange() PotentialMasterList
Returns the maximum range of any potential held by this potential master
getMaxSleep() DeviceDelaySlider
getMaxSteps() ActionIntegrate
Accessor method for the number of doStep calls to be
performed by this integrator after it is started.
getMaxSteps() ActivityIntegrate
getMaxWidth() SVGConverter
getMaxWidth() ScientificFormat
getMaxX() G3DSys
getMaxY() G3DSys
getMaxZ() G3DSys
getMCMove() MCMoveEvent
getMCMove() MCMoveTrialCompletedEvent
getMCMove() MCMoveTrialFailedEvent
getMCMove() MCMoveTrialInitiatedEvent
getMCMoveClusterTorsionMulti() CollectionPotentialAtomicLike
getMCMoveMoleculeExchange() IntegratorGEMC
Returns the object that performs the molecule-exchange move in the GE
simulation.
getMCMoveMoleculeExchange() IntegratorRGEMC
Returns the object that performs the molecule-exchange move in the GE
simulation.
getMCMoves() MCMoveManager
Constructs and returns array of all moves added to the integrator.
getMCMoveVolumeExchange() IntegratorGEMC
Returns the object that performs the volume-exchange move in the GE
simulation.
getMediaType() SVGConverter
getMembraneDim() ConfigurationMembrane
getMembraneDim() ConfigurationMembraneWater
The dimension of the membrane (0=x, 1=y, 2=z).
getMembraneThickness() ConfigurationMembraneWater
Returns the thickness (angstroms) of each layer of the membrane
(see getNumMembraneLayers)
getMembraneThicknessPerLayer() ConfigurationMembrane
getMembraneWidth() ConfigurationMembrane
getMembraneWidth() ConfigurationMembraneWater
Returns the width of the membrane.
getMessage() SVGConverterException
getMetadata() Edge
getMetadata() EdgeImpl
getMetadata() NodeImpl
getMetadata() Node
getMeterPotentialEnergy() IntegratorBox
getMeterTemperature() IntegratorMD
getMillerIndex(int) LatticePlane
Returns the current value of the i-th Miller index.
getMinBondedAtomDistance() AssociationHelperBranched
getMinBondedAtomDistance() AssociationHelperDouble
getMinBondedMoleculeDistance() AssociationHelperMolecule
getMinConfigIndex() MeterGs
getMinDistance() AtomTestDeviation
getMinimum() DeviceSlider
getMinimum() DeviceSpinner
getMinimumFractionDigits() ScientificFormat
getMinimumIntegerDigits() ScientificFormat
getMinNumAtoms() MCMoveOverlapListener
getMinPrevSample() MeterCorrelation
getMinRadicalSites() P2SquareWellSurface
getMinX() G3DSys
getMinY() G3DSys
getMinZ() G3DSys
getMobileSpecies() GrainBoundaryTiltConfiguration
getModelSelectedSpecies() AppModelMixtureBuilder
getModelSpeciesSelection() AppModelMixtureBuilder
getModeNum() MCMoveHarmonic
getModeSigns() CalcVibrationalModes
Returns a one dimensional array of length 3 with the total number of
positive, negative, and imaginary modes.
getModifier() ActionToggle
Returns the boolean modifier used by this action.
getModifier() DeviceBox
Accessor method for the modifier that receives the edit.
getModifier() DeviceCheckBox
Specifies the boolean modifier that is set between true and false by the button.
getModifier() DeviceSlider
getModifier() DeviceSpinner
getModifier() DeviceThermoSlider
getModifier() DeviceToggleRadioButtons
Specifies the boolean modifier that is set between true and false by the button.
getModifier() DeviceThermoSliderGEMC
getModifier() DeviceEigenvaluesSlider
getModifier() DeviceWaveVectorSlider
getMolecularModelDisplayName() IMolecularModel_SpeciesFactory
getMolecularModelDisplayName() MolecularModel2CLJQ_SpeciesCO2
getMolecularModelDisplayName() MolecularModel2CLJQ_SpeciesEthane
getMolecularModelDisplayName() MolecularModel2CLJQ_SpeciesLJ
getMolecularModelDisplayName() MolecularModelEMP2_SpeciesCO2
getMolecularModelDisplayName() MolecularModelLJ_SpeciesLJ
getMolecularModelDisplayName() MolecularModelLJQ_SpeciesLJ
getMolecularModelDisplayName() MolecularModelSKS_SpeciesAlkane
getMolecularModelDisplayName() MolecularModelSPCE_SpeciesH2O
getMolecularModelDisplayName() MolecularModelTRAPPE_SpeciesAlkane
getMolecularModelDisplayName() MolecularModelTrappe_SpeciesCO2
getMolecule() MoleculeSourceRandomDimer
getMolecule() MoleculeSourceRandomMonomer
getMolecule() BoxMoleculeEvent
getMolecule() MoleculeIteratorSinglet
getMolecule() MoleculeSource
Returns an atom.
getMolecule() MoleculeSourceRandomMolecule
returns a random molecule from the box
getMoleculeDataInfo() DataSourceMolecular
getMoleculeDataInfo() MeterMoleculeTemperature
getMoleculeDataInfo() MeterNMolecules
getMoleculeDataInfo() MeterOrientation
getMoleculeDisplayName() IMolecularModel_SpeciesFactory
getMoleculeDisplayName() MolecularModel2CLJQ_SpeciesCO2
getMoleculeDisplayName() MolecularModel2CLJQ_SpeciesEthane
getMoleculeDisplayName() MolecularModel2CLJQ_SpeciesLJ
getMoleculeDisplayName() MolecularModelEMP2_SpeciesCO2
getMoleculeDisplayName() MolecularModelLJ_SpeciesLJ
getMoleculeDisplayName() MolecularModelLJQ_SpeciesLJ
getMoleculeDisplayName() MolecularModelSKS_SpeciesAlkane
getMoleculeDisplayName() MolecularModelSPCE_SpeciesH2O
getMoleculeDisplayName() MolecularModelTRAPPE_SpeciesAlkane
getMoleculeDisplayName() MolecularModelTrappe_SpeciesCO2
getMoleculeList() Box
getMoleculeList(IMolecule) MoleculeToMoleculeList
Returns the ArrayList that this instance associates with the given atom.
getMoleculeList(IMolecule) MoleculeToMoleculeListSpecies
getMoleculeList(IMolecule) MoleculeToMoleculeSetFixed
getMoleculeList(ISpecies) Box
Returns the list of molecules of the given species.
getMoleculeListDisplayLSM() ViewSpeciesSelection
getMoleculeListDisplayLSM() ViewSpeciesSelection
getMoleculeListDisplayString() ModelSpeciesSelection
getMoleculeListDisplayTable() ViewSpeciesSelection
getMoleculeListDisplayTable() ViewSpeciesSelection
getMoleculeListDisplayTM() ViewSpeciesSelection
getMoleculeListDisplayTM() ViewSpeciesSelection
getMoleculeListDisplayTMListener() ViewSpeciesSelection
getMoleculeListDisplayTMListener() ViewSpeciesSelection
getMoleculeOffset() ConfigurationCatalysis
getMoleculeOffset() ConfigurationSAM
getMoleculeOrientation(IMolecule) CoordinateDefinitionNitrogen
getMoleculeOrientation(IMolecule) CoordinateDefinitionNitrogenSuperBox
getMoleculeOrientation(IMolecule) CoordinateDefinitionHSDimer
return the initial Orientation of the molecule
getMolecules() ParmedStructure
Gets the list of all molecules in the Structure, initialized with their coordinates in space.
getMolecules(Box) Debug
Returns an AtomPair containing the two atoms with global indices
ATOM1_INDEX and ATOM2_INDEX within the given box.
getMoleculeSource() MCMoveMoleculeExchange
Returns the AtomSource this class uses to pick molecules to delete.
getMoment() VLESim
getMoment(int) MolecularModel2CLJQ_SpeciesCO2
getMoment(int) MolecularModel2CLJQ_SpeciesEthane
getMoment(int) MolecularModel2CLJQ_SpeciesLJ
getMomentAndAxes(IAtomOriented) P2SemiclassicalAtomic.AtomInfo
Returns the moment of inertia as a vector containing Ix, Iy, Iz and also the principle axes.
getMomentAndAxes(IMolecule) P2SemiclassicalMolecular.MoleculeInfo
Returns the moment of inertia as a vector containing Ix, Iy, Iz
and also the principle axes.
getMomentAndAxes(IMolecule) P2SemiclassicalMolecular.MoleculeInfoBrute
getMomentOfInertia() AtomTypeOriented
Returns the principal components of the moment of inertia of the
atom within the body-fixed frame.
getMomentOfInertia() ISpecies
getMomentOfInertia() SpeciesGeneral
getMomentOfInertia() SpeciesGeneralMutable
getMomentSquare(int) MolecularModelLJQ_SpeciesLJ
getMonomerColor() ColorSchemeSmer
Returns the color used for all dimers.
getMove() DataSourceAcceptanceRatio
getMoveEventManager() IntegratorManagerMC
getMoveEventManager() IntegratorMC
getMoveManager() IntegratorManagerMC
getMoveManager() IntegratorMC
getMSMCGraphs(boolean) MayerIonicDiagram1qbond
getMSMCGraphs(boolean) MayerIonicDiagram2qbonds
getMSMCGraphs(boolean) MayerIonicDiagram4qbonds
getMSMCGraphs(boolean) WertheimDiagrams2SiteRho
getMSMCGraphs(boolean) WertheimDiagrams3SiteRho
getMSMCGraphs(boolean, boolean) VirialDiagrams
getMSMCGraphs(boolean, int) VirialDiagramsPT
getMSMCGraphs(boolean, int, int[]) VirialDiagramsMix2
getMSMCGraphsEX(boolean) ExternalVirialDiagrams
getMu() MCMoveInsertDelete
Accessor method for the chemical potential of th insertion/deletion species.
getMuDimension() MCMoveInsertDelete
Indicates that chemical potential has dimensions of energy.
getMultiBDcount() ClusterWheatleyMultibodyDerivatives
getMultiBDfrac() ClusterWheatleyMultibodyDerivatives
getMultiBonds() ClusterBondsNonAdditive
Returns the list of multiBonds to multiply.
getMulticount() ClusterWheatleyMultibodyDerivatives
getn() ClusterWheatleyPartitionScreening.FrequencyCounter
getN() NormalModeAnalysisDisplay3D
getN() P4TorsionDreiding
getN1() AbstractSearchState
getN1() NodePair
getN1(byte) AbstractSearchState
getN2() AbstractSearchState
getN2() NodePair
getN2(byte) AbstractSearchState
getNA() SelfAssemblySim
getName() AtomType
getName() DataSet.DataSetSink
getName() MeterDihedralAngle
getName() MeterMomentumCOM
getName() MeterPositionCOM
getName() MeterRDF
getName() MeterRDFPC
getName() MeterTensorVelocity
getName() PropertyImpl
getName() VariableImpl
getName() Parser.Property
getName() Parser.Variable
getName() SVGConverterDocumentSource
getName() SVGConverterFileSource
getName() SVGConverterSource
Returns the name of the source.
getName() SVGConverterURLSource
getName() EtomicaTheme
getName() MeterMappedRdf
getName() ArrayProperty
getName() AtomListProperty
getName() InstanceProperty
getName() MoleculeListProperty
getName() Property
getName() VectorProperty
getName() MeterDimerFraction
getName() MeterHarmonicSingleEnergy
getName() MeterNormalMode
getName() EtomicaServer
getName() MeterBondLength
getName() EnumStereoMode
getName(int) DataSet
getNaturalIsotope(int) Elements
getNB() SelfAssemblySim
getNB1() SelfAssemblySim
getNB2() SelfAssemblySim
getNBennetPoints() AccumulatorOverlapAverageUa2
getNBennetPoints() AccumulatorVirialOverlapSingleAverage
getNBins() AccumulatorHistogram
getNBins() Histogram
Returns the number of bins in the histogram.
getNBins() HistogramDiscrete
getNBins() HistogramNotSoSimple
getNBins() HistogramReweightedData
getNBins() HistogramSimple
getNbrAtoms(Box) P1ConstraintNbr
getNbrCellIterator() Api1ACell
getNbrCellIterator() AtomsetIteratorCellular
getNbrCellIterator() MoleculesetIteratorCellular
getNbrCellIterator() Mpi1ACell
getNbrCellIterator() MpiAACell
getNbrCellManager(Box) PotentialMasterCell
getNbrCellManager(Box) PotentialMasterListMolecular
getNbrCellManager(Box) PotentialMasterList
getNbrCellManager(Box) PotentialMasterHybrid
getNbrDistance() MCMoveAtomSwap
getNbrMax() AtomNbrClusterer
getNbrMax() ColorSchemeCluster
getNbrMax() DataSourcePercolation
getNbrMax() DataSourcePercolation0
getNbrMax() ColorSchemeCluster
getNCellModifier() DeviceCellNum3DSlider
getNCellNum() DeviceCellNum3DSlider
getNCellNum() NormalModes3D
getNCells() NormalModeAnalysisDisplay2D
getNCells() NormalModeAnalysisDisplay3D
getNCellsX() ConfigurationCatalysis
getNCellsX() ConfigurationSAM
getNCellsZ() ConfigurationCatalysis
getNCellsZ() ConfigurationSAM
getNCrossLinkersAcid() ChainEquilibriumSim
getNData() DataGroup
Returns the number of data objects encapsulated by this DataGroup.
getNDataInfo() DataGroup.DataInfoGroup
getNDiAcid() ChainEquilibriumSim
getNDiagrams() ClusterDiagramTree
getNDiol() ChainEquilibriumSim
getNegativePrefix() ScientificFormat
getNegativeSuffix() ScientificFormat
getNeighborCellManager() NeighborListManager
getNeighborCriteria() PotentialMasterListMolecular
getNeighborDistance() CellLattice.NeighborIterator
getNeighborManager(Box) PotentialMasterListMolecular
getNeighborManager(Box) PotentialMasterList
getNeighborManager(Box) PotentialMasterHybrid
getNeighborRange() CriterionPositionWall
getNeighborRange() CriterionSimple
getNeighborRange() CriterionSimpleMolecular
getNeighborRangeDimension() CriterionPositionWall
getNeighborRangeDimension() CriterionSimple
getNeighborRangeDimension() CriterionSimpleMolecular
getNeighborVertexesArrays() Geodesic
getNewId() SimulationModel
getNewPartners() PotentialReactive.BondChangeData
getNewValue() PropertyUpdate
getNextAtom() AtomNbrClusterer
getNGraft() ConfigurationColloid
getNInsert() MeterWidomCavity
Accessor to number of Widom insertions attempted with each call to
currentValue
getNInsert() MeterWidomInsertion
Accessor to number of Widom insertions attempted with each call to
currentValue
getNInsert() MeterWidomInsertionCorrection
Accessor to number of Widom insertions attempted with each call to
currentValue
getNInsert() MeterWidomInsertionP
Accessor to number of Widom insertions attempted with each call to
currentValue
getNMajor() DeviceSlider
getNMax() AccumulatorAutocorrelationPTensor
getNMax() AccumulatorAutocorrelationShearStress
getNMinor() DeviceSlider
getNMolecules(ISpecies) Box
getNMonoAcid() ChainEquilibriumSim
getNMonoOl() ChainEquilibriumSim
getNode(byte) Graph
getNode(byte) GraphImpl
getNoisyAdjustment() MCMoveStepTracker
getNominalFluctuation() HSNPT.ColorSchemeDisplacement
getNominalFrequency() MCMove
Returns a nominal, unnormalized frequency for performing this move,
relative to the other moves that have been added to the integrator.
getNonBondedInteractionModel() IMolecularModel_SpeciesFactory
getNonBondedInteractionModel() MolecularModel2CLJQ_SpeciesCO2
getNonBondedInteractionModel() MolecularModel2CLJQ_SpeciesEthane
getNonBondedInteractionModel() MolecularModel2CLJQ_SpeciesLJ
getNonBondedInteractionModel() MolecularModelEMP2_SpeciesCO2
getNonBondedInteractionModel() MolecularModelLJ_SpeciesLJ
getNonBondedInteractionModel() MolecularModelLJQ_SpeciesLJ
getNonBondedInteractionModel() MolecularModelSKS_SpeciesAlkane
getNonBondedInteractionModel() MolecularModelSPCE_SpeciesH2O
getNonBondedInteractionModel() MolecularModelTRAPPE_SpeciesAlkane
getNonBondedInteractionModel() MolecularModelTrappe_SpeciesCO2
getNoneCliqueCount() ClusterWheatleyExtendSW
getNoneCliques() ClusterWheatleyExtendSW
getNonPolarizationEnergy(IMoleculeList) PNCO2GCPM
This returns the pairwise-additive portion of the GCPM potential for a
pair of atoms (dispersion + fixed-charge electrostatics)
getNonPolarizationEnergy(IMoleculeList) PNGCPM
This returns the pairwise-additive portion of the GCPM potential for a
pair of atoms (dispersion + fixed-charge electrostatics)
getNonPolarizationEnergy(IMoleculeList) PNWaterGCPM
This returns the pairwise-additive portion of the GCPM potential for a
pair of atoms (dispersion + fixed-charge electrostatics)
getNonPolarizationEnergy(IMoleculeList) PNWaterGCPMReactionField
This returns the pairwise-additive portion of the GCPM potential for a
pair of atoms (dispersion + fixed-charge electrostatics)
getNoOfSpheres() ViewAlkaneLengthSelection
getNoOfSteps() ModelSimulationEnvironment
getNoOfSteps() ModelTemperatureAndSteps
getNoOfStepsField() ViewSimEnvironmentSelection
getNorm() Quaternion
Returns the norm of the Quaternion q defined as N = sqrt(q*q)
getNormal() Quaternion
getNormalDirected(Vector3f) Quaternion
getNormalFromCenter(Point3f, Point3f, Point3f, Point3f, boolean, Vector3f) Measure
getNormalModes() HarmonicCrystal
getNormalModes() HarmonicCrystalSsFccNxy
getNormalModes() MCMoveAtomCoupledBennet
getNormalModes() MCMoveAtomCoupledUmbrella
getNormalThroughPoints(Point3f, Point3f, Point3f, Vector3f, Vector3f, Vector3f) Measure
getNormalToLine(Point3f, Point3f, Vector3f) Measure
getNormixCount() Normix
getNormixV(Vector3f, BitSet) Normix
getnPoints() ModelSimulationEnvironment
getnReactCO() ReactionManagerCO
getNRows() DataTable.DataInfoTable
Returns the number of rows in the table
getNRows() DataTable.DataInfoTableFactory
Returns the number of rows.
getNRows() DataTable
Returns the number of rows in each and every column of the table.
getNSpheres() MolecularModelSKS_SpeciesAlkane
getNSpheres() MolecularModelTRAPPE_SpeciesAlkane
getNthSpeciesAdded() ModelSelectedSpecies
getNthSpeciesSelectedIndex() ModelSpeciesSelection
getNullPotential(AtomType) IntegratorHard
getNumAlpha() MeterMBAR
getNumAlpha() AlphaSource
Returns the number of possible alpha values.
getNumAlpha() MeterOverlap
getNumAlpha() DataProcessorVirialOverlap
getNumAlpha() SimulationVirialOverlap2
Returns the number of alpha values used for the production stage of the
simulation
getNumAtoms() ConfigurationFileXYZ
getNumBDChecks() ClusterWheatleySoftDerivatives
getNumBeads() MCMoveClusterRingPartialRegrow
getNumber() StrainColorScheme
getNumCheckVisits() ClusterWheatleySoftDerivatives
getNumClusters() DataClusterer
getNumCO() ConfigurationCatalysis
getNumCollapseBins() HistoryCollapsing
getNumConnections() ClusterDiagram
returns the number of active connections in the cluster.
getNumDataSinks() DataDistributer
getNumDataSinks() DataGroupSplitter
getNumDataSinks() DataSplitter
getNumDataSinks() DataOverlap.DataSourceOverlapAvgCollapsing
getNumDataSinks() DataOverlap.DataSourceOverlapAvgCollapsingSplit
getNumDelete() MCMoveOverlapListener
getNumDigitColumns() DisplayTable
getNumDr() CorrelationSelf2
getNumDt() CorrelationSelf2
getNumerator() Coefficient
getNumerator() CoefficientImpl
getNumFieldPoints() Mul.MulParameters
getNumInsert() MCMoveOverlapListener
getNumMembraneLayers() ConfigurationMembrane
getNumMembraneLayers() ConfigurationMembraneWater
Returns the number of membrane layers.
getNumNodes() ClusterCollapsedTreeNode
getNumNodes() ClusterTreeNode
getNumO2() ConfigurationCatalysis
getNumRawData() AccumulatorAverageBootstrap
getNumRawData() AccumulatorAverageCollapsingLog
getNumRootPoints() ClusterDiagram
getNumSubSteps() IntegratorOverlap
Retruns the number of total number of integrator steps the sub-integrators
perform for every step of the overlap integrator.
getNumSubSteps() IntegratorOverlap
Deprecated.
Retruns the number of total number of integrator steps the sub-integrators
perform for every step of the overlap integrator.
getNumSurfaceSites() P2SquareWellBonding
getNumSurfaceSites() P2SquareWellBondingCO
getNumTargets() DataVirialOverlap
getNumTrial() MCMoveClusterRingPartialRegrow
getNumTrial() MCMoveClusterRingRegrow
getNumTrial() MCMoveClusterRingRegrowExchange
getNumUpdates() NeighborListManager
Returns the number of times the neighbor lists have been updated.
getNumValues() ClusterAbstractMultivalue
getNumValues() ClusterCoupledFlippedMultivalue
getNumValues() ClusterSumIC
getNumValues() ClusterWheatleyMultibodyDerivatives
getNumValues() ClusterWheatleyMultibodyDerivativesBD
getNumValues() ClusterWheatleyPT
getNumValues() ClusterWheatleySoftDerivatives
getNumValues() ClusterWheatleySoftDerivativesBD
getNumXCells() Sam
getNumZCells() Sam
getNValues() DataSourceUniform
Accessor method for number of values.
getObject() ModifierGeneral
getObject(int) ArrayMoleculeDisplayList
getOctant(Point3f) Quadric
getOelement() SimpleElementForSimilarSpecies
getOffset() P1ImageHarmonic
getOffset() P1Sinusoidal
getOldPartners() PotentialReactive.BondChangeData
getOmegaSquared() NormalModes
Returns an array giving the frequencies (squared) corresponding to the normal-mode
motions.
getOmegaSquared() NormalModes1DHR
getOmegaSquared() NormalModes2D
getOmegaSquared() NormalModes3D
getOmegaSquared() NormalModesFromFile
getOmegaSquared() NormalModesMolecular
getOmegaSquared() NormalModesPotential
getOmegaSquared() NormalModesSoftSpherical
getOneEValButtonsVisibility() DeviceEigenvaluesSlider
getOneWVButtonsVisibility() DeviceWaveVectorSlider
getOperation() BinaryOpImpl
getOperation() UnaryOpImpl
getOperation() Parser.BinaryOp
getOperation() Parser.UnaryOp
getOptionDescription() Main.OptionHandler
Returns the description for this option
getOptionValuesLength() Main.NoValueOptionHandler
getOptionValuesLength() Main.OptionHandler
Returns the number of values which the option handler requires.
getOptionValuesLength() Main.SingleValueOptionHandler
getOrderBeta() VirialDiagramsPT
getOrientation() AtomOriented
getOrientation() AtomOrientedDynamic
getOrientation() IAtomOriented
Returns the orientation of the IAtom.
getOrientation() Quaternion
Returns an orientation corresponding to the rotation of cartesian coordinate frame {i,j,k}
by the axis and angle associated with the Quaternion q.
getOrientation() IMoleculeOriented
Returns the orientation of the IAtom.
getOrientation() MoleculeOriented
getOrientationIndex(Vector) FindPairMoleculeIndex
getOrientationIndex(Vector) FindPairMoleculeIndexBetaN2
getOrigin() DisplayBox
getOrigin() DisplayPolytope
getOrigin() LatticePlane
getOtherAngles() MeterTargetRPMolecule
getOtherDensities() MeterDDP
getOtherDensities() MeterDP
getOtherTemperature() MeterBoltzmannHTTP
getOtherTemperatures() MeterTargetTPMolecule
getOtherTemperatures() MeterTargetTP
getOut() DataSinkConsole
Method called to express incredulity.
getOutDegree() ClusterSumHS
Returns outDegee (number of bonds for each point) of the configuration
passed to checkConfig
getOutDegree() ClusterWheatley
Returns outDegee (number of bonds for each point) of the configuration
passed to checkConfig
getOutDegree() ClusterWheatleyHS
Returns outDegee (number of bonds for each point) of the configuration
passed to checkConfig
getOutDegree() ClusterWheatleyPartitionScreening
Returns outDegee (number of bonds for each point) of the configuration
passed to checkConfig
getOutDegree(byte) Graph
getOutDegree(byte) GraphImpl
getOutDegreeCore() ClusterWheatleyExtendSW
getOutDegreeWell() ClusterWheatleyExtendSW
getOuterGraph() CartesianIterator
getOuterIterator() ApiInnerVariable
Accessor method for the outer-loop atom iterator.
getOuterIterator() ApiIntergroup
Accessor method for the outer-loop atom iterator.
getOuterIterator() CartesianIterator
getOuterIterator() MpiInnerFixed
Accessor method for the outer-loop atom iterator.
getOuterIterator() MpiInnerVariable
Accessor method for the outer-loop atom iterator.
getOuterList() ApiInterArrayList
Returns the outer list used to generate the pairs.
getOuterList() MpiInterArrayList
Returns the outer list used to generate the pairs.
getOuterPermutation() CartesianPermutator
getOuterPermutator() CartesianPermutator
getOuterRadius() AtomTypeSpheroPolyhedron
getOutNode(byte, byte) Graph
getOutNode(byte, byte) GraphImpl
getOverlapAverage() DataVirialOverlap
Returns the ratio of the reference to target overlap-to-virial ratios
(which reduces to reference/target) for the optimal value of the Bennett
parameter.
getOverlapAverage(int) DataVirialOverlap
Returns the ratio of the reference to target overlap-to-virial ratios
(which reduces to target/reference) for the given value of the Bennet
parameter.
getOverlapAverageAndError() DataOverlapCaching
getOverlapAverageAndError() DataOverlap
Returns the ratio of the reference to target overlap-to-virial ratios
(which reduces to reference/target) for the optimal value of the Bennett
parameter.
getOverlapAverageAndError() DataSourceVirialOverlap
Returns the ratio of the reference to target overlap-to-virial ratios
(which reduces to reference/target) for the optimal value of the Bennett
parameter.
getOverlapAverageAndErrorForAlpha(double) DataVirialOverlap
Returns the overlap average and uncertainty for a given value of alpha.
getOverlapAverageForAlpha(double) DataSourceVirialOverlap
getP(int) MeterDDP
getP(int) MeterDP
getp1Counter() P1ConstraintNbrHcp
getPaddingSigma() DisplayBox
Returns the amount of padding added around the edge of the drawing area.
getPaintAction(Box) SimulationGraphic
getPaintAction()
getPairAgent(AtomType, AtomType) PNGCPM
getPairAgent(AtomType, AtomType) PNGCPMX
getPairArray(int, int) VirialPolymerOverlapMC
getPairedAtom1() P2HardSphereCavity
getPairedAtom2() P2HardSphereCavity
getPairMoleculesIndex(IMolecule, IMolecule, boolean) FindPairMoleculeIndex
getPairMoleculesIndex(IMolecule, IMolecule, boolean) FindPairMoleculeIndexBetaN2
getPairSiteValidation(String, IMolecularModel_SpeciesFactory[]) BuilderCollectionPotential
getPalette(String) EnumPalette
getPaletteID(String) EnumPalette
getPaletteName(byte) EnumPalette
getPanel() DeviceSlider
getPanel() DeviceSpinner
getPanel() DisplayPlotXChart
getPanel() SimulationGraphic
A visual display of the simulation via a JPanel.
getPanel() ClipPlaneEditor
getPanel() LatticeEditor
getParallelAxis(IMolecule) PNGCPM.GCPMAgent
getParamAndValues() IMolecularModel_SpeciesFactory
getParamAndValues() MolecularModel2CLJQ_SpeciesCO2
getParamAndValues() MolecularModel2CLJQ_SpeciesEthane
getParamAndValues() MolecularModel2CLJQ_SpeciesLJ
getParamAndValues() MolecularModelEMP2_SpeciesCO2
getParamAndValues() MolecularModelLJ_SpeciesLJ
getParamAndValues() MolecularModelLJQ_SpeciesLJ
getParamAndValues() MolecularModelSKS_SpeciesAlkane
getParamAndValues() MolecularModelSPCE_SpeciesH2O
getParamAndValues() MolecularModelTRAPPE_SpeciesAlkane
getParamAndValues() MolecularModelTrappe_SpeciesCO2
getParameter(double) BetaPhaseLatticeParameter
getParameter(double) BetaPhaseLatticeParameterLS
getParameter(int) BetaPhaseLatticeParameterNA
getParameterCount() IMolecularModel_SpeciesFactory
getParameterCount() MolecularModel2CLJQ_SpeciesCO2
getParameterCount() MolecularModel2CLJQ_SpeciesEthane
getParameterCount() MolecularModel2CLJQ_SpeciesLJ
getParameterCount() MolecularModelEMP2_SpeciesCO2
getParameterCount() MolecularModelLJ_SpeciesLJ
getParameterCount() MolecularModelLJQ_SpeciesLJ
getParameterCount() MolecularModelSKS_SpeciesAlkane
getParameterCount() MolecularModelSPCE_SpeciesH2O
getParameterCount() MolecularModelTRAPPE_SpeciesAlkane
getParameterCount() MolecularModelTrappe_SpeciesCO2
getParameters() HSMD3D
getParametersArray() IMolecularModel_SpeciesFactory
getParametersArray() MolecularModel2CLJQ_SpeciesCO2
getParametersArray() MolecularModel2CLJQ_SpeciesEthane
getParametersArray() MolecularModel2CLJQ_SpeciesLJ
getParametersArray() MolecularModelEMP2_SpeciesCO2
getParametersArray() MolecularModelLJ_SpeciesLJ
getParametersArray() MolecularModelLJQ_SpeciesLJ
getParametersArray() MolecularModelSKS_SpeciesAlkane
getParametersArray() MolecularModelSPCE_SpeciesH2O
getParametersArray() MolecularModelTRAPPE_SpeciesAlkane
getParametersArray() MolecularModelTrappe_SpeciesCO2
getParameterValue(String) DevicePlotPoints
Returns the value of the function parameter slider.
getParameterWrapper() ParseArgs
Returns the parameter wrapper.
getParameterWrapper() ReadParameters
Returns the parameter wrapper.
getParameterWrapper() WriteParameters
Returns the parameter wrapper.
getParamType(int) Token
getParentGroup() Atom
getParentGroup() IAtom
getParsers() ParameterBase
getPartner(int) P1ImageHarmonic
getPauseFlag() Controller.ControllerHandle
getPbcEnforcer() NeighborListManagerMolecular
getPbcEnforcer() NeighborListManager
getPCenter(int) MeterDDP
getPCenter(int) MeterDP
getPdbBondInfo(int) JmolConstants
getPerimeter() Cube
Returns 12*edgeLength
getPerimeter() Cuboid
getPerimeter() Parallelepiped
getPerimeter() Parallelogram
getPerimeter() Polygon
Returns the sum of the length of the edges of the polygon
getPerimeter() Polyhedron
Returns the sum of the length of the edges of the polyhedron
getPerimeter() Rectangle
Returns the perimeter of the rectangle.
getPeriodicity() Boundary
getPeriodicity(int) BoundaryDeformablePeriodicSwitch
getPeriodicity(int) BoundaryRectangularPeriodicSwitch
getPeriodicity(int) Boundary
Returns true if the boundary is periodic in the given direction (as
defined by the getEdgeVector method).
getPeriodicity(int) BoundaryDeformablePeriodic
getPeriodicity(int) BoundaryRectangularNonperiodic
getPeriodicity(int) BoundaryRectangularPeriodic
getPeriodicity(int) BoundaryRectangularPore
getPeriodicity(int) BoundaryRectangularSlit
getPeriodicity(int) BoundaryTruncatedOctahedron
getPerp(Vector, Vector, Vector) P2CO2H2OWheatley
getPerp(Vector, Vector, Vector) P2CO2Hellmann.P2CO2SC
getPerp(Vector, Vector, Vector) P2NitrogenHellmann.P2N2QFH
getPerspectiveDepth() G3DSys
getPhaseAngles() MeterStructureFactor
getPhaseAngles() NormalModesVariable
getPhi() P4TorsionDreiding
getPhongExponent() GData
getPickedDiagram() ClusterDiagramTree
getPickedDiagram() DiagramSource
getPixelDepth() G3DSys
Gets the pixel depth of the display (zbuffer)
getPixelHeight() G3DSys
Gets the pixel height of the display
getPixelUnit() DisplayBox
getPixelUnit() DisplayCanvas
Returns unit for conversion between simulation units and display pixels.
getPixelUnit() DisplayPolytope
Returns unit for conversion between simulation units and display pixels.
getPixelUnitToMillimeter() SVGConverter
getPixelWidth() G3DSys
Gets the pixel width of the display
getPlane() LatticePlane
getPlaneColor() DisplayBoxCanvasG3DSys
Gets the color of the plane.
getPlaneProjection(Point3f, Point4f, Point3f, Vector3f) Measure
getPlaneThroughPoint(Point3f, Vector3f, Point4f) Measure
getPlaneThroughPoints(Point3f, Point3f, Point3f, Vector3f, Vector3f, Vector3f, Point4f) Measure
getPlot() DisplayPlot
Accessor method to plot class so that its properties can be edited.
getPlot() DisplayPlotXChart
getPlotSizeSlider(int) DevicePlotPoints
Returns the plot scale slider for the given parameter (values can be
DevicePlotPoints.MIN_X, MAX_X, MIN_Y or MAX_Y.
getPoint() Ball
getPoint() Ellipse
getPolarizationEnergy(IMoleculeList) PNCO2GCPM
This returns the polarizable portion of the GCPM potential for any
number of atoms.
getPolarizationEnergy(IMoleculeList) PNGCPM
This returns the polarizable portion of the GCPM potential for any
number of atoms.
getPolarizationEnergy(IMoleculeList) PNWaterGCPM
This returns the polarizable portion of the GCPM potential for any
number of atoms.
getPolarizationEnergy(IMoleculeList) PNWaterGCPMReactionField
This returns the polarizable portion of the GCPM potential for any
number of atoms.
getPolarizationEnergy(IMoleculeList) PotentialPolarizable
Returns the polarization contribution (non pairwise-additive) to the
energy for the given AtomSet.
getPolytope() DisplayPolytope
getPoreCenters() P1WCAPorousWall
getPoreDim() BoundaryRectangularPore
Returns index of periodic dimension.
getPoreRadius() P1WCAPorousWall
getPos(int) P2CO2Hellmann
getPosition() Atom
getPosition() IAtom
getPosition() LatticePlane
Returns the position i, such the the plane is located at the i-th from the origin.
getPosition() Hypersphere
getPosition() Polytope
Returns the geometric center of the polytope.
getPosition() IMoleculePositioned
Returns the position of the IMolecule.
getPosition() MoleculeOriented
getPositionDataInfo() DataSourcePositioned
getPositionDataInfo() DataSourcePositionedBoltzmannFactor
getPositionDefinition() BoxImposePbc
getPositionDefinition() MeterProfileByAtoms
getPositionDefinition() MeterProfileByVolume
getPositionDefinition() MCMoveRotateMolecule3D
getPositionDefinition() CoordinateDefinitionMolecule
getPositionDefinition() CoordinateDefinitionMoleculeVolumeFluctuation
getPositionDefinition() CoordinatePairMoleculeSet
getPositionSource() MeterProfile
Returns the RandomPositionSource used by this meter.
getPositionSource() MeterWidomInsertion
Returns the RandomPositionSource used by this meter.
getPositionSource() MCMoveInsertDelete
Returns the RandomPositionSource used by this move.
getPositionSource() MCMoveMoleculeExchange
Returns the RandomPositionSource used by this move.
getPositionSource() MeterWidomInsertionCorrection
Returns the RandomPositionSource used by this meter.
getPositionSource() MeterWidomInsertionP
Returns the RandomPositionSource used by this meter.
getPositivePrefix() ScientificFormat
getPositiveSuffix() ScientificFormat
getPostAction() SimulationRestart
getPostAction() Device
getPotential() MeterEnergy
getPotential() ClusterSumIC.FR2
getPotential() IMolecularModel_SpeciesFactory
getPotential() MolecularModel2CLJQ_SpeciesCO2
getPotential() MolecularModel2CLJQ_SpeciesEthane
getPotential() MolecularModel2CLJQ_SpeciesLJ
getPotential() MolecularModelEMP2_SpeciesCO2
getPotential() MolecularModelLJ_SpeciesLJ
getPotential() MolecularModelLJQ_SpeciesLJ
getPotential() MolecularModelSKS_SpeciesAlkane
getPotential() MolecularModelSPCE_SpeciesH2O
getPotential() MolecularModelTRAPPE_SpeciesAlkane
getPotential() MolecularModelTrappe_SpeciesCO2
getPotential() MayerD2FDT2Spherical
getPotential() MayerDFDTSpherical
getPotential() MayerDFQFHDTSpherical
getPotential() MayerEGeneral
getPotential() MayerENonGeneral
getPotential() MayerESpherical
getPotential() MayerFunction
getPotential() MayerFunctionProductGeneral
getPotential() MayerFunctionSum
getPotential() MayerFunctionSumGeneral
getPotential() MayerFunctionTemperature
getPotential() MayerGeneral
getPotential() MayerGeneralAtomic
getPotential() MayerGeneralSpherical
getPotential() MayerHardSphere
getPotential() MayerHSMixture
getPotential() MayerPTAtt
getPotential() MayerPUGeneral
getPotential() MayerSphericalPTAtt
getPotential() MayerSSSeries
getPotential() MayerWell
getPotential() MayerXSpherical
getPotential() MuFGeneral
getPotential() MuGeneral
getPotential() VirialB2WaterTIP4P_DHS_difference.MuDeltaEBond
getPotential() VirialB3C1TIP4Pwater.MuFBond
getPotential() VirialB3C2TIP4Pwater.fPlusBetaEU
getPotential() VirialB3C2TIP4Pwater.MuProduct
getPotential(ISpecies[]) PotentialMaster
Returns the potential that applies to the specified types,
or null of no existing potential applies.
getPotential1BodyList(IAtom) NeighborListManager
getPotential1BodyList(IMolecule) NeighborListManagerMolecular
getPotentialCalculation() MeterMappedRdf
getPotentialCalculation() MeterMappedU
getPotentialCalculation() MeterMappedVirial
getPotentialCalculation() MeterMappedVirialV
getPotentialCollectionFactory() ModelSimulationConstructor
getPotentialEnergy() MeterEnergy
getPotentialEnergy() IntegratorBox
getPotentialEnergy() MCMoveAtomCoupledUmbrella
getPotentialGroupInterNonBondedLike() CollectionPotentialAtomicLike
getPotentialGroupInterNonBondedUnlike() CollectionPotentialAtomicUnlike
getPotentialGroupIntraBonded() CollectionPotentialAtomicLike
getPotentialIndex(IPotential) PotentialArray
Returns the index that this type has assigned to the given
potential.
getPotentialIndex(IPotential) PotentialArrayByType
Returns the index that this type has assigned to the given
potential.
getPotentialIndex(IPotentialMolecular) PotentialArrayMolecular
Returns the index that this type has assigned to the given
potential.
getPotentialIntraBondedTorsion() CollectionPotentialAtomicLike
getPotentialJList() ViewSpeciesSelection
getPotentialJList() ViewSpeciesSelection
getPotentialJListListener() ViewSpeciesSelection
getPotentialJListListener() ViewSpeciesSelection
getPotentialListDisplayLSM() ViewSpeciesSelection
getPotentialListDisplayLSM() ViewSpeciesSelection
getPotentialMaster() IntegratorBox
getPotentialMaster() MeterPressure2
Returns the integrator associated with this instance.
getPotentialMasterCell() PotentialMasterHybrid
getPotentialMasterList() PotentialMasterHybrid
getPotentialMasters() SimulationWrapper
getPotentialMolecularNonBondedLike() CollectionPotentialMolecularLike
getPotentialMolecularUnlike() CollectionPotentialMolecularUnlike
getPotentialParamAndValuesString() ModelSpeciesSelection
getPotentialParamDispayTable() ViewSpeciesSelection
getPotentialParamDispayTable() ViewSpeciesSelection
getPotentialParamDisplayLSM() ViewSpeciesSelection
getPotentialParamDisplayLSM() ViewSpeciesSelection
getPotentialParamDisplayTM() ViewSpeciesSelection
getPotentialParamDisplayTM() ViewSpeciesSelection
getPotentialParamDisplayTMListener() ViewSpeciesSelection
getPotentialParamDisplayTMListener() ViewSpeciesSelection
getPotentialParamString() ModelSpeciesSelection
getPotentialPlus() MayerSphericalPlus
getPotentialRange() NeighborCellManagerMolecular
Returns the potential range.
getPotentialRange() NeighborCellManager
Returns the potential range.
getPotentials() PotentialArray
getPotentials() PotentialArrayByType
getPotentials() PotentialArrayMolecular
getPotentials() PotentialGroup
getPotentials() PotentialMaster
Returns an array containing all molecular Potentials.
getPotentialsClassList() ModelSpeciesSelection
getPotentialsCollectionBuilder() ModelSimulationConstructor
getPotentialSiteAtIndex(int) IMolecularModel_SpeciesFactory
getPotentialSiteAtIndex(int) MolecularModel2CLJQ_SpeciesCO2
getPotentialSiteAtIndex(int) MolecularModel2CLJQ_SpeciesEthane
getPotentialSiteAtIndex(int) MolecularModel2CLJQ_SpeciesLJ
getPotentialSiteAtIndex(int) MolecularModelEMP2_SpeciesCO2
getPotentialSiteAtIndex(int) MolecularModelLJ_SpeciesLJ
getPotentialSiteAtIndex(int) MolecularModelLJQ_SpeciesLJ
getPotentialSiteAtIndex(int) MolecularModelSKS_SpeciesAlkane
getPotentialSiteAtIndex(int) MolecularModelSPCE_SpeciesH2O
getPotentialSiteAtIndex(int) MolecularModelTRAPPE_SpeciesAlkane
getPotentialSiteAtIndex(int) MolecularModelTrappe_SpeciesCO2
getPotentialSites() IMolecularModel_SpeciesFactory
getPotentialSites() MolecularModel2CLJQ_SpeciesCO2
getPotentialSites() MolecularModel2CLJQ_SpeciesEthane
getPotentialSites() MolecularModel2CLJQ_SpeciesLJ
getPotentialSites() MolecularModelEMP2_SpeciesCO2
getPotentialSites() MolecularModelLJ_SpeciesLJ
getPotentialSites() MolecularModelLJQ_SpeciesLJ
getPotentialSites() MolecularModelSKS_SpeciesAlkane
getPotentialSites() MolecularModelSPCE_SpeciesH2O
getPotentialSites() MolecularModelTRAPPE_SpeciesAlkane
getPotentialSites() MolecularModelTrappe_SpeciesCO2
getPotentialSites(int) MolecularModel2CLJQ_SpeciesCO2
getPotentialSites(int) MolecularModel2CLJQ_SpeciesEthane
getPotentialSites(int) MolecularModelEMP2_SpeciesCO2
getPotentialSites(int) MolecularModelSKS_SpeciesAlkane
getPotentialSites(int) MolecularModelSPCE_SpeciesH2O
getPotentialSites(int) MolecularModelTRAPPE_SpeciesAlkane
getPotentialSites(int) MolecularModelTrappe_SpeciesCO2
getPotentialsList() ModelSpeciesSelection
getPotentialsSelectedIndex() ModelSpeciesSelection
getPreAction() Device
Returns the action to be performed before the primary action executed
by the device.
getPrecision() DataDoubleBDArray.DataInfoDoubleBDArray
getPrecision() DataDoubleBDArray.DataInfoDoubleBDArrayFactory
getPrecision() DecimalSlider
Accessor method for precision of slider, defined as number of
digits after the decimal that will be distinguished by slider.
getPrecision() DeviceBox
Accessor method of the precision, which specifies the number of significant figures to be displayed.
getPrecision() DeviceSlider
getPrecision() DisplayTable
Accessor method of the precision, which specifies the number of
significant figures to be displayed.
getPrecision() DisplayTextBox
Accessor method of the precision, which specifies the number of significant figures to be displayed.
getPrecision() DisplayTextBoxesCAE
Accessor method of the precision, which specifies the number of significant figures to be displayed.
getPrecision() PotentialCalculationEnergySumBigDecimal
getPreferredSize() DisplayPlotXChart
getPrefix() PrefixedUnit
getPressure() MCMoveVolumeAssociated
getPressure() MCMoveVolumeAssociatedMolecule
getPressure() MCMoveVolume
getPressure() PotentialCalculationMappedVirial
getPressure() PotentialCalculationMappedVirialV
getPressure() MCMoveVolumeN2
getPressure() MCMoveVolumeMonoclinicScaled
getPressure() MCMoveVolumeSolid
getPressure() MCMoveVolumeSolidNPTMolecular
getPressure() ColorSchemeScaledOverlap
getPressure() DisplayBoxCanvas2DNpTScaling
getPressure() HSNPT2DGraphic
getPressure() P1HardMovingBoundary
getPressure(int, int, double, double) SoftSphereSolidEOS
getPressure1() PotentialCalculationSolidSuperCut
getPressureDimension() MCMoveVolumeAssociated
getPressureDimension() MCMoveVolumeAssociatedMolecule
getPressureDimension() MCMoveVolume
getPressureDimension() MCMoveVolumeN2
getPressureDimension() MCMoveVolumeMonoclinicScaled
getPressureDimension() MCMoveVolumeSolid
getPressureDimension() MCMoveVolumeSolidNPTMolecular
getPressureDimension() P1HardMovingBoundary
getPressureTensor() PotentialCalculationForcePressureSumGB
Returns the virial portion of pressure tensor calculated during the last
potential calculation.
getPressureTensor() IntegratorRigidIterative
Returns the pressure tensor based on the forces calculated during the
last time step.
getPressureTensor() IntegratorRigidMatrixIterative
Returns the pressure tensor based on the forces calculated during the
last time step.
getPressureTensor() IntegratorVelocityVerlet
Returns the pressure tensor based on the forces calculated during the
last time step.
getPressureTensor() IntegratorVerlet
Returns the pressure tensor based on the forces calculated during the
last time step.
getPressureTensor() IntegratorDroplet
Returns the pressure tensor based on the forces calculated during the
last time step.
getPressureTensor() PotentialCalculationForcePressureSum
Returns the virial portion of pressure tensor calculated during the last
potential calculation.
getPressureTensor() PotentialCalculationPressureTensor
Returns the pressure tensor based on a previous call to
PotentialMaster.calculate
getPressureTensor() IntegratorVelocityVerletQuaternion
Returns the pressure tensor based on the forces calculated during the
last time step.
getPrevConfigIndex() AtomSignalMobility
getPrevConfigIndex() AtomSignalMotion
getPrevSampleIndex() MeterCorrelation
getPrevX() DisplayCanvas
getPrevY() DisplayCanvas
getPrimitive() BravaisLattice
Returns the primitive object used to construct this lattice.
getPrimitive() CoordinateDefinition
getPrimitiveFcc() LatticeCubicFcc
Returns a new PrimitiveFcc instance corresponding to the fcc lattice.
getPrimitiveHexagonal() LatticeOrthorhombicHexagonal
Returns a new PrimitiveFcc instance corresponding to the fcc lattice.
getPriority() BoxImposePbc
getPrivateKey() Graphics3D
getProductOfFrequencies() CalcVibrationalModes
getProfileDataInfo() DataSourceTensorVirialHardProfile
getProfileDim() MeterProfile
Accessor method for vector describing the direction along which the profile is measured.
getProfileDim() MeterProfileByAtoms
Accessor method for vector describing the direction along which the profile is measured.
getProfileDim() MeterProfileByVolume
Accessor method for vector describing the direction along which the profile is measured.
getProfileDim() DataProcessorInterfacialTensionProfile
getPrompt() ConsoleUI
getProperty() CommandPropertyValueImpl
getProperty() Parser.CommandPropertyValue
getProperty() DeviceSlider
getProperty() DeviceSpinner
getProperty() ModifierGeneral
getProperty() PropertyUpdate
getPropertyNames() Environment
getPropertyNames() EnvironmentImpl
getPropertyType() ArrayProperty
getPropertyType() AtomListProperty
getPropertyType() InstanceProperty
getPropertyType() MoleculeListProperty
getPropertyType() Property
getPropertyType() VectorProperty
getPropertyValue(String) Environment
getPropertyValue(String) EnvironmentImpl
getPump() DataStreamStore.DataPlumbing
getPushInterval() DataAccumulator
Accumulated data are pushed to the data sinks after every pushInterval calls
to putData.
getpVelocity(double, double, double, double) MeterMeanField
getPYCorrection(byte) PYGenerator
Returns graphs included in the correction to the PY approximation at the
n-th order.
getPzxy() PotentialCalculationSolidSuperCut
getq() PotentialCalculationMappedRdf
getQ() Charge
getQ() PotentialCalculationMappedVirial
getQ() PotentialCalculationMappedVirialV
getQ() P2WaterSzalewicz
getQ() DataSourceFs
getQ(int) P2CO2Hellmann
getQ0() Quaternion
Returns the q0 component of the Quaternion
getQ1() Quaternion
Returns the q1 component of the Quaternion
getQ2() Quaternion
Returns the q2 component of the Quaternion
getQ3() Quaternion
Returns the q3 component of the Quaternion
getqp() PotentialCalculationMappedEnergy
getQP_Q() PotentialCalculationMappedEnergy
getQU() PotentialCalculationMappedVirial
getQU() PotentialCalculationMappedVirialV
getQuadrupolarMomentSquare() P2LJQ
getQuadrupolarMomentSquare() P2LJQQ
getQuality() SVGConverter
getQuardricZ(double, double, double[], double[]) Quadric
getQuaternion() AtomOrientedQuaternion
getQuaternionFrame(Point3f, Tuple3f, Tuple3f) Quaternion
getQuaternionFrameV(Vector3f, Vector3f, Vector3f, boolean) Quaternion
getQuotedAttribute(String, String) Parser
getQuotedStringAt(String, int) Parser
getQuotedStringNext(String, int[]) Parser
getR0() P2Harmonic
Separation at which potential is at its minimum.
getR0Dimension() P2Harmonic
getr2(int, int) CoordinatePairLeafSet
Returns atom pair for ith and jth atoms in set.
getr2(int, int) CoordinatePairMoleculeSet
Returns atom pair for ith and jth atoms in set.
getr2(int, int) CoordinatePairSet
Returns atom pair for ith and jth atoms in set.
getr2d2udr2(int, double, Potential2SoftSpherical) BnPY_1QC_Helium
getRadius() Hypersphere
getRadius() P1SoftBoundary
Returns the radius.
getRadius(int) Quadric
getRadiusDimension() P1SoftBoundary
getRandom() Simulation
getRandomizeProbability() IntegratorImageHarmonicMD
getRandomNumberGenerator() AtomSourceRandomDimer
Returns the random number generator used to pick atoms
getRandomNumberGenerator() AtomSourceRandomSmer
Returns the random number generator used to pick atoms
getRandomNumberGenerator() MoleculeSourceRandomDimer
Returns the random number generator used to pick atoms
getRandomNumberGenerator() AtomSourceRandomLeaf
Returns the random number generator used to pick atoms
getRandomNumberGenerator() AtomSourceRandomSpecies
Returns the random number generator used to pick atoms
getRandomNumberGenerator() MoleculeSourceRandomMolecule
Returns the random number generator used to pick molecules
getRandomSeeds() Simulation
getRandSeedArray() RandomNumberGeneratorUnix
Convenience method that returns an array of integers, useful as seeds to
another RNG.
getRange() P1WCAWall
getRange() P2EAM
getRange() PotentialCuLREP
getRange() PotentialEAM_LS
getRange() PotentialEAM
getRange() PotentialEFS
getRange() P1ImageHarmonic
getRange() RectangularLatticeNbrIteratorSquare
Returns (a copy of) the array specifying the neighbor range.
getRange() Potential2SoftSphericalLSMulti
Returns infinity.
getRange() Potential2SoftSphericalLSMultiLat
Returns infinity.
getRange() P2CO2H2OWheatley
getRange() P2CO2H2OWheatley.P2CO2H2OSC
getRange() P2CO2H2OWheatley.P2CO2H2OSCTI
getRange() P2CO2Hellmann
getRange() P2CO2Hellmann.P2CO2SC
getRange() PNCO2GCPM
getRange() PNCO2GCPM.P3GCPMAxilrodTeller
getRange() PNGCPM
getRange() PNGCPM.P3GCPMAxilrodTeller
getRange() PNGCPM.PNGCPMCached
getRange() P0LatticeEnergyCorrec
getRange() P2Nitrogen
getRange() P2NitrogenAB
getRange() P2NitrogenAnisotropic
getRange() P2NitrogenShellModel
getRange() PRotConstraint
getRange() P2Water3P
getRange() P2Water3PSoft
getRange() P2Water4P
getRange() P2Water4PSoft
getRange() P2WaterSzalewicz
getRange() P2WaterSzalewicz.P2H2OSC
getRange() P2WaterTIP4P
getRange() P2WaterTIP4PHardCore
getRange() PNWaterGCPM
getRange() PNWaterGCPM.PNWaterGCPMCached
getRange() PNWaterGCPMReactionField
getRange() P1Wall
getRange() P2SquareWellBonding
getRange() P2SquareWellBondingCO
getRange() P2SquareWellSurface
getRange() P1Wall
getRange() P1WCAPorousWall
getRange() P1WCAWall
getRange() P1Smash
getRange() P2Cohesion
getRange() P1Tension
getRange() P2SquareWellOneSide
getRange() P1Sinusoidal
getRange() P1WCAWall
getRange() PotentialMasterCell
getRange() NeighborListManagerMolecular
getRange() PotentialMasterListMolecular
Returns the range that determines how far to look for neighbors.
getRange() NeighborListManager
getRange() PotentialMasterList
Returns the range that determines how far to look for neighbors.
getRange() PotentialMasterHybrid
getRange() P1ConstraintNbr
getRange() P1ConstraintNbrHcp
getRange() P2XOrder
Returns infinity.
getRange() PotentialDepletion
getRange() P2HardSpherePoly
getRange() EwaldSummation
getRange() EwaldSummation.P2EwaldReal
getRange() EwaldSumMolecules
getRange() IPotential
Returns the range over which the potential applies.
getRange() P1ExternalField
getRange() P1HardBoundary
getRange() P1HydrogenMielke
getRange() P22CLJmuQ
getRange() P22CLJQ
getRange() P2CO2EMP
getRange() P2DiscreteFeynmanHibbs
getRange() P2DLPOLY
getRange() P2DoubleWell
getRange() P2EffectiveFeynmanHibbs
getRange() P2HardAssociation
Returns the well diameter.
getRange() P2HardAssociationCone
Returns infinity.
getRange() P2HardAssociationConeDoubleSites
Returns infinity.
getRange() P2HardAssociationConeFourSites
Returns infinity.
getRange() P2HardAssociationConeFourSitesSW
Returns infinity.
getRange() P2HardAssociationConeOneSite
Returns infinity.
getRange() P2HardAssociationConeReference
Returns infinity.
getRange() P2HardAssociationConeReferenceFourSites
Returns infinity.
getRange() P2HardAssociationConeSW
Returns sigma * cutoffFactor.
getRange() P2HardBond
Returns infinity.
getRange() P2HardBondedList
getRange() P2HardSphere
getRange() P2HardWrapper
getRange() P2HC2Yukawa
getRange() P2HePCKLJS.P2HeQFH
getRange() P2HePCKLJS.P2HeTI
getRange() P2HeSimplified.P2HeQFH
getRange() P2HeSimplified.P2HeTI
getRange() P2HSDipole
getRange() P2HydrogenHinde
getRange() P2HydrogenHindeAtomic
getRange() P2HydrogenHindePatkowski
getRange() P2HydrogenHindePatkowskiAtomic
getRange() P2HydrogenPatkowski
getRange() P2HydrogenPatkowskiAtomic
getRange() P2Ideal
Returns zero.
getRange() P2LJDipole
getRange() P2LJQ
getRange() P2MoleculeMonatomic
getRange() P2MoleculeSoftTruncatedSwitched
Returns the truncation radius.
getRange() P2MoleculeTruncated
Returns the truncation radius.
getRange() P2NitrogenHellmann
getRange() P2NitrogenHellmann.P2N2QFH
getRange() P2O2Bartolomei
getRange() P2O2Bartolomei.P2O2TI
getRange() P2PenetrableBond
Returns infinity.
getRange() P2PenetrableSphere
getRange() P2PenetrableSquareWell
getRange() P2QChem
getRange() P2ReactionFieldDipole
The radius of the sphere within which molecules contribute to the reaction
field of a given molecule.
getRange() P2ReactionFieldDipoleTruncated
getRange() P2ReactionFieldDipoleTruncated.P0ReactionField
getRange() P2SemiclassicalAtomic
getRange() P2SemiclassicalMolecular
getRange() P2SoftSphericalTruncated
Returns the truncation radius.
getRange() P2SoftSphericalTruncatedSwitched
Returns the truncation radius.
getRange() P2SoftTruncated
Returns the truncation radius.
getRange() P2SpheroPolyhedron
getRange() P2SquareWell
getRange() P2SquareWellRobust
getRange() P2Tether
Returns the tether length.
getRange() P2TriangleWell
getRange() P2WaterPotentialsJankowski
getRange() P2WCA
Returns the range of the potential, which is the point of truncation.
getRange() P2WCAP
Returns the range of the potential, which is the point of truncation.
getRange() P3AxilrodTeller
getRange() P3BondAngle
getRange() P3BondAngleDreiding
getRange() P3CPSNonAdditiveHe
getRange() P3CPSNonAdditiveHeLessSimplified
getRange() P3CPSNonAdditiveHeOrig
getRange() P3CPSNonAdditiveHeSimplified
getRange() P3HydrogenATM
getRange() P3HydrogenManzhos
getRange() P3Induction
getRange() P3NitrogenHellmannNonAdditive
getRange() P4BondTorsion
getRange() P4BondTorsionAlkaneXCCH
getRange() P4TorsionDreiding
getRange() Potential
getRange() Potential0
Returns zero.
getRange() Potential1
Returns zero.
getRange() Potential2SoftSpherical
Returns infinity.
getRange() Potential2SoftSphericalLS
Returns infinity.
getRange() PotentialAtomicSum
getRange() PotentialDLPOLY
getRange() PotentialEmul
getRange() PotentialGroup
Returns the maximum of the range of all potentials in the group.
getRange() PotentialMolecular
getRange() PotentialMolecularMonatomic
getRange() PotentialMolecularSum
getRange() PotentialNonAdditiveDifference
getRange() P2LJDipole
getRange() P2Spin
Returns 0, because potential operates on a lattice and range
should not be needed.
getRange() P2Spin
Returns 0, becuase potential operates on a lattice and range
should not be needed.
getRange() P2HSPolymer
getRange() P1IntraLambda
getRange() PotentialCommonAtomic
getRange() PotentialGroup3PI.PotentialGroup3PISkip
getRange() PotentialGroupPI.PotentialGroupPISkip
getRange() PotentialNonAdditive
getRange() PotentialNonAdditive.PotentialNonAdditiveNB
getRange() VirialB2WaterTIP4P_DHS_difference.P2WaterDHS
getRangedPotentials() PotentialMasterNbr
getRangedPotentials(AtomType) PotentialMasterNbr
getRangedPotentials(ISpecies) PotentialMasterNbrMolecular
getRangedPotentials1Body(AtomType) PotentialMasterNbr
getRatios() MCMoveOverlapListener
Returns overlap sampling results (ratio of partition functions between
sequential number of atoms).
getRawData() AccumulatorAverageBlockless
getRawData() AccumulatorAverageBlocklessSlim
getRawData() AccumulatorAverageBootstrap
getRawData() AccumulatorAverageCollapsingLog
getRawDataBlockSize() AccumulatorAverageBootstrap
getRawDataBlockSize() AccumulatorAverageCollapsingLog
getRawLogAccumulator() AccumulatorAverageBootstrap
getRawLogAccumulator() AccumulatorAverageCollapsingLog
getRawLogDataCorrelation() AccumulatorAverageCollapsingLog
Returns the correlation between consecutive values of the log of the "raw"
data held by the accumulator.
getRCut() EwaldSummation
Returns real-space cutoff
getrdfdr(int, double, double) BnHNCLJ
getrdfdr(int, double, double) BnPYLJ
getrdfdr(int, double, double) BnSCALJ
getrdfdr(int, double, double, Potential2SoftSpherical) BnIETP2Spherical
getrdudr(int, double, Potential2SoftSpherical) BnPY_1QC_Helium
getRe() P2ModifiedMorse
getRe() P2Morse
getReal() FastFourierTransform
array value calls
getRealEigenvalues() MyEigenvalueDecomposition
Return the real parts of the eigenvalues
getRealEigenvalues() Eigen
Return the real parts of the eigenvalues
getReferenceDataInterval() SimOverlapModule
getRefPref() MeterSamplingHarmonic
getRefPref() MeterSamplingTarget
getRefPref() MeterWorkBennetHarmonic
getRefPref() MeterWorkBennetTarget
getRefPref() MeterWorkHarmonicBennet
getRefPref() MeterWorkHarmonicUmbrella
getRefPref() MeterWorkTargetBennet
getRefPref() MeterWorkTargetUmbrella
getRefPref() MeterWorkUmbrellaHarmonic
getRefPref() MeterWorkUmbrellaTarget
getRefPref() SimBennet
getRefPref() SimHarmonicUmbrella
getRefPref() SimTargetUmbrella
getRefPref() SimUmbrella
getRefPref() SimUmbrellaSoftSphere
getRefSource() DataOverlap
Returns object capable of retrieving data from the reference system.
getRefStepFraction() IntegratorOverlap
getRefTimeFraction() IntegratorOverlap
getReinitButton() DeviceTrioControllerButton
getRelativeDisplacement(IAtom) ConfigFromFileLAMMPS.ColorSchemeDeviation
getRelativeDisplacement(IAtom) ColorSchemeDeviation
getRemove() ViewSpeciesSelection
getRemoveSpecies1() ViewSpeciesSelection
getRemoveSpecies2() ViewSpeciesSelection
getRemoveSpecies3() ViewSpeciesSelection
getRenderHeight() GData
gets g3d height
getRenderWidth() GData
gets g3d width
getReset() ViewSpeciesSelection
getReset() ViewSpeciesSelection
getResetAction() DeviceNSelector
Returns the action used to "reset" the simulation after changing the
number of molecules, SimulationRestart by default.
getResetAveragesButton() DeviceTrioControllerButton
getResizeOnNewBox() DisplayBox
Get the flag indicating whether the graphic should resize from its
currently displayed size when a new box is set.
getResults(Potential2SoftSpherical, double, double, double, boolean) B2ForSphericallySymmetricUByTrapezoidRule
getReverseEdgeColor(char) MetadataImpl
getRm() P2Exp6Buckingham
getRmax() P2Exp6Buckingham
getRmsd(Point3f[][], Quaternion) Measure
getRootColorMap() ConstructorColoredImpl
getRootColorMap() Parser.ConstructorColored
getRootNodes() ConstructorMonoImpl
getRootNodes() Parser.ConstructorMono
getRotationAxis() FindBetaN2AngleFromParameter
getRotationMatrix() Quaternion
Returns the rotation matrix associated with the Quaternion q as a Jama.Matrix
getRotationScale(Matrix3f) Matrix4f
Gets the upper 3x3 values of this matrix and places them into the matrix
m1.
getRow(int, float[]) Matrix3f
Copies the matrix values in the specified row into the array parameter.
getRow(int, float[]) Matrix4f
Copies the matrix values in the specified row into the array parameter.
getRowCount() DataSinkTable
Returns the length of the longest column.
getRowCount() DeviceTableModelGeneric
Get the number of rows in the table (including blank rows).
getRowCount() ModelMoleculeListDisplayTable_new
getRowCount() ModelMoleculeListDisplayTable
getRowCount() ModelPotParamDisplayTable
getRowHeader(int) DataSinkTable
getRowHeader(int) DataTable.DataInfoTable
Returns the row header for row i or an empty string if there are no
row headers.
getRowHeaders() DataTable.DataInfoTableFactory
Returns a copy of the row headers or null if no row headers exist.
getRowLabelColumnHeader() DisplayTable
Returns the header of the row-label column.
getRowLabels() DisplayTable
Descriptive text for each row.
getRPow() MCMoveClusterAtomDiscrete
getRun() ViewSpeciesSelection
getRun() ViewSpeciesSelection
getRunControls() DeviceTrioControllerButton
getSafetyFactor() CriterionPositionWall
returns the safety factor
getSafetyFactor() CriterionSimple
getSafetyFactor() PotentialMasterListMolecular
Returns the safety factor.
getSafetyFactor() PotentialMasterList
Returns the safety factor.
getSafetyFactor() CriterionSimpleMolecular
getSampleCluster() BoxCluster
returns the cluster used for sampling in this box
getSampleClusters() SimulationVirialOverlap2
getSampleCount() AccumulatorAverage
getSampleCount() AccumulatorAverageBlockless
getSampleCount() AccumulatorAverageBlocklessSlim
getSampleCount() History
Returns the number of data samples currently held by the History.
getSampleCount() HistoryCollapsing
getSampleCount() HistoryComplete
getSampleCount() HistoryScrolling
getSampleCount() DataOverlap.DataSourceOverlapAvg
getSampleCount() DataOverlap.DataSourceOverlapAvgCollapsing
getSampleCount() DataOverlap.DataSourceOverlapAvgSimple
getSampleInterval() ConfigurationStorage
getSampleLogVariance() AccumulatorAverageBootstrap
getSampleLogVariance() AccumulatorAverageCollapsingLog
getSampleVariance() AccumulatorAverageBootstrap
getSampleVariance() AccumulatorAverageCollapsingLog
getSavedConfig(int) ConfigurationStorage
getSavedSteps() ConfigurationStorage
getSavedTimes() ConfigurationStorage
getSavedVel(int) ConfigurationStorage
getSaveValues() ViewAlkaneLengthSelection
getSaveValues() ViewSimEnvironmentSelection
getScalar() Quaternion
Returns the scalar part of the Quaternion
getScale() BoxInflate
getScale() DisplayBox
getScale() DisplayPolytope
getScaledCoordinates() Basis
Returns scaled coordinates
getScalingDataSource() MeterPressureByVolumeChange
Returns the data source for volume scalings.
getScreenImage() Graphics3D
getScreenImage() GData
getSecondaryDirection() IOrientationFull3D
Returns a unit vector pointing in the orientation's secondary direction.
getSecondaryDirection() OrientationFull3D
getSecondVector() ConformationChainZigZag
getSecondVector() ConformationChainZigZag2
getSecurityOff() SVGConverter
Returns whether or not scripts will be run securely
getSeed() RandomMersenneTwister
getSeedArray() RandomMersenneTwister
getSeen() AbstractTraversal
getSegments() FFTDecomposition
getSelectedMove() MCMoveManager
getSelectedRows() DeviceTable
Returns the indices of all the selected rows on the table.
getSelectedSpecies() ModelSpeciesSelection
getSelector() DeviceSelector
getSelector() DeviceThermoSelector
getSeries(String) DisplayPlotXChart
getSet(GraphIterator) IteratorToSet
getSettableTokFromString(String) Token
getSgima() P1HardPeriodic
getShadeIndex(float, float, float) Shader
getShadeIndex(short) Graphics3D
getShadeIndexNormalized(float, float, float) Shader
getShades(int, boolean) Shader
getShades(short) Colix
getShades(short) GData
getShadesArgb(int, boolean) Colix
getShadesGreyscale(short) Colix
getShakeAgentManager() IntegratorVelocityVerletShake
getShakeTolerance() IntegratorVelocityVerletShake
getShape() MeterLocalDensity
getShape() MeterLocalMoleFraction
Returns the subvolume shape for the mole fraction calculation.
getShape() DeviceTrioControllerButton
getShape() Boundary
getShapeClassName(int, boolean) JmolConstants
getShapeOrigin() MeterLocalMoleFraction
Returns the origin of the subvolume.
getShapeVisibilityFlag(int) JmolConstants
getShearRate() IntegratorPolymer
getShearRateNumber() IntegratorPolymer
getShift() ConfigurationLammps
getShifts(Boundary, Vector, double) OverflowShift
Provides information needed so that drawing can be done of portions of
the periodic images of an atom that overflow into the volume (because the
periodic image is just outside the volume).
getShiftX() DisplayCanvas
getShiftY() DisplayCanvas
getShowBoundary() DisplayBox
Get the flag indicating if the boundary should be drawn.
getShowSlider() DeviceSlider
getShowValues() DeviceSlider
getSigma() P1WCAWall
Returns the radius.
getSigma() P2Water3P
getSigma() P2Water3PSoft
getSigma() P2Water4P
getSigma() P2Water4PSoft
getSigma() P2WaterTIP4P
getSigma() P2WaterTIP4PHardCore
getSigma() P1Wall
getSigma() P1Wall
getSigma() P1WCAPorousWall
Returns the radius.
getSigma() P1WCAWall
Returns the radius.
getSigma() P1WCAWall
Returns the radius.
getSigma() VLESim
getSigma() P22CLJQ
getSigma() P2HardAssociationCone
Accessor method for Lennard-Jones size parameter
getSigma() P2HardAssociationConeDoubleSites
Accessor method for Lennard-Jones size parameter
getSigma() P2HardAssociationConeFourSites
Accessor method for Lennard-Jones size parameter
getSigma() P2HardAssociationConeFourSitesSW
Accessor method for Lennard-Jones size parameter
getSigma() P2HardAssociationConeOneSite
Accessor method for Lennard-Jones size parameter
getSigma() P2HardAssociationConeReference
Accessor method for Lennard-Jones size parameter
getSigma() P2HardAssociationConeReferenceFourSites
Accessor method for Lennard-Jones size parameter
getSigma() P2HardAssociationConeSW
Accessor method for Lennard-Jones size parameter
getSigma() P2HC2Yukawa
Accessor methods for size and energy parameters.
getSigma() P2HSDipole
getSigma() P2LennardJones
Accessor method for Lennard-Jones size parameter.
getSigma() P2LennardJonesDreiding
Accessor method for Lennard-Jones size parameter.
getSigma() P2LJDipole
getSigma() P2LJQ
getSigma() P2LJQQ
getSigma() P2SoftSphere
Accessor method for soft-sphere size parameter.
getSigma() P2WCA
Accessor method for the size parameter.
getSigma() P2WCAP
Accessor method for the size parameter.
getSigma() P2LJDipole
getSigma() LJ
getSigma() MayerEHardSphere
Returns the HS diameter.
getSigma() MayerHardSphere
Returns the HS diameter.
getSigma() VirialB2WaterTIP4P_DHS_difference.P2WaterDHS
getSigma(int) MolecularModel2CLJQ_SpeciesCO2
getSigma(int) MolecularModel2CLJQ_SpeciesEthane
getSigma(int) MolecularModel2CLJQ_SpeciesLJ
getSigma(int) MolecularModelEMP2_SpeciesCO2
getSigma(int) MolecularModelLJ_SpeciesLJ
getSigma(int) MolecularModelLJQ_SpeciesLJ
getSigma(int) MolecularModelSKS_SpeciesAlkane
getSigma(int) MolecularModelSPCE_SpeciesH2O
getSigma(int) MolecularModelTRAPPE_SpeciesAlkane
getSigma(int) MolecularModelTrappe_SpeciesCO2
getSigma(int, int) MCMoveClusterMoleculeHSChain
getSigma(int, int) MCMoveClusterMoleculeHSChainB3
getSigma(int, int) MCMoveClusterAtomHSChain
getSigma(int, int) MCMoveClusterAtomHSChainMix
getSigma(int, int) MCMoveClusterAtomHSTree
getSigma(int, int) MCMoveClusterAtomHSTreeMix
getSigma(int, int) MCMoveClusterAtomSQWChain
getSigma(int, int) MCMoveClusterAtomSQWTree
getSigma(int, int) MCMoveClusterMoleculeHSChain
getSigmaC() P2CO2EMP
getSigmaCO() P2CO2EMP
getSigmaColloid() ConfigurationColloid
getSigmaDimension() P2HardAssociationCone
getSigmaDimension() P2HardAssociationConeDoubleSites
getSigmaDimension() P2HardAssociationConeFourSites
getSigmaDimension() P2HardAssociationConeFourSitesSW
getSigmaDimension() P2HardAssociationConeOneSite
getSigmaDimension() P2HardAssociationConeReference
getSigmaDimension() P2HardAssociationConeReferenceFourSites
getSigmaDimension() P2HardAssociationConeSW
getSigmaDimension() P2LennardJones
getSigmaDimension() P2LennardJonesDreiding
getSigmaDimension() P2ModifiedMorse
getSigmaDimension() P2Morse
getSigmaDimension() P2SoftSphere
getSigmaDimension() P2WCA
getSigmaDimension() P2WCAP
getSigmaHSRef() MolecularModel2CLJQ_SpeciesCO2
getSigmaHSRef() MolecularModel2CLJQ_SpeciesEthane
getSigmaHSRef() MolecularModel2CLJQ_SpeciesLJ
getSigmaHSRef() MolecularModelEMP2_SpeciesCO2
getSigmaHSRef() MolecularModelLJ_SpeciesLJ
getSigmaHSRef() MolecularModelLJQ_SpeciesLJ
getSigmaHSRef() MolecularModelSKS_SpeciesAlkane
getSigmaHSRef() MolecularModelSPCE_SpeciesH2O
getSigmaHSRef() MolecularModelTRAPPE_SpeciesAlkane
getSigmaHSRef() MolecularModelTrappe_SpeciesCO2
getSigmaHSRef(int) ModelSimulationEnvironment
getSigmaHSRefField(int) ViewSimEnvironmentSelection
getSigmaHSRefFieldA() ViewSimEnvironmentSelection
getSigmaHSRefFieldB() ViewSimEnvironmentSelection
getSigmaHSRefFieldC() ViewSimEnvironmentSelection
getSigmaHSRefSpecies(IMolecularModel_SpeciesFactory) ModelSimulationEnvironment
getSigmaMonomer() ConfigurationColloid
getSigmaO() P2CO2EMP
getSignalSource() MeterStructureFactor
getSignature() Graph
getSignature() GraphImpl
getSignature(Graph) GlobalFilter.SignatureMaker
getSimEnvController() ControllerSpeciesSelection
getSimId() DataStreamStore.DataPlumbing
getSimRestart() DeviceTrioControllerButton
getSimulation() DeviceTrioControllerButton
Returns the simulation affected by the buttons.
getSimulation() SimulationGraphic
getSimulation() SimulationModel
getSimulation() PotentialMasterNbrMolecular
Returns the simulation associated with this PotentialMaster
getSimulation() SimulationContainer
getSindtheta() MeterMeanField
getSint0() MeterMeanField
getSite() EnumSiteName
getSite(IAtom) NeighborSiteManager
getSiteDisplacementIndex() FindPairMoleculeIndex
getSiteDisplacementIndex(Vector) FindPairMoleculeIndexBetaN2
getSiteFactor() HSNPT.ColorSchemeDisplacement
getSiteManager() CoordinateDefinition
getSites(Space) P2WaterSzalewicz
getSitesNotParticipating(IMolecularModel_SpeciesFactory) BuilderCollectionPotential
getSitesOnSpecies() ModelSpeciesSelection
getSize() DisplayBox
Gets the size of the box graphic.
getSize() Primitive
Returns a new array with values equal to the lengths of the primitive vectors.
getSize() FiniteLattice
Returns an array with elements giving the maximum number of
index values in each dimension.
getSize() RectangularLattice
getSizeA() PrimitiveMonoclinic
getSizeA() PrimitiveOrthorhombic
getSizeA() PrimitiveOrthorhombicHexagonal
getSizeA() PrimitiveTriclinic
getSizeAB() PrimitiveHexagonal
getSizeAB() PrimitiveHexagonal2D
getSizeAB() PrimitiveTetragonal
getSizeABC() PrimitiveCubic
Returns the common length of all primitive vectors.
getSizeB() PrimitiveMonoclinic
getSizeB() PrimitiveOrthorhombic
getSizeB() PrimitiveTriclinic
getSizeC() PrimitiveHexagonal
getSizeC() PrimitiveMonoclinic
getSizeC() PrimitiveOrthorhombic
getSizeC() PrimitiveTetragonal
getSizeC() PrimitiveTriclinic
getSizeIncreaseRatio() AtomArrayList
getSizeIncreaseRatio() MoleculeArrayList
getSkewLog() AccumulatorAverageBootstrap
Returns the standard deviation of the log of the block averages, for all
block sizes.
getSkewLog() AccumulatorAverageCollapsingLog
Returns the standard deviation of the log of the block averages, for all
block sizes.
getSlab() DisplayBoxCanvasG3DSys
Get depth percentage
getSlab() DisplayPolytopeCanvasG3DSys
Get depth percentage
getSlab() GData
gets g3d slab
getSlabColor() MeshSurface
getSlabObject(int, Object, boolean, Object) MeshSurface
getSlabPercent() G3DSys
getSlabTranslucency() MeshSurface
getSlabType() MeshSurface
getSlabWithinRange(float, float) MeshSurface
getSleepPeriod() Controller
getSlider() DeviceSlider
getSlider(String) DevicePlotPoints
Returns the slider for the given parameter.
getSlitDim() BoundaryRectangularSlit
Returns index of non-periodic dimension.
getSnapshotTime() SVGConverter
Returns the document to to seek to before rasterizing.
getSoftBDcount() ClusterWheatleySoftDerivatives
getSoftBDfrac() ClusterWheatleySoftDerivatives
getSoftcount() ClusterWheatleySoftDerivatives
getSoluteMoleFraction() ConfigurationMembrane
getSoluteMoleFraction() ConfigurationMembraneWater
Returns the mole fraction of solutes within the solute chamber.
getSolutionChamberDensity() ConfigurationMembrane
getSolutionChamberDensity() ConfigurationMembraneWater
Returns the number density of the solution chamber
getSolventChamberDensity() ConfigurationMembrane
getSolventChamberDensity() ConfigurationMembraneWater
Returns the number density of the solvent chamber
getSolventThermoFrac() P2SquareWellBonded
Returns the fraction of well energy that is gained or lost by an atom
pair when they hop in or leave their well.
getSolventThermoFrac() P2SquareWellRadical
Returns the fraction of well energy that is gained or lost by an atom
pair when they hop in or leave their well.
getSources() SVGConverter
getSpace() Box
getSpace() ConfigurationLattice.MyLattice
getSpace() DataTensor.DataInfoTensor
getSpace() DataTensor.DataInfoTensorFactory
Returns the Space
getSpace() DataVector.DataInfoVector
getSpace() DataVector.DataInfoVectorFactory
Returns the Space
getSpace() BravaisLattice
getSpace() Primitive
getSpace() SpaceLattice
getSpace() Simulation
getSpace() ISpecies
getSpace() SpeciesGeneral
getSpace() SpeciesGeneralMutable
getSpace() IMolecularModel_SpeciesFactory
getSpace() MolecularModel2CLJQ_SpeciesCO2
getSpace() MolecularModel2CLJQ_SpeciesEthane
getSpace() MolecularModel2CLJQ_SpeciesLJ
getSpace() MolecularModelEMP2_SpeciesCO2
getSpace() MolecularModelLJ_SpeciesLJ
getSpace() MolecularModelLJQ_SpeciesLJ
getSpace() MolecularModelSKS_SpeciesAlkane
getSpace() MolecularModelSPCE_SpeciesH2O
getSpace() MolecularModelTRAPPE_SpeciesAlkane
getSpace() MolecularModelTrappe_SpeciesCO2
getSpacePosition() LatticePlane
Gets the position of the plane as the distance from the
origin in the direction of the normal.
getSpecialAtomName(int) JmolConstants
getSpecies() AtomType
getSpecies() BoxMoleculeCountEvent
getSpecies() MeterWidomCavity
Accessor for the species for which chemical potential is evaluated
getSpecies() DataSourcePositionedBoltzmannFactor
Returns the ISpecies for which the chemical potential is to be measured.
getSpecies() MeterDensity
getSpecies() MeterLocalMoleFraction
Accessor method to get the current value of the species index
getSpecies() MeterMoleculeTemperature
getSpecies() MeterMoleFraction
getSpecies() MeterNMolecules
getSpecies() MeterProfileByAtoms
getSpecies() MeterProfileByVolume
getSpecies() MeterWidomInsertion
Accessor for the species for which chemical potential is evaluated
getSpecies() DeviceNSelector
getSpecies() MCMoveInsertDelete
getSpecies() MCMoveSemigrand
Accessor method for the set of species that can participate in an exchange move.
getSpecies() MeterWidomInsertionCorrection
Accessor for the species for which chemical potential is evaluated
getSpecies() MeterWidomInsertionP
Accessor for the species for which chemical potential is evaluated
getSpecies() MCMoveVolumeN2
getSpecies() P0LatticeEnergyCorrec
getSpecies() MeterFlux
getSpecies() CriterionSpecies
Returns the Species accepted by this criterion.
getSpecies() CriterionSpeciesPair
Returns the Species accepted by this NeighborCriterionMolecular
getSpecies() DeviceCellNum3DSlider
getSpecies() DeviceCellNumXYSlider
getSpecies() ParmedStructure
getSpecies(int) Simulation
Returns one of the simulation ISpecies.
getSpecies(int) ModelSelectedSpecies
getSpecies(IPotentialMolecular) PotentialMaster
getSpecies1() ConfigurationZincblende
getSpecies2() ConfigurationZincblende
getSpeciesAFixed() GrainBoundaryConfiguration
getSpeciesAllocation(ISpecies) ConfigurationLatticeWithPlane
Sets the initial allocation of the species on the left side
of the plane.
getSpeciesAMobile() GrainBoundaryConfiguration
getSpeciesBFixed() GrainBoundaryConfiguration
getSpeciesBMobile() GrainBoundaryConfiguration
getSpeciesco2Potentialslist() ModelSpeciesSelection
getSpeciesCount() Simulation
getSpeciesCount1() ViewSpeciesSelection
getSpeciesCount2() ViewSpeciesSelection
getSpeciesCount3() ViewSpeciesSelection
getSpeciesDataModel() ModelSelectedSpecies
getSpeciesDataModel(int) ModelSelectedSpecies
getSpeciesDM() ControllerAlkaneLengthSelection
getSpeciesethanePotentiallist() ModelSpeciesSelection
getSpeciesh2oPotentiallist() ModelSpeciesSelection
getSpeciesID() MolecularModel2CLJQ_SpeciesCO2
getSpeciesID() MolecularModel2CLJQ_SpeciesEthane
getSpeciesID() MolecularModel2CLJQ_SpeciesLJ
getSpeciesIdentifier(int) ModelSpeciesSelection
getSpeciesIndex() CollectionPotentialAtomicLike
getSpeciesIndex() CollectionPotentialAtomicUnlike
getSpeciesIndex() CollectionPotentialMolecularLike
getSpeciesIndex() CollectionPotentialMolecularUnlike
getSpeciesIndex(int) CollectionPotentialAtomicUnlike
getSpeciesIndex(int) CollectionPotentialMolecularUnlike
getSpeciesInteractionIndex() ModelSelectedSpecies
getSpeciesJList() ViewSpeciesSelection
getSpeciesJList() ViewSpeciesSelection
getSpeciesJListListener() ViewSpeciesSelection
getSpeciesJListListener() ViewSpeciesSelection
getSpeciesList() Simulation
getSpeciesList() ModelSpeciesSelection
getSpeciesListDisplayLSM() ViewSpeciesSelection
getSpeciesListDisplayLSM() ViewSpeciesSelection
getSpeciesljPotentialslist() ModelSpeciesSelection
getSpeciesMembrane() ConfigurationMembrane
getSpeciesMembrane() ConfigurationMembraneWater
getSpeciesmethanePotentiallist() ModelSpeciesSelection
getSpeciesMoleculeCount() ModelSelectedSpecies
getSpeciesMoleculeCount(int) ModelSelectedSpecies
getSpeciesnalkanePotentiallist() ModelSpeciesSelection
getSpeciespropanePotentiallist() ModelSpeciesSelection
getSpeciesRemovalMsgBox() ViewSpeciesSelection
getSpeciesSelectedIndex() ModelSpeciesSelection
getSpeciesSelectedIndex(int) ModelSpeciesSelection
getSpeciesSelectionDM() ModelAlertMsgDialog
getSpeciesSolute() ConfigurationMembrane
getSpeciesSolute1() ConfigurationMembraneWater
getSpeciesSolute2() ConfigurationMembraneWater
getSpeciesSolvent() ConfigurationMembrane
getSpeciesSolvent() ConfigurationMembraneWater
getSpecular() GData
getSpecularExponent() GData
getSpecularPercent() GData
getSpecularPower() GData
getSphereData(int) MeshSurface
Calculates the data (faces, vertices, normals) for a sphere.
getSphericalInterpolationFraction(double, double, double, double) MeshSurface
getSpin(IAtom) MeterMeanField
getSpinner() DeviceSpinner
getSpinnerPanel() ViewSpeciesSelection
getSplines() P2QChemInterpolated
getSplitDisconnectedVirialGraphs(Graph) VirialDiagrams
getSplitDisconnectedVirialGraphs(Graph) VirialDiagramsMix2
getSplitDisconnectedVirialGraphs(Graph) VirialDiagramsPT
getSplitDisconnectedVirialGraphs(Set<Graph>) MayerIonicDiagram1qbond
getSplitDisconnectedVirialGraphs(Set<Graph>) MayerIonicDiagram2qbonds
getSplitDisconnectedVirialGraphs(Set<Graph>) MayerIonicDiagram4qbonds
getSplitDisconnectedVirialGraphs(Set<Graph>) WertheimDiagrams2SiteRho
getSplitDisconnectedVirialGraphs(Set<Graph>) WertheimDiagrams3SiteRho
getSplitGraphString(Set<Graph>, VirialDiagramsMix2, boolean) VirialCH4AlkaneEHMix
getSplitGraphString(Set<Graph>, VirialDiagramsMix2, boolean) VirialCO2AlkaneEHMix
getSplitGraphString(Set<Graph>, VirialDiagramsMix2, boolean) VirialCO2AlkaneUAMix
getSplitGraphString(Set<Graph>, VirialDiagramsMix2, boolean) VirialCO2N2Mix
getSplitGraphString(Set<Graph>, VirialDiagramsMix2, boolean) VirialN2AlkaneEHMix
getSplitGraphString(Set<Graph>, VirialDiagramsMix2, boolean) VirialN2AlkaneUAMix
getSplitGraphString(Set<Graph>, VirialDiagramsMix2, boolean) VirialN2CH4Mix
getSplitGraphString(Set<Graph>, VirialDiagramsMix2, boolean) VirialSF6LJAlkaneUAMix
getSplitGraphString(Set<Graph>, VirialDiagrams, boolean) VirialPolymerOverlapMC
getSplitGraphString(Set<Graph>, VirialDiagrams, boolean) VirialPolymerOverlapWithMD
getSplitGraphString(Set<Graph>, VirialDiagrams, boolean) VirialPolymerOverlapWithMDB3
getSplitGraphString(Set<Graph>, VirialDiagrams, boolean) VirialAlkaneEHTest
getSplitGraphString(Set<Graph>, VirialDiagrams, boolean) VirialAlkaneFull
getSplitGraphString(Set<Graph>, VirialDiagrams, boolean) VirialCO2PI
getSplitGraphString(Set<Graph>, VirialDiagrams, boolean) VirialH2PI
getSplitGraphString(Set<Graph>, VirialDiagrams, boolean) VirialHePI
getSplitGraphString(Set<Graph>, VirialDiagrams, boolean) VirialHePISysErr
getSpringConstant() P1Tension
getSpringConstant() P1Harmonic
getSpringConstant() P1HarmonicSite
getSpringConstant() P2Anharmonic
Accessor method for harmonic energy parameter
getSpringConstant() P2Harmonic
Accessor method for harmonic energy parameter
getSpringConstantDimension() P1Tension
Not implemented correctly.
getSpringConstantDimension() P1Harmonic
getSpringConstantDimension() P1HarmonicSite
getSpringConstantDimension() P2Anharmonic
Not implemented correctly.
getSpringConstantDimension() P2Harmonic
Not implemented correctly.
getSqErr(double[], double[]) FitTanh
getSqErr(double[], double[]) FitTanh
getStandardPdbHydrogenCount(int) JmolConstants
getStart() Line
getStartAtom() MCMoveClusterAtomMulti
getState() DeviceCheckBox
Returns the currents true/false state of the button.
getState() DeviceToggleButton
Returns the current true/false state of the button.
getState() DeviceToggleRadioButtons
Returns the currents true/false state of the button.
getStaticGraphics(Object, boolean) ApiPlatform
getStaticGraphics(Object, boolean) Platform
getStatus() StatusAction
getStdev() AccumulatorAverageBootstrap
Returns the standard deviation of the block averages, for all block
sizes.
getStdev() AccumulatorAverageCollapsingLog
Returns the standard deviation of the block averages, for all block
sizes.
getStdevantibiasedLog() AccumulatorAverageCollapsingLogAB
Returns the standard deviation of the log of the block averages, for all
block sizes.
getStdevLog() AccumulatorAverageBootstrap
Returns the standard deviation of the log of the block averages, for all
block sizes.
getStdevLog() AccumulatorAverageCollapsingLog
Returns the standard deviation of the log of the block averages, for all
block sizes.
getStepCount() Integrator
Returns the number of steps performed by the integrator since it was
initialized.
getStepFreq0() IntegratorOverlap
Deprecated.
getStepSize() MCMoveBoxStep
getStepSize() MCMoveStep
getStepSize() MCMoveStepDependent
returns the current step size.
getStepSizeDimension() MCMoveBoxStep
getStepSizeDimension() MCMoveStep
getStepSizeMax() MCMoveBoxStep
getStepSizeMax() MCMoveStep
getStepSizeMax() MCMoveStepDependent
Returns the maximum allowable steps size.
getStepSizeMaxDimension() MCMoveBoxStep
getStepSizeMaxDimension() MCMoveStep
getStepSizeMin() MCMoveBoxStep
getStepSizeMin() MCMoveStep
getStepSizeMin() MCMoveStepDependent
Returns the minimum allowable steps size.
getStepSizeMinDimension() MCMoveBoxStep
getStepSizeMinDimension() MCMoveStep
getStereoMode(String) EnumStereoMode
getStiffness() MCMoveChangeBondLength
getStiffness() MCMoveClusterRingRegrowOrientation
getStockComponent(char, char) MetadataImpl
getStore() Graph
getStore() GraphImpl
getStrands() FFTDecomposition
getStrands() IsFFT
getStreamsForSim(String) DataStreamResource
getStress() AtomHardStressCollector
getStress() AtomStressSource
getStress() PotentialCalculationForceSumGlass
getSubCluster() ClusterCoupledFlipped
getSubCluster() ClusterCoupledFlippedMultivalue
getSubCluster() ClusterCoupledFlippedPartial
getSubCluster() ClusterWeightAbs
getSubDataInfo() DataSourceGroup
getSubDataInfo() DataGroup.DataInfoGroupFactory
getSubDataInfo(int) DataGroup.DataInfoGroup
Returns the DataInfo corresponding to the group's given wrapped
Data object.
getSum() PotentialCalculationEnergySumEAM
Returns the current value of the energy sum.
getSum() DataSourceEnergies.PotentialCalculationEnergies
getSum() DataSourceEnergies.PotentialCalculationEnergiesEAM
getSum() PotentialCalculationDUDW
getSum() MeterWallForce.PotentialCalculationWallForce
getSum() PotentialCalculationEFSSP
Returns the current value of the energy sum.
getSum() PotentialCalculationLJSP
Returns the current value of the energy sum.
getSum() PotentialCalculationEnergySum
Returns the current value of the energy sum.
getSum() PotentialCalculationEnergySumBigDecimal
Returns the current value of the energy sum.
getSum() PotentialCalculationFSum
Returns the current value of the energy sum.
getSum() PotentialCalculationHyperVirialSum
Returns the current value of the energy sum.
getSum() PotentialCalculationMolecularVirialSum
Returns the current value of the energy sum.
getSum() PotentialCalculationPhiSum
Returns the current value of the energy sum.
getSum() PotentialCalculationPhiSumHeisenberg
Returns the current value of the energy sum.
getSum() PotentialCalculationVirialSum
Returns the current value of the energy sum.
getSum() PotentialCalculationFSum
getSum() PotentialCalculationSumquare
getSum1() DataSourceEnergies.PotentialCalculationEnergies
getSum2() DataSourceEnergies.PotentialCalculationEnergies
getSum2() DataSourceEnergies.PotentialCalculationEnergiesEAM
getSumAEE() PotentialCalculationPair
getSumJEEMJEJE() PotentialCalculationHeisenberg
getSumJEEMJEJE() PotentialCalculationMoleculeAgentSum
getSumJEEMJEJE() PotentialCalculationMoleculeAgentSumMinusIdealPair
getSumJEEMJEJE() PotentialCalculationMoleculeAgentSumPair
getSumJEEMJEJE() PotentialCalculationPair
getSumJEMUE() PotentialCalculationHeisenberg
getSumJEMUEx() PotentialCalculationHeisenberg
getSumJEMUEx() PotentialCalculationPair
getSumJEMUExIdeal() PotentialCalculationHeisenberg
getSumJEMUExSquare() PotentialCalculationHeisenberg
getSumJEMUEy() PotentialCalculationHeisenberg
getSumJEMUEy() PotentialCalculationPair
getSumJEMUEyIdeal() PotentialCalculationHeisenberg
getSumJEMUEySquare() PotentialCalculationHeisenberg
getSums() PotentialCalculationEnergySumCutoff
Returns the current value of the energy sum.
getSums() PotentialCalculationSumCutoffLS
Returns the current value of the energy sum.
getSumU_Con() PotentialCalculationMoleculeAgentSumMinusIdealPair
getSumU_Map() PotentialCalculationFreeEnergy
getSumU_Map() PotentialCalculationMoleculeAgentSumMinusIdealPair
getSumUEE() PotentialCalculationHeisenberg
getSumUEE() PotentialCalculationMoleculeAgentSum
getSumUEE() PotentialCalculationMoleculeAgentSumMinusIdealPair
getSumUEE() PotentialCalculationMoleculeAgentSumPair
getSumUEE() PotentialCalculationPair
getSurfaceArea() Cube
Returns 6*edgeLength^2
getSurfaceArea() Cuboid
getSurfaceArea() Parallelepiped
getSurfaceArea() Polyhedron
Returns the sum the area of the faces of the polyhedron
getSurfaceColor() ColorSchemeDropletSurface
getSurfaceDimension() DataProcessorInterfacialTension
Returns the dimension of the surfaces.
getSurfaceYOffset() ConfigurationCatalysis
getSurfaceYOffset() ConfigurationSAM
getSweepRadius() AtomTypeSpheroPolyhedron
getSwitchFac() P2MoleculeSoftTruncatedSwitched
getSwitchFac() P2SoftSphericalTruncatedSwitched
getSymbol() Element
getSymbol() IElement
getSystemSigmaHSRef() ModelSimulationEnvironment
getT1() HTTPSoftSphereApplet
getT2() HTTPSoftSphereApplet
getTableModel() DevicePlotPoints
getTableUpdateInterval() DataTableAverages
getTag() MeterEnthalpyVolume
getTag() MeterCavityMapped
getTag() MeterRDFMapped
getTag() MeterWidomCavity
getTag() DataDistributer
Returns the DataTag associated with this DataSplitter
getTag() DataDump
getTag() DataFork
getTag() DataGroupSplitter
Returns the DataTag associated with this DataGroupSplitter
getTag() DataPipe
getTag() DataProcessor
getTag() DataSourceAtomic
getTag() DataSourceFunction
getTag() DataSourceGroup
getTag() DataSourceMolecular
getTag() DataSourcePoints
getTag() DataSourcePositioned
getTag() DataSourcePositionedBoltzmannFactor
getTag() DataSourceRmsVelocity
getTag() DataSourceScalar
getTag() DataSourceTensorVirialHard
getTag() DataSourceUniform
getTag() DataSplitter
Returns the DataTag associated with this DataSplitter
getTag() HistogramDataSource
getTag() IDataSource
getTag() MeterDihedralAngle
getTag() MeterDipoleSumSquaredMappedAverage
getTag() MeterHyperVirial
getTag() MeterMomentumCOM
getTag() MeterPositionCOM
getTag() MeterPressureByVolumeChange.DataSourceExp
getTag() MeterPressureByVolumeChange
getTag() MeterPressureHardTensor
getTag() MeterPressureTensor
getTag() MeterPressureTensorFromIntegrator
getTag() MeterProfile
getTag() MeterProfileByAtoms
getTag() MeterProfileByVolume
getTag() MeterRDF
getTag() MeterRDFPC
getTag() MeterStructureFactor
getTag() MeterTensorVelocity
getTag() DataSourceEnergies
getTag() IntegratorPT.BoxTracker
getTag() MeterPotentialEnergyCutoff
getTag() MeterPU
getTag() MeterPUCut
getTag() MeterPUCutLS
getTag() MeterWidomInsertionCorrection
getTag() MeterMappedRdf
getTag() MeterMeanForce
getTag() MeterDensityDistribution
getTag() MeterBoltzmann
getTag() MeterBoltzmannRotPerturb
getTag() MeterNormalizedCoord
getTag() MeterNormalizedCoordBeta
getTag() MeterOrientationDistribution
getTag() MeterRotationDistributionGroup
getTag() MeterTargetRPMolecule
getTag() MeterTargetTPMolecule
getTag() DataSourceDensityFunction
getTag() DataSourceWallPressureCatalysis
getTag() MeterChainLength
getTag() MeterDeformation
getTag() AccumulatorPTensor
getTag() CorrelationSelf2.MeterCorrelationSelf2
getTag() DataSourceAlpha2
getTag() DataSourceBlockAvgCor
getTag() DataSourceCorrelation.Meter
getTag() DataSourceF
getTag() DataSourceFOld
getTag() DataSourceFs
getTag() DataSourceHisogram
getTag() DataSourceHistogramMSD
getTag() DataSourceMSD
getTag() DataSourceMSDcorP.DataSourceMSDcovP
getTag() DataSourceMSDcorP
getTag() DataSourcePercolation.Chi4Source
getTag() DataSourcePercolation
getTag() DataSourcePercolation.ImmFractionByTypeSource
getTag() DataSourcePercolation.ImmFractionSource
getTag() DataSourcePercolation.PercolationByImmFrac
getTag() DataSourcePercolation0
getTag() DataSourcePMSDHistory
getTag() DataSourceQ4
getTag() DataSourceQ4.MeterChi4
getTag() DataSourceStrings
getTag() DataSourceVAC
getTag() GlassGraphic.MeterFromDumps
getTag() MeterCorrelation
getTag() MeterCorrelationSelf
getTag() MeterGs
getTag() MeterStructureFactorStress3
getTag() StructureFactorComponentCorrelation.Meter
getTag() DataSourceTensorVirialHardProfile.DataSourceVirialProfile
getTag() MeterOrientation
getTag() DataSourceWallPressureMu
getTag() MeterMBAR
getTag() MultiharmonicGraphicMC.DataSourceAlphaChi
getTag() MultiharmonicGraphicMC.DataSourceAlphaAlpha
getTag() MultiharmonicGraphicMC.DataSourceAlphaChi
getTag() MultiharmonicGraphicMC.DataSourceAlphaFE
getTag() MultiharmonicGraphicMC.DataSourceFunctionRaw
getTag() MeterUmbrella
getTag() MultiharmonicGraphicMC.DataSourceAlphaAlpha
getTag() MultiharmonicGraphicMC.DataSourceAlphaChi
getTag() MeterClusterSizes
getTag() MeterDimerFraction
getTag() MeterFlux
getTag() MeterOsmoticPressure
getTag() MeterTilt
getTag() DataCollector
getTag() DataSourceFE
getTag() DataSourceFEHistogram
getTag() DataSourceImposedFEFit
getTag() DataSourceImposedFEHistogram
getTag() DataSourcePMu
getTag() DataSourcePN
getTag() MeterAtomicDisplacement
getTag() MeterBoltzmann
getTag() MeterBoltzmannHarmonic
getTag() MeterBoltzmannHTTP
getTag() MeterBoltzmannTarget
getTag() MeterDADB
getTag() MeterDDP
getTag() MeterDirectSamplingHarmonic
getTag() MeterDirectSamplingTarget
getTag() MeterDP
getTag() MeterHarmonicSingleEnergy
getTag() MeterNormalMode
getTag() MeterOverlapSwitch
getTag() MeterPlaneSlip
getTag() MeterSamplingHarmonic
getTag() MeterSamplingTarget
getTag() MeterSolidDA
getTag() MeterSolidDACut
getTag() MeterSolidMirror
getTag() MeterSolidProps
getTag() MeterSolidPropsLJ
getTag() MeterTargetTP
getTag() MeterTilt
getTag() MeterTiltHistogram
getTag() MeterTiltRotation
getTag() MeterTiltRotationHistogram
getTag() MeterTiltRotationStdev
getTag() MeterWorkBennetHarmonic
getTag() MeterWorkBennetTarget
getTag() MeterWorkHarmonicBennet
getTag() MeterWorkHarmonicPhaseSpace
getTag() MeterWorkHarmonicTargetandReweighting
getTag() MeterWorkHarmonicUmbrella
getTag() MeterWorkTargetBennet
getTag() MeterWorkTargetHarmonicandReweighting
getTag() MeterWorkTargetPhaseSpace
getTag() MeterWorkTargetUmbrella
getTag() MeterWorkUmbrellaHarmonic
getTag() MeterWorkUmbrellaTarget
getTag() MeterOverlap
getTag() MeterDipoleMoment
getTag() MeterEnergyMeanField
getTag() MeterMappedAveraging
getTag() MeterMappedAveraging3Pair
getTag() MeterMappedAveragingCorrelation
getTag() MeterMappedAveragingCV
getTag() MeterMappedAveragingFreeEnergy
getTag() MeterMappedAveragingPair
getTag() MeterMappedAveragingPairExcess
getTag() MeterMappedAveragingSum
getTag() MeterMappedAveragingVSum
getTag() MeterMappedAveragingVSum3Pair
getTag() MeterMappedAveragingVSumPair
getTag() MeterMeanField
getTag() MeterBondLength
getTag() MeterSamplingWeight
getTag() MeterVirial
getTag() MeterVirialBD
getTag() MeterVirialBDBin
getTag() MeterVirialExternalField
getTag() MeterVirialExternalFieldConfined
getTag() MeterVirialExternalFieldOverlapConfined
getTag() MeterVirialExternalFieldOverlapConfinedRho
getTag() MeterVirialExternalFieldOverlapConfinedSW
getTag() MeterVirialExternalFieldOverlapRho
getTag() MeterVirialExternalFieldRho
getTag() MeterVirialExternalFieldSW
getTag() MeterVirialIC
getTag() MeterVirialSWWE
getTag(int) DataProcessorBounds
getTag(int) MeterTiltRotationHistogram
getTag(AccumulatorAverage.StatType) AccumulatorAverage
getTag(AccumulatorAverage.StatType) AccumulatorRatioAverageCovariance
getTag(AccumulatorAverage.StatType) AccumulatorRatioAverageCovarianceFull
getTag(AccumulatorAverageBlockless.StatType) AccumulatorAverageBlockless
getTags() DataInfo
Returns the array of tags held by this DataInfo instance.
getTags() DataInfoFactory
getTags() IDataInfo
Returns the array of tags held by this DataInfo instance.
getTags() IDataInfoFactory
Returns the factory's tags as an array.
getTargetAtom() IteratorDirective
getTargetCluster() MeterVirialBDBin
getTargetCluster() MeterVirialBDBinMultiThreaded
getTargetCluster() MeterVirialBinMultiThreaded
getTargetCluster() MeterVirialEBinMultiThreaded
getTargetDataInterval() SimOverlapModule
getTargetDensity() BoxInflate
Returns the target density of the action.
getTargetMolecule() IteratorDirective
getTargetSource() DataOverlap
Returns object capable of retrieving data from the target system.
getTemperature() AtomActionRandomizeVelocity
getTemperature() BoxQuench
Returns the quench temperature.
getTemperature() BoxRandomizeMomenta
getTemperature() BoxScaleMomenta
getTemperature() DeviceThermoSlider
getTemperature() DeviceThermoSliderGEMC
getTemperature() IntegratorBox
getTemperature() IntegratorManagerMC
getTemperature() MeterTargetRPMolecule
getTemperature() MeterTargetTPMolecule
getTemperature() BoltzmannProcessor
getTemperature() DataProcessorBoltzmannFactor
getTemperature() MCMoveAtomCoupledBennet
getTemperature() MCMoveAtomCoupledUmbrella
getTemperature() MeterBoltzmannHarmonic
getTemperature() MeterBoltzmannHTTP
getTemperature() MeterDDP
getTemperature() MeterDirectSamplingHarmonic
getTemperature() MeterDP
getTemperature() MeterTargetTP
getTemperature() MeterWorkHarmonicBennet
getTemperature() MeterWorkHarmonicPhaseSpace
getTemperature() MeterWorkHarmonicTargetandReweighting
getTemperature() P2LJDipole
getTemperature() P2LJQ
getTemperature() P2LJQQ
getTemperature() MaxwellBoltzmann.Distribution
getTemperature() ClusterSum
getTemperature() ClusterSumNonAdditiveTrimerEnergy
getTemperature() ClusterSumPolarizable
getTemperature() ClusterSumPolarizableWertheimProduct
getTemperature() ClusterSumPolarizableWertheimProduct4Pt
getTemperature() ClusterSumPolarizableWertheimProduct4PtFinal
getTemperature() ModelSimulationEnvironment
getTemperature() ModelTemperatureAndSteps
getTemperatureDimension() IntegratorBox
getTemperatureDimension() MaxwellBoltzmann.Distribution
getTemperatureField() ViewSimEnvironmentSelection
getTetherLength() P2Tether
Accessor method for the tether distance
getTetherLengthDimension() P2Tether
getTextBackground() DeviceBox
getTextField() DeviceSlider
getTextPixels(String, JmolFont, Object, Object, int, int, int) ApiPlatform
getTextPixels(String, JmolFont, Object, Object, int, int, int) Platform
getThermostat() IntegratorMD
getThermostatInterval() IntegratorMD
getTheta() BiasVolumeSphereOriented
getTheta() BiasVolumeSphereOrientedDoubleSites
getTheta() P2HardAssociationGCPMReference
getTheta() PNWaterGCPMThreeSite
getTheta() P2HardAssociationCone
Accessor method for angle describing width of cone.
getTheta() P2HardAssociationConeDoubleSites
Accessor method for angle describing width of cone.
getTheta() P2HardAssociationConeFourSites
Accessor method for angle describing width of cone.
getTheta() P2HardAssociationConeFourSitesSW
Accessor method for angle describing width of cone.
getTheta() P2HardAssociationConeOneSite
Accessor method for angle describing width of cone.
getTheta() P2HardAssociationConeReference
Accessor method for angle describing width of cone.
getTheta() P2HardAssociationConeReferenceFourSites
Accessor method for angle describing width of cone.
getTheta() P2HardAssociationConeSW
Accessor method for angle describing width of cone.
getTheta() P2QChemInterpolated
getTheta() MolecularModelSKS_SpeciesAlkane
getTheta() MolecularModelTRAPPE_SpeciesAlkane
getTheta() Quaternion
getTheta0() MeterMeanField
getThetaDimension() P2HardAssociationCone
getThetaDimension() P2HardAssociationConeDoubleSites
getThetaDimension() P2HardAssociationConeFourSites
getThetaDimension() P2HardAssociationConeFourSitesSW
getThetaDimension() P2HardAssociationConeOneSite
getThetaDimension() P2HardAssociationConeReference
getThetaDimension() P2HardAssociationConeReferenceFourSites
getThetaDimension() P2HardAssociationConeSW
getThetaDirected(Point4f) Quaternion
getThetaDirectedV(Vector3f) Quaternion
getThetaDot(IAtom) MeterMeanField
getThetaFrac() MCMoveVolumeSolidNPTMolecularOriented
getThetaRadians() Quaternion
getTHigh() ColorSchemeTemperature
getThreshold() ConfigFromFileLAMMPS.AtomTestDeviation
getTilt() AkimaSplineSmootherApp.PlotAction
getTilt() AkimaSplineSmootherDyApp.PlotAction
getTimeBD() ClusterWheatleySoftDerivatives
getTimeDataSource() AccumulatorHistory
Returns the DataSource used for the "time" component of the history.
getTimer() DisplayTimer
Returns the data source used to count the time, to permit
access to its methods for reset, etc.
getTimeStep() IntegratorMD
getTitle() DeviceToggleRadioButtons
getTLow() ColorSchemeTemperature
getTLowDimension() ColorSchemeTemperature
getTM() G3DSys
getTokenFromName(String) Token
getTokens(String) Parser
getTokensAt(String, int) Parser
getTokensLike(String) Token
getTokFromName(String) Token
getTolerance() ActionMinimizeEnergy
getTolerance() FitTanh
getTolerance() FitTanh
getToNode(byte) Graph
getToNode(byte) GraphImpl
getToPixels() DisplayBox
getToPixels() DisplayPolytope
getTorsionpotentiala0() MolecularModelSKS_SpeciesAlkane
getTorsionpotentiala0() MolecularModelTRAPPE_SpeciesAlkane
getTorsionpotentiala1() MolecularModelSKS_SpeciesAlkane
getTorsionpotentiala1() MolecularModelTRAPPE_SpeciesAlkane
getTorsionpotentiala2() MolecularModelSKS_SpeciesAlkane
getTorsionpotentiala2() MolecularModelTRAPPE_SpeciesAlkane
getTorsionpotentiala3() MolecularModelSKS_SpeciesAlkane
getTorsionpotentiala3() MolecularModelTRAPPE_SpeciesAlkane
getTotalCount() MeterVirialBDBinMultiThreaded
getTotalCount() MeterVirialBinMultiThreaded
getTotalCount() MeterVirialEBinMultiThreaded
gettotcount() ClusterCoupledFlippedMultivalue
getTracker() MCMove
getTranscoder() DestinationType
Returns a transcoder object of the result image type.
getTransformationTensor() AtomActionTransformed
getTransformationTensor() AtomActionTransformed
getTransformedVertexVectors() Graphics3D
getTransformedVertexVectors() GData
getTransformMatrix4(List<Point3f>, List<Point3f>, Matrix4f, Point3f) Measure
getTranslationVector() AtomActionTranslateBy
Returns the translation vector, the distance that the
atom will be moved by this action.
getTranslationVector() MoleculeActionTranslateTo
Returns the vector that was used to accomplish the most recent translation action.
getTrimThreshold() AtomArrayList
getTrimThreshold() MoleculeArrayList
getTrueLabel() ActionToggle
getTrueLabel() DeviceToggleButton
getTrueLabel() DeviceToggleRadioButtons
getTruncatedPotential() Potential0Lrc
Returns the potential whose truncation this lrcPotential exists to correct.
getTruncation() PotentialGroupSoft
getTruncationRadius() P2MoleculeSoftTruncatedSwitched
Accessor method for the radial cutoff distance.
getTruncationRadius() P2MoleculeTruncated
Accessor method for the radial cutoff distance.
getTruncationRadius() P2SoftSphericalTruncated
Accessor method for the radial cutoff distance.
getTruncationRadius() P2SoftSphericalTruncatedSwitched
Accessor method for the radial cutoff distance.
getTruncationRadius() P2SoftTruncated
Accessor method for the radial cutoff distance.
getTruncationRadius() BoundaryDeformablePeriodic
getTruncationRadiusDimension() P2MoleculeSoftTruncatedSwitched
Returns the dimension (length) of the radial cutoff distance.
getTruncationRadiusDimension() P2MoleculeTruncated
Returns the dimension (length) of the radial cutoff distance.
getTruncationRadiusDimension() P2SoftSphericalTruncated
Returns the dimension (length) of the radial cutoff distance.
getTruncationRadiusDimension() P2SoftSphericalTruncatedSwitched
Returns the dimension (length) of the radial cutoff distance.
getTruncationRadiusDimension() P2SoftTruncated
Returns the dimension (length) of the radial cutoff distance.
getTSelement() SimpleElementForSimilarSpecies
getTunable() MCMoveStepTracker
getType() Atom
getType() IAtom
getType() Edge
getType() EdgeImpl
getType() MetadataImpl
getType() NodeImpl
getType() Metadata
getType() Node
getType() IMolecule
Returns the ISpecies of this IMolecule.
getType() Molecule
getTypeA() SelfAssemblySim
getTypeB1() SelfAssemblySim
getTypeB2() SelfAssemblySim
getTypeByName(String) ISpecies
Get the AtomType with a given name used in this Species.
getTypeByName(String) SpeciesGeneral
getTypeByName(String) SpeciesGeneralMutable
getTypeInteraction() WriteConfigurationP2DLPOLY
getTypeMax() DataSourceUniform
Accessor method for the type of the right limit.
getTypeMin() DataSourceUniform
Accessor method for the type of the left limit.
getTypes() PotentialArrayByType
getU_DipoleDipole() P2WaterTIP4PHardCore
getU123ADD(P2QChemInterpolated, double, double, double) P3AdditiveQChem
getU123SCF(double, double, int) P3QChem
getUa2(int) AccumulatorOverlapAverageUa2
Returns average value of expression used to determine optimal
Bennet parameter (value[1]/(value[1]+expX[iParam]).
getUDisp(double) P2QChemInterpolated
getUlat0(int, int) SoftSphereSolidEOS
getUlat0(int, int) SoftSphereSolidEOSCalculator
getULatFunction() MCMoveVolumeMonoclinicScaled
getULatFunction() MCMoveVolumeSolid
getULatFunction() MCMoveVolumeSolidNPTMolecular
getULatFunction() MeterDDP
getULatFunction() MeterDP
getULatTruncFunction() MCMoveVolumeSolid
getULJAtDipoleCenter() P2WaterTIP4PHardCore
getUnit() Device
getUnit() DimensionedDoubleEditor
getUnit() DisplayTextBox
Returns the physical units of the displayed value.
getUnit() DisplayTextBoxesCAE
getUnit(int) DisplayTable
Returns the unit assign to the i-th column (as defined before any
transpose).
getUnit(UnitSystem) Angle
getUnit(UnitSystem) Area
getUnit(UnitSystem) Charge
getUnit(UnitSystem) CompoundDimension
getUnit(UnitSystem) Current
getUnit(UnitSystem) Dimension
Returns the unit of this dimension as derived in the given system of units.
getUnit(UnitSystem) DimensionRatio
getUnit(UnitSystem) Dipole
getUnit(UnitSystem) ElectricPotential
getUnit(UnitSystem) Energy
getUnit(UnitSystem) Force
getUnit(UnitSystem) Fraction
getUnit(UnitSystem) Frequency
getUnit(UnitSystem) Length
getUnit(UnitSystem) LuminousIntensity
getUnit(UnitSystem) Mass
getUnit(UnitSystem) Momentum
getUnit(UnitSystem) Null
Returns UNIT, regardless of the given unit system.
getUnit(UnitSystem) Power
getUnit(UnitSystem) Pressure
getUnit(UnitSystem) Pressure2D
getUnit(UnitSystem) Quantity
getUnit(UnitSystem) Temperature
getUnit(UnitSystem) Time
getUnit(UnitSystem) Undefined
Returns UNIT, regardless of the given unit system.
getUnit(UnitSystem) Velocity
getUnit(UnitSystem) Viscosity
getUnit(UnitSystem) Volume
getUnit(UnitSystem) Wavenumber
getUnitVectors(double[][], Vector3f[], float[]) Eigen
getUnscreenedCount() MeterVirialBDBin
getUpdatedDimensions() ConfigurationFileXYZ
getUpdateInterval() NeighborListManagerMolecular
Returns the interval for which neighbor update checks are performed.
getUpdateInterval() NeighborListManager
Returns the interval for which neighbor update checks are performed.
getUpList() AtomNeighborLists
Returns an array of uplist-neighbor-atom lists.
getUpList() MoleculeNeighborLists
Returns an array of uplist-neighbor-molecule lists.
getUpList(IAtom) NeighborListManager
getUpList(IMolecule) NeighborListManagerMolecular
getUpNeighbors() RectangularLattice
getUpsilon(int, double, double) SoftSphereSolidEOS
getUpsilon(int, double, double) SoftSphereSolidEOSCalculator
getuReactCO() ReactionManagerCO
getuReactCORev() ReactionManagerCO
getURI() SVGConverterDocumentSource
getURI() SVGConverterFileSource
getURI() SVGConverterSource
Returns a URI string corresponding to this source
getURI() SVGConverterURLSource
getUSCF(double) P2QChemInterpolated
getUserStylesheet() SVGConverter
getUseSurfaceOnly() P2Cohesion
getUSums() PotentialCalculationSumCutoff
Returns the current value of the energy sum.
getV() MyEigenvalueDecomposition
Return the eigenvector matrix
getVacancyFraction(double) HardSphereSolid
Returns the fraction of lattice sites with a vacancy for the given
lattice density.
getVacancyFreeEnergy(double) HardSphereSolid
Returns the Helmholtz free energy difference due to the presence of
vacancies at the given lattice density.
getVacancyPressure(double) HardSphereSolid
Returns the difference between the pressure with vacancies from the
pressure without vacancies for the given lattice density.
getValidate() SVGConverter
getValue() ConfigFromFileLAMMPS.ModifierConfiguration
getValue() CommandPropertyValueImpl
getValue() CommandValueImpl
getValue() CommandVariableValueImpl
getValue() ValueImpl
getValue() Parser.CommandPropertyValue
getValue() Parser.CommandValue
getValue() Parser.CommandVariableValue
getValue() Parser.Value
getValue() Coefficient
getValue() CoefficientImpl
getValue() DeviceBoxValueChangedEvent
getValue() DeviceSlider
getValue() DeviceSpinner
getValue() DimensionedDoubleEditor
Returns the value in simulation units.
getValue() LjMd3D.ValueCache
getValue() ValueCache
getValue() Modifier
Gets the current value of the property.
getValue() ModifierFunctionWrapper
Applies inverse of function to property before returning it.
getValue() ModifierGeneral
getValue() ModifierNMolecule
getValue() ModifyAction
getValue() ModifierPMu
getValue() ColloidGraphic.WallRangeModifier
getValue() LatticeEditor.NModifier
getValue() IntegratorDCVGCMD.Mu1Modulator
getValue() IntegratorDCVGCMD.Mu2Modulator
getValue() DropletGraphic.ModifierBoxSize
getValue() InterfacialSWGraphic.ModifierBoxSize
getValue() MuGraphic.ModifierAtomDiameter
getValue() MuGraphic.ModifierEpsilon
getValue() MuGraphic.ModifierLambda
getValue() NucleationGraphic.ModifierDensity
getValue() ModifierPistonPressure
getValue() PistonCylinderGraphic.ModifierAtomDiameter
getValue() PistonCylinderGraphic.ModifierPistonDensity
getValue() ReverseOsmosisGraphic.ModifierAtomDiameter
getValue() ReverseOsmosisGraphic.ModifierEpsilon
getValue() ReverseOsmosisWaterGraphic.ModifierAtomDiameter
getValue() ReverseOsmosisWaterGraphic.ModifierEpsilon
getValue() ReverseOsmosisWaterGraphic.ModifierSoluteCharge
getValue() SamGraphic.ModifierWallPosition
getValue() SwmdGraphic.ModifierAtomDiameter
getValue() ModifierCells3D
getValue() ModifierXCells2D
getValue() ModifierYCells2D
getValue() ModifierTPI
getValue(double, double, double) FunctionCosIntegral
thetaDot for mean-field mapping of XY model, calculation of correlation function via 2nd free-energy derivative
getValue(int) IData
Returns the i-th data value.
getValue(int) DataDouble
Returns this instance's value if argument is 0, otherwise throw exception
getValue(int) DataDoubleArray
Returns the i-th value of the wrapped array.
getValue(int) DataDoubleBDArray
Returns the i-th value of the wrapped array.
getValue(int) DataGroup
getValue(int) DataTable
Returns the i-th data value, where the values are numbered by counting down the first column,
then the next, and so on.
getValue(int) DataTensor
Returns the i-th tensor value, indexing across the first row, then the
second, etc.
getValue(int) DataVector
Returns the i-th vector value.
getValue(int[]) DataDoubleArray
Returns the element of the array indicated by the given set of indices.
getValue(int[]) DataDoubleBDArray
Returns the element of the array indicated by the given set of indices.
getValue(int, int) DataSinkTable
getValue(String) Grabber.ActionCornerSetter
getValueAt(int, int) DeviceTableModelGeneric
Get the value in the given table cell.
getValueAt(int, int) ModelMoleculeListDisplayTable_new
getValueAt(int, int) ModelMoleculeListDisplayTable
getValueAt(int, int) ModelPotParamDisplayTable
getValueProperties() Wrapper
getValues() DestinationType
Defines valid image types.
getValues() Wrapper
getValueString(Object, Field) ParameterParser
Returns the value of obj's field as a string if this parser is
appropirate for the given field, or throws an exception if it's not.
getValueString(Field) ParameterBase
Actually writes field name and value to a file using fileWriter.
getVanderwaalsMar(int, EnumVdw) Elements
getVaporColor() ColorSchemeLiquidVapor
getVar() MeterVirialBinMultiThreaded.MyData
getVar(int) MeterVirialEBinMultiThreaded.MyData
getVar(MathContext) MeterVirialBDBinMultiThreaded.MyData
getVarDouble() MeterVirialBDBinMultiThreaded.MyData
getVariable() AssignmentImpl
getVariable() CommandVariableImpl
getVariable() CommandVariableValueImpl
getVariable() Parser.Assignment
getVariable() Parser.CommandVariable
getVariable() Parser.CommandVariableValue
getVariable(Object) ScriptVariable
getVariableAD(double[]) ScriptVariable
getVariableAF(float[]) ScriptVariable
getVariableAFF(float[][]) ScriptVariable
getVariableAI(int[]) ScriptVariable
getVariableAII(int[][]) ScriptVariable
getVariableAP(Point3f[]) ScriptVariable
getVariableAS(String[]) ScriptVariable
getVariableAV(ScriptVariable[]) ScriptVariable
getVariableList(List<?>) ScriptVariable
getVariableMap(Object) ScriptVariable
getVariableNames() Environment
getVariableNames() EnvironmentImpl
getVariableValue(String) Environment
getVariableValue(String) EnvironmentImpl
getVdwLabel() EnumVdw
getVdwType(String) EnumVdw
getVdwType2(String) EnumVdw
getVector() Quaternion
Returns the vector part of the Quaternion as Vector
getVector(int) Quaternion
getVectorAsDoubleArray() Quaternion
Returns the vector associated with the Quaternion as a double array
getVectorMagnitude() Quaternion
Returns the magnitude of the vector associated with the Quaternion
getVectorScale() BoxInflate
Returns the current value of the inflation scale in each dimension.
getVectorsFromFile(String) ArrayReader1D
getVectorsFromFile(String) ArrayReader1D
getVelocity() AtomLeafDynamic
getVelocity() IAtomKinetic
getVelocity() IMoleculeKinetic
getVelocity() MoleculeOrientedDynamic
getVelocityAverage(IMolecule) AtomGroupVelocityAverage
Returns the mass-average velocity of the given Atom and
all its children.
getVertex1() Triangle
getVertex2() Triangle
getVertex3() Triangle
getVertexCount() Polytope
Number of vertices in the polytrope.
getVertexCount(int) Geodesic
getVertexVector(int) Geodesic
getVertexVectors() Geodesic
getVertexVectors() Normix
getVertGBC() SimulationPanel
getVertices() AtomTypeSpheroPolyhedron
getVertices() LineSegment
getVertices() Polytope
Returns an array of all vertices of the polytrope.
getVertices() MeshSurface
getVib0(int, int) SoftSphereSolidEOS
getVib0(int, int) SoftSphereSolidEOSCalculator
getViewSpeciesSelection() AppViewMixtureBuilder
getVirialGraphs() MayerIonicDiagram1qbond
getVirialGraphs() MayerIonicDiagram2qbonds
getVirialGraphs() MayerIonicDiagram4qbonds
getVirialGraphs() VirialDiagrams
getVirialGraphs() VirialDiagramsPT
getVirialGraphs() WertheimDiagrams2SiteRho
getVirialGraphs() WertheimDiagrams3SiteRho
getVirialProfile() DataSourceTensorVirialHardProfile
Current value of the meter, obtained by dividing sum of collision virial contributions by time elapsed since last call.
getVirialSum() PotentialCalculationSolidSuper
getVirialSum() PotentialCalculationSolidSuperCut
getVolume() Circle
Returns the volume for the present sphere radius.
getVolume() Cube
Returns edgeLength^3.
getVolume() Cuboid
getVolume() Hypersphere
getVolume() LineSegment
getVolume() Parallelepiped
Calculated parallelepiped volume using (a X b) .
getVolume() Point
Returns zero.
getVolume() Polygon
Returns the 2-D volume of the polygon, which is its area
getVolume() PolyhedronGeneral
Returns the 3-D volume of the polyhedron, which is its conventional volume
getVolume() Polytope
Returns the (hyper)volume enclosed by the polytope.
getVolume() Shape
Returns the (hyper-)volume of the enclosed region.
getVolume() Sphere
Returns the volume for the present sphere radius.
getVolume() TruncatedOctahedron
getVSums() PotentialCalculationSumCutoff
Returns the current value of the energy sum.
getVZero() P2Yukawa
getW() P1ImageHarmonic
getW(int) ClusterOperations
Returns all diagrams of order n in the sum [eta(r) + b(r)] (i.e., the sum of the indirect correlation
function and the bridge function).
getWallDim() P1WCAWall
getWallDim() P1WCAWall
getWallDim() P1WCAWall
getWallForce() IPotentialCalculationWallForce
getWallForce() PotentialCalculationForceSumWallForce
getWallForce() PotentialCalculationTorqueSumWallForce
getWallForce() PotentialCalculationForceSumWall
getWallPosition() P1WCAWall
getWallPosition() CriterionPositionWall
Returns the position of the wall.
getWallPosition() P1HardMovingBoundary
getWallPositionDimension() CriterionPositionWall
getWallPositionDimension() P1HardMovingBoundary
getWallPotential() PotentialCalculationForceSumWall
getWallVelocity() P1HardMovingBoundary
getWallVelocityDimension() P1HardMovingBoundary
getWaveVectorFactory() CalcJacobian
getWaveVectorFactory() LatticeSumMolecularCrystal
getWaveVectorFactory() MeterNormalMode
getWaveVectorFactory() NormalModes
Returns a factory that provides the wave vectors and coefficients for
the periodic system.
getWaveVectorFactory() NormalModes1DHR
getWaveVectorFactory() NormalModes2D
getWaveVectorFactory() NormalModes3D
getWaveVectorFactory() NormalModesFromFile
getWaveVectorFactory() NormalModesMolecular
getWaveVectorFactory() NormalModesPotential
getWaveVectorFactory() NormalModesSoftSpherical
getWaveVectorNum() DeviceWaveVectorSlider
getWaveVectorNum() IntegratorHarmonic
getWaveVectors() MeterStructureFactor
getWaveVectors() IntegratorHarmonic
getWaveVectors() MeterNormalMode
getWaveVectors() NormalModesVariable
getWaveVectors() WaveVectorFactory
Returns the wave vectors generated by makeWaveVectors
getWaveVectors() WaveVectorFactory1D
getWaveVectors() WaveVectorFactory2D
getWaveVectors() WaveVectorFactoryFcc
getWaveVectors() WaveVectorFactoryFromFile
getWaveVectors() WaveVectorFactorySimple
getWeight() ClusterDiagram
getWeightCoefficients() ClusterMultivalueUmbrella
getWeightCoefficients() ClusterWeightUmbrella
getWeights() ClusterSum
getWeightUpdateInterval() IntegratorTMMC
Accessor method for number of doStep calls between updating of weights.
getWellCutoffFactor() P2HardAssociationCone
Accessor method for attractive-well diameter divided by sigma
getWellCutoffFactor() P2HardAssociationConeDoubleSites
Accessor method for attractive-well diameter divided by sigma
getWellCutoffFactor() P2HardAssociationConeFourSites
Accessor method for attractive-well diameter divided by sigma
getWellCutoffFactor() P2HardAssociationConeFourSitesSW
Accessor method for attractive-well diameter divided by sigma
getWellCutoffFactor() P2HardAssociationConeOneSite
Accessor method for attractive-well diameter divided by sigma
getWellCutoffFactor() P2HardAssociationConeSW
Accessor method for attractive-well diameter divided by sigma
getWellCutoffFactorDimension() P2HardAssociationCone
getWellCutoffFactorDimension() P2HardAssociationConeDoubleSites
getWellCutoffFactorDimension() P2HardAssociationConeFourSites
getWellCutoffFactorDimension() P2HardAssociationConeFourSitesSW
getWellCutoffFactorDimension() P2HardAssociationConeOneSite
getWellCutoffFactorDimension() P2HardAssociationConeSW
getWellDiameter() P2HardAssociation
Accessor for well diameter.
getWellDiameterDimension() P2HardAssociation
getWellEdgeCount() ClusterWheatleyExtendSW
getWellEpsilon() P2HardAssociationCone
Accessor method for attractive-well depth parameter.
getWellEpsilon() P2HardAssociationConeDoubleSites
Accessor method for attractive-well depth parameter.
getWellEpsilon() P2HardAssociationConeFourSites
Accessor method for attractive-well depth parameter.
getWellEpsilon() P2HardAssociationConeFourSitesSW
Accessor method for attractive-well depth parameter.
getWellEpsilon() P2HardAssociationConeOneSite
Accessor method for attractive-well depth parameter.
getWellEpsilon() P2HardAssociationConeSW
Accessor method for attractive-well depth parameter.
getWellEpsilonDimension() P2HardAssociationCone
getWellEpsilonDimension() P2HardAssociationConeDoubleSites
getWellEpsilonDimension() P2HardAssociationConeFourSites
getWellEpsilonDimension() P2HardAssociationConeFourSitesSW
getWellEpsilonDimension() P2HardAssociationConeOneSite
getWellEpsilonDimension() P2HardAssociationConeSW
getWidth() SVGConverter
getWindow(Container) Platform
getWrapped() Wrapper
getWrappedClass() Wrapper
getWrappedCriterion() CriterionAdapter
Returns the criterion wrapped by this adapter
getWrappedCriterion() CriterionAdapterMolecular
Returns the criterion wrapped by this adapter
getWrappedId() Wrapper
getWrappedModifier() ModifyAction
getWrappedModifier() ModifyBooleanAction
getWrappedPotential() P2XOrder
getWrappedPotential() P2HardWrapper
getWrappedPotential() P2MoleculeMonatomic
getWrappedPotential() P2MoleculeSoftTruncatedSwitched
Returns the wrapped potential.
getWrappedPotential() P2MoleculeTruncated
Returns the wrapped potential.
getWrappedPotential() P2SoftSphericalTruncated
Returns the wrapped potential.
getWrappedPotential() P2SoftSphericalTruncatedShifted
Returns the wrapped potential.
getWrappedPotential() P2SoftSphericalTruncatedSwitched
Returns the wrapped potential.
getWrappedPotential() P2SoftTruncated
Returns the wrapped potential.
getWrappedRandom() RandomNumberGenerator
getWrapper(Object) SimulationModel
getWrapper(Object, SimulationModel) WrapperIndex
getWrapperById(long) SimulationModel
getWrapperClass(String) ReadParameters
getWriteInterval() DataLogger
getWriteOnFinishDataSource() DataLogger
getWriteScale() DisplayCanvas
getWriteVelocity() WriteConfigurationDLPOLY
getWriteVelocity() WriteConfigurationP2DLPOLY
getX() Ball
getX() Ellipse
getX(int) Vector
Vector components corresponding to the given index.
getX(int) Vector1D
getX(int) Vector2D
getX(int) Vector3D
getX(int) VectorND
getX0() PotentialCalculationMappedRdf
getX0() PotentialCalculationMappedEnergy
getX0() PotentialCalculationMappedVirial
getX0() PotentialCalculationMappedVirialV
getX0() P1Harmonic
getX0Dimension() P1Harmonic
getXCellModifier() DeviceCellNumXYSlider
getXCellNum() DeviceCellNumXYSlider
getXDataSource() MeterCavityMapped
getXDataSource() MeterRDFMapped
getXDataSource() MeterDihedralAngle
getXDataSource() MeterProfileByVolume
getXDataSource() MeterRDF
getXDataSource() MeterRDFPC
getXDataSource() PotentialCalculationRDF
getXDataSource() DataFunction.DataInfoFunction
getXDataSource() DataFunction.DataInfoFunctionFactory
Returns a copy of array of independent DataInfo.
getXDataSource() MeterMappedRdf
getXDataSource() PotentialCalculationMappedRdf
getXDataSource() MeterCorrelation
getXDataSource() MeterGs
getXDataSource() MeterBondLength
getXMax() DataSourceUniform
Accessor method for the right limit of the range.
getXMin() DataSourceUniform
Accessor method for the left limit of the range.
getXRange() Histogram
Returns the range of x values (min and max) used in the histogram.
getXRange() HistogramDiscrete
getXRange() HistogramNotSoSimple
getXRange() HistogramReweightedData
getXRange() HistogramSimple
getXRot() DisplayCanvas
getXSource() DataSourceFunction
Returns the DataSourceUniform instance that generates the x values.
getXValues() History
Returns an array containing the x values that have been added to the
History.
getXValues() HistoryCollapsing
getXValues() HistoryComplete
getXValues() HistoryScrolling
getXValues() HistoryStatistics
getXzOrientationTensor() CoordinateDefinitionNitrogen
getY() Ball
getY() Ellipse
getYCellModifier() DeviceCellNumXYSlider
getYCellNum() DeviceCellNumXYSlider
getYesButton() ViewAlertMsgBoxSpeciesRemoval
getyOrientationTensor() CoordinateDefinitionNitrogen
getYRot() DisplayCanvas
getZ() P1WCAPorousWall
getZ() Ball
getZ() Ellipse
getZ1() P2ModifiedMorse
getZ2() P2ModifiedMorse
getZero() BigValue
getZero() IBigValue
Returns an instance of the class representing the value zero.
getZero() MyBigDecimal
getZFraction() MyMCMove
Returns the zFraction.
getZFraction() MyMCMove
getZFraction() MyMCMove
Returns the zFraction.
getZoom() DisplayCanvas
ghostBox LatticeSumCrystalMolecular
ghostBox MinimizationBetaNitrogenModelLS
ghostBox MinimizeBetaNitrogenLatticeParameterLSFromFile
gi P2CO2H2OWheatley.P2CO2H2OSCTI
gi P2CO2Hellmann.P2CO2SC
gi P2WaterSzalewicz.P2H2OSC
gi P2NitrogenHellmann.P2N2QFH
GIGA Prefix
gjke(AtomOrientedQuaternion, AtomOrientedQuaternion) P2SpheroPolyhedron
GlassClustering etomica.modules.glass
GlassClustering() GlassClustering
GlassClustering.SimParams etomica.modules.glass
GlassGraphic etomica.modules.glass
GlassGraphic(SimGlass) GlassGraphic
GlassGraphic.DataProcessorTensorTrace etomica.modules.glass
Inner class to find the total pressure of the system from the pressure
tensor.
GlassGraphic.MeterFromDumps etomica.modules.glass
GlassGraphic.SFacButtonAction etomica.modules.glass
GlassParams() SimGlass.GlassParams
GlassProd etomica.modules.glass
GlassProd() GlassProd
GlassProd.SimParams etomica.modules.glass
globalAtomLeafIndexChanged(int) BoxEventManager
GlobalFilter etomica.graph.iterators.filters
A GlobalFilter is one that must see the entire graph stream before returning any graph.
GlobalFilter(GraphIterator) GlobalFilter
GlobalFilter(GraphIterator, GlobalFilter.SignatureMaker) GlobalFilter
GlobalFilter.SignatureMaker etomica.graph.iterators.filters
globalMoveProbability IntegratorManagerMC
GMIfac GCRestrictedGibbsHS.simParams
go() AkimaSplineSmootherApp
go() AkimaSplineSmootherDyApp
goButton MyApplet
goFastButton PistonCylinderGraphic
GOLD Colix
Gperp IntegratorDimerRT
Gperplast IntegratorDimerRT
Gpol P2WaterSzalewicz
gR() PotentialCalculationMappedRdf
grabber Grabber.ActionCornerSetter
grabber Grabber.CornerSetListener
grabber Grabber.DefaultMouseListener
Grabber etomica.util
Grabber(String) Grabber
Grabber.ActionCornerSetter etomica.util
Grabber.CornerData etomica.util
Grabber.CornerSetListener etomica.util
Grabber.DefaultMouseListener etomica.util
Grabber.ImagePanel etomica.util
grabPixels(Object, int, int, int[], int, int) ApiPlatform
grabPixels(Object, int, int, int[], int, int) Platform
grad P1Wall
gradient P1WCAWall
gradient P2EAM
gradient PotentialCuLREP
gradient PotentialEAM_LS
gradient PotentialEAM
gradient PotentialEFS
gradient P1ImageHarmonic
gradient Potential2SoftSphericalLSMulti
gradient Potential2SoftSphericalLSMultiLat
gradient P2Nitrogen
gradient P2NitrogenAB
gradient P2NitrogenShellModel
gradient P2Water3PSoft
gradient P2Water4PSoft
gradient P1WCAWall
gradient P1Smash
gradient P1Tether
gradient P1Sinusoidal
gradient P1WCAWall
gradient EwaldSummation
gradient P2ReactionFieldDipoleTruncated.P0ReactionField
gradient P2SoftSphericalTruncatedSwitched
gradient P2SoftTruncated
gradient P3BondAngle
gradient P3BondAngleDreiding
gradient P3CPSNonAdditiveHe
gradient P3CPSNonAdditiveHeLessSimplified
gradient P3CPSNonAdditiveHeOrig
gradient P3CPSNonAdditiveHeSimplified
gradient P4BondTorsion
gradient P4BondTorsionAlkaneXCCH
gradient P4TorsionDreiding
gradient Potential2SoftSpherical
gradient Potential2SoftSphericalLS
gradient(IAtomList) P1WCAWall
gradient(IAtomList) P1LepsHarmonic
gradient(IAtomList) P2EAM
gradient(IAtomList) PotentialCuLREP
gradient(IAtomList) PotentialEAM_LS
gradient(IAtomList) PotentialEAM
gradient(IAtomList) PotentialEFS
gradient(IAtomList) P1ImageHarmonic
gradient(IAtomList) P1Wall
gradient(IAtomList) Potential2SoftSphericalLSMulti
Gradient of the pair potential as given by the du(double) method.
gradient(IAtomList) Potential2SoftSphericalLSMultiLat
Gradient of the pair potential as given by the du(double) method.
gradient(IAtomList) P2CO2H2OWheatley
gradient(IAtomList) P2CO2Hellmann
gradient(IAtomList) P2WaterSzalewicz
gradient(IAtomList) P1WCAPorousWall
gradient(IAtomList) P1WCAWall
gradient(IAtomList) P1Smash
gradient(IAtomList) P2Cohesion
gradient(IAtomList) P1Tension
gradient(IAtomList) P1Tether
gradient(IAtomList) P1Sinusoidal
gradient(IAtomList) P1WCAWall
gradient(IAtomList) EwaldSummation
gradient(IAtomList) EwaldSummation.P2EwaldReal
gradient(IAtomList) P1Harmonic
gradient(IAtomList) P1HarmonicSite
gradient(IAtomList) P1SoftBoundary
gradient(IAtomList) P2HardAssociationConeDoubleSites
gradient(IAtomList) P2HardAssociationConeFourSites
gradient(IAtomList) P2HardAssociationConeOneSite
gradient(IAtomList) P2Ideal
Returns a zero vector.
gradient(IAtomList) P2LJQ
gradient(IAtomList) P2NitrogenHellmann
gradient(IAtomList) P2SoftSphericalTruncated.P0Lrc
gradient(IAtomList) P2SoftSphericalTruncatedSwitched
gradient(IAtomList) P2SoftTruncated
Returns the derivative (r du/dr) of the wrapped potential if the separation
is less than the cutoff value
gradient(IAtomList) P3BondAngle
gradient(IAtomList) P3BondAngleDreiding
gradient(IAtomList) P3CPSNonAdditiveHe
gradient(IAtomList) P3CPSNonAdditiveHeLessSimplified
gradient(IAtomList) P3CPSNonAdditiveHeOrig
gradient(IAtomList) P3CPSNonAdditiveHeSimplified
gradient(IAtomList) P4BondTorsion
gradient(IAtomList) P4BondTorsionAlkaneXCCH
gradient(IAtomList) P4TorsionDreiding
gradient(IAtomList) Potential2SoftSpherical
Gradient of the pair potential as given by the du(double) method.
gradient(IAtomList) Potential2SoftSphericalLS
Gradient of the pair potential as given by the du(double) method.
gradient(IAtomList) PotentialSoft
Returns the gradient of the potential as it applies to each atom in the
given AtomSet, indicating how the energy would change as the position of
the first atom is varied.
gradient(IAtomList) P2Spin
do nothing
gradient(IAtomList, Tensor) P1WCAWall
gradient(IAtomList, Tensor) P1LepsHarmonic
gradient(IAtomList, Tensor) P2EAM
gradient(IAtomList, Tensor) PotentialCuLREP
gradient(IAtomList, Tensor) PotentialEAM_LS
gradient(IAtomList, Tensor) PotentialEAM
gradient(IAtomList, Tensor) PotentialEFS
gradient(IAtomList, Tensor) P1ImageHarmonic
gradient(IAtomList, Tensor) P1Wall
gradient(IAtomList, Tensor) Potential2SoftSphericalLSMulti
gradient(IAtomList, Tensor) Potential2SoftSphericalLSMultiLat
gradient(IAtomList, Tensor) P2CO2H2OWheatley
gradient(IAtomList, Tensor) P2CO2Hellmann
gradient(IAtomList, Tensor) P2WaterSzalewicz
gradient(IAtomList, Tensor) P1WCAPorousWall
gradient(IAtomList, Tensor) P1WCAWall
gradient(IAtomList, Tensor) P1Smash
gradient(IAtomList, Tensor) P2Cohesion
gradient(IAtomList, Tensor) P1Tension
gradient(IAtomList, Tensor) P1Tether
gradient(IAtomList, Tensor) P1Sinusoidal
gradient(IAtomList, Tensor) P1WCAWall
gradient(IAtomList, Tensor) EwaldSummation
gradient(IAtomList, Tensor) EwaldSummation.P2EwaldReal
gradient(IAtomList, Tensor) P1Harmonic
gradient(IAtomList, Tensor) P1HarmonicSite
gradient(IAtomList, Tensor) P1SoftBoundary
gradient(IAtomList, Tensor) P2HardAssociationConeDoubleSites
gradient(IAtomList, Tensor) P2HardAssociationConeFourSites
gradient(IAtomList, Tensor) P2HardAssociationConeOneSite
gradient(IAtomList, Tensor) P2Ideal
gradient(IAtomList, Tensor) P2LJQ
gradient(IAtomList, Tensor) P2NitrogenHellmann
gradient(IAtomList, Tensor) P2SoftSphericalTruncated.P0Lrc
gradient(IAtomList, Tensor) P2SoftSphericalTruncatedSwitched
gradient(IAtomList, Tensor) P2SoftTruncated
Returns the derivative (r du/dr) of the wrapped potential if the separation
is less than the cutoff value
gradient(IAtomList, Tensor) P3BondAngle
gradient(IAtomList, Tensor) P3BondAngleDreiding
gradient(IAtomList, Tensor) P3CPSNonAdditiveHe
gradient(IAtomList, Tensor) P3CPSNonAdditiveHeLessSimplified
gradient(IAtomList, Tensor) P3CPSNonAdditiveHeOrig
gradient(IAtomList, Tensor) P3CPSNonAdditiveHeSimplified
gradient(IAtomList, Tensor) P4BondTorsion
gradient(IAtomList, Tensor) P4BondTorsionAlkaneXCCH
gradient(IAtomList, Tensor) P4BondTorsionOPLS
gradient(IAtomList, Tensor) P4TorsionDreiding
gradient(IAtomList, Tensor) Potential2SoftSpherical
gradient(IAtomList, Tensor) Potential2SoftSphericalLS
gradient(IAtomList, Tensor) PotentialSoft
Returns the same gradient as gradient(AtomSet) and also adds in the
contribution of the AtomSet to the pressureTensor.
gradient(IAtomList, Tensor) P2Spin
do nothing
gradient(IMoleculeList) P2Nitrogen
gradient(IMoleculeList) P2NitrogenAB
gradient(IMoleculeList) P2NitrogenShellModel
gradient(IMoleculeList) P2Water3PSoft
gradient(IMoleculeList) P2Water4PSoft
gradient(IMoleculeList) P22CLJmuQ
gradient(IMoleculeList) P2HSDipole
gradient(IMoleculeList) P2LJDipole
gradient(IMoleculeList) P2MoleculeSoftTruncatedSwitched
gradient(IMoleculeList) P2ReactionFieldDipole
gradient(IMoleculeList) P2ReactionFieldDipoleTruncated
gradient(IMoleculeList) P2ReactionFieldDipoleTruncated.P0ReactionField
gradient(IMoleculeList) PotentialGroupSoft
gradient(IMoleculeList) PotentialMolecularSoft
Returns the gradient of the potential as it applies to each atom in the
given AtomSet, indicating how the energy would change as the position of
the first atom is varied.
gradient(IMoleculeList) P2LJDipole
gradient(IMoleculeList, Tensor) P2Nitrogen
gradient(IMoleculeList, Tensor) P2NitrogenAB
gradient(IMoleculeList, Tensor) P2NitrogenShellModel
gradient(IMoleculeList, Tensor) P2Water3PSoft
gradient(IMoleculeList, Tensor) P2Water4PSoft
gradient(IMoleculeList, Tensor) P22CLJmuQ
gradient(IMoleculeList, Tensor) P2HSDipole
gradient(IMoleculeList, Tensor) P2LJDipole
gradient(IMoleculeList, Tensor) P2MoleculeSoftTruncatedSwitched
gradient(IMoleculeList, Tensor) P2ReactionFieldDipole
gradient(IMoleculeList, Tensor) P2ReactionFieldDipoleTruncated
gradient(IMoleculeList, Tensor) P2ReactionFieldDipoleTruncated.P0ReactionField
gradient(IMoleculeList, Tensor) PotentialGroupSoft
gradient(IMoleculeList, Tensor) PotentialMolecularSoft
Returns the same gradient as gradient(IMoleculeList) and also adds in
the contribution of the molecules to the pressureTensor.
gradient(IMoleculeList, Tensor) P2LJDipole
gradient2 EwaldSummation.P2EwaldReal
gradientAndTorque P2CO2H2OWheatley
gradientAndTorque P2CO2Hellmann
gradientAndTorque P2Nitrogen
gradientAndTorque P2Water3PSoft
gradientAndTorque P2Water4PSoft
gradientAndTorque P2HSDipole
gradientAndTorque P2LJDipole
gradientAndTorque P2MoleculeSoftTruncatedSwitched
gradientAndTorque P2NitrogenHellmann
gradientAndTorque P2ReactionFieldDipole
gradientAndTorque P2ReactionFieldDipoleTruncated
gradientAndTorque P2LJDipole
gradientAndTorque(IAtomList) P2CO2H2OWheatley
gradientAndTorque(IAtomList) P2CO2Hellmann
gradientAndTorque(IAtomList) P2WaterSzalewicz
gradientAndTorque(IAtomList) IPotentialTorque
gradientAndTorque(IAtomList) P2NitrogenHellmann
gradientAndTorque(IAtomList) P2Spin
gradientAndTorque(IAtomList, Tensor) P2Spin
do nothing
gradientAndTorque(IMoleculeList) P2Nitrogen
gradientAndTorque(IMoleculeList) P2Water3PSoft
gradientAndTorque(IMoleculeList) P2Water4PSoft
gradientAndTorque(IMoleculeList) IPotentialMolecularTorque
gradientAndTorque(IMoleculeList) P2HSDipole
gradientAndTorque(IMoleculeList) P2LJDipole
gradientAndTorque(IMoleculeList) P2MoleculeSoftTruncatedSwitched
gradientAndTorque(IMoleculeList) P2ReactionFieldDipole
gradientAndTorque(IMoleculeList) P2ReactionFieldDipoleTruncated
gradientAndTorque(IMoleculeList) P2LJDipole
gradients PotentialGroupSoft
GraftAction(int) ColloidGraphic.GraftAction
graftVectors ConfigurationColloid
graftVectors ConformationStarPolymerGraft
GrainBoundaryConfiguration etomica.config
GrainBoundaryConfiguration(BravaisLatticeCrystal, BravaisLatticeCrystal, Space) GrainBoundaryConfiguration
Construct class that will place atoms on sites of the given lattices,
proceeding in the order resulting from iteration through the given index
iterator.
GrainBoundaryTiltConfiguration etomica.config
GrainBoundaryTiltConfiguration(BravaisLatticeCrystal, BravaisLatticeCrystal, ISpecies[], double, Space) GrainBoundaryTiltConfiguration
Gram etomica.units
Graph etomica.graph.model
GraphExtract etomica.graph.operations
This class takes the given nodes from the given graph and returns a new
graph consisting only of those nodes (and the bonds between them).
GraphExtract() GraphExtract
GraphFactory etomica.graph.model
GraphFactory() GraphFactory
graphHasEdgeColor(Graph, char) DecorateWertheim2Site
graphHasEdgeColor(Graph, char) DecorateWertheim2SiteRho
graphHasEdgeColor(Graph, char) DecorateWertheimNaphthalene2Rho
graphHasEdgeColor(Graph, char) VirialDiagrams
graphHasEdgeColor(Graph, char) VirialDiagramsMix2
graphHasEdgeColor(Graph, char) VirialDiagramsPT
graphic EllipseDisplayAction
graphic() DefaultToolbar
graphic() Device
graphic() DeviceBox
graphic() DeviceButton
Returns the GUI element for display in the simulation.
graphic() DeviceButtonGroup
graphic() DeviceCheckBox
Returns the GUI box element for display in the simulation.
graphic() DeviceDelaySlider
graphic() DevicePlotPoints
Returns the top level panel that the function plot components sit on.
graphic() DeviceRunControls
graphic() DeviceSelector
Returns the GUI element for display in the simulation.
graphic() DeviceSlider
Returns the GUI element for display in the simulation.
graphic() DeviceSpinner
Returns the GUI element for display in the simulation.
graphic() DeviceTable
Returns the top level panel that the table components sit on.
graphic() DeviceThermoSelector
Returns the GUI element for display in the simulation.
graphic() DeviceThermoSlider
graphic() DeviceToggleRadioButtons
Returns the GUI button element for display in the simulation.
graphic() DeviceTrioControllerButton
Returns the JPanel that contains the buttons.
graphic() Display
Method of Simulation.GraphicElement interface.
graphic() DisplayBox
Simulation.GraphicalElement interface method.
graphic() DisplayPlot
Overrides superclass method to return a JPanel holding the plot.
graphic() DisplayPlotXChart
graphic() DisplayPolytope
Simulation.GraphicalElement interface method.
graphic() DisplayTable
graphic() DisplayTextBox
graphic() DisplayTextBoxesCAE
graphic() DeviceThermoSliderGEMC
graphic() Osmosis.InitializeMolecules
graphic() DeviceCellNum3DSlider
graphic() DeviceCellNumXYSlider
graphic() DeviceEigenvaluesSlider
graphic() DeviceWaveVectorSlider
graphic() DeviceButtonSingle
Returns the GUI element for display in the simulation.
Graphic() LJMC3D.Graphic
Graphic() LJMC3DDimer.Graphic
GRAPHIC_ONLY SimulationGraphic
graphicOut MyApplet
graphicOut2 MyApplet
graphics SimFe.LjMC3DParams
graphics SimIdealGas.LjMC3DParams
graphics SimLattice.LjMC3DParams
graphics SimLJ.LjMC3DParams
graphics LJMC.LjMC3DParams
graphics LJMD.LJMDParams
graphics LjMC3D.LjMC3DParams
graphics LjMd3D.LjMd3DParams
graphics LjMd3Dv2y.LjMd3DParams
graphics MappedU.LJMDParams
graphics MappedVirialLJ.LJMDParams
graphics MappedVirialLJVGr.LJMDParams
graphics SimHSMDVacancy.HSMDVParams
graphics SimLJVacancy.LJParams
graphics AshtonWildingOsmoticVirial.simParams
graphics BnFlexibleContributionTraPPEUAMethanol
graphics VirialRowleyAlcohol
graphics VirialTraPPEAlcohol
Graphics3D org.jmol.g3d
Provides high-level graphics primitives for 3D visualization
for the software renderers.
Graphics3D() Graphics3D
graphicsForMetrics GData
graphicsPanel SimulationPanel
graphicsToggler MyApplet
GraphicsToggler() MyApplet.GraphicsToggler
GraphImpl etomica.graph.model.impl
GraphImpl(byte) GraphImpl
GraphImpl(byte, byte) GraphImpl
GraphImpl(byte, byte, Bitmap) GraphImpl
GraphImpl(byte, byte, Bitmap, Coefficient) GraphImpl
GraphImpl(byte, Bitmap) GraphImpl
GraphImpl(Node[]) GraphImpl
GraphIterator etomica.graph.model
GraphList etomica.graph.model
GraphList() GraphList
GraphList(Comparator<Graph>) GraphList
GraphMap etomica.graph.viewer
GraphMap(Set<Graph>, JComponent) GraphMap
GraphNumber etomica.graph.util
GraphNumber() GraphNumber
graphOp MaxIsomorph.MaxIsomorphParameters
GraphOp etomica.graph.operations
Interface for a simple operation that takes a Graph and returns a Graph.
GraphOp.GraphOpNull etomica.graph.operations
A dummy implementation of GraphOp that does nothing.
GraphOpMaxRoot etomica.graph.operations
GraphOp class that adjusts root points in each component so that
+ the number of root points is maintained
+ no component has more than one root point
+ all root points are included in all the "earliest" components
+ if a component has a root point, it is the first node in that component
This class only makes sense if the specific identity of each root
point is unimportant (Metadata.ROOT_POINTS_SPECIAL=false).
GraphOpMaxRoot() GraphOpMaxRoot
GraphOpNull() GraphOp.GraphOpNull
graphs Match
graphSegment FFTDecomposition
graphSplitter Unfactor
GRAY Colix
GREATER_THAN Feature
GREEN Colix
greys ColorSchemeRadical
greyscalerendering Token
group Token
GROUP EnumPalette
group1 Token
groupid Token
GROUPID_AMINO_MAX JmolConstants
GROUPID_ARGININE JmolConstants
GROUPID_ASPARAGINE JmolConstants
GROUPID_ASPARTATE JmolConstants
GROUPID_CYSTEINE JmolConstants
GROUPID_GLUTAMATE JmolConstants
GROUPID_GLUTAMINE JmolConstants
GROUPID_HISTIDINE JmolConstants
GROUPID_LYSINE JmolConstants
GROUPID_NUCLEIC_MAX JmolConstants
GROUPID_PROLINE JmolConstants
GROUPID_TRYPTOPHAN JmolConstants
groupindex Token
groupScaler BoxInflate
groupStart VirialDiagrams
groupTag MeterTiltRotationHistogram
groupTranslationVector BiasVolume2SiteAceticAcid
groupTranslationVector BiasVolumeAceticAcid
groupTranslationVector MCMoveBiasUBMolecule
groupTranslationVector MCMoveVolumeAssociatedMolecule
groupTranslationVector MCMoveMolecule
groupTransVect MCMoveMoleculeCoupledInitPert
groupTransVect MCMoveMoleculeCoupledSuperBox
groupTransVect MCMoveMoleculeCoupled
growto(BigInteger) Prime
extend the list of known primes up to n
gruneisen_knu MeterSolidPropsLJ
gSat P1Wall
gScaled Rgb16
gSet1 UnaryChain
gsSum MeterGs
GSTAR Gamma
gSum MeterCavityMapped
gSum MeterRDFMapped
gSum MeterDihedralAngle
gSum MeterRDF
gSum PotentialCalculationRDF
gSum PotentialCalculationMappedRdf
gSum MeterCorrelation
gSum MeterBondLength
gSum2 MeterRDFMapped
gSum2 PotentialCalculationMappedRdf
gsys DisplayBoxCanvasG3DSys
gtmp P4BondTorsion
gtmp P4BondTorsionAlkaneXCCH
GUI ConfigFromFileLAMMPS.ConfigFromFileLAMMPSParam
i(double, int) IntegratorDroplet
I P3Induction
I PotentialCalculationPressureTensor
I(int, double) BesselFunction
I0_AD P2HePCJS
I0_BO P2HePCJS
I0_QED P2HePCJS
I0_REL P2HePCJS
I1_AD P2HePCJS
I1_BO P2HePCJS
I1_QED P2HePCJS
I1_REL P2HePCJS
I1I0 MeterMeanField
I2etc MeterMeanField
i2roots() BigIntegerPoly
Generate the factors which are 2nd degree polynomials.
iA MeshSurface
IAction etomica.action
General interface for performing an action, allowing the defined behavior to be separated from the driver that causes
it.
IAPIPotential etomica.normalmode
Preliminary interface for proposed IPotential interface
iasdone P2WaterPotentialsJankowski
IAssociationHelper etomica.association
Interface for a class that is capable of populating a list of atoms in an
smer as well as checking the validity of the bonding
IAssociationHelperMolecule etomica.association
Interface for a class that is capable of populating a list of molecules in an
smer as well as checking the validity of the bonding
IAtom etomica.atom
IAtom is an interface for atoms in the simulation.
IAtomKinetic etomica.atom
Interface for an atom that holds vectors for velocity.
IAtomList etomica.atom
Interface for a list of IAtoms.
IAtomOriented etomica.atom
Interface for a IAtom that includes an IVector that defines the atom's
orientation.
IAtomOrientedKinetic etomica.atom
Interface for an Atom that has a position, orientation, velocity and angular
velocity.
iB MeshSurface
IB MeterEnthalpyVolume
IBigValue etomica.veos
iBondCount DataClusterer
iBonds DataClusterer
iC MeshSurface
icc P2WaterPotentialsJankowski
ICollectionPotential etomica.virial.GUI.components
IConformation etomica.config
IConformationOriented etomica.config
iCorner Grabber.ActionCornerSetter
iCorner Grabber.CornerSetListener
id ActionMinimizeEnergy
id DataSourceEnergies
id MeterWallForce
id MeterDADB
id MeterSolidProps
id MeterSolidPropsLJ
id P2SemiclassicalMolecular.MoleculeInfoBrute
id PropertyUpdate
id EnumPalette
ID CoordinatePairLeafSet
ID CoordinatePairMoleculeSet
IData etomica.data
Abstract container of simulation data and information describing it.
IDataInfo etomica.data
IDataInfoFactory etomica.data
IDataSink etomica.data
A recipient of Data.
IDataSource etomica.data
Interface for an object that can provide IData objects
on request.
IDEAL_GAS PistonCylinderGraphic
IdenticalFree etomica.graph.operations
Operation that removes identical graphs
IdenticalFree() IdenticalFree
IdenticalGraphFilter etomica.graph.iterators.filters
Filter that combines graphs that are identical
IdenticalGraphFilter(GraphIterator) IdenticalGraphFilter
identifier Token
identify Token
identity P2CO2H2OWheatley.P2CO2H2OSC
identity P2CO2Hellmann.P2CO2SC
identity P2Nitrogen
identity P2WaterSzalewicz.P2H2OSC
identity IntegratorDroplet
identity EwaldSummation
identity P2NitrogenHellmann.P2N2QFH
Identity() Function.Identity
idFontFace JmolFont
idFontStyle JmolFont
idFreeEnergy(double) HardSphere
Returns the ideal gas free energy for the given density.
idFreeEnergy(double) HardSphereSolid
Returns the ideal gas free energy for the given density.
iDiagram ClusterSumStickyEF
iDipole P2ReactionFieldDipole
iDipole P2ReactionFieldDipoleTruncated
iDipoleMoment PNWaterGCPMReactionField
idonl P2WaterPotentialsJankowski
ids PotentialEmulCached
idx Primitive
idx DataSourceCorrelation.Meter
idx DataSourceCorrelation.Receiver
idx DataAccPusher
idxProduct P2HardSphereCavity
idxSum P2HardSphereCavity
IEGenerator etomica.virial
IEGenerator() IEGenerator
IElement etomica.chem.elements
iEmbed P2WaterPotentialsJankowski
IEvent etomica.util
ifactor() BigIntegerPoly
Factorization into integer polynomials.
Ifactor etomica.veos.bigdecimal
Factored integers.
Ifactor(int) Ifactor
Constructor given an integer.
Ifactor(Ifactor) Ifactor
Copy constructor.
Ifactor(BigInteger) Ifactor
Constructor given a BigInteger .
Ifactor(Vector<Integer>) Ifactor
Constructor given a list of exponents of the prime factor decomposition.
IFLGST Gamma
IFunction etomica.math.function
ig MeterDensitySides
ignoredAtomType MeterChainLength
ignoreOverlap SimulationRestart
ignoreOverlap P2SquareWellOneSide
ignoreOverlap P2HardSpherePoly
ignoreOverlap P2HardSphere
ignoreOverlap P2PenetrableSquareWell
ignoreOverlap P2SquareWell
ignoreOverlap P2SquareWellRobust
IgnoreProperty etomica.meta.annotations
When applied to a get method, this annotation marks the property as ignored when introspecting the
simulation.
ignoreResetForFrac IntegratorOverlap
iGraph VirialLJBridge.VirialLJParam
ijInit(double[], double[][], Unit) P2CO2Hellmann
ijk P2WaterSzalewicz
ijRTensor P2CO2H2OWheatley.P2CO2H2OSC
ijRTensor P2CO2Hellmann.P2CO2SC
ijRTensor P2WaterSzalewicz.P2H2OSC
ijRTensor P2NitrogenHellmann.P2N2QFH
ijTensor P2CO2H2OWheatley.P2CO2H2OSC
ijTensor P2CO2Hellmann.P2CO2SC
ijTensor P2WaterSzalewicz.P2H2OSC
ijTensor P2NitrogenHellmann.P2N2QFH
IListener E extends IEvent > - Interface in etomica.util
imageOrigins(int) Boundary
Set of vectors describing the displacements needed to translate the
central image to all of the periodic images.
imageOrigins(int) BoundaryDeformablePeriodic
imageOrigins(int) BoundaryRectangular
Returns a set of image origins for a set of periodic image shells.
imageOrigins(int) BoundaryRectangularNonperiodic
Returns a zero-length vector.
imageOrigins(int) BoundaryTruncatedOctahedron
imageOut(String) GraphMap
ImagePanel() Grabber.ImagePanel
Constructor sets default size of the plot
ImagePanel(Color, int, int) Grabber.ImagePanel
ImageShell g3dsys.images
ImageShell(G3DSys) ImageShell
imagestate Token
imaginary() Complex
Imaginary part of this Complex number,the y-coordinate in rectangular coordinates.
imaginaryT MeterHarmonicCoordinate
imaginaryT MeterHarmonicEnergy
imaginaryT MeterHarmonicSingleEnergy
imaginaryT MeterNormalMode
imgPanel Grabber
iminDr CorrelationSelf2
imm2Total DataSourcePercolation
immFracByTypeTag DataSourcePercolation
immFracData DataSourcePercolation
immFracDataByType DataSourcePercolation
immFracDataByTypeInfo DataSourcePercolation
immFracDataInfo DataSourcePercolation
immFracPercData DataSourcePercolation
immFracPercDataInfo DataSourcePercolation
immFracPercTag DataSourcePercolation
immFracs DataSourcePercolation0
immFracTag DataSourcePercolation
immFractionByType DataSourcePercolation
ImmFractionByTypeSource(AtomType) DataSourcePercolation.ImmFractionByTypeSource
ImmFractionSource() DataSourcePercolation.ImmFractionSource
immTotal DataSourcePercolation
IMolecularModel_SpeciesFactory etomica.virial.GUI.models
iMolecule MCMoveClusterRingPartialRegrow
iMolecule MCMoveClusterRingScale
IMolecule etomica.molecule
Interface for an IMolecule
IMoleculeKinetic etomica.molecule
Interface for an molecule that holds vectors for velocity.
IMoleculeList etomica.molecule
Interface for a set of IMolecules.
IMoleculeOriented etomica.molecule
Interface for a IAtom that includes an IVector that defines the atom's
position.
IMoleculeOrientedKinetic etomica.molecule
Interface for an Atom that has a position, orientation, velocity and angular
velocity.
IMoleculePositionDefinition etomica.molecule
Returns a vector given a molecule, thereby defining the position
of the molecule.
IMoleculePositioned etomica.molecule
iMon VirialH2O.VirialH2OParam
iMonomer P2WaterPotentialsJankowski
imposePBC MCMoveClusterAtomMulti
inc() Bitmap
Increments the integer value of this bitmap by one: bitmap++.
inc() AbstractBitmap
includeAntibiasErr DataOverlap
includeLrc IteratorDirective
Flag indicating whether long-range correction contributions should
be included in calculation.
includeM ClathrateHarmonicFE.SimParams
includeM MinimizationTIP4P.SimParams
includeM ProtonDisorderGenerator.SimParams
INCLUSIVE DataSourceUniform.LimitType
Limit type indicating that limit is included in range, and that it equals the extreme value.
INCOMPATIBLE_TYPES Feature
increment(int) ScriptVariable
increment(int[]) RectangularLattice
ind_beta P2WaterSzalewicz
ind_C10 P2WaterSzalewicz
ind_C6 P2WaterSzalewicz
ind_C8 P2WaterSzalewicz
ind_charge P2WaterSzalewicz
ind_d1 P2WaterSzalewicz
ind_d10 P2WaterSzalewicz
ind_d6 P2WaterSzalewicz
ind_d8 P2WaterSzalewicz
ind_lin P2WaterSzalewicz
ind3_beta P2WaterSzalewicz
ind3_gamma P2WaterSzalewicz
ind3_R0 P2WaterSzalewicz
inDataInfo AccumulatorAverageBlocklessSlim
index Atom
index AtomType
index ApiIndexList
index BoxAtomIndexEvent
index BoxIndexEvent
index BoxMoleculeIndexEvent
index AccumulatorAverage.StatType
index AccumulatorAverageBlockless.StatType
index AccumulatorAverageBlocklessSlim.StatType
index DataSet.DataSetSink
index FindPairMoleculeIndex
index FindPairMoleculeIndexBetaN2
index MeterMBAR
index Molecule
index ScriptVariable
index Point3fi
indexaC SpeciesEthanol
indexaC SpeciesMethanol
indexaH SpeciesEthanol
indexaH SpeciesMethanol
indexAtom1 SpeciesHSDimer
indexAtom2 SpeciesHSDimer
indexC SpeciesMethane
indexC SpeciesTraPPECO2
indexC SpeciesAceticAcid
indexC SpeciesEthanol
indexC SpeciesWater4PCOM
indexC1 SpeciesAnthracene3site545
indexC1 SpeciesPh3site464
indexC1 SpeciesPh3site545
indexC1 SpeciesTraPPEAnthracene
indexC1 SpeciesTraPPENaphthalene
indexC1 SpeciesTraPPEPhenanthrene
indexC2 SpeciesTraPPEAnthracene
indexC2 SpeciesTraPPENaphthalene
indexC2 SpeciesTraPPEPhenanthrene
indexC3 SpeciesTraPPEAnthracene
indexC3 SpeciesTraPPEPhenanthrene
indexC4 SpeciesTraPPEAnthracene
indexC4 SpeciesTraPPEPhenanthrene
indexCenter SpeciesN2ShellModel
indexCH1 SpeciesAnthracene3site545
indexCH1 SpeciesPh3site464
indexCH1 SpeciesPh3site545
indexCH1 SpeciesTraPPEAnthracene
indexCH1 SpeciesTraPPENaphthalene
indexCH1 SpeciesTraPPEPhenanthrene
indexCH10 SpeciesTraPPEAnthracene
indexCH10 SpeciesTraPPEPhenanthrene
indexCH2 SpeciesAnthracene3site545
indexCH2 SpeciesPh3site464
indexCH2 SpeciesPh3site545
indexCH2 SpeciesTraPPEAnthracene
indexCH2 SpeciesTraPPENaphthalene
indexCH2 SpeciesTraPPEPhenanthrene
indexCH3 SpeciesAceticAcid
indexCH3 SpeciesTraPPEAnthracene
indexCH3 SpeciesTraPPENaphthalene
indexCH3 SpeciesTraPPEPhenanthrene
indexCH4 SpeciesTraPPEAnthracene
indexCH4 SpeciesTraPPENaphthalene
indexCH4 SpeciesTraPPEPhenanthrene
indexCH5 SpeciesTraPPEAnthracene
indexCH5 SpeciesTraPPENaphthalene
indexCH5 SpeciesTraPPEPhenanthrene
indexCH6 SpeciesTraPPEAnthracene
indexCH6 SpeciesTraPPENaphthalene
indexCH6 SpeciesTraPPEPhenanthrene
indexCH7 SpeciesTraPPEAnthracene
indexCH7 SpeciesTraPPENaphthalene
indexCH7 SpeciesTraPPEPhenanthrene
indexCH8 SpeciesTraPPEAnthracene
indexCH8 SpeciesTraPPENaphthalene
indexCH8 SpeciesTraPPEPhenanthrene
indexCH9 SpeciesTraPPEAnthracene
indexCH9 SpeciesTraPPEPhenanthrene
indexDBO SpeciesAceticAcid
indexed SVGConverter
Should output Image be indexed .
indexer DataDistributer
indexF1 Species7SiteRigidSF6
indexF2 Species7SiteRigidSF6
indexF3 Species7SiteRigidSF6
indexF4 Species7SiteRigidSF6
indexF5 Species7SiteRigidSF6
indexF6 Species7SiteRigidSF6
indexH SpeciesAceticAcid
indexH1 SpeciesMethane
indexH1 SpeciesMethanol
indexH1 SpeciesWater4P
indexH1 SpeciesWater4PCOM
indexH1a SpeciesEthanol
indexH1b SpeciesEthanol
indexH2 SpeciesMethane
indexH2 SpeciesWater4P
indexH2 SpeciesWater4PCOM
indexH2a SpeciesEthanol
indexH2a SpeciesMethanol
indexH2b SpeciesEthanol
indexH2b SpeciesMethanol
indexH2c SpeciesEthanol
indexH3 SpeciesMethane
indexH4 SpeciesMethane
indexIterator ConfigurationLattice
indexIterator ConfigurationLatticeSimple
IndexIterator etomica.lattice
Loops through the set of indexes appropriate to a lattice of given size.
IndexIterator g3dsys.control
IndexIteratorIncreasing etomica.lattice
Iterator that returns indices in increasing order, starting at 0 and ending
including all indices where |i| <= max, where i are the components of the
index.
IndexIteratorIncreasing(int) IndexIteratorIncreasing
IndexIteratorRectangular etomica.lattice
Iterates arrays of int, such that 0 <= a[0] <= size[0], 0 <= a[1] <= size[1], etc.,
thereby spanning a rectangular region.
IndexIteratorRectangular(int) IndexIteratorRectangular
Constructs iterator that returns int arrays of length D.
IndexIteratorReflecting etomica.lattice
Generates iterates by alternately keeping or flipping the sign of each element of
iterates generated by another iterator.
IndexIteratorReflecting(IndexIterator) IndexIteratorReflecting
Constructs iterator to generate reflections from iterates of
given iterator.
IndexIteratorSizable etomica.lattice
Interface for an iterator in which the number of indices
in each dimension may be specified.
IndexIteratorTriangular etomica.lattice
Iterates arrays of int such that a[0] >= a[1] >= ...
IndexIteratorTriangular(int) IndexIteratorTriangular
Constructs iterator that will return int arrays of length D.
IndexIteratorTriangularPermutations etomica.lattice
Generates all unique iterates formed as permutations of iterates given by IndexIteratorTriangular with
allowEqualElements set to true.
IndexIteratorTriangularPermutations(int) IndexIteratorTriangularPermutations
indexM SpeciesWater4P
indexM SpeciesWater4PCOM
IndexMap V > - Class in etomica.util.collections
An specialized implementation of Map which is designed for mapping
an index to a value.
IndexMap() IndexMap
Creates a new map with the default initial capacity of 10 and
default reservoir size of 30.
IndexMap(int) IndexMap
Creates a new map with the given initial capacity and default
reservoir size of 30.
IndexMap(int, int) IndexMap
Creates a new map with the given initial capacity and reservoir size.
indexN1 SpeciesN2
indexN1 SpeciesN2ShellModel
indexN2 SpeciesN2
indexN2 SpeciesN2ShellModel
indexO SpeciesEthanol
indexO SpeciesMethanol
indexO SpeciesWater4P
indexO SpeciesWater4PCOM
indexOf(IAtom) AtomArrayList
indexOf(IAtom) P2HardBondedList.BondArrayList
indexOf(IMolecule) MoleculeArrayList
indexOf(Object) AtomPair
indexOf(Object) AtomSetSinglet
indexOf(Object) MoleculePair
indexOf(Object) MoleculeSetSinglet
indexOf(String) StringXBuilder
indexOf2(String, int) StringXBuilder
indexOleft SpeciesTraPPECO2
indexOright SpeciesTraPPECO2
indexP1left SpeciesN2
indexP1left SpeciesN2ShellModel
indexP1right SpeciesN2
indexP1right SpeciesN2ShellModel
indexP2left SpeciesN2
indexP2right SpeciesN2
indexS Species7SiteRigidSF6
indexSBO SpeciesAceticAcid
indexSelectedSpecies ExceptionDoNotRemoveSpecies
indexX SpeciesEthanol
indexX SpeciesMethanol
indices PermutationIterator
indN_iter() P2WaterSzalewicz
Compute the iterative induction between N water molecules
using several polarization centers in the molecular plane
INDUCTION PNCO2GCPM.Component
INDUCTION PNGCPM.Component
INDUCTION P2WaterSzalewicz.Component
INDUCTION PNWaterGCPM.Component
INeighborListListener etomica.nbr.list
INeighborListListenerMolecular etomica.nbr.list.molecule
inflate MCMoveBoxSize
inflate MCMoveVolume
inflate MCMoveVolumeN2
inflate CoordinateDefinitionMolecule
inflate CoordinateDefinitionMoleculeVolumeFluctuation
inflate MCMoveVolumeMonoclinic
inflate MCMoveVolumeMonoclinicAngle
inflate MCMoveVolumeMonoclinicScaled
inflate MCMoveVolumeSolid
inflate MCMoveVolumeSolidNPTMolecular
inflate(Boundary) BoundaryEventManager
inflateEvent Boundary
info Token
info(String) DefaultLogger
info(String) Logger
og* Writes a log at INFO level.
info(String) LoggerInterface
Writes a log at INFO level.
info2 EFSTungsten
inGreyscaleMode GData
INHERIT_ALL Colix
INHERIT_COLOR Colix
init() GraphMap
init() DeviceNSelector
init() DisplayPolytope.Applet
init() AkimaSplineSmootherApp.Applet
init() AkimaSplineSmootherDyApp.Applet
init() AdsorptionGraphic.Applet
init() CatalysisGraphic.Applet
init() ChainEquilibriumGraphic.Applet
init() FreeRadicalPolymerizationGraphic.Applet
init() MyApplet
init() ColloidGraphic.Applet
init() CrystalViewer.Applet
init() DCVGCMDGraphic.Applet
init() DropletAtomicGraphic.Applet
init() DropletGraphic.Applet
init() LJMCGraphic.Applet
init() InsertionGraphic.Applet
init() InterfacialSWGraphic.Applet
init() LjmdGraphic.Applet
init() MaterialFractureGraphic.Applet
init() MuGraphic.Applet
init() MultiharmonicGraphicMC.Applet
init() MultiharmonicGraphic.Applet
init() MultiharmonicGraphicMC.Applet
init() MultiharmonicGraphicMC.Applet
init() MultiharmonicGraphicMC.Applet
init() PistonCylinderGraphic.Applet
init() PistonCylinderGraphic
Initialize all the bits based on previously set doConfigButton and doRDF.
init() ReactionEquilibriumGraphic.Applet
init() RheologyGraphic.Applet
init() ReverseOsmosisGraphic.Applet
init() ReverseOsmosisWaterGraphic.Applet
init() SamGraphic.Applet
init() SwmdGraphic.Applet
init() B2Fit.Applet
init() VLE.Applet
init() DeviceCellNumXYSlider
init() HTTPSoftSphereApplet.Applet
init() MCMovePhaseAngle
init() MCMoveWV
init() NormalModeAnalysisDisplay1D.Applet
init() NormalModeAnalysisDisplay1DGraphic.Applet
init() NormalModeAnalysisDisplay2DGraphic.Applet
init() NormalModeAnalysisDisplay3D.Applet
init() NormalModeAnalysisDisplay3DGraphic.Applet
init() SimLJVacancy.Applet
init() DipoleBox.Applet
init() DipoleBoxMatrix.Applet
init() SingleDipole.Applet
init() SingleDumbellRattle.Applet
init() SingleDumbellShake.Applet
init() SingleWater.Applet
init() SingleWaterMatrix.Applet
init() SingleWaterRattle.Applet
init() SingleWaterShake.Applet
init() WaterBox.Applet
init() WaterDroplet.Applet
init() WaterDropletMatrix.Applet
init() WaterDropletRattle.Applet
init() WaterDropletShake.Applet
init() WaterTrimer.Applet
init() WaterTrimerRattle.Applet
init() WaterTrimerShake.Applet
init() LJMD3D.Applet
init() LJMD3DNbr.Applet
init() Wigner3jGUI
init() VirialDiagrams
init() VirialDiagramsPT
init() SimulationVirial
init() SimulationVirialOverlap2
init(int) AkimaSplineSmootherApp
init(int) AkimaSplineSmootherDyApp
init(EndpointConfig) ConfigurationWebsocket.ConfigurationUpdateEncoder
init(EndpointConfig) DataStreamWebsocket.DataAndInfoEncoder
initAlpha() MeterTargetRPMolecule
initAlpha() MeterTargetTPMolecule
initAlpha() MeterOverlapSwitch
initAlpha() MeterTargetTP
initAtomOldCoord() MSDCoordWriter.AfterPBC
initBlockAccumulator() SimulationVirialOverlap2
initBox(Box) P1ConstraintNbr
Assigns & keeps track of a set of neighbors for each box
initC MinimizeHCP.SimOverlapParam
initCellEditor(TableModel) DeviceTable
initComponents() ViewSpeciesSelection
initComponents() ViewSpeciesSelection
initConfig() SimGlass
initEta PolydisperseHS.HSPolyParam
initGraphics() SimulationGraphic
initHistogram(int, IDataSink) AccumulatorAverageBootstrap
initialize() AssociationManager
initialize() AssociationManagerMolecule
initialize() DisplayPolytopeCanvas2D
initialize() P2QChemInterpolated
initialize(long) SimOverlapAlphaN2TP
initialize(long) SimOverlapBetaN2RPScaling
initialize(long) SimOverlapBetaN2TP
initialize(long) SimOverlapDisorderedAlphaN2RPScaling
initialize(long) SimOverlapDisorderedAlphaN2TP
initialize(long) SimEinStep2
initialize(long) SimEinStep2HCP
initialize(long) SimLJHTTISuper
initialize(long) SimLJHTTISuperHCP
initialize(long) SimLJHTTISuperHCP2
initialize(long) SimLJHTTISuperSFMD
initialize(long) SimOverlapSoftSphereDP
initialize(long) SimOverlapSoftSphereEin
initialize(long) SimOverlapSoftSphereTP
initialize(long) SimOverlapSoftSphereTPHCP
initialize(long) SimOverlapSoftSphereTPSlantedBox
initialize(Bootstrap<EtomicaServerConfig>) EtomicaServer
initialize(ApiPlatform) Graphics3D
initialize(ApiPlatform) GData
initializeConfigFromFile(String) SimDirectBetaN2RPAngleToNoAngle
initializeConfigFromFile(String) SimDirectBetaN2RPInitPert
initializeConfigFromFile(String) SimDirectDisorderedAlphaN2RPInitPert
initializeConfigFromFile(String) SimOverlapAlphaN2TP
initializeConfigFromFile(String) SimOverlapBetaN2RPScaling
initializeConfigFromFile(String) SimOverlapBetaN2TP
initializeConfigFromFile(String) SimOverlapDisorderedAlphaN2RPScaling
initializeConfigFromFile(String) SimOverlapDisorderedAlphaN2TP
initializeConfigFromFile(String) SimFluidSoftSphere
initializeConfiguration(String) SimDimerLJadatom
initializeConfiguration(String) SimKMCLJadatom
initializeConformation(IMolecule) ISpecies
Initializes the molecule's IAtoms in their standard arrangement.
initializeConformation(IMolecule) SpeciesGeneral
initializeConformation(IMolecule) SpeciesGeneralMutable
initializeCoordinates() IntegratorDimerApproach
initializeCoordinates(int[]) CoordinateDefinitionNitrogen
initializeCoordinates(int[]) CoordinateDefinitionNitrogenSuperBox
initializeCoordinates(int[]) CoordinateDefinition
initializeCoordinates(int[]) CoordinateDefinitionHSDimer
initializeCoordinates(int[]) CoordinateDefinitionLeafSuperBox
initializeCoordinates(int[]) CoordinateDefinitionMolecule
initializeCoordinates(int[]) CoordinateDefinitionMoleculeVolumeFluctuation
initializeCoordinates(Box) Configuration
Defines the placement of the molecules.
initializeCoordinates(Box) ConfigurationFile
initializeCoordinates(Box) ConfigurationFileBinary
initializeCoordinates(Box) ConfigurationLattice
Places the molecules in the given box on the positions of the
lattice.
initializeCoordinates(Box) ConfigurationLatticeRandom
initializeCoordinates(Box) ConfigurationLatticeSimple
Places the molecules in the given box on the positions of the
lattice.
initializeCoordinates(Box) ConfigurationLatticeWithPlane
Places the molecules in the given box on the positions of the
lattice.
initializeCoordinates(Box) ConfigurationResourceFile
initializeCoordinates(Box) ConfigurationZincblende
Initializes positions of atoms to the zincblende structure.
initializeCoordinates(Box) GrainBoundaryConfiguration
Places the molecules in the given box on the positions of the
lattice.
initializeCoordinates(Box) GrainBoundaryTiltConfiguration
initializeCoordinates(Box) ConfigurationLammps
initializeCoordinates(Box) ConfigurationFileTIP4P
initializeCoordinates(Box) ConfigurationCatalysis
initializeCoordinates(Box) ConfigurationLatticeFreeRadical
Places the molecules in the given box on the positions of the
lattice.
initializeCoordinates(Box) ConfigurationColloid
initializeCoordinates(Box) ConfigurationLatticeTube
initializeCoordinates(Box) ConfigurationDroplet
initializeCoordinates(Box) ConfigurationPolymer
initializeCoordinates(Box) ConfigurationMembrane
initializeCoordinates(Box) ConfigurationMembraneWater
initializeCoordinates(Box) ConfigurationSAM
initializeCoordinates(Box) ConfigurationWater108
initializeCoordinates(Box) ConfigurationWater108TIP4P
initializeCoordinates(Box) ConfigurationWater256
initializeCoordinates(Box) ConfigurationWater3_3P
initializeCoordinates(Box) ConfigurationWater3
initializeCoordinates(Box) ConfigurationAligned
Sets all spins to be aligned in the +x direction
initializeCoordinates(Box) ConfigurationCluster
initializeCoordinates(Box) ConfigurationClusterChain
initializeCoordinates(Box) ConfigurationClusterChainFourSites
initializeCoordinates(Box) ConfigurationClusterMove
initializeCoordinates(Box) ConfigurationClusterWertheimGCPM
initializeCoordinates(Box) ConfigurationClusterWertheimGCPM4Pt
initializeCoordinates(Box) ConfigurationFileXYZ
initializeCoordinates(Box, boolean, boolean) ConfigurationClusterAceticAcid
initializeCoordinates(Box, ISpecies) ConfigurationLattice
initializeCoordinates2(Box) ConfigurationClusterWertheimGCPM
initializeCoordinates2(Box) ConfigurationClusterWertheimGCPM4Pt
initializeCoordinates2(Box, boolean, boolean) ConfigurationClusterAceticAcid
initializeCoordinates3(Box) ConfigurationClusterWertheimGCPM
initializeCoordinates3(Box) ConfigurationClusterWertheimGCPM4Pt
initializeCoordinates4(Box) ConfigurationClusterWertheimGCPM
initializeCoordinates4(Box) ConfigurationClusterWertheimGCPM4Pt
initializeCoordinates4Mol(Box, char, char, char, char, char, int, int) ConfigurationClusterAceticAcid
initializeCoordinates5(Box) ConfigurationClusterWertheimGCPM
initializeCoordinates5(Box) ConfigurationClusterWertheimGCPM4Pt
initializeCoordinatesBranch(Box) ConfigurationClusterWertheimGCPMDirectSampling
initializeCoordinatesER(Box) ConfigurationClusterWertheimGCPM
initializeCoordinatesER(Box) ConfigurationClusterWertheimGCPM4Pt
initializeCoordinatesRef(Box) ConfigurationClusterWertheimGCPM4Pt
initializeCoordinatesTetramer(Box) ConfigurationClusterWertheimGCPMDirectSampling
initializeCoordinatesTrimer(Box) ConfigurationClusterWertheimGCPMDirectSampling
initialized Integrator
initialized OrientationCalcWater3P
initialized OrientationCalcWater4P
initialized NeighborListManagerMolecular
initialized NeighborListManager
initialized SimulationVirialOverlap2
initialized() IntegratorEventManager
InitializeMolecules(ConfigurationLatticeWithPlane, SimulationRestart) Osmosis.InitializeMolecules
initializePositions(IAtomList) ConformationAlkaneEH
initializePositions(IAtomList) ConformationMethane
initializePositions(IAtomList) ConformationChain
Places a set of atoms in a linearly connected fashion.
initializePositions(IAtomList) ConformationChainLinear
initializePositions(IAtomList) ConformationGeneric
initializePositions(IAtomList) ConformationLinear
initializePositions(IAtomList) ConformationWater
initializePositions(IAtomList) IConformation
Defined by subclass to assign coordinates to the atoms in the given list.
initializePositions(IAtomList) ConformationCO2
initializePositions(IAtomList) ConformationNitrogen
initializePositions(IAtomList) ConformationNitrogenShellModel
initializePositions(IAtomList) ConformationAceticAcid
initializePositions(IAtomList) ConformationEthanol
initializePositions(IAtomList) ConformationMethanol
initializePositions(IAtomList) ConformationWater3P
initializePositions(IAtomList) ConformationWaterGCPM
initializePositions(IAtomList) ConformationWaterGCPMCOM
initializePositions(IAtomList) ConformationWaterTIP4P
initializePositions(IAtomList) OrientationCalcWater3P
initializePositions(IAtomList) OrientationCalcWater4P
initializePositions(IAtomList) ConformationTube
initializePositions(IAtomList) ConformationHSDimer
initializePositions(IAtomList) ConformationStarPolymerGraft
initializePositions(IAtomList) Conformation7SiteRigidSF6
initializePositions(IAtomList) ConformationAnthracene3site
initializePositions(IAtomList) ConformationAnthraceneTraPPE
initializePositions(IAtomList) ConformationNaphthaleneTraPPE
initializePositions(IAtomList) ConformationPh3site
initializePositions(IAtomList) ConformationPhenanthreneTraPPE
initializePositions(IAtomList, IOrientation) IConformationOriented
Assign coordinates to the atoms in the given list using the
given orientation for the molecule.
initializePositions(IAtomList, IOrientation) ConformationHSDimer
initializePositions(IAtomList, Vector) ConformationNitrogen
initializing ReactionEquilibrium
initializing ReactionEquilibriumGraphic
initialLatticeEnergy MinimizationBetaNitrogenModelLS
initialSeed AccumulatorAverageBootstrap
initialSeed AccumulatorAverageCollapsingLog
initialSolute OsmosisSim
initialSolvent OsmosisSim
initialState(Graph, Graph) Match
Initial search state with the default isomorphism test algorithm.
initialU ClathrateHarmonicFE
initialU MinimizationTIP4P
initialU MinimizationBetaNitrogenModel
initLat MinimizeBetaNitrogenLatticeParameterFromFile
initMetaDataComparator() VirialDiagrams
initMetaDataComparator() VirialDiagramsPT
initMolecOrientation CalcAnalytical2ndDerivativeNitrogen
initMolecOrientation MCMoveRotateMolecule3DConstraint
initMolecOrientation MCMoveRotateMolecule3DFixedAngle
initMolecOrientation MCMoveRotateMolecule3DN2AveCosThetaConstraint
initNominalU(IMoleculeList) CoordinateDefinitionNitrogen
Override if nominal U is more than the lattice position of the molecule
Number of molecules equals to basis atoms
initNominalU(IMoleculeList) CoordinateDefinitionNitrogenSuperBox
Override if nominal U is more than the lattice position of the molecule
Number of molecules equals to basis atoms
initNomial is the method to define the initial orientation of the molecule
initNominalU(IMoleculeList) CoordinateDefinition
Initializes the CoordinateDefinition for the given molecule and
associates the molecule with the given index.
initNominalU(IMoleculeList) CoordinateDefinitionLeaf
initNominalU(IMoleculeList) CoordinateDefinitionMolecule
Override if nominal U is more than the lattice position of the molecule
initNominalU(IMoleculeList) CoordinateDefinitionMoleculeVolumeFluctuation
Override if nominal U is more than the lattice position of the molecule
initP() MeterDDP
initP() MeterDP
initPotential(Space, ISpecies, PotentialGroup) MethanolPotentialHelper
initPotential(Space, SpeciesGeneral, PotentialGroup) AceticAcidModPotentialHelper
initPotential(Space, SpeciesGeneral, PotentialGroup) AceticAcidPotentialHelper
initPotential(Space, SpeciesGeneral, PotentialGroup, boolean) EthanolPotentialHelper
initPotential(Space, SpeciesGeneral, PotentialGroup, boolean, double, double) MethanolPotentialHelper
initRefPref(String, long) SimOverlapNitrogenModel
initRefPref(String, long) SimOverlap
initRefPref(String, long) SimOverlapLJ
initRefPref(String, long) SimOverlapModule
initRefPref(String, long) SimOverlapSoftSphere
initRefPref(String, long) SimOverlapSoftSphereHCP
initRefPref(String, long) SimOverlapSoftSphereReweighting
initRefPref(String, long) SimOverlapSoftSphereSuperBox
initRefPref(String, long) SimOverlapSSnxy
initRefPref(String, long) SimulationVirialOverlap2
initRefPref(String, long, boolean) SimulationVirialOverlap2
initRqFactor() PNWaterGCPMReactionField
initU MCMoveMoleculeCoupledInitPert
initU MeterDirectInitPert
initVolume CoordinateDefinitionMolecule
initVolume CoordinateDefinitionMoleculeVolumeFluctuation
innersegment CoordinateDefinitionNitrogenSuperBox
inPlane(Vector) LatticePlane
Returns true if the given point is inside the plane (within some small tolerance).
inPlane(Vector) Plane
Returns true if the given point is within a distance epsilon of this plane.
input ConfigFromFileLAMMPS.ConfigFromFileLAMMPSParam
inputDataInfo AccumulatorAutocorrelationPTensor
inputDataInfo AccumulatorAutocorrelationShearStress
inputDataInfo StatisticsMCGraphic.DataProcessorUndo
inRadius AtomTypeSpheroPolyhedron
insert MCMoveInsertDelete
insertCandidates MCMoveInsertDeleteLatticeVacancy
insertCandidates MCMoveInsertDeleteVacancy
inserted MCMoveClusterAtomHSRing
inserted MCMoveClusterAtomHSTree
inserted MCMoveClusterPolyhedraTree
insertion Token
Insertion etomica.modules.insertion
Insertion(Space) Insertion
INSERTION EnumPalette
InsertionGraphic etomica.modules.insertion
InsertionGraphic(Insertion) InsertionGraphic
InsertionGraphic.Applet etomica.modules.insertion
InsertionGraphic.MeterWidom etomica.modules.insertion
INSTANCE AtomIteratorNull
INSTANCE Argon
INSTANCE Carbon
INSTANCE Chlorine
INSTANCE Copper
INSTANCE Fluorine
INSTANCE Helium
INSTANCE Hydrogen
INSTANCE Iron
INSTANCE Nitrogen
INSTANCE Oxygen
INSTANCE Silver
INSTANCE Sodium
INSTANCE Sulfur
INSTANCE Tin
INSTANCE Tungsten
INSTANCE Function.Abs
INSTANCE Function.Exp
INSTANCE Function.Identity
INSTANCE Function.Log
INSTANCE Function.Reciprocal
INSTANCE Function.Sqrt
INSTANCE IteratorFactory
InstanceProperty etomica.meta.properties
Container class for mapping an instance to a property.
InstanceProperty(Object, PropertyDescriptor) InstanceProperty
Int etomica.graph.operations
Int() Int
Int2IntHash org.jmol.util
Int2IntHash(int) Int2IntHash
intArrayList AccumulatorAverageBootstrap
intArrayList AccumulatorAverageCollapsingLog
integer Token
integral(double) P2HardAssociationConeDoubleSites
integral(double) P2HardAssociationConeFourSites
integral(double) P2HardAssociationConeOneSite
integral(double) P2Ideal
Returns zero.
integral(double) P2LJQ
integral(double) P2SoftSphericalTruncated.P0Lrc
integral(double) P2SoftTruncated
Returns the value of uInt for the wrapped potential.
integral(double) Potential2Soft
Integral used to evaluate correction to truncation of potential.
integral(double) Potential2SoftSpherical
Same as uInt.
integrand(double) HardSphere
integrate(ClusterDiagram[]) ClusterOperations
Replaces each cluster in the given array with another having the same
topology, but with the highest-index root point converted into a field
point.
integrator IntegratorActionAdapter
integrator CH4NVT
integrator DHS_NVT
integrator DLJ_NVT_1site
integrator TestAceticAcidMC3D_NPT
integrator SimGCPMWaterMCNPT
integrator SimGCPMWaterMCNVT
integrator TestIGAssociationMC3D_NPT_DoubleSites
integrator TestLJAssociationMC3D_NPT_DoubleSites
integrator TestLJAssociationMC3D_NPT
integrator TestLJAssociationMC3D_NVTOld
integrator HSMDCavity
The Integrator performing the dynamics.
integrator HSMDWidom
The Integrator performing the dynamics.
integrator DataProcessorChemicalPotential
integrator DataSourceCountCollisions
integrator DataSourceCountSteps
integrator DataSourceCountTime
integrator DataSourcePositionedBoltzmannFactor
integrator MeterPressureTensorFromIntegrator
integrator DHS_NVT
integrator DLJ_NVT_1site
integrator TIP4P_NVT
integrator EFSTungsten
integrator SimFe
integrator SimIdealGas
integrator SimLJ
integrator DisplayTimer
integrator IntegratorHard.Agent
integrator MCMoveInsertDeleteLatticeVacancy
integrator MCMoveInsertDeleteVacancy
integrator LJMC
integrator LJMD
integrator LjMC3D
integrator LjMd3D
integrator LjMd3D.ValueCache
integrator ValueCache
integrator SimMappedRdf
integrator MappedU
integrator MappedVirialLJ
integrator MappedVirialLJVGr
integrator LJmuVT
integrator LJNPT
integrator LJNVT
integrator MeterBoltzmann
integrator MeterBoltzmannDirect
integrator MeterDirectInitPert
integrator SimOverlapAlphaN2TP
integrator SimOverlapBetaN2RPScaling
integrator SimOverlapBetaN2TP
integrator SimOverlapDisorderedAlphaN2RPScaling
integrator SimOverlapDisorderedAlphaN2TP
integrator SimulationAlphaNitrogenModel
integrator SimulationBetaNitrogenModel
integrator SimulationBetaNitrogenModelTest
integrator SimulationGammaNitrogenModel
integrator TestEwaldTIP4PWater
integrator ModifierPMu
integrator P1Wall
integrator Catalysis
integrator ColloidSim
integrator Droplet
integrator DropletAtomic
integrator LJMC
integrator AccumulatorPTensor
integrator DataSourceBlockAvgCor
integrator DataSourceHisogram
integrator DataSourceHistogramMSD
integrator DataSourceMSDcorP
integrator DataSourcePMSDHistory
integrator SimGlass
integrator Insertion
integrator InterfacialSW
integrator Ljmd
integrator MaterialFracture
integrator Mu
integrator MuGraphic.DataProcessorMu
integrator MuGraphic.ModifierEpsilon
integrator MuGraphic.ModifierLambda
integrator DataOverlapCaching
integrator MultiharmonicMC
integrator OsmosisSim
integrator PistonCylinder
integrator MeterNormalStress
integrator MeterViscosity
integrator SimulationRheology
integrator MeterFlux
integrator ReverseOsmosis
integrator ReverseOsmosisWater
integrator Sam
integrator AccumulatorMimicMu
integrator DataProcessorMu
integrator Swmd
integrator DeviceWaveVectorSlider
integrator HessianDB
integrator HSDimerNPT
integrator HSNPT
integrator HTTPSoftSphereSim
integrator MeterBoltzmann
integrator MeterDirectSamplingTarget
integrator MeterSamplingHarmonic
integrator MeterSamplingTarget
integrator MeterWorkBennetHarmonic
integrator MeterWorkBennetTarget
integrator MeterWorkHarmonicUmbrella
integrator MeterWorkTargetBennet
integrator MeterWorkTargetHarmonicandReweighting
integrator MeterWorkTargetPhaseSpace
integrator MeterWorkTargetUmbrella
integrator MeterWorkUmbrellaHarmonic
integrator MeterWorkUmbrellaTarget
integrator NormalModeAnalysisDisplay1D
integrator NormalModeAnalysisDisplay2D
integrator NormalModeAnalysisDisplay3D
integrator HSNPT2DSim
integrator SimBennet
integrator SimCalcJ
integrator SimCalcS
integrator SimCalcSLJ
integrator SimCalcSMorse
integrator SimCalcSSoftSphere2D
integrator SimCalcSSoftSphereFCC
integrator SimCalcSSoftSphereFCCSuperBox
integrator SimEinStep1
integrator SimEinStep1HCP
integrator SimEinStep2
integrator SimEinStep2HCP
integrator SimFluidSoftSphere
integrator SimHarmonic
integrator SimHarmonicUmbrella
integrator SimHSMDVacancy
integrator SimLJHTTISuper
integrator SimLJHTTISuperHCP
integrator SimLJHTTISuperHCP2
integrator SimLJHTTISuperSFMD
integrator SimLJVacancy
integrator SimModesJ
integrator SimOverlapSoftSphereDP
integrator SimOverlapSoftSphereEin
integrator SimOverlapSoftSphereTP
integrator SimOverlapSoftSphereTPHCP
integrator SimOverlapSoftSphereTPSlantedBox
integrator SimTarget
integrator SimTargetUmbrella
integrator SimUmbrella
integrator SimUmbrellaSoftSphere
integrator AshtonWildingLJ
integrator AshtonWildingOsmoticVirial
integrator AshtonWildingVirial
integrator GCRestrictedGibbsHS
integrator GCWidomInsertHS
integrator NVTWidomInsertLJ
integrator PolydisperseHS
The Integrator performing the dynamics.
integrator PotentialCalculationPressureTensor
integrator DipoleBox
integrator DipoleBoxMatrix
integrator ChainHSMD3D
integrator GEMCWithRotation
integrator HSMC2D
integrator HSMD2D_noNbr
integrator HSMD2D
integrator HSMD3D
The Integrator performing the dynamics.
integrator HSMD3DNoNbr
integrator LJMC3D
integrator LJMC3DDimer
integrator LJMD2D
integrator LJMD3D
integrator LJMD3DNbr
integrator SoftSphere3d
integrator SWMD2D
integrator SWMD3D
integrator StarPolymerMD
integrator LJMC
integrator TestHSMD3D
integrator TestLammpsLJ
integrator TestLJGCMC3D
integrator TestLJMC3D
integrator TestLJMD3D
integrator TestSWChain
integrator ModifierTPI
integrator SimulationVirial
integrator TestLJAssociationMC3D_NPT
integrator ZeoliteSimulation
The Integrator performing the dynamics.
Integrator etomica.integrator
Integrator implements the algorithm used to move the atoms around and
generate new configurations in one or more boxs.
Integrator() Integrator
Integrator.Forcible etomica.integrator
Integrator agent that holds a force vector.
Integrator.Torquable etomica.integrator
Integrator agent that holds a torque vector.
integrator1 DeviceThermoSliderGEMC
integrator1 MCMoveMoleculeExchange
integrator1 GCRestrictedGibbsHS
integrator2 DeviceThermoSliderGEMC
integrator2 MCMoveMoleculeExchange
integrator2 GCRestrictedGibbsHS
integrator3 DeviceThermoSliderGEMC
integratorA MultiharmonicMC
integratorA MultiharmonicMC
IntegratorAction etomica.action
Elementary action performed on an integrator.
IntegratorActionAdapter etomica.action
Convenience class used to define a IntegratorAction.
IntegratorActionAdapter() IntegratorActionAdapter
IntegratorActionAdapter(Integrator) IntegratorActionAdapter
Constructs the Action with the given descriptive label.
integratorAgentManager PotentialCalculationForceSum
integratorB MultiharmonicMC
integratorB MultiharmonicMC
IntegratorBox etomica.integrator
Superclass of integrators that acts on a single box.
IntegratorBox(PotentialMaster, double, Box) IntegratorBox
integratorDCV DCVGCMD
integratorDCV DCVGCMD
IntegratorDCVGCMD etomica.dcvgcmd
IntegratorDCVGCMD etomica.modules.dcvgcmd
IntegratorDCVGCMD(PotentialMaster, double, ISpecies, ISpecies, Box) IntegratorDCVGCMD
IntegratorDCVGCMD(PotentialMaster, double, ISpecies, ISpecies, Box) IntegratorDCVGCMD
IntegratorDCVGCMD.Mu1Modulator etomica.modules.dcvgcmd
IntegratorDCVGCMD.Mu2Modulator etomica.modules.dcvgcmd
integratorDimer SimDimerLJadatom
integratorDimer SimKMCLJadatom
IntegratorDimerApproach etomica.action
IntegratorDimerApproach(PotentialMaster, Box) IntegratorDimerApproach
integratorDimerMin SimDimerLJadatom
IntegratorDimerMin etomica.dimer
Henkelman's Dimer Method (Minimum Energy Path).
IntegratorDimerMin(Simulation, PotentialMaster, double, ISpecies[], Boolean, Box) IntegratorDimerMin
IntegratorDimerMin(Simulation, PotentialMaster, ISpecies[], Boolean, Box) IntegratorDimerMin
IntegratorDimerRT etomica.dimer
Henkelman's Dimer Method (Rotation and Translation).
IntegratorDimerRT(Simulation, PotentialMaster, ISpecies[], Box) IntegratorDimerRT
IntegratorDimerRT(Simulation, PotentialMaster, IRandom, double, ISpecies[], Box) IntegratorDimerRT
IntegratorDroplet etomica.modules.droplet
Mesoscale integrator for Droplet module.
IntegratorDroplet(PotentialMaster, IRandom, double, double, Box) IntegratorDroplet
IntegratorDroplet(Simulation, PotentialMaster, Box) IntegratorDroplet
IntegratorDroplet.MyAgent etomica.modules.droplet
IntegratorEnergyMap etomica.dimer
IntegratorEnergyMap(Simulation, PotentialMaster, IAtom, String, Box) IntegratorEnergyMap
IntegratorEvent etomica.integrator
IntegratorEvent(Integrator) IntegratorEvent
IntegratorEventManager etomica.integrator
IntegratorEventManager(Integrator) IntegratorEventManager
IntegratorFixedWall etomica.interfacial
IntegratorFixedWall(PotentialMaster, IRandom, double, double, Box) IntegratorFixedWall
integratorForceComputed(IntegratorEvent) IntegratorListenerMD
Invoked after the integrator has computed the forces on all atoms
in the system.
integratorForceComputed(IntegratorEvent) FixedWall
integratorForcePrecomputed(IntegratorEvent) IntegratorListenerMD
Invoked before the integrator computes the forces on all atoms
in the system.
integratorForcePrecomputed(IntegratorEvent) FixedWall
IntegratorGear4 etomica.integrator
Gear 4th-order predictor-corrector integrator.
IntegratorGear4(PotentialMaster, IRandom, double, double, Box) IntegratorGear4
IntegratorGear4(Simulation, PotentialMaster, Box) IntegratorGear4
IntegratorGear4.Agent etomica.integrator
integratorGEMC VLESim
integratorGEMC SWVLESim
integratorGEMC VLESim
IntegratorGEMC etomica.integrator
Simple Gibbs-ensemble Monte Carlo integrator.
IntegratorGEMC(IRandom, Space) IntegratorGEMC
integratorHard MeterCavityMapped
integratorHard MeterPairedFraction
integratorHard MeterPressureCollisionCount
integratorHard MeterRDFMapped
integratorHard DataSourceTensorVirialHard
integratorHard MeterPressureHard
integratorHard DataSourceWallPressureCatalysis
integratorHard ChainEquilibriumSim
integratorHard FreeRadicalPolymerizationSim
integratorHard DataSourceWallPressureMu
integratorHard SelfAssemblySim
IntegratorHard etomica.integrator
Integrator for hard potentials.
IntegratorHard(PotentialMaster, IRandom, double, double, Box) IntegratorHard
IntegratorHard(Simulation, PotentialMaster, Box) IntegratorHard
IntegratorHard.Agent etomica.integrator
Agent defined by this integrator.
IntegratorHard.CollisionHandlerUp etomica.integrator
IntegratorHard.CollisionListener etomica.integrator
integratorHard1 ReactionEquilibrium
IntegratorHardMDMC etomica.normalmode
Custom DMD integrator that handles hybrid simulations with
insertion/deletions.
IntegratorHardMDMC(Simulation, PotentialMaster, Box) IntegratorHardMDMC
IntegratorHardPiston etomica.modules.pistoncylinder
Integrator for DMD with a piston (P1HardMovingBoundary)
IntegratorHardPiston(Simulation, PotentialMaster, P1HardMovingBoundary, Box) IntegratorHardPiston
integratorHarmonic SimOverlapNitrogenModel
IntegratorHarmonic etomica.normalmode
Integrator that is used for the harmonic osciallating system
IntegratorHarmonic(IRandom, double, double, Box, CoordinateDefinition, Vector[]) IntegratorHarmonic
integratorHybrid Adsorption
IntegratorHybrid etomica.modules.adsorption
IntegratorHybrid(PotentialMasterHybrid, IntegratorMD, IntegratorMC, double) IntegratorHybrid
IntegratorImageHarmonicMD etomica.freeenergy.npath
Created by andrew on 4/30/17.
IntegratorImageHarmonicMD(PotentialMaster, IRandom, double, double, Box) IntegratorImageHarmonicMD
IntegratorImageMultistepMD etomica.freeenergy.npath
This integrator implements velocity Verlet algorithm and Tuckerman's
multi-step time step algorithm to handle propagating the spring forces.
IntegratorImageMultistepMD(PotentialMaster, IRandom, double, double, Box) IntegratorImageMultistepMD
integratorInitialized(IntegratorEvent) DataPumpListener
integratorInitialized(IntegratorEvent) DataPumpListenerPow
integratorInitialized(IntegratorEvent) DataPumpListenerPowStrict
integratorInitialized(IntegratorEvent) IntegratorListener
Invoked when integration begins.
integratorInitialized(IntegratorEvent) IntegratorListenerAction
integratorInitialized(IntegratorEvent) IntegratorListenerGroupSeries
integratorInitialized(IntegratorEvent) FixedWall
integratorInitialized(IntegratorEvent) ReactionManagerCO
integratorInitialized(IntegratorEvent) ConfigurationStorage
integratorInitialized(IntegratorEvent) MeterMBAR
integratorInitialized(IntegratorEvent) NeighborListManagerMolecular
integratorInitialized(IntegratorEvent) NeighborListManager
integratorKMC SimKMCLJadatom
integratorKMC() SimKMCLJadatom
IntegratorKMC etomica.kmc
IntegratorKMC(Simulation, PotentialMaster, double, IRandom, ISpecies[], Box) IntegratorKMC
integratorKMCCluster SimKMCLJadatom
integratorKMCCluster(double, int, int) SimKMCLJadatom
IntegratorKMCCluster etomica.kmc
IntegratorKMCCluster(Simulation, PotentialMaster, double, int, IRandom, ISpecies[], Box) IntegratorKMCCluster
integratorLiquid VLESim
integratorLiquid SWVLESim
integratorLiquid VLESim
IntegratorListener etomica.integrator
IntegratorListenerAction etomica.integrator
An IntegratorListener that performs an action after every integrator step,
optionally with a given interval of integrator steps.
IntegratorListenerAction(IAction) IntegratorListenerAction
IntegratorListenerAction(IAction, int) IntegratorListenerAction
IntegratorListenerGroupSeries etomica.integrator
A composition of IntegratorListeners that must be performed together and in sequence.
IntegratorListenerGroupSeries() IntegratorListenerGroupSeries
IntegratorListenerGroupSeries(IntegratorListener[]) IntegratorListenerGroupSeries
IntegratorListenerMD etomica.integrator
IntegratorManagerMC etomica.integrator
Integrator manages other Integrators which either act on a Box, or manage
still other Integrators.
IntegratorManagerMC(IRandom) IntegratorManagerMC
integratorMC IntegratorMD
integratorMC MCMoveIDBiasAction
integratorMC LjMd3D
integratorMC Adsorption
integratorMC IntegratorHybrid
integratorMC SimGlass
integratorMC SimHSMDVacancy
integratorMC MCMoveGeometricCluster
integratorMC MCMoveSpinCluster
integratorMC StarPolymerMC
IntegratorMC etomica.integrator
Integrator to perform Metropolis Monte Carlo sampling.
IntegratorMC(PotentialMaster, IRandom, double, Box) IntegratorMC
IntegratorMC(Simulation, PotentialMaster, Box) IntegratorMC
integratorMD SimDimerLJadatom
integratorMD Adsorption
integratorMD IntegratorHybrid
integratorMD StarPolymerMD
IntegratorMD etomica.integrator
Superclass of all molecular-dynamics integrators.
IntegratorMD(PotentialMaster, IRandom, double, double, Box) IntegratorMD
Constructs integrator with a default for non-isothermal sampling.
IntegratorMD.ThermostatType etomica.integrator
IntegratorMD.VectorSource etomica.integrator
An AgentSource that permits another vector to be associated with each atom.
IntegratorMDHarmonicMC etomica.freeenergy.npath
Created by andrew on 4/30/17.
IntegratorMDHarmonicMC(PotentialMaster, IRandom, double, double, Box) IntegratorMDHarmonicMC
integratorOS MultiharmonicMC
integratorOS MultiharmonicGraphicMC.DataSourceUa2
integratorOS MultiharmonicMC
integratorOS SimulationVirialOverlap2
integratorOverlap SimOverlapBetaN2RP
integratorOverlap SimOverlapNitrogenModel
integratorOverlap SimOverlap
integratorOverlap SimOverlapLJ
integratorOverlap SimOverlapLJModule
integratorOverlap SimOverlapModule
integratorOverlap SimOverlapSoftSphere
integratorOverlap SimOverlapSoftSphereEinHarm
integratorOverlap SimOverlapSoftSphereHCP
integratorOverlap SimOverlapSoftSphereReweighting
integratorOverlap SimOverlapSoftSphereSoftness
integratorOverlap SimOverlapSoftSphereSuperBox
integratorOverlap SimOverlapSSnxy
IntegratorOverlap etomica.overlap
This integrator class manages (2) sub-integrators for an overlap
sampling simulation.
IntegratorOverlap etomica.virial.overlap
Deprecated.
IntegratorOverlap(Integrator[]) IntegratorOverlap
IntegratorOverlap(Integrator[]) IntegratorOverlap
Deprecated.
IntegratorOverlap.ReferenceFracSource etomica.overlap
IntegratorPolymer etomica.modules.rheology
Integrator for Brownian dynamics of a polymer in a flow field.
IntegratorPolymer(PotentialMaster, IRandom, double, double, Box) IntegratorPolymer
IntegratorPT etomica.integrator
Parallel-tempering integrator.
IntegratorPT(IRandom, IntegratorPT.MCMoveSwapFactory, Space) IntegratorPT
IntegratorPT(IRandom, Space) IntegratorPT
IntegratorPT.BoxTracker etomica.integrator
Meter that tracks the swapping of the boxes in parallel-tempering
simulation.
IntegratorPT.MCMoveSwap etomica.integrator
Interface for a move that swaps two boxes.
IntegratorPT.MCMoveSwapFactory etomica.integrator
Interface for a class that can make a MCMove that will swap
the configurations of two boxes.
IntegratorReset etomica.action
Action that calls the reset method of an integrator.
IntegratorReset() IntegratorReset
IntegratorReset(Integrator, boolean) IntegratorReset
IntegratorRGEMC etomica.osmoticvirial
Simple Gibbs-ensemble Monte Carlo integrator.
IntegratorRGEMC(IRandom, Space, ISpecies) IntegratorRGEMC
IntegratorRigidIterative etomica.integrator
IntegratorRigidIterative(Simulation, PotentialMaster, double, double, Box) IntegratorRigidIterative
IntegratorRigidIterative(Simulation, PotentialMaster, Box) IntegratorRigidIterative
IntegratorRigidIterative.AtomForceAgent etomica.integrator
IntegratorRigidIterative.MoleculeAgent etomica.integrator
IntegratorRigidMatrixIterative etomica.integrator
Integrator implementation of Omelyan's leapfrog integrator for rotational
motion.
IntegratorRigidMatrixIterative(Simulation, PotentialMaster, double, double, Box) IntegratorRigidMatrixIterative
IntegratorRigidMatrixIterative(Simulation, PotentialMaster, Box) IntegratorRigidMatrixIterative
IntegratorRigidMatrixIterative.BoxImposePbcMolecule etomica.integrator
integrators IntegratorManagerMC
integrators SimOverlapBetaN2RP
integrators SimOverlapNitrogenModel
integrators SimOverlap
integrators SimOverlapLJ
integrators SimOverlapLJModule
integrators SimOverlapModule
integrators SimOverlapSoftSphere
integrators SimOverlapSoftSphereEinHarm
integrators SimOverlapSoftSphereHCP
integrators SimOverlapSoftSphereReweighting
integrators SimOverlapSoftSphereSoftness
integrators SimOverlapSoftSphereSuperBox
integrators SimOverlapSSnxy
integrators SimulationVirialOverlap2
IntegratorSmoother(AkimaSplineSmoother) AkimaSplineSmootherApp.IntegratorSmoother
IntegratorSmoother(AkimaSplineSmoother) AkimaSplineSmootherDyApp.IntegratorSmoother
integratorStep() BenchSimCatalysis
integratorStep() BenchSimDCVGCMD
integratorStep() BenchSimHSMD3D
integratorStep() BenchSimLammpsLJ
integratorStep() BenchSimLJGCMC3D
integratorStep() BenchSimLJMC3D
integratorStep() BenchSimLJMD3D
integratorStep() BenchSimSurfacetensionLJMC
integratorStep() BenchSimSWChain
integratorStep() BenchSimVirialLJ
integratorStep() BenchSimVirialH2OGCPMD
integratorStepFinished(IntegratorEvent) DataPumpListener
integratorStepFinished(IntegratorEvent) DataPumpListenerPow
integratorStepFinished(IntegratorEvent) DataPumpListenerPowStrict
integratorStepFinished(IntegratorEvent) IntegratorListener
Invoked at the end of each integrator step.
integratorStepFinished(IntegratorEvent) IntegratorListenerAction
integratorStepFinished(IntegratorEvent) IntegratorListenerGroupSeries
integratorStepFinished(IntegratorEvent) FixedWall
integratorStepFinished(IntegratorEvent) ReactionManagerCO
integratorStepFinished(IntegratorEvent) ConfigurationStorage
integratorStepFinished(IntegratorEvent) MeterMBAR
integratorStepFinished(IntegratorEvent) NeighborListManagerMolecular
integratorStepFinished(IntegratorEvent) NeighborListManager
integratorStepStarted(IntegratorEvent) DataPumpListener
integratorStepStarted(IntegratorEvent) DataPumpListenerPow
integratorStepStarted(IntegratorEvent) DataPumpListenerPowStrict
integratorStepStarted(IntegratorEvent) IntegratorListener
Invoked at the beginning of each integrator step.
integratorStepStarted(IntegratorEvent) IntegratorListenerAction
integratorStepStarted(IntegratorEvent) IntegratorListenerGroupSeries
integratorStepStarted(IntegratorEvent) FixedWall
integratorStepStarted(IntegratorEvent) ReactionManagerCO
integratorStepStarted(IntegratorEvent) ConfigurationStorage
integratorStepStarted(IntegratorEvent) MeterMBAR
integratorStepStarted(IntegratorEvent) NeighborListManagerMolecular
integratorStepStarted(IntegratorEvent) NeighborListManager
integratorTarg SimDirectBetaN2RP
integratorTarget SimOverlapNitrogenModel
integratorTarget SimOverlap
IntegratorTMMC etomica.tmmc
Integrator that implements Transition-Matrix Monte Carlo method.
IntegratorTMMC(PotentialMaster, IRandom, double, Box) IntegratorTMMC
IntegratorTMMC(Simulation, PotentialMaster, Box) IntegratorTMMC
integratorVapor VLESim
integratorVapor SWVLESim
integratorVapor VLESim
IntegratorVelocityVerlet etomica.integrator
IntegratorVelocityVerlet(PotentialMaster, IRandom, double, double, Box) IntegratorVelocityVerlet
IntegratorVelocityVerlet(Simulation, PotentialMaster, Box) IntegratorVelocityVerlet
IntegratorVelocityVerletQuaternion etomica.rotation
IntegratorVelocityVerletQuaternion(Simulation, PotentialMaster, double, double, Box) IntegratorVelocityVerletQuaternion
IntegratorVelocityVerletQuaternion(Simulation, PotentialMaster, Box) IntegratorVelocityVerletQuaternion
IntegratorVelocityVerletQuaternion.MoleculeAgent etomica.rotation
IntegratorVelocityVerletQuaternion.MyTypeAgent etomica.rotation
IntegratorVelocityVerletRattle etomica.integrator
Integrator implementing RATTLE algorithm.
IntegratorVelocityVerletRattle(Simulation, PotentialMaster, Box) IntegratorVelocityVerletRattle
IntegratorVelocityVerletRattle(Simulation, PotentialMaster, IRandom, double, double, Box) IntegratorVelocityVerletRattle
IntegratorVelocityVerletSAM etomica.modules.sam
Special integrator subclass that has the ability to prevent sulfur atoms
from moving in the Y direction.
IntegratorVelocityVerletSAM(PotentialMaster, IRandom, double, double, Box) IntegratorVelocityVerletSAM
IntegratorVelocityVerletShake etomica.integrator
Integrator implementing SHAKE algorithm.
IntegratorVelocityVerletShake(Simulation, PotentialMaster, Box) IntegratorVelocityVerletShake
IntegratorVelocityVerletShake(Simulation, PotentialMaster, IRandom, double, double, Box) IntegratorVelocityVerletShake
IntegratorVelocityVerletShake.BondConstraints etomica.integrator
IntegratorVerlet etomica.integrator
IntegratorVerlet(PotentialMaster, IRandom, double, double, Box) IntegratorVerlet
IntegratorVerlet(Simulation, PotentialMaster, Box) IntegratorVerlet
IntegratorVerlet.Agent etomica.integrator
intenseFraction Shader
interactionAgentManager DataSourceWallPressureCatalysis
interactionAgentManager MeterDensityCO
interactionAgentManager MeterDensityCO2
interactionAgentManager MeterDensityO2
interactionRange CriterionSimple
interactionRange CriterionSimpleMolecular
interactionS Heisenberg.Param
interactionS Heisenberg3Pair.Param
interactionS HeisenbergPair.Param
interactionTracker Catalysis
InteractionTracker etomica.modules.catalysis
InteractionTracker(Box, ISpecies) InteractionTracker
InteractionTracker.CatalysisAgent etomica.modules.catalysis
InterfacialSW etomica.modules.interfacial
Simulation for interfacial tension module.
InterfacialSW(Space) InterfacialSW
InterfacialSWGraphic etomica.modules.interfacial
Graphic UI for interfacial tension module.
InterfacialSWGraphic(InterfacialSW, Space) InterfacialSWGraphic
InterfacialSWGraphic.Applet etomica.modules.interfacial
InterfacialSWGraphic.DataProcessorTensorSplitter etomica.modules.interfacial
Inner class to find the total pressure of the system from the pressure
tensor.
InterfacialSWGraphic.ModifierBoxSize etomica.modules.interfacial
interiorColor ColorSchemeDropletSurface
intermolecular Token
internal MeterCavityMapped
internal MeterPairedFraction
internal MeterRDFMapped
INTERNAL_BOUNCE P2HardSphereCavity.CollisionType
internalCollisions DataProcessorCavity
internalCollisions MeterCavityMapped
internalCollisions MeterContactRatio
internalCollisions MeterRDFMapped
internalDataSink DataTableWriter
interpolatedDy AkimaSpline
interpolatedY AkimaSpline
interPotential ParserLAMMPS.Stuff
Interpreter etomica.graph.engine
Interpreter(ConsoleContainer, Environment, Parser) Interpreter
Interpreter.InterpreterException etomica.graph.engine
InterpreterException(String) Interpreter.InterpreterException
InterpreterException(String, Throwable) Interpreter.InterpreterException
intersectPlane(Point4f, float, int) BoxInfo
returns a set of points defining the geometric object within the given
plane that spans the unit cell within the given margins
intersectPlane(Point4f, List<Object>, int) TriangleData
a generic cell - plane intersector -- used for finding the plane through a
unit cell
intersects(BitSet) BitSet
Returns true if the specified BitSet has any bits set to
true that are also set to true in this BitSet.
interType Potential0Lrc
interval DataPumpListener
interval DataPumpListenerPow
interval DataPumpListenerPowStrict
interval HistoryCollapsing
interval Integrator
interval AccumulatorPTensor
interval ConfigurationStorage
interval DataSourceHisogram
interval DataSourceHistogramMSD
interval DataSourcePMSDHistory
interval GlassClustering.SimParams
interval ReadCluster.ReadClusterParams
interval StarPolymerMC.PolymerParam
interval StarPolymerMD.PolymerParam
intervalCount DataPumpListener
intervalCount DataPumpListenerPowStrict
intervalCount HistoryCollapsing
intervalCountdown ConfigurationStorage
intervals DataPumpListenerPow
intoTruncatedOctahedron BoundaryTruncatedOctahedron
intparam Token
IntParameters etomica.graph.operations
IntParameters(byte) IntParameters
intproperty Token
intramolecular Token
intraPotential ParserLAMMPS.Stuff
introspect(Object, String, BeanInfo) Dimension
Method to determine the dimension of a property via introspection.
IntSet etomica.virial
An IntSet holds an array of integers and can act as a has key.
IntSet(int[]) IntSet
IntSet.PropertyBin etomica.virial
intToken(int) Token
intValue Token
inv() Quaternion
invalidatePolygons() MeshSurface
inverse() Quaternion
Returns the inverse of the Quaternion q given by q^-1 = 1/(norm^2) * q*
inverse(double) Function.Exp
inverse(double) Function.Identity
inverse(double) Function.Linear
inverse(double) Function.Log
inverse(double) Function.Reciprocal
inverse(double) Function.Sqrt
inverse(double) FunctionChain
Inverts function by calling inverse methods of subfunctions, in reverse order of their addition.
inverse(double) FunctionInvertible
inverse(double) StatisticsMCGraphic.MyFunctionInvertible
inverse(double) MaxwellBoltzmann.Distribution
inverseProduct3D(Vector, Vector, Vector) P2SpheroPolyhedron
inverseProduct4D(Vector, Vector, Vector) P2SpheroPolyhedron
invert() LatticePlane
Changes the direction of the normal vector so that it points
toward the other side of the plane from its present orientation.
invert() Plane
Changes the direction of the normal vector so that it points
toward the other side of the plane from its present orientation.
invert() FastFourierTransform
Reverse Transformation of discrete data sets
invert() Tensor
Replaces this tensor with its inverse.
invert() Tensor1D
invert() Tensor2D
invert() RotationTensor3D
invert() Tensor3D
invert() TensorND
invert() Matrix3f
Sets the value of this matrix to its inverse.
invert() Matrix4f
Sets the value of this matrix to its inverse.
invertInPlace(BitSet, int) BitSetUtil
inverts the bitset bits 0 through n-1,
and returns a reference to the modified bitset
invertM(Matrix3f) Matrix3f
Sets the value of this matrix to the matrix inverse of the passed matrix
m1.
invertM(Matrix4f) Matrix4f
Sets the value of this matrix to the matrix inverse of the passed matrix
m1.
invertRound(BigComplex) BigDecimalMath
Build the inverse and maintain the approximate accuracy.
invokeAdder(Object) ArrayProperty
invokeAdder(Object) AtomListProperty
invokeAdder(Object) InstanceProperty
invokeAdder(Object) MoleculeListProperty
invokeAdder(Object) Property
invokeAdder(Object) VectorProperty
invokeCount() ArrayProperty
invokeCount() AtomListProperty
invokeCount() InstanceProperty
invokeCount() MoleculeListProperty
invokeCount() Property
invokeCount() VectorProperty
invokeReader() ArrayProperty
invokeReader() AtomListProperty
invokeReader() InstanceProperty
invokeReader() MoleculeListProperty
invokeReader() Property
invokeReader() VectorProperty
invokeReader(int) ArrayProperty
invokeReader(int) AtomListProperty
invokeReader(int) InstanceProperty
invokeReader(int) MoleculeListProperty
invokeReader(int) Property
invokeReader(int) VectorProperty
invokeRemover(Object) ArrayProperty
invokeRemover(Object) AtomListProperty
invokeRemover(Object) InstanceProperty
invokeRemover(Object) MoleculeListProperty
invokeRemover(Object) Property
invokeRemover(Object) VectorProperty
invokeWriter(int, Object...) ArrayProperty
invokeWriter(int, Object...) AtomListProperty
invokeWriter(int, Object...) InstanceProperty
invokeWriter(int, Object...) MoleculeListProperty
invokeWriter(int, Object...) Property
invokeWriter(int, Object...) VectorProperty
invokeWriter(Object...) ArrayProperty
invokeWriter(Object...) AtomListProperty
invokeWriter(Object...) InstanceProperty
invokeWriter(Object...) MoleculeListProperty
invokeWriter(Object...) Property
invokeWriter(Object...) VectorProperty
ionic Token
IONIC EnumVdw
iopt P2WaterPotentialsJankowski
iOrder ClusterWheatleyPT.ClusterRetrieveOrders
iOrientation AtomOriented
iOrientation AtomOrientedDynamic
iOrientation MCMoveRotate
IOrientation etomica.space
Interface for a class that specifies an orientation in space.
IOrientation2D etomica.space2d
Interface for a class that specifies an orientation in a 2D space.
IOrientation3D etomica.space3d
Interface for an orientation in 3D.
IOrientationFull3D etomica.space3d
Interface representing an orientation in 3D.
iparams P2CO2H2OWheatley
iPosition CoordinatePairMoleculeSet
IPotential etomica.potential
IPotential0Lrc etomica.potential
Interface for a long-range correction potential.
IPotential0MoleculeLrc etomica.potential
Interface for a long-range correction potential.
IPotentialAtomic etomica.potential
IPotentialAtomicMultibody etomica.potential
Interface for an atomic non-additive potential.
IPotentialAtomicSecondDerivative etomica.potential
IPotentialCalculationWallForce etomica.modules.rosmosis
IPotentialMolecular etomica.potential
IPotentialMolecularSecondDerivative etomica.potential
IPotentialMolecularTorque etomica.potential
IPotentialTorque etomica.potential
iPotParts P2WaterPotentialsJankowski
ipr P2WaterPotentialsJankowski
iRand MCMoveHarmonic
IRandom etomica.util.random
Interface for random number generation.
Iron etomica.chem.elements
Class for the Iron element.
Iron(String) Iron
Iron(String, double) Iron
iroots() BigIntegerPoly
Generate the integer roots of the polynomial.
irpowex P2HydrogenPatkowski
irpowex P2HydrogenPatkowskiAtomic
irpowsp P2HydrogenPatkowski
irpowsp P2HydrogenPatkowskiAtomic
IS_EMPTY Feature
IS_EQUAL Feature
is864 CoordinateDefinitionLeafSuperBox
is864() CoordinateDefinitionLeafSuperBox
isAB(Object) Escape
isAccepted() MCMoveTrialCompletedEvent
isActive() DataAccumulator
isActiveLevel(int) Logger
Tells if a logging level is active.
isAD(Object) Escape
isAdiabatic() DeviceThermoSlider
isAdiabatic() DeviceThermoSliderGEMC
isAdjustStepFraction() IntegratorOverlap
Sets whether to adjust the number of relative number of steps for each
sub-integrator.
isAdjustStepFreq() IntegratorOverlap
Deprecated.
Sets whether to adjust the number of relative number of steps for each
sub-integrator.
isAF(Object) Escape
isAFF(Object) Escape
isAFFF(Object) Escape
isAFloat(Object) Escape
isAI(Object) Escape
isAII(Object) Escape
isAllEVal() DeviceEigenvaluesSlider
isAllowEqualElements() IndexIteratorTriangular
isAllWV() DeviceWaveVectorSlider
isAlpha CoordinateDefinitionNitrogen
isAlpha CoordinateDefinitionNitrogenSuperBox
isAntialiased() GData
is full scene / oversampling antialiasing in effect
isAP(Object) Escape
isAppend() XYZWriter
isAppending() DataLogger
isApplyToMolecules() BoxImposePbc
Returns the value of applyToMolecules.
isaromatic Token
isArticulated(Graph, int, int) FactorFFT
isArticulationPair(int, int) ClusterGenerator
determines if the given pair of points is an articulation pair.
isArticulationPair(Graph, int, int) IsArticulationPair
IsArticulationPair etomica.graph.property
IsArticulationPair() IsArticulationPair
isArticulationPoint(int) ClusterGenerator
Determines if the given point is an articulation point.
isArticulationPoint(Graph, int) IsArticulationPoint
IsArticulationPoint etomica.graph.property
IsArticulationPoint() IsArticulationPoint
isAS(Object) Escape
isASS(Object) Escape
isAssociated(IAtom, IAtom) AssociationDefinition
isAssociated(IAtom, IAtom) BiasVolume
isAssociated(IAtom, IAtom) BiasVolumeCube
Function to check for bonding
isAssociated(IAtom, IAtom) BiasVolumeSphere
Function to check for bonding
calculate the distance between atom1 and atom2
isAssociated(IAtom, IAtom) BiasVolumeSphereOriented
Function to check for bonding
calculate the distance between atom1 and atom2
isAssociated(IAtom, IAtom) BiasVolumeSphereOrientedDoubleSites
Function to check for bonding
calculate the distance between atom1 and atom2
isAssociated(IMolecule, IMolecule) AssociationDefinitionMolecule
isAssociated(IMolecule, IMolecule) BiasVolume2SiteAceticAcid
Function to check for bonding
calculate the distance between atom1 and atom2
isAssociated(IMolecule, IMolecule) BiasVolumeAceticAcid
Function to check for bonding
calculate the distance between atom1 and atom2
isAssociated(IMolecule, IMolecule) BiasVolumeMolecule
isAssociation P2AceticAcidTwoSite
isAssociation P2HardAssociationGCPMReference
isAssociation PNWaterGCPMThreeSite
isAtomInString(IAtom) ColorSchemeDeviation
isAV(Object) Escape
isB ClusterWheatleyExtendSW
isBeta CoordinateDefinitionNitrogen
isBeta SimOverlapBetaN2TP.SimOverlapParam
isBeta SimOverlapDisorderedAlphaN2TP.SimOverlapParam
isBetaHCP CoordinateDefinitionNitrogen
isBetaHCP SimOverlapBetaN2TP.SimOverlapParam
isBetaHCP SimOverlapDisorderedAlphaN2TP.SimOverlapParam
isBetaLatticeSum CoordinateDefinitionNitrogen
isBetaPhase MeterTargetTPMolecule
isBetaPhase() MeterTargetTPMolecule
isBi ComparatorBiConnected
isBi ReeHoover
isBi FFTDecomposition
isBiColor() EnumStereoMode
IsBiconnected etomica.graph.property
IsBiconnected() IsBiconnected
isBigInteger() BigSurd
True if the value is integer.
isBigInteger() Rational
True if the value is integer.
isBonded() CriterionBondedSimple
isBonded(IAtomList) P2HardBondedList
isBonded(IAtom, IAtom) P2HardBondedList
Returns true if the pair of atoms are on each others' bonded list; false otherwise.
isBoundaryWall() CriterionPositionWall
Returns true if the walls are at the box boundaries.
isBroken MultiharmonicGraphicMC.DataSourceAlphaChi
isCartesianExport() Graphics3D
isCellEditable(int, int) DeviceTableModelGeneric
isCellEditable(int, int) ModelMoleculeListDisplayTable_new
isCellEditable(int, int) ModelMoleculeListDisplayTable
isCellEditable(int, int) ModelPotParamDisplayTable
isClipped(int, int) GData
isClipped3(int, int, int) GData
isClippedXY(int, int, int) GData
isClippedZ(int) GData
isCloseFileEachTime() DataLogger
isCO2 Virial2CLJmuQ.Virial2CLJQParam
isCO2 Virial2CLJQ.Virial2CLJQParam
isColixColorInherited(short) Colix
isColixLastAvailable(short) Colix
isColixTranslucent(short) Colix
isCollapseOnReset() HistoryComplete
Returns true if the history is collapsed (to 100 data points) when reset
is called.
isColorSolid MeshSurface
isCompatible(Edge) Edge
isCompatible(Edge) EdgeImpl
isCompatible(Metadata) MetadataImpl
isCompatible(Metadata) Metadata
isCompatible(Node) NodeImpl
isCompatible(Node) Node
isCon SplitGraph
isConnected HasSimpleArticulationPoint
isConnected() HasSimpleArticulationPoint
isConnected() ClusterGenerator
Determines if the cluster is connected.
isConnected(int) ClusterGenerator
Determines if the cluster is connected after removal of the
given node.
IsConnected etomica.graph.property
IsConnected() IsConnected
isContextClass(Class) Construction
isDead() SearchState
isDead() UllmanSearchState
isDead() VF2SearchState
isDead() VFSearchState
isDecimalMode() ScientificFormat
isDecimalSeparatorAlwaysShown() ScientificFormat
isDirectedTowardsCamera(short) Graphics3D
isDirectedTowardsCamera(short) GData
isDisplayAntialiased() GData
is full scene / oversampling antialiasing GENERALLY in effect
isDoClear() DisplayPlot
isDoLatticeSum CoordinateDefinitionNitrogen
isDoLegend() DisplayPlot
Accessor for flag determining if a legend is to be shown.
isDoPBC() BoundaryDeformablePeriodicSwitch
isDoPBC() BoundaryRectangularPeriodicSwitch
isDoScaling() MeterTargetRPMolecule
isDoWiggle() ModelSimulationEnvironment
isDynamic() ISpecies
Returns whether the Species is dynamic.
isDynamic() SpeciesGeneral
isDynamic() SpeciesGeneralMutable
isEditable() DeviceBox
isElementary() ClusterGenerator
Convenience method to determine whether the cluster is elementary or not.
isEmpty() AtomArrayList
isEmpty() AtomPair
isEmpty() AtomSetSinglet
isEmpty() GraphList
isEmpty() MoleculeArrayList
isEmpty() MoleculePair
isEmpty() MoleculeSetSinglet
isEmpty() IndexMap
isEmpty() BitSet
Returns true if this BitSet contains no bits that are set to
true.
isEmpty(IAtom) P2SquareWellRadical
isEmpty(Graph) FactorFFT
isEnabled Grabber.DefaultMouseListener
isEnabled() DeviceSlider
isEnabled() PotentialMaster
isEnabled() PotentialMasterLrc
isEnabled() Grabber.ActionCornerSetter
isEnabled(IPotentialAtomic) PotentialGroup
Returns true if the potential is in this group and has not been disabled
via a previous call to setEnabled; returns false otherwise.
isEnabled(IPotentialAtomic) PotentialMaster
Returns true if the potential is in this group and has not been disabled
via a previous call to setEnabled; returns false otherwise.
isEnabled(IPotentialMolecular) PotentialMaster
Returns true if the potential is in this group and has not been disabled
via a previous call to setEnabled; returns false otherwise.
isEnablePBC() P2Nitrogen
isEqualTo(Quaternion) Quaternion
Returns whether the Quaternion is equal to another given Quaternion p
isExpanded InterfacialSWGraphic
isExponentialMode() ScientificFormat
isFatal SVGConverterException
Defines whether or not this is a fatal error condition
isFatal() SVGConverterException
isFeasiblePair(NodePair) SearchState
isFeasiblePair(NodePair) UllmanSearchState
isFeasiblePair(NodePair) VF2SearchState
isFeasiblePair(NodePair) VFSearchState
IsFFT etomica.graph.property
Property class that determines if a diagram can be decomposed by FFT.
IsFFT etomica.virial
IsFFT() IsFFT
IsFFT() IsFFT
isFile(File) SVGConverter
Returns true if f is a File.
isFitToWindow() DisplayTable
Accessor method for flag determining if table is squeezed to fit in
window.
isFlexibleMode() ScientificFormat
isFoundReverse HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
isFoundReverse HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
isFoundReverse HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
isFoundReverse HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
isFoundReverse HarmonicBetaNitrogenModelPairMoleculeSequentialLS
isFoundReverse HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
isFoundReverse HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
isGamma CoordinateDefinitionNitrogen
isGamma CoordinateDefinitionNitrogenSuperBox
isGoal() SearchState
isGoal() UllmanSearchState
isGoal() VF2SearchState
isGoal() VFSearchState
isGraphic CH4NVT.Param
isGraphic DHS_NVT.Param
isGraphic DLJ_NVT_1site.Param
isGraphic DHS_NVT.Param
isGraphic DLJ_NVT_1site.Param
isGraphic TIP4P_NVT.Param
isGraphics MinimizationTIP4P.SimParams
isGraphics ProtonDisorderGenerator.SimParams
isGraphics PolydisperseHS.HSPolyParam
isGroupingUsed() ScientificFormat
isHeadless() ApiPlatform
isHeadless() Platform
isHetero(String) JmolConstants
isIce ClathrateHarmonicFE.SimParams
isIce MinimizationTIP4P.SimParams
isIce ProtonDisorderGenerator.SimParams
isIce ConfigurationFileTIP4P
isIgnoreOverlap() ActivityIntegrate
isIgnoreOverlap() IntegratorReset
isIgnoreOverlap() SimulationRestart
isIgnoreOverlap() ZeoliteSimStart
isIllegal() Quaternion
Returns true if even a single component of the quaternion is either infinite or NaN
isIncludeAdiabatic() DeviceThermoSelector
isIncludeLrc() MeterHyperVirial
Indicates whether calculated energy should include
long-range correction for potential truncation (true) or not (false).
isIncludeLrc() MeterPotentialEnergy
Indicates whether calculated energy should include
long-range correction for potential truncation (true) or not (false).
isIncludeLrc() MeterPressure
Indicates whether calculated energy should include
long-range correction for potential truncation (true) or not (false).
isIncludeLrc() MeterPressureMolecular
Indicates whether calculated energy should include
long-range correction for potential truncation (true) or not (false).
isIncludeLrc() MeterPressureTensor
Indicates whether calculated energy should include
long-range correction for potential truncation (true) or not (false).
isIncludeLrc() MeterPU
Indicates whether calculated energy should include
long-range correction for potential truncation (true) or not (false).
isIncludeLrc() MeterPressure2
Indicates whether calculated energy should include
long-range correction for potential truncation (true) or not (false).
isIncludeLrc() MeterPressureSuperBox
Indicates whether calculated energy should include
long-range correction for potential truncation (true) or not (false).
isIncludeLrc() SimEinStep2.MeterPotentialEnergyComposite
isIncludeLrc() SimEinStep2HCP.MeterPotentialEnergyComposite
isIncludeLrc() SimOverlapSoftSphereEin.MeterPotentialEnergyComposite
isIncludeLrc() SimOverlapSoftSphereEinHarm.MeterPotentialEnergyComposite
isIncludeLrc() IteratorDirective
Sets flag indicating if lrc potentials (long-range correction) should be
included.
isIndexedProperty() ArrayProperty
isIndexedProperty() AtomListProperty
isIndexedProperty() InstanceProperty
isIndexedProperty() MoleculeListProperty
isIndexedProperty() Property
isIndexedProperty() VectorProperty
isInDisplayRange(int, int) GData
Ising etomica.spin.ising
Simulation of a simple 2D Ising model.
Ising() Ising
Ising(Space, int) Ising
isInitialized() Integrator
isInteger() DeviceBox
isInteger() Rational
True if the value is integer and in the range of the standard integer.
isIntegerDisplay() DisplayTextBox
isIntegerFrac() Rational
True if the value is a fraction of two integers in the range of the standard integer.
isInteractingList MoleculePotentialList
isInteractive MayerIonicDiagram1qbond
isInteractive MayerIonicDiagram2qbonds
isInteractive MayerIonicDiagram4qbonds
isInteractive VirialDiagrams
isInteractive VirialDiagramsMix
isInteractive VirialDiagramsMix2
isInteractive VirialDiagramsPT
isInteractive WertheimDiagrams2SiteRho
isInteractive WertheimDiagrams3SiteRho
isInTetrahedron(Point3f, Point3f, Point3f, Point3f, Point3f, Point4f, Vector3f, Vector3f, Vector3f, boolean) Measure
isIsoFree() ConstructorColoredImpl
isIsoFree() ConstructorMonoImpl
isIsoFree() Parser.ConstructorColored
isIsoFree() Parser.ConstructorMono
isIsomorphOf(ClusterDiagram) ClusterDiagram
Returns true if this cluster is an isomorph of the given cluster.
isIsothermal() DeviceThermoSlider
isIsothermal() DeviceThermoSliderGEMC
isIsothermal() IntegratorBox
iskiosk Token
isLazySafe() IndexIterator
Indicates whether it is appropriate to simply scale the original
boundary lines when in 'large box' mode.
isLiquid DataSourceDensityFunction
isLJ MeterSolidProps
isLS PotentialCalculationEFSSP
isMatch(String, String, boolean, boolean) TextFormat
isMaximumScore() ClusterGenerator
Determines if the cluster has a maximum score.
isMerged MeshSurface
ISMORPHS_COUNT Match
isMovable() DisplayCanvas
isMovable() DisplayPolytope
isNaN() IData
Returns true if any data value is true for Double.isNaN
isNaN() DataDouble
Returns true if the this instance's value is NaN.
isNaN() DataDoubleArray
Returns true if any element of the encapsulated array is not-a-number, as
given by Double.isNaN.
isNaN() DataDoubleBDArray
isNaN() DataGroup
isNaN() DataTensor
Returns true if any vector element is not-a-number, as given by
Double.isNaN.
isNaN() DataVector
Returns true if any vector element is not-a-number, as given by Double.isNaN.
isNaN() Tensor
isNaN() Vector
Returns true if any element of the vector is not-a-number.
isNaN() Tensor1D
isNaN() Vector1D
isNaN() Tensor2D
isNaN() Vector2D
isNaN() Tensor3D
isNaN() Vector3D
isNaN() TensorND
isNaN() VectorND
isNaturalIsotope(String) Elements
isNewPair FindPairMoleculeIndex
isNewPair FindPairMoleculeIndexBetaN2
isNodalPoint(int) ClusterGenerator
Determines if the given node is a nodal point.
isNominallyPerParticleFrequency() MCMoveBox
Indicates whether this move should nominally be performed at a frequency
proportional to the number of molecules in the box.
isoFree Split
IsoFree etomica.graph.operations
IsoFree() IsoFree
IsoFree.IsoFreeParams etomica.graph.operations
IsoFreeParams() IsoFree.IsoFreeParams
IsomorphismFilter etomica.graph.iterators.filters
IsomorphismFilter(GraphIterator) IsomorphismFilter
IsomorphismFilter(GraphIterator, GlobalFilter.SignatureMaker) IsomorphismFilter
IsomorphismPrefilteredPartitionedIterator etomica.graph.iterators
IsomorphismPrefilteredPartitionedIterator(Map<Character, Byte>, Map<Character, Byte>) IsomorphismPrefilteredPartitionedIterator
isOneEVal() DeviceEigenvaluesSlider
isOneEVal() IntegratorHarmonic
isOneOf(String, String) Parser
isOneWV() DeviceWaveVectorSlider
isOneWV() IntegratorHarmonic
isosurface Token
isosurfacekey Token
isosurfacepropertysmoothing Token
isosurfacepropertysmoothingpower Token
isothermal IntegratorBox
isPaletteVariable(byte) EnumPalette
isPass2 GData
isPass2() GData
isPaused() Controller
ISpecies etomica.species
An ISpecies holds information about how to construct a molecule, and creates molecules on demand.
isPeriodic RectangularLatticeNbrIterator
isPolydisperse PolydisperseHS.HSPolyParam
isPositive() BigValue
isPositive() IBigValue
Returns true if this instance has a value greater than zero.
isPositive() MyBigDecimal
isPositiveSide(Vector) LatticePlane
Returns true if the given point is on the side of the
plane toward which the normal vector points.
isPositiveSide(Vector) Plane
Returns true if the given point is on the side of the
plane or over the side of the plane by epsilon or less
toward which the normal vector points.
isPotentialHard PotentialMaster
isPotentialHard() PotentialMaster
Flag indicating indicating that the only energetic interactions are based on hard potentials, which
prohibit overlap but otherwise have zero energy.
isPotentialSite(String, IMolecularModel_SpeciesFactory) BuilderCollectionPotential
IsPotentialSiteMoreThanOne() MolecularModelEMP2_SpeciesCO2
IsPotentialSiteMoreThanOne() MolecularModelSKS_SpeciesAlkane
IsPotentialSiteMoreThanOne() MolecularModelSPCE_SpeciesH2O
IsPotentialSiteMoreThanOne() MolecularModelTRAPPE_SpeciesAlkane
IsPotentialSiteMoreThanOne() MolecularModelTrappe_SpeciesCO2
isPT2 P2O2Bartolomei
isPT2 VirialO2.VirialO2Param
isPT2 VirialO2PI.VirialO2Param
isPureQuaternion() Quaternion
Returns whether the Quaternion is pure or not
isqrt(int) BigIntegerMath
Evaluate floor(sqrt(n)).
isqrt(long) BigIntegerMath
Evaluate floor(sqrt(n)).
isqrt(BigInteger) BigIntegerMath
Evaluate floor(sqrt(n)).
isQuiet() NeighborListManagerMolecular
isQuiet() NeighborListManager
isRadical InteractionTracker.CatalysisAgent
isRadical(IAtom) P2SquareWellRadical
This function return true if the given atom is a radical (meaning that
it has only one unreacted site).
isRational() BigSurd
True if the value is rational.
isReadable() SVGConverterDocumentSource
isReadable() SVGConverterFileSource
isReadable() SVGConverterSource
Checks if source can be read
isReadable() SVGConverterURLSource
isReference MeterOverlap
isRejectable IntegratorHarmonic
isRejectable MCMoveHarmonic
isRejectable() MCMoveHarmonic
isRemoveSpeciesAfterAlertFlag() ModelSpeciesSelection
isRescalingToFitVolume() ConfigurationLattice
Returns the resizeLatticeToFitVolume flag.
isResidual() MeterWidomInsertion
Accessor for flag specifying if full or residual chemical potential is
computed
isResizable() DisplayCanvas
isResizable() DisplayPolytope
isRootPoint(int) ClusterDiagram
returns true if the given point is a root point
isRunningActivityStep() Controller
isSameAs(String) SVGConverterDocumentSource
isSameAs(String) SVGConverterFileSource
isSameAs(String) SVGConverterSource
Checks if same as source described by srcStr
isSameAs(String) SVGConverterURLSource
isSameColor(Edge) Edge
isSameColor(Edge) EdgeImpl
isSameColor(Metadata) MetadataImpl
isSameColor(Metadata) Metadata
isSameColor(Node) NodeImpl
isSameColor(Node) Node
isSameFileEachTime() DataLogger
isSameId(Edge) Edge
isSameId(Edge) EdgeImpl
isSameId(Node) NodeImpl
isSameId(Node) Node
isSameType(Metadata) EdgeImpl
isSameType(Metadata) MetadataImpl
isSameType(Metadata) NodeImpl
isSameType(Metadata) Metadata
isSatisfied(FeatureSet) ClassRequirement
isSatisfied(FeatureSet) FeatureRequirement
isSatisfied(FeatureSet) Requirement
isSatisfied(FeatureSet) RequirementSet
isSelected(String) DeviceButtonGroup
Returns true if the button of the given label is selected.
isSelectMode MCMoveHarmonic
isShapeSecondary(int) JmolConstants
isShowBorder() DeviceSlider
isShowBorder() DeviceSpinner
isShowingColumnHeaders() DisplayTable
isShowingRowLabels() DisplayTable
Accessor method for flag indicating if table should include a column of
"x" values.
isShowingUnits() DisplayTable
isSingleThreaded() ApiPlatform
isSingleThreaded() Platform
isSpecies1AtomicFlag() BuilderCollectionPotential
isSpecies2AtomicFlag() BuilderCollectionPotential
isSpeciesAlreadyAdded(int) ModelSpeciesSelection
isSpeciesSelectionChanged() ModelSpeciesSelection
isSPP(BigInteger, BigInteger) Prime
Test whether a number n is a strong pseudoprime to base a.
issquare() Ifactor
Test whether this is a square of an integer (perfect square).
isStationary() P1HardMovingBoundary
isStopSimulation() ModelSimulationEnvironment
isString ColorSchemeDeviation
isStringArray(String) Escape
isThermalEllipsoid Quadric
isThermostatNoDrift() IntegratorMD
isTransposed() DisplayTable
If true, each data set fills a row; if false, data are arranged to fill
columns.
isTrial BoxCluster
isTriangleSet MeshSurface
isUnitQuaternion() Quaternion
Returns whether the norm of the Quaternion is 1 or not
isUpdatingOnAnyChange() DataSet
isUpperBound DataProcessorBounds
iSurf P2WaterPotentialsJankowski
iSurf VirialH2O.VirialH2OParam
isUsePermutations() ClusterBonds
Returns the usePermutations flag.
isValid(double[][][]) ClusterSumAssociation.ClusterCriteria
isValueProperty() ArrayProperty
isValueProperty() AtomListProperty
isValueProperty() InstanceProperty
isValueProperty() MoleculeListProperty
isValueProperty() Property
isValueProperty() VectorProperty
isVariableType(Object) ScriptVariable
isVisited DataSourcePercolation
isVisited DataSourcePercolation0
isVolFluctuation() MeterNormalizedCoord
isWild(String) TextFormat
isWithin(Point3f) BoxInfo
isWriteable(File) SVGConverter
Checks if the application is allowed to write to the file.
isWriteOnInterval() DataLogger
isXComp() DeviceCellNumXYSlider
isXFlipped() G3DSys
isYComp() DeviceCellNumXYSlider
isYFlipped() G3DSys
isyst P2WaterPotentialsJankowski
isZero() Vector
Returns true if all components of this vector are zero; false otherwise.
isZero() Vector1D
isZero() Vector2D
isZero() Vector3D
isZero() VectorND
isZero() BigIntegerPoly
Test whether this polynomial value is zero.
isZero() BigValue
isZero() IBigValue
Returns true if this instance has a value of zero.
isZero() MyBigDecimal
iT PotentialCalculationPhiSum
iTag MeterTiltRotationHistogram
itemStateChanged(ItemEvent) DimensionedDoubleEditor
ItemListener interface implementation.
itemStateChanged(ItemEvent) MyApplet.BondInteractionTypeToggler
itemStateChanged(ItemEvent) MyApplet.BondTypeToggler
itemStateChanged(ItemEvent) MyApplet.ConnectedToggler
itemStateChanged(ItemEvent) MyApplet.GraphicsToggler
itemStateChanged(ItemEvent) MyApplet.NumbersToggler
itemStateChanged(ItemEvent) MyApplet.PointsToggler
itemStateChanged(ItemEvent) MyApplet.ReeHooverToggler
iterator MeterDihedralAngle
iterator MeterRDF
iterator MCMoveMultiHarmonic
iterator MCMoveHarmonic
iterator MCMoveHarmonicStep
iterator MeterRmin
iterator MeterRminSpecies
iterator PotentialGroup.PotentialLinker
iterator PotentialMaster.PotentialLinker
iterator() AtomPair
iterator() AtomSetSinglet
iterator() GraphList
iterator() MoleculePair
iterator() MoleculeSetSinglet
Iterator(int) RectangularLattice.Iterator
iteratorDirective MeterHyperVirial
iteratorDirective MeterPotentialEnergy
iteratorDirective MeterPressureTensor
iteratorDirective MeterPotentialEnergyCutoff
iteratorDirective MeterPU
iteratorDirective MeterPUCut
iteratorDirective MeterPUCutLS
IteratorDirective etomica.potential
Encapsulation of a set of instructions that an AtomsetIterator
uses to select the atoms it presents on iteration.
IteratorDirective() IteratorDirective
IteratorDirective(IteratorDirective.Direction) IteratorDirective
IteratorDirective(IteratorDirective.Direction, IAtom) IteratorDirective
IteratorDirective(IteratorDirective.Direction, IMolecule) IteratorDirective
IteratorDirective.Direction etomica.potential
IteratorEF(byte, boolean) PYGenerator.IteratorEF
iteratorFactory PotentialMaster
IteratorFactory etomica.molecule.iterator
Class for construction of iterators of molecules.
IteratorFactory() IteratorFactory
IteratorToSet etomica.graph.iterators
IteratorToSet() IteratorToSet
IteratorWrapper etomica.graph.iterators
IteratorWrapper(Iterator<Graph>) IteratorWrapper
IteratorWrapper(Iterator<Graph>, boolean) IteratorWrapper
iThread MeterVirialBDBinMultiThreaded
iThread MeterVirialBinMultiThreaded
iThread MeterVirialEBinMultiThreaded
iThread VirialHSBinMultiThreaded.SimulationWorker
iThread VirialSQWBinMultiThreaded.SimulationWorker
itypus P2WaterPotentialsJankowski
iValue(Token) ScriptVariable
iweight P2WaterPotentialsJankowski
iy AkimaSplineSmootherDy
m PotentialEAM_LS
m PotentialEAM
m IndexIteratorIncreasing
m AkimaSpline
m AkimaSplineSmoother
m ClusterMultiToSingle
M FittingFunctionNonLinear
M RandomMersenneTwister
M_AD P2HePCJS
M_BO P2HePCJS
M_QED P2HePCJS
M_REL P2HePCJS
m00 Matrix3f
The first element of the first row.
m00 Matrix4f
The first element of the first row.
m01 Matrix3f
The second element of the first row.
m01 Matrix4f
The second element of the first row.
m02 Matrix3f
third element of the first row.
m02 Matrix4f
third element of the first row.
m03 Matrix4f
The fourth element of the first row.
m10 Matrix3f
The first element of the second row.
m10 Matrix4f
The first element of the second row.
m11 Matrix3f
The second element of the second row.
m11 Matrix4f
The second element of the second row.
m12 Matrix3f
The third element of the second row.
m12 Matrix4f
The third element of the second row.
m13 Matrix4f
The fourth element of the second row.
m2 P2EAM
m20 Matrix3f
The first element of the third row.
m20 Matrix4f
The first element of the third row.
m21 Matrix3f
The second element of the third row.
m21 Matrix4f
The second element of the third row.
m22 Matrix3f
The third element of the third row.
m22 Matrix4f
The third element of the third row.
m23 Matrix4f
The fourth element of the third row.
m2s(IMoleculeList) ClusterSumMultibody
m30 Matrix4f
The first element of the fourth row.
m31 Matrix4f
The second element of the fourth row.
m32 Matrix4f
The third element of the fourth row.
m33 Matrix4f
The fourth element of the fourth row.
m4dSum DataSourceAlpha2
MacrostateManager etomica.tmmc
Interface for class that defines the macrostates.
madMultipleBondSmallMaximum JmolConstants
MAG_DOT MeterCorrelationSelf.CorrelationType
MAGENTA Colix
MAGNITUDE CorrelationSelf2.CorrelationType
MAGNITUDE MeterCorrelation.CorrelationType
MAGNITUDE MeterCorrelationSelf.CorrelationType
main(String[]) CH4NVT
main(String[]) DHS_NVT
main(String[]) DLJ_NVT_1site
main(String[]) TestAceticAcidMC3D_NPT
main(String[]) Wertheim2SiteAceticAcid
main(String[]) SimGCPMWaterMCNPT
main(String[]) SimGCPMWaterMCNVT
main(String[]) WertheimGCPM3PtEBondDecomp
main(String[]) WertheimGCPM3PtThreeSite
main(String[]) WertheimGCPM4PtEBondDecomp
main(String[]) WertheimGCPM4PtEBondDecompFinal
main(String[]) WertheimGCPM4PtThreeSite
main(String[]) WertheimGCPM4PtThreeSiteEDecompDirectSampling
main(String[]) TestIGAssociationMC3D_NPT_DoubleSites
main(String[]) TestLJAssociationMC3D_NPT_DoubleSites
main(String[]) TestLJAssociationMC3D_NPT
main(String[]) TestLJAssociationMC3D_NVTOld
main(String[]) BenchApiAACell
main(String[]) BenchNbrUpdates
main(String[]) HSMDCavity
main(String[]) HSMDWidom
main(String[]) AccumulatorAverageBootstrap
main(String[]) AccumulatorAverageCollapsingLog
main(String[]) DataSourceUniform
Main method to demonstrate and check class.
main(String[]) DCVGCMD
main(String[]) DCVGCMDGraphic
main(String[]) DHS_NVT
main(String[]) DLJ_NVT_1site
main(String[]) TIP4P_NVT
main(String[]) SimDimerLJadatom
main(String[]) EFSTungsten
main(String[]) ReaderIn
main(String[]) ConfigFromFileLAMMPS
main(String[]) SimFe
main(String[]) SimIdealGas
main(String[]) SimLattice
main(String[]) SimLJ
main(String[]) Launcher
main(String[]) DropOrphanNodes
main(String[]) FFTDecomposition
main(String[]) IsFFT
main(String[]) GraphNumber
main(String[]) Main
main(String[]) ColorScheme
main(String[]) DeviceButton
Method to demonstrate and test the use of this class.
main(String[]) DeviceNSelector
main(String[]) DeviceTable
main method to demonstrate and test this class.
main(String[]) DeviceThermoSelector
main(String[]) DeviceToggleButton
Method to demonstrate and test the use of this class.
main(String[]) DeviceTrioControllerButton
main method to show how to work with this class
main(String[]) DisplayTable
Demonstrates how this class is implemented.
main(String[]) DisplayTextBoxesCAE
main(String[]) SimulationGraphic
Demonstrates how this class is implemented.
main(String[]) VLE
main(String[]) VLESim
main(String[]) IntegratorRigidIterative
main(String[]) LJMC
main(String[]) LJMD
main(String[]) SimKMCLJadatom
main(String[]) PrimitiveFcc
main(String[]) PrimitiveHexagonal
main(String[]) PrimitiveMonoclinic
main(String[]) PrimitiveTriclinic
main(String[]) IndexIteratorIncreasing
main(String[]) IndexIteratorRectangular
main method to test and demonstrate class.
main(String[]) IndexIteratorReflecting
Method to test and demonstrate class.
main(String[]) IndexIteratorTriangular
Method to test and demonstrate class.
main(String[]) IndexIteratorTriangularPermutations
Method to test and demonstrate class.
main(String[]) RectangularLatticeNbrIteratorAdjacent
Method to test the neighbor iterator.
main(String[]) RectangularLatticeNbrIteratorSquare
Method to test the neighbor iterator.
main(String[]) LjMC3D
main(String[]) LjMd3D
main(String[]) LjMd3Dv2y
main(String[]) Main
main(String[]) SimMappedRdf
main(String[]) MappedU
main(String[]) MappedVirialLJ
main(String[]) MappedVirialLJVGr
main(String[]) PotentialCalculationMappedEnergy
main(String[]) PotentialCalculationMappedVirial
main(String[]) PotentialCalculationMappedVirialV
main(String[]) CombinationIterator
main(String[]) FixedSumIterator
main(String[]) PermutationDegenerateIterator
main(String[]) PermutationIterator
main(String[]) Gamma
main(String[]) LineSegment
main(String[]) Plane
main(String[]) AkimaSpline
main(String[]) AkimaSplineSmootherApp
main(String[]) AkimaSplineSmootherDyApp
main(String[]) AkimaSplineSmootherMain
main(String[]) FastFourierTransform
main(String[]) LinearFit
main(String[]) PadeApproximation
main(String[]) PolynomialFit
main(String[]) VirialOptimizer
main(String[]) SpecialFunctions
main(String[]) DataSourceIndex
main(String[]) LJmuVT
main(String[]) LJNPT
main(String[]) LJNVT
main(String[]) ClathrateHarmonicFE
main(String[]) MinimizationTIP4P
main(String[]) ProtonDisorderGenerator
main(String[]) P2CO2H2OWheatley
Randomly moves molcules all over, computing and checking 2nd derivative
main(String[]) P2CO2Hellmann
main(String[]) PNCO2GCPM
main(String[]) PNGCPM
main(String[]) FindBetaN2AngleFromParameter
main(String[]) FindTransitionTemperature
main(String[]) HarmonicAlphaNitrogenModel
main(String[]) HarmonicAlphaNitrogenModelDecomposed
main(String[]) HarmonicAlphaNitrogenModelLatticeSum
main(String[]) HarmonicAlphaNitrogenModelPairMolecule
main(String[]) HarmonicAlphaNitrogenModelPairMoleculeSequential
main(String[]) HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2
main(String[]) HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
main(String[]) HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
main(String[]) HarmonicBetaNitrogenModel
main(String[]) HarmonicBetaNitrogenModelDecomposed
main(String[]) HarmonicBetaNitrogenModelLatticeSum
main(String[]) HarmonicBetaNitrogenModelPairMoleculeSequential
main(String[]) HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
main(String[]) HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2
main(String[]) HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
main(String[]) HarmonicBetaNitrogenModelPairMoleculeSequentialLS
main(String[]) HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
main(String[]) HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
main(String[]) MinimizationBetaNitrogenModel
main(String[]) MinimizationBetaNitrogenModelLS
main(String[]) MinimizeBetaNitrogenLatticeParameter
main(String[]) MinimizeBetaNitrogenLatticeParameterFromFile
main(String[]) MinimizeBetaNitrogenLatticeParameterLSFromFile
main(String[]) MinimizeBetaNitrogenTranslationDOF
main(String[]) MinimizeGammaNitrogenLatticeParameter
main(String[]) SimDirectBetaN2RP
main(String[]) SimDirectBetaN2RPAngleToNoAngle
main(String[]) SimDirectBetaN2RPInitPert
main(String[]) SimDirectDisorderedAlphaN2RPInitPert
main(String[]) SimOverlapAlphaN2TP
main(String[]) SimOverlapBetaN2RP
main(String[]) SimOverlapBetaN2RPScaling
main(String[]) SimOverlapBetaN2TP
main(String[]) SimOverlapDisorderedAlphaN2RPScaling
main(String[]) SimOverlapDisorderedAlphaN2TP
main(String[]) SimOverlapNitrogenModel
main(String[]) SimulationAlphaNitrogenModel
main(String[]) SimulationBetaNitrogenModel
main(String[]) SimulationBetaNitrogenModelTest
main(String[]) SimulationGammaNitrogenModel
main(String[]) TestRotationVector
main(String[]) DimerApproach
main(String[]) MassProductionVirialRowleyAlcohol
main(String[]) P2WaterSzalewicz
main(String[]) TestEwaldTIP4PWater
main(String[]) Adsorption
main(String[]) AdsorptionGraphic
main(String[]) Catalysis
main(String[]) CatalysisGraphic
main(String[]) ChainEquilibriumGraphic
main(String[]) FreeRadicalPolymerizationGraphic
main(String[]) ColloidGraphic
main(String[]) ColloidSim
main(String[]) CrystalViewer
main(String[]) DCVGCMD
main(String[]) DCVGCMDGraphic
main(String[]) Droplet
main(String[]) DropletAtomic
main(String[]) DropletAtomicGraphic
main(String[]) DropletGraphic
main(String[]) LJMC
main(String[]) LJMCGraphic
main(String[]) GlassClustering
main(String[]) GlassGraphic
main(String[]) GlassProd
main(String[]) ReadCluster
main(String[]) SimGlass
main(String[]) Insertion
main(String[]) InsertionGraphic
main(String[]) FitTanh
main(String[]) InterfacialSW
main(String[]) InterfacialSWGraphic
main(String[]) Ljmd
main(String[]) LjmdGraphic
main(String[]) MaterialFractureGraphic
/* main method
main(String[]) ModuleLauncher
main(String[]) Mu
main(String[]) MuGraphic
main(String[]) MultiharmonicGraphicMC
main(String[]) MultiharmonicGraphic
main(String[]) MultiharmonicGraphicMC
main(String[]) MultiharmonicGraphicMC
main(String[]) MultiharmonicGraphicMC
main(String[]) NucleationGraphic
main(String[]) SWVLE
main(String[]) Osmosis
main(String[]) OsmosisSim
main(String[]) PistonCylinderGraphic
main(String[]) ReactionEquilibriumGraphic
main(String[]) RheologyGraphic
main(String[]) SimulationRheology
main(String[]) ReverseOsmosis
main(String[]) ReverseOsmosisGraphic
main(String[]) ReverseOsmosisWater
main(String[]) ReverseOsmosisWaterGraphic
main(String[]) Sam
main(String[]) SamGraphic
main(String[]) SelfAssemblyGraphic
main(String[]) StatisticsMCGraphic
main(String[]) Swmd
main(String[]) SwmdGraphic
main(String[]) B2Fit
main(String[]) LJQB2
main(String[]) VLE
main(String[]) VLESim
main(String[]) ArrayA2B
main(String[]) ArrayB2A
main(String[]) CalcHarmonicA
main(String[]) HarmonicCrystal
main(String[]) HarmonicCrystalSoftSphereBCC
main(String[]) HarmonicCrystalSoftSphereFCC
main(String[]) HarmonicCrystalSoftSphereHCP
main(String[]) HarmonicCrystalSsFccNxy
main(String[]) HessianDB
main(String[]) HessianFromFile
main(String[]) HSDimerNPT
Demonstrates how this class is implemented.
main(String[]) HSNPT
Demonstrates how this class is implemented.
main(String[]) HTTPSoftSphereApplet
main(String[]) LJVacancyMin
main(String[]) MeterHarmonicEnergy
main(String[]) MinimizeHCP
main(String[]) NormalModeAnalysisDisplay1D
main(String[]) NormalModeAnalysisDisplay1DGraphic
main(String[]) NormalModeAnalysisDisplay2D
main(String[]) NormalModeAnalysisDisplay2DGraphic
main(String[]) NormalModeAnalysisDisplay3D
main(String[]) NormalModeAnalysisDisplay3DGraphic
main(String[]) NormalModeEigenGetter
main(String[]) NormalModes1DHR
main(String[]) NormalModes3D
main(String[]) HSNPT2DGraphic
Demonstrates how this class is implemented.
main(String[]) SimBennet
main(String[]) SimCalcJ
main(String[]) SimCalcS
main(String[]) SimCalcSLJ
main(String[]) SimCalcSMorse
main(String[]) SimCalcSSoftSphere2D
main(String[]) SimCalcSSoftSphereFCC
main(String[]) SimCalcSSoftSphereFCCSuperBox
main(String[]) SimEinStep1
main(String[]) SimEinStep1HCP
main(String[]) SimEinStep2
main(String[]) SimEinStep2HCP
main(String[]) SimFluidSoftSphere
main(String[]) SimHarmonic
main(String[]) SimHarmonicUmbrella
main(String[]) SimHSMDVacancy
main(String[]) SimLJHTTISuper
main(String[]) SimLJHTTISuperHCP
main(String[]) SimLJHTTISuperHCP2
main(String[]) SimLJHTTISuperSFMD
main(String[]) SimLJVacancy
main(String[]) SimModesJ
main(String[]) SimOverlap
main(String[]) SimOverlapLJ
main(String[]) SimOverlapLJModule
main(String[]) SimOverlapSoftSphere
main(String[]) SimOverlapSoftSphereDP
main(String[]) SimOverlapSoftSphereEin
main(String[]) SimOverlapSoftSphereEinHarm
main(String[]) SimOverlapSoftSphereHCP
main(String[]) SimOverlapSoftSphereReweighting
main(String[]) SimOverlapSoftSphereSoftness
main(String[]) SimOverlapSoftSphereSuperBox
main(String[]) SimOverlapSoftSphereTP
main(String[]) SimOverlapSoftSphereTPHCP
main(String[]) SimOverlapSoftSphereTPSlantedBox
main(String[]) SimOverlapSSnxy
main(String[]) SimTarget
main(String[]) SimTargetUmbrella
main(String[]) SimUmbrella
main(String[]) SimUmbrellaSoftSphere
main(String[]) SoftSphereSolidEOS
main(String[]) SoftSphereSolidEOSCalculator
main(String[]) WaveVectorFactory1D
main(String[]) WaveVectorFactory2D
main(String[]) WaveVectorFactoryFcc
main(String[]) WaveVectorFactorySimple
main(String[]) AshtonWildingLJ
main(String[]) AshtonWildingOsmoticVirial
main(String[]) AshtonWildingVirial
main(String[]) GCRestrictedGibbsHS
main(String[]) GCWidomInsertHS
main(String[]) NVTWidomInsertLJ
main(String[]) ParserLAMMPS
main(String[]) PolydisperseHS
main(String[]) P2ArgonSlavicekEtAl2003
main(String[]) P2ArgonTangAndToennies2003
main(String[]) P2DiscreteFeynmanHibbs
main(String[]) P2EffectiveFeynmanHibbs
main(String[]) P2HePCJS
main(String[]) P2HePCKLJS
main(String[]) P2HydrogenHinde
main(String[]) P2HydrogenPatkowski
main(String[]) P2HydrogenPatkowskiIso
main(String[]) P2MoleculeSoftTruncatedSwitched
main(String[]) P2NitrogenHellmann
main(String[]) P2O2Bartolomei
main(String[]) P2QChemInterpolated
main(String[]) P2SoftSphericalTruncatedSwitched
main(String[]) P2WaterPotentialsJankowski
main(String[]) P3AdditiveQChem
main(String[]) P3BondAngle
main(String[]) P3CPSNonAdditiveHe
main(String[]) P3CPSNonAdditiveHeLessSimplified
main(String[]) P3CPSNonAdditiveHeOrig
main(String[]) P3CPSNonAdditiveHeSimplified
main(String[]) P3HydrogenATM
main(String[]) P3HydrogenManzhos
main(String[]) P3Induction
main(String[]) P3QChem
main(String[]) P4BondTorsion
main(String[]) P4BondTorsionAlkaneXCCH
main(String[]) P4BondTorsionOPLS
main(String[]) PotentialEmul
main(String[]) DipoleBox
main(String[]) DipoleBoxMatrix
main(String[]) IntegratorVelocityVerletQuaternion
main(String[]) P2LJDipole
main(String[]) SingleDipole
main(String[]) SingleDumbellRattle
main(String[]) SingleDumbellShake
main(String[]) SingleWater
main(String[]) SingleWaterMatrix
main(String[]) SingleWaterRattle
main(String[]) SingleWaterShake
main(String[]) WaterBox
main(String[]) WaterDroplet
main(String[]) WaterDropletMatrix
main(String[]) WaterDropletRattle
main(String[]) WaterDropletShake
main(String[]) WaterTrimer
main(String[]) WaterTrimerRattle
main(String[]) WaterTrimerShake
main(String[]) EtomicaServer
main(String[]) BenchSimCatalysis
main(String[]) BenchSimLammpsLJ
main(String[]) BenchSimLJMD3D
main(String[]) BenchSimSWChain
main(String[]) BenchSimVirialLJ
main(String[]) ChainHSMD3D
main(String[]) GEMCWithRotation
main(String[]) HSMC2D
main(String[]) HSMD2D_noNbr
Demonstrates how this class is implemented.
main(String[]) HSMD2D
Demonstrates how this class is implemented.
main(String[]) HSMD3D
Demonstrates how this class is implemented.
main(String[]) HSMD3DNoNbr
main(String[]) LJMC3D.Graphic
main(String[]) LJMC3D
main(String[]) LJMC3DDimer.Graphic
main(String[]) LJMC3DDimer
main(String[]) LJMD3D
main(String[]) LJMD3DNbr
main(String[]) SoftSphere3d
main(String[]) SWMD3D
Demonstrates how this class is implemented.
main(String[]) BenchVector
main(String[]) BenchVector3D
main(String[]) RotationTensor3D
Method to test rotation tensor.
main(String[]) SpeciesFileParser
main(String[]) FunctionCosIntegral
main(String[]) Heisenberg
main(String[]) Heisenberg3Pair
main(String[]) HeisenbergPair
main(String[]) Ising
main(String[]) StarPolymerMC
main(String[]) StarPolymerMD
main(String[]) VirialPolymerOverlapMC
main(String[]) VirialPolymerOverlapWithMD
main(String[]) VirialPolymerOverlapWithMDB3
main(String[]) HardSphere
main(String[]) HardSphereSolid
main(String[]) LennardJones
main(String[]) FitTanh
main(String[]) LJMC
main(String[]) TestHSMD3D
Demonstrates how this class is implemented.
main(String[]) TestLammpsLJ
main(String[]) TestLJGCMC3D
main(String[]) TestLJMC3D
main(String[]) TestLJMD3D
main(String[]) TestSWChain
main(String[]) UnitFilter
main(String[]) UnitGraphics
main(String[]) BuildProperties
main(String[]) Constants
main(String[]) Grabber
main(String[]) MathTiming
main(String[]) RandomNumberGeneratorUnix
main(String[]) ReadParameters
main(String[]) ScientificFormat
main(String[]) Strings
main(String[]) EulerPhi
Test program.
main(String[]) Ifactor
Test program.
main(String[]) PartitionsP
Test program.
main(String[]) Prime
Test program.
main(String[]) Wigner3j
Test programs.
main(String[]) Wigner3jGUI
Main entry point.
main(String[]) BigValue
main(String[]) MyBigDecimal
main(String[]) QSeries
main(String[]) Ushcats
main(String[]) B2ForSphericallySymmetricUByTrapezoidRule
main(String[]) B2Ionic
main(String[]) B3ForSphericallySymmetricU
main(String[]) B3LJ
main(String[]) B3NonAddForSphericallySymmetricU
main(String[]) B4FFTLJ
main(String[]) B5FFTLJ
main(String[]) B6FFTLJ
main(String[]) BnHNCLJ
main(String[]) BnHSIonic
main(String[]) BnIETP2Spherical
main(String[]) BnJHBVArgon_Analytic
main(String[]) BnPCJSDHe
main(String[]) BnPY_1QC_Helium
main(String[]) BnPYCHe
main(String[]) BnPYHardSphere
main(String[]) BnPYLJ
main(String[]) BnSCALJ
main(String[]) CalcFFT
main(String[]) ClusterDiagram
main(String[]) ClusterGenerator
Demonstrates how to use this class.
main(String[]) ClusterOperations
main(String[]) DCF
main(String[]) ExternalVirialDiagrams
main(String[]) MayerIonicDiagram1qbond
main(String[]) MayerIonicDiagram2qbonds
main(String[]) MayerIonicDiagram4qbonds
main(String[]) PermutationIterator
main(String[]) Standard
main(String[]) VirialDiagrams
main(String[]) VirialDiagramsMix
main(String[]) VirialDiagramsMix2
main(String[]) VirialDiagramsPT
main(String[]) WertheimDiagrams2SiteRho
main(String[]) WertheimDiagrams3SiteRho
main(String[]) ClusterBonds
main(String[]) ClusterChainHS
main(String[]) ClusterSinglyConnected
main(String[]) ClusterWheatleyPartitionScreening
main(String[]) ApplicationMixtureBuilder
main(String[]) ControllerAlkaneLengthSelection
main(String[]) ControllerSpeciesSelection
main(String[]) ModelMoleculeListDisplayTable_new
main(String[]) ModelMoleculeListDisplayTable
main(String[]) ModelPotParamDisplayTable
main(String[]) MolecularModel2CLJQ_SpeciesCO2
main(String[]) MolecularModel2CLJQ_SpeciesEthane
main(String[]) MolecularModel2CLJQ_SpeciesLJ
main(String[]) MolecularModelLJQ_SpeciesLJ
main(String[]) MolecularModelSKS_SpeciesAlkane
main(String[]) MolecularModelTRAPPE_SpeciesAlkane
main(String[]) ViewSpeciesSelection
main(String[]) ViewAlkaneLengthSelection
main(String[]) ViewSpeciesSelection
main(String[]) HNCGenerator
main(String[]) IsFFT
main(String[]) MCMoveClusterAtomHSRing
main(String[]) PotentialNonAdditive
main(String[]) PYGenerator
main(String[]) BenchSimVirialH2OGCPMD
main(String[]) BnFlexibleContributionTraPPEUAMethanol
main(String[]) DirectSamplingTargetQCArReferenceAzizAr
main(String[]) DoubleAssociationSitesFluid2Pt
main(String[]) DoubleAssociationSitesFluid3Pt
main(String[]) DoubleAssociationSitesFluid4Pt
main(String[]) FourAssociationSitesFluid2Pt
main(String[]) LJTSRefLJ
main(String[]) ReeHooverMC
main(String[]) SimulationVirialUmbrella
main(String[]) SingleAssociationSiteFluid
main(String[]) SingleAssociationSiteFluid2
main(String[]) SingleAssociationSiteFluid2Pt
main(String[]) SingleAssociationSiteFluid3Pt
main(String[]) SingleAssociationSiteFluid4Points
main(String[]) SingleAssociationSiteFluid4Pt
main(String[]) SingleAssociationSiteFluidGraph
main(String[]) TestLJAssociationMC3D_NPT
main(String[]) Virial2CLJmuQ
main(String[]) Virial2CLJQ
main(String[]) Virial7SiteRigidSF6
main(String[]) VirialAceticAcid
main(String[]) VirialAceticAcidFlex
main(String[]) VirialAlkane
main(String[]) VirialAlkaneEHTest
main(String[]) VirialAlkaneFlex
main(String[]) VirialAlkaneFull
main(String[]) VirialAlkaneMix_Kong
main(String[]) VirialAlkaneMix
main(String[]) VirialAlkaneMix2_Kong
main(String[]) VirialAlkaneMix2
main(String[]) VirialAlkaneSKS
main(String[]) VirialAnthracene464
main(String[]) VirialAnthracene545
main(String[]) VirialAnthraceneTraPPE
main(String[]) VirialAssociatingFluid
main(String[]) VirialAssociatingFluid4points
main(String[]) VirialB2WaterTIP4P_DHS_difference
main(String[]) VirialB3C1HSDipole
main(String[]) VirialB3C1TIP4Pwater
main(String[]) VirialB3C2HSDipole
main(String[]) VirialB3C2TIP4Pwater
main(String[]) VirialCH4AlkaneEHMix
main(String[]) VirialCO2
main(String[]) VirialCO2AlkaneEHMix
main(String[]) VirialCO2AlkaneUAMix
main(String[]) VirialCO2anthracene464
main(String[]) VirialCO2anthracene545
main(String[]) VirialCO2AnthraceneTraPPE
main(String[]) VirialCO2CH4Mix
main(String[]) VirialCO2CH4UAMix
main(String[]) VirialCO2CH4UAMixWheatley
main(String[]) VirialCO2H2OGCPM
main(String[]) VirialCO2H2OGCPMX
main(String[]) VirialCO2H2OSC
main(String[]) VirialCO2LJQ
main(String[]) VirialCO2N2Mix
main(String[]) VirialCO2NaphthaleneLJQ
main(String[]) VirialCO2NaphthaleneTraPPE
main(String[]) VirialCO2PI
main(String[]) VirialCO2SKSMix
main(String[]) VirialCO2TraPPE
main(String[]) VirialCPSHeliumNonAdditive
main(String[]) VirialCPSHeliumNonAdditiveClassical_Correction
main(String[]) VirialCPSHeliumNonAdditiveClassical
main(String[]) VirialEmulNonAdditive
main(String[]) VirialExternalFieldConfinedOverlap
main(String[]) VirialExternalFieldConfinedOverlapRho
main(String[]) VirialExternalFieldConfinedOverlapSW
main(String[]) VirialExternalFieldOverlapRho
main(String[]) VirialGCPM
main(String[]) VirialGCPMGraphic
main(String[]) VirialH2O
main(String[]) VirialH2OGCPMD
main(String[]) VirialH2PI
main(String[]) VirialH2PIBoltzmann
main(String[]) VirialH2PISimple
main(String[]) VirialH2PIXC
main(String[]) VirialH2PYCorrection
main(String[]) VirialHardAssociationCone
main(String[]) VirialHardAssociationConeDoubleSites
main(String[]) VirialHeD
main(String[]) VirialHeNonAdditive
main(String[]) VirialHeNonAdditiveD
main(String[]) VirialHeNonAdditiveWheatley
main(String[]) VirialHePCKLJS
main(String[]) VirialHePCKLJSCHNCCorrection
main(String[]) VirialHePCKLJSPYCorrection
main(String[]) VirialHePCKLJSTempDeriv
main(String[]) VirialHePI_PotentialCorrection
main(String[]) VirialHePI
main(String[]) VirialHePIGraphic
main(String[]) VirialHePISysErr
main(String[]) VirialHePIXC
main(String[]) VirialHePIXCEven
main(String[]) VirialHePIXCOdd
main(String[]) VirialHePYCorrection
main(String[]) VirialHeSC
main(String[]) VirialHS
main(String[]) VirialHSBinMultiThreaded
main(String[]) VirialHSMixture
main(String[]) VirialHSMixtureOverlap
main(String[]) VirialHSOrC
main(String[]) VirialLJ
main(String[]) VirialLJBridge
main(String[]) VirialLJCHNCCorrection
main(String[]) VirialLJD
main(String[]) VirialLJDU
main(String[]) VirialLJMultiOverlap
main(String[]) VirialLJOrC
main(String[]) VirialLJOrICPYC
main(String[]) VirialLJPT
main(String[]) VirialLJPYCorrection
main(String[]) VirialLJSeries
main(String[]) VirialMethaneEH
main(String[]) VirialN2
main(String[]) VirialN2AlkaneEHMix
main(String[]) VirialN2AlkaneUAMix
main(String[]) VirialN2AlkaneUARigid
main(String[]) VirialN2CH4Mix
main(String[]) VirialN2CH4UAMix
main(String[]) VirialN2PI
main(String[]) VirialN2TraPPE
main(String[]) VirialNaphthaleneTraPPE
main(String[]) VirialO2
main(String[]) VirialO2PI
main(String[]) VirialPh464
main(String[]) VirialPh545
main(String[]) VirialPhenanthreneTraPPE
main(String[]) VirialPolyhedra
main(String[]) VirialPolyhedra2
main(String[]) VirialRowleyAlcohol
main(String[]) VirialSF6LJAlkaneUAMix
main(String[]) VirialSQWBinMultiRecalcW
main(String[]) VirialSQWBinMultiThreaded
main(String[]) VirialSQWRecalcSmallMem
main(String[]) VirialSW
main(String[]) VirialSwsPT
main(String[]) VirialSWWE
main(String[]) VirialTraPPE
main(String[]) VirialTraPPEAlcohol
main(String[]) VirialWaterOverlap
main(String[]) DataCutter
main(String[]) DeviceButtonSingle
Method to demonstrate and test the use of this class.
main(String[]) Zeolite
main(String[]) ZeoliteSimulation
Demonstrates how this class is implemented.
Main etomica.graph.view.rasterizer
Handles command line parameters to configure the SVGConverter
and rasterizer images.
Main etomica
Main() Main
Main(String[]) Main
Main.AbstractOptionHandler etomica.graph.view.rasterizer
This abstract implementation of the OptionHandler interface
throws an exception if the number of arguments passed to the
handleOption method does not match the number of expected
optionValues.
Main.ColorOptionHandler etomica.graph.view.rasterizer
Base class for options which expect a Color optionValue.
Main.FloatOptionHandler etomica.graph.view.rasterizer
Base class for options which expect the single optionValue to
be a float.
Main.NoValueOptionHandler etomica.graph.view.rasterizer
Base class for options with no option value (i.e., the presence
of the option means something in itself.
Main.OptionHandler etomica.graph.view.rasterizer
Interface for handling one command line option
Main.RectangleOptionHandler etomica.graph.view.rasterizer
Base class for options which expect a Rectangle optionValue.
Main.SingleValueOptionHandler etomica.graph.view.rasterizer
Base class for options with a single option value.
Main.TimeOptionHandler etomica.graph.view.rasterizer
Base class for options which expect the single optionValue to
be a time value.
main1(String[]) P2CO2Hellmann
main1(String[]) P2WaterSzalewicz
main2(String[]) PotentialCalculationMappedVirialV
main2(String[]) P2CO2H2OWheatley
main2(String[]) PNCO2GCPM
main2(String[]) PNGCPM
main2(String[]) P2WaterSzalewicz
main2DGrid(String[]) P2CO2H2OWheatley
Writes x-y grid of energies
main3(String[]) P2WaterSzalewicz
mainCO2(String[]) PNGCPM
mainQ(String[]) P2CO2H2OWheatley
Check charges (all sums should be 0 for neutral molecules)
mainTestU(String[]) P2CO2H2OWheatley
Reads geometry.txt file and computes energy for each configuration
makeAccumulator() AccumulatorFactory
makeAdjacentPairIterator() ApiBuilder
Pair iterator that constructs pairs from the childlist atoms of a basis,
each with the atom adjacent to it in the list.
makeAgent(AtomType) AtomTypeAgentManager.AgentSource
Returns an agent for the given AtomType.
makeAgent(AtomType) PotentialMasterMonatomic
makeAgent(IAtom, Box) ActionMinimizeEnergy
makeAgent(IAtom, Box) AssociationManager
makeAgent(IAtom, Box) ColorSchemeSmer
makeAgent(IAtom, Box) MCMoveVolumeAssociated
makeAgent(IAtom, Box) AtomLeafAgentManager.AgentSource
Returns an agent for the given Atom.
makeAgent(IAtom, Box) IntegratorDimerRT
makeAgent(IAtom, Box) ColorSchemeCollectiveAgent
makeAgent(IAtom, Box) ColorSchemeRandom
makeAgent(IAtom, Box) DisplayBoxCanvasG3DSys
AgentSource methods
makeAgent(IAtom, Box) DisplayBoxCanvasG3DSys.OrientedAgentSource
makeAgent(IAtom, Box) IntegratorGear4
makeAgent(IAtom, Box) IntegratorHard
Produces the Agent for this integrator.
makeAgent(IAtom, Box) IntegratorMD.VectorSource
makeAgent(IAtom, Box) IntegratorRigidIterative
makeAgent(IAtom, Box) IntegratorVelocityVerlet
makeAgent(IAtom, Box) IntegratorVerlet
makeAgent(IAtom, Box) MeterMappedRdf
makeAgent(IAtom, Box) MinimizationTIP4P.ChargeAgentSourceRPM
makeAgent(IAtom, Box) ChargeAgentSourceTIP4PWater
makeAgent(IAtom, Box) InteractionTracker
makeAgent(IAtom, Box) AtomTestChainLength
makeAgent(IAtom, Box) ChainEquilibriumSim
Implementation of AtomAgentManager.AgentSource interface.
makeAgent(IAtom, Box) ColorSchemeRadical
makeAgent(IAtom, Box) FreeRadicalPolymerizationSim
Implementation of AtomAgentManager.AgentSource interface.
makeAgent(IAtom, Box) MeterChainLength
makeAgent(IAtom, Box) AtomTestLiquidAtomic
makeAgent(IAtom, Box) IntegratorDroplet
makeAgent(IAtom, Box) ReactionEquilibrium
Implementation of Atom.AgentSource interface.
makeAgent(IAtom, Box) P1Tether
makeAgent(IAtom, Box) AtomTestChainLength
makeAgent(IAtom, Box) NeighborCellManager
Returns the cell containing the given atom.
makeAgent(IAtom, Box) CriterionPositionWall
makeAgent(IAtom, Box) CriterionSimple
makeAgent(IAtom, Box) NeighborListManager.AtomPotential1ListSource
makeAgent(IAtom, Box) NeighborListManager
makeAgent(IAtom, Box) NeighborSiteManager
makeAgent(IAtom, Box) CoordinateDefinition.SiteSource
makeAgent(IAtom, Box) HSNPT.ActionSummer
makeAgent(IAtom, Box) P2HardBondedList
makeAgent(IAtom, Box) P2SquareWellRobust
makeAgent(IAtom, Box) MeterDipoleMoment
makeAgent(IAtom, Box) MeterMappedAveraging
makeAgent(IAtom, Box) MeterMappedAveraging3Pair
makeAgent(IAtom, Box) MeterMappedAveragingCorrelation
makeAgent(IAtom, Box) MeterMappedAveragingFreeEnergy
makeAgent(IAtom, Box) MeterMappedAveragingPair
makeAgent(IAtom, Box) MeterMappedAveragingPairExcess
makeAgent(IAtom, Box) MeterMappedAveragingSum
makeAgent(IAtom, Box) MeterMappedAveragingVSum
makeAgent(IAtom, Box) MeterMappedAveragingVSum3Pair
makeAgent(IAtom, Box) MeterMappedAveragingVSumPair
makeAgent(IAtom, Box) MeterMeanField
makeAgent(IAtom, Box) PotentialCalculationMeanField
makeAgent(Box) BoxAgentManager.BoxAgentSource
makeAgent(Box) BoxAgentSourceAtomManager
makeAgent(Box) BoxAgentSourceMoleculeManager
makeAgent(Box) NeighborListManagerColloid.NeighborListAgentSourceColloid
makeAgent(Box) BoxAgentSourceCellManager
makeAgent(Box) BoxAgentSourceCellManagerMolecular
makeAgent(Box) BoxAgentSourceCellManagerListMolecular
makeAgent(Box) NeighborListManagerSlantyMolecular.NeighborListSlantyAgentSourceMolecular
makeAgent(Box) PotentialMasterListMolecular.NeighborListAgentSourceMolecular
makeAgent(Box) NeighborListAgentSource
makeAgent(Box) NeighborListManagerSlanty.NeighborListSlantyAgentSource
makeAgent(Box) P2SquareWellRobust
makeAgent(IMolecule) AssociationManagerMolecule
makeAgent(IMolecule) MCMoveVolumeAssociatedMolecule
makeAgent(IMolecule) MeterDipoleSumSquaredMappedAverage
makeAgent(IMolecule) ColorSchemeRandomByMolecule
makeAgent(IMolecule) IntegratorRigidIterative
makeAgent(IMolecule) IntegratorRigidMatrixIterative
makeAgent(IMolecule) CoordinateDefinitionNitrogen.OrientationAgentSource
makeAgent(IMolecule) CoordinateDefinitionNitrogenSuperBox.OrientationAgentSource
makeAgent(IMolecule) MeterFlux
makeAgent(IMolecule) CriterionTether3
makeAgent(IMolecule) MoleculeAgentManager.MoleculeAgentSource
Returns an agent for the given Atom.
makeAgent(IMolecule) NeighborCellManagerMolecular
Returns the cell containing the given atom.
makeAgent(IMolecule) NeighborCellManagerListMolecular
makeAgent(IMolecule) NeighborListManagerMolecular
makeAgent(IMolecule) NeighborListManagerMolecular.MoleculePotential1ListSource
makeAgent(IMolecule) CriterionSimpleMolecular
makeAgent(IMolecule) CoordinateDefinitionMolecule.MoleculeSiteSource
makeAgent(IMolecule) CoordinateDefinitionMoleculeVolumeFluctuation.MoleculeSiteSource
makeAgent(IMolecule) IntegratorVelocityVerletQuaternion
makeAgent(ISpecies) IntegratorRigidIterative
makeAgent(ISpecies) IntegratorRigidMatrixIterative
makeAgent(ISpecies) IntegratorVelocityVerletShake
makeAgent(ISpecies) IntegratorVelocityVerletQuaternion
makeAgent(ISpecies) SpeciesAgentManager.AgentSource
Returns an agent for the given AtomType.
makeAndDisplayFrame() SimulationGraphic
makeAndDisplayFrame(String) SimulationGraphic
makeAndDisplayFrame(JPanel) SimulationGraphic
makeAndDisplayFrame(JPanel, String) SimulationGraphic
makeArrayD(double) Space
makeArrayD(double) Space1D
makeArrayD(double) Space2D
makeArrayD(double) Space3D
makeArrayD(int) Space
makeArrayD(int) Space1D
makeArrayD(int) Space2D
makeArrayD(int) Space3D
makeAtom(AtomType) SpeciesGeneral.AtomFactory
makeAxilrodTeller() PNCO2GCPM
makeAxilrodTeller() PNGCPM
makeBigValue(double) Ushcats
makeBigValue(IBigValue) Ushcats
makeBond(IAtomList, Object) DisplayBoxCanvasG3DSys
Add a bond to the graphical display between the given pairs.
makeBox() Simulation
Creates a new Box with the default Boundary and adds it to the Simulation.
makeBox(Boundary) Simulation
Creates a new Box and adds it to the Simulation.
makeCachedPairPolarization() PNGCPM
makeCachedPairPolarization() PNWaterGCPM
makeChi4Meter() DataSourceQ4
makeChi4Source() DataSourcePercolation
makeClusterBDBD(int) ClusterWheatleySoftDerivativesBD
makeClusterBDBD(int) ClusterWheatleySoftDerivativesMixBD
makeClusterOrder(int) ClusterWheatleyPT
makeCopy() ClusterAbstract
Returns another instance of an identical cluster (shallow copy).
makeCopy() ClusterChainHS
makeCopy() ClusterChainSoft
makeCopy() ClusterConstant
makeCopy() ClusterCoupledAtomFlipped
makeCopy() ClusterCoupledFlipped
makeCopy() ClusterCoupledFlippedMultivalue
makeCopy() ClusterCoupledFlippedPartial
makeCopy() ClusterDifference
makeCopy() ClusterExchange
makeCopy() ClusterMultiToSingle
makeCopy() ClusterMultivalueUmbrella
makeCopy() ClusterSinglyConnected
makeCopy() ClusterSum
makeCopy() ClusterSumAssociation
makeCopy() ClusterSumEF
makeCopy() ClusterSumHS
makeCopy() ClusterSumIC
makeCopy() ClusterSumMultibody
makeCopy() ClusterSumMultibodyShell
makeCopy() ClusterSumNonAdditiveTrimerEnergy
makeCopy() ClusterSumPolarizable
makeCopy() ClusterSumPolarizableWertheimProduct
makeCopy() ClusterSumPolarizableWertheimProduct4Pt
makeCopy() ClusterSumPolarizableWertheimProduct4PtFinal
makeCopy() ClusterSumShell
makeCopy() ClusterTree
makeCopy() ClusterTreeEF
makeCopy() ClusterWeightAbs
makeCopy() ClusterWeightSumWall
makeCopy() ClusterWeightUmbrella
makeCopy() ClusterWheatleyExtendSW
makeCopy() ClusterWheatleyHS
makeCopy() ClusterWheatleyMultibody
makeCopy() ClusterWheatleyMultibodyBD
makeCopy() ClusterWheatleyMultibodyDerivatives.ClusterRetrievePrimes
makeCopy() ClusterWheatleyMultibodyDerivatives
makeCopy() ClusterWheatleyMultibodyDerivativesBD.ClusterRetrievePrimes
makeCopy() ClusterWheatleyMultibodyDerivativesBD
makeCopy() ClusterWheatleyMultibodyMix
makeCopy() ClusterWheatleyPartitionScreening
makeCopy() ClusterWheatleyPT.ClusterRetrieveOrders
makeCopy() ClusterWheatleyPT.ClusterRetrievePrimesBD
makeCopy() ClusterWheatleyPT
makeCopy() ClusterWheatleySoft
makeCopy() ClusterWheatleySoftBD
makeCopy() ClusterWheatleySoftDerivatives.ClusterRetrievePrimes
makeCopy() ClusterWheatleySoftDerivatives.ClusterRetrievePrimesBD
makeCopy() ClusterWheatleySoftDerivatives
makeCopy() ClusterWheatleySoftDerivativesBD.ClusterRetrievePrimes
makeCopy() ClusterWheatleySoftDerivativesBD
makeCopy() ClusterWheatleySoftDerivativesMix
makeCopy() ClusterWheatleySoftDerivativesMixBD
makeCopy() ClusterWheatleySoftMix
makeCopy() ClusterWheatleySoftMixBD
makeCopy() VirialH2OGCPMD.Clusterfoo
makeCov() DataSourceMSDcorP
makeData() IDataInfo
Returns a Data object appropriate for this DataInfo instance.
makeData() DataDouble.DataInfoDouble
makeData() DataDoubleArray.DataInfoDoubleArray
makeData() DataDoubleBDArray.DataInfoDoubleBDArray
makeData() DataFunction.DataInfoFunction
makeData() DataGroup.DataInfoGroup
makeData() DataTable.DataInfoTable
makeData() DataTensor.DataInfoTensor
makeData() DataVector.DataInfoVector
makeData(int) MeterVirialEBinMultiThreaded
makeData(int, int) DataTable
makeDataInfo() DataInfoFactory
Creates a new DataInfo object using the information held by this factory.
makeDataInfo() IDataInfoFactory
Creates a new DataInfo object using the information held by this factory.
makeDataInfo() DataDouble.DataInfoDoubleFactory
makeDataInfo() DataDoubleArray.DataInfoDoubleArrayFactory
makeDataInfo() DataDoubleBDArray.DataInfoDoubleBDArrayFactory
makeDataInfo() DataFunction.DataInfoFunctionFactory
makeDataInfo() DataGroup.DataInfoGroupFactory
makeDataInfo() DataTable.DataInfoTableFactory
makeDataInfo() DataTensor.DataInfoTensorFactory
makeDataInfo() DataVector.DataInfoVectorFactory
makeDataProcessor() AccumulatorFactory
makeDataSink() DataSet
makeDataSink(int) DataSplitter.IDataSinkFactory
makeDataSink(IDataInfo) DataSinkTable
makeDataSink(String) DataSet
makeDipole() SingleDipole
makeDropShape() DropletAtomic
makeDWPlot MultiharmonicGraphicMC
makeF(Potential2Spherical, double) CalcFFT
makeFccVectors(double) MCMoveInsertDeleteLatticeVacancy
makeFullStar() ClusterDiagram
Turns this cluster into a full star -- each point in the cluster is
connected to every other point in the cluster.
makeGContactSink() DataProcessorWidomContact
makeGraph(long) GraphNumber
makeGraph(long, byte) GraphNumber
makeGraphicsPanel() MyApplet
makeGraphList() MayerIonicDiagram1qbond
makeGraphList() MayerIonicDiagram2qbonds
makeGraphList() MayerIonicDiagram4qbonds
makeGraphList() VirialDiagrams
makeGraphList() VirialDiagramsMix
makeGraphList() VirialDiagramsMix2
makeGraphList() VirialDiagramsPT
makeGraphList() WertheimDiagrams2SiteRho
makeGraphList() WertheimDiagrams3SiteRho
makeHcpVectors(double) MCMoveInsertDeleteLatticeVacancy
makeHistogram() AccumulatorAverageBootstrap.HistogramFactory
makeHistoryPlot(ArrayList<DataPump>, DataSourceCountSteps, JPanel, DataPumpListener, String) StatisticsMCGraphic
makeImmFractionSource() DataSourcePercolation
makeImmFractionSource(AtomType) DataSourcePercolation
makeInitConfigActivity() SimGlass
makeInputFile(IMoleculeList) PotentialEmul
makeInputFile(Vector, Vector) P2QChem
makeIntegratorListener(PotentialMaster, Box) P2EAM
Creates and returns an integrator listener that makes the integrator's
force sum work properly by running an energy calculation first.
makeIntergroupTypeIterator(AtomType[]) ApiBuilder
Returns an intergroup iterator that filters the iterates so that only
those having the given type instances are returned.
makeInterspeciesPairIterator(ISpecies[]) IteratorFactory
creates a pair iterator which loops over all pairs in a neighbor list
between two groups
makeIntraspeciesPairIterator(ISpecies) IteratorFactory
creates a pair iterator which loops over all pairs in a neighbor list
within one group
makeLrc P2SoftSphericalTruncated
makeLrcPotential(AtomType[]) P2SoftSphericalTruncated
Returns the zero-body potential that evaluates the contribution to the
energy and its derivatives from pairs that are separated by a distance
exceeding the truncation radius.
makeLrcPotential(AtomType[]) P2SoftSphericalTruncatedShifted
Returns null because the shift can't be corrected.
makeLrcPotential(AtomType[]) P2SoftTruncated
Returns the zero-body potential that evaluates the contribution to the
energy and its derivatives from pairs that are separated by a distance
exceeding the truncation radius.
makeLrcPotential(AtomType[]) PotentialTruncated
Returns a class that calculates the long-range contribution to the potential
that becomes neglected by the truncation.
makeMCMoveListener() NeighborCellManagerMolecular
makeMCMoveListener() NeighborCellManager
makeMCMoveSwap(IntegratorBox, IntegratorBox, Space) IntegratorPT.MCMoveSwapFactory
makeMCMoveSwap(IntegratorBox, IntegratorBox, Space) MCMoveSwapConfiguration.SwapFactory
makeMCMoveSwap(IntegratorBox, IntegratorBox, Space) MCMoveSwapCluster.SwapFactory
makeMeter(int) CorrelationSelf2
makeMeter(int) DataSourceCorrelation
makeMeter(int) StructureFactorComponentCorrelation
makeMolecule() ISpecies
Builds and returns the IMolecule of this ISpecies.
makeMolecule() SpeciesGeneral
makeMolecule() SpeciesGeneralMutable
makeMoleculeIterator(ISpecies[]) IteratorFactory
Selects an appropriate iterator for the given species array.
makeMuHistoryPlot(ArrayList<DataPump>, DataSourceCountSteps, JPanel, DataPumpListener, String) StatisticsMCGraphic
makeNB(int) PotentialNonAdditive
makeNonAdjacentPairIterator() ApiBuilder
Pair iterator that constructs pairs from the childlist atoms of a basis,
each with all atoms that are not adjacent to it in the list.
makeNonAdjacentPairIterator(int) ApiBuilder
makeOrientation() Space
makeOrientation() Space1D
makeOrientation() Space2D
makeOrientation() Space3D
makeP0() P2ReactionFieldDipole
makeP0() P2ReactionFieldDipoleTruncated
Returns a 0-body potential that should be added along with this
potential.
makeP1IntraSimple(PotentialMaster, Potential2, Potential2) P1IntraSimple
makeP2EwaldReal() EwaldSummation
makePairPotentialsUnlike(int, int) BuilderCollectionPotential
makeParameters(char[], byte) MulFlexible.MulFlexibleParameters
Parameters that specify that the resulting product should include graphs
containing up to nFieldNodes field nodes and that nodes of a color
included in flexColors never be superimposed unless one of the nodes is
unbonded.
makeParametersOnlyRootPt(char[], byte) MulFlexible.MulFlexibleParameters
makeParametersWithNodes(char[], byte, byte, byte) MulFlexible.MulFlexibleParameters
Parameters that specify that the resulting product should include graphs
containing up to nFieldNodes field nodes and that node1ID from the first
graph and node2ID from the second graph should be superimposed (if
possible).
makePerclationByImmFracSource() DataSourcePercolation
makePotentialGroup(int) PotentialMasterNbrMolecular
makePotentialGroup(int) PotentialMasterHybrid
makePotentialGroup(int) PotentialMasterNbr
makePotentialGroup(int) PotentialMaster
Returns an nBody PotentialGroup appropriate for this type of
PotentialMaster.
makePressureSink() DataClusterer
makePressureSink() DataClusterWriter
makeQFH(double) P2HePCKLJS
makeQFH(double) P2HeSimplified
makeQFH(double) P2NitrogenHellmann
makeReceiver(int) DataSourceCorrelation
makeReciprocal() Primitive
Method defining and constructing reciprocal primitive;
makeReciprocal() PrimitiveBcc
makeReciprocal() PrimitiveCubic
makeReciprocal() PrimitiveFcc
makeReciprocal() PrimitiveGeneral
makeReciprocal() PrimitiveHexagonal
makeReciprocal() PrimitiveHexagonal2D
makeReciprocal() PrimitiveMonoclinic
makeReciprocal() PrimitiveOrthorhombic
makeReciprocal() PrimitiveOrthorhombicHexagonal
makeReciprocal() PrimitiveTetragonal
makeReciprocal() PrimitiveTriclinic
makeReciprocal() PrimitiveTrigonal
makeReeHoover(ClusterDiagram) ClusterOperations
Creates a set of Ree-Hoover clusters from the given cluster.
makeReeHoover(ClusterDiagram[]) ClusterOperations
makeReferenceF(Space, int, double[][], Boundary) MayerHSMixture
makeRhoCluster(MayerFunction, boolean) ExternalVirialDiagrams
makeRhoDiagrams() ExternalVirialDiagrams
makeRhoDiagrams() MayerIonicDiagram1qbond
makeRhoDiagrams() MayerIonicDiagram2qbonds
makeRhoDiagrams() MayerIonicDiagram4qbonds
makeRhoDiagrams() VirialDiagrams
makeRhoDiagrams() VirialDiagramsMix
makeRhoDiagrams() VirialDiagramsMix2
makeRhoDiagrams() VirialDiagramsPT
makeRhoDiagrams() WertheimDiagrams2SiteRho
makeRhoDiagrams() WertheimDiagrams3SiteRho
makeRotationTensor() Space
makeRotationTensor() Space1D
makeRotationTensor() Space2D
makeRotationTensor() Space3D
makeScaledCoordinates(Space, Basis, int[]) BasisBigCell
makeSemiclassical(double) P2CO2H2OWheatley
Creates a Feynman-Hibbs implementation of a semi-classical potential based on this model for the given temperature.
makeSemiclassical(double) P2CO2Hellmann
makeSemiclassical(double) P2WaterSzalewicz
makeSemiclassicalTI(double) P2CO2H2OWheatley
Creates a Takahashi-Imada implementation of a semi-classical potential based on this model for the given temperature.
makeSim(VirialH2OGCPMD.VirialParam) BenchSimVirialH2OGCPMD
makeSingleVirialClusters(ClusterSum, MayerFunction[][], int, int[]) VirialDiagramsMix2
makeSingleVirialClusters(ClusterSum, MayerFunction, MayerFunction) MayerIonicDiagram1qbond
makeSingleVirialClusters(ClusterSum, MayerFunction, MayerFunction) MayerIonicDiagram2qbonds
makeSingleVirialClusters(ClusterSum, MayerFunction, MayerFunction) MayerIonicDiagram4qbonds
makeSingleVirialClusters(ClusterSum, MayerFunction, MayerFunction) VirialDiagrams
makeSingleVirialClusters(ClusterSum, MayerFunction, MayerFunction) WertheimDiagrams2SiteRho
makeSingleVirialClusters(ClusterSum, MayerFunction, MayerFunction) WertheimDiagrams3SiteRho
makeSingleVirialClusters(ClusterSum, MayerFunction, MayerFunction[], int) VirialDiagramsPT
makeSingleVirialClustersMulti(ClusterSumMultibody, MayerFunction, MayerFunctionNonAdditive) VirialDiagrams
makeSingleWater() SingleDumbellRattle
makeSingleWater() SingleDumbellShake
makeSingleWater() SingleWater
makeSingleWater() SingleWaterMatrix
makeSingleWater() SingleWaterRattle
makeSingleWater() SingleWaterShake
makeSink(int, MeterStructureFactor) StructureFactorComponentCorrelation
makeSink(String) DisplayPlotXChart
makeSite(AbstractLattice, int[]) SiteFactory
Constructs a site for placement in a lattice.
makeSite(AbstractLattice, int[]) Cell.CellFactory
makeSite(AbstractLattice, int[]) CellMolecular.CellFactory
makeSpecies(Space) SpeciesFactoryMethanol
makeSpecies(Space) SpeciesFactory
makeSpecies(Space) SpeciesFactorySpheres
makeSpecies(Space) SpeciesFactoryWaterGCPM
makeSpeciesB(int, int) SelfAssemblySim
makeStuff(String, ParserLAMMPS.Options) ParserLAMMPS
makeStuffFromLines(List<String>, ParserLAMMPS.Options) ParserLAMMPS
makeTargetF(Space, int, double[][], Boundary) MayerHSMixture
makeTemperatureSink() AccumulatorPTensor
makeTensor() Space
makeTensor() Space1D
makeTensor() Space2D
makeTensor() Space3D
makeTerminalSink() DataArrayWriter
makeTerminalSink() DataTableWriter
makeTI(double) P2HePCKLJS
makeTI(double) P2HeSimplified
makeTI(double) P2O2Bartolomei
makeUniqueElementSymbol(String) Simulation
Method to allow generation of unique string to identify Elements in the Simulation.
makeVector() Space
makeVector() Space1D
makeVector() Space2D
makeVector() Space3D
makeVector(double...) Space
makeVector(int) Space
Returns a Vector from the space of the given dimension.
makeVector(int...) Space
makeVectorArray(int) Space
Makes an array of Vectors.
makeVirialCluster(MayerFunction) VirialDiagrams
makeVirialCluster(MayerFunction[][], int, int[]) VirialDiagramsMix2
makeVirialCluster(MayerFunction, MayerFunction) MayerIonicDiagram1qbond
makeVirialCluster(MayerFunction, MayerFunction) MayerIonicDiagram2qbonds
makeVirialCluster(MayerFunction, MayerFunction) MayerIonicDiagram4qbonds
makeVirialCluster(MayerFunction, MayerFunction) WertheimDiagrams3SiteRho
makeVirialCluster(MayerFunction, MayerFunction[]) VirialDiagramsPT
makeVirialCluster(MayerFunction, MayerFunctionNonAdditive) VirialDiagrams
makeVirialCluster(MayerFunction, MayerFunctionNonAdditive, boolean) VirialDiagrams
makeVirialCluster(Set<Graph>, MayerFunction[][], int, int[]) VirialDiagramsMix2
makeVirialCluster(Set<Graph>, MayerFunction, MayerFunction[]) VirialDiagramsPT
makeVirialCluster(Set<Graph>, MayerFunction, MayerFunctionNonAdditive) VirialDiagrams
makeVirialClusterHS(Set<Graph>, MayerFunction) VirialDiagrams
makeVirialClusterSecondTemperatureDerivative(MayerFunction, MayerFunction, MayerFunction, MayerFunction) VirialDiagrams
makeVirialClusterTempDeriv(MayerFunction, MayerFunction, MayerFunction) VirialDiagrams
makeVirialDiagrams() MayerIonicDiagram1qbond
makeVirialDiagrams() MayerIonicDiagram2qbonds
makeVirialDiagrams() MayerIonicDiagram4qbonds
makeVirialDiagrams() VirialDiagrams
makeVirialDiagrams() VirialDiagramsMix
makeVirialDiagrams() VirialDiagramsMix2
makeVirialDiagrams() VirialDiagramsPT
makeVirialDiagrams() WertheimDiagrams3SiteRho
makeWaterBox() WaterBox
makeWaterDroplet() WaterDroplet
makeWaterDroplet() WaterDropletMatrix
makeWaterDroplet() WaterDropletRattle
makeWaterDroplet() WaterDropletShake
makeWaterDroplet() WaterTrimer
makeWaterDroplet() WaterTrimerRattle
makeWaterDroplet() WaterTrimerShake
makeWaveVector(double) MeterStructureFactor
makeWaveVectorMap(Vector[], int) StructureFactorComponentCorrelation
makeWaveVectors(Box) WaveVectorFactory
Tells the instance to make wave vectors appropriate for the given box.
makeWaveVectors(Box) WaveVectorFactory1D
makeWaveVectors(Box) WaveVectorFactory2D
makeWaveVectors(Box) WaveVectorFactoryFcc
makeWaveVectors(Box) WaveVectorFactoryFromFile
makeWaveVectors(Box) WaveVectorFactorySimple
makeWaveVectors(Box) WaveVectorFactorySuperBox
makeWeightCluster(ClusterAbstract) ClusterWeightAbs
makeWeightCluster(ClusterAbstract[]) ClusterWeight.Factory
makeWeightClusters(ClusterAbstract[]) ClusterWeightAbs
makeWertheimCluster(MayerFunction, MayerFunction) WertheimDiagrams2SiteRho
makeWertheimDiagrams() WertheimDiagrams2SiteRho
makeWrapper(Object) SimulationModel
Ensures that a wrapper is defined for the given object and, recursively, all other objects referenced by it.
makeWrapperObject(Class) ReadParameters
makeX() StatisticsMCGraphic.DataProcessorUndo
manager NeighborListManager.AtomPotential1ListSource
managerPanel MyApplet
map(byte) RelabelParameters
map(IFunction) IData
Maps the function on all data values, replace each with the value given
by the function applied to it.
map(IFunction) DataDouble
Maps the function on this instance's value, replacing it with the value
returned by the function.
map(IFunction) DataDoubleArray
Replaces all values by the value of the function applied to each.
map(IFunction) DataDoubleBDArray
Replaces all values by the value of the function applied to each.
map(IFunction) DataGroup
map(IFunction) DataTensor
Maps the function on all vector elements, replacing each with the value
given by the function applied to it.
map(IFunction) DataVector
Maps the function on all vector elements, replacing each with the
value given by the function applied to it.
map(IFunction) Tensor
Applies given function to each element of this tensor.
map(IFunction) Vector
Applies the given function to each element of the vector.
map(IFunction) Tensor1D
map(IFunction) Vector1D
map(IFunction) Tensor2D
map(IFunction) Vector2D
map(IFunction) Tensor3D
map(IFunction) Vector3D
map(IFunction) TensorND
map(IFunction) VectorND
MappedU etomica.mappedvirial
MappedU(Space, int, double, double, double) MappedU
MappedU.LJMDParams etomica.mappedvirial
MappedVirialLJ etomica.mappedvirial
MappedVirialLJ(Space, int, double, double, double) MappedVirialLJ
MappedVirialLJ.LJMDParams etomica.mappedvirial
MappedVirialLJVGr etomica.mappedvirial
MappedVirialLJVGr(Space, int, double, double, double) MappedVirialLJVGr
MappedVirialLJVGr.LJMDParams etomica.mappedvirial
mappingCut HSMDWidom.HSMDParam
mappingCut2 MeterCavityMapped
mappingCut2 MeterRDFMapped
mapValue(String) ScriptVariable
markDirty() AkimaSpline
markLines(String, char) Parser
MAROON Colix
maskSingleBit(int) BitmapOfLong
Returns a long with a single bit set, corresponding to the bit offset of the given
bit index.
maskSingleBit(int) BitmapOfLongVector
Returns a long with a single bit set, corresponding to the bit offset of the given
bit index.
maskSingleLong() BitmapOfLong
Returns a bitmask corresponding to the valid bits of the long with the given index.
maskSingleLong(int) BitmapOfLongVector
Returns a bitmask corresponding to the valid bits of the long with the given index.
mass ElementChemical
mass ElementSimple
mass P2CO2Hellmann
mass P2WaterSzalewicz
mass PistonCylinderGraphic
mass ReactionEquilibriumGraphic.MassEditor
mass SwmdGraphic
mass P2DiscreteFeynmanHibbs
mass P2EffectiveFeynmanHibbs
mass P2HePCKLJS.P2HeQFH
mass P2HePCKLJS.P2HeTI
mass P2HeSimplified.P2HeQFH
mass P2HeSimplified.P2HeTI
mass P2O2Bartolomei.P2O2TI
mass LJ
mass Token
mass() CGS
mass() LJ
mass() MKS
mass() UnitSystem
mass() UnitSystem.Sim
Mass etomica.units.dimensions
Dimension for all units of mass.
mass0 P2CO2H2OWheatley.P2CO2H2OSC
mass0 P2CO2H2OWheatley.P2CO2H2OSCTI
mass1 P2CO2H2OWheatley
massBox PistonCylinderGraphic
massBox ReverseOsmosisGraphic
massBox ReverseOsmosisWaterGraphic
massBox SwmdGraphic
MassEditor(SpeciesGeneral, String) ReactionEquilibriumGraphic.MassEditor
massH PNWaterGCPM
massH PNWaterGCPMReactionField
massH VirialH2PISimple
massMembrane ReverseOsmosisGraphic
massN VirialN2
massN VirialN2PI
massN2 P2NitrogenHellmann
massO PNWaterGCPM
massO PNWaterGCPMReactionField
massO VirialO2PI
MassProductionVirialRowleyAlcohol etomica.models.rowley
MassProductionVirialRowleyAlcohol() MassProductionVirialRowleyAlcohol
massSolute ReverseOsmosisGraphic
massSolvent ReverseOsmosisGraphic
mat4 MeshSurface
match(SearchState) Match
Execution of an isomorphism test with a provided initial state.
match(Graph, Graph, boolean) Match
Execution of an isomorphism test with the default algorithm.
Match etomica.graph.isomorphism
Match() Match
MaterialFracture etomica.modules.materialfracture
MaterialFracture() MaterialFracture
MaterialFractureGraphic etomica.modules.materialfracture
Graphical components for Material Fracture module
MaterialFractureGraphic(MaterialFracture) MaterialFractureGraphic
MaterialFractureGraphic.Applet etomica.modules.materialfracture
MathTiming etomica.util
This class benchmarks various mathematical functions.
MathTiming() MathTiming
MATRIX_A RandomMersenneTwister
matrix3f Token
Matrix3f org.jmol.util
A single precision floating point 3 by 3 matrix.
Matrix3f() Matrix3f
Constructs and initializes a Matrix3f to all zeros.
matrix4f Token
Matrix4f org.jmol.util
A single precision floating point 4 by 4 matrix.
Matrix4f() Matrix4f
matrixPermutation(int[], int[][]) PermutationIterator
Returns a new matrix formed by permuting the rows and columns of the
given matrix according to the permuation list p.
matrixToScript(Object) Escape
max IndexIteratorIncreasing
max Token
max(Ifactor) Ifactor
Maximum of two values.
max(Rational) Rational
Compares the value of this with another constant.
max(Vector<Ifactor>) Ifactor
Maximum of a list of values.
MAX_INT Rational
The maximum and minimum value of a standard Java integer, 2^31.
max_l P2HydrogenPatkowski
max_l P2HydrogenPatkowskiAtomic
MAX_X DevicePlotPoints
MAX_Y DevicePlotPoints
maxAdjustInterval MCMoveStepTracker
maxAngle MCMoveRotateMoleculePhiTheta
maxBias MCMoveClusterAtomHSRing
maxBiasMinN MCMoveIDBiasAction
maxBiasR MCMoveClusterAtomHSRing
maxBlocks AccumulatorAverageCollapsing
maxBlockSize VirialHSOrC.VirialLJrParam
maxBlockSize VirialLJOrC.VirialLJrParam
maxBlockSize VirialLJOrICPYC.VirialLJrParam
maxBonds AssociationHelperBranched
maxBonds AssociationHelperMolecule
maxcf MinimizeHCP.SimOverlapParam
maxChainLength TestIGAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
maxChainLength TestLJAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
maxChainLength AtomTestChainLength
maxChainLength AtomTestChainLength
maxCount FieldNodeCount
maxCount FieldNodeCountMax
maxDistance MCMoveInsertDeleteLatticeVacancy
maxDistance MCMoveInsertDeleteVacancy
maxDr2 DataSourceQ4
maxExchangeNodes ExchangeSplit.ExchangeSplitParameters
maxFloat DisplayTable
maxHeight SVGConverter
Maximum output image height.
maximum() DoubleRange
The maximum defined by this range.
MAXIMUM_AUTO_BOND_COUNT JmolConstants
MAXIMUM_QUALITY SVGConverter
Maximum quality value
maxIndex PermutationIterator
maxIndex() BetaSource
Returns k such that beta[j] == 0 for all j > k.
maxIndex() HardRods
maxIndex() VanderWaals
maxInsertDistance MCMoveInsertDeleteLatticeVacancy
maxInsertDistance MCMoveInsertDeleteVacancy
maxIsomorph FFTDecomposition
maxIsomorph IsFFT
MaxIsomorph etomica.graph.operations
Returns a set of graphs with each one corresponding to a graph in the
original set.
MaxIsomorph() MaxIsomorph
MaxIsomorph.MaxIsomorphParameters etomica.graph.operations
Parameters class for MaxIsomorph which defines a graph operation and
property to select for.
MaxIsomorphCriteriaMixture() VirialDiagramsMix2.MaxIsomorphCriteriaMixture
MaxIsomorphParameters(GraphOp, Property) MaxIsomorph.MaxIsomorphParameters
MaxIsomorphWertheim etomica.graph.operations
Returns a set of graphs with each one corresponding to a graph in the
original set.
MaxIsomorphWertheim() MaxIsomorphWertheim
MaxIsomorphWertheim.MaxIsomorphWertheimParameters etomica.graph.operations
MaxIsomorphWertheimParameters(CombineABSite.CombineABSiteParameters) MaxIsomorphWertheim.MaxIsomorphWertheimParameters
MaxIsomorphWertheimParameters(Property, CombineABSite.CombineABSiteParameters) MaxIsomorphWertheim.MaxIsomorphWertheimParameters
maxIterations IntegratorRigidIterative
maxIterations IntegratorRigidMatrixIterative
maxIterations IntegratorVelocityVerletShake
maxIterations DataClusterer
maxIterations ReadCluster.ReadClusterParams
maxIterations FitTanh
maxIterations FitTanh
maxLength MCMoveAtomMonomer
maxLength MCMoveAtomSmer
maxLength MCMoveMoleculeMonomer
maxLength MCMoveMoleculeRotateAssociated
maxLength MCMoveMoleculeSmer
maxLength MCMoveRotateAssociated
maxLPN SpecialFunctions
maxMolecule MCMoveVolumeSolidNPTMolecularOriented
maxN MCMoveInsertDeleteBiased
maxNbrsVapor AtomTestLiquidAtomic
maxNumAtoms MCMoveIDBiasAction
maxNumAtoms PotentialEmulCached
maxNumBeads MCMoveClusterRingPartialRegrow
maxNumBlocks AccumulatorAverageBootstrap
maxpar1 P2WaterPotentialsJankowski
maxpar2 P2WaterPotentialsJankowski
maxPhi MCMoveVolumeSolidNPTMolecularOriented
maxRatio DataPumpListenerPow
maxRunNumber VirialSQWBinMultiRecalcW.VirialHSParam
maxRunNumber VirialSQWRecalcSmallMem.VirialHSParam
maxSample AccumulatorAverageCollapsingLogAB
maxSampleValue MeterVirialBDBin
maxSleep DeviceDelaySlider
maxSphereCache Shader
maxSteps ActionIntegrate
maxSteps ActionMinimizeEnergy
maxVacancy MCMoveIDBiasAction
MaxwellBoltzmann etomica.statmech
Non-instantiable class with static methods for implementing features of the
Maxwell-Boltzmann velocity distribution.
MaxwellBoltzmann.Distribution etomica.statmech
Function giving the Maxwell-Boltzmann distribution of speeds.
maxwidth ScientificFormat
maxWidth SVGConverter
Maximum output image width.
maybeTrimToSize() AtomArrayList
maybeTrimToSize() MoleculeArrayList
MayerD2FDT2Spherical etomica.virial
Required for computing second derivatives of virial coefficients w/r to temperature
MayerD2FDT2Spherical(Potential2Spherical) MayerD2FDT2Spherical
Constructor for MayerESpherical.
MayerDFDTSpherical etomica.virial
Required for computing temperature derivatives of virial coefficients
MayerDFDTSpherical(Potential2Spherical) MayerDFDTSpherical
Constructor for MayerESpherical.
MayerDFQFHDTSpherical etomica.virial
Required for computing temperature derivatives of virial coefficients computed with quadratic Feynmann-Hibbs modification
to the potential.
MayerDFQFHDTSpherical(P2EffectiveFeynmanHibbs) MayerDFQFHDTSpherical
Constructor for MayerESpherical.
MayerEGeneral etomica.virial
MayerEGeneral(IPotentialMolecular) MayerEGeneral
Constructor Mayer function using given potential.
MayerEHardSphere etomica.virial
MayerEHardSphere() MayerEHardSphere
Constructor for MayerEHardSphere.
MayerEHardSphere(double) MayerEHardSphere
MayerENonGeneral etomica.virial
MayerENonGeneral(IPotentialMolecular, double) MayerENonGeneral
Constructor Mayer function using given potential.
MayerESpherical etomica.virial
MayerESpherical(Potential2Spherical) MayerESpherical
Constructor for MayerESpherical.
MayerFunction etomica.virial
MayerFunctionMolecularThreeBody etomica.virial
MayerFunctionMolecularThreeBody(IPotentialMolecular) MayerFunctionMolecularThreeBody
MayerFunctionNonAdditive etomica.virial
Interface for a Mayer f-function, which takes 3+ atoms and
returns exp(-(u(atoms)-u(pairs))/kT) - 1
MayerFunctionNonAdditiveFull etomica.virial
MayerFunctionNonAdditiveFull(IPotentialMolecular) MayerFunctionNonAdditiveFull
MayerFunctionProductGeneral etomica.virial
MayerFunctionProductGeneral(Space, MayerFunction[], double[]) MayerFunctionProductGeneral
MayerFunctionSphericalThreeBody etomica.virial
Non-additive Mayer function class for "spherical" potentials
MayerFunctionSphericalThreeBody(IPotentialAtomicMultibody) MayerFunctionSphericalThreeBody
MayerFunctionSum etomica.virial
MayerFunctionSum(MayerFunction[], double[]) MayerFunctionSum
MayerFunctionSumGeneral etomica.virial
MayerFunctionSumGeneral(Space, MayerFunction[], double[]) MayerFunctionSumGeneral
MayerFunctionTemperature etomica.virial
Mayer function that wraps another MayerFunction and ignores
the temperature passed to f(), asking the wrapped MayerFunction
for its value at the MayerFunction Temperature's temperature.
MayerFunctionTemperature(MayerFunction, double) MayerFunctionTemperature
MayerFunctionThreeBody etomica.virial
This class acts as a non-additive Mayer function for molecules that
interact with only a 3-body potential.
MayerFunctionThreeBody() MayerFunctionThreeBody
MayerGeneral etomica.virial
MayerGeneral(IPotentialMolecular) MayerGeneral
Constructor Mayer function using given potential.
MayerGeneralAtomic etomica.virial
MayerGeneralAtomic(IPotentialAtomic) MayerGeneralAtomic
Constructor Mayer function using given potential.
MayerGeneralSpherical etomica.virial
MayerGeneralSpherical(Potential2Spherical) MayerGeneralSpherical
Constructor Mayer function using given potential.
MayerHardSphere etomica.virial
MayerHardSphere() MayerHardSphere
Constructor for MayerHardSphere.
MayerHardSphere(double) MayerHardSphere
MayerHSMixture etomica.virial
This class represents a Mayer function for any pair of species from a
hard sphere mixture.
MayerHSMixture(int, double[][], double, boolean, Space, Boundary) MayerHSMixture
MayerIonicDiagram1qbond etomica.virial.cluster
modified from WertheimNaphthalene class
cluster diagrams generator for ionic solutions, based on Mayer's theory
f-bond is splitted to k-bond, (kg1+g1)
diagrams with g chain(s) are reduced to lower order of diagrams(here they are just simply discarded)
g1/kg1 is magically changed to represent q1-bond [exp(-kappa * r / (4*pi*r)] with different domain, but g1 is still in use
kg1 represents [exp(-kappa * r / (4*pi*r)] instead of [exp(-alpha * r / (4*pi*r)] (kq1 essentially)
===> then q1 is substituted by (xq1-kg1), where xq1 has domain:[sigmaHS, infinity]
qi represent xqi bonds, gi represent REAL q bonds
the final result contains q1(represent xq1) and kg1(represent q1)
can handle 4pt
just xq1 & kq1 & k in the final set of S
MayerIonicDiagram1qbond(int, boolean, boolean, boolean, boolean) MayerIonicDiagram1qbond
MayerIonicDiagram1qbond(int, boolean, boolean, int, boolean) MayerIonicDiagram1qbond
MayerIonicDiagram2qbonds etomica.virial.cluster
Mayer's theory on ionic solution
f-bond is splitted to k-bond, (kg+g),(kg2+g2)
diagrams with g chain(s) are reduced to lower order of diagrams(here they are just simply discarded)
gi is substituted by (qi - kgi)
qi represent modified q bonds, gi represent REAL q bonds
even number of q bonds , the final result contains q1,q2,kg1,kg2bonds
MayerIonicDiagram2qbonds(int, boolean, boolean, boolean, boolean) MayerIonicDiagram2qbonds
MayerIonicDiagram2qbonds(int, boolean, boolean, int, boolean) MayerIonicDiagram2qbonds
MayerIonicDiagram4qbonds etomica.virial.cluster
cluster diagrams generator for ionic solutions, based on Mayer's theory
f-bond is split into k-bond(HS f-hond), (kg+g),(kg2+g2),(kg3+g3),(kg4+g4)truncation
diagrams with g chain(s) are reduced to lower order of diagrams(here they are just simply discarded)
gi is substituted by (qi - kgi), where qi represents modified q bonds( domain [sigmaHS,infinity), gi represent REAL q bonds, i represents q bonds power
the final sets of diagrams contains q1,q2,q3,q4;kg1,kg2,kg3,kg4 bonds
2 pt diagrams with q2 bond is discarded ( cycle diagram)
cannot handle 4 points due to the insufficiency of calculations
MayerIonicDiagram4qbonds(int, boolean, boolean, boolean, boolean) MayerIonicDiagram4qbonds
MayerIonicDiagram4qbonds(int, boolean, boolean, int, boolean) MayerIonicDiagram4qbonds
MayerPTAtt etomica.virial
Mayer function class that returns temperature expansion bond of the desired
order using molecular potentials.
MayerPTAtt(IPotentialMolecular, IPotentialMolecular, int) MayerPTAtt
Constructor takes reference potential, attractive component and order in temperature.
MayerPUGeneral etomica.virial
f + u
f: exp(-beta U)
u: 0 for r < sigmaHS, dipole energy otherwise
a Potential2 object.
MayerPUGeneral(Space, double, double, IPotentialMolecular) MayerPUGeneral
MayerSphericalPlus etomica.virial
MayerSphericalPlus(Potential2Spherical, Potential2Spherical) MayerSphericalPlus
Constructor Mayer function using given potential.
MayerSphericalPTAtt etomica.virial
Mayer function class that returns temperature expansion bond of the desired
order.
MayerSphericalPTAtt(Potential2Spherical, Potential2Spherical, int) MayerSphericalPTAtt
Constructor takes reference potential, attractive component and order in temperature.
MayerSSSeries etomica.virial
MayerSSSeries(int) MayerSSSeries
Constructor for MayerHardSphere.
MayerWell etomica.virial
MayerWell(double, double) MayerWell
MayerXSpherical etomica.virial
MayerXSpherical(Potential2SoftSpherical) MayerXSpherical
Constructor for MayerESpherical.
mBond MayerIonicDiagram1qbond
mBond MayerIonicDiagram2qbonds
mBond MayerIonicDiagram4qbonds
mBond VirialDiagrams.ArticulatedAt0
mBond VirialDiagrams
mBond VirialDiagramsMix
mBond VirialDiagramsPT.ArticulatedAt0
mBond VirialDiagramsPT
mBond WertheimDiagrams2SiteRho
mBond WertheimDiagrams3SiteRho
MBond VirialDiagramsMix
mc PotentialCalculationEnergySumBigDecimal
mc ClusterWheatleySoftBD
mc ClusterWheatleySoftDerivativesBD
mc MeterVirialBDBinMultiThreaded
mc MeterVirialEBinMultiThreaded
mCapF1Bond WertheimDiagrams3SiteRho
mCapF2Bond WertheimDiagrams3SiteRho
mCapFACBond DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
mCapFACBond WertheimDiagrams3SiteRho
mCapFBCBond DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
mCapFBCBond WertheimDiagrams3SiteRho
mCapFBond WertheimDiagrams3SiteRho
mCapFCABond DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
mCapFCABond WertheimDiagrams3SiteRho
mCapFCBBond DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
mCapFCBBond WertheimDiagrams3SiteRho
mCluster ClusterGenerator
mcmove Ising
mcMove MCMoveOverlapListener
mcMove MCMoveStepTracker
mcMove LJMD
mcMove MeterSamplingHarmonic
mcMove MeterSamplingTarget
mcMove MeterWorkUmbrellaHarmonic
mcMove MeterWorkUmbrellaTarget
mcMove Heisenberg
mcMove Heisenberg3Pair
mcMove HeisenbergPair
mcMove MCMoveClusterAtomQ
MCMove etomica.integrator.mcmove
Parent class for all elementary Monte Carlo move classes, as used by
IntegratorMC class.
MCMove(PotentialMaster) MCMove
MCMove(PotentialMaster, MCMoveTracker) MCMove
mcMoveAtom TestLJAssociationMC3D_NVTOld
mcMoveAtom SimIdealGas
mcMoveAtom SimLJ
mcMoveAtom LjMC3D
mcMoveAtom LJNPT
mcMoveAtom LJNVT
mcMoveAtom LJMC
mcMoveAtom AshtonWildingLJ
mcMoveAtom AshtonWildingOsmoticVirial
mcMoveAtom AshtonWildingVirial
mcMoveAtom GCRestrictedGibbsHS
mcMoveAtom GCWidomInsertHS
mcMoveAtom NVTWidomInsertLJ
mcMoveAtom HSMC2D
mcMoveAtom SoftSphere3d
mcMoveAtom LJMC
mcMoveAtom TestLJGCMC3D
mcMoveAtom TestLJMC3D
MCMoveAtom etomica.integrator.mcmove
Standard Monte Carlo atom-displacement trial move.
MCMoveAtom(IRandom, PotentialMaster, Space) MCMoveAtom
Constructs the move with default stepSize = 1.0, stepSizeMax = 15.0, fixOverlap = false
MCMoveAtom(IRandom, PotentialMaster, Space, double, double, boolean) MCMoveAtom
MCMoveAtom(IRandom, PotentialMaster, Space, double, double, boolean, MeterPotentialEnergy) MCMoveAtom
Constructs with specification of special-purpose energy meter.
mcMoveAtomBigStep LJMC
mcMoveAtomCoupled SimIdealGas
mcMoveAtomCoupled SimLJ
MCMoveAtomCoupled etomica.freeenergy.npath
Created by andrew on 4/11/17.
MCMoveAtomCoupled etomica.normalmode
Standard Monte Carlo atom-displacement trial move.
MCMoveAtomCoupled(PotentialMaster, MeterPotentialEnergy, IRandom, Space) MCMoveAtomCoupled
MCMoveAtomCoupled(PotentialMaster, MeterPotentialEnergy, IRandom, Space, double, double, boolean) MCMoveAtomCoupled
MCMoveAtomCoupled(PotentialMaster, IRandom, Space, double, double, boolean) MCMoveAtomCoupled
MCMoveAtomCoupled(IRandom, PotentialMaster, Space) MCMoveAtomCoupled
MCMoveAtomCoupledBennet etomica.normalmode
Standard Monte Carlo atom-displacement trial move.
MCMoveAtomCoupledBennet(PotentialMaster, IRandom, CoordinateDefinition, NormalModes, double, Space) MCMoveAtomCoupledBennet
MCMoveAtomCoupledUmbrella etomica.normalmode
Standard Monte Carlo atom-displacement trial move.
MCMoveAtomCoupledUmbrella(PotentialMaster, IRandom, CoordinateDefinition, NormalModes, double, Space) MCMoveAtomCoupledUmbrella
mcMoveAtomDimer TestLJAssociationMC3D_NPT
mcMoveAtomDimer TestLJAssociationMC3D_NPT
MCMoveAtomDimer etomica.association
MCMoveAtomDimer(PotentialMaster, IRandom, Space, double, double, boolean) MCMoveAtomDimer
MCMoveAtomDimer(Simulation, PotentialMaster, Space) MCMoveAtomDimer
MCMoveAtomInRegion etomica.integrator.mcmove
MC move that operates only on atoms within a given region of x values.
MCMoveAtomInRegion(IRandom, PotentialMaster, Space) MCMoveAtomInRegion
mcMoveAtomMonomer TestIGAssociationMC3D_NPT_DoubleSites
mcMoveAtomMonomer TestLJAssociationMC3D_NPT_DoubleSites
mcMoveAtomMonomer TestLJAssociationMC3D_NPT
mcMoveAtomMonomer TestLJAssociationMC3D_NPT
MCMoveAtomMonomer etomica.association
MCMoveAtomMonomer(PotentialMaster, IRandom, Space, double, double, boolean) MCMoveAtomMonomer
MCMoveAtomMonomer(Simulation, PotentialMaster, Space) MCMoveAtomMonomer
MCMoveAtomNbr etomica.interfacial
MCMoveAtomNbr(IRandom, PotentialMaster, Space) MCMoveAtomNbr
MCMoveAtomNoSmer etomica.association
MCMoveAtomNoSmer(IRandom, PotentialMaster, Space) MCMoveAtomNoSmer
MCMoveAtomNPath etomica.freeenergy.npath
Created by andrew on 4/11/17.
MCMoveAtomNPath(IRandom, PotentialMaster, Space, P1ImageHarmonic) MCMoveAtomNPath
mcMoveAtomSmer TestIGAssociationMC3D_NPT_DoubleSites
mcMoveAtomSmer TestLJAssociationMC3D_NPT_DoubleSites
MCMoveAtomSmer etomica.association
MCMoveAtomSmer(PotentialMaster, IRandom, Space, double, double, boolean) MCMoveAtomSmer
MCMoveAtomSmer(Simulation, PotentialMaster, Space) MCMoveAtomSmer
MCMoveAtomSuperBox etomica.normalmode
Standard Monte Carlo atom-displacement trial move.
MCMoveAtomSuperBox(PotentialMaster, IRandom, Space, CoordinateDefinitionLeafSuperBox) MCMoveAtomSuperBox
MCMoveAtomSwap etomica.freeenergy.npath
Created by andrew on 4/11/17.
MCMoveAtomSwap(IRandom, PotentialMaster, Space, P1ImageHarmonic) MCMoveAtomSwap
mcMoveBiasUB TestAceticAcidMC3D_NPT
mcMoveBiasUB TestIGAssociationMC3D_NPT_DoubleSites
mcMoveBiasUB TestLJAssociationMC3D_NPT_DoubleSites
mcMoveBiasUB TestLJAssociationMC3D_NPT
mcMoveBiasUB TestLJAssociationMC3D_NPT
MCMoveBiasUB etomica.association
MCMoveBiasUB(PotentialMasterCell, BiasVolume, IRandom, Space) MCMoveBiasUB
MCMoveBiasUBMolecule etomica.association
MCMoveBiasUBMolecule(PotentialMaster, BiasVolumeMolecule, IRandom, Space) MCMoveBiasUBMolecule
MCMoveBondLength etomica.starpolymer
An MC Move for cluster simulations that "wiggles" a chain molecule.
MCMoveBondLength(PotentialMaster, IRandom, double, int, Space) MCMoveBondLength
MCMoveBondLength(Simulation, PotentialMaster, int, Space) MCMoveBondLength
MCMoveBox etomica.integrator.mcmove
MCMove parent class for moves that operate on a single Box.
MCMoveBox(PotentialMaster) MCMoveBox
MCMoveBox(PotentialMaster, MCMoveTracker) MCMoveBox
MCMoveBoxSize etomica.integrator.mcmove
Monte Carlo move for changing the box dimensions at constant volume.
MCMoveBoxSize(PotentialMaster, IRandom, Space) MCMoveBoxSize
MCMoveBoxSize(Simulation, PotentialMaster, Space) MCMoveBoxSize
MCMoveBoxStep etomica.integrator.mcmove
MCMove parent class for moves that have a step size and operate on a single
Box.
MCMoveBoxStep(PotentialMaster) MCMoveBoxStep
MCMoveBoxStep(PotentialMaster, MCMoveStepTracker) MCMoveBoxStep
MCMoveChangeBondLength etomica.virial
MCMoveChangeBondLength(PotentialMaster, IRandom, Space, double) MCMoveChangeBondLength
MCMoveClusterAngleBend etomica.virial
An MC Move for cluster simulations that bends the bond angle for 3-atom
molecule.
MCMoveClusterAngleBend(PotentialMaster, IRandom, double, Space) MCMoveClusterAngleBend
MCMoveClusterAngleBend(Simulation, PotentialMaster, Space) MCMoveClusterAngleBend
MCMoveClusterAngleBendAceticAcid etomica.virial
An MC Move for cluster simulations that bends the bond angle for 3-atom
molecule.
MCMoveClusterAngleBendAceticAcid(PotentialMaster, IRandom, double, Space) MCMoveClusterAngleBendAceticAcid
MCMoveClusterAngleBendAceticAcid(Simulation, PotentialMaster, Space) MCMoveClusterAngleBendAceticAcid
MCMoveClusterAtom etomica.virial
Overrides MCMoveAtom to prevent index-0 molecule from being displaced
MCMoveClusterAtom(IRandom, Space) MCMoveClusterAtom
MCMoveClusterAtomChainHSTail etomica.virial
Grows configurations of chains with the pair probability distribution that
is flat for some distance and then has a power-law decay tail.
MCMoveClusterAtomChainHSTail(IRandom, Space, double, double) MCMoveClusterAtomChainHSTail
MCMoveClusterAtomDiscrete etomica.virial
Extension of MCMoveClusterAtom that moves only the second atom and only
along the x axis.
MCMoveClusterAtomDiscrete(IRandom, Space, double) MCMoveClusterAtomDiscrete
MCMoveClusterAtomHSChain etomica.virial
Class that samples molecule positions based on a chain of hard spheres of
diameter sigma.
MCMoveClusterAtomHSChain(IRandom, Space, double) MCMoveClusterAtomHSChain
MCMoveClusterAtomHSChainMix etomica.virial
Class that samples molecule positions based on a chain of hard spheres of
various sizes.
MCMoveClusterAtomHSChainMix(IRandom, Space, double[][]) MCMoveClusterAtomHSChainMix
MCMoveClusterAtomHSRing etomica.virial
MCMoveClusterAtomHSRing(IRandom, Space, double) MCMoveClusterAtomHSRing
MCMoveClusterAtomHSTree etomica.virial
Class that samples molecule positions based on a tree of hard spheres of
diameter sigma.
MCMoveClusterAtomHSTree(IRandom, Space, double) MCMoveClusterAtomHSTree
MCMoveClusterAtomHSTreeMix etomica.virial
Class that samples molecule positions based on a tree of hard spheres of
various sizes.
MCMoveClusterAtomHSTreeMix(IRandom, Space, double[][]) MCMoveClusterAtomHSTreeMix
MCMoveClusterAtomInBox etomica.virial
Class that samples molecule positions by randomly placing hard spheres
in the box.
MCMoveClusterAtomInBox(IRandom, Space) MCMoveClusterAtomInBox
MCMoveClusterAtomMulti etomica.virial
MCMoveClusterAtomMulti(IRandom, Space) MCMoveClusterAtomMulti
MCMoveClusterAtomQ etomica.virial
MCMoveClusterAtomQ(IRandom, Space, MCMoveAtom) MCMoveClusterAtomQ
MCMoveClusterAtomRotateMulti etomica.virial
Extension of MCMoveAtom that does trial in which several atom orientations are
perturbed.
MCMoveClusterAtomRotateMulti(IRandom, Space) MCMoveClusterAtomRotateMulti
MCMoveClusterAtomSQWChain etomica.virial
MCMoveClusterAtomSQWChain(IRandom, Space, double, double) MCMoveClusterAtomSQWChain
MCMoveClusterAtomSQWTree etomica.virial
MCMoveClusterAtomSQWTree(IRandom, Space, double, double) MCMoveClusterAtomSQWTree
MCMoveClusterBondLength etomica.starpolymer
An MC Move for cluster simulations that "wiggles" a chain molecule.
MCMoveClusterBondLength(PotentialMaster, IRandom, double, int, Space) MCMoveClusterBondLength
MCMoveClusterBondLength(Simulation, PotentialMaster, int, Space) MCMoveClusterBondLength
MCMoveClusterConformationMDTest etomica.starpolymer
MCMoveClusterConformationMDTest(SimulationVirialOverlap2, Space, double, int, int, boolean, boolean) MCMoveClusterConformationMDTest
MCMoveClusterDiagram etomica.virial
Move that attempts to perform changes in the cluster diagram.
MCMoveClusterDiagram(PotentialMaster) MCMoveClusterDiagram
MCMoveClusterMolecule etomica.virial
Standard Monte Carlo molecule-displacement trial move for cluster integrals.
MCMoveClusterMolecule(Simulation, Space) MCMoveClusterMolecule
MCMoveClusterMolecule(IRandom, Space, double) MCMoveClusterMolecule
MCMoveClusterMoleculeHSChain etomica.starpolymer
Class that samples molecule positions based on a chain of hard spheres of
diameter sigma.
MCMoveClusterMoleculeHSChain etomica.virial
Class that samples molecule positions based on a chain of hard spheres of
diameter sigma.
MCMoveClusterMoleculeHSChain(IRandom, Space, double) MCMoveClusterMoleculeHSChain
MCMoveClusterMoleculeHSChain(IRandom, Space, double) MCMoveClusterMoleculeHSChain
MCMoveClusterMoleculeHSChainB3 etomica.starpolymer
Class that samples molecule positions based on a chain of hard spheres of
diameter sigma.
MCMoveClusterMoleculeHSChainB3(IRandom, Space, double) MCMoveClusterMoleculeHSChainB3
MCMoveClusterMoleculeLayerMove etomica.virial
Monte Carlo molecule-displacement from 1 layer to the other layer trial move for cluster integrals.
MCMoveClusterMoleculeLayerMove(Simulation, Space) MCMoveClusterMoleculeLayerMove
MCMoveClusterMoleculeMulti etomica.virial
MCMoveClusterMoleculeMulti(PotentialMaster, IRandom, Space, double) MCMoveClusterMoleculeMulti
MCMoveClusterMoleculeMulti(Simulation, Space) MCMoveClusterMoleculeMulti
MCMoveClusterPolyhedraChain etomica.virial
MCMoveClusterPolyhedraChain(IRandom, Space, double, IPotentialAtomic, double[][]) MCMoveClusterPolyhedraChain
MCMoveClusterPolyhedraTree etomica.virial
MCMoveClusterPolyhedraTree(IRandom, Space, double, IPotentialAtomic, double[][]) MCMoveClusterPolyhedraTree
MCMoveClusterReptateMulti etomica.virial
An MC move for cluster simulations which performs reptation moves on molecules.
MCMoveClusterReptateMulti(PotentialMaster, IRandom, int) MCMoveClusterReptateMulti
MCMoveClusterReptateMulti(Simulation, PotentialMaster, int) MCMoveClusterReptateMulti
MCMoveClusterRingPartialRegrow etomica.virial
MCMove that partially regrows the beads of a ring polymer, accepting or
rejecting the move based on the sampling weight.
MCMoveClusterRingPartialRegrow(PotentialMaster, IRandom, Space) MCMoveClusterRingPartialRegrow
MCMoveClusterRingPartialRegrow(PotentialMaster, IRandom, Space, int[][]) MCMoveClusterRingPartialRegrow
MCMoveClusterRingRegrow etomica.virial
MCMove that fully regrows the beads of a ring polymer, accepting or
rejecting the move based on the sampling weight.
MCMoveClusterRingRegrow(IRandom, Space) MCMoveClusterRingRegrow
MCMoveClusterRingRegrow(IRandom, Space, int[][]) MCMoveClusterRingRegrow
MCMoveClusterRingRegrowExchange etomica.virial
MCMove that fully regrows the beads of a ring polymer, accepting or
rejecting the move based on the sampling weight.
MCMoveClusterRingRegrowExchange(IRandom, Space) MCMoveClusterRingRegrowExchange
MCMoveClusterRingRegrowOrientation etomica.virial
MCMove that fully regrows the beads of a ring polymer by rotating the images, accepting or
rejecting the move based on the sampling weight.
MCMoveClusterRingRegrowOrientation(IRandom, Space, int) MCMoveClusterRingRegrowOrientation
MCMoveClusterRingScale etomica.virial
MCMove that scales the atoms of a molecule in or out.
MCMoveClusterRingScale(PotentialMaster, IRandom, Space) MCMoveClusterRingScale
MCMoveClusterRingScale(PotentialMaster, IRandom, Space, int[][]) MCMoveClusterRingScale
MCMoveClusterRotateArm etomica.starpolymer
An MC Move for cluster simulations that "wiggles" a chain molecule.
MCMoveClusterRotateArm(PotentialMaster, IRandom, double, int, Space) MCMoveClusterRotateArm
MCMoveClusterRotateArm(Simulation, PotentialMaster, int, Space) MCMoveClusterRotateArm
MCMoveClusterRotateCH3 etomica.virial
Monte Carlo CH3 rotation for cluster integrals(Alkane TraPPE-EH).
MCMoveClusterRotateCH3(PotentialMaster, IRandom, double, int, Space) MCMoveClusterRotateCH3
MCMoveClusterRotateCH3(Simulation, PotentialMaster, int, Space) MCMoveClusterRotateCH3
MCMoveClusterRotateMolecule3D etomica.virial
MC move for Mayer Sampling that rotates a single molecule
MCMoveClusterRotateMolecule3D(PotentialMaster, IRandom, Space) MCMoveClusterRotateMolecule3D
MCMoveClusterRotateMoleculeMulti etomica.virial
MCMove for use in a Mayer sampling simulation that rotates all molecules in
a Box except the first molecule, which is never moved.
MCMoveClusterRotateMoleculeMulti(IRandom, Space) MCMoveClusterRotateMoleculeMulti
MCMoveClusterTorsionAceticAcid etomica.virial
An MC Move for cluster simulations that performs torsion moves on acetic acid.
MCMoveClusterTorsionAceticAcid(PotentialMaster, Space, IRandom) MCMoveClusterTorsionAceticAcid
MCMoveClusterTorsionAlkaneEH etomica.virial
MC move for alkane-TraPPE-EH torsion
pick up carbons in the box only, but move update all the atoms(carbons and hydrogens)
MCMoveClusterTorsionAlkaneEH(PotentialMaster, Space, IRandom, double, P4BondTorsion, int) MCMoveClusterTorsionAlkaneEH
MCMoveClusterTorsionAlkaneEH(Simulation, PotentialMaster, Space, P4BondTorsion) MCMoveClusterTorsionAlkaneEH
MCMoveClusterTorsionMulti etomica.virial
An MC Move for cluster simulations that performs torsion moves on a chain
molecule (of length N>=4).
MCMoveClusterTorsionMulti(PotentialMaster, Space, IRandom, double, P4BondTorsion, int) MCMoveClusterTorsionMulti
MCMoveClusterTorsionMulti(Simulation, PotentialMaster, Space, P4BondTorsion) MCMoveClusterTorsionMulti
MCMoveClusterWiggleAceticAcid etomica.virial
An MC Move for cluster simulations that "wiggles" a chain molecule.
MCMoveClusterWiggleAceticAcid(PotentialMaster, IRandom, double, Space) MCMoveClusterWiggleAceticAcid
MCMoveClusterWiggleAceticAcid(Simulation, PotentialMaster, Space) MCMoveClusterWiggleAceticAcid
MCMoveClusterWiggleAlkaneEH etomica.virial
Wiggle move for alkane, TraPPE-EH
hydrogens attached to the 3 carbons are updated, keeping bond lengths and angles fixed
*********** outline ************
// update j if j == 0 or j == n-1
// update 3 H on j
// if j==0, update 2H on (j+1)
// if j==n-1, update 2H on (j-1)
&& 0
MCMoveClusterWiggleAlkaneEH(PotentialMaster, IRandom, double, int, Space) MCMoveClusterWiggleAlkaneEH
Constructor for MCMoveAtomMulti.
MCMoveClusterWiggleAlkaneEH(Simulation, PotentialMaster, int, Space) MCMoveClusterWiggleAlkaneEH
MCMoveClusterWiggleMulti etomica.virial
An MC Move for cluster simulations that "wiggles" a chain molecule.
MCMoveClusterWiggleMulti(PotentialMaster, IRandom, double, int, Space) MCMoveClusterWiggleMulti
MCMoveClusterWiggleMulti(Simulation, PotentialMaster, int, Space) MCMoveClusterWiggleMulti
mcMoveDiagram SimulationVirialDiagram
mcMoveDimer TestLJAssociationMC3D_NPT
mcMoveDimer TestLJAssociationMC3D_NVTOld
mcMoveDimer TestLJAssociationMC3D_NPT
MCMoveDimer etomica.association
Standard Monte Carlo atom-displacement trial move of dimer
MCMoveDimer etomica.integrator.mcmove
Standard Monte Carlo atom-displacement trial move.
MCMoveDimer(PotentialMasterCell, IRandom, Space, double, double, boolean, IPotentialAtomic) MCMoveDimer
MCMoveDimer(Simulation, PotentialMasterCell, Space, IPotentialAtomic) MCMoveDimer
MCMoveDimer(Simulation, PotentialMasterCell, Space, IPotentialAtomic) MCMoveDimer
MCMoveDimer(Simulation, PotentialMasterCell, IRandom, Space, double, double, boolean, IPotentialAtomic) MCMoveDimer
mcMoveDimerRotate TestLJAssociationMC3D_NPT
mcMoveDimerRotate TestLJAssociationMC3D_NVTOld
mcMoveDimerRotate TestLJAssociationMC3D_NPT
MCMoveDimerRotate etomica.association
Standard Monte Carlo atom-displacement trial move.
MCMoveDimerRotate etomica.integrator.mcmove
Standard Monte Carlo atom-displacement trial move.
MCMoveDimerRotate(PotentialMasterCell, IRandom, Space, double, double, boolean, IPotentialAtomic) MCMoveDimerRotate
MCMoveDimerRotate(Simulation, PotentialMasterCell, Space, IPotentialAtomic) MCMoveDimerRotate
MCMoveDimerRotate(Simulation, PotentialMasterCell, Space, IPotentialAtomic) MCMoveDimerRotate
MCMoveDimerRotate(Simulation, PotentialMasterCell, IRandom, Space, double, double, boolean, IPotentialAtomic) MCMoveDimerRotate
MCMoveEinsteinCrystal etomica.normalmode
MC move whose purpose in life is to sample an Einstein crystal.
MCMoveEinsteinCrystal(Space, IRandom) MCMoveEinsteinCrystal
MCMoveEvent etomica.integrator.mcmove
MCMoveEvent() MCMoveEvent
mcMoveGeometricCluster AshtonWildingOsmoticVirial
mcMoveGeometricCluster GCWidomInsertHS
MCMoveGeometricCluster etomica.osmoticvirial
Implementation of geometric cluster move of Liu and Luijten.
MCMoveGeometricCluster(PotentialMaster, Space, IRandom, IntegratorMC, ISpecies) MCMoveGeometricCluster
MCMoveGeometricClusterRestrictedGE etomica.osmoticvirial
Implementation of geometric cluster move for restricted gibbs ensemble by Liu, Luijten and Wilding.
MCMoveGeometricClusterRestrictedGE(PotentialMaster, Space, IRandom, Box, Box, ISpecies) MCMoveGeometricClusterRestrictedGE
mcMoveHarmonic MeterBoltzmannHarmonic
mcMoveHarmonic MeterDirectSamplingHarmonic
mcMoveHarmonic MeterHarmonicEnergyFromMove
mcMoveHarmonic MeterWorkHarmonicBennet
mcMoveHarmonic MeterWorkHarmonicPhaseSpace
mcMoveHarmonic MeterWorkHarmonicTargetandReweighting
MCMoveHarmonic etomica.normalmode
MCMoveHarmonic(IRandom) MCMoveHarmonic
MCMoveHarmonicEin etomica.normalmode
MC move whose purpose in life is to sample a system whose energy is a
combination of normal mode contributions and Einstein crystal
contributions.
MCMoveHarmonicEin(IRandom) MCMoveHarmonicEin
MCMoveHarmonicStep etomica.normalmode
MCMove that performs random displacements in the harmonic coordinates for
the k=0 wave vector.
MCMoveHarmonicStep(PotentialMaster, IRandom) MCMoveHarmonicStep
mcMoveID MCMoveIDBiasAction
mcMoveID LJmuVT
mcMoveID LJMC
mcMoveID DataSourceImposedFEFit
mcMoveID DataSourceImposedFEHistogram
mcMoveID SimHSMDVacancy
mcMoveID SimLJVacancy
mcMoveID TestLJGCMC3D
mcMoveIDA Adsorption
mcMoveIDB Adsorption
MCMoveIDBiasAction etomica.integrator.mcmove
IAction which takes data from an MCMoveOverlapListener about acceptance
probabilities for insert/delete moves and uses them to update biasing of
the move.
MCMoveIDBiasAction(IntegratorMC, MCMoveInsertDeleteBiased, int, double, MCMoveOverlapListener, int) MCMoveIDBiasAction
mcMoveInsertDelete AshtonWildingOsmoticVirial
mcMoveInsertDelete GCWidomInsertHS
MCMoveInsertDelete etomica.integrator.mcmove
Elementary Monte Carlo move in which a molecule of a specified species is
inserted into or removed from a box.
MCMoveInsertDelete(PotentialMaster, IRandom, Space) MCMoveInsertDelete
Constructs using default isPotentialHard = false
mcMoveInsertDelete1 GCRestrictedGibbsHS
mcMoveInsertDelete2 GCRestrictedGibbsHS
MCMoveInsertDeleteBiased etomica.integrator.mcmove
Biased MCMove for insertion and deletion.
MCMoveInsertDeleteBiased(PotentialMaster, IRandom, Space, int, int) MCMoveInsertDeleteBiased
MCMoveInsertDeleteLatticeVacancy etomica.integrator.mcmove
Looks for atoms without a full set of first nearest neighbors and attempts
insertions adjacent to one of those atoms.
MCMoveInsertDeleteLatticeVacancy(PotentialMasterNbr, IRandom, Space, Integrator, double, int, int) MCMoveInsertDeleteLatticeVacancy
MCMoveInsertDeleteLatticeVacancy.AtomIteratorBruteForce etomica.integrator.mcmove
MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbr etomica.integrator.mcmove
MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbrCell etomica.integrator.mcmove
MCMoveInsertDeleteVacancy etomica.integrator.mcmove
Looks for atoms without a full set of first nearest neighbors and attempts
insertions adjacent to one of those atoms.
MCMoveInsertDeleteVacancy(PotentialMaster, IRandom, Space, Integrator, double, int, int) MCMoveInsertDeleteVacancy
mcMoveList MCMoveManager
MCMoveListenerRGE etomica.osmoticvirial
MCMoveListenerRGE(AccumulatorAverage, Box, ISpecies, int) MCMoveListenerRGE
MCMoveManager etomica.integrator.mcmove
MCMoveManager(IRandom) MCMoveManager
MCMoveMolecular etomica.integrator.mcmove
An interface that contains MoleculeIterator
mcMoveMolecule SimGCPMWaterMCNPT
mcMoveMolecule SimGCPMWaterMCNVT
MCMoveMolecule etomica.integrator.mcmove
Standard Monte Carlo molecule-displacement trial move.
MCMoveMolecule(PotentialMaster, IRandom, Space, double, double) MCMoveMolecule
MCMoveMolecule(Simulation, PotentialMaster, Space) MCMoveMolecule
MCMoveMoleculeCoupled etomica.normalmode
Standard Monte Carlo molecule-displacement trial move.
MCMoveMoleculeCoupled(PotentialMaster, IRandom, Space) MCMoveMoleculeCoupled
MCMoveMoleculeCoupledInitPert etomica.models.nitrogen
Standard Monte Carlo molecule-displacement trial move.
MCMoveMoleculeCoupledInitPert(PotentialMaster, IRandom, Space, CoordinateDefinitionNitrogen) MCMoveMoleculeCoupledInitPert
MCMoveMoleculeCoupledSuperBox etomica.models.nitrogen
Standard Monte Carlo molecule-displacement trial move for superbox.
MCMoveMoleculeCoupledSuperBox(PotentialMaster, IRandom, Space, Box, int, int, CoordinateDefinitionNitrogenSuperBox) MCMoveMoleculeCoupledSuperBox
MCMoveMoleculeExchange etomica.integrator.mcmove
Performs a trial that results in the exchange of a molecule from one box to another.
MCMoveMoleculeExchange(PotentialMaster, IRandom, Space, IntegratorBox, IntegratorBox) MCMoveMoleculeExchange
MCMoveMoleculeExchangeVLE etomica.integrator.mcmove
MCMoveMoleculeExchangeVLE(PotentialMaster, IRandom, Space, IntegratorBox, IntegratorBox) MCMoveMoleculeExchangeVLE
mcMoveMoleculeMonomer TestAceticAcidMC3D_NPT
MCMoveMoleculeMonomer etomica.association
Monte Carlo molecule-displacement trial move for monomer molecules
MCMoveMoleculeMonomer(PotentialMaster, IRandom, Space, double, double) MCMoveMoleculeMonomer
MCMoveMoleculeMonomer(Simulation, PotentialMaster, Space) MCMoveMoleculeMonomer
mcMoveMoleculeRotate TestAceticAcidMC3D_NPT
MCMoveMoleculeRotateAssociated etomica.association
Performs a rotation of a molecule that has an orientation coordinate.
MCMoveMoleculeRotateAssociated(PotentialMaster, IRandom, Space) MCMoveMoleculeRotateAssociated
mcMoveMoleculeSmer TestAceticAcidMC3D_NPT
MCMoveMoleculeSmer etomica.association
Monte Carlo molecule-displacement trial move for a molecule in smer
MCMoveMoleculeSmer(PotentialMaster, IRandom, Space, double, double) MCMoveMoleculeSmer
MCMoveMoleculeSmer(Simulation, PotentialMaster, Space) MCMoveMoleculeSmer
MCMoveMultiHarmonic etomica.modules.multiharmonic
MCMove which moves all atoms.
MCMoveMultiHarmonic(P1Harmonic, IRandom) MCMoveMultiHarmonic
MCMoveOverlapListener etomica.integrator.mcmove
MCMoveOverlapListener(MCMoveInsertDeleteBiased, int, double, int, double) MCMoveOverlapListener
mcMoveOverlapMeter MCMoveIDBiasAction
mcMoveOverlapMeter DataSourceAvgPressure
mcMoveOverlapMeter DataSourceAvgPressure2
mcMoveOverlapMeter DataSourceFE
mcMoveOverlapMeter DataSourceFEHistogram
mcMoveOverlapMeter DataSourceImposedFEFit
mcMoveOverlapMeter DataSourceImposedFEHistogram
mcMoveOverlapMeter DataSourceMuRoot
mcMoveOverlapMeter DataSourceMuRoot1
mcMoveOverlapMeter DataSourceMuRootPMatch
mcMoveOverlapMeter DataSourcePMu
MCMovePhaseAngle etomica.normalmode
MCMovePhaseAngle(Space, NormalModesVariable, CoordinateDefinition, IRandom) MCMovePhaseAngle
mcMoveReptate SimulationVirial
mcMoveRotate TestIGAssociationMC3D_NPT_DoubleSites
mcMoveRotate TestLJAssociationMC3D_NPT_DoubleSites
mcMoveRotate TestLJAssociationMC3D_NVTOld
mcMoveRotate SimulationVirial
mcMoveRotate SimulationVirialOverlap2
mcMoveRotate TestLJAssociationMC3D_NPT
MCMoveRotate etomica.integrator.mcmove
Performs a rotation of an atom (not a molecule) that has an orientation coordinate.
MCMoveRotate(PotentialMaster, IRandom, Space) MCMoveRotate
MCMoveRotate3Pair etomica.spin.heisenberg
MCMoveRotate3Pair(IPotentialAtomic, IRandom, Space) MCMoveRotate3Pair
MCMoveRotateArm etomica.starpolymer
An MC Move for cluster simulations that "wiggles" a chain molecule.
MCMoveRotateArm(PotentialMaster, IRandom, double, int, Space) MCMoveRotateArm
MCMoveRotateArm(Simulation, PotentialMaster, int, Space) MCMoveRotateArm
MCMoveRotateAssociated etomica.association
Performs a rotation of an atom (not a molecule) that has an orientation coordinate.
MCMoveRotateAssociated(PotentialMaster, IRandom, Space) MCMoveRotateAssociated
mcMoveRotateMolecule SimGCPMWaterMCNPT
mcMoveRotateMolecule SimGCPMWaterMCNVT
MCMoveRotateMolecule3D etomica.integrator.mcmove
MCMoveRotateMolecule3D(PotentialMaster, IRandom, Space) MCMoveRotateMolecule3D
MCMoveRotateMolecule3DConstraint etomica.models.nitrogen
MCMoveRotate that moves the molecules according to pre-set constraint angle
which is given by the parameter "angle"
This class does not consider rotational energy, so the variable "energyChange"
always returns zero
getB() always returns positive one is to ensure the proposed move is always
accepted
MCMoveRotateMolecule3DConstraint(PotentialMaster, IRandom, Space, double, CoordinateDefinitionNitrogen, Box) MCMoveRotateMolecule3DConstraint
MCMoveRotateMolecule3DFixedAngle etomica.models.nitrogen
MCMoveRotate that moves the molecules according to pre-set constraint angle
which is given by the parameter "angle"
This class does not consider rotational energy, so the variable "energyChange"
always returns zero
getB() always returns positive one is to ensure the proposed move is always
accepted
the proposed angle criteria is based on u3 and u4 distribution
MCMoveRotateMolecule3DFixedAngle(PotentialMaster, IRandom, Space, double, CoordinateDefinitionNitrogen, Box) MCMoveRotateMolecule3DFixedAngle
MCMoveRotateMolecule3DN2AveCosThetaConstraint etomica.models.nitrogen
Impose constraint to prevent the alpha-N2 phase from becoming orientationally-disordered
the constraint imposed is the average cosine theta, where
theta is the orientation angle off the molecular nominal orientation
MCMoveRotateMolecule3DN2AveCosThetaConstraint(PotentialMaster, IRandom, Space, CoordinateDefinitionNitrogen, double) MCMoveRotateMolecule3DN2AveCosThetaConstraint
MCMoveRotateMolecule3DSuperBox etomica.models.nitrogen
MC Rotate Move 3D for superbox
The potential master that being passed in this class is a "full-strength" potential without
multiplying by 0.5 for the speciesA and speciesB interaction.
MCMoveRotateMolecule3DSuperBox(PotentialMaster, IRandom, Space, int, int, CoordinateDefinitionNitrogenSuperBox) MCMoveRotateMolecule3DSuperBox
MCMoveRotateMoleculePhiTheta etomica.normalmode
MCMoveRotateMoleculePhiTheta(PotentialMaster, IRandom, Space, Vector[], boolean) MCMoveRotateMoleculePhiTheta
MCMoveRotateNoSmer etomica.association
MCMoveRotateNoSmer(PotentialMaster, IRandom, Space) MCMoveRotateNoSmer
MCMoveRotatePair etomica.spin.heisenberg
MCMoveRotatePair(IPotentialAtomic, IRandom, Space) MCMoveRotatePair
mcMoves() IntegratorDCVGCMD
mcMoves() IntegratorDCVGCMD
MCMoveSemigrand etomica.integrator.mcmove
Basic Monte Carlo move for semigrand-ensemble simulations.
MCMoveSemigrand(PotentialMaster, IRandom, Space) MCMoveSemigrand
MCMoveSingleMode etomica.normalmode
A Monte Carlo move which selects each individual modes to move
the atoms accordingly
MCMoveSingleMode(PotentialMaster, IRandom) MCMoveSingleMode
mcMoveSmer TestIGAssociationMC3D_NPT_DoubleSites
mcMoveSmer TestLJAssociationMC3D_NPT_DoubleSites
MCMoveSmer etomica.association
Standard Monte Carlo atom-displacement trial move of Trimer
MCMoveSmer(PotentialMasterCell, IRandom, Space, double, double, boolean, IPotentialAtomic) MCMoveSmer
MCMoveSmer(Simulation, PotentialMasterCell, Space, IPotentialAtomic) MCMoveSmer
mcMoveSmerRotate TestIGAssociationMC3D_NPT_DoubleSites
mcMoveSmerRotate TestLJAssociationMC3D_NPT_DoubleSites
MCMoveSmerRotate etomica.association
Standard Monte Carlo atom-displacement trial move.
MCMoveSmerRotate(PotentialMasterCell, IRandom, Space, double, double, boolean, IPotentialAtomic) MCMoveSmerRotate
MCMoveSmerRotate(Simulation, PotentialMasterCell, Space, IPotentialAtomic) MCMoveSmerRotate
MCMoveSpinCluster etomica.spin.heisenberg
Cluster move as described by Wolff in PRL v62 361 (1989)
MCMoveSpinCluster(Space, IRandom, PotentialMasterSite, IntegratorMC, double) MCMoveSpinCluster
MCMoveSpinFlip etomica.spin.ising
TODO To change the template for this generated type comment go to
Window - Preferences - Java - Code Style - Code Templates
MCMoveSpinFlip(PotentialMaster, IRandom) MCMoveSpinFlip
MCMoveStep etomica.integrator.mcmove
MCMoveStep(PotentialMaster) MCMoveStep
MCMoveStep(PotentialMaster, MCMoveStepTracker) MCMoveStep
MCMoveStepDependent etomica.integrator.mcmove
MCMoveStepTracker etomica.integrator.mcmove
This Class tracks acceptance statistics for an MCMove and also manages the
move's step size.
MCMoveStepTracker() MCMoveStepTracker
mcMoveSwap SimFe
mcMoveSwap SimIdealGas
mcMoveSwap SimLJ
MCMoveSwap etomica.modules.glass
MC Move class that swaps the position of two atoms of different species.
MCMoveSwap(Space, IRandom, PotentialMaster, ISpecies, ISpecies) MCMoveSwap
MCMoveSwapCluster etomica.virial.paralleltempering
Swaps configurations and pairSet between boxes for a virial clustering simulation.
MCMoveSwapCluster(IntegratorMC, IntegratorMC, Space) MCMoveSwapCluster
MCMoveSwapCluster.SwapFactory etomica.virial.paralleltempering
MCMoveSwapConfiguration etomica.integrator.mcmove
Basic MCMove for swapping coordinates of atoms in two boxes.
MCMoveSwapConfiguration(IntegratorBox, IntegratorBox, Space) MCMoveSwapConfiguration
MCMoveSwapConfiguration.SwapFactory etomica.integrator.mcmove
mcMoveTorsion TestAceticAcidMC3D_NPT
MCMoveTorsionAceticAcid etomica.integrator.mcmove
An MC Move for cluster simulations that performs torsion moves on acetic acid.
MCMoveTorsionAceticAcid(PotentialMaster, Space, IRandom) MCMoveTorsionAceticAcid
MCMoveTracker etomica.integrator.mcmove
This class is responsible for tracking acceptance statistics for an MCMove.
MCMoveTracker() MCMoveTracker
mcMoveTranslate SimulationVirial
mcMoveTranslate SimulationVirialOverlap2
MCMoveTrialCompletedEvent etomica.integrator.mcmove
MCMoveTrialCompletedEvent(MCMoveManager, boolean) MCMoveTrialCompletedEvent
MCMoveTrialFailedEvent etomica.integrator.mcmove
MC move event that indicates the move's trial failed, meaning that
MCMove.doTrial() returned false.
MCMoveTrialFailedEvent(MCMoveManager) MCMoveTrialFailedEvent
MCMoveTrialInitiatedEvent etomica.integrator.mcmove
MCMoveTrialInitiatedEvent(MCMoveManager) MCMoveTrialInitiatedEvent
mcMoveVolume TestAceticAcidMC3D_NPT
mcMoveVolume SimGCPMWaterMCNPT
mcMoveVolume TestIGAssociationMC3D_NPT_DoubleSites
mcMoveVolume TestLJAssociationMC3D_NPT_DoubleSites
mcMoveVolume TestLJAssociationMC3D_NPT
mcMoveVolume TestLJAssociationMC3D_NVTOld
mcMoveVolume LjMd3D
mcMoveVolume LJNPT
mcMoveVolume LJMC
mcMoveVolume SimHSMDVacancy
mcMoveVolume SimLJVacancy
mcMoveVolume TestLJAssociationMC3D_NPT
MCMoveVolume etomica.integrator.mcmove
Standard Monte Carlo volume-change move for simulations in the NPT ensemble.
MCMoveVolume(PotentialMaster, IRandom, Space, double) MCMoveVolume
MCMoveVolume(Simulation, PotentialMaster, Space) MCMoveVolume
MCMoveVolumeAssociated etomica.association
Standard Monte Carlo volume-change move for simulations in the NPT ensemble.
MCMoveVolumeAssociated(PotentialMaster, IRandom, Space, double) MCMoveVolumeAssociated
MCMoveVolumeAssociated(Simulation, PotentialMaster, Space) MCMoveVolumeAssociated
MCMoveVolumeAssociated.Agent etomica.association
MCMoveVolumeAssociatedMolecule etomica.association
Monte Carlo volume-change move for associating fluids simulations in the NPT ensemble.
MCMoveVolumeAssociatedMolecule(Simulation, PotentialMaster, Space) MCMoveVolumeAssociatedMolecule
MCMoveVolumeAssociatedMolecule(Simulation, PotentialMaster, IRandom, Space, double) MCMoveVolumeAssociatedMolecule
MCMoveVolumeAssociatedMolecule.Agent etomica.association
MCMoveVolumeExchange etomica.integrator.mcmove
Elementary Monte Carlo trial that exchanges volume between two boxes.
MCMoveVolumeExchange(PotentialMaster, IRandom, Space, IntegratorBox, IntegratorBox) MCMoveVolumeExchange
MCMoveVolumeExchangeVLE etomica.integrator.mcmove
MCMoveVolumeExchangeVLE(PotentialMaster, IRandom, Space, IntegratorBox, IntegratorBox) MCMoveVolumeExchangeVLE
MCMoveVolumeMonoclinic etomica.normalmode
Standard Monte Carlo volume-change move for simulations in the NPT ensemble.
MCMoveVolumeMonoclinic(PotentialMaster, IRandom, Space) MCMoveVolumeMonoclinic
MCMoveVolumeMonoclinicAngle etomica.normalmode
Standard Monte Carlo volume-change move for simulations in the NPT ensemble.
MCMoveVolumeMonoclinicAngle(PotentialMaster, IRandom, Space, Box) MCMoveVolumeMonoclinicAngle
MCMoveVolumeMonoclinicScaled etomica.normalmode
Monte Carlo volume-change move for simulations of crystalline solids in the
NPT ensemble (molecular model).
MCMoveVolumeMonoclinicScaled(PotentialMaster, IRandom, Space, double) MCMoveVolumeMonoclinicScaled
MCMoveVolumeMonoclinicScaled(PotentialMaster, IRandom, Space, double, int) MCMoveVolumeMonoclinicScaled
MCMoveVolumeN2 etomica.models.nitrogen
Monte Carlo volume-change move for simulations in the NPT ensemble.
MCMoveVolumeN2(PotentialMaster, IRandom, Space, double) MCMoveVolumeN2
MCMoveVolumeN2(Simulation, PotentialMaster, Space) MCMoveVolumeN2
MCMoveVolumeSolid etomica.normalmode
Monte Carlo volume-change move for simulations of crystalline solids in the
NPT ensemble.
MCMoveVolumeSolid(PotentialMaster, CoordinateDefinition, IRandom, Space, double) MCMoveVolumeSolid
MCMoveVolumeSolidNPTMolecular etomica.normalmode
Monte Carlo volume-change move for simulations of crystalline solids in the
NPT ensemble (molecular model).
MCMoveVolumeSolidNPTMolecular(PotentialMaster, IRandom, Space, double) MCMoveVolumeSolidNPTMolecular
MCMoveVolumeSolidNPTMolecular(PotentialMaster, IRandom, Space, double, int) MCMoveVolumeSolidNPTMolecular
MCMoveVolumeSolidNPTMolecularOriented etomica.normalmode
Class which handles orientation of linear molecules during volume change
trials.
MCMoveVolumeSolidNPTMolecularOriented(PotentialMaster, IRandom, Space, double, Vector[]) MCMoveVolumeSolidNPTMolecularOriented
mcMoveWiggle TestAceticAcidMC3D_NPT
mcMoveWiggle SimulationVirial
mcMoveWiggle SimulationVirialOverlap2
MCMoveWiggle etomica.starpolymer
An MC Move for cluster simulations that "wiggles" a chain molecule.
MCMoveWiggle(PotentialMaster, IRandom, double, int, Space) MCMoveWiggle
MCMoveWiggle(Simulation, PotentialMaster, int, Space) MCMoveWiggle
MCMoveWiggleAceticAcid etomica.integrator.mcmove
An MC Move for cluster simulations that "wiggles" for acetic acid.
MCMoveWiggleAceticAcid(PotentialMaster, IRandom, double, Space) MCMoveWiggleAceticAcid
MCMoveWiggleAceticAcid(Simulation, PotentialMaster, Space) MCMoveWiggleAceticAcid
MCMoveWV etomica.normalmode
MCMoveWV(Space, NormalModesVariable, CoordinateDefinition, IRandom) MCMoveWV
mConnections ClusterDiagram
mcSteps IntegratorMD
mcSteps LJMD.LJMDParams
ME(IData) IData
Minus-equals (-=) operation.
ME(IData) DataDouble
Minus-equals (-=) operation.
ME(IData) DataDoubleArray
Minus-equals (-=) operation.
ME(IData) DataDoubleBDArray
Minus-equals (-=) operation.
ME(IData) DataGroup
ME(IData) DataTensor
Minus-equals (-=) operation.
ME(IData) DataVector
Minus-equals (-=) operation.
ME(Tensor) Tensor
"Minus equals" (-=) operation, subtracting the elements of the given tensor from the
respective elements of this tensor.
ME(Tensor) Tensor1D
ME(Tensor) Tensor2D
ME(Tensor) Tensor3D
ME(Tensor) TensorND
ME(Vector) Vector
Minus-equals (-=) operation.
ME(Vector) Vector1D
ME(Vector) Vector2D
ME(Vector) Vector3D
ME(Vector) VectorND
measure Token
Measure org.jmol.util
Measure() Measure
MEASURE_DEFAULT_FONTSIZE JmolConstants
measureallmodels Token
measurementlabels Token
measurements Token
measurementunits Token
mediaType SVGConverter
Media type for which the SVG image should be rendered
MEGA Prefix
membrane DCVGCMD
membraneDim ConfigurationMembrane
membraneDim ConfigurationMembraneWater
membraneThicknessPerLayer ConfigurationMembrane
membraneThicknessSlider ReverseOsmosisGraphic
membraneThicknessSlider ReverseOsmosisWaterGraphic
membraneTotalThickness ConfigurationMembraneWater
membraneWidth ConfigurationMembrane
membraneWidth ConfigurationMembraneWater
membraneWidthSlider ReverseOsmosisWaterGraphic
mERBond WertheimDiagrams3SiteRho
mergeData(Map<IntSet, MeterVirialBDBinMultiThreaded.MyData>) MeterVirialBDBinMultiThreaded
mergeData(Map<IntSet, MeterVirialBinMultiThreaded.MyData>) MeterVirialBinMultiThreaded
mergeData(Map<IntSet, MeterVirialEBinMultiThreaded.MyData>) MeterVirialEBinMultiThreaded
mergePolygonCount0 MeshSurface
mergeVertexCount0 MeshSurface
mesh Token
meshRibbon Token
meshscale Token
MeshSurface org.jmol.util
MeshSurface() MeshSurface
meshType MeshSurface
MESSAGE_ABOUT_TO_TRANSCODE Main
MESSAGE_ABOUT_TO_TRANSCODE_SOURCE Main
MESSAGE_CONVERSION_FAILED Main
MESSAGE_CONVERSION_SUCCESS Main
Messages etomica.graph.view.rasterizer
This class manages the message for the bridge module.
Messages() Messages
This class does not need to be instantiated.
messagestylechime Token
Metadata etomica.graph.model
metaDataComparator MetadataImpl
MetadataImpl etomica.graph.model.impl
MetadataImpl(char, char) MetadataImpl
meter MeterProfile
Meter that defines the property being profiled.
meter MeterProfileByAtoms
Meter that defines the property being profiled.
meter MeterProfileByVolume
Meter that defines the property being profiled.
meter SimOverlapAlphaN2TP
meter SimOverlapBetaN2RPScaling
meter SimOverlapBetaN2TP
meter SimOverlapDisorderedAlphaN2RPScaling
meter SimOverlapDisorderedAlphaN2TP
meter AtomTestLiquid
meter DataSourceTensorVirialHardProfile.DataSourceVirialProfile
meter HTTPSoftSphereApplet
meter SimOverlapLJModule.MeterPotentialEnergyDifference
meter SimOverlapSoftSphereDP
meter SimOverlapSoftSphereEin
meter SimOverlapSoftSphereTP
meter SimOverlapSoftSphereTPHCP
meter SimOverlapSoftSphereTPSlantedBox
meter Ising
meter SimulationVirial
meter VirialHSBinMultiThreaded.SimulationWorker
meter VirialSQWBinMultiThreaded.SimulationWorker
Meter etomica.units
The meter unit of length, equal to 10^10 angstroms.
Meter(int) DataSourceCorrelation.Meter
Meter(int) StructureFactorComponentCorrelation.Meter
meterA MultiharmonicGraphicMC.DataSourceFE
MeterAPIPotentialEnergy etomica.normalmode
Meter that returns the potential energy using an IAPIPotential.
MeterAPIPotentialEnergy(IAPIPotential) MeterAPIPotentialEnergy
MeterAtomicDisplacement etomica.normalmode
Calculates the average atomic displacement from their lattice sites
MeterAtomicDisplacement(Space, CoordinateDefinition) MeterAtomicDisplacement
MeterAvgBondLength etomica.data.meter
MeterAvgBondLength() MeterAvgBondLength
meterB MultiharmonicGraphicMC.DataSourceFE
MeterBoltzmann etomica.models.nitrogen
Meter used for overlap sampling in the target-sampled system.
MeterBoltzmann etomica.normalmode
Meter used for overlap sampling in the target-sampled system.
MeterBoltzmann(IntegratorBox, MeterPotentialEnergy) MeterBoltzmann
MeterBoltzmann(IntegratorBox, MeterPotentialEnergy, double, double) MeterBoltzmann
MeterBoltzmannDirect etomica.models.nitrogen
Meter used for overlap sampling in the target-sampled system.
MeterBoltzmannDirect(IntegratorBox, MeterPotentialEnergy) MeterBoltzmannDirect
MeterBoltzmannHarmonic etomica.normalmode
Meter used for overlap sampling in the harmonic-sampled system.
MeterBoltzmannHarmonic(MCMoveHarmonic, PotentialMaster) MeterBoltzmannHarmonic
MeterBoltzmannHTTP etomica.normalmode
Same as TargetTP class but is used by MethodBoltzmannHTTP
It is to illustrate the idea of HTTP method.
MeterBoltzmannHTTP(PotentialMaster, ISpecies, Simulation, CoordinateDefinition) MeterBoltzmannHTTP
MeterBoltzmannRotPerturb etomica.models.nitrogen
Meter used for overlap sampling in the target-sampled system.
MeterBoltzmannRotPerturb(IntegratorMC, PotentialMaster, ISpecies, Space, Simulation, CoordinateDefinitionNitrogen) MeterBoltzmannRotPerturb
MeterBoltzmannTarget etomica.normalmode
Meter used for overlap sampling in the target-sampled system.
MeterBoltzmannTarget(DataSourceScalar, DataSourceScalar) MeterBoltzmannTarget
MeterBondLength etomica.starpolymer
Meter for tabulation of the atomic radial distribution function (RDF).
MeterBondLength(Box, int, int) MeterBondLength
Creates meter with default to compute pair correlation for all
leaf atoms in a box.
MeterCavity etomica.cavity
Meter collects RDF but is hardcoded to look at only those atoms that are
overlapping.
MeterCavity(Space, P2HardSphereCavity) MeterCavity
MeterCavityMapped etomica.cavity
Meter for the cavity function using mapped averaging.
MeterCavityMapped(IntegratorHard) MeterCavityMapped
MeterChainLength etomica.modules.chainequilibrium
MeterChainLength(AtomLeafAgentManager<IAtom[]>) MeterChainLength
MeterChainLength.AtomTag etomica.modules.chainequilibrium
MeterChi4() DataSourceQ4.MeterChi4
meterClusterSizes NucleationGraphic
MeterClusterSizes etomica.modules.nucleation
Computes the cluster sizes and returns them as a histogram
MeterClusterSizes(Box) MeterClusterSizes
MeterContactRatio etomica.cavity
MeterContactRatio(IntegratorHard) MeterContactRatio
MeterConversion etomica.modules.chainequilibrium
Meter for the reaction conversion (fraction of reacted sites).
MeterConversion(Box, AtomLeafAgentManager) MeterConversion
MeterCorrelation etomica.modules.glass
Meter for tabulation of the atomic radial distribution function (RDF).
MeterCorrelation(ConfigurationStorage) MeterCorrelation
MeterCorrelation(ConfigurationStorage, MeterCorrelation.CorrelationType) MeterCorrelation
MeterCorrelation.CorrelationType etomica.modules.glass
MeterCorrelationSelf etomica.modules.glass
MeterCorrelationSelf(ConfigurationStorage) MeterCorrelationSelf
MeterCorrelationSelf(ConfigurationStorage, MeterCorrelationSelf.CorrelationType) MeterCorrelationSelf
MeterCorrelationSelf.CorrelationType etomica.modules.glass
MeterCorrelationSelf2(int) CorrelationSelf2.MeterCorrelationSelf2
meterCountAtoms ModifierPMu
meterCycles PistonCylinderGraphic
meterCycles HSMC2D
meterCycles SoftSphere3d
MeterDADB etomica.normalmode
MeterDADB(Space, DataSourceScalar, PotentialMaster, CoordinateDefinition, double) MeterDADB
MeterDDP etomica.normalmode
Meter that measures the overlap averages for perturbing from a solid at one
density into other densities.
MeterDDP(PotentialMaster, ISpecies, Space, Simulation) MeterDDP
meterDeformation Droplet
MeterDeformation etomica.modules.droplet
MeterDeformation(Space) MeterDeformation
MeterDensity etomica.data.meter
Meter for measurement of the total molecule number density in a box
Molecule number density is defined (number of molecules)/(volume of box)
MeterDensity(Box) MeterDensity
MeterDensityCO etomica.modules.catalysis
MeterDensityCO(Box, ISpecies, AtomLeafAgentManager) MeterDensityCO
MeterDensityCO2 etomica.modules.catalysis
MeterDensityCO2(Box, ISpecies, AtomLeafAgentManager) MeterDensityCO2
MeterDensityDistribution etomica.metastable
MeterDensityDistribution(Space, Box, int) MeterDensityDistribution
MeterDensityO2 etomica.modules.catalysis
MeterDensityO2(Box, ISpecies, AtomLeafAgentManager) MeterDensityO2
MeterDensitySides etomica.modules.mu
MeterDensitySides(Box, ISpecies, boolean) MeterDensitySides
MeterDihedralAngle etomica.data.meter
Meter for tabulation of a dihedral angle distribution between nearest neighbors.
MeterDihedralAngle(Space) MeterDihedralAngle
Creates meter with default to compute dihedral angle for all
leaf atoms in a box.
meterDimerFraction ReactionEquilibrium
MeterDimerFraction etomica.modules.reactionequilibrium
MeterDimerFraction(AtomLeafAgentManager) MeterDimerFraction
MeterDimerMoleFraction etomica.association
Meter for measurement of species mole fraction within a specified subvolume
MeterDimerMoleFraction(Space, Box) MeterDimerMoleFraction
MeterDipoleMoment etomica.spin.heisenberg
MeterDipoleMoment(Box) MeterDipoleMoment
MeterDipoleMoment.ForceTorque etomica.spin.heisenberg
MeterDipoleSumSquared1site etomica.data.meter
meter for (sum dipole)^2, used for dielectric constant calculation
MeterDipoleSumSquared1site(Space, Box, double) MeterDipoleSumSquared1site
MeterDipoleSumSquaredMappedAverage etomica.data.meter
meter for AEE use mapping average
MeterDipoleSumSquaredMappedAverage(Space, Box, Simulation, double, double, PotentialMaster) MeterDipoleSumSquaredMappedAverage
MeterDipoleSumSquaredTIP4PWater etomica.data.meter
meter for (sum dipole)^2
used for dielectric constant calculation
MeterDipoleSumSquaredTIP4PWater(Space, Box) MeterDipoleSumSquaredTIP4PWater
MeterDirectInitPert etomica.models.nitrogen
Meter used for overlap sampling in the target-sampled system.
MeterDirectInitPert(IntegratorBox, MeterPotentialEnergy, CoordinateDefinitionNitrogen, IRandom) MeterDirectInitPert
MeterDirectSamplingHarmonic etomica.normalmode
Meter used for overlap sampling in the harmonic-sampled system.
MeterDirectSamplingHarmonic(MCMoveHarmonic, PotentialMaster) MeterDirectSamplingHarmonic
MeterDirectSamplingTarget etomica.normalmode
Meter used for overlap sampling in the target-sampled system.
MeterDirectSamplingTarget(IntegratorBox, MeterHarmonicEnergy) MeterDirectSamplingTarget
MeterDisplacementMoleculeRMS etomica.normalmode
MeterDisplacementMoleculeRMS(Space, CoordinateDefinitionMolecule) MeterDisplacementMoleculeRMS
MeterDisplacementRMS etomica.normalmode
MeterDisplacementRMS(Space, CoordinateDefinition) MeterDisplacementRMS
MeterDP etomica.normalmode
Meter that measures the overlap averages for perturbing from a solid at one
density into other densities.
MeterDP(PotentialMaster, ISpecies, Space, Simulation) MeterDP
meterE2E ColloidGraphic
MeterElongation etomica.modules.materialfracture
MeterElongation() MeterElongation
MeterEnd2End etomica.modules.colloid
Measures the end-to-end squared distance for the colloid system, averaged
across the grafted chains.
MeterEnd2End(Space) MeterEnd2End
MeterEndToEnd etomica.modules.rheology
Meter that measures that end to end distance of the molecules
MeterEndToEnd(Space) MeterEndToEnd
meterEnergy MeterBoltzmann
meterEnergy MeterBoltzmannDirect
meterEnergy MeterDirectInitPert
meterEnergy MeterBoltzmann
meterEnergy MeterBoltzmannHarmonic
meterEnergy MeterBoltzmannTarget
meterEnergy MeterDirectSamplingHarmonic
meterEnergy MeterDirectSamplingTarget
meterEnergy MeterWorkHarmonicBennet
meterEnergy MeterWorkHarmonicPhaseSpace
meterEnergy MeterWorkHarmonicTargetandReweighting
meterEnergy MeterWorkTargetBennet
meterEnergy MeterWorkTargetHarmonicandReweighting
meterEnergy MeterWorkTargetPhaseSpace
meterEnergy SimUmbrella
meterEnergy SimUmbrellaSoftSphere
MeterEnergy etomica.data.meter
Meter for measurement of the total (potential and kinetic) energy in a box
This meter is constructed from kinetic-energy and a potential-energy meters
An instance of this meter is placed in each box to allow for energy measurements in the box
MeterEnergy(PotentialMaster, Box) MeterEnergy
MeterEnergyMeanField etomica.spin.heisenberg
MeterEnergyMeanField(Space, Box, double, PotentialMaster, double) MeterEnergyMeanField
MeterEnergyMeanField.PotentialCalculationCSsum etomica.spin.heisenberg
Used to compute and store sums of cos(theta) and sin(theta) over neighbors of each atom.
MeterEnthalpyVolume etomica.association.GCPMWater
MeterEnthalpyVolume(IntegratorBox, double) MeterEnthalpyVolume
MeterExcessAdsorbed etomica.modules.adsorption
MeterExcessAdsorbed(ISpecies, EOSSW) MeterExcessAdsorbed
MeterFlux etomica.dcvgcmd
MeterFlux etomica.modules.dcvgcmd
MeterFlux etomica.modules.rosmosis
Meter to measure flux across a boundary or boundaries.
MeterFlux(MyMCMove, IntegratorDCVGCMD) MeterFlux
MeterFlux(MyMCMove, IntegratorDCVGCMD) MeterFlux
MeterFlux(Simulation, Space) MeterFlux
meterFlux0 DCVGCMD
meterFlux0 DCVGCMD
meterFlux1 DCVGCMD
meterFlux1 DCVGCMD
meterFlux2 DCVGCMD
meterFlux2 DCVGCMD
meterFlux3 DCVGCMD
meterFlux3 DCVGCMD
MeterFreeEnergy etomica.modules.multiharmonic
Computes the free-enery difference through free-energy perturbation.
MeterFreeEnergy(P1Harmonic, P1Harmonic) MeterFreeEnergy
MeterFromDumps(DataDump[]) GlassGraphic.MeterFromDumps
MeterGs etomica.modules.glass
Meter for tabulation of the atomic Gs.
MeterGs(ConfigurationStorage) MeterGs
meterHarm MinimizationTIP4P
meterHarm MinimizationBetaNitrogenModel
meterHarmonic MeterWorkBennetHarmonic
meterHarmonic MeterWorkBennetTarget
meterHarmonic MeterWorkHarmonicUmbrella
meterHarmonic MeterWorkTargetUmbrella
meterHarmonicCoordinate NormalModeAnalysisDisplay3DGraphic
MeterHarmonicCoordinate etomica.normalmode
MeterHarmonicCoordinate(CoordinateDefinition) MeterHarmonicCoordinate
meterHarmonicEnergy SimOverlapNitrogenModel
meterHarmonicEnergy MeterDirectSamplingTarget
meterHarmonicEnergy MeterWorkTargetBennet
meterHarmonicEnergy MeterWorkTargetHarmonicandReweighting
meterHarmonicEnergy MeterWorkTargetPhaseSpace
meterHarmonicEnergy SimBennet
meterHarmonicEnergy SimHarmonicUmbrella
meterHarmonicEnergy SimOverlap
meterHarmonicEnergy SimOverlapSoftSphere
meterHarmonicEnergy SimOverlapSoftSphereHCP
meterHarmonicEnergy SimOverlapSoftSphereReweighting
meterHarmonicEnergy SimOverlapSSnxy
meterHarmonicEnergy SimTargetUmbrella
meterHarmonicEnergy SimUmbrella
meterHarmonicEnergy SimUmbrellaSoftSphere
MeterHarmonicEnergy etomica.normalmode
Meter that calculates the harmonic energy of a configuration given
eigenvectors and omegas corresponding to wave vectors.
MeterHarmonicEnergy(CoordinateDefinition, NormalModes) MeterHarmonicEnergy
MeterHarmonicEnergyFromMove etomica.normalmode
Meter that returns the harmonic energy from the MC move as a data source.
MeterHarmonicEnergyFromMove(MCMoveHarmonic) MeterHarmonicEnergyFromMove
MeterHarmonicSingleEnergy etomica.normalmode
Meter that calculates the Boltzmann-factored harmonic energy of each normal mode for a
configuration given eigenvectors and omegas corresponding to wave vectors.
MeterHarmonicSingleEnergy(CoordinateDefinition, NormalModes) MeterHarmonicSingleEnergy
MeterHyperVirial etomica.data.meter
Meter for measurement of the hypervirial, r^2 d2u/dr2 + r du/dr
MeterHyperVirial() MeterHyperVirial
MeterHyperVirial(Space, boolean) MeterHyperVirial
If full is true, then the pressure is also calculated and three values
are returned.
meterJacobian MCMovePhaseAngle
meterJacobian MCMoveWV
MeterJacobian etomica.normalmode
MeterJacobian(CoordinateDefinition, NormalModesVariable) MeterJacobian
meterKE MeterTemperature
meterKE IntegratorMD
MeterKineticEnergy etomica.data.meter
Meter for the total kinetic energy in a box Computes total KE by summing values of KE returned by every atom in the
box.
MeterKineticEnergy(Box) MeterKineticEnergy
MeterKineticEnergy(Box, AtomIteratorBoxDependent) MeterKineticEnergy
MeterKineticEnergyFromIntegrator etomica.data.meter
Acts as a DataSource to retrieve the energy from the integrator
MeterKineticEnergyFromIntegrator() MeterKineticEnergyFromIntegrator
MeterKineticEnergyFromIntegrator(IntegratorMD) MeterKineticEnergyFromIntegrator
MeterKineticEnergyRigid etomica.data.meter
Meter for the total kinetic energy in a box
Computes total KE by summing values of KE returned by every atom in the box.
MeterKineticEnergyRigid(Space, Simulation) MeterKineticEnergyRigid
MeterKineticEnergyRigid(Space, Simulation, Box) MeterKineticEnergyRigid
meterLargestCluster NucleationGraphic
MeterLargestCluster etomica.modules.nucleation
MeterLargestCluster(Box) MeterLargestCluster
MeterLoad etomica.modules.materialfracture
Meter that calculates the stress within the gage cell.
MeterLoad(PotentialCalculationForceStress) MeterLoad
MeterLocalDensity etomica.data.meter
Meter for measurement of density within a specified subvolume
MeterLocalDensity(Box) MeterLocalDensity
MeterLocalMoleFraction etomica.data.meter
Meter for measurement of species mole fraction within a specified subvolume
MeterLocalMoleFraction(Space, Box) MeterLocalMoleFraction
MeterMappedAveraging etomica.spin.heisenberg
MeterMappedAveraging(Space, Box, Simulation, double, double, double, PotentialMaster, int) MeterMappedAveraging
MeterMappedAveraging3Pair etomica.spin.heisenberg
MeterMappedAveraging3Pair(Space, Box, Simulation, double, double, double, IPotentialAtomic, int) MeterMappedAveraging3Pair
MeterMappedAveragingCorrelation etomica.spin.heisenberg
MeterMappedAveragingCorrelation(Simulation, double, double, PotentialMaster, int) MeterMappedAveragingCorrelation
MeterMappedAveragingCorrelation.CorrelationAgent etomica.spin.heisenberg
MeterMappedAveragingCV etomica.spin.heisenberg
MeterMappedAveragingCV(Simulation, double, double, PotentialMaster) MeterMappedAveragingCV
MeterMappedAveragingFreeEnergy etomica.spin.heisenberg
MeterMappedAveragingFreeEnergy(Space, Box, Simulation, double, double, double, PotentialMaster) MeterMappedAveragingFreeEnergy
MeterMappedAveragingPair etomica.spin.heisenberg
MeterMappedAveragingPair(Space, Box, Simulation, double, double, double, IPotentialAtomic, int) MeterMappedAveragingPair
MeterMappedAveragingPairExcess etomica.spin.heisenberg
Computes pair-mapped average for a single spin pair
MeterMappedAveragingPairExcess(AtomPair, Space, Box, Simulation, double, double, double, PotentialMaster, P2Spin, int) MeterMappedAveragingPairExcess
MeterMappedAveragingSum etomica.spin.heisenberg
MeterMappedAveragingSum(Space, Box, Simulation, double, double, double, PotentialMaster) MeterMappedAveragingSum
MeterMappedAveragingSum.MoleculeAgent etomica.spin.heisenberg
MeterMappedAveragingVSum etomica.spin.heisenberg
MeterMappedAveragingVSum(Space, Box, Simulation, double, double, double, PotentialMaster, boolean, boolean, boolean, boolean, boolean, int) MeterMappedAveragingVSum
MeterMappedAveragingVSum3Pair etomica.spin.heisenberg
MeterMappedAveragingVSum3Pair(Space, Box, Simulation, double, double, double, IPotentialAtomic, int) MeterMappedAveragingVSum3Pair
MeterMappedAveragingVSumPair etomica.spin.heisenberg
MeterMappedAveragingVSumPair(Space, Box, Simulation, double, double, double, IPotentialAtomic, int) MeterMappedAveragingVSumPair
MeterMappedRdf etomica.mappedRdf
Calculates pair distribution using mapped averaging
MeterMappedRdf(double, Space, PotentialMaster, Box, int, double) MeterMappedRdf
MeterMappedU etomica.mappedvirial
MeterMappedU(Space, PotentialMaster, Box, int) MeterMappedU
MeterMappedVirial etomica.mappedvirial
MeterMappedVirial(Space, PotentialMaster, Box, int) MeterMappedVirial
MeterMappedVirialV etomica.mappedvirial
MeterMappedVirialV(Space, PotentialMaster, Box, int) MeterMappedVirialV
MeterMaxExpansion etomica.normalmode
measures the maximum amount by which by which the HS diameter could increase
without causing overlap
MeterMaxExpansion(Space, Box, NeighborListManager) MeterMaxExpansion
MeterMBAR etomica.modules.multiharmonic.mbar
MeterMBAR(DataSourceScalar[], double) MeterMBAR
meterMeanField MeterMappedAveragingCorrelation
meterMeanField MeterMappedAveragingVSum
MeterMeanField etomica.spin.heisenberg
MeterMeanField(Space, Box, double, PotentialMaster, double) MeterMeanField
MeterMeanField.ForceTorque etomica.spin.heisenberg
MeterMeanForce etomica.mappedvirial
MeterMeanForce(Space, PotentialMaster, Potential2SoftSpherical, Box, int) MeterMeanForce
MeterMeanSquareDisplacement etomica.data.meter
Computes the mean square displacement for a set of atoms.
MeterMeanSquareDisplacement(Space, IntegratorBox) MeterMeanSquareDisplacement
MeterMeanSquareDisplacement(Space, IntegratorBox, AtomIteratorBoxDependent) MeterMeanSquareDisplacement
MeterMoleculeTemperature etomica.data.meter
Meter for recording the total number of molecules in the box
MeterMoleculeTemperature() MeterMoleculeTemperature
MeterMoleFraction etomica.data.meter
Meter for measurement of the species mole fraction in a box.
MeterMoleFraction() MeterMoleFraction
MeterMomentumCOM etomica.data.meter
Returns the instantaneous total center-of-mass momentum, summed over all
leaf atoms in a box.
MeterMomentumCOM(Space) MeterMomentumCOM
MeterNMolecules etomica.data.meter
Meter for recording the total number of molecules in the box
MeterNMolecules() MeterNMolecules
MeterNormalizedCoord etomica.models.nitrogen
Sample the distribution of the normalized coordinate for the atoms/ molecules
from coordinate definition, calcU method.
MeterNormalizedCoord(Box, CoordinateDefinition, ISpecies) MeterNormalizedCoord
MeterNormalizedCoord(Box, CoordinateDefinition, ISpecies, boolean) MeterNormalizedCoord
MeterNormalizedCoordBeta etomica.models.nitrogen
Sample the distribution of the normalized coordinate for the atoms/ molecules
from coordinate definition, calcU method.
MeterNormalizedCoordBeta(Box, CoordinateDefinition, ISpecies) MeterNormalizedCoordBeta
meterNormalMode WriteS
MeterNormalMode etomica.normalmode
Calculates the S-matrix for a configuration.
MeterNormalMode() MeterNormalMode
MeterNormalStress etomica.modules.rheology
Meter to measure normal stress of a polymer in a shear field.
MeterNormalStress(Space) MeterNormalStress
MeterOrientation etomica.modules.interfacial
Meter for collecting the molecular orientation of the dimer.
MeterOrientation(Space) MeterOrientation
MeterOrientationDistribution etomica.models.nitrogen
Meter that measures the spherical coordinate angles
angle[0]: is theta, angle between the projection vector (molecular axis vector onto xy plane)
and x-axis
angle[1]: is phi, angle between the molecular axis vector and z-axis
MeterOrientationDistribution(Box, CoordinateDefinitionNitrogen, ISpecies) MeterOrientationDistribution
MeterOrientationOrderParameter etomica.models.nitrogen
Meter used to sample orientation order parameter
MeterOrientationOrderParameter(CoordinateDefinitionNitrogen) MeterOrientationOrderParameter
MeterOsmoticPressure etomica.modules.osmosis
Osmotic pressure meter that calculates the difference in
MeterOsmoticPressure etomica.modules.rosmosis
Meter to measure flux across a boundary or boundaries.
MeterOsmoticPressure(IPotentialCalculationWallForce, Box) MeterOsmoticPressure
MeterOsmoticPressure(P1HardBoundary[], IntegratorHard) MeterOsmoticPressure
MeterOverlap etomica.overlap
MeterOverlap(IDataSource, IDataSource, double, boolean) MeterOverlap
Meter to measure the "overlap" function for free energy calculations,
used as input to an AccumulatorVirialOverlapSingleAverage.
meterOverlapA MultiharmonicGraphicMC.DataSourceAlphaChi
meterOverlapA MultiharmonicMC
meterOverlapB MultiharmonicGraphicMC.DataSourceAlphaChi
meterOverlapB MultiharmonicMC
MeterOverlapSwitch etomica.normalmode
Meter whose purpose in life is to measure the overlap between systems
defined by a combination of two energy meters.
MeterOverlapSwitch(PotentialMaster, PotentialMaster) MeterOverlapSwitch
MeterPairedFraction etomica.cavity
MeterPairedFraction(IntegratorHard) MeterPairedFraction
MeterPairSum etomica.spin.heisenberg
MeterPairSum(Space, Box, Simulation, double, double, double, PotentialMaster) MeterPairSum
meterPE IntegratorBox
meterPE ClathrateHarmonicFE
meterPE MinimizationTIP4P
meterPE MinimizationBetaNitrogenModel
meterPE DimerApproach
meterPE MCMoveSwap
meterPE InsertionGraphic.MeterWidom
meterPE MeterMBAR
meterPE MeterDADB
meterPE MeterSolidProps
meterPE MeterSolidPropsLJ
meterPE NormalModeAnalysisDisplay3D
meterPE ClusterSumExternalField
meterPE VirialRowleyAlcohol
meterPE1 SimEinStep2.MeterPotentialEnergyComposite
meterPE1 SimEinStep2HCP.MeterPotentialEnergyComposite
meterPE1 SimOverlapSoftSphereEin.MeterPotentialEnergyComposite
meterPE1 SimOverlapSoftSphereEinHarm.MeterPotentialEnergyComposite
meterPE2 SimEinStep2.MeterPotentialEnergyComposite
meterPE2 SimEinStep2HCP.MeterPotentialEnergyComposite
meterPE2 SimOverlapSoftSphereEin.MeterPotentialEnergyComposite
meterPE2 SimOverlapSoftSphereEinHarm.MeterPotentialEnergyComposite
MeterPhiDeviation etomica.normalmode
Meter that measures the average tilt angle (not the angle of average tilt!)
MeterPhiDeviation(Space) MeterPhiDeviation
MeterPlaneSlip etomica.normalmode
Meter that measures the average tilt angle (not the angle of average tilt!)
MeterPlaneSlip(Space, ISpecies, int, int, int) MeterPlaneSlip
MeterPositionCOM etomica.data.meter
Returns the instantaneous center-of-mass position, summed over all
leaf atoms in a box, dividing by the number of atoms.
MeterPositionCOM(Space) MeterPositionCOM
meterPotential CalcNumerical2ndDerivative
meterPotential FiniteDifferenceDerivativeCGNitrogenBeta
meterPotential MeterTargetRPMolecule
meterPotential MeterTargetTPMolecule
meterPotential MinimizeBetaNitrogenLatticeParameter
meterPotential MinimizeBetaNitrogenLatticeParameterFromFile
meterPotential MinimizeBetaNitrogenTranslationDOF
meterPotential MeterBoltzmannHTTP
meterPotential MeterDDP
meterPotential MeterDP
meterPotential MeterTargetTP
meterPotentialEnergy MeterBoltzmann
meterPotentialEnergy MeterBoltzmannDirect
meterPotentialEnergy MeterDirectInitPert
meterPotentialEnergy MeterBoltzmann
MeterPotentialEnergy etomica.data.meter
Meter for evaluation of the potential energy in a box.
MeterPotentialEnergy(PotentialMaster) MeterPotentialEnergy
MeterPotentialEnergy(PotentialMaster, Box) MeterPotentialEnergy
MeterPotentialEnergyComposite(PotentialMaster, PotentialMaster, double) SimOverlapSoftSphereEin.MeterPotentialEnergyComposite
MeterPotentialEnergyComposite(PotentialMaster, PotentialMaster, double) SimOverlapSoftSphereEinHarm.MeterPotentialEnergyComposite
MeterPotentialEnergyComposite(PotentialMaster, PotentialMaster, double, int) SimEinStep2.MeterPotentialEnergyComposite
MeterPotentialEnergyComposite(PotentialMaster, PotentialMaster, double, int) SimEinStep2HCP.MeterPotentialEnergyComposite
MeterPotentialEnergyCutoff etomica.liquidLJ
Meter for evaluation of the potential energy in a box.
MeterPotentialEnergyCutoff(PotentialMaster, Space, double[]) MeterPotentialEnergyCutoff
MeterPotentialEnergyDifference(DataSourceScalar, double) SimOverlapLJModule.MeterPotentialEnergyDifference
MeterPotentialEnergyFromIntegrator etomica.data.meter
Acts as a DataSource to retrieve the energy from the integrator
MeterPotentialEnergyFromIntegrator() MeterPotentialEnergyFromIntegrator
MeterPotentialEnergyFromIntegrator(IntegratorBox) MeterPotentialEnergyFromIntegrator
meterPotentialMeasured MeterBoltzmannRotPerturb
meterPotentialMeasured MeterRotPerturbMolecule
meterPotentialSampled MeterBoltzmannRotPerturb
meterPotentialSampled MeterRotPerturbMolecule
meterPressure HSMD2D_noNbr
MeterPressure etomica.data.meter
Meter for evaluation of the soft-potential pressure in a box.
MeterPressure(Space) MeterPressure
MeterPressure2 etomica.modules.vle
Meter for evaluation of the soft-potential pressure in a box.
MeterPressure2(Space) MeterPressure2
MeterPressureByVolumeChange etomica.data.meter
Evaluates the pressure by examining the change in energy accompanying
small changes in volume.
MeterPressureByVolumeChange(Space) MeterPressureByVolumeChange
MeterPressureByVolumeChange(Space, boolean[]) MeterPressureByVolumeChange
MeterPressureByVolumeChange(Space, boolean[], BoxInflateDeformable) MeterPressureByVolumeChange
MeterPressureByVolumeChange(Space, BoxInflateDeformable) MeterPressureByVolumeChange
MeterPressureByVolumeChange.DataSourceExp etomica.data.meter
Transforms the scaling from linear (-s to +s) to exponential (exp(-s) to exp(+s))
MeterPressureCollisionCount etomica.cavity
Meter for the pressure by counting the number of collisions (assumes HS potential)
MeterPressureCollisionCount(IntegratorHard) MeterPressureCollisionCount
MeterPressureHard etomica.data.meter
Meter for the pressure (given as the compressibility factor) of a hard potential.
MeterPressureHard(IntegratorHard) MeterPressureHard
MeterPressureHardTensor etomica.data.meter
MeterPressureHardTensor(Space) MeterPressureHardTensor
MeterPressureMolecular etomica.data.meter
Meter for evaluation of the soft-potential (molecular) pressure in a box.
MeterPressureMolecular(Space) MeterPressureMolecular
MeterPressureSuperBox etomica.normalmode
Meter for evaluation of the soft-potential pressure in a box.
MeterPressureSuperBox(Space) MeterPressureSuperBox
MeterPressureTensor etomica.data.meter
Meter for evaluation of the soft-potential pressure tensor in a box.
MeterPressureTensor(PotentialMaster, Space) MeterPressureTensor
MeterPressureTensorFromIntegrator etomica.data.meter
Acts as a DataSource to retrieve the pressure from the integrator.
MeterPressureTensorFromIntegrator(Space) MeterPressureTensorFromIntegrator
MeterProfile etomica.data.meter
Meter that takes a (scalar) Meter and records its property as a
1-dimensional function of position in the simulation volume.
MeterProfile(Space, IRandom) MeterProfile
Default constructor sets profile along the x-axis, with 100 points in
the profile.
MeterProfileByAtoms etomica.data.meter
Meter that takes a (scalar) Meter and records its property as a
1-dimensional function of position in the simulation volume.
MeterProfileByAtoms(Space) MeterProfileByAtoms
Default constructor sets profile along the y-axis, with 100 histogram points.
MeterProfileByVolume etomica.data.meter
Meter that takes a (scalar) Meter and records its property as a
1-dimensional function of position in the simulation volume.
MeterProfileByVolume(Space) MeterProfileByVolume
Default constructor sets profile along the y-axis, with 100 histogram points.
MeterProfileByVolumeAdsorption etomica.modules.adsorption
MeterProfileByVolumeAdsorption(Space) MeterProfileByVolumeAdsorption
MeterPU etomica.liquidLJ
Meter for evaluation of the soft-potential pressure in a box.
MeterPU(Space) MeterPU
MeterPUCut etomica.liquidLJ
Meter for evaluation of the soft-potential pressure in a box.
MeterPUCut(Space, double[]) MeterPUCut
MeterPUCutLS etomica.liquidLJ
Meter for evaluation of the soft-potential pressure in a box.
MeterPUCutLS(Space, int) MeterPUCutLS
MeterRadiusGyration etomica.data.meter
Meter for tabulation of the radius of gyration of a set of chain molecules.
MeterRadiusGyration(Space) MeterRadiusGyration
MeterRDF etomica.data.meter
Meter for tabulation of the atomic radial distribution function (RDF).
MeterRDF(Space) MeterRDF
Creates meter with default to compute pair correlation for all
leaf atoms in a box.
MeterRDF(Space, boolean) MeterRDF
MeterRDFCylinder etomica.modules.pistoncylinder
MeterRDF sublcass that properly calculates the RDF for the Piston/Cylinder
apparatus.
MeterRDFCylinder(Space) MeterRDFCylinder
MeterRDFMapped etomica.cavity
Meter for the cavity function using mapped averaging.
MeterRDFMapped(IntegratorHard) MeterRDFMapped
MeterRDFPC etomica.data.meter
Meter for tabulation of the atomic radial distribution function (RDF).
MeterRDFPC(Space, PotentialMaster, Box) MeterRDFPC
Creates meter with default to compute pair correlation for all
leaf atoms in a box.
meterRef MeterOverlapSwitch
meterRefEnergy MeterBoltzmannTarget
MeterRmin etomica.osmoticvirial
Calculates minimum pair distance from all the possible pairs of atoms as required by
Ashton and Wilding's method
MeterRmin(Space, Box) MeterRmin
MeterRminSpecies etomica.osmoticvirial
Calculates minimum pair distance from all the possible pairs of atoms of a particular species
as required by Ashton and Wilding's method
MeterRminSpecies(Space, Box, ISpecies) MeterRminSpecies
MeterRMSD etomica.data.meter
Measured root mean squared displacement of all atoms in the box.
MeterRMSD(Box, Space) MeterRMSD
MeterRotationDistributionGroup etomica.models.nitrogen
Meter that measures the spherical coordinate angles
angle[0]: is theta, angle between the projection vector (molecular axis vector onto xy plane)
and x-axis
angle[1]: is phi, angle between the molecular axis vector and z-axis
MeterRotationDistributionGroup(Box, CoordinateDefinitionNitrogen) MeterRotationDistributionGroup
MeterRotPerturbMolecule etomica.models.nitrogen
Meter that returns a Boltzmann factor difference between 2 systems: system 1 and 0
1: (Target System) sampled with an angle constraint, e.g.
MeterRotPerturbMolecule(IntegratorMC, PotentialMaster, ISpecies, Space, Simulation, CoordinateDefinitionNitrogen) MeterRotPerturbMolecule
meters SimOverlapBetaN2RP
meters SimOverlapNitrogenModel
meters SimOverlap
meters SimOverlapLJ
meters SimOverlapLJModule.APIPotentialReference
meters SimOverlapLJModule
meters SimOverlapModule
meters SimOverlapSoftSphere
meters SimOverlapSoftSphereEinHarm
meters SimOverlapSoftSphereHCP
meters SimOverlapSoftSphereReweighting
meters SimOverlapSoftSphereSoftness
meters SimOverlapSoftSphereSuperBox
meters SimOverlapSSnxy
meters SimulationVirialOverlap2
MeterSamplingHarmonic etomica.normalmode
Meter used for compute for the probability of the harmonic sampling
< e0 / (e1 + alpha * e0)>umb
MeterSamplingHarmonic(IntegratorBox, MCMoveAtomCoupledUmbrella) MeterSamplingHarmonic
MeterSamplingTarget etomica.normalmode
Meter used for compute for the probability of the target system sampling
< e1 / (e1 + alpha * e0)>umb
MeterSamplingTarget(IntegratorBox, MCMoveAtomCoupledUmbrella) MeterSamplingTarget
MeterSamplingWeight etomica.virial
Measures value of clusters in a box and returns the values
divided by the sampling bias from the sampling cluster.
MeterSamplingWeight(DataSourceAtomDistance) MeterSamplingWeight
Constructor for MeterVirial.
meterSFac DataSinkBlockAveragerSFac
MeterSolidDA etomica.normalmode
Meter for evaluation of the soft-potential pressure in a box.
MeterSolidDA(Space, PotentialMaster, CoordinateDefinition, boolean) MeterSolidDA
MeterSolidDACut etomica.normalmode
Meter for evaluation of the soft-potential pressure in a box.
MeterSolidDACut(Space, PotentialMaster, CoordinateDefinition, double[]) MeterSolidDACut
MeterSolidMirror etomica.normalmode
Meter uses harmonically-mapped averages to compute properties and also
couples configurations with their mirror images to obtain cancellation
of error at very low temperatures.
MeterSolidMirror(Space, IDataSource, CoordinateDefinition) MeterSolidMirror
MeterSolidProps etomica.normalmode
MeterSolidProps(Space, DataSourceScalar, PotentialMaster, CoordinateDefinition, double, double, double, double, double, boolean) MeterSolidProps
MeterSolidPropsLJ etomica.normalmode
MeterSolidPropsLJ(Space, DataSourceScalar, PotentialMaster, CoordinateDefinition, double, double, double, double, double, double, double, double, double, double) MeterSolidPropsLJ
MeterSpin etomica.spin.ising
Meter that provides the x-component of the vector average of
spin values (which is represented by the atom's position
vector).
MeterSpin(Space) MeterSpin
MeterSpinMSquare etomica.spin.heisenberg
returns the average of square of total dipole moment.
MeterSpinMSquare(Space, Box, double) MeterSpinMSquare
MeterStrain etomica.modules.materialfracture
MeterStrain() MeterStrain
MeterStress etomica.modules.materialfracture
Meter that calculates the stress within the gage cell.
MeterStress(PotentialCalculationForceStress) MeterStress
MeterStructureFactor etomica.data.meter
Meter for calculation of structure factor of atoms for all wave vectors less
than a cutoff.
MeterStructureFactor(Box, double) MeterStructureFactor
Creates meter with default to compute the structure factor for all atoms
in the box.
MeterStructureFactor(Box, double, MeterStructureFactor.AtomSignalSource) MeterStructureFactor
MeterStructureFactor.AtomSignalSource etomica.data.meter
MeterStructureFactor.AtomSignalSourceByType etomica.data.meter
MeterStructureFactorStress3 etomica.modules.glass
MeterStructureFactorStress3(MeterStructureFactor[]) MeterStructureFactorStress3
meterTarget MeterOverlapSwitch
meterTarget MeterWorkBennetHarmonic
meterTarget MeterWorkBennetTarget
meterTarget MeterWorkHarmonicUmbrella
meterTarget MeterWorkTargetUmbrella
MeterTargetRPMolecule etomica.models.nitrogen
Rotational Perturbation for beta-phase Nitrogen
- scaling of the rotational angle to better map the phase space
of the perturbing systems.
MeterTargetRPMolecule(PotentialMaster, ISpecies, Space, Simulation, CoordinateDefinitionNitrogen, PRotConstraint) MeterTargetRPMolecule
MeterTargetTP etomica.normalmode
Meter that measures the overlap averages for perturbing from a solid at one
temperature into other the system at other temperatures.
MeterTargetTP(PotentialMaster, ISpecies, Simulation, CoordinateDefinition) MeterTargetTP
MeterTargetTPMolecule etomica.models.nitrogen
For molecular model, e.g., diatomic Nitrogen model, with 5 d.o.f.
MeterTargetTPMolecule(PotentialMaster, ISpecies, Simulation, CoordinateDefinitionNitrogen) MeterTargetTPMolecule
meterTemperature BoxQuench
meterTemperature IntegratorMD
MeterTemperature etomica.data.meter
Meter for measurement of the temperature based on kinetic-energy
equipartition.
MeterTemperature(Box, int) MeterTemperature
MeterTemperature(Simulation, Box, int) MeterTemperature
MeterTensorVelocity etomica.data.meter
A meter to compute the velocity component of the pressure tensor.
MeterTensorVelocity(Space) MeterTensorVelocity
MeterThetaDeviation etomica.normalmode
Meter that measures the average tilt angle (not the angle of average tilt!)
MeterThetaDeviation(Space) MeterThetaDeviation
MeterTilt etomica.modules.sam
Meter that measures the average tilt angle (not the angle of average tilt!)
MeterTilt etomica.normalmode
Meter that measures the average tilt angle (not the angle of average tilt!)
MeterTilt(Space, ISpecies) MeterTilt
MeterTilt(Space, ISpecies, int) MeterTilt
MeterTiltHistogram etomica.normalmode
Meter that measures the average tilt angle (not the angle of average tilt!)
MeterTiltHistogram(Space, ISpecies) MeterTiltHistogram
MeterTiltRotation etomica.normalmode
Meter that measures the average tilt angle (not the angle of average tilt!)
MeterTiltRotation(Space, ISpecies, int) MeterTiltRotation
MeterTiltRotationHistogram etomica.normalmode
Meter that measures the average tilt angle (not the angle of average tilt!)
MeterTiltRotationHistogram(Space, ISpecies, int) MeterTiltRotationHistogram
MeterTiltRotationStdev etomica.normalmode
Meter that measures the average tilt angle (not the angle of average tilt!)
MeterTiltRotationStdev(Space, ISpecies, int) MeterTiltRotationStdev
meterUmbrella MultiharmonicMC
MeterUmbrella etomica.modules.multiharmonic.umbrella
MeterUmbrella(IDataSource, IDataSource, double) MeterUmbrella
Meter to measure the "overlap" function for free energy calculations,
used as input to an AccumulatorVirialOverlapSingleAverage.
MeterVirial etomica.virial
Measures value of clusters in a box and returns the values
divided by the sampling bias from the sampling cluster.
MeterVirial(ClusterAbstract[]) MeterVirial
Constructor for MeterVirial.
MeterVirialBD etomica.virial
This meter handles direct sampling with BigDecimal precision for averages.
MeterVirialBD(ClusterAbstract[]) MeterVirialBD
Constructor for MeterVirial.
MeterVirialBDBin etomica.virial
Measures value of clusters in a box and returns the values
divided by the sampling bias from the sampling cluster.
MeterVirialBDBin(ClusterWheatley, IRandom) MeterVirialBDBin
Constructor for MeterVirial.
MeterVirialBDBinMultiThreaded etomica.virial
Measures cluster averages for virial coefficients.
MeterVirialBDBinMultiThreaded(ClusterWheatley, IRandom, IntSet.PropertyBin) MeterVirialBDBinMultiThreaded
Constructor for MeterVirial.
MeterVirialBDBinMultiThreaded(ClusterWheatley, IRandom, IntSet.PropertyBin, long[], Map<IntSet, MeterVirialBDBinMultiThreaded.MyData>, int, boolean) MeterVirialBDBinMultiThreaded
MeterVirialBDBinMultiThreaded.MyData etomica.virial
MeterVirialBinMultiThreaded etomica.virial
Measures cluster averages for virial coefficients.
MeterVirialBinMultiThreaded(ClusterWheatley, IRandom, IntSet.PropertyBin) MeterVirialBinMultiThreaded
Constructor for MeterVirial.
MeterVirialBinMultiThreaded(ClusterWheatley, IRandom, IntSet.PropertyBin, long[], Map<IntSet, MeterVirialBinMultiThreaded.MyData>, int, boolean) MeterVirialBinMultiThreaded
MeterVirialBinMultiThreaded.MyData etomica.virial
MeterVirialEBinMultiThreaded etomica.virial
Measures cluster averages for virial coefficients.
MeterVirialEBinMultiThreaded(ClusterWheatleyExtendSW, IRandom, IntSet.PropertyBin, int) MeterVirialEBinMultiThreaded
Constructor for MeterVirial.
MeterVirialEBinMultiThreaded(ClusterWheatleyExtendSW, IRandom, IntSet.PropertyBin, long[], Map<IntSet, MeterVirialEBinMultiThreaded.MyData>, int, boolean, int) MeterVirialEBinMultiThreaded
MeterVirialEBinMultiThreaded.MyData etomica.virial
MeterVirialEBinMultiThreaded.MyDataCov etomica.virial
MeterVirialExternalField etomica.virial
Measures value of clusters in a box and returns the values
divided by the sampling bias from the sampling cluster.
MeterVirialExternalField(ClusterAbstract, double[]) MeterVirialExternalField
Constructor for MeterVirial.
MeterVirialExternalFieldConfined etomica.virial
Measures value of clusters in a box and returns the values
divided by the sampling bias from the sampling cluster.
MeterVirialExternalFieldConfined(ClusterAbstract, double[], double[]) MeterVirialExternalFieldConfined
Constructor for MeterVirial.
MeterVirialExternalFieldOverlapConfined etomica.virial
Measures value of clusters in a box and returns the values
divided by the sampling bias from the sampling cluster.
MeterVirialExternalFieldOverlapConfined(ExternalVirialDiagrams, MayerFunction, double[], double) MeterVirialExternalFieldOverlapConfined
Constructor for MeterVirial.
MeterVirialExternalFieldOverlapConfined.RangeComparator etomica.virial
MeterVirialExternalFieldOverlapConfinedRho etomica.virial
Measures value of clusters in a box and returns the values
divided by the sampling bias from the sampling cluster.
MeterVirialExternalFieldOverlapConfinedRho(ExternalVirialDiagrams, MayerFunction, double[], double, double, double, double) MeterVirialExternalFieldOverlapConfinedRho
Constructor for MeterVirial.
MeterVirialExternalFieldOverlapConfinedSW etomica.virial
Measures value of clusters in a box and returns the values
divided by the sampling bias from the sampling cluster.
MeterVirialExternalFieldOverlapConfinedSW(ExternalVirialDiagrams, MayerFunction, double[], double, double, double) MeterVirialExternalFieldOverlapConfinedSW
Constructor for MeterVirial.
MeterVirialExternalFieldOverlapRho etomica.virial
Measures value of clusters in a box and returns the values
divided by the sampling bias from the sampling cluster.
MeterVirialExternalFieldOverlapRho(ExternalVirialDiagrams, MayerFunction, double[]) MeterVirialExternalFieldOverlapRho
Constructor for MeterVirial.
MeterVirialExternalFieldRho etomica.virial
Measures value of clusters in a box and returns the values
divided by the sampling bias from the sampling cluster.
MeterVirialExternalFieldRho(ExternalVirialDiagrams, MayerFunction, double[]) MeterVirialExternalFieldRho
Constructor for MeterVirial.
MeterVirialExternalFieldSW etomica.virial
Measures value of clusters in a box and returns the values
divided by the sampling bias from the sampling cluster.
MeterVirialExternalFieldSW(ClusterAbstract, double[], double, double, double) MeterVirialExternalFieldSW
Constructor for MeterVirial.
MeterVirialExternalFieldSW.Near etomica.virial
MeterVirialIC etomica.virial
Returns cluster and distribution function values from ClusterSumIC
MeterVirialIC(ClusterSumIC) MeterVirialIC
Constructor for MeterVirial.
MeterVirialSWWE etomica.virial
MeterVirialSWWE(ClusterWheatleyExtendSW) MeterVirialSWWE
MeterViscosity etomica.modules.rheology
Meter to measure the viscosity of a polymer in a shear field.
MeterViscosity(Space) MeterViscosity
MeterVolume etomica.data.meter
Meter for measurement of the box volume.
MeterVolume() MeterVolume
MeterWallForce etomica.interfacial
MeterWallForce(Space, PotentialMaster, Box, ISpecies) MeterWallForce
MeterWallForce.PotentialCalculationWallForce etomica.interfacial
Sums the force on each iterated atom and adds it to the integrator agent
associated with the atom.
MeterWallPosition etomica.interfacial
MeterWallPosition(Box, ISpecies, double) MeterWallPosition
MeterWallPressure etomica.modules.sam
MeterWallPressure(PotentialCalculationForceSumWall) MeterWallPressure
meterWidom InsertionGraphic
MeterWidom() InsertionGraphic.MeterWidom
MeterWidomCavity etomica.cavity
MeterWidomCavity(Box, IRandom, PotentialMaster) MeterWidomCavity
MeterWidomInsertion etomica.data.meter
Meter to measure the chemical potential (as its exponent: exp(-mu/kT)) of a
species via the Widom insertion method.
MeterWidomInsertion(Space, IRandom) MeterWidomInsertion
MeterWidomInsertionCorrection etomica.liquidLJ
Meter to measure the chemical potential (as its exponent: exp(-mu/kT)) of a
species via the Widom insertion method.
MeterWidomInsertionCorrection(Space, IRandom) MeterWidomInsertionCorrection
MeterWidomInsertionP etomica.liquidLJ
Meter to measure the chemical potential (as its exponent: exp(-mu/kT)) of a
species via the Widom insertion method.
MeterWidomInsertionP(Space, IRandom) MeterWidomInsertionP
MeterWorkBennetHarmonic etomica.normalmode
Meter used for direct sampling in the harmonic-sampled system.
MeterWorkBennetHarmonic(IntegratorBox, MeterHarmonicEnergy) MeterWorkBennetHarmonic
MeterWorkBennetTarget etomica.normalmode
Meter used for direct sampling in the target-sampled system.
MeterWorkBennetTarget(IntegratorBox, MeterHarmonicEnergy) MeterWorkBennetTarget
MeterWorkHarmonicBennet etomica.normalmode
Meter used for overlap sampling in the harmonic-sampled system.
MeterWorkHarmonicBennet(MCMoveHarmonic, PotentialMaster, double) MeterWorkHarmonicBennet
MeterWorkHarmonicPhaseSpace etomica.normalmode
Meter used for overlap sampling in the harmonic-sampled system.
MeterWorkHarmonicPhaseSpace(MCMoveHarmonic, PotentialMaster) MeterWorkHarmonicPhaseSpace
MeterWorkHarmonicTargetandReweighting etomica.normalmode
Meter used for overlap sampling in the harmonic-sampled system.
MeterWorkHarmonicTargetandReweighting(MCMoveHarmonic, PotentialMaster, double) MeterWorkHarmonicTargetandReweighting
MeterWorkHarmonicUmbrella etomica.normalmode
Meter used for direct sampling in the harmonic-sampled system.
MeterWorkHarmonicUmbrella(IntegratorBox, MeterHarmonicEnergy) MeterWorkHarmonicUmbrella
MeterWorkTargetBennet etomica.normalmode
Meter used for overlap sampling in the target-sampled system.
MeterWorkTargetBennet(IntegratorBox, MeterHarmonicEnergy, double) MeterWorkTargetBennet
MeterWorkTargetHarmonicandReweighting etomica.normalmode
Meter used for overlap sampling in the target-sampled system.
MeterWorkTargetHarmonicandReweighting(IntegratorBox, MeterHarmonicEnergy, double) MeterWorkTargetHarmonicandReweighting
MeterWorkTargetPhaseSpace etomica.normalmode
Meter used for overlap sampling in the target-sampled system.
MeterWorkTargetPhaseSpace(IntegratorBox, MeterHarmonicEnergy) MeterWorkTargetPhaseSpace
MeterWorkTargetUmbrella etomica.normalmode
Meter used for direct sampling in the target-sampled system.
MeterWorkTargetUmbrella(IntegratorBox, MeterHarmonicEnergy) MeterWorkTargetUmbrella
MeterWorkUmbrellaHarmonic etomica.normalmode
Meter used for direct sampling in the harmonic-sampled system.
MeterWorkUmbrellaHarmonic(IntegratorBox, MCMoveAtomCoupledUmbrella) MeterWorkUmbrellaHarmonic
MeterWorkUmbrellaTarget etomica.normalmode
Meter used for direct sampling in the target-sampled system.
MeterWorkUmbrellaTarget(IntegratorBox, MCMoveAtomCoupledUmbrella) MeterWorkUmbrellaTarget
MethanolPotentialHelper etomica.models.rowley
MethanolPotentialHelper etomica.models.traPPE
MethanolPotentialHelper() MethanolPotentialHelper
MethanolPotentialHelper() MethanolPotentialHelper
MethanolRouteParams etomica.models.rowley
MethanolRouteParams() MethanolRouteParams
MethodNotImplementedException etomica.exception
Exception that indicates a method is defined for a class (perhaps to adhere
to an interface), but its implementation is not yet completed.
MethodNotImplementedException() MethodNotImplementedException
Constructor for MethodNotImplementedException.
MethodNotImplementedException(String) MethodNotImplementedException
Constructor for MethodNotImplementedException.
MethodNotImplementedException(String, Throwable) MethodNotImplementedException
Constructor for MethodNotImplementedException.
MethodNotImplementedException(Throwable) MethodNotImplementedException
Constructor for MethodNotImplementedException.
metricPanel SimulationPanel
MEv1v2(Vector, Vector) Tensor
"Minus equals" (-=) operation with a dyad argument.
MEv1v2(Vector, Vector) Tensor1D
MEv1v2(Vector, Vector) Tensor2D
MEv1v2(Vector, Vector) Tensor3D
MEv1v2(Vector, Vector) TensorND
mfp ComponentSubst.ComponentSubstParameters
mfp Decorate.DecorateParameters
mfp DecorateWertheim2Site.DecorateWertheimParameters2Site
mfp DecorateWertheim2SiteRho.DecorateWertheimParameters2Site
mfp DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
mfp DecorateWertheimNaphthalene2Rho.DecorateNaphthalene2Site
mfp ExchangeSplit.ExchangeSplitParameters
mH P2WaterPotentialsJankowski
mH2O P2WaterPotentialsJankowski
MICRO Prefix
millerRabin(BigInteger) Prime
Miller-Rabin primality tests.
MILLI Prefix
mimeTypeMap Main
Static map containing all the mime types understood by the
rasterizer
min Token
min(Ifactor) Ifactor
Minimum of two values.
min(Rational) Rational
Compares the value of this with another constant.
min(Vector<Ifactor>) Ifactor
Minimum of a list of values.
MIN_INT Rational
MIN_X DevicePlotPoints
MIN_Y DevicePlotPoints
minAdjustStep MCMoveStepTracker
minbonddistance Token
mincf MinimizeHCP.SimOverlapParam
minConfigIndex MeterGs
minDiffLocation() DataSourceVirialOverlap
Returns the index of the Bennet parameter which minimizes the differences
between the Bennet "sums" from the target and references accumulators.
minDiffLocation() DataVirialOverlap
Deprecated.
minDistance MCMoveInsertDeleteVacancy
minDistance AtomTestDeviation
minDrFilter GlassProd.SimParams
minFlipDistance ClusterCoupledFlipped
minFlipDistance ClusterCoupledFlippedMultivalue
minFloat DisplayTable
minFound IntegratorDimerMin
MINIMIZATION_ATOM_MAX JmolConstants
MinimizationBetaNitrogenModel etomica.models.nitrogen
Lattice-Energy Minimization for Beta-Nitrogen Structure
using gradient
MinimizationBetaNitrogenModel(Space, int[], double) MinimizationBetaNitrogenModel
MinimizationBetaNitrogenModelLS etomica.models.nitrogen
Lattice-Energy Minimization for Beta-Nitrogen Structure
using gradient with lattice sum
MinimizationBetaNitrogenModelLS(Space, double, double) MinimizationBetaNitrogenModelLS
minimizationcriterion Token
minimizationrefresh Token
minimizationsilent Token
minimizationsteps Token
MinimizationTIP4P etomica.models.clathrates
MinimizationTIP4P(Space, double, double, double[], int[], int, boolean, double, String, boolean) MinimizationTIP4P
MinimizationTIP4P.ChargeAgentSourceRPM etomica.models.clathrates
MinimizationTIP4P.SimParams etomica.models.clathrates
minimize(double[], double[], double, int) SteepestDescent
minimize(double[], double, int) NewtonMinimization
MINIMIZE_FIXED_RANGE JmolConstants
MinimizeBetaNitrogenLatticeParameter etomica.models.nitrogen
This class is written to minimize the lattice energy of the beta-phase
Nitrogen, which has HCP packing with 2 basis atoms using line minimization
The varying parameters are:
unit cell A: molecule 1 (u[0] through u[4]) and molecule 2 (u[5] through u[9])
unit cell B: molecule 1 (u[0] through u[4]) and molecule 2 (u[5] through u[9])
- 3 translational + 2 rotational
There are total of 20 degrees of freedom.
MinimizeBetaNitrogenLatticeParameter(Space, int[], double) MinimizeBetaNitrogenLatticeParameter
MinimizeBetaNitrogenLatticeParameterFromFile etomica.models.nitrogen
This class is written to minimize the lattice energy of the beta-phase
Nitrogen, which has HCP packing with 2 basis atoms using line minimization
The varying parameters are:
unit cell A: molecule 1 (u[0] through u[4]) and molecule 2 (u[5] through u[9])
unit cell B: molecule 1 (u[0] through u[4]) and molecule 2 (u[5] through u[9])
- 3 translational + 2 rotational
There are total of 20 degrees of freedom.
MinimizeBetaNitrogenLatticeParameterFromFile(Space, int[], double, double[]) MinimizeBetaNitrogenLatticeParameterFromFile
MinimizeBetaNitrogenLatticeParameterLSFromFile etomica.models.nitrogen
This class is written to minimize the lattice energy of the beta-phase
Nitrogen, which has HCP packing with 2 basis atoms using line minimization
The varying parameters are:
unit cell A: molecule 1 (u[0] through u[4]) and molecule 2 (u[5] through u[9])
unit cell B: molecule 1 (u[0] through u[4]) and molecule 2 (u[5] through u[9])
- 3 translational + 2 rotational
There are total of 20 degrees of freedom.
MinimizeBetaNitrogenLatticeParameterLSFromFile(Space, double, double[], double) MinimizeBetaNitrogenLatticeParameterLSFromFile
MinimizeBetaNitrogenTranslationDOF etomica.models.nitrogen
This class is written to minimize the lattice energy of the beta-phase
Nitrogen, which has HCP packing with 2 basis atoms using line minimization
The varying parameters are all the translational d.o.f of the molecules
NO rotational d.o.f.
MinimizeBetaNitrogenTranslationDOF(Space, int[], double, String, double) MinimizeBetaNitrogenTranslationDOF
MinimizeGammaNitrogenLatticeParameter etomica.models.nitrogen
Determine c/a ratio for tetragonal unit cell that minimizes
the lattice energy of gamma-N2 crystal structure
MinimizeGammaNitrogenLatticeParameter(Space, int, double, double) MinimizeGammaNitrogenLatticeParameter
MinimizeHCP etomica.normalmode
Determines c/a ratio of primitive vector lengths corresponding to the
minimum energy HCP structure.
MinimizeHCP(Space, int, double, int, double, double) MinimizeHCP
MinimizeHCP.SimOverlapParam etomica.normalmode
Inner class for parameters understood by the HSMD3D constructor
minimum() DoubleRange
The minimium defined by this range.
minimum(P2QChemInterpolated) P2QChemInterpolated
minimumScreening(int, int, double, double) VirialOptimizer
minInterval CorrelationSelf2
minInterval DataSinkBlockAveragerSFac
minInterval DataSourceAlpha2
minInterval DataSourceBlockAvgCor
minInterval DataSourceFs
minInterval DataSourceMSD
minInterval DataSourceVAC
minInterval MeterCorrelationSelf
minInterval StructureFactorComponentCorrelation
minMulti VirialHeNonAdditive.VirialParam
minMultiP VirialDiagrams
minMultiP VirialDiagramsPT
minN MCMoveInsertDeleteBiased
minNumAtoms MCMoveOverlapListener
minOCOr2 P2SquareWellBonding
minOOr2 P2SquareWellBondingCO
minor(BigInteger[][], int, int) BigIntegerMath
Minor of an integer matrix.
minpixelselradius Token
minPrevSample MeterCorrelation
minR P2CO2H2OWheatley
minR2 AssociationHelperBranched
minR2 AssociationHelperDouble
minR2 AssociationHelperMolecule
minRadicalSites P2SquareWellSurface
minSearch SimDimerLJadatom
minus(Complex) Complex
Subtraction of Complex numbers (doesn't change this Complex number).
minus_half_sqrt_bondlength ConformationPh3site
mip FFTDecomposition
mip IsFFT
MIXED Dimension
Dimension used to indicate that a group of values are not all of
the same dimension.
mixedPM MCMoveGeometricCluster
mixedPM MCMoveGeometricClusterRestrictedGE
mixF ClusterWheatleySoftDerivativesMix
mixF ClusterWheatleySoftDerivativesMixBD
mixF ClusterWheatleySoftMix
mixF ClusterWheatleySoftMixBD
mixFMulti3 ClusterWheatleyMultibodyMix
mixID VirialLJMultiOverlap.VirialMixParam
mixPotentials ReverseOsmosisGraphic.ModifierEpsilon
mixPotentials ReverseOsmosisWaterGraphic.ModifierEpsilon
mixPotentialsM ReverseOsmosisWaterGraphic.ModifierSoluteCharge
mixPotentialsP ReverseOsmosisWaterGraphic.ModifierSoluteCharge
MKS etomica.units.systems
Meter-Kilogram-Second system of units
MKS() MKS
mLREP PotentialCuLREP
mmBond VirialDiagrams
mmBond VirialDiagramsPT
mNumBody ClusterDiagram
mNumIdenticalPermutations ClusterDiagram
mo Token
mO P2WaterPotentialsJankowski
mobFrac DataSourceStrings
mobileAtoms DataSourceQ4
mobileSpecies GrainBoundaryTiltConfiguration
mod() BenchVector3D
mod(Vector) Vector
Replaces each component of this vector with its value modulo
the corresponding component in u
mod(Vector) Vector1D
mod(Vector) Vector2D
mod(Vector) Vector3D
mod(Vector) VectorND
mod(Vector1D) Vector1D
mod(Vector3D) Vector3D
mod(String, String, Class<?>) EtomicaModuleInfo
mod(String, String, Class<?>, String) EtomicaModuleInfo
mod2pi(BigDecimal) BigDecimalMath
Reduce value to the interval [0,2*Pi].
model Token
ModelAlertMsgDialog etomica.virial.GUI.models
ModelAlertMsgDialog(String) ModelAlertMsgDialog
ModelAlkaneLengthSelection etomica.virial.GUI.models
ModelAlkaneLengthSelection() ModelAlkaneLengthSelection
modelindex Token
modelIndex Point3fi
MODELKIT_ZAP_STRING JmolConstants
MODELKIT_ZAP_TITLE JmolConstants
modelkitmode Token
ModelMoleculeListDisplayTable etomica.virial.GUI.models
ModelMoleculeListDisplayTable() ModelMoleculeListDisplayTable
ModelMoleculeListDisplayTable_new etomica.virial.GUI.models
ModelMoleculeListDisplayTable_new() ModelMoleculeListDisplayTable_new
ModelParams(AtomType[], double[], double[], double[]) P2PotentialGroupBuilder.ModelParams
ModelPotParamDisplayTable etomica.virial.GUI.models
ModelPotParamDisplayTable() ModelPotParamDisplayTable
modelSelectedSpecies AppModelMixtureBuilder
ModelSelectedSpecies etomica.virial.GUI.models
ModelSelectedSpecies() ModelSelectedSpecies
ModelSimulationConstructor etomica.virial.GUI.models
ModelSimulationConstructor() ModelSimulationConstructor
ModelSimulationEnvironment etomica.virial.GUI.models
ModelSimulationEnvironment() ModelSimulationEnvironment
ModelSimulationEnvironment(double, int) ModelSimulationEnvironment
ModelSimulationEnvironment(double, int, ModelSelectedSpecies) ModelSimulationEnvironment
modelSpeciesSelection AppModelMixtureBuilder
ModelSpeciesSelection etomica.virial.GUI.models
ModelSpeciesSelection() ModelSpeciesSelection
ModelTemperatureAndSteps etomica.virial.GUI.models
modeNum MCMoveHarmonic
modes MCMoveHarmonicStep
modeSigns SimDimerLJadatom
Modifier etomica.modifier
A Modifier object permits changes to be made to a property of another object.
ModifierAtomDiameter() PistonCylinderGraphic.ModifierAtomDiameter
ModifierAtomDiameter() SwmdGraphic.ModifierAtomDiameter
ModifierAtomDiameter(MuGraphic, SpeciesGeneral, P2SquareWellOneSide, P2SquareWellOneSide, P2SquareWellOneSide) MuGraphic.ModifierAtomDiameter
ModifierAtomDiameter(SpeciesGeneral, P2LennardJones, P2LennardJones[], P2LennardJones[], DiameterHashByType) ReverseOsmosisWaterGraphic.ModifierAtomDiameter
ModifierAtomDiameter(SpeciesGeneral, P2LennardJones, SpeciesGeneral[], P2LennardJones[], DiameterHashByType) ReverseOsmosisGraphic.ModifierAtomDiameter
ModifierBoolean etomica.modifier
Interface that permits changes to be made to a boolean property of another object.
ModifierBoxSize(Space, Box, int, IAction) DropletGraphic.ModifierBoxSize
ModifierBoxSize(Space, Box, int, IAction) InterfacialSWGraphic.ModifierBoxSize
ModifierCells3D etomica.normalmode
Modifier class that enables change of the number of cells in 2D
ModifierCells3D(Box, ISpecies) ModifierCells3D
ModifierConfiguration(Box, List<Vector[]>, List<Vector[]>, List<DataFunction>, List<DataFunction.DataInfoFunction>, DataTag) ConfigFromFileLAMMPS.ModifierConfiguration
ModifierDensity() NucleationGraphic.ModifierDensity
ModifierEpsilon(P2SquareWellOneSide, P2SquareWellOneSide, P2SquareWellOneSide, IntegratorBox) MuGraphic.ModifierEpsilon
ModifierEpsilon(P2LennardJones, P2LennardJones[], P2LennardJones[]) ReverseOsmosisGraphic.ModifierEpsilon
ModifierEpsilon(P2LennardJones, P2LennardJones[], P2LennardJones[]) ReverseOsmosisWaterGraphic.ModifierEpsilon
ModifierFunctionWrapper etomica.modifier
Extends the configurable modifier to permit a function to be applied to
a value before the modified property is set.
ModifierFunctionWrapper(Object[], String) ModifierFunctionWrapper
ModifierFunctionWrapper(Object, String) ModifierFunctionWrapper
ModifierGeneral etomica.modifier
Implements the Modifier functionality using introspection to obtain the accessor methods for a property.
ModifierGeneral(Object[], String) ModifierGeneral
Constructor connecting the modifier's getValue and setValue methods to the set/get accessor
methods of the object being modifier.
ModifierGeneral(Object, String) ModifierGeneral
Modifier for property of a single object (most common use)
ModifierLambda(P2SquareWellOneSide, P2SquareWellOneSide, P2SquareWellOneSide, IntegratorBox) MuGraphic.ModifierLambda
ModifierNMolecule etomica.modifier
Modifier class that enables change of the number of molecules of a particular species
in a particular box.
ModifierNMolecule(Box, ISpecies) ModifierNMolecule
ModifierPistonDensity() PistonCylinderGraphic.ModifierPistonDensity
ModifierPistonPressure etomica.modules.pistoncylinder
Modifier for the piston pressure.
ModifierPistonPressure(Space, P1HardMovingBoundary, Dimension) ModifierPistonPressure
ModifierPMu etomica.modules.adsorption
ModifierPMu(P2SquareWell, IntegratorBox, EOSSW, MyMCMove, MeterExcessAdsorbed) ModifierPMu
ModifierSoluteCharge(P2Electrostatic, P2Electrostatic, P2Electrostatic, P2Electrostatic[], P2Electrostatic[]) ReverseOsmosisWaterGraphic.ModifierSoluteCharge
ModifierTPI etomica.virial.simulations
ModifierTPI(double, int, MCMoveClusterRingRegrow, MCMoveClusterRingRegrow, ClusterAbstract) ModifierTPI
ModifierWallPosition(Sam) SamGraphic.ModifierWallPosition
ModifierXCells2D etomica.normalmode
Modifier class that enables change of the number of cells in 2D
ModifierXCells2D(Box, ISpecies, int) ModifierXCells2D
ModifierYCells2D etomica.normalmode
Modifier class that enables change of the number of cells in 2D
ModifierYCells2D(Box, ISpecies, int) ModifierYCells2D
modify Token
modifyAction DeviceBox
Modifier connecting the slider to the property
modifyAction DeviceCheckBox
modifyAction DeviceSlider
Modifier connecting the slider to the property
modifyAction DeviceSpinner
Modifier connecting the spinner to the property
ModifyAction etomica.modifier
Wraps a Modifier instance so that the modification can be performed
as the consequence of an action.
ModifyAction(Modifier) ModifyAction
Constuctor requires the wrapped Modifier, which is final.
ModifyBooleanAction etomica.modifier
Wraps a ModifierBoolean instance so that the modification can be performed
as the consequence of an action.
ModifyBooleanAction(ModifierBoolean) ModifyBooleanAction
Constuctor requires the wrapped ModifierBoolean
modifyorcreate Token
modpi(BigDecimal) BigDecimalMath
Reduce value to the interval [-Pi/2,Pi/2].
moduleClass EtomicaModuleInfo
ModuleLauncher etomica.modules
ModuleLauncher() ModuleLauncher
moduleName EtomicaModuleInfo
moduleNum StatisticsMCGraphic.StatsParams
modulus() Complex
Modulus of this Complex number, the distance from the origin in polar coordinates.
moebius() Ifactor
The Moebius function.
mol MoleculeSetSinglet
mol0 MoleculePair
mol1 MoleculePair
molAVec FindPairMoleculeIndex
molAVec FindPairMoleculeIndexBetaN2
molAxis MCMoveRotateMolecule3DN2AveCosThetaConstraint
molBVec FindPairMoleculeIndex
molBVec FindPairMoleculeIndexBetaN2
Mole etomica.units
The mole unit of quantity, approximately equal to 6.022e23 simulation units.
molecOrientation MCMoveRotateMolecule3DConstraint
molecOrientation MCMoveRotateMolecule3DFixedAngle
MolecularModel2CLJQ_SpeciesCO2 etomica.virial.GUI.models
MolecularModel2CLJQ_SpeciesCO2() MolecularModel2CLJQ_SpeciesCO2
MolecularModel2CLJQ_SpeciesEthane etomica.virial.GUI.models
MolecularModel2CLJQ_SpeciesEthane() MolecularModel2CLJQ_SpeciesEthane
MolecularModel2CLJQ_SpeciesLJ etomica.virial.GUI.models
MolecularModel2CLJQ_SpeciesLJ() MolecularModel2CLJQ_SpeciesLJ
MolecularModelEMP2_SpeciesCO2 etomica.virial.GUI.models
MolecularModelEMP2_SpeciesCO2() MolecularModelEMP2_SpeciesCO2
MolecularModelExp6_SpeciesAlkane etomica.virial.GUI.models
MolecularModelExp6_SpeciesAlkane() MolecularModelExp6_SpeciesAlkane
MolecularModelLJ_SpeciesLJ etomica.virial.GUI.models
MolecularModelLJ_SpeciesLJ() MolecularModelLJ_SpeciesLJ
MolecularModelLJQ_SpeciesLJ etomica.virial.GUI.models
MolecularModelLJQ_SpeciesLJ() MolecularModelLJQ_SpeciesLJ
MolecularModelSKS_SpeciesAlkane etomica.virial.GUI.models
MolecularModelSKS_SpeciesAlkane() MolecularModelSKS_SpeciesAlkane
MolecularModelSKS_SpeciesAlkane(int) MolecularModelSKS_SpeciesAlkane
MolecularModelSPCE_SpeciesH2O etomica.virial.GUI.models
MolecularModelSPCE_SpeciesH2O() MolecularModelSPCE_SpeciesH2O
MolecularModelTRAPPE_SpeciesAlkane etomica.virial.GUI.models
MolecularModelTRAPPE_SpeciesAlkane() MolecularModelTRAPPE_SpeciesAlkane
MolecularModelTRAPPE_SpeciesAlkane(int) MolecularModelTRAPPE_SpeciesAlkane
MolecularModelTrappe_SpeciesCO2 etomica.virial.GUI.models
MolecularModelTrappe_SpeciesCO2() MolecularModelTrappe_SpeciesCO2
molecularPotentials PotentialMasterLrc
MolecularWeightAvg etomica.modules.chainequilibrium
Takes output from MeterChainLength as input and outputs the number-average
molecular weight.
MolecularWeightAvg() MolecularWeightAvg
MolecularWeightAvg2 etomica.modules.chainequilibrium
Takes output from MeterChainLength as input and outputs the weight-average
molecular weight.
MolecularWeightAvg2() MolecularWeightAvg2
molecule BoxMoleculeEvent
molecule MCMoveMolecule
molecule Token
Molecule etomica.molecule
Molecule(ISpecies, int) Molecule
MOLECULE EnumPalette
molecule0 MCMoveMoleculeCoupledInitPert
molecule0 MCMoveMoleculeCoupledSuperBox
molecule0 MCMoveMoleculeCoupled
molecule1 MCMoveMoleculeCoupledInitPert
molecule1 MCMoveMoleculeCoupledSuperBox
molecule1 MCMoveMoleculeCoupled
MOLECULE1_INDEX Debug
Molecule index of a molecule of interest.
MOLECULE2_INDEX Debug
Global index of a molecule of interest.
MoleculeAction etomica.action
Interface for a class that can perform an action on an atom.
MoleculeActionRelaxWater3P etomica.virial
MoleculeActionRelaxWater3P(Space) MoleculeActionRelaxWater3P
MoleculeActionTranslateTo etomica.action
Moves (translates) an atom to a specified position.
MoleculeActionTranslateTo(Space) MoleculeActionTranslateTo
Creates new action with atom position defined by its
center of mass (via MoleculePositionCOM).
moleculeAdded(IMolecule) BoxEventManager
MoleculeAgent etomica.spin.heisenberg
Holds fields needed by the meter that calculates dielectric constant using mapped averaging.
MoleculeAgent() MeterMappedAveragingSum.MoleculeAgent
MoleculeAgent(int) MoleculeAgent
MoleculeAgent(Space) IntegratorRigidIterative.MoleculeAgent
MoleculeAgent(Space) IntegratorVelocityVerletQuaternion.MoleculeAgent
moleculeAgentManager MCMoveVolumeAssociatedMolecule
moleculeAgentManager MeterDipoleSumSquaredMappedAverage
moleculeAgentManager IntegratorRigidIterative
moleculeAgentManager IntegratorRigidMatrixIterative
moleculeAgentManager PotentialCalculationTorqueSum
moleculeAgentManager IntegratorVelocityVerletQuaternion
MoleculeAgentManager E > - Class in etomica.molecule
MoleculeAgentManager acts on behalf of client classes (an AgentSource) to
manage agents in every IMolecule in a box.
MoleculeAgentManager(Simulation, Box, MoleculeAgentManager.MoleculeAgentSource<E>) MoleculeAgentManager
MoleculeAgentManager(Simulation, Box, Function<IMolecule, ? extends E>) MoleculeAgentManager
MoleculeAgentManager(Simulation, Box, Function<IMolecule, ? extends E>, BiConsumer<? super E, IMolecule>) MoleculeAgentManager
MoleculeAgentManager.MoleculeAgentSource E > - Interface in etomica.molecule
Interface for an object that wants an agent associated with each
IMolecule a Box.
MoleculeArrayList etomica.molecule
MoleculeArrayList() MoleculeArrayList
MoleculeArrayList(int) MoleculeArrayList
MoleculeArrayList(Collection<IMolecule>) MoleculeArrayList
moleculeCell0 LatticeSumCrystalMolecular
moleculeCenter BoxInflate
moleculeCenter MCMoveVolumeMonoclinicScaled
moleculeCenter MCMoveVolumeSolidNPTMolecular
MoleculeChildAtomAction etomica.action
Wraps an AtomAction, and performs the wrapped action on the atom
only if it is a leaf atom; if given an atom group (as indicated
by the atom's node), performs action instead on all the atom's
child atoms.
MoleculeChildAtomAction(AtomAction) MoleculeChildAtomAction
Constructor takes wrapped action, which is final.
moleculeCOM MCMoveClusterMoleculeHSChain
moleculeCOM MCMoveClusterMoleculeHSChainB3
moleculeCOM MCMoveClusterMoleculeHSChain
moleculeIndexChanged(IMolecule, int) BoxEventManager
moleculeIndices ClusterWheatleyMultibody
moleculeIndices ClusterWheatleyMultibodyBD
moleculeIndices ClusterWheatleyMultibodyDerivatives
moleculeIndices ClusterWheatleyMultibodyDerivativesBD
moleculeIndices ClusterWheatleyMultibodyMix
MoleculeInfoBrute(Space) P2SemiclassicalMolecular.MoleculeInfoBrute
moleculeIterator MCMoveVolumeAssociatedMolecule
MoleculeIterator etomica.molecule.iterator
Interface for classes that loop over a set of atoms.
MoleculeIterator0() PotentialMaster.MoleculeIterator0
MoleculeIteratorAll etomica.molecule.iterator
Iterator for all the molecules of a set of species in a box.
MoleculeIteratorAll(ISpecies[]) MoleculeIteratorAll
MoleculeIteratorAll(ISpecies[], boolean) MoleculeIteratorAll
MoleculeIteratorAllMolecules etomica.molecule.iterator
Iterator for all the molecules in a box.
MoleculeIteratorAllMolecules() MoleculeIteratorAllMolecules
MoleculeIteratorAllMolecules(Box) MoleculeIteratorAllMolecules
Returns a new iterator ready to iterate over the molecules of the given
box.
MoleculeIteratorArrayList etomica.molecule.iterator
An atom iterator of the elements from an AtomArrayList (in proper
sequence).
MoleculeIteratorArrayList(IteratorDirective.Direction, int, MoleculeToIndex, MoleculeToMoleculeList) MoleculeIteratorArrayList
MoleculeIteratorArrayListSimple etomica.molecule.iterator
An atom iterator of the elements from an AtomArrayList (in proper
sequence).
MoleculeIteratorArrayListSimple() MoleculeIteratorArrayListSimple
Constructs new iterator with an empty list.
MoleculeIteratorArrayListSimple(IMoleculeList) MoleculeIteratorArrayListSimple
Constructs new iterator set to iterate given list (upon reset).
MoleculeIteratorBoxDependent etomica.molecule.iterator
Interface indicating that an atom iterator can determine appropriate
atoms for iteration given an arbitrary box.
MoleculeIteratorMolecule etomica.molecule.iterator
Iterator for the molecules of a single species in a box.
MoleculeIteratorMolecule(ISpecies) MoleculeIteratorMolecule
MoleculeIteratorMoleculeDependent etomica.molecule.iterator
Interface for an atom iterator that can be altered by setting
of an atom.
MoleculeIteratorSinglet etomica.molecule.iterator
Iterator that expires after returning a single atom, which is
specified by a call to the setAtom method, or via the constructor.
MoleculeIteratorSinglet() MoleculeIteratorSinglet
Constructs iterator without defining atom.
MoleculeIteratorSinglet(IMolecule) MoleculeIteratorSinglet
Constructs iterator specifying that it return the given atom.
moleculeList IntegratorDimerApproach
moleculeList MCMoveInsertDelete
moleculeList MoleculeToMoleculeListSpecies
moleculeList EwaldSummation
moleculeList EwaldSumMolecules
moleculeList ClusterSumMultibody
moleculeList PotentialNonAdditive
MoleculeListProperty etomica.meta.properties
Created by kofke on 7/24/17.
MoleculeListProperty(Object, PropertyDescriptor) MoleculeListProperty
moleculeLists Box
MoleculeNeighborLists etomica.nbr.list.molecule
Class used to maintain neighbor lists.
MoleculeNeighborLists() MoleculeNeighborLists
Constructs sequencer for the given molecule.
moleculeOffset ConfigurationCatalysis
moleculeOffset ConfigurationSAM
MoleculeOriented etomica.molecule
Molecule class appropriate for a rigid molecule.
MoleculeOriented(Space, ISpecies, int) MoleculeOriented
MoleculeOriented(Space, ISpecies, int, boolean) MoleculeOriented
MoleculeOrientedDynamic etomica.molecule
Molecule class appropriate for a rigid molecule in a dynamic context.
MoleculeOrientedDynamic(Space, ISpecies, int) MoleculeOrientedDynamic
moleculePair ANIntergroupExchange
moleculePair PotentialMasterListMolecular
MoleculePair etomica.molecule
Data structure that contains two mutable atom instances.
MoleculePair() MoleculePair
MoleculePair(IMolecule, IMolecule) MoleculePair
MoleculePositionCOM etomica.molecule
Calculates the center of mass (COM) over a set of atoms.
MoleculePositionCOM(Space) MoleculePositionCOM
MoleculePositionFirstAtom etomica.molecule
Returns the position of the first child leaf atom.
MoleculePositionFirstAtom() MoleculePositionFirstAtom
MoleculePositionGeometricCenter etomica.molecule
Calculates the geometric center over a set of atoms.
MoleculePositionGeometricCenter(Space) MoleculePositionGeometricCenter
MoleculePositionGeometricCenterAlkaneEH etomica.molecule
Calculates the geometric center over a set of atoms.
MoleculePositionGeometricCenterAlkaneEH(Space, ISpecies) MoleculePositionGeometricCenterAlkaneEH
MoleculePositionGeometricCenterPBC etomica.molecule
Calculates the geometric center over a set of atoms.
MoleculePositionGeometricCenterPBC(Space, Boundary) MoleculePositionGeometricCenterPBC
MoleculePotential1ListSource(PotentialMasterListMolecular) NeighborListManagerMolecular.MoleculePotential1ListSource
MoleculePotentialList etomica.nbr.list.molecule
Class used to maintain list of whether each 1-body potential that
applies to a species is currently in effect or not for an Molecule.
MoleculePotentialList() MoleculePotentialList
Constructs sequencer for the given atom.
moleculeRemoved(IMolecule) BoxEventManager
molecules CoordinateDefinition.BasisCell
molecules ClusterWheatleyMultibody
molecules ClusterWheatleyMultibodyBD
molecules ClusterWheatleyMultibodyDerivatives
molecules ClusterWheatleyMultibodyDerivativesBD
molecules ClusterWheatleyMultibodyMix
MoleculesetIterator etomica.molecule.iterator
Interface for classes that loop over a set of atoms.
MoleculesetIteratorBasisDependent etomica.molecule.iterator
Interface for an MoleculeIterator that can be conditioned with
target and basis molecules.
MoleculesetIteratorBoxDependent etomica.molecule.iterator
Interface indicating that an iterator can determine appropriate
atoms for iteration given an arbitrary box.
MoleculesetIteratorCellular etomica.nbr.cell.molecule
Interface for moleculeset iterators that use cell-based neighbor
lists for iteration.
MoleculesetIteratorPDT etomica.molecule.iterator
This is an interface for iterators that are box dependent, directable,
and targetable.
MoleculesetIteratorTargetable etomica.molecule.iterator
Interface for an iterator that can be targeted at one or more atoms.
moleculeSetSinglet NeighborListManagerMolecular
moleculeSetSinglet PotentialMasterListMolecular
MoleculeSetSinglet etomica.molecule
Data structure that contains a single mutable atom instance.
MoleculeSetSinglet() MoleculeSetSinglet
MoleculeSetSinglet(IMolecule) MoleculeSetSinglet
moleculeSite NeighborCellManagerMolecular
moleculeSite CriterionSimpleMolecular
moleculeSiteManager CoordinateDefinitionMolecule
moleculeSiteManager CoordinateDefinitionMoleculeVolumeFluctuation
MoleculeSiteSource(Space, IMoleculePositionDefinition) CoordinateDefinitionMolecule.MoleculeSiteSource
MoleculeSiteSource(Space, IMoleculePositionDefinition) CoordinateDefinitionMoleculeVolumeFluctuation.MoleculeSiteSource
moleculeSource MCMoveMolecule
moleculeSource MCMoveMoleculeCoupledInitPert
moleculeSource MCMoveMoleculeCoupledSuperBox
moleculeSource MCMoveMoleculeCoupled
moleculeSource MCMoveClusterAngleBend
moleculeSource MCMoveClusterAngleBendAceticAcid
MoleculeSource etomica.molecule
Interface for objects when return atoms (meeting some specification)
from a box.
MoleculeSourceRandomDimer etomica.association
MoleculeSourceRandomDimer() MoleculeSourceRandomDimer
MoleculeSourceRandomMolecule etomica.molecule
MoleculeSource that returns a completely random molecule.
MoleculeSourceRandomMolecule() MoleculeSourceRandomMolecule
MoleculeSourceRandomMonomer etomica.association
MoleculeSourceRandomMonomer() MoleculeSourceRandomMonomer
MoleculeToIndex etomica.molecule
Interface for class that associates an integer with an atom.
MoleculeToMoleculeList etomica.molecule
Interface for class that determines an AtomArrayList given an atom.
MoleculeToMoleculeListSpecies etomica.molecule
MoleculeToMoleculeListSpecies(ISpecies) MoleculeToMoleculeListSpecies
MoleculeToMoleculeSetFixed etomica.molecule
MoleculeToMoleculeSetFixed() MoleculeToMoleculeSetFixed
moleFractionLeft Osmosis
moleFractionRight Osmosis
molIndex MCMoveMoleculeCoupledSuperBox
molIndex MCMoveRotateMolecule3DSuperBox
molNum MCMoveRotateMolecule3DSuperBox
molSpeciesA MCMoveMoleculeCoupledSuperBox
molSpeciesB MCMoveMoleculeCoupledSuperBox
moment VLESim
moment P2CO2Hellmann.P2CO2SC
moment P2WaterSzalewicz.P2H2OSC
moment VLESim
moment P2NitrogenHellmann
moment P2SemiclassicalMolecular.MoleculeInfoBrute
moment Virial2CLJmuQ.Virial2CLJQParam
moment Virial2CLJQ.Virial2CLJQParam
MOMENT EnumPotentialParamDescription
moment0 P2CO2H2OWheatley.P2CO2H2OSC
moment0 P2CO2H2OWheatley.P2CO2H2OSCTI
moment1 P2CO2H2OWheatley.P2CO2H2OSC
moment1 P2CO2H2OWheatley.P2CO2H2OSCTI
momentj P2SemiclassicalMolecular.MoleculeInfoBrute
momentOfIntertia AtomTypeOriented
MOMENTSQR EnumPotentialParamDescription
momentum BoxScaleMomenta
momentum IntegratorMD
Momentum etomica.units.dimensions
Dimension for all units of momentum, Mass-Length/Time
monatomic(Space, AtomType) SpeciesGeneral
monatomic(Space, AtomType, boolean) SpeciesGeneral
monitorenergy Token
MONOMER EnumPalette
monomer1 ApiIntergroupExchange
monomerA IntegratorDimerApproach
monomerB IntegratorDimerApproach
monomerColor ColorSchemeSmer
monomerMonomerBondManager ColloidSim
monomerMonomerBondManager ConfigurationColloid
monomerMonomerBondManager P1Wall
moreDefaultColors ColorSchemeByType
MOST_RECENT AccumulatorAverage
MOST_RECENT AccumulatorAverageBlockless
mostRecent AccumulatorAverage
mostRecent AccumulatorAverageBlockless
mostRecentBlock AccumulatorAverageFixed
mostRecentBlock AccumulatorAverageFixedOutputFile
mostRecentValue ModifierCells3D
mostRecentValue ModifierXCells2D
mostRecentValue ModifierYCells2D
MOUSE_NONE JmolConstants
mouseClicked(MouseEvent) MyApplet.MouseEventClusterPanel
mouseClicked(MouseEvent) Grabber.CornerSetListener
mouseClicked(MouseEvent) Grabber.DefaultMouseListener
mousedragfactor Token
mouseEntered(MouseEvent) MyApplet.MouseEventClusterPanel
mouseEntered(MouseEvent) Grabber.CornerSetListener
mouseEntered(MouseEvent) Grabber.DefaultMouseListener
MouseEventClusterPanel() MyApplet.MouseEventClusterPanel
mouseExited(MouseEvent) MyApplet.MouseEventClusterPanel
mouseExited(MouseEvent) Grabber.CornerSetListener
mouseExited(MouseEvent) Grabber.DefaultMouseListener
mousePressed(MouseEvent) DisplayPlot.PopupListener
mousePressed(MouseEvent) MyApplet.MouseEventClusterPanel
mousePressed(MouseEvent) Grabber.CornerSetListener
mousePressed(MouseEvent) Grabber.DefaultMouseListener
mouseReleased(MouseEvent) DisplayPlot.PopupListener
mouseReleased(MouseEvent) MyApplet.MouseEventClusterPanel
mouseReleased(MouseEvent) Grabber.CornerSetListener
mouseReleased(MouseEvent) Grabber.DefaultMouseListener
mousewheelfactor Token
movable SimDimerLJadatom
movable SimKMCLJadatom
movableAtoms IntegratorDimerMin
movableAtoms IntegratorDimerRT
movableSet SimDimerLJadatom
movableSet SimKMCLJadatom
movableSpecies IntegratorDimerMin
movableSpecies IntegratorDimerRT
move DataSourceAcceptanceRatio
move SimMappedRdf
move MappedU
move MappedVirialLJ
move MappedVirialLJVGr
move SimOverlapBetaN2TP
move SimOverlapDisorderedAlphaN2TP
move ModifierPMu
move HessianDB
move SimOverlap
move SimOverlapSoftSphere
move SimOverlapSoftSphereHCP
move SimOverlapSoftSphereReweighting
move SimOverlapSSnxy
move SimUmbrella
move SimUmbrellaSoftSphere
moveA MultiharmonicMC
moveB MultiharmonicMC
moved IntegratorVelocityVerletShake
moveEventManager IntegratorMC
moveHarmonic SimOverlapNitrogenModel
moveManager IntegratorManagerMC
moveManager IntegratorMC
moveMolecule CH4NVT
moveMolecule DHS_NVT
moveMolecule DLJ_NVT_1site
moveMolecule DHS_NVT
moveMolecule DLJ_NVT_1site
moveMolecule TIP4P_NVT
moveMoleculeAction BiasVolume2SiteAceticAcid
moveMoleculeAction BiasVolumeAceticAcid
moveMoleculeAction MCMoveBiasUBMolecule
moveMoleculeAction MCMoveVolumeAssociatedMolecule
moveMoleculeAction MCMoveMolecule
moveMoleculeAction MCMoveMoleculeCoupledInitPert
moveMoleculeAction MCMoveMoleculeCoupledSuperBox
moveMoleculeAction MCMoveMoleculeCoupled
moveto Token
moveTo(Vector) Plane
Shifts the plane at fixed orientation so that it contains the given point.
moveTracker MCMove
moveWallAction SamGraphic
Mpi1ACell etomica.nbr.cell.molecule
Generates pairs that are cell-based neighbors of a specific Molecule.
Mpi1ACell(int, double, BoxAgentManager) Mpi1ACell
Constructor makes iterator that must have box specified and then be
reset() before iteration.
MpiAACell etomica.nbr.cell.molecule
Returns iterates formed from all cell-based neighbor pairs.
MpiAACell(int, double, Box) MpiAACell
Constructor makes iterator that must have box specified and then be
reset() before iteration.
MpiInnerFixed etomica.molecule.iterator
Pair iterator synthesized from two atom iterators, such that the inner-loop
iteration is independent of the outer-loop atom.
MpiInnerFixed(MoleculeIterator, MoleculeIterator, boolean) MpiInnerFixed
Construct a pair iterator using the given atom iterators, indicating
whether the atoms ordering in the AtomPair should be swapped from the
default behavior.
MpiInnerVariable etomica.molecule.iterator
Pair iterator synthesized from two atom iterators, such that the inner-loop
iteration depends on the outer-loop atom.
MpiInnerVariable(MoleculeIterator, MoleculeIteratorMoleculeDependent, boolean) MpiInnerVariable
Construct a pair iterator using the given atom iterators, indicating
whether the atoms ordering in the AtomPair should be swapped from the
default behavior.
MpiInterArrayList etomica.molecule.iterator
Returns all pairs formed from two different untabbed lists of molecules.
MpiInterArrayList() MpiInterArrayList
Construct iterator with an empty lists.
MpiInterArrayList(IMoleculeList, IMoleculeList) MpiInterArrayList
Constructs iterator to return pairs from the given lists.
MpiInterspecies1A etomica.molecule.iterator
Gives pairs formed from the molecules of two different species in a box,
taking one molecule of one species with all molecules of the other.
MpiInterspecies1A(ISpecies[]) MpiInterspecies1A
Sorts given array of species according to species index, then constructs iterator
such that atom0 of the pair iterates is in (sorted) species[0], and atom1 is in
(sorted) species[1], regardless of which is specified via setTarget.
MpiInterspeciesAA etomica.molecule.iterator
Gives pairs formed from the molecules of two different species in a box.
MpiInterspeciesAA(ISpecies[]) MpiInterspeciesAA
Constructs iterator that provides iterates taken from the molecules of
two species.
MpiIntraArrayList etomica.molecule.iterator
Returns all pairs formed from a single list of molecules.
MpiIntraArrayList() MpiIntraArrayList
Construct iterator with an empty list.
MpiIntraArrayList(IMoleculeList) MpiIntraArrayList
Constructs iterator to return pairs from the given list.
MpiIntraspecies1A etomica.molecule.iterator
Gives pairs formed from the molecules of a species in a box, taking one
molecule the species with all of its other molecules.
MpiIntraspecies1A(ISpecies) MpiIntraspecies1A
MpiIntraspecies1A(ISpecies, MoleculeToMoleculeListSpecies) MpiIntraspecies1A
MpiIntraspeciesAA etomica.molecule.iterator
Gives pairs formed from the molecules of a single species in a box.
MpiIntraspeciesAA(ISpecies) MpiIntraspeciesAA
MpiMolecule etomica.molecule.iterator
Adapater class that wraps three atomPair iterators, one suitable for
iterating over all molecule pairs in a box (AA), another suitable for
iterating over all molecule pairs formed with a target molecule (1A), and the
third suitable for iterating over a single molecule pair (11).
MpiMolecule(MoleculesetIteratorPDT, MoleculesetIteratorBoxDependent) MpiMolecule
Constructs iterator by wrapping three others.
mReeHooverFactor ClusterDiagram
MSD ConfigurationStorage.StorageType
msd2Sum DataSourceMSD
msd2Sum DataSourceMSDcorP
msdCalc(MeterMeanSquareDisplacement) IntegratorKMCCluster
MSDCoordWriter etomica.zeolite
MSDCoordWriter(Integrator, Box, String, int) MSDCoordWriter
MSDCoordWriter.AfterPBC etomica.zeolite
MSDProcessor etomica.zeolite
MSDProcessor(Space, String, String) MSDProcessor
msdSinks DataSourceMSD
msdSum DataSourceAlpha2
msdSum DataSourceMSD
msdSum DataSourceMSDcorP
msdSumBlock DataSourceMSD
mspMinus PYGenerator.IteratorEF
mspPlus PYGenerator.IteratorEF
mSquare DLJ_NVT_1site.Param
mSquare TIP4P_NVT.Param
mSquare Heisenberg.Param
mSquare Heisenberg3Pair.Param
mSquare HeisenbergPair.Param
mt RandomMersenneTwister
mti RandomMersenneTwister
mu MCMoveInsertDelete
mu LJmuVT.LJMCParams
mu PNCO2GCPM
mu PNGCPM
mu SimHSMDVacancy.HSMDVParams
mu SimLJVacancy.LJParams
mu PotentialCalculationFSum
mu MeterMappedAveraging
mu MeterMappedAveraging3Pair
mu MeterMappedAveragingFreeEnergy
mu MeterMappedAveragingPair
mu MeterMappedAveragingPairExcess
mu MeterMappedAveragingSum
mu MeterMappedAveragingVSum
mu MeterMappedAveragingVSum3Pair
mu MeterMappedAveragingVSumPair
mu MeterPairSum
mu PotentialCalculationFreeEnergy
mu PotentialCalculationFSum
mu PotentialCalculationHeisenberg
mu PotentialCalculationMoleculeAgentSum
mu PotentialCalculationMoleculeAgentSumMinusIdeal
mu PotentialCalculationMoleculeAgentSumMinusIdealPair
mu PotentialCalculationMoleculeAgentSumPair
mu PotentialCalculationPair
mu PotentialCalculationSumquare
mu PotentialCalculationVSum
mu HardSphereSolid.EOSParams
mu(double) EOSSW
mu(double) EOSSWPatel
mu(double) VEOS3SW
Mu etomica.modules.mu
Mu(Space) Mu
mu0 LJmuVT.LJMCParams
Mu1Modulator() IntegratorDCVGCMD.Mu1Modulator
mu2 VirialB3C1HSDipole.VirialParam
mu2 VirialB3C2HSDipole.VirialParam
Mu2Modulator() IntegratorDCVGCMD.Mu2Modulator
MuDeltaEBond(Space, P2WaterTIP4PHardCore, VirialB2WaterTIP4P_DHS_difference.P2WaterDHS) VirialB2WaterTIP4P_DHS_difference.MuDeltaEBond
MuFBond(Space, P2WaterTIP4PHardCore) VirialB3C1TIP4Pwater.MuFBond
MuFGeneral etomica.virial
MuFGeneral(double, IPotentialMolecular) MuFGeneral
muForPressure(double) EOSSW
muForPressure(double) EOSSWPatel
muForPressure(double) VEOS3SW
MuGeneral etomica.virial
MuGeneral(double, IPotentialMolecular) MuGeneral
MuGraphic etomica.modules.mu
MuGraphic(Mu, Space) MuGraphic
MuGraphic.Applet etomica.modules.mu
MuGraphic.DataProcessorMu etomica.modules.mu
MuGraphic.DataSinkExcludeOverlap etomica.modules.mu
MuGraphic.ModifierAtomDiameter etomica.modules.mu
MuGraphic.ModifierEpsilon etomica.modules.mu
MuGraphic.ModifierLambda etomica.modules.mu
muHistory MuGraphic.DataProcessorMu
mul(float) Matrix4f
Multiplies each element of this matrix by a scalar.
mul(float) Quaternion
mul(Matrix3f) Matrix3f
Sets the value of this matrix to the result of multiplying itself with
matrix m1.
mul(Matrix4f) Matrix4f
Sets the value of this matrix to the result of multiplying itself with
matrix m1.
Mul etomica.graph.operations
Mul() Mul
Mul(double[], double[]) CalcFFT
Mul.MulParameters etomica.graph.operations
mul2(Matrix3f, Matrix3f) Matrix3f
Sets the value of this matrix to the result of multiplying the two argument
matrices together.
mul2(Matrix4f, Matrix4f) Matrix4f
Sets the value of this matrix to the result of multiplying the two argument
matrices together.
mulf(float) Matrix3f
Multiplies each element of this matrix by a scalar.
mulFlex BiComponentSubst
mulFlex ComponentSubst
mulFlex Unfactor
MulFlexible etomica.graph.operations
Perform graph multiplication for flexible molecules.
MulFlexible() MulFlexible
MulFlexible.MulFlexibleParameters etomica.graph.operations
MulFlexibleParameters(char[], byte, byte, byte, boolean) MulFlexible.MulFlexibleParameters
mulParameters() ConvParameters
MulParameters(byte) Mul.MulParameters
mulQ(Quaternion) Quaternion
mulScalar BiComponentSubst
mulScalar ComponentSubst
mulScalar PYGenerator.IteratorEF
MulScalar etomica.graph.operations
Multiply graphs by a scalar (coefficient)
MulScalar() MulScalar
MulScalarParameters etomica.graph.operations
MulScalarParameters(int, int) MulScalarParameters
MulScalarParameters(Coefficient) MulScalarParameters
multGcdLcm(Ifactor, int) Ifactor
Multiply with another positive integer.
MultiBDcount ClusterWheatleyMultibodyDerivatives
multibody MayerIonicDiagram1qbond
multibody MayerIonicDiagram2qbonds
multibody MayerIonicDiagram4qbonds
multibody VirialDiagrams
multibody VirialDiagramsMix
multibody VirialDiagramsPT
multibody WertheimDiagrams2SiteRho
multibody WertheimDiagrams3SiteRho
MULTIBOND_ALWAYS JmolConstants
MULTIBOND_NEVER JmolConstants
MULTIBOND_NOTSMALL JmolConstants
MULTIBOND_WIREFRAME JmolConstants
multiBonds ClusterBondsNonAdditive
Multiharmonic etomica.modules.multiharmonic
TODO To change the template for this generated type comment go to
Window - Preferences - Java - Code Style - Code Templates
Multiharmonic() Multiharmonic
MultiharmonicGraphic etomica.modules.multiharmonic
MultiharmonicGraphic(Multiharmonic, Space) MultiharmonicGraphic
MultiharmonicGraphic.Applet etomica.modules.multiharmonic
MultiharmonicGraphicMC etomica.modules.multiharmonic.mbar
MultiharmonicGraphicMC etomica.modules.multiharmonic
MultiharmonicGraphicMC etomica.modules.multiharmonic.overlap
MultiharmonicGraphicMC etomica.modules.multiharmonic.umbrella
MultiharmonicGraphicMC(MultiharmonicMC, Space) MultiharmonicGraphicMC
MultiharmonicGraphicMC(MultiharmonicMC, Space) MultiharmonicGraphicMC
MultiharmonicGraphicMC(MultiharmonicMC, Space) MultiharmonicGraphicMC
MultiharmonicGraphicMC(MultiharmonicMC, Space) MultiharmonicGraphicMC
MultiharmonicGraphicMC.Applet etomica.modules.multiharmonic.mbar
MultiharmonicGraphicMC.Applet etomica.modules.multiharmonic
MultiharmonicGraphicMC.Applet etomica.modules.multiharmonic.overlap
MultiharmonicGraphicMC.Applet etomica.modules.multiharmonic.umbrella
MultiharmonicGraphicMC.DataProcessAHT etomica.modules.multiharmonic.overlap
MultiharmonicGraphicMC.DataSinkReweightedDeltaU etomica.modules.multiharmonic.overlap
MultiharmonicGraphicMC.DataSourceAlphaAlpha etomica.modules.multiharmonic.overlap
MultiharmonicGraphicMC.DataSourceAlphaAlpha etomica.modules.multiharmonic.umbrella
MultiharmonicGraphicMC.DataSourceAlphaChi etomica.modules.multiharmonic.mbar
MultiharmonicGraphicMC.DataSourceAlphaChi etomica.modules.multiharmonic.overlap
MultiharmonicGraphicMC.DataSourceAlphaChi etomica.modules.multiharmonic.umbrella
MultiharmonicGraphicMC.DataSourceAlphaFE etomica.modules.multiharmonic.overlap
MultiharmonicGraphicMC.DataSourceBias etomica.modules.multiharmonic.overlap
MultiharmonicGraphicMC.DataSourceChiSlope etomica.modules.multiharmonic.overlap
MultiharmonicGraphicMC.DataSourceFE etomica.modules.multiharmonic.mbar
MultiharmonicGraphicMC.DataSourceFunctionRaw etomica.modules.multiharmonic.overlap
MultiharmonicGraphicMC.DataSourceUa etomica.modules.multiharmonic.overlap
MultiharmonicGraphicMC.DataSourceUa2 etomica.modules.multiharmonic.overlap
MultiharmonicMC etomica.modules.multiharmonic.mbar
MC version of multi-harmonic simulation.
MultiharmonicMC etomica.modules.multiharmonic
MC version of multi-harmonic simulation.
MultiharmonicMC etomica.modules.multiharmonic.overlap
MC version of multi-harmonic simulation.
MultiharmonicMC etomica.modules.multiharmonic.umbrella
MC version of multi-harmonic simulation.
MultiharmonicMC() MultiharmonicMC
MultiharmonicMC() MultiharmonicMC
MultiharmonicMC() MultiharmonicMC
MultiharmonicMC() MultiharmonicMC
multiP VirialDiagramsMix
multiplebondradiusfactor Token
multiplebondspacing Token
multiply(int) BigSurd
Multiply by an integer.
multiply(int) Ifactor
Multiply with another positive integer.
multiply(int) Rational
Multiply by an integer.
multiply(Coefficient) Coefficient
multiply(Coefficient) CoefficientImpl
multiply(BigIntegerPoly) BigIntegerPoly
Multiply by another polynomial
multiply(BigSurd) BigSurd
Multiply by another square root.
multiply(BigSurd) BigSurdVec
Multiply by another square root.
multiply(Ifactor) Ifactor
Multiply with another positive integer.
multiply(Rational) BigSurd
Multiply by a rational number.
multiply(Rational) Rational
Multiply by another fraction.
multiply(BigInteger) BigIntegerPoly
Multiply by a constant factor.
multiply(BigInteger) BigSurd
Multiply by a BigInteger.
multiply(BigInteger) Ifactor
Multiply with another positive integer.
multiply(BigInteger) Rational
Multiply by a BigInteger.
Multiply(Set<Graph>, Set<Graph>) IEGenerator
multiplyRound(BigComplex, BigComplex) BigDecimalMath
Multiply and round.
multiplyRound(BigComplex, BigDecimal) BigDecimalMath
Multiply and round.
multiplyRound(BigDecimal, int) BigDecimalMath
Multiply and round.
multiplyRound(BigDecimal, Rational) BigDecimalMath
Multiply and round.
multiplyRound(BigDecimal, BigDecimal) BigDecimalMath
Multiply and round.
multiplyRound(BigDecimal, BigInteger) BigDecimalMath
Multiply and round.
multiprocessor Token
multiTol ClusterWheatleyMultibody
multiTol ClusterWheatleyMultibodyDerivatives
MulUnion etomica.graph.operations
This operation multiplies two graphs (or each pair of graphs from two sets)
by superimposing all points (with the idea that all nodes are
distinguishable).
MulUnion() MulUnion
mUnit PistonCylinderGraphic
mUnit SwmdGraphic
MuProduct(P2WaterTIP4PHardCore) VirialB3C2TIP4Pwater.MuProduct
muProfileMeter InterfacialSWGraphic
Mv1Squared(Vector) Vector
Returns square of vector resulting from subtracting given vector
from this one.
Mv1Squared(Vector) Vector1D
Mv1Squared(Vector) Vector2D
Mv1Squared(Vector) Vector3D
Mv1Squared(Vector) VectorND
mxcBond VirialDiagrams
mxcBond VirialDiagramsPT
MxcBond VirialDiagrams
MxcBond VirialDiagramsPT
mxter P2O2Bartolomei
myAcceptNotify() MCMoveInsertDeleteBiased
myAcceptNotify() MCMoveInsertDeleteLatticeVacancy
myAcceptNotify() MCMoveInsertDeleteVacancy
MyAgent(double[], Vector[], double[], Vector[]) P3Induction.MyAgent
MyAgent(double, double) P3AxilrodTeller.MyAgent
MyAgent(Space) IntegratorDroplet.MyAgent
MyAgent(Space) HSNPT.MyAgent
MyApplet etomica.modules.clustergenerator
MyApplet() MyApplet
MyApplet.BondInteractionTypeToggler etomica.modules.clustergenerator
Options for type of bond-interaction (e-bonds, f-bonds, etc)
MyApplet.BondTypeToggler etomica.modules.clustergenerator
Options for type of bond array
MyApplet.ComponentEventMyPanel etomica.modules.clustergenerator
This class is to be notified to graphicOut2 when the window of applet is resized
MyApplet.ConnectedToggler etomica.modules.clustergenerator
MyApplet.GraphicsToggler etomica.modules.clustergenerator
MyApplet.MouseEventClusterPanel etomica.modules.clustergenerator
This class is for showing bonds of selected cluster in GraphicPanel
MyApplet.NumbersToggler etomica.modules.clustergenerator
Options for showing index of particle or not
MyApplet.PointsToggler etomica.modules.clustergenerator
Option of showing particles or not
MyApplet.ReeHooverToggler etomica.modules.clustergenerator
Options for type of bond-interaction (e-bonds, f-bonds, etc)
MyApplet.Starter etomica.modules.clustergenerator
MyApplet.Stopper etomica.modules.clustergenerator
myAtom MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbr
myAtom MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbrCell
myAtoms MCMoveClusterRingPartialRegrow
myAtoms MCMoveClusterRingRegrow
myAtoms MCMoveClusterRingRegrowExchange
myAtoms MCMoveClusterRingScale
MyBigDecimal etomica.veos
Data class to handle operations involving large numbers.
MyBigDecimal() MyBigDecimal
Default constructor sets value to 0.0
MyBigDecimal(double) MyBigDecimal
Constructs using the given value.
MyBigDecimal(IBigValue) MyBigDecimal
Copy constructor.
MyBigDecimal(BigDecimal) MyBigDecimal
myCharge ChargeAgentSourceTIP4PWater
MyCharge(double) EwaldSummation.MyCharge
MyCharge(double) EwaldSumMolecules.MyCharge
myData MuGraphic.DataSinkExcludeOverlap
myData NucleationGraphic.DataSinkExcludeOverlap
myData ReverseOsmosisGraphic.DataSinkExcludeOverlap
myData ReverseOsmosisWaterGraphic.DataSinkExcludeOverlap
myData SwmdGraphic.DataSinkExcludeOverlap
MyData() MeterVirialBDBinMultiThreaded.MyData
MyData() MeterVirialBinMultiThreaded.MyData
MyData(int) MeterVirialEBinMultiThreaded.MyData
MyDataCov(int) MeterVirialEBinMultiThreaded.MyDataCov
mydt CorrelationSelf2.MeterCorrelationSelf2
MyEigenvalueDecomposition etomica.eigenstuff
Eigenvalues and eigenvectors of a real matrix.
MyEigenvalueDecomposition(int, double[][]) MyEigenvalueDecomposition
Check for symmetry, then construct the eigenvalue decomposition
myEllipse3D Ellipse
MyForceTorque(Space) ActionMinimizeEnergy.MyForceTorque
MyFunctionInvertible(double) StatisticsMCGraphic.MyFunctionInvertible
myIds VirialDiagrams
myImage Grabber.ImagePanel
myLat ConfigurationLattice
MyLattice(SpaceLattice, Vector, Vector) ConfigurationLattice.MyLattice
myListener Grabber.ActionCornerSetter
MyMCMove etomica.dcvgcmd
MyMCMove etomica.modules.adsorption
MyMCMove etomica.modules.dcvgcmd
MyMCMove(IntegratorBox, IRandom, Space, double) MyMCMove
MyMCMove(IntegratorBox, IRandom, Space, double) MyMCMove
MyMCMove(IntegratorBox, IRandom, Space, double, double, int) MyMCMove
myMoleculeIndices MayerFunctionThreeBody
myPanel MyApplet
myRejectNotify() MCMoveInsertDeleteBiased
myRq PNWaterGCPMReactionField
myRqFactor PNWaterGCPMReactionField
mySeeds VirialHSBinMultiThreaded.SimulationWorker
mySeeds VirialSQWBinMultiThreaded.SimulationWorker
MySpeciesEditor(SpeciesGeneral, String) ReactionEquilibriumGraphic.MySpeciesEditor
mysum HSNPT.ColorSchemeDisplacement
MyTypeAgent(OrientationCalcQuaternion) IntegratorVelocityVerletQuaternion.MyTypeAgent
MyWall() Osmosis.MyWall
N
n PotentialEAM_LS
n PotentialEAM
n DecorateWertheim2Site.DecorateWertheimParameters2Site
n FactorialBenchmark
n LnFactorialBenchmark
n PadeApproximation.VirialParam
n NormalModeAnalysisDisplay3D
n P4TorsionDreiding
n Ifactor
The standard representation of the number
n BnPCJSDHe.BnPCJSDHeParams
n BnPYCHe.BnPYHeParams
n MayerIonicDiagram1qbond
n MayerIonicDiagram2qbonds
n MayerIonicDiagram4qbonds
n VirialDiagrams
n VirialDiagramsMix
n VirialDiagramsMix2
n VirialDiagramsPT
n WertheimDiagrams2SiteRho
n WertheimDiagrams3SiteRho
n ClusterChainHS
n ClusterChainSoft
n ClusterSinglyConnected
n ClusterSumHS
n ClusterWheatleyExtendSW
n ClusterWheatleyHS
n ClusterWheatleyMultibodyDerivatives.ClusterRetrievePrimes
n ClusterWheatleyMultibodyDerivativesBD.ClusterRetrievePrimes
n ClusterWheatleyPartitionScreening
n ClusterWheatleyPT.ClusterRetrievePrimesBD
n ClusterWheatleyPT
n ClusterWheatleySoft
n ClusterWheatleySoftBD
n ClusterWheatleySoftDerivatives.ClusterRetrievePrimes
n ClusterWheatleySoftDerivatives.ClusterRetrievePrimesBD
n ClusterWheatleySoftDerivatives
n ClusterWheatleySoftDerivativesBD.ClusterRetrievePrimes
n ClusterWheatleySoftDerivativesBD
n MeterVirialEBinMultiThreaded.MyData
n MeterVirialEBinMultiThreaded
n MeterVirialSWWE
n ReeHooverMC.VirialParam
N IntegratorDimerMin
N IntegratorDimerRT
N FittingFunctionNonLinear
N P3HydrogenManzhos
N MeterMappedAveragingCorrelation
N MeterMappedAveragingCV
N MeterMappedAveragingVSum
N RandomMersenneTwister
N CalcFFT
N_BASE Dimension
Number of base dimensions, equal to seven.
n_max P2HydrogenPatkowski
n_max P2HydrogenPatkowskiAtomic
n_min P2HydrogenPatkowski
n_min P2HydrogenPatkowskiAtomic
n0 P2HydrogenHinde
n0 P2HydrogenHindeAtomic
n0 P2HydrogenHindePatkowski
n0 P2HydrogenHindePatkowskiAtomic
n0 P2HydrogenPatkowski
n0 P2HydrogenPatkowskiAtomic
N0_AD P2HePCJS
N0_BO P2HePCJS
N0_QED P2HePCJS
N0_REL P2HePCJS
n1 AbstractSearchState
n1 P2HydrogenHinde
n1 P2HydrogenHindeAtomic
n1 P2HydrogenHindePatkowski
n1 P2HydrogenHindePatkowskiAtomic
n1 P2HydrogenPatkowski
n1 P2HydrogenPatkowskiAtomic
N1 IntegratorDimerRT
N1_AD P2HePCJS
N1_BO P2HePCJS
N1_QED P2HePCJS
N1_REL P2HePCJS
n2 P2EAM
n2 AbstractSearchState
nA MCMoveMoleculeCoupledSuperBox
nA MCMoveRotateMolecule3DSuperBox
nA SimGlass.GlassParams
nA SelfAssemblySim
nA NormalModes1DHR
Na P2QChemInterpolated
naamax P2WaterPotentialsJankowski
nAccBlocks LjMC3D.LjMC3DParams
nAccBlocks LjMd3D.LjMd3DParams
nAccBlocks LjMd3Dv2y.LjMd3DParams
nAccept MCMoveTracker
nAccepted IntegratorMD
nAccepted AkimaSplineSmoother
nada Token
NADA EnumVdw
nAlpha MeterMBAR
name Feature
name MeterHarmonicSingleEnergy
nameOf(int) Token
note: nameOf is a very inefficient mechanism for getting
the name of a token.
nand(Bitmap) Bitmap
Updates this bitmap with the result of the bitwise AND with the other bitmap: bitmap
= ~(bitmap & other).
nand(Bitmap) AbstractBitmap
nand(Bitmap) BitmapOfLong
TIME = O(1) for a compatible instance.
nand(Bitmap) BitmapOfLongVector
NANO Prefix
nAtoms MCMoveVolumeAssociated.Agent
nAtoms HSMDCavity.CavityParam
nAtoms HSMDWidom.HSMDParam
nAtoms MeterProfileByAtoms
nAtoms HSMD3D.HSMD3DParam
Number of atoms, default = 256
nAtomTypes PNGCPM
nAttempt AkimaSplineSmoother
nAttempted IntegratorMDHarmonicMC
nAttempts MCMoveAtomInRegion
navfps Token
navigate Token
navigatesurface Token
navigationdepth Token
navigationmode Token
navigationperiodic Token
navigationslab Token
navigationspeed Token
navx Token
navy Token
NAVY Colix
navz Token
nB SimGlass.GlassParams
nB SelfAssemblySim
nB1 SelfAssemblySim
nB2 SelfAssemblySim
nBasis ClathrateHarmonicFE.SimParams
nBasis MinimizationTIP4P.SimParams
nBasis ProtonDisorderGenerator.SimParams
nBasis MeterSolidPropsLJ
nbbmax P2WaterPotentialsJankowski
nBeads ModifierTPI
nBeads VirialCO2PI.VirialH2PIParam
nBeads VirialH2PI.VirialH2PIParam
nBeads VirialH2PISimple.VirialH2PISimpleParam
nBeads VirialHePI_PotentialCorrection.VirialHePIParam
nBeads VirialHePI.VirialHePIParam
nBeads VirialHePISysErr.VirialHePIParam
nBeads VirialHePIXCEven.VirialHePIParam
nBeads VirialHePIXCOdd.VirialHePIParam
nBeads VirialN2PI.VirialN2Param
nBeads VirialO2PI.VirialO2Param
nbin P2O2Bartolomei
nbins PotentialCalculationMappedRdf
nbins PotentialCalculationMappedEnergy
nbins PotentialCalculationMappedVirial
nbins PotentialCalculationMappedVirialV
nBins HSMDCavity.CavityParam
nBins HistogramNotSoSimple
nBins HistogramReweightedData
nBins HistogramSimple
nBins DataSourceTensorVirialHardProfile
nBinsRDF PolydisperseHS.HSPolyParam
nBlocks SimMappedRdf.LJMDParams
nBlocks MappedU.LJMDParams
nBlocks MappedVirialLJ.LJMDParams
nBlocks MappedVirialLJVGr.LJMDParams
nBlocks AccumulatorAutocorrelationPTensor
nBlocks AccumulatorAutocorrelationShearStress
nBlocks AshtonWildingLJ.simParams
nBlocks AshtonWildingOsmoticVirial.simParams
nBlocks AshtonWildingVirial.simParams
nBlocks GCWidomInsertHS.simParams
nBlocks NVTWidomInsertLJ.simParams
nBlockSamplesX AccumulatorPTensor
nBlockSamplesX DataSourceHisogram
nBlockSamplesX DataSourceMSDcorP
nBlockSamplesX DataSourcePMSDHistory
nBody Wertheim2SiteAceticAcid.WertheimParam
nBody WertheimGCPM4PtThreeSite.VirialAssociatingFluidParam
nBody ANIntergroupCoupled
nBody ANIntragroupExchange
nBody MyApplet
nBody PotentialMolecular
nBody PotentialCommonAtomic
nBody PotentialNonAdditive
nBody VirialAceticAcid.VirialParam
nBody VirialAceticAcidFlex.VirialParam
nBody() ANIntergroupCoupled
nBody() ANIntergroupExchange
nBody() ANIntragroupExchange
nBody() ApiIndexList
Returns 2, indicating that this is a pair iterator.
nBody() ApiInnerVariable
nBody() ApiInterArrayList
Returns 2, indicating that this is a pair iterator
nBody() ApiIntergroup
nBody() ApiIntraArrayList
Returns 2, indicating that this is a pair iterator
nBody() ApiIntragroup
nBody() AtomIteratorArrayListAdjacent
Returns 1, indicating that this is an atom AtomSet iterator.
nBody() AtomIteratorArrayListSimple
Returns 1, indicating that this is an atom iterator.
nBody() AtomIteratorNull
nBody() AtomIteratorSinglet
nBody() Atomset3IteratorIndexList
Returns 3, indicating that this is a set of three iterator.
nBody() Atomset4IteratorIndexList
Returns 4, indicating that this is a set of four iterator.
nBody() AtomsetIterator
Returns the number of atoms given in each iterate, i.e., the
size of the atom array returned with each call to next().
nBody() AtomsetIteratorAllLeafAtoms
nBody() MCMoveInsertDeleteLatticeVacancy.AtomIteratorBruteForce
nBody() MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbr
nBody() MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbrCell
nBody() P2CO2H2OWheatley
nBody() P2CO2H2OWheatley.P2CO2H2OSC
nBody() P2CO2H2OWheatley.P2CO2H2OSCTI
nBody() P2CO2Hellmann
nBody() P2CO2Hellmann.P2CO2SC
nBody() PNCO2GCPM.P3GCPMAxilrodTeller
nBody() PNGCPM.P3GCPMAxilrodTeller
nBody() PNGCPM.PNGCPMCached
nBody() P2WaterSzalewicz
nBody() P2WaterSzalewicz.P2H2OSC
nBody() PNWaterGCPM.PNWaterGCPMCached
nBody() P1Wall
nBody() P1Wall
nBody() P1Smash
nBody() P1Tension
nBody() P1Sinusoidal
nBody() MoleculeIteratorAll
nBody() MoleculeIteratorArrayListSimple
Returns 1, indicating that this is an atom iterator.
nBody() MoleculeIteratorSinglet
nBody() MpiInnerFixed
nBody() MpiInnerVariable
nBody() MpiInterArrayList
Returns 2, indicating that this is a pair iterator
nBody() MpiInterspecies1A
nBody() MpiInterspeciesAA
Returns 2, indicating that this is a pair iterator
nBody() MpiIntraArrayList
Returns 2, indicating that this is a pair iterator
nBody() MpiIntraspecies1A
nBody() MpiIntraspeciesAA
Returns 2, indicating that this is a pair iterator
nBody() MpiMolecule
Returns 2, indicating that this is a pair iterator.
nBody() Api1ACell
Returns 2, indicating that this is a pair iterator.
nBody() Mpi1ACell
Returns 2, indicating that this is a pair iterator.
nBody() MpiAACell
Returns 2, indicating that this is a pair iterator.
nBody() Api1ASite
Returns 2, indicating that this is a pair iterator.
nBody() P1ConstraintNbr
nBody() P1ConstraintNbrHcp
nBody() EwaldSummation
nBody() EwaldSummation.P2EwaldReal
nBody() EwaldSumMolecules
nBody() IPotential
The number of atoms on which the potential depends.
nBody() P1HardBoundary
nBody() P1HydrogenMielke
nBody() P1HydrogenMielke.P2HydrogenMielkeAtomic
nBody() P2DiscreteFeynmanHibbs
nBody() P2EffectiveFeynmanHibbs
nBody() P2HardWrapper
nBody() P2HePCKLJS.P2HeQFH
nBody() P2HePCKLJS.P2HeTI
nBody() P2HeSimplified.P2HeQFH
nBody() P2HeSimplified.P2HeTI
nBody() P2HydrogenHinde
nBody() P2HydrogenHindeAtomic
nBody() P2HydrogenHindePatkowski
nBody() P2HydrogenHindePatkowskiAtomic
nBody() P2HydrogenPatkowski
nBody() P2HydrogenPatkowskiAtomic
nBody() P2MoleculeMonatomic
nBody() P2NitrogenHellmann
nBody() P2NitrogenHellmann.P2N2QFH
nBody() P2O2Bartolomei
nBody() P2O2Bartolomei.P2O2TI
nBody() P2SemiclassicalAtomic
nBody() P2SemiclassicalMolecular
nBody() P2WaterPotentialsJankowski
nBody() P2WCAP
nBody() P3AxilrodTeller
nBody() P3HydrogenATM
nBody() P3HydrogenManzhos
nBody() P3Induction
nBody() P3NitrogenHellmannNonAdditive
nBody() Potential
The number of atoms on which the potential depends.
nBody() PotentialAtomicSum
nBody() PotentialMaster.AtomIterator0
nBody() PotentialMaster.MoleculeIterator0
nBody() PotentialMolecular
The number of atoms on which the potential depends.
nBody() PotentialMolecularSum
nBody() P1IntraLambda
nBody() PotentialCommonAtomic
nBody() PotentialGroup3PI.PotentialGroup3PISkip
nBody() PotentialGroupPI.PotentialGroupPISkip
nBody() PotentialNonAdditive
nBody() PotentialNonAdditive.PotentialNonAdditiveNB
nBodyField MyApplet
nBodyPretend PotentialNonAdditive.PotentialNonAdditiveNB
nbrCsum MeterEnergyMeanField
nbrCsum MeterEnergyMeanField.PotentialCalculationCSsum
nbrCsum MeterMappedAveragingCorrelation
nbrCsum MeterMappedAveragingVSum
nbrDistance MCMoveAtomSwap
nbrDistance MCMoveInsertDeleteLatticeVacancy
nbrDistance DataClusterer
nbrList MCMoveAtomSwap
nbrList AtomNbrClusterer
nbrMax2 AtomNbrClusterer
nbrMax2 DataSourceStrings
nbrs MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbr
nbrs MeterMappedAveragingCV
nbrSsum MeterEnergyMeanField
nbrSsum MeterEnergyMeanField.PotentialCalculationCSsum
nbrSsum MeterMappedAveragingCorrelation
nbrSsum MeterMappedAveragingVSum
nbrVectors MCMoveInsertDeleteLatticeVacancy
nC ClathrateHarmonicFE.SimParams
nC MinimizationTIP4P.SimParams
nC ProtonDisorderGenerator.SimParams
nC MinimizeBetaNitrogenLatticeParameter
nC MinimizeBetaNitrogenLatticeParameterFromFile
nC MinimizeBetaNitrogenLatticeParameterLSFromFile
nC MinimizeBetaNitrogenTranslationDOF
nC SimOverlapAlphaN2TP.SimOverlapParam
nC HSDimerNPT.HSMD3DParameters
nC NormalModesMolecular
nC PolydisperseHS.HSPolyParam
nC ClusterChainHS
nC ClusterChainSoft
nCell FindPairMoleculeIndex
nCell FindPairMoleculeIndexBetaN2
nCell MinimizeGammaNitrogenLatticeParameter
nCell SimOverlapNitrogenModel
nCellNum NormalModes3D
nCells SimOverlapBetaN2RP
nCells HessianDB
nCells LJVacancyMin
nCells MeterSolidPropsLJ
nCells NormalModeAnalysisDisplay1D
nCells NormalModeAnalysisDisplay2D
nCells NormalModeAnalysisDisplay3D
nCells SimBennet
nCells SimCalcSLJ
nCells SimCalcSMorse
nCells SimCalcSSoftSphere2D
nCells SimCalcSSoftSphereFCC
nCells SimCalcSSoftSphereFCCSuperBox
nCells SimEinStep1
nCells SimEinStep1HCP
nCells SimEinStep2
nCells SimEinStep2HCP
nCells SimHarmonic
nCells SimHarmonicUmbrella
nCells SimLJHTTISuper
nCells SimLJHTTISuperHCP
nCells SimLJHTTISuperHCP2
nCells SimLJHTTISuperSFMD
nCells SimOverlap
nCells SimOverlapLJ
nCells SimOverlapLJModule
nCells SimOverlapSoftSphere
nCells SimOverlapSoftSphereDP
nCells SimOverlapSoftSphereEin
nCells SimOverlapSoftSphereEinHarm
nCells SimOverlapSoftSphereHCP
nCells SimOverlapSoftSphereReweighting
nCells SimOverlapSoftSphereSoftness
nCells SimOverlapSoftSphereSuperBox
nCells SimOverlapSoftSphereTP
nCells SimOverlapSoftSphereTPHCP
nCells SimOverlapSoftSphereTPSlantedBox
nCells SimOverlapSSnxy
nCells SimTargetUmbrella
nCells SimUmbrella
nCells SimUmbrellaSoftSphere
nCells Heisenberg.Param
nCellsX ConfigurationCatalysis
nCellsX ConfigurationSAM
nCellsZ ConfigurationCatalysis
nCellsZ ConfigurationSAM
nCheck ClusterWheatleySoft
nCheck ClusterWheatleySoftDerivatives
nCheckTot ClusterWheatleySoftDerivatives
nci Token
nClusters ReadCluster.ReadClusterParams
nCO ConfigurationCatalysis
nColumns DisplayTable
nColumnsA MeterSolidPropsLJ
nComp1 VirialAlkaneMix2_Kong.VirialAlkaneMixParam
nComp1 VirialAlkaneMix2.VirialAlkaneMixParam
nComp2 VirialAlkaneMix2_Kong.VirialAlkaneMixParam
nComp2 VirialAlkaneMix2.VirialAlkaneMixParam
NCopy etomica.graph.operations
NCopy() NCopy
nCrossLinkersAcid ChainEquilibriumSim
nCutoffs DataProcessorReweight
nCutoffs DataProcessorReweightRatio
nData AccumulatorAverageBootstrap
nData AccumulatorAverageCollapsingLog
nData AccumulatorHistory
nData DataSinkBlockAveragerSFac
nData DataSourceCorrelation
nData MultiharmonicGraphicMC.DataSourceAlphaFE
nDataInfo AccumulatorAverageBootstrap
nDataInfo AccumulatorAverageCollapsingLog
nDataInfo MultiharmonicGraphicMC.DataSourceAlphaFE
nDataP DataClusterer
nDataP DataClusterWriter
nDataSource DataProcessorDyDLnx
NDelta IntegratorDimerMin
NDelta IntegratorDimerRT
nDer ClusterCoupledFlippedMultivalue
nDer ClusterWheatleyMultibodyDerivatives
nDer ClusterWheatleyMultibodyDerivativesBD
nDer ClusterWheatleySoftDerivatives
nDer ClusterWheatleySoftDerivativesBD
nDer VirialH2OGCPMD.VirialParam
nDer VirialHeD.VirialParam
nDer VirialHeNonAdditiveD.VirialParam
nDer VirialLJD.VirialLJParam
nDer VirialLJDU.VirialLJParam
nDer VirialTraPPE.VirialParam
nDiAcid ChainEquilibriumSim
nDimension() DimensionRatio
nDiol ChainEquilibriumSim
nEachIndices PermutationIterator
nEachIndicesCheck PermutationIterator
Near() MeterVirialExternalFieldSW.Near
nearestImage(Vector) BoundaryDeformablePeriodicSwitch
nearestImage(Vector) BoundaryRectangularPeriodicSwitch
nearestImage(Vector) Boundary
The nearest image is the pair of atom images that are closest when all
periodic-boundary images are considered.
nearestImage(Vector) BoundaryDeformablePeriodic
nearestImage(Vector) BoundaryRectangularNonperiodic
Does nothing.
nearestImage(Vector) BoundaryRectangularPeriodic
nearestImage(Vector) BoundaryRectangularPore
nearestImage(Vector) BoundaryRectangularSlit
nearestImage(Vector) Vector
nearestImage(Vector) Vector1D
nearestImage(Vector) Vector2D
nearestImage(Vector) BoundaryTruncatedOctahedron
nearestImage(Vector) Vector3D
nearestImage(Vector) VectorND
nearestImageOpt() BenchVector
nearestImageOriginal() BenchVector
needNeighborUpdate RectangularLatticeNbrIterator
needSetupIterators ANIntergroupCoupled
needSetupIterators ANIntergroupExchange
needSetupIterators ANIntragroupExchange
needSetupIterators ApiIntergroup
needUpdate EtomicaPlot
needUpdate(IAtom) ColloidSim.CriterionNone
needUpdate(IAtom) CriterionTether3
needUpdate(IAtom) CriterionAdapter
Indicates whether the neighbor list for the given atom should be updated,
according to the wrapped criterion.
needUpdate(IAtom) CriterionAll
Always returns false, indicating that neighbor list never needs updating.
needUpdate(IAtom) CriterionNone
Always returns false, indicating that neighbor list never needs updating.
needUpdate(IAtom) CriterionPositionWall
needUpdate(IAtom) CriterionSimple
needUpdate(IAtom) NeighborCriterion
Indicates whether the neighbor list for the given atom should
be updated, according to this criterion.
needUpdate(IMolecule) CriterionAdapterMolecular
Indicates whether the neighbor list for the given atom should be updated,
according to the wrapped criterion.
needUpdate(IMolecule) CriterionAllMolecular
Always returns false, indicating that neighbor list never needs updating.
needUpdate(IMolecule) CriterionSimpleMolecular
needUpdate(IMolecule) NeighborCriterionMolecular
Indicates whether the neighbor list for the given molecule should
be updated, according to this criterion.
Neff IntegratorDimerRT
negate() BigSurd
Compute the negative.
negate() BigSurdVec
Compute the negative.
negate() Rational
Compute the negative.
negate() Quaternion
negativeChop AccumulatorAverageBlockless
negativeChop AccumulatorAverageBlocklessSlim
negativeChop AccumulatorAverageFixed
negativeChop AccumulatorAverageFixedOutputFile
negativeExchange ExchangeSplit.ExchangeSplitParameters
neighborAtoms P1ConstraintNbr
neighborAtoms P1ConstraintNbrHcp
NeighborCellManager etomica.nbr.cell
Class that defines and manages construction and use of lattice of cells
for cell-based neighbor listing.
NeighborCellManager(Box, double) NeighborCellManager
Constructs manager for neighbor cells in the given box.
NeighborCellManager(Box, double, IMoleculePositionDefinition) NeighborCellManager
Construct manager for neighbor cells in the given box.
NeighborCellManagerListMolecular etomica.nbr.list.molecule
Subclass of NeighborCellManager that notifies the NeighborListManager when
an atom added to the box gets a cell.
NeighborCellManagerListMolecular(Simulation, Box, double, IMoleculePositionDefinition, Space) NeighborCellManagerListMolecular
NeighborCellManagerListMolecular(Simulation, Box, double, Space) NeighborCellManagerListMolecular
NeighborCellManagerMolecular etomica.nbr.cell.molecule
Class that defines and manages construction and use of lattice of cells
for cell-based neighbor listing.
NeighborCellManagerMolecular(Simulation, Box, double, IMoleculePositionDefinition, Space) NeighborCellManagerMolecular
Construct manager for neighbor cells in the given box.
NeighborCellManagerMolecular(Simulation, Box, double, Space) NeighborCellManagerMolecular
Constructs manager for neighbor cells in the given box.
neighborClusterDistance ReadCluster.ReadClusterParams
neighborCount RectangularLatticeNbrIterator
NeighborCriterion etomica.nbr
Atom filter used to specify whether two atoms are considered neighbors,
for the purpose of tabulating neighbor lists.
NeighborCriterionMolecular etomica.nbr.molecule
Atom filter used to specify whether two atoms are considered neighbors,
for the purpose of tabulating neighbor lists.
NeighborIterator etomica.nbr
NeighborIterator(int, double) CellLattice.NeighborIterator
NeighborIterator.AtomPairConsumer etomica.nbr
NeighborIteratorCell etomica.nbr.cell
NeighborIteratorCell(NeighborCellManager) NeighborIteratorCell
NeighborIteratorSite etomica.nbr.site
NeighborIteratorSite(NeighborSiteManager, Box) NeighborIteratorSite
neighborListAgentManager PotentialMasterListMolecular
neighborListAgentSource PotentialMasterListMolecular
NeighborListAgentSource etomica.nbr.list
NeighborListAgentSource(double) NeighborListAgentSource
NeighborListAgentSourceColloid(double) NeighborListManagerColloid.NeighborListAgentSourceColloid
NeighborListAgentSourceMolecular(double, Space) PotentialMasterListMolecular.NeighborListAgentSourceMolecular
NeighborListEventManager etomica.nbr.list
NeighborListEventManager() NeighborListEventManager
NeighborListEventManagerMolecular etomica.nbr.list.molecule
NeighborListEventManagerMolecular() NeighborListEventManagerMolecular
NeighborListManager etomica.nbr.list
Initiates the process of updating the neighbor lists.
NeighborListManager(PotentialMasterList, double, Box) NeighborListManager
NeighborListManager(PotentialMasterList, NeighborCellManager, double, Box) NeighborListManager
NeighborListManager.AtomPotential1ListSource etomica.nbr.list
NeighborListManagerColloid etomica.modules.colloid
NeighborListManagerColloid(PotentialMasterList, double, Box) NeighborListManagerColloid
NeighborListManagerColloid.NeighborListAgentSourceColloid etomica.modules.colloid
NeighborListManagerMolecular etomica.nbr.list.molecule
Initiates the process of updating the neighbor lists.
NeighborListManagerMolecular(PotentialMasterListMolecular, double, Box, Space) NeighborListManagerMolecular
Configures instance for use by the given PotentialMaster.
NeighborListManagerMolecular.MoleculePotential1ListSource etomica.nbr.list.molecule
NeighborListManagerSlanty etomica.nbr.list
Implements neighbor listing for a slanty box.
NeighborListManagerSlanty(PotentialMasterList, double, Box) NeighborListManagerSlanty
Configures instance for use by the given PotentialMaster.
NeighborListManagerSlanty.NeighborListSlantyAgentSource etomica.nbr.list
Constructs instances of NeighborListManagerSlanty on behalf of the
PotentialMaster
NeighborListManagerSlantyMolecular etomica.nbr.list.molecule
Implements neighbor listing for a slanty box.
NeighborListManagerSlantyMolecular(PotentialMasterListMolecular, double, Box, Space) NeighborListManagerSlantyMolecular
Configures instance for use by the given PotentialMaster.
NeighborListManagerSlantyMolecular.NeighborListSlantyAgentSourceMolecular etomica.nbr.list.molecule
Constructs instances of NeighborListManagerSlanty on behalf of the
PotentialMaster
neighborListNeighborsUpdated() IntegratorHard
neighborListNeighborsUpdated() INeighborListListener
neighborListNeighborsUpdated() INeighborListListenerMolecular
NeighborListSlantyAgentSource(double) NeighborListManagerSlanty.NeighborListSlantyAgentSource
NeighborListSlantyAgentSourceMolecular(double, Space) NeighborListManagerSlantyMolecular.NeighborListSlantyAgentSourceMolecular
neighborManager ColorSchemeOverlap
neighborManager MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbr
neighborManager P1MagicWall
neighborManager MeterMaxExpansion
neighborRadius2 CriterionSimple
neighborRadius2 CriterionSimpleMolecular
neighborRadiusSq P1ConstraintNbr
neighborRadiusSq P1ConstraintNbrHcp
neighbors RectangularLatticeNbrIterator
neighbors MCMoveGeometricCluster
neighbors MCMoveSpinCluster
neighbors1 MCMoveGeometricClusterRestrictedGE
neighbors2 MCMoveGeometricClusterRestrictedGE
neighborSetup() NeighborListManagerColloid
neighborSetup() NeighborListManagerMolecular
Reassigns all interacting atoms to cells, then loops over all cell-list
neighbor pairs, determines for each pair whether a potential applies to it,
and if so, puts each in the other's neighbor list.
neighborSetup() NeighborListManagerSlantyMolecular
Reassigns all interacting atoms to cells, then loops over all atom
pairs, determines for each pair whether a potential applies to it,
and if so, puts each in the other's neighbor list.
neighborSetup() NeighborListManager
Reassigns all interacting atoms to cells, then loops over all cell-list
neighbor pairs, determines for each pair whether a potential applies to it,
and if so, puts each in the other's neighbor list.
neighborSetup() NeighborListManagerSlanty
Reassigns all interacting atoms to cells, then loops over all atom
pairs, determines for each pair whether a potential applies to it,
and if so, puts each in the other's neighbor list.
NeighborSiteManager etomica.nbr.site
Neighbor manager for system in which there is an unchanging, one-to-one
correspondence between atoms and lattice cells.
NeighborSiteManager(Box, int) NeighborSiteManager
Constructs manager for neighbor cells in the given box.
neighborsUpdated() NeighborListEventManagerMolecular
neighborsUpdated() NeighborListEventManager
nEthane VirialAlkaneMix_Kong.VirialAlkaneMixParam
nEthane VirialAlkaneMix.VirialAlkaneMixParam
new3(float, float, float) Point3f
new3(float, float, float) Vector3f
new3(int, int, int) Point3i
new4(float, float, float, float) AxisAngle4f
Constructs and initializes an AxisAngle4f from the specified x, y, z, and
angle.
new4(float, float, float, float) Point4f
new4(float, float, float, float) Quaternion
newA(float[]) Matrix3f
Constructs and initializes a Matrix3f from the specified 9 element array.
newA(float[]) Matrix4f
Constructs and initializes a Matrix4f from the specified 16 element array.
newAA(AxisAngle4f) AxisAngle4f
Constructs and initializes a AxisAngle4f from the specified AxisAngle4f.
newAA(AxisAngle4f) Quaternion
newAndSetBit(int) BitSetUtil
newAntialiasing GData
newBitSet(int) BitSetUtil
newBitSet2(int, int) BitSetUtil
newBufferedImage(Object, int, int) ApiPlatform
newBufferedImage(Object, int, int) Platform
newByte2(int) ArrayUtil
newColor0 SplitOne.SplitOneParameters
newColor0() SplitParameters
newColor1 SplitOne.SplitOneParameters
newColor1() SplitParameters
newConfigruation() ConfigurationStorage.ConfigurationStorageListener
newConfigruation() ConfigurationStoragePumper
newConfigruation() CorrelationSelf2
newConfigruation() DataSourceAlpha2
newConfigruation() DataSourceF
newConfigruation() DataSourceFOld
newConfigruation() DataSourceFs
newConfigruation() DataSourceMSD
newConfigruation() DataSourcePercolation
newConfigruation() DataSourceQ4
newConfigruation() DataSourceStrings
newConfigruation() DataSourceVAC
newConfigruation() MeterCorrelation
newConfigruation() MeterCorrelationSelf
newConfigruation() MeterGs
newestgSum PotentialCalculationMappedRdf
newFloat2(int) ArrayUtil
newFloat3(int, int) ArrayUtil
newFont(String, boolean, boolean, float) ApiPlatform
newFont(String, boolean, boolean, float) Platform
newgSum PotentialCalculationMappedRdf
newI(int) Rgb16
newInt2(int) ArrayUtil
newInt4(int) ArrayUtil
newLnA MCMoveInsertDeleteLatticeVacancy
newLnA MCMoveInsertDeleteVacancy
newM(double[][]) Eigen
newM(Matrix3f) Matrix3f
Constructs a new matrix with the same values as the Matrix3f parameter.
newM(Matrix3f) Quaternion
newM(Matrix4f) Matrix4f
Constructs a new matrix with the same values as the Matrix4f parameter.
newMesh(boolean, Tuple3f[], int, int[][], Tuple3f[], int) MeshSurface
newMV(Matrix3f, Vector3f) Matrix4f
Constructs and initializes a Matrix4f from the rotation matrix
and translation.
newN(int) BitSet
Creates a bit set whose initial size is large enough to explicitly
represent bits with indices in the range 0 through nbits-1.
newN(int) StringXBuilder
newOffScreenImage(int, int) ApiPlatform
newOffScreenImage(int, int) Platform
newOriginB IntegratorDimerApproach
newP(Tuple3f) Point3f
newP4(Point4f) Quaternion
newPartners PotentialReactive.BondChangeData
newPosition IntegratorDimerRT
newPositionC BiasVolume2SiteAceticAcid
newPositionC BiasVolumeAceticAcid
newPt(Point4f) Point4f
newQ(Quaternion) Quaternion
newR MCMoveClusterAtomDiscrete
newS(String) StringXBuilder
newScriptVariableBs(BitSet, int) ScriptVariable
newScriptVariableIntValue(int, int, Object) ScriptVariable
newScriptVariableToken(Token) ScriptVariable
newSeeds SimulationVirial
newShort2(int) ArrayUtil
newSlab(Point3f[], int, float[], int[][], int, int) MeshSurface
newSmerList MCMoveSmer
newSmerList MCMoveSmerRotate
newToken(int, int) Token
newTokenIntVal(int, int, Object) Token
newTokenObj(int, Object) Token
Newton etomica.units
The Newton unit of force, equal to 1 kg-m/s^2.
NewtonMinimization etomica.math.numerical
NewtonMinimization(FunctionMultiDimensionalDifferentiable, boolean) NewtonMinimization
newtonRaphson(double, int, double, double, P1IntraMolecular) VirialH2PIXC
newTotalCosTheta MCMoveRotateMolecule3DN2AveCosThetaConstraint
newU MeterDirectInitPert
newV(Tuple3f) Vector3f
newVA(Tuple3f, float) Quaternion
newVA(Vector3f, float) AxisAngle4f
Constructs and initializes an AxisAngle4f from the specified axis and
angle.
newValue PropertyUpdate
newVariable(int, Object) ScriptVariable
newVertexBitSet() Normix
newWindowHeight GData
newWindowWidth GData
nex P2HydrogenPatkowski
nex P2HydrogenPatkowskiAtomic
NexpStretchFit HardSphereFluid
NexpVirial HardSphereFluid
next IndexIteratorIncreasing
next FunctionChain.Link
next MoleculeIteratorAll
next PotentialGroup.PotentialLinker
next Token
next() ANIntergroupCoupled
next() ANIntergroupExchange
next() ANIntragroupExchange
next() ApiIndexList
Returns the iterator's pair and unsets iterator.
next() ApiInnerVariable
Returns the next pair of atoms.
next() ApiInterArrayList
Returns the next iterate pair.
next() ApiIntergroup
Returns the next pair of atoms.
next() ApiIntergroupCoupled
Returns the next pair of atoms.
next() ApiIntergroupExchange
Returns the next pair of atoms.
next() ApiIntergroupIntraSpecies
Returns the next pair of atoms.
next() ApiIntraArrayList
Returns the next iterate pair.
next() ApiIntragroup
next() AtomIteratorArrayListAdjacent
Same as nextAtom.
next() AtomIteratorArrayListSimple
Same as nextAtom().
next() AtomIteratorBasisFilteredType
next() AtomIteratorBasisFilteredType2
next() AtomIteratorLeafFilteredType
next() AtomIteratorNull
next() AtomIteratorSinglet
next() AtomLeafsetIterator
Returns the next AtomSet iterate, or null if hasNext() is false.
next() Atomset3IteratorIndexList
Same as nextSet().
next() Atomset4IteratorIndexList
next() AtomsetIteratorAllLeafAtoms
next() CartesianIterator
next() CartesianPermutator
next() ChainedIterator
next() DefaultIterator
next() DefaultPermutator
next() EdgelessIterator
next() GlobalFilter
next() LocalFilter
next() FixedEdgeCountIterator
next() IteratorWrapper
next() RangePermutator
next() StoredIterator
next() MCMoveInsertDeleteLatticeVacancy.AtomIteratorBruteForce
next() MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbr
next() MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbrCell
next() IndexIterator
next() IndexIteratorIncreasing
Returns the next index.
next() IndexIteratorRectangular
Returns the next iterate, or null if hasNext is false.
next() IndexIteratorReflecting
next() IndexIteratorTriangular
Returns the next iterate.
next() IndexIteratorTriangularPermutations
next() RectangularLattice.Iterator
next() RectangularLatticeNbrIterator
Returns the next site in the iteration sequence, or null
if hasNext is false.
next() SiteIterator
Returns the next iterate.
next() CombinationIterator
next() FixedSumIterator
next() PermutationDegenerateIterator
Returns the next iterate, or null if hasNext is false.
next() PermutationIterator
next() ApiFilteredCylinder
next() MoleculeIteratorAll
next() MoleculeIteratorArrayListSimple
Same as nextAtom().
next() MoleculeIteratorSinglet
next() MoleculesetIterator
Returns the next AtomSet iterate, or null if hasNext() is false.
next() MpiInnerFixed
Returns the next pair of atoms.
next() MpiInnerVariable
Returns the next pair of atoms.
next() MpiInterArrayList
Returns the next iterate pair.
next() MpiInterspecies1A
next() MpiInterspeciesAA
Returns the next iterate pair.
next() MpiIntraArrayList
Returns the next iterate pair.
next() MpiIntraspecies1A
next() MpiIntraspeciesAA
Returns the next iterate pair.
next() MpiMolecule
Same as nextPair.
next() Api1ACell
next() Mpi1ACell
next() Api1ASite
next() PotentialMaster.AtomIterator0
next() PotentialMaster.MoleculeIterator0
next() PermutationIterator
next() PYGenerator.IteratorEF
next() IndexIterator
Get the next set of indices
nextAtom MCMoveVolumeAssociated.Agent
nextAtom AtomNbrClusterer
nextAtom DataSourceStrings
nextAtom() AtomIterator
Returns the next atom in the iteration sequence, or
null if hasNext() is false.
nextAtom() AtomIteratorArrayList
Returns the next iterate and advances the iterator.
nextAtom() AtomIteratorArrayListAdjacent
Returns the next iterator, or null if hasNext is false.
nextAtom() AtomIteratorArrayListSimple
Returns the next iterate and advances the iterator.
nextAtom() AtomIteratorBasisFilteredType
nextAtom() AtomIteratorBasisFilteredType2
nextAtom() AtomIteratorLeafFilteredType
nextAtom() AtomIteratorNull
nextAtom() AtomIteratorSinglet
Returns the iterator's atom and unsets iterator.
nextAtom() MCMoveInsertDeleteLatticeVacancy.AtomIteratorBruteForce
nextAtom() MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbr
nextAtom() MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbrCell
nextClearBit(int) BitSet
Returns the index of the first bit that is set to false that occurs
on or after the specified starting index.
nextCursor MoleculeIteratorAll
nextDouble() IRandom
Returns a pseudorandom double, uniformly distributed between
0.0 (exclusive) and 1.0 (exclusive).
nextDouble() RandomMersenneTwister
nextDouble() RandomNumberGenerator
nextDouble() RandomNumberGeneratorUnix
Returns a random double, uniformly distributed between 0 and 1.
nextFixedDouble() IRandom
Returns a pseudorandom double, uniformly distributed between
0.0 (inclusive) and 1.0 (exclusive).
nextFixedDouble() RandomMersenneTwister
nextFixedDouble() RandomNumberGenerator
nextFixedDouble() RandomNumberGeneratorUnix
nextFloat() RandomMersenneTwister
nextFloat() RandomNumberGeneratorUnix
Returns a random float, uniformly distributed between 0 and 1.
nextGaussian RandomMersenneTwister
nextGaussian RandomNumberGeneratorUnix
nextGaussian() IRandom
Returns a pseudorandom double, Gaussian ("normally") distributed
value with mean 0.0 and standard deviation 1.0.
nextGaussian() RandomMersenneTwister
nextGaussian() RandomNumberGenerator
nextGaussian() RandomNumberGeneratorUnix
Returns a double taken from a Gaussian distribution with 0 mean and
variance of 1.
nextIndex() RectangularLattice.Iterator
nextIndex() RectangularLatticeNbrIterator
Returns the index of the next iterate while advancing the
iterator.
nextIndex() SiteIterator
Returns the index of the next iterate while advancing iterator.
nextInt() RandomMersenneTwister
nextInt() RandomNumberGeneratorUnix
Returns a random int (32-bit integer).
nextInt(int) IRandom
Returns a pseudorandom integer, uniformly distributed between
0 (inclusive) and maxInt (exclusive).
nextInt(int) RandomMersenneTwister
Returns a random int ranging from 0 to max-1.
nextInt(int) RandomNumberGenerator
nextInt(int) RandomNumberGeneratorUnix
Returns a random int ranging from 0 to max-1.
nextLeft TreeLinker
nextLong() RandomMersenneTwister
nextLong() RandomNumberGeneratorUnix
Returns a random long (64-bit integer).
nextLong(long) RandomNumberGeneratorUnix
Returns a random long ranging from 0 to max-1.
nextMolecule MCMoveVolumeAssociatedMolecule.Agent
nextMolecule() MoleculeIterator
Returns the next atom in the iteration sequence, or
null if hasNext() is false.
nextMolecule() MoleculeIteratorArrayList
Returns the next iterate and advances the iterator.
nextMolecule() MoleculeIteratorArrayListSimple
Returns the next iterate and advances the iterator.
nextMolecule() MoleculeIteratorSinglet
Returns the iterator's atom and unsets iterator.
nextOp UnaryChain
nextPair() MpiAACell
nextPair(NodePair) SearchState
nextPair(NodePair) UllmanSearchState
nextPair(NodePair) VF2SearchState
nextPair(NodePair) VFSearchState
nextParams UnaryChain.ChainParameters
nextprime(BigInteger) Prime
return the smallest prime larger than n
nextRandom8Bit() Shader
Implements RANDU algorithm for random noise in lighting/shading.
nextReweightStep MeterVirialBDBin
nextReweightStep MeterVirialBDBinMultiThreaded
nextReweightStep MeterVirialBinMultiThreaded
nextReweightStep MeterVirialEBinMultiThreaded
nextRight TreeLinker
nextSet() Atomset3IteratorIndexList
Returns the iterator's pair and unsets iterator.
nextSetBit(int) BitSet
Returns the index of the first bit that is set to true that occurs
on or after the specified starting index.
nextVector() ConformationChain
nextVector() ConformationChain2D
nextVector() ConformationChain3D
nextVector() ConformationChainZigZag
nextVector() ConformationChainZigZag2
nf ClusterChainSoft
nf ClusterSinglyConnected
nf ClusterWheatleyExtendSW
nf ClusterWheatleyPartitionScreening
nf ClusterWheatleyPT
nf1 ClusterChainHS
nfBond PYGenerator.IteratorEF
nfctmx P2O2Bartolomei
nFieldPoints Mul.MulParameters
nGraft ColloidGraphic.GraftAction
nGraft ColloidSim
nGraft ConfigurationColloid
nIn Shader
nIndices PermutationIterator
nInner MinimizationTIP4P.SimParams
Nitrogen etomica.chem.elements
Class for the Nitrogen element.
Nitrogen(String) Nitrogen
Nitrogen(String, double) Nitrogen
nKs EwaldSummation
nLayer HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
nLayer HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
nLayer HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
nLayer HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
nLayer HarmonicBetaNitrogenModelPairMoleculeSequentialLS
nLayer HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
nLayer HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
nLayer MinimizationBetaNitrogenModelLS
nLayer MinimizeBetaNitrogenLatticeParameterLSFromFile
nLeafAtoms ANIntergroupCoupled
nLeafAtoms ANIntergroupExchange
nlin P2WaterSzalewicz
nlin3 P2WaterSzalewicz
nlm BenchNbrUpdates
nLookUp Vector3D
nLREP PotentialCuLREP
nm HessianDB
nm NormalModeAnalysisDisplay1D
nm NormalModeAnalysisDisplay2D
nm NormalModeAnalysisDisplay3D
nMax AccumulatorAutocorrelationPTensor
nMax AccumulatorAutocorrelationShearStress
nMax Heisenberg.Param
nMax Heisenberg3Pair.Param
nMax HeisenbergPair.Param
nMax MeterMappedAveraging
nMax MeterMappedAveraging3Pair
nMax MeterMappedAveragingFreeEnergy
nMax MeterMappedAveragingPair
nMax MeterMappedAveragingPairExcess
nMax MeterMappedAveragingVSum
nMax MeterMappedAveragingVSum3Pair
nMax MeterMappedAveragingVSumPair
nMax PotentialCalculationHeisenberg
nMax PotentialCalculationMoleculeAgentSum
nMax PotentialCalculationMoleculeAgentSumMinusIdeal
nMax PotentialCalculationMoleculeAgentSumMinusIdealPair
nMax PotentialCalculationMoleculeAgentSumPair
nMax PotentialCalculationPair
nMax PotentialCalculationVSum
nMax PartitionsP
The maximum integer covered by the high end of the list.
nMax Prime
The maximum integer covered by the high end of the list.
nMethane VirialAlkaneMix_Kong.VirialAlkaneMixParam
nMethane VirialAlkaneMix.VirialAlkaneMixParam
NModifier() LatticeEditor.NModifier
nMol MeterSolidProps
nMol MeterSolidPropsLJ
nMol PotentialCalculationEFSSP
nMol PotentialCalculationLJSP
nMolecules MCMoveVolumeAssociatedMolecule.Agent
nMolecules SimEinStep2.MeterPotentialEnergyComposite
nMolecules SimEinStep2HCP.MeterPotentialEnergyComposite
nMolecules SimulationVirialOverlap2
nMoments AccumulatorAverageBootstrap
nMoments AccumulatorAverageCollapsingLog
nMonoAcid ChainEquilibriumSim
nMonoOl ChainEquilibriumSim
nmrurlformat Token
nMu LjMd3D.DataProcessorCorrection
nMu DataSourcePMu
nNominalAtoms DropletAtomic
nO2 ConfigurationCatalysis
nocontourlines Token
Node etomica.graph.model
NODE_NULL Traversal
node1ID MulFlexible.MulFlexibleParameters
node2ID MulFlexible.MulFlexibleParameters
nodeColor VirialDiagrams
nodeColor VirialDiagramsMix
nodeColor VirialDiagramsPT
nodeColors VirialDiagramsMix
nodeColors VirialDiagramsMix2
nodeCount() Graph
nodeCount() GraphImpl
nodeId FactorOnce.FactorOnceParameters
nodeId() ConvParameters
nodeId() IntParameters
NodeImpl etomica.graph.model.impl
NodeImpl(byte, char, char) NodeImpl
NodePair etomica.graph.isomorphism
NodePair(Byte, Byte) NodePair
nodes() Graph
nodes() GraphImpl
nodesToString() Graph
nodesToString() GraphImpl
NodeVisitor etomica.graph.model
NoDoNotRemoveSpeciesButtonListener() ControllerAlertMsgBoxSpeciesRemoval.NoDoNotRemoveSpeciesButtonListener
nodots Token
nofill Token
noisyAdjustment MCMoveStepTracker
NOJMOL EnumVdw
nomesh Token
nominalBlockSize AccumulatorAverageCollapsing
nominalBondL SpeciesAlkane
NominalbondL EnumPotentialParamDescription
nominalBondTheta SpeciesAlkane
nominalBoxSize MCMoveVolumeSolid
nominalDiameter EllipseDisplayAction
nominalFluctuation HSNPT.ColorSchemeDisplacement
nominalFrequency MCMove
Value giving nominal frequency for performing this move.
nominalNumAtoms DataSourcePN
nominalScale HSNPT2DGraphic
nominalTheta MeterThetaDeviation
nominalWeight MeterVirialBDBinMultiThreaded
nominalWeight MeterVirialBinMultiThreaded
nominalWeight MeterVirialEBinMultiThreaded
NON_PAIR P2WaterSzalewicz.Component
nonAdd VirialHSMixture.VirialHSParam
nonAdd VirialHSMixtureOverlap.VirialHSParam
nonAdditive VirialCO2H2OGCPM.VirialParam
nonAdditive VirialCO2H2OGCPMX.VirialParam
nonAdditive VirialCO2H2OSC.VirialCO2SCParam
nonAdditive VirialH2O.VirialH2OParam
nonAdditive VirialH2OGCPMD.VirialParam
nonAdditive VirialN2.VirialN2Param
nonAdditive VirialN2PI.VirialN2Param
nonAdditiveOnly ClusterWheatleyMultibodyMix
nonAssociationPotential ConfigurationClusterWertheimGCPM
nonAssociationPotential ConfigurationClusterWertheimGCPM4Pt
nonAssociationPotential ConfigurationClusterWertheimGCPMDirectSampling
none Token
NONE ParserLAMMPS.Truncation
NONE EnumPalette
NONE EnumStereoMode
NONE ClusterOperations
NoOfSpheres ViewAlkaneLengthSelection
noOfSteps ModelTemperatureAndSteps
nOrder ClusterWheatleyPT
noReset MCMoveStepTracker
norm Quaternion
norm PNCO2GCPM.P3GCPMAxilrodTeller
norm PNGCPM.P3GCPMAxilrodTeller
norm0 P2SpheroPolyhedron
norm1 P2SpheroPolyhedron
norm2 P2SpheroPolyhedron
normal SimDimerLJadatom
normalCount MeshSurface
normalD IntegratorDimerMin
normalDir SimDimerLJadatom
normalize() Quaternion
Normalizes the Quaternion q i.e.
normalize() Vector
Normalizes this vector, so this.squared() == 1.
normalize() Vector1D
normalize() Vector2D
normalize() Vector3D
normalize() VectorND
normalize() BigSurd
Normalize to squarefree discriminant.
normalize() BigSurdVec
Combine terms that can be written as a single surd.
normalize() Rational
Normalize to coprime numerator and denominator.
normalize() Vector3f
Normalizes this vector in place.
normalizeByN MeterStructureFactor
normalizeG() BigSurd
Normalize to coprime numerator and denominator in prefactor and discriminant
NormalModeAnalysisDisplay1D etomica.normalmode
NormalModeAnalysisDisplay1D() NormalModeAnalysisDisplay1D
NormalModeAnalysisDisplay1D.Applet etomica.normalmode
NormalModeAnalysisDisplay1DGraphic etomica.normalmode
NormalModeAnalysisDisplay1DGraphic(NormalModeAnalysisDisplay1D, Space) NormalModeAnalysisDisplay1DGraphic
NormalModeAnalysisDisplay1DGraphic.Applet etomica.normalmode
NormalModeAnalysisDisplay2D etomica.normalmode
Harmonic anaylsis for 2-D soft-sphere model
NormalModeAnalysisDisplay2D() NormalModeAnalysisDisplay2D
NormalModeAnalysisDisplay2DGraphic etomica.normalmode
NormalModeAnalysisDisplay2DGraphic(NormalModeAnalysisDisplay2D, Space) NormalModeAnalysisDisplay2DGraphic
NormalModeAnalysisDisplay2DGraphic.Applet etomica.normalmode
NormalModeAnalysisDisplay3D etomica.normalmode
NormalModeAnalysisDisplay3D() NormalModeAnalysisDisplay3D
NormalModeAnalysisDisplay3D.Applet etomica.normalmode
NormalModeAnalysisDisplay3DGraphic etomica.normalmode
Harmonic Oscillator 3D
NormalModeAnalysisDisplay3DGraphic(NormalModeAnalysisDisplay3D, Space) NormalModeAnalysisDisplay3DGraphic
NormalModeAnalysisDisplay3DGraphic.Applet etomica.normalmode
NormalModeEigenGetter etomica.normalmode
NormalModeEigenGetter() NormalModeEigenGetter
normalModes SimOverlapNitrogenModel
normalModes MCMoveAtomCoupledBennet
normalModes MCMoveAtomCoupledUmbrella
normalModes MCMovePhaseAngle
normalModes MCMoveWV
normalModes MeterHarmonicEnergy
normalModes MeterHarmonicSingleEnergy
normalModes MeterJacobian
normalModes SimBennet
normalModes SimHarmonic
normalModes SimHarmonicUmbrella
normalModes SimModesJ
normalModes SimOverlap
normalModes SimOverlapLJ
normalModes SimOverlapLJModule
normalModes SimOverlapSoftSphere
normalModes SimOverlapSoftSphereEinHarm
normalModes SimOverlapSoftSphereHCP
normalModes SimOverlapSoftSphereReweighting
normalModes SimOverlapSoftSphereSuperBox
normalModes SimOverlapSSnxy
normalModes SimTargetUmbrella
normalModes SimUmbrella
normalModes SimUmbrellaSoftSphere
NormalModes etomica.normalmode
Provides information about all the normal modes for a periodic system.
NormalModes1DHR etomica.normalmode
Normal-mode quantities for a 1-dimensional system of hard rods.
NormalModes1DHR(Boundary, int) NormalModes1DHR
NormalModes2D etomica.normalmode
NormalModes2D(Space, Boundary, Primitive, Basis) NormalModes2D
NormalModes3D etomica.normalmode
NormalModes3D(Space, Primitive, Basis) NormalModes3D
NormalModesFromFile etomica.normalmode
Provides normal-mode information as obtained from a file read at
construction.
NormalModesFromFile(String, int) NormalModesFromFile
NormalModesMolecular etomica.normalmode
Uses analysis of 2nd derivatives to compute the normal modes for a Bravais lattice with a basis,
occupied by atoms that interact with a simple, spherically-symmetric soft potential.
NormalModesMolecular(SpeciesGeneral, boolean, PotentialMaster, Box, int[], Primitive, int, LatticeSumMolecularCrystal.AtomicTensorAtomicPair, Space) NormalModesMolecular
NormalModesPotential etomica.normalmode
Uses analysis of 2nd derivatives to compute the normal modes for a Bravais lattice with a basis,
occupied by atoms that interact with a simple, spherically-symmetric soft potential.
NormalModesPotential(int[], Primitive, Basis, Potential2SoftSpherical, Space) NormalModesPotential
NormalModesSoftSpherical etomica.normalmode
Computes the normal modes for a Bravais lattice occupied by atoms that interact
with a simple, spherically-symmetric soft potential, using analysis of second
derivatives.
NormalModesSoftSpherical(int[], Primitive, Potential2SoftSpherical, Space) NormalModesSoftSpherical
NormalModesVariable etomica.normalmode
NormalModesVariable(Space, int, CoordinateDefinition) NormalModesVariable
normals MeshSurface
normalsTemp MeshSurface
normalVector MCMoveClusterAtomHSRing
normalWidth MCMoveClusterAtomHSRing
Normix org.jmol.util
Provides quantization of normalized vectors so that shading for
lighting calculations can be handled by a simple index lookup
Normix() Normix
NORMIX_NULL Normix
normixCount MeshSurface
noRotScale SimOverlapAlphaN2TP.SimOverlapParam
NORTH Constants.CompassDirection
not() Bitmap
Inverts the bits of this bitmap: bitmap = ~bitmap.
not() AbstractBitmap
not() BitmapOfLong
TIME = O(1).
not() BitmapOfLongVector
NOT_ALLOWED Prefix
Constant used when invoking constructor of SimpleUnit class to indicate
that the unit does not permit the use of a prefix.
NOTE_SCRIPT_FILE JmolConstants
notfrontonly Token
notifyEndOfRendering() ApiPlatform
notifyEndOfRendering() Platform
notifyEnergyChange(double) IntegratorMC
Notifies the IntegratorMC that the energy changed allowing
the internal potential energy field to be updated.
notifyNeedUpdate() EtomicaPlot
Notify that the displayPlot has new data, but we're not showing.
notifyNewMolecules(ISpecies, int, int) Box
notriangles Token
notzero ClusterWheatleyHS
notzero ClusterWheatleyPartitionScreening
nOut Shader
nOuter MinimizationTIP4P.SimParams
NoValueOptionHandler() Main.NoValueOptionHandler
nOverlaps ColorSchemeOverlap
nOverlaps ColorSchemeScaledOverlap
nP AccumulatorPTensor
npairs ClusterWheatleyExtendSW
npairs MeterVirialSWWE
nPairs MeterMappedAveragingCorrelation
nPairs() Potential0Lrc
Returns the number of pairs formed from molecules of the current
species, in the given box.
nPerm P3HydrogenManzhos
nPermutations ClusterBonds
nPermutations() ClusterBonds
Number of permutations of (and including) the basic cluster used when
calculating its value for a configuration
nPoint SingleAssociationSiteFluidGraph.VirialAssociatingFluidParam
nPoints P2DiscreteFeynmanHibbs
nPoints VirialPolymerOverlapMC.VirialHSParam
nPoints VirialPolymerOverlapWithMD.VirialHSParam
nPoints VirialPolymerOverlapWithMDB3.VirialHSParam
nPoints ClusterBonds
nPoints DirectSamplingTargetQCArReferenceAzizAr.VirialLJParam
nPoints LJTSRefLJ.VirialLJParam
nPoints Virial2CLJmuQ.Virial2CLJQParam
nPoints Virial2CLJQ.Virial2CLJQParam
nPoints Virial7SiteRigidSF6.VirialSF6Param
nPoints VirialAlkane.VirialSiepmannSpheresParam
nPoints VirialAlkaneEHTest.VirialParam
nPoints VirialAlkaneFlex.VirialSiepmannSpheresParam
nPoints VirialAlkaneFull.VirialSiepmannSpheresParam
nPoints VirialAlkaneMix_Kong.VirialAlkaneMixParam
nPoints VirialAlkaneMix.VirialAlkaneMixParam
nPoints VirialAlkaneMix2_Kong.VirialAlkaneMixParam
nPoints VirialAlkaneMix2.VirialAlkaneMixParam
nPoints VirialAlkaneSKS.VirialSiepmannSpheresParam
nPoints VirialAnthracene464.VirialAnthracene545Param
nPoints VirialAnthracene545.VirialAnthracene545Param
nPoints VirialAnthraceneTraPPE.VirialAnthraceneTraPPEParam
nPoints VirialB3C1HSDipole.VirialParam
nPoints VirialB3C2HSDipole.VirialParam
nPoints VirialCH4AlkaneEHMix.VirialMixParam
nPoints VirialCO2.VirialCO2Param
nPoints VirialCO2AlkaneEHMix.VirialMixParam
nPoints VirialCO2AlkaneUAMix.VirialMixParam
nPoints VirialCO2anthracene464.VirialCO2anthracene545Param
nPoints VirialCO2anthracene545.VirialCO2anthracene545Param
nPoints VirialCO2AnthraceneTraPPE.VirialCO2AnthraceneTraPPEParam
nPoints VirialCO2CH4Mix.VirialMixParam
nPoints VirialCO2CH4UAMix.VirialMixParam
nPoints VirialCO2CH4UAMixWheatley.VirialMixParam
nPoints VirialCO2LJQ.VirialCO2LJQParam
nPoints VirialCO2N2Mix.VirialMixParam
nPoints VirialCO2NaphthaleneLJQ.VirialCO2NaphthaleneLJQParam
nPoints VirialCO2NaphthaleneTraPPE.VirialCO2TraPPEParam
nPoints VirialCO2PI.VirialH2PIParam
nPoints VirialCO2SKSMix.VirialCO2Param
nPoints VirialCO2TraPPE.VirialCO2TraPPEParam
nPoints VirialCPSHeliumNonAdditive.VirialParam
nPoints VirialCPSHeliumNonAdditiveClassical_Correction.VirialParam
nPoints VirialCPSHeliumNonAdditiveClassical.VirialParam
nPoints VirialEmulNonAdditive.VirialParam
nPoints VirialExternalFieldConfinedOverlap.VirialExternalFieldParam
nPoints VirialExternalFieldConfinedOverlapRho.VirialExternalFieldParam
nPoints VirialExternalFieldConfinedOverlapSW.VirialExternalFieldParam
nPoints VirialExternalFieldOverlapRho.VirialExternalFieldParam
nPoints VirialGCPM.VirialGCPMParam
nPoints VirialH2O.VirialH2OParam
nPoints VirialH2OGCPMD.VirialParam
nPoints VirialH2PI.VirialH2PIParam
nPoints VirialH2PIBoltzmann.VirialHePIParam
nPoints VirialH2PISimple.VirialH2PISimpleParam
nPoints VirialH2PIXC.VirialHePIParam
nPoints VirialH2PYCorrection.VirialH2PYCParam
nPoints VirialHardAssociationCone.VirialLJParam
nPoints VirialHardAssociationConeDoubleSites.VirialLJParam
nPoints VirialHeD.VirialParam
nPoints VirialHeNonAdditive.VirialParam
nPoints VirialHeNonAdditiveD.VirialParam
nPoints VirialHeNonAdditiveWheatley.VirialParam
nPoints VirialHePCKLJSTempDeriv.VirialParam
nPoints VirialHePI_PotentialCorrection.VirialHePIParam
nPoints VirialHePI.VirialHePIParam
nPoints VirialHePISysErr.VirialHePIParam
nPoints VirialHePIXC.VirialHePIParam
nPoints VirialHePIXCEven.VirialHePIParam
nPoints VirialHePYCorrection.VirialHePYCParam
nPoints VirialHeSC.VirialHePYCParam
nPoints VirialHS.VirialHSParam
nPoints VirialHSBinMultiThreaded.SimulationWorker
nPoints VirialHSBinMultiThreaded.VirialHSBinParam
nPoints VirialHSMixture.VirialHSParam
nPoints VirialHSMixtureOverlap.VirialHSParam
nPoints VirialHSOrC.VirialLJrParam
nPoints VirialLJ.VirialLJParam
nPoints VirialLJD.VirialLJParam
nPoints VirialLJDU.VirialLJParam
nPoints VirialLJMultiOverlap.VirialMixParam
nPoints VirialLJOrC.VirialLJrParam
nPoints VirialLJOrICPYC.VirialLJrParam
nPoints VirialLJPT.VirialLJParam
nPoints VirialLJSeries.VirialLJParam
nPoints VirialMethaneEH.VirialMethaneParam
nPoints VirialN2.VirialN2Param
nPoints VirialN2AlkaneEHMix.VirialMixParam
nPoints VirialN2AlkaneUAMix.VirialMixParam
nPoints VirialN2AlkaneUARigid.VirialMixParam
nPoints VirialN2CH4Mix.VirialMixParam
nPoints VirialN2CH4UAMix.VirialMixParam
nPoints VirialN2PI.VirialN2Param
nPoints VirialN2TraPPE.VirialN2Param
nPoints VirialNaphthaleneTraPPE.VirialNaphthaleneTraPPEParam
nPoints VirialO2.VirialO2Param
nPoints VirialO2PI.VirialO2Param
nPoints VirialPh464.VirialPh3site464Param
nPoints VirialPh545.VirialPh3site545Param
nPoints VirialPhenanthreneTraPPE.VirialPhenanthreneTraPPEParam
nPoints VirialPolyhedra.VirialHSParam
nPoints VirialPolyhedra2.VirialHSParam
nPoints VirialSF6LJAlkaneUAMix.VirialMixParam
nPoints VirialSQWBinMultiRecalcW.VirialHSParam
nPoints VirialSQWBinMultiThreaded.SimulationWorker
nPoints VirialSQWBinMultiThreaded.VirialHSBinParam
nPoints VirialSQWRecalcSmallMem.VirialHSParam
nPoints VirialSW.VirialSWParam
nPoints VirialSwsPT.VirialSiepmannSpheresParam
nPoints VirialSWWE.VirialSWWEParam
nPoints VirialTraPPE.VirialParam
npol P2WaterSzalewicz
npowers P2WaterPotentialsJankowski
nPretendPoints AkimaSplineSmootherDyApp
nPts ClusterWheatleyPartitionScreening
nPtsTabulated ClusterWheatleyPartitionScreening
nPtsTabulated VirialHS.VirialHSParam
nPtsTabulated VirialHSBinMultiThreaded.SimulationWorker
nPtsTabulated VirialHSBinMultiThreaded.VirialHSBinParam
npun P2O2Bartolomei
nRawData AccumulatorAverageBootstrap
nRawData AccumulatorAverageCollapsingLog
nRawDataDoubles AccumulatorAverageBootstrap
nRawDataDoubles AccumulatorAverageCollapsingLog
nrcMax LjMC3D.LjMC3DParams
nrcMax LjMd3Dv2y.LjMd3DParams
nReactCO ReactionManagerCO
nReacted MeterConversion
nRealPoints VirialAlkaneFlex.VirialSiepmannSpheresParam
nRealShells EwaldSummation
nRejected IntegratorMD
nReservoirTrials MyMCMove
nReservoirTrialsAccepted MyMCMove
nRootField MyApplet
nRows DataTable.DataInfoTable
nRows DataTable.DataInfoTableFactory
nRowsA MeterSolidPropsLJ
nSample AccumulatorPTensor
nSamples CorrelationSelf2
nSamples DataSinkBlockAveragerSFac
nSamples DataSourceAlpha2
nSamples DataSourceCorrelation
nSamples DataSourceF
nSamples DataSourceFOld
nSamples DataSourceFs
nSamples DataSourceMSD
nSamples DataSourceMSDcorP
nSamples DataSourcePercolation
nSamples DataSourceQ4
nSamples DataSourceVAC
nSamples MeterCorrelationSelf
nSamples MeterWorkHarmonicTargetandReweighting
nSamples MeterWorkTargetHarmonicandReweighting
nSamples2 StructureFactorComponentCorrelation
nSamplesCor StructureFactorComponentCorrelation
nSamplesCorX DataSourceBlockAvgCor
nSamplesP DataClusterer
nSamplesP DataClusterWriter
nSets MeshSurface
nShapes VirialPolyhedra.VirialHSParam
nShells PotentialEAM_LS
nShells Potential2SoftSphericalLSMulti
nShells Potential2SoftSphericalLSMultiLat
nShells Potential2SoftSphericalLS
nsite3 P2WaterSzalewicz
nsitea P2WaterPotentialsJankowski
nsiteb P2WaterPotentialsJankowski
nsitemax P2WaterPotentialsJankowski
nsites P2CO2Hellmann
nSlider DropletGraphic
nSlider InterfacialSWGraphic
nSlider PistonCylinderGraphic
nSlider ReactionEquilibriumGraphic.MySpeciesEditor
nsp P2HydrogenPatkowski
nsp P2HydrogenPatkowskiAtomic
nSpheres CollectionBondedPotentialAlkanes
nSpheres VirialAlkane.VirialSiepmannSpheresParam
nSpheres VirialAlkaneEHTest.VirialParam
nSpheres VirialAlkaneFlex.VirialSiepmannSpheresParam
nSpheres VirialAlkaneFull.VirialSiepmannSpheresParam
nSpheres VirialAlkaneSKS.VirialSiepmannSpheresParam
nSpheres VirialCH4AlkaneEHMix.VirialMixParam
nSpheres VirialCO2AlkaneEHMix.VirialMixParam
nSpheres VirialCO2AlkaneUAMix.VirialMixParam
nSpheres VirialCO2SKSMix.VirialCO2Param
nSpheres VirialH2PIBoltzmann.VirialHePIParam
nSpheres VirialH2PIXC.VirialHePIParam
nSpheres VirialHePIXC.VirialHePIParam
nSpheres VirialN2AlkaneEHMix.VirialMixParam
nSpheres VirialN2AlkaneUAMix.VirialMixParam
nSpheres VirialN2AlkaneUARigid.VirialMixParam
nSpheres VirialSF6LJAlkaneUAMix.VirialMixParam
nSpheres1 VirialAlkaneMix_Kong.VirialAlkaneMixParam
nSpheres1 VirialAlkaneMix.VirialAlkaneMixParam
nSpheres1 VirialAlkaneMix2_Kong.VirialAlkaneMixParam
nSpheres1 VirialAlkaneMix2.VirialAlkaneMixParam
nSpheres2 VirialAlkaneMix_Kong.VirialAlkaneMixParam
nSpheres2 VirialAlkaneMix.VirialAlkaneMixParam
nSpheres2 VirialAlkaneMix2_Kong.VirialAlkaneMixParam
nSpheres2 VirialAlkaneMix2.VirialAlkaneMixParam
Nstar IntegratorDimerMin
Nstar IntegratorDimerRT
NstarDelta IntegratorDimerMin
NstarDelta IntegratorDimerRT
nStates IntegratorTMMC
nStrings DataSourceStrings
nSubPoints AkimaSplineSmootherApp.PlotAction
nSubPoints AkimaSplineSmootherDyApp.PlotAction
nSurfaceBonds InteractionTracker.CatalysisAgent
nSurfaceSites P2SquareWellBonding
nSurfaceSites P2SquareWellBondingCO
nSurfactantSlider InterfacialSWGraphic
nTag AccumulatorAverageBootstrap
nTag AccumulatorAverageCollapsingLog
nTag DataProcessorDyDLnx
nTag MultiharmonicGraphicMC.DataSourceAlphaFE
nThreads VirialHSBinMultiThreaded.VirialHSBinParam
nThreads VirialSQWBinMultiThreaded.VirialHSBinParam
nTimes VirialH2O.VirialH2OParam
nTimes VirialN2.VirialN2Param
nTimes VirialO2.VirialO2Param
nTimes VirialO2PI.VirialO2Param
ntpot P2WaterPotentialsJankowski
nTrial AkimaSplineSmoother
nTrial MCMoveClusterRingPartialRegrow
nTrial MCMoveClusterRingRegrow
nTrial MCMoveClusterRingRegrowExchange
nTrials MCMoveTracker
ntypemax P2WaterPotentialsJankowski
nTypes ClusterWheatleySoftDerivativesMix
nTypes ClusterWheatleySoftDerivativesMixBD
nTypes ClusterWheatleySoftMix
nTypes ClusterWheatleySoftMixBD
nTypes VirialCH4AlkaneEHMix.VirialMixParam
nTypes VirialCO2AlkaneEHMix.VirialMixParam
nTypes VirialCO2AlkaneUAMix.VirialMixParam
nTypes VirialCO2anthracene464.VirialCO2anthracene545Param
nTypes VirialCO2anthracene545.VirialCO2anthracene545Param
nTypes VirialCO2AnthraceneTraPPE.VirialCO2AnthraceneTraPPEParam
nTypes VirialCO2CH4Mix.VirialMixParam
nTypes VirialCO2CH4UAMix.VirialMixParam
nTypes VirialCO2CH4UAMixWheatley.VirialMixParam
nTypes VirialCO2H2OGCPM.VirialParam
nTypes VirialCO2H2OGCPMX.VirialParam
nTypes VirialCO2H2OSC.VirialCO2SCParam
nTypes VirialCO2N2Mix.VirialMixParam
nTypes VirialCO2NaphthaleneLJQ.VirialCO2NaphthaleneLJQParam
nTypes VirialCO2NaphthaleneTraPPE.VirialCO2TraPPEParam
nTypes VirialCO2SKSMix.VirialCO2Param
nTypes VirialLJMultiOverlap.VirialMixParam
nTypes VirialN2AlkaneEHMix.VirialMixParam
nTypes VirialN2AlkaneUAMix.VirialMixParam
nTypes VirialN2AlkaneUARigid.VirialMixParam
nTypes VirialN2CH4Mix.VirialMixParam
nTypes VirialN2CH4UAMix.VirialMixParam
nTypes VirialSF6LJAlkaneUAMix.VirialMixParam
nTypes VirialTraPPE.VirialParam
NucleationGraphic etomica.modules.nucleation
NucleationGraphic(Swmd) NucleationGraphic
NucleationGraphic.DataSinkExcludeOverlap etomica.modules.nucleation
NucleationGraphic.ModifierDensity etomica.modules.nucleation
nucleic Token
nufac0 PNCO2GCPM.P3GCPMAxilrodTeller
Null etomica.units.dimensions
Dimension specified dimensionless quantities which have no other interpretation
(e.g., the quantity is not known to be an angle, or a fraction).
NULL Prefix
NULL_NODE SearchState
nullCollisionTime IntegratorHard.Agent
nullPair() NodePair
nullPotential IntegratorHard.Agent
nullRegionMethod VirialCPSHeliumNonAdditive.VirialParam
nullRegionMethod VirialHeNonAdditive.VirialParam
nullRegionMethod VirialHeNonAdditiveWheatley.VirialParam
num ClusterICPYC
numAlpha MCMoveOverlapListener
numAlpha MeterTargetRPMolecule
numAlpha MeterTargetTPMolecule
numAlpha SimOverlapAlphaN2TP.SimOverlapParam
numAlpha SimOverlapBetaN2RP.SimOverlapParam
numAlpha SimOverlapBetaN2RPScaling.SimOverlapParam
numAlpha SimOverlapBetaN2TP.SimOverlapParam
numAlpha SimOverlapDisorderedAlphaN2RPScaling.SimOverlapParam
numAlpha SimOverlapDisorderedAlphaN2TP.SimOverlapParam
numAlpha MeterOverlapSwitch
numAlpha MeterTargetTP
numAlpha SimOverlapSoftSphereEin.SimOverlapParam
numAlpha SimOverlapSoftSphereEinHarm
numAlpha SimOverlapSoftSphereEinHarm.SimOverlapParam
numAlpha SimOverlapSoftSphereSoftness.SimOverlapParam
numAlpha SimOverlapSoftSphereTP.SimOverlapParam
numAlpha SimOverlapSoftSphereTPHCP.SimOverlapParam
numAlpha SimOverlapSoftSphereTPSlantedBox.SimOverlapParam
numAlpha MeterOverlap
numAlpha SimulationVirialOverlap2
numAssociatedAtoms MCMoveVolumeAssociated
numAssociatedMolecules MCMoveVolumeAssociatedMolecule
numAtomInString DataSourceStrings
numatoms EFSTungsten.Params
numAtoms TestAceticAcidMC3D_NPT.AceticAcidMCParam
numAtoms TestIGAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
numAtoms TestLJAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
numAtoms TestLJAssociationMC3D_NPT.VirialAssociatingFluidParam
numAtoms TestLJAssociationMC3D_NVTOld.VirialAssociatingFluidParam
numAtoms SimFe.LjMC3DParams
numAtoms SimIdealGas.LjMC3DParams
numAtoms SimLattice.LjMC3DParams
numAtoms SimLJ.LjMC3DParams
numAtoms VLESim.GEMCParams
numAtoms MCMoveIDBiasAction
numAtoms LjMC3D.LjMC3DParams
numAtoms LjMd3D.LjMd3DParams
numAtoms LjMd3Dv2y.LjMd3DParams
numAtoms SimMappedRdf.LJMDParams
numAtoms MappedU.LJMDParams
numAtoms MappedVirialLJ.LJMDParams
numAtoms MappedVirialLJVGr.LJMDParams
numAtoms LJmuVT.LJMCParams
numAtoms LJNPT.LJMCParams
numAtoms LJNVT.LJMCParams
numAtoms DataSourcePercolation
numAtoms DataSourcePercolation0
numAtoms DataSourceStrings
numAtoms NucleationGraphic.DataSinkExcludeOverlap
numAtoms SwmdGraphic.DataSinkExcludeOverlap
numAtoms HSNPT.HSMD3DParameters
numAtoms LJVacancyMin.SimOverlapParam
numAtoms NormalModeAnalysisDisplay1D
numAtoms SimHSMDVacancy.HSMDVParams
numAtoms SimLJHTTISuper.SimOverlapParam
numAtoms SimLJHTTISuperHCP.SimOverlapParam
numAtoms SimLJHTTISuperHCP2.SimOverlapParam
numAtoms SimLJHTTISuperSFMD.SimOverlapParam
numAtoms SimLJVacancy.LJParams
numAtoms SimOverlapSoftSphereTP.SimOverlapParam
numAtoms AshtonWildingLJ.simParams
numAtoms AshtonWildingOsmoticVirial.simParams
numAtoms AshtonWildingVirial.simParams
numAtoms GCRestrictedGibbsHS.simParams
numAtoms GCWidomInsertHS.simParams
numAtoms NVTWidomInsertLJ.simParams
numAtoms PolydisperseHS.HSPolyParam
numAtoms LJMC3D.SimParams
numAtoms LJMC3DDimer.SimParams
numAtoms LJMC.LJMCParams
numAtoms TestHSMD3D.SimParams
numAtoms TestLJGCMC3D.SimParams
numAtoms TestLJMC3D.SimParams
numAtoms TestLJMD3D.SimParams
numAtoms TestSWChain.SimParams
numAtoms CoordinatePairLeafSet
numAtoms CoordinatePairMoleculeSet
numAtoms TestLJAssociationMC3D_NPT.VirialAssociatingFluidParam
numAtomsByType DataSourcePercolation
numAtomsLattice MCMoveOverlapListener
numAtomsMove MCMoveClusterWiggleAlkaneEH
numBeads MCMoveClusterRingPartialRegrow
NUMBER EnumPotentialParamDescription
numberMolecules CH4NVT.Param
numberMolecules DHS_NVT.Param
numberMolecules DLJ_NVT_1site.Param
numberMolecules DHS_NVT.Param
numberMolecules DLJ_NVT_1site.Param
numberMolecules TIP4P_NVT.Param
numberMolecules Heisenberg3Pair.Param
numberMolecules(ISpecies, int) BoxEventManager
numberOfStates(Box) MacrostateManager
Number of expected macrostates in the box.
NumbersToggler() MyApplet.NumbersToggler
numCarbons ConformationAlkaneEH
numCarbons MCMoveClusterWiggleAlkaneEH
numCells NeighborCellManagerMolecular
numCells NeighborCellManager
numCellsSlider SamGraphic
numCH2 ConformationAlkaneEH
numCollapseBins HistoryCollapsing
numDelete MCMoveOverlapListener
numDeleteCandidateNbrs MCMoveInsertDeleteLatticeVacancy
numDeleteCandidateNbrs MCMoveInsertDeleteVacancy
numDiagram Wertheim2SiteAceticAcid.WertheimParam
numDiagram WertheimGCPM3PtEBondDecomp.VirialAssociatingFluidParam
numDiagram WertheimGCPM3PtThreeSite.VirialAssociatingFluidParam
numDiagram WertheimGCPM4PtEBondDecomp.WertheimAssociatingFluidParam
numDiagram WertheimGCPM4PtEBondDecompFinal.VirialAssociatingFluidParam
numDiagram WertheimGCPM4PtThreeSite.VirialAssociatingFluidParam
numDiagram WertheimGCPM4PtThreeSiteEDecompDirectSampling.VirialAssociatingFluidParam
numDiagrams() ClusterChainHS
numDiagrams() ClusterChainSoft
numDiagrams() ClusterSinglyConnected
numer() Rational
Get the numerator.
numerator Rational
numerator() Rational
Returns the numerator.
NumericFeature etomica.compatibility
NumericFeature(String, double) NumericFeature
numEval NormalModeAnalysisDisplay3DGraphic
numExtraTargetClusters SimulationVirialOverlap2
NumFieldNodes etomica.graph.property
Simple class that returns the number of field nodes.
NumFieldNodes() NumFieldNodes
numH ConformationAlkaneEH
numIncomingValues DataProcessorVirialOverlap
numInnerSteps IntegratorImageMultistepMD
numInnerSteps SimFe.LjMC3DParams
numInsert MCMoveOverlapListener
numInserts MCMoveClusterAtomHSRing
numMembraneLayers ConfigurationMembrane
numMembraneLayers ConfigurationMembraneWater
numMer MCMoveVolumeAssociated
numMer MCMoveVolumeAssociatedMolecule
numMol MeterOrientationOrderParameter
numMolec MCMoveVolumeN2
numMolec P0LatticeEnergyCorrec
numMolecule MCMoveRotateMolecule3DN2AveCosThetaConstraint
numMolecule MinimizeBetaNitrogenLatticeParameter
numMolecule MinimizeBetaNitrogenLatticeParameterFromFile
numMolecule MinimizeBetaNitrogenTranslationDOF
numMolecule MinimizeGammaNitrogenLatticeParameter
numMolecules SimGCPMWaterMCNPT.GCPMWaterMCParam
numMolecules SimGCPMWaterMCNVT.GCPMWaterMCParam
numMolecules SimDirectBetaN2RP.SimOverlapParam
numMolecules SimOverlapAlphaN2TP.SimOverlapParam
numMolecules SimOverlapBetaN2RP.SimOverlapParam
numMolecules SimOverlapBetaN2RPScaling.SimOverlapParam
numMolecules SimOverlapBetaN2TP.SimOverlapParam
numMolecules SimOverlapDisorderedAlphaN2RPScaling.SimOverlapParam
numMolecules SimOverlapDisorderedAlphaN2TP.SimOverlapParam
numMolecules SimOverlapNitrogenModel.SimOverlapParam
numMolecules MinimizeHCP
numMolecules MinimizeHCP.SimOverlapParam
numMolecules SimBennet.SimBennetParam
numMolecules SimEinStep1.SimOverlapParam
numMolecules SimEinStep1HCP.SimOverlapParam
numMolecules SimEinStep2.SimOverlapParam
numMolecules SimEinStep2HCP.SimOverlapParam
numMolecules SimHarmonicUmbrella.SimBennetParam
numMolecules SimOverlap.SimOverlapParam
numMolecules SimOverlapLJ.SimOverlapParam
numMolecules SimOverlapLJModule.SimOverlapParam
numMolecules SimOverlapSoftSphere.SimOverlapParam
numMolecules SimOverlapSoftSphereDP.SimOverlapParam
numMolecules SimOverlapSoftSphereEin.SimOverlapParam
numMolecules SimOverlapSoftSphereEinHarm.SimOverlapParam
numMolecules SimOverlapSoftSphereHCP.SimOverlapParam
numMolecules SimOverlapSoftSphereReweighting.SimOverlapParam
numMolecules SimOverlapSoftSphereSoftness.SimOverlapParam
numMolecules SimOverlapSoftSphereSuperBox.SimOverlapParam
numMolecules SimOverlapSoftSphereTPHCP.SimOverlapParam
numMolecules SimOverlapSoftSphereTPSlantedBox.SimOverlapParam
numMolecules SimOverlapSSnxy.SimOverlapParam
numMolecules SimTargetUmbrella.SimBennetParam
numMolecules SimUmbrella.SimBennetParam
numMolecules SimUmbrellaSoftSphere.SimBennetParam
numMolecules EwaldSumMolecules
numMolecules BenchSimSWChain
numMolecules BnFlexibleContributionTraPPEUAMethanol.VirialParam
numMolecules SimulationVirial
numMolecules VirialHePCKLJS.VirialParam
numMolecules VirialHePCKLJSCHNCCorrection.VirialLJParam
numMolecules VirialHePCKLJSPYCorrection.VirialLJParam
numMolecules VirialLJBridge.VirialLJParam
numMolecules VirialLJCHNCCorrection.VirialLJParam
numMolecules VirialLJPYCorrection.VirialLJParam
numMolecules VirialRowleyAlcohol.VirialParam
numMolecules VirialTraPPEAlcohol.VirialParam
numMolecules0 LjMd3D.DataProcessorReweight
numNeighborCandidatesOnDelete MCMoveInsertDeleteLatticeVacancy
numNeighborCandidatesOnDelete MCMoveInsertDeleteVacancy
numNeighbors MCMoveInsertDeleteLatticeVacancy
numNeighbors MCMoveInsertDeleteVacancy
numNewDeleteCandidates MCMoveInsertDeleteLatticeVacancy
numNewDeleteCandidates MCMoveInsertDeleteVacancy
numNonAdditiveNeeded ClusterSumMultibody
numP MeterDDP
numP MeterDP
numP SimOverlapSoftSphereDP.SimOverlapParam
NumRootNodes etomica.graph.property
Simple class that returns the number of root nodes.
NumRootNodes() NumRootNodes
numRuns LJmuVT.LJMCParams
numRuns LJNPT.LJMCParams
numRuns LJNVT.LJMCParams
numSamples MeterGs
numSavedBlockData AccumulatorAverageFixed
numsteps EFSTungsten.Params
numSteps TestAceticAcidMC3D_NPT.AceticAcidMCParam
numSteps Wertheim2SiteAceticAcid.WertheimParam
numSteps SimGCPMWaterMCNPT.GCPMWaterMCParam
numSteps SimGCPMWaterMCNVT.GCPMWaterMCParam
numSteps WertheimGCPM3PtEBondDecomp.VirialAssociatingFluidParam
numSteps WertheimGCPM3PtThreeSite.VirialAssociatingFluidParam
numSteps WertheimGCPM4PtEBondDecomp.WertheimAssociatingFluidParam
numSteps WertheimGCPM4PtEBondDecompFinal.VirialAssociatingFluidParam
numSteps WertheimGCPM4PtThreeSite.VirialAssociatingFluidParam
numSteps WertheimGCPM4PtThreeSiteEDecompDirectSampling.VirialAssociatingFluidParam
numSteps TestIGAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
numSteps TestLJAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
numSteps TestLJAssociationMC3D_NPT.VirialAssociatingFluidParam
numSteps TestLJAssociationMC3D_NVTOld.VirialAssociatingFluidParam
numSteps VLESim.GEMCParams
numSteps SimMappedRdf.LJMDParams
numSteps MappedU.LJMDParams
numSteps MappedVirialLJ.LJMDParams
numSteps MappedVirialLJVGr.LJMDParams
numSteps LJmuVT.LJMCParams
numSteps LJNPT.LJMCParams
numSteps LJNVT.LJMCParams
numSteps SimDirectBetaN2RP.SimOverlapParam
numSteps SimOverlapAlphaN2TP.SimOverlapParam
numSteps SimOverlapBetaN2RP.SimOverlapParam
numSteps SimOverlapBetaN2RPScaling.SimOverlapParam
numSteps SimOverlapBetaN2TP.SimOverlapParam
numSteps SimOverlapDisorderedAlphaN2RPScaling.SimOverlapParam
numSteps SimOverlapDisorderedAlphaN2TP.SimOverlapParam
numSteps SimOverlapNitrogenModel.SimOverlapParam
numSteps GlassClustering.SimParams
numSteps GlassProd.SimParams
numSteps HSDimerNPT.HSMD3DParameters
numSteps HSNPT.HSMD3DParameters
numSteps SimBennet.SimBennetParam
numSteps SimEinStep1.SimOverlapParam
numSteps SimEinStep1HCP.SimOverlapParam
numSteps SimEinStep2.SimOverlapParam
numSteps SimEinStep2HCP.SimOverlapParam
numSteps SimHarmonicUmbrella.SimBennetParam
numSteps SimLJHTTISuper.SimOverlapParam
numSteps SimLJHTTISuperHCP.SimOverlapParam
numSteps SimLJHTTISuperHCP2.SimOverlapParam
numSteps SimLJHTTISuperSFMD.SimOverlapParam
numSteps SimOverlap.SimOverlapParam
numSteps SimOverlapLJ.SimOverlapParam
numSteps SimOverlapLJModule.SimOverlapParam
numSteps SimOverlapSoftSphere.SimOverlapParam
numSteps SimOverlapSoftSphereDP.SimOverlapParam
numSteps SimOverlapSoftSphereEin.SimOverlapParam
numSteps SimOverlapSoftSphereEinHarm.SimOverlapParam
numSteps SimOverlapSoftSphereHCP.SimOverlapParam
numSteps SimOverlapSoftSphereReweighting.SimOverlapParam
numSteps SimOverlapSoftSphereSoftness.SimOverlapParam
numSteps SimOverlapSoftSphereSuperBox.SimOverlapParam
numSteps SimOverlapSoftSphereTP.SimOverlapParam
numSteps SimOverlapSoftSphereTPHCP.SimOverlapParam
numSteps SimOverlapSoftSphereTPSlantedBox.SimOverlapParam
numSteps SimOverlapSSnxy.SimOverlapParam
numSteps SimTargetUmbrella.SimBennetParam
numSteps SimUmbrella.SimBennetParam
numSteps SimUmbrellaSoftSphere.SimBennetParam
numSteps AshtonWildingLJ.simParams
numSteps AshtonWildingOsmoticVirial.simParams
numSteps AshtonWildingVirial.simParams
numSteps GCRestrictedGibbsHS.simParams
numSteps GCWidomInsertHS.simParams
numSteps NVTWidomInsertLJ.simParams
numSteps BenchSimSWChain
numSteps StarPolymerMC.PolymerParam
numSteps StarPolymerMD.PolymerParam
numSteps VirialPolymerOverlapMC.VirialHSParam
numSteps VirialPolymerOverlapWithMD.VirialHSParam
numSteps VirialPolymerOverlapWithMDB3.VirialHSParam
numSteps TestHSMD3D.SimParams
numSteps TestLJGCMC3D.SimParams
numSteps TestLJMC3D.SimParams
numSteps TestLJMD3D.SimParams
numSteps TestSWChain.SimParams
numSteps BnFlexibleContributionTraPPEUAMethanol.VirialParam
numSteps DoubleAssociationSitesFluid2Pt.VirialAssociatingFluidParam
numSteps DoubleAssociationSitesFluid3Pt.VirialAssociatingFluidParam
numSteps DoubleAssociationSitesFluid4Pt.VirialAssociatingFluidParam
numSteps FourAssociationSitesFluid2Pt.VirialAssociatingFluidParam
numSteps SingleAssociationSiteFluid.VirialAssociatingFluidParam
numSteps SingleAssociationSiteFluid2.VirialAssociatingFluidParam
numSteps SingleAssociationSiteFluid2Pt.VirialAssociatingFluidParam
numSteps SingleAssociationSiteFluid3Pt.VirialAssociatingFluidParam
numSteps SingleAssociationSiteFluid4Points.VirialAssociatingFluidParam
numSteps SingleAssociationSiteFluid4Pt.VirialAssociatingFluidParam
numSteps SingleAssociationSiteFluidGraph.VirialAssociatingFluidParam
numSteps TestLJAssociationMC3D_NPT.VirialAssociatingFluidParam
numSteps Virial2CLJmuQ.Virial2CLJQParam
numSteps Virial2CLJQ.Virial2CLJQParam
numSteps Virial7SiteRigidSF6.VirialSF6Param
numSteps VirialAceticAcid.VirialParam
numSteps VirialAceticAcidFlex.VirialParam
numSteps VirialAlkane.VirialSiepmannSpheresParam
numSteps VirialAlkaneEHTest.VirialParam
numSteps VirialAlkaneFlex.VirialSiepmannSpheresParam
numSteps VirialAlkaneFull.VirialSiepmannSpheresParam
numSteps VirialAlkaneMix_Kong.VirialAlkaneMixParam
numSteps VirialAlkaneMix.VirialAlkaneMixParam
numSteps VirialAlkaneMix2_Kong.VirialAlkaneMixParam
numSteps VirialAlkaneMix2.VirialAlkaneMixParam
numSteps VirialAlkaneSKS.VirialSiepmannSpheresParam
numSteps VirialAnthracene464.VirialAnthracene545Param
numSteps VirialAnthracene545.VirialAnthracene545Param
numSteps VirialAnthraceneTraPPE.VirialAnthraceneTraPPEParam
numSteps VirialAssociatingFluid.VirialAssociatingFluidParam
numSteps VirialAssociatingFluid4points.VirialAssociatingFluidParam
numSteps VirialB2WaterTIP4P_DHS_difference.VirialParam
numSteps VirialB3C1HSDipole.VirialParam
numSteps VirialB3C1TIP4Pwater.VirialParam
numSteps VirialB3C2HSDipole.VirialParam
numSteps VirialB3C2TIP4Pwater.VirialParam
numSteps VirialCH4AlkaneEHMix.VirialMixParam
numSteps VirialCO2.VirialCO2Param
numSteps VirialCO2AlkaneEHMix.VirialMixParam
numSteps VirialCO2AlkaneUAMix.VirialMixParam
numSteps VirialCO2anthracene464.VirialCO2anthracene545Param
numSteps VirialCO2anthracene545.VirialCO2anthracene545Param
numSteps VirialCO2AnthraceneTraPPE.VirialCO2AnthraceneTraPPEParam
numSteps VirialCO2CH4Mix.VirialMixParam
numSteps VirialCO2CH4UAMix.VirialMixParam
numSteps VirialCO2CH4UAMixWheatley.VirialMixParam
numSteps VirialCO2H2OGCPM.VirialParam
numSteps VirialCO2H2OGCPMX.VirialParam
numSteps VirialCO2H2OSC.VirialCO2SCParam
numSteps VirialCO2LJQ.VirialCO2LJQParam
numSteps VirialCO2N2Mix.VirialMixParam
numSteps VirialCO2NaphthaleneLJQ.VirialCO2NaphthaleneLJQParam
numSteps VirialCO2NaphthaleneTraPPE.VirialCO2TraPPEParam
numSteps VirialCO2PI.VirialH2PIParam
numSteps VirialCO2SKSMix.VirialCO2Param
numSteps VirialCO2TraPPE.VirialCO2TraPPEParam
numSteps VirialCPSHeliumNonAdditive.VirialParam
numSteps VirialEmulNonAdditive.VirialParam
numSteps VirialExternalFieldConfinedOverlap.VirialExternalFieldParam
numSteps VirialExternalFieldConfinedOverlapRho.VirialExternalFieldParam
numSteps VirialExternalFieldConfinedOverlapSW.VirialExternalFieldParam
numSteps VirialExternalFieldOverlapRho.VirialExternalFieldParam
numSteps VirialGCPM.VirialGCPMParam
numSteps VirialH2O.VirialH2OParam
numSteps VirialH2OGCPMD.VirialParam
numSteps VirialH2PI.VirialH2PIParam
numSteps VirialH2PIBoltzmann.VirialHePIParam
numSteps VirialH2PISimple.VirialH2PISimpleParam
numSteps VirialH2PIXC.VirialHePIParam
numSteps VirialH2PYCorrection.VirialH2PYCParam
numSteps VirialHardAssociationCone.VirialLJParam
numSteps VirialHardAssociationConeDoubleSites.VirialLJParam
numSteps VirialHeD.VirialParam
numSteps VirialHeNonAdditive.VirialParam
numSteps VirialHeNonAdditiveD.VirialParam
numSteps VirialHeNonAdditiveWheatley.VirialParam
numSteps VirialHePCKLJS.VirialParam
numSteps VirialHePCKLJSCHNCCorrection.VirialLJParam
numSteps VirialHePCKLJSPYCorrection.VirialLJParam
numSteps VirialHePCKLJSTempDeriv.VirialParam
numSteps VirialHePI.VirialHePIParam
numSteps VirialHePISysErr.VirialHePIParam
numSteps VirialHePIXC.VirialHePIParam
numSteps VirialHePIXCEven.VirialHePIParam
numSteps VirialHePYCorrection.VirialHePYCParam
numSteps VirialHeSC.VirialHePYCParam
numSteps VirialHS.VirialHSParam
numSteps VirialHSBinMultiThreaded.VirialHSBinParam
numSteps VirialHSMixture.VirialHSParam
numSteps VirialHSMixtureOverlap.VirialHSParam
numSteps VirialHSOrC.VirialLJrParam
numSteps VirialLJ.VirialLJParam
numSteps VirialLJBridge.VirialLJParam
numSteps VirialLJCHNCCorrection.VirialLJParam
numSteps VirialLJD.VirialLJParam
numSteps VirialLJDU.VirialLJParam
numSteps VirialLJMultiOverlap.VirialMixParam
numSteps VirialLJOrC.VirialLJrParam
numSteps VirialLJOrICPYC.VirialLJrParam
numSteps VirialLJPT.VirialLJParam
numSteps VirialLJPYCorrection.VirialLJParam
numSteps VirialLJSeries.VirialLJParam
numSteps VirialMethaneEH.VirialMethaneParam
numSteps VirialN2.VirialN2Param
numSteps VirialN2AlkaneEHMix.VirialMixParam
numSteps VirialN2AlkaneUAMix.VirialMixParam
numSteps VirialN2AlkaneUARigid.VirialMixParam
numSteps VirialN2CH4Mix.VirialMixParam
numSteps VirialN2CH4UAMix.VirialMixParam
numSteps VirialN2PI.VirialN2Param
numSteps VirialN2TraPPE.VirialN2Param
numSteps VirialNaphthaleneTraPPE.VirialNaphthaleneTraPPEParam
numSteps VirialO2.VirialO2Param
numSteps VirialO2PI.VirialO2Param
numSteps VirialPh464.VirialPh3site464Param
numSteps VirialPh545.VirialPh3site545Param
numSteps VirialPhenanthreneTraPPE.VirialPhenanthreneTraPPEParam
numSteps VirialPolyhedra.VirialHSParam
numSteps VirialPolyhedra2.VirialHSParam
numSteps VirialRowleyAlcohol.VirialParam
numSteps VirialSF6LJAlkaneUAMix.VirialMixParam
numSteps VirialSQWBinMultiThreaded.VirialHSBinParam
numSteps VirialSW.VirialSWParam
numSteps VirialSwsPT.VirialSiepmannSpheresParam
numSteps VirialSWWE.VirialSWWEParam
numSteps VirialTraPPE.VirialParam
numSteps VirialTraPPEAlcohol.VirialParam
numStepsComp PolydisperseHS.HSPolyParam
numStepsEq GlassProd.SimParams
numStepsEqu PolydisperseHS.HSPolyParam
numStepsProd PolydisperseHS.HSPolyParam
numSubSteps IntegratorOverlap
numSum MeterWorkHarmonicBennet
numSum MeterWorkHarmonicTargetandReweighting
numSum MeterWorkTargetBennet
numSum MeterWorkTargetHarmonicandReweighting
numSum MeterWorkUmbrellaHarmonic
numSum MeterWorkUmbrellaTarget
numSwaps MCMoveGeometricClusterRestrictedGE
numtm P2WaterPotentialsJankowski
numTrials MCMoveClusterAtomHSRing
numTypes DataSourcePercolation
numV SimHSMDVacancy.HSMDVParams
numV SimLJVacancy.LJParams
numWV NormalModeAnalysisDisplay3DGraphic
numXCells Sam
numZCells Sam
nValue(Token) ScriptVariable
nve SimFe.LjMC3DParams
nvt HSNPT.HSMD3DParameters
NVTWidomInsertLJ etomica.osmoticvirial
Calculate osmotic virial coefficients for Lennard-Jones potential in Canonical ensemble
from Free-Energy Perturbation Approach utilizing Widom's Insertion.
NVTWidomInsertLJ(int, double, double, double, double, boolean) NVTWidomInsertLJ
NVTWidomInsertLJ.simParams etomica.osmoticvirial
nWidomCavity HSMDWidom.HSMDParam
nx MeterPlaneSlip
ny MeterPlaneSlip
O
O EnumSiteName
obj TreeLinker
object DataTagBag
object ModifierGeneral
ObjectWrapper T > - Class in etomica.meta.wrappers
ObjectWrapper(T, SimulationModel, boolean) ObjectWrapper
objectWriter() EtomicaServer
occupancy Token
occupants() Cell
occupants() CellMolecular
Oelement SimpleElementForSimilarSpecies
of(double...) Vector
Returns a Vector initialized to the given set of values.
of(int...) Vector
Returns a Vector initialized to the given set of values (cast to double).
off Token
officialRelease JmolConstants
offScreen DisplayCanvas
offset P1ImageHarmonic
offset LatticeSumCrystalMolecular
offset P1Sinusoidal
offset SimOverlapLJModule.MeterPotentialEnergyDifference
offset MeterMappedAveragingCorrelation
offset PotentialGroup3PI.PotentialGroup3PISkip
offset PotentialGroupPI.PotentialGroupPISkip
offset MeshSurface
offset0 MeterPlaneSlip
offsetDim SimFe.LjMC3DParams
offsetDim SimIdealGas.LjMC3DParams
offsetDim SimLattice.LjMC3DParams
offsetDim SimLJ.LjMC3DParams
OH EnumSiteName
old ClusterChainHS
oldB MCMoveInsertDeleteLatticeVacancy
oldB MCMoveInsertDeleteVacancy
oldBalls DisplayBoxCanvas3DGlass
oldBondlengths MCMoveClusterRingRegrowExchange
oldBoxSize MCMoveInsertDeleteLatticeVacancy
oldCenter MCMoveClusterTorsionAlkaneEH
oldCenter MCMoveClusterTorsionMulti
oldColors ColorSchemeSmer
oldDiagram ClusterSumStickyEF
oldDirtyAtom ClusterSumPolarizableWertheimProduct
oldDirtyAtom ClusterSumPolarizableWertheimProduct4Pt
oldDirtyAtom ClusterSumPolarizableWertheimProduct4PtFinal
oldDirtyAtom ClusterTree
oldEigenVectors MCMoveWV
oldEnergy IntegratorMD
oldEpsilon B2Fit.FunctionMayerB2LJQ
oldG EllipseDisplayAction
oldGraphs Match
oldLnA MCMoveInsertDeleteLatticeVacancy
oldLnA MCMoveInsertDeleteVacancy
oldMu PNCO2GCPM
oldMu PNGCPM
oldOrientation MCMoveRotate
oldOrientations MCMoveClusterRingRegrowExchange
oldPartners PotentialReactive.BondChangeData
oldPhaseAngles MCMovePhaseAngle
oldPosition MCMoveAtomInRegion
oldPosition MCMoveInsertDeleteLatticeVacancy
oldPosition MCMoveInsertDeleteVacancy
oldPosition MCMoveGeometricCluster
oldPosition MCMoveGeometricClusterRestrictedGE
oldPositionAgentManager IntegratorMD
oldPositions MCMoveClusterRingPartialRegrow
oldPositions MCMoveClusterRingRegrow
oldPositions MCMoveClusterRingRegrowExchange
oldPositions MCMoveClusterTorsionAlkaneEH
oldPositions MCMoveClusterTorsionMulti
oldPotentialEnergy IntegratorMD
oldQ B2Fit.FunctionMayerB2LJQ
oldR MCMoveClusterAtomDiscrete
oldSigma B2Fit.FunctionMayerB2LJQ
oldStep MeterFlux
oldTime MeterFlux
oldTotalCosTheta MCMoveRotateMolecule3DN2AveCosThetaConstraint
oldValue ModifierPMu
oldValue ModifierTPI
oldWaveVectors MCMoveWV
OLIVE Colix
omdth IntegratorPolymer
omega Token
omega() Ifactor
The sum of the prime factor exponents, without multiplicity.
omega2 NormalModeAnalysisDisplay3DGraphic
omega2Table NormalModeAnalysisDisplay1DGraphic
omega2Table NormalModeAnalysisDisplay2DGraphic
omegaSquared MeterHarmonicEnergy
omegaSquared MeterHarmonicSingleEnergy
omegaTensor IntegratorRigidMatrixIterative
omegaTolerance IntegratorRigidIterative
omegaTolerance IntegratorRigidMatrixIterative
on Token
ON Debug
true if any debugging should be done
onClose(Session) ConfigurationWebsocket
onClose(Session) DataStreamWebsocket
ONE BitmapFactory
ONE BigSurd
The value of one.
ONE BigSurdVec
The value of one.
ONE Ifactor
oneEVal IntegratorHarmonic
oneIterate MoleculeIteratorAll
onError(Session, Throwable) ConfigurationWebsocket
onError(Session, Throwable) DataStreamWebsocket
ones DataDoubleBDArray
oneWV IntegratorHarmonic
onlyDoublyConnectedCB MyApplet
onlyRootPt MulFlexible.MulFlexibleParameters
onlySinglyConnectedCB MyApplet
onlyUnique AllIsomorphs.AllIsomorphsParameters
onMessage(Session, String) EchoServer
onOpen(Session) EchoServer
onOpen(Session, String) ConfigurationWebsocket
onOpen(Session, String, String) DataStreamWebsocket
onSourceTranscodingSuccess(SVGConverterSource, File) DefaultSVGConverterController
Invoked when the rasterizer successfully transcoded
the input source.
onSourceTranscodingSuccess(SVGConverterSource, File) Main
onSourceTranscodingSuccess(SVGConverterSource, File) SVGConverterController
Invoked when the rasterizer successfully transcoded
the input source.
onSwitch PRotConstraint
OO1 BiasVolume2SiteAceticAcid
OO1 BiasVolumeAceticAcid
OO2 BiasVolume2SiteAceticAcid
OO2 BiasVolumeAceticAcid
oops PNCO2GCPM
oops PNGCPM
oos DataClusterWriter
op UnaryChain
OPAQUE_MASK Colix
open() Viewer
open() ClusterViewer
openAlkaneView() ViewAlkaneLengthSelection
openFW(String) MeterTargetTPMolecule
Writes collected overlap data (for the "middle" alpha) to a file.
openFW(String) MeterTargetTP
Writes collected overlap data (for the "middle" alpha) to a file.
openResourceFile(String, Class<?>) Resources
openSimEnvParamView() ViewSimEnvironmentSelection
openStream() SVGConverterDocumentSource
openStream() SVGConverterFileSource
openStream() SVGConverterSource
Gets a TranscoderInput for that source
openStream() SVGConverterURLSource
opEQ Token
optimizeHigherbVirial(int, int, double, double) VirialOptimizer
optimizeRvdwWMin(P2QChemInterpolated) P2QChemInterpolated
optimizeRvdwWuTT3757(P2QChemInterpolated) P2QChemInterpolated
optionMap Main
Static map containing all the option handlers able to analyze the
various options.
Options() ParserLAMMPS.Options
opToggle Token
or(Bitmap) Bitmap
Updates this bitmap with the result of the bitwise AND with the other bitmap: bitmap
= (bitmap | other).
or(Bitmap) AbstractBitmap
or(Bitmap) BitmapOfLong
TIME = O(1) for a compatible instance.
or(Bitmap) BitmapOfLongVector
or(BitSet) BitSet
Performs a logical OR of this bit set with the bit set argument.
or01 P2CO2H2OWheatley
or01 P2CO2Hellmann.P2CO2SC
or01 P2NitrogenHellmann.P2N2QFH
or02 P2CO2H2OWheatley
or02 P2CO2Hellmann.P2CO2SC
or02 P2NitrogenHellmann.P2N2QFH
or11 P2CO2Hellmann.P2CO2SC
or11 P2NitrogenHellmann.P2N2QFH
or12 P2CO2Hellmann.P2CO2SC
or12 P2NitrogenHellmann.P2N2QFH
or2 P2WaterSzalewicz
or3 P3Induction
ORANGE Colix
order MayerPTAtt
order MayerSphericalPTAtt
order VirialSwsPT.VirialSiepmannSpheresParam
orderBeta VirialDiagramsPT
org.jmol.api - package org.jmol.api
org.jmol.awt - package org.jmol.awt
org.jmol.constant - package org.jmol.constant
org.jmol.g3d - package org.jmol.g3d
org.jmol.script - package org.jmol.script
org.jmol.util - package org.jmol.util
org.jmol.viewer - package org.jmol.viewer
orH2O3 P2CO2H2OWheatley
orientation FindPairMoleculeIndexBetaN2
orientation MoleculeOriented
orientation CoordinateDefinitionHSDimer
orientation MCMoveVolumeSolidNPTMolecularOriented
Orientation1D etomica.space1d
Orientation in a 1-dimensional space.
Orientation1D() Orientation1D
Construct with default orientation of +1.
Orientation2D etomica.space2d
Orientation in a 2-dimensional space.
Orientation2D() Orientation2D
Default constructor sets orientation angle to zero.
Orientation2D(Vector) Orientation2D
Constructs with orientation as specified by the given angle theta.
Orientation3D etomica.space3d
Orientation3D(Space) Orientation3D
Default constructor sets orientation to point in the X direction.
OrientationAgentSource() CoordinateDefinitionNitrogen.OrientationAgentSource
OrientationAgentSource() CoordinateDefinitionNitrogenSuperBox.OrientationAgentSource
OrientationCalc etomica.molecule
Interface for a class that can calculate the orientation of a molecule or
to set the orientation of a molecule.
OrientationCalcAtom etomica.molecule
OrientationCalc implementation that handles a monotomic oriented molecule.
OrientationCalcAtom() OrientationCalcAtom
OrientationCalcQuaternion etomica.molecule
OrientationCalc interface that handles quaternions (as a a double array)
instead of an Orientation object.
OrientationCalcWater3P etomica.models.water
OrientationCalcWater3P(Space) OrientationCalcWater3P
OrientationCalcWater4P etomica.models.water
OrientationCalcWater4P(Space) OrientationCalcWater4P
orientationColor DisplayBoxCanvas2D
OrientationFull3D etomica.space3d
OrientationFull3D(Space) OrientationFull3D
Default constructor sets orientation to point in the X direction.
orientationLength DisplayBoxCanvas2D
orientationManager CoordinateDefinitionNitrogen
orientationManager CoordinateDefinitionNitrogenSuperBox
orientationPlot InterfacialSWGraphic
orientationProfileMeter InterfacialSWGraphic
orientationProfilePump InterfacialSWGraphic
orientationSelector CoordinateDefinitionHSDimer
orientationX ConformationHSDimer
OrientedAgentSource() DisplayBoxCanvasG3DSys.OrientedAgentSource
OrientedFullSite(Vector, Color, double) DisplayBoxCanvasG3DSys.OrientedFullSite
OrientedSite(double, Color, double) DisplayBoxCanvasG3DSys.OrientedSite
orientVector CoordinateDefinitionNitrogen
originalBox MCMoveGeometricClusterRestrictedGE
originalGageLength MeterElongation
originalGageLength MeterStrain
originalPosition MeterRMSD
origins BoundaryRectangularNonperiodic
OrnsteinZernike etomica.virial
OrnsteinZernike() OrnsteinZernike
ortho IntegratorDimerRT
ortho2 IntegratorDimerRT
osg DisplayCanvas
osg Plot
osg Grabber.ImagePanel
Osmosis etomica.modules.osmosis
Osmosis module.
Osmosis(OsmosisSim, Space) Osmosis
Osmosis.InitializeMolecules etomica.modules.osmosis
Osmosis.MyWall etomica.modules.osmosis
osmosisPMeter Osmosis
OsmosisSim etomica.modules.osmosis
Osmosis simulation.
OsmosisSim(Space) OsmosisSim
otherAngles MeterTargetRPMolecule
otherAngles SimOverlapBetaN2RPScaling.SimOverlapParam
otherAngles SimOverlapDisorderedAlphaN2RPScaling.SimOverlapParam
otherDensities MeterDDP
otherDensities MeterDP
otherFrac MeterOverlapSwitch
otherFrac SimOverlapSoftSphereEin.SimOverlapParam
otherPotentials ReverseOsmosisGraphic.ModifierAtomDiameter
otherPurePotentials ReverseOsmosisGraphic.ModifierEpsilon
otherPurePotentials ReverseOsmosisWaterGraphic.ModifierAtomDiameter
otherPurePotentials ReverseOsmosisWaterGraphic.ModifierEpsilon
otherRho SimOverlapSoftSphereDP.SimOverlapParam
otherSpecies ReverseOsmosisGraphic.ModifierAtomDiameter
otherTemperature MeterBoltzmannHTTP
otherTemperatures MeterTargetTPMolecule
otherTemperatures SimOverlapAlphaN2TP.SimOverlapParam
otherTemperatures SimOverlapBetaN2TP.SimOverlapParam
otherTemperatures SimOverlapDisorderedAlphaN2TP.SimOverlapParam
otherTemperatures MeterTargetTP
otherTemperatures SimOverlapSoftSphereTP.SimOverlapParam
otherTemperatures SimOverlapSoftSphereTPHCP.SimOverlapParam
otherTemperatures SimOverlapSoftSphereTPSlantedBox.SimOverlapParam
out LJmuVT.LJMCParams
out LJNPT.LJMCParams
out LJNVT.LJMCParams
outData DataDistributer
outData DataGroupSplitter
outData DataSplitter
outDegree ClusterSumHS
outDegree ClusterWheatleyHS
outDegree ClusterWheatleyPartitionScreening
outDegreeCore ClusterWheatleyExtendSW
outDegreeWell ClusterWheatleyExtendSW
outNData DataProcessorDyDLnx
outNDataInfo DataProcessorDyDLnx
output MyApplet
outputArea Grabber
outRadius AtomTypeSpheroPolyhedron
oValue(ScriptVariable) ScriptVariable
OverflowShift etomica.graphics
overlapAvgA MultiharmonicGraphicMC
overlapAvgB MultiharmonicGraphicMC
overlapBlockCovSum AccumulatorVirialOverlapSingleAverage
overlapCorrelationSum AccumulatorVirialOverlapSingleAverage
overlapFirstBlock AccumulatorVirialOverlapSingleAverage
overlapMostRecentBlock AccumulatorVirialOverlapSingleAverage
Oxygen etomica.chem.elements
Class for the Oxygen element.
Oxygen(String) Oxygen
Oxygen(String, double) Oxygen
oy AkimaSplineSmoother
P
p RandomPositionSourceDeformable
p RandomPositionSourceRectangular
p MeterDDP
p MeterDP
p DisplayBoxCanvas2DNpTScaling
p P2HydrogenPatkowski
p P2HydrogenPatkowskiAtomic
p PotentialAtomicSum
p PotentialMolecularSum
p MayerIonicDiagram1qbond
p MayerIonicDiagram2qbonds
p MayerIonicDiagram4qbonds
p VirialDiagrams
p VirialDiagramsMix
p VirialDiagramsMix2
p VirialDiagramsPT
p WertheimDiagrams2SiteRho
p WertheimDiagrams3SiteRho
p PotentialNonAdditive
P ANIntergroupExchange
P ANIntragroupExchange
P ApiIntergroupExchange
P SimOverlapSoftSphereDP.SimOverlapParam
P P2HePCKLJS
P MCMoveClusterRingRegrowExchange
P_AD P2HePCJS
P_BO P2HePCJS
P_QED P2HePCJS
P_REL P2HePCJS
p0 MCMoveClusterAtomHSRing
P0LatticeEnergyCorrec etomica.models.nitrogen
The lattice energy correction for Nitrogen model
zero-body interaction
All the parameters are determined from the fitted equation.
P0LatticeEnergyCorrec(Space) P0LatticeEnergyCorrec
P0Lrc(Space, Potential2Soft, Potential2Soft, AtomType[]) P2SoftSphericalTruncated.P0Lrc
P0ReactionField(Space, P2ReactionFieldDipoleTruncated) P2ReactionFieldDipoleTruncated.P0ReactionField
p1 MyMCMove
p1 IntegratorImageHarmonicMD
p1 IntegratorImageMultistepMD
p1 IntegratorMDHarmonicMC
p1 MCMoveAtomCoupled
p1 MCMoveAtomNPath
p1 MCMoveAtomSwap
p1 ColloidGraphic.WallRangeModifier
p1 MCMoveMultiHarmonic
p1 MeterBoltzmannHTTP
p1 MeterDDP
p1 MeterDP
p1 MeterTargetTP
p1 P2HydrogenPatkowski
p1 P2HydrogenPatkowskiAtomic
p1 ClusterExchange
p1 P1IntraLambda
p1BoundaryA Mu
p1BoundaryB Mu
p1Constraint HTTPSoftSphereSim
p1Constraint SimCalcSLJ
p1Constraint SimCalcSSoftSphereFCC
p1Constraint SimOverlapLJ
p1Constraint SimOverlapSoftSphereHCP
p1Constraint SimOverlapSoftSphereTPHCP
P1Constraint etomica.normalmode
P1Constraint(Space, double, Box, CoordinateDefinition) P1Constraint
P1ConstraintNbr etomica.normalmode
P1ConstraintNbr(Space, double) P1ConstraintNbr
P1ConstraintNbr(Space, double, double) P1ConstraintNbr
P1ConstraintNbrHcp etomica.normalmode
P1ConstraintNbrHcp(Space, double, Box) P1ConstraintNbrHcp
p1Counter P1ConstraintNbrHcp
P1ExternalField etomica.potential
P1ExternalField(Space) P1ExternalField
P1HardBoundary etomica.potential
Potential that places hard repulsive walls coinciding with the
boundary of the box, which is assumed to be rectangular in shape.
P1HardBoundary(Space) P1HardBoundary
P1HardBoundary(Space, boolean) P1HardBoundary
P1HardMovingBoundary etomica.potential
Potential that places hard repulsive walls that move and
accelerate subject to an external force field (pressure).
P1HardMovingBoundary(Space, Boundary, int, double, boolean) P1HardMovingBoundary
Constructor for a hard moving (and accelerating) boundary.
P1HardPeriodic etomica.potential
pseudo-potential for a "collision" time to update colliders for periodic boundaries
P1HardPeriodic(Space) P1HardPeriodic
Returns an instance of P1HardPeriodic with sigma = NaN.
P1HardPeriodic(Space, double) P1HardPeriodic
Returns an instance of P1HardPeriodic with the given value of sigma (the
maximum distance between two atoms where they interact)
P1HardWall etomica.modules.osmosis
P1HardWall(Space) P1HardWall
P1HardWall(Space, double) P1HardWall
P1Harmonic etomica.potential
Potential in which attaches a harmonic spring between each affected atom and
the nearest boundary in each direction.
P1Harmonic(Space) P1Harmonic
P1HarmonicSite etomica.potential
Potential in which attaches a harmonic spring between each affected atom a
nominal site for that atom, as defined by an agent manager.
P1HarmonicSite(Space) P1HarmonicSite
P1HydrogenMielke etomica.potential
P1HydrogenMielke(Space) P1HydrogenMielke
P1HydrogenMielke.P1HydrogenMielkeAtomic etomica.potential
P1HydrogenMielke.P2HydrogenMielkeAtomic etomica.potential
P1HydrogenMielkeAtomic(Space) P1HydrogenMielke.P1HydrogenMielkeAtomic
p1ImageHarmonic SimFe
p1ImageHarmonic SimIdealGas
p1ImageHarmonic SimLJ
P1ImageHarmonic etomica.freeenergy.npath
Created by andrew on 4/11/17.
P1ImageHarmonic(Space, Vector, double, boolean) P1ImageHarmonic
p1Intra Sam
P1IntraLambda etomica.virial
P1IntraLambda(Space, double, P1IntraMolecular, double) P1IntraLambda
P1IntraMolecular etomica.potential
P1IntraSimple etomica.potential
Generic intramolecular potential group, having one potential for bonded
atoms, and a different potential for unbonded ones.
P1IntraSimple() P1IntraSimple
P1LepsHarmonic etomica.dimer
A combination of the basic LEPS potential describing 3 atoms moving in 1-dimension, paired with a harmonic potential.
P1LepsHarmonic(Space) P1LepsHarmonic
P1MagicWall etomica.modules.mu
P1MagicWall(Space, PotentialMasterList) P1MagicWall
P1MagneticField etomica.spin.ising
TODO To change the template for this generated type comment go to
Window - Preferences - Java - Code Style - Code Templates
P1MagneticField(Space) P1MagneticField
P1Sinusoidal etomica.modules.sam
P1Sinusoidal(Space) P1Sinusoidal
p1Smash Droplet
p1Smash DropletAtomic
P1Smash etomica.modules.droplet
Gravity-like potential that pushes the molecules toward the center.
P1Smash(Space) P1Smash
P1SoftBoundary etomica.potential
P1SoftBoundary(Space) P1SoftBoundary
P1SoftBoundary(Space, double) P1SoftBoundary
p1SurfaceBond Sam
p1Tension MaterialFracture
P1Tension etomica.modules.materialfracture
P1Tension(Space) P1Tension
P1Tether etomica.modules.rosmosis
Potential for a harmonic tether.
P1Tether(Box, ISpecies, Space) P1Tether
P1Wall etomica.interfacial
P1Wall etomica.modules.adsorption
P1Wall etomica.modules.colloid
P1Wall(Space) P1Wall
P1Wall(Space, double, double, double) P1Wall
P1Wall(Space, AtomLeafAgentManager) P1Wall
p1WallA Adsorption
p1WallA Mu
p1WallB Adsorption
p1WallB Mu
p1WallColloid ColloidSim
p1WallMonomer ColloidSim
P1WCAPorousWall etomica.modules.dcvgcmd
This acts as a 1-body WCA potential wall perpendicular to the z direction
with a hole.
P1WCAPorousWall(Space) P1WCAPorousWall
P1WCAPorousWall(Space, double, double) P1WCAPorousWall
P1WCAWall etomica.dcvgcmd
1-D potential that has a WCA form in the Z direction.
P1WCAWall etomica.modules.dcvgcmd
1-D potential that has a WCA form in the Z direction.
P1WCAWall etomica.modules.sam
1-D potential that has a WCA form in the Z direction.
P1WCAWall(Space, int) P1WCAWall
P1WCAWall(Space, int) P1WCAWall
P1WCAWall(Space, int) P1WCAWall
P1WCAWall(Space, int, double, double) P1WCAWall
P1WCAWall(Space, int, double, double) P1WCAWall
P1WCAWall(Space, int, double, double) P1WCAWall
p2 ColorSchemePaired
p2 MeterCavity
p2 PotentialCalculationEnergySumEAM
p2 DataSourceEnergies.PotentialCalculationEnergiesEAM
p2 VLESim
p2 PotentialCalculationMappedRdf
p2 MeterMeanForce
p2 PotentialCalculationMappedVirialV.UShift
p2 PotentialCalculationMappedVirialV.USine
p2 MeterDensityDistribution
p2 ModifierPMu
p2 Droplet
p2 MuGraphic.ModifierAtomDiameter
p2 MuGraphic.ModifierEpsilon
p2 MuGraphic.ModifierLambda
p2 SWVLESim
p2 P2HydrogenPatkowski
p2 P2HydrogenPatkowskiAtomic
p2 PotentialNonAdditiveDifference
p2 MCMoveRotate3Pair
p2 MCMoveRotatePair
p2 MeterMappedAveraging3Pair
p2 MeterMappedAveragingPair
p2 MeterMappedAveragingVSum3Pair
p2 MeterMappedAveragingVSumPair
p2 MCMoveClusterPolyhedraChain
p2 MCMoveClusterPolyhedraTree
P22CLJmuQ etomica.potential
Two-centered Lennard Jones heteronuclear molecule with a mu2 and quadrupole.
P22CLJmuQ(Space, double, double, double, double, double, double, double) P22CLJmuQ
P22CLJQ etomica.potential
Two-centered Lennard Jones molecule with a quadrupole.
P22CLJQ(Space) P22CLJQ
P22CLJQ(Space, double, double, double) P22CLJQ
p2AA Adsorption
p2AA ChainEquilibriumSim
p2AA FreeRadicalPolymerizationSim
p2AA SimGlass
p2AA SelfAssemblySim
p2AB Adsorption
p2AB FreeRadicalPolymerizationSim
p2AB1 SelfAssemblySim
p2AB2 SelfAssemblySim
P2AceticAcidTwoSite etomica.models.OPLS
P2AceticAcidTwoSite(double, boolean, int) P2AceticAcidTwoSite
P2Anharmonic etomica.potential
Harmonic Well interatomic potential.
P2Anharmonic(Space, double) P2Anharmonic
P2ArgonAziz1993 etomica.potential
Pair potential for argon from Aziz (1993) JCP 99(6): 4518.
P2ArgonAziz1993(Space) P2ArgonAziz1993
P2ArgonSlavicekEtAl2003 etomica.potential
Ab initio pair potential for argon from Slavicek et al.
P2ArgonSlavicekEtAl2003(Space) P2ArgonSlavicekEtAl2003
P2ArgonTangAndToennies2003 etomica.potential
Pair potential for argon from Tang and Toennies 2003.
P2ArgonTangAndToennies2003(Space) P2ArgonTangAndToennies2003
p2B1B1 SelfAssemblySim
p2B1B2 SelfAssemblySim
p2B2B2 SelfAssemblySim
p2BB Adsorption
p2BB ChainEquilibriumSim
p2BB FreeRadicalPolymerizationSim
p2Bond InterfacialSW
p2Bond SelfAssemblySim
p2BondCC Sam
p2BondCS Sam
p2CH2 Sam
p2CH2CH3 Sam
p2CH2CH3t Sam
p2CH2Surface Sam
p2CH2t Sam
p2CH3 Sam
p2CH3t Sam
p2Classy P2DiscreteFeynmanHibbs
p2Classy P2EffectiveFeynmanHibbs
p2Classy P2SemiclassicalAtomic
p2Classy P2SemiclassicalMolecular
P2CO2EMP etomica.potential
3-point potential for CO2.
P2CO2EMP(Space, double, double, double, double, double, double, double) P2CO2EMP
P2CO2EMP1 etomica.potential
EPM model for CO2.
P2CO2EMP1(Space) P2CO2EMP1
P2CO2EMP2 etomica.potential
EPM2 model for CO2
P2CO2EMP2(Space) P2CO2EMP2
P2CO2H2OSC(double) P2CO2H2OWheatley.P2CO2H2OSC
P2CO2H2OSCTI(double) P2CO2H2OWheatley.P2CO2H2OSCTI
P2CO2H2OWheatley etomica.models.co2
Ab initio potential for CO2-H2O by Wheatley and Harvey
http://dx.doi.org/10.1063/1.3574345
The CO2 molecule is expected first
P2CO2H2OWheatley(Space) P2CO2H2OWheatley
P2CO2H2OWheatley.P2CO2H2OSC etomica.models.co2
P2CO2H2OWheatley.P2CO2H2OSCTI etomica.models.co2
P2CO2Hellmann etomica.models.co2
Ab initio potential for CO2-CO2 developed by R.
P2CO2Hellmann(Space, P2CO2Hellmann.Parameters) P2CO2Hellmann
P2CO2Hellmann.P2CO2SC etomica.models.co2
P2CO2Hellmann.Parameters etomica.models.co2
P2CO2SC(double) P2CO2Hellmann.P2CO2SC
P2CO2TraPPE etomica.potential
I used this original EPM2model to describe TraPPECO2 model
the two models are different in parameters.
P2CO2TraPPE(Space) P2CO2TraPPE
P2Cohesion etomica.modules.droplet
Cohesive potential for mesoscale droplet simulation
P2Cohesion(Space) P2Cohesion
P2DiscreteFeynmanHibbs etomica.potential
Effective 2 body potential approximating the quantum behavior of atomic
interactions.
P2DiscreteFeynmanHibbs(Space, Potential2Spherical) P2DiscreteFeynmanHibbs
P2DiscreteFeynmanHibbs.P2HeEmpericalQuantum etomica.potential
P2DLPOLY etomica.potential
P2DLPOLY(Space) P2DLPOLY
P2DoubleWell etomica.potential
Double-well potential.
P2DoubleWell(Space) P2DoubleWell
P2DoubleWell(Space, double, double, double, double) P2DoubleWell
P2Dreiding etomica.potential
Dreiding potential.
P2Dreiding(Space, double, double) P2Dreiding
P2EAM etomica.eam
EAM (Embedded Atom Method) potential that pretends to be a pair potential.
P2EAM(Space, double, double, double, double, double, double, double) P2EAM
P2EffectiveFeynmanHibbs etomica.potential
Effective 2 body potential approximating the quantum behavior of atomic
interactions.
P2EffectiveFeynmanHibbs(Space, Potential2SoftSpherical) P2EffectiveFeynmanHibbs
P2Electrostatic etomica.potential
Simple electrostatic potential class.
P2Electrostatic(Space) P2Electrostatic
P2ElectrostaticWithHardCore etomica.potential
Simple electrostatic potential class.
P2ElectrostaticWithHardCore(Space) P2ElectrostaticWithHardCore
P2EwaldReal() EwaldSummation.P2EwaldReal
P2Exp6 etomica.potential
Exponential-6 atom-atom repulsion-dispersion potential.
P2Exp6(Space) P2Exp6
P2Exp6(Space, double, double, double) P2Exp6
P2Exp6Buckingham etomica.potential
The Buckingham Exponential-6 atom-atom dispersion potential.
P2Exp6Buckingham(Space, double, double, double, double) P2Exp6Buckingham
P2Fene etomica.potential
Finite elastic nonlinear extensible (FENE) spring potential.
P2Fene(Space) P2Fene
P2Fene(Space, double, double) P2Fene
P2H2OSC(double) P2WaterSzalewicz.P2H2OSC
P2HardAssociation etomica.potential
Purely attractive square-well potential with no repulsive core.
P2HardAssociation(Space) P2HardAssociation
P2HardAssociation(Space, double, double) P2HardAssociation
P2HardAssociationCone etomica.potential
Lennard-Jones potential with a square-well cone of attraction.
P2HardAssociationCone(Space) P2HardAssociationCone
P2HardAssociationCone(Space, double, double, double, double) P2HardAssociationCone
P2HardAssociationConeDoubleSites etomica.potential
Lennard-Jones potential with a square-well cone of attraction.
P2HardAssociationConeDoubleSites(Space, double, double, double, double) P2HardAssociationConeDoubleSites
P2HardAssociationConeFourSites etomica.potential
Lennard-Jones potential with a square-well cone of attraction.
P2HardAssociationConeFourSites(Space, double, double, double, double) P2HardAssociationConeFourSites
P2HardAssociationConeFourSitesSW etomica.potential
Square-Well cone of attraction for associating fluid theory
Four association sites
P2HardAssociationConeFourSitesSW(Space, double, double, double, double) P2HardAssociationConeFourSitesSW
P2HardAssociationConeOneSite etomica.potential
Lennard-Jones potential with a square-well cone of attraction.
P2HardAssociationConeOneSite(Space) P2HardAssociationConeOneSite
P2HardAssociationConeOneSite(Space, double, double, double, double) P2HardAssociationConeOneSite
P2HardAssociationConeReference etomica.potential
potential with a square-well cone of attraction for reference system.
P2HardAssociationConeReference(Space, double) P2HardAssociationConeReference
P2HardAssociationConeReferenceFourSites etomica.potential
potential with a square-well cone of attraction for reference system.
P2HardAssociationConeReferenceFourSites(Space, double) P2HardAssociationConeReferenceFourSites
P2HardAssociationConeSW etomica.potential
Square-Well cone of attraction for associating fluid theory
double association sites
P2HardAssociationConeSW(Space, double, double, double, double) P2HardAssociationConeSW
P2HardAssociationGCPMReference etomica.models.water
P2HardAssociationGCPMReference(Space, boolean) P2HardAssociationGCPMReference
P2HardAssociationRefAceticAcidTwoSite etomica.models.OPLS
P2HardAssociationRefAceticAcidTwoSite() P2HardAssociationRefAceticAcidTwoSite
P2HardBond etomica.potential
Potential that acts like a hard string connecting the centers of two atoms.
P2HardBond(Space) P2HardBond
P2HardBond(Space, double, double, boolean) P2HardBond
P2HardBondedList etomica.potential
Hard potential that wraps two others.
P2HardBondedList(Simulation, PotentialHard, PotentialHard) P2HardBondedList
P2HardBondedList.BondArrayList etomica.potential
P2HardSphere etomica.potential
Basic hard-(rod/disk/sphere) potential.
P2HardSphere(Space) P2HardSphere
P2HardSphere(Space, double, boolean) P2HardSphere
P2HardSphereCavity etomica.cavity
P2HardSphereCavity(Space) P2HardSphereCavity
P2HardSphereCavity(Space, IRandom, double) P2HardSphereCavity
P2HardSphereCavity.CollisionType etomica.cavity
P2HardSphereMC etomica.modules.colloid
P2HardSphereMC(Space, AtomLeafAgentManager<? extends IAtomList>, ISpecies) P2HardSphereMC
P2HardSpherePoly etomica.polydisperseHS
Basic hard-(rod/disk/sphere) potential.
P2HardSpherePoly(Space, double[], boolean) P2HardSpherePoly
P2HardWrapper etomica.potential
Hard potential class that wraps another hard potential.
P2HardWrapper(Space, PotentialHard) P2HardWrapper
P2Harmonic etomica.potential
Harmonic Well interatomic potential.
P2Harmonic(Space, double) P2Harmonic
P2Harmonic(Space, double, double) P2Harmonic
P2HC2Yukawa etomica.potential
Hard-core plus two Yukawa fluid (HC2Yukawa): A Lennard-Jones like potential.
P2HC2Yukawa(Space) P2HC2Yukawa
P2HC2Yukawa(Space, double, double) P2HC2Yukawa
p2Head InterfacialSW
p2HeadHead InterfacialSW
p2HeadTail InterfacialSW
P2HeEmpericalQuantum(Space, P2HePCKLJS, double) P2DiscreteFeynmanHibbs.P2HeEmpericalQuantum
P2HePCJS etomica.potential
pair potential for Helium Przybytek et al.
P2HePCJS(Space) P2HePCJS
P2HePCJS(Space, double) P2HePCJS
P2HePCKLJS etomica.potential
Ab initio pair potential for helium from Przybytek et al.
P2HePCKLJS(Space) P2HePCKLJS
P2HePCKLJS(Space, double) P2HePCKLJS
P2HePCKLJS.P2HeQFH etomica.potential
This inner class can calculates the Feynman-Hibbs semiclassical
approximation for the potential.
P2HePCKLJS.P2HeTI etomica.potential
P2HeQFH(double) P2HePCKLJS.P2HeQFH
P2HeQFH(double) P2HeSimplified.P2HeQFH
P2HeSimplified etomica.potential
Simplified pair potential for Helium.
P2HeSimplified(Space) P2HeSimplified
P2HeSimplified.P2HeQFH etomica.potential
This inner class can calculates the Feynman-Hibbs semiclassical
approximation for the potential.
P2HeSimplified.P2HeTI etomica.potential
P2HeTI(double) P2HePCKLJS.P2HeTI
P2HeTI(double) P2HeSimplified.P2HeTI
p2Hinde P2HydrogenHindePatkowski
p2Hinde P2HydrogenHindePatkowskiAtomic
P2HSDipole etomica.potential
Hard sphere molecule with a dipole sitting at the center.
P2HSDipole(Space) P2HSDipole
P2HSDipole(Space, double) P2HSDipole
P2HSDipole(Space, double, double) P2HSDipole
P2HSDipole(Space, double, double, double) P2HSDipole
P2HSPolymer etomica.starpolymer
P2HSPolymer(int, Space, IPotentialAtomic) P2HSPolymer
P2HydrogenHinde etomica.potential
P2HydrogenHinde(Space) P2HydrogenHinde
P2HydrogenHinde.P2HydrogenHindeAtomic etomica.potential
P2HydrogenHinde.P2HydrogenHindeMolecular etomica.potential
P2HydrogenHindeAtomic etomica.potential
P2HydrogenHindeAtomic(Space) P2HydrogenHinde.P2HydrogenHindeAtomic
P2HydrogenHindeAtomic(Space) P2HydrogenHindeAtomic
P2HydrogenHindeMolecular(Space) P2HydrogenHinde.P2HydrogenHindeMolecular
P2HydrogenHindePatkowski etomica.potential
P2HydrogenHindePatkowski(Space) P2HydrogenHindePatkowski
P2HydrogenHindePatkowski.P2HydrogenHindePatkowskiAtomic etomica.potential
P2HydrogenHindePatkowski.P2HydrogenHindePatkowskiMolecular etomica.potential
P2HydrogenHindePatkowskiAtomic etomica.potential
P2HydrogenHindePatkowskiAtomic(Space) P2HydrogenHindePatkowski.P2HydrogenHindePatkowskiAtomic
P2HydrogenHindePatkowskiAtomic(Space) P2HydrogenHindePatkowskiAtomic
P2HydrogenHindePatkowskiMolecular(Space) P2HydrogenHindePatkowski.P2HydrogenHindePatkowskiMolecular
P2HydrogenMielkeAtomic(Space) P1HydrogenMielke.P2HydrogenMielkeAtomic
P2HydrogenPatkowski etomica.potential
P2HydrogenPatkowski(Space) P2HydrogenPatkowski
P2HydrogenPatkowski.P2HydrogenPatkowskiAtomic etomica.potential
P2HydrogenPatkowski.P2HydrogenPatkowskiMolecular etomica.potential
P2HydrogenPatkowskiAtomic etomica.potential
P2HydrogenPatkowskiAtomic(Space) P2HydrogenPatkowski.P2HydrogenPatkowskiAtomic
P2HydrogenPatkowskiAtomic(Space) P2HydrogenPatkowskiAtomic
P2HydrogenPatkowskiIso etomica.potential
P2HydrogenPatkowskiIso(Space) P2HydrogenPatkowskiIso
P2HydrogenPatkowskiMolecular(Space) P2HydrogenPatkowski.P2HydrogenPatkowskiMolecular
P2Ideal etomica.potential
Ideal-gas two-body potential, which defines no interactions and zero energy
for all pairs given to it.
P2Ideal(Space) P2Ideal
P2LennardJones etomica.potential
Lennard-Jones interatomic potential.
P2LennardJones(Space) P2LennardJones
P2LennardJones(Space, double, double) P2LennardJones
P2LennardJonesDreiding etomica.potential
Dreiding: Lennard-Jones non-bonding potential.
P2LennardJonesDreiding(Space) P2LennardJonesDreiding
P2LennardJonesDreiding(Space, double, double) P2LennardJonesDreiding
p2LJ DropletAtomic
p2LJ MaterialFracture
p2LJ SimLJVacancy
P2LJDipole etomica.potential
Lennard Jones molecule with a point dipole sitting in the center.
P2LJDipole etomica.rotation
r^-12 potential plus a point dipole, force shifted, as used in
Kol, Laird and Leimkuhler, JCP 107 (1997) 2580-2588.
P2LJDipole(Space) P2LJDipole
P2LJDipole(Space, double, double, double) P2LJDipole
P2LJDipole(Space, double, double, double, double) P2LJDipole
p2LJQ VLESim
P2LJQ etomica.potential
Lennard Jones molecule with a quadrupole.
P2LJQ(Space) P2LJQ
P2LJQ(Space, double, double, double) P2LJQ
P2LJQQ etomica.potential
Lennard Jones molecule with a quadrupole.
P2LJQQ(Space) P2LJQQ
P2LJQQ(Space, double, double, double) P2LJQQ
p2LJt DropletAtomic
p2mc ColloidSim
p2mc NeighborListManagerColloid
p2Mix MuGraphic.ModifierAtomDiameter
p2Mix MuGraphic.ModifierEpsilon
p2Mix MuGraphic.ModifierLambda
p2mm ColloidSim
p2MM DCVGCMD
P2ModifiedMorse etomica.potential
P2ModifiedMorse(Space) P2ModifiedMorse
P2ModifiedMorse(Space, double, double, double, double, double, double) P2ModifiedMorse
P2MoleculeMonatomic etomica.potential
P2MoleculeMonatomic(IPotentialAtomic) P2MoleculeMonatomic
P2MoleculeSoftTruncatedSwitched etomica.potential
Wraps a soft-spherical potential to apply a truncation to it.
P2MoleculeSoftTruncatedSwitched(IPotentialMolecularTorque, double, Space) P2MoleculeSoftTruncatedSwitched
P2MoleculeTruncated etomica.potential
Wraps a soft-spherical potential to apply a truncation to it.
P2MoleculeTruncated(IPotentialMolecular, double, Space, IMoleculePositionDefinition) P2MoleculeTruncated
P2Morse etomica.potential
P2Morse(Space) P2Morse
P2Morse(Space, double, double, double) P2Morse
p2N2HellmannA VirialN2.VirialN2Param
P2N2QFH(double) P2NitrogenHellmann.P2N2QFH
P2Nitrogen etomica.models.nitrogen
P2 6-point potential for Nitrogen.
P2Nitrogen(Space, double) P2Nitrogen
P2NitrogenAB etomica.models.nitrogen
P2 6-point potential for Nitrogen.
P2NitrogenAB(Space, double) P2NitrogenAB
P2NitrogenAnisotropic etomica.models.nitrogen
P2 6-point potential for Nitrogen with anisotropic contribution
Reference: 1.
P2NitrogenAnisotropic(Space, double) P2NitrogenAnisotropic
P2NitrogenHellmann etomica.potential
P2NitrogenHellmann(Space) P2NitrogenHellmann
P2NitrogenHellmann.P2N2QFH etomica.potential
P2NitrogenShellModel etomica.models.nitrogen
CAUTION!!!!!! The potential DOES NOT really describe the ALPHA and GAMMA structure at
NON-ZERO temperature condition!!
(through observation [SimulationGraphic]
and pressure calculation[MeterPressureMolecular])
P2 shell-model potential for Nitrogen.
P2NitrogenShellModel(Space, double) P2NitrogenShellModel
P2O2Bartolomei etomica.potential
P2O2Bartolomei(Space) P2O2Bartolomei
P2O2Bartolomei.P2O2TI etomica.potential
P2O2TI(double) P2O2Bartolomei.P2O2TI
p2Other MuGraphic.ModifierAtomDiameter
p2Other MuGraphic.ModifierEpsilon
p2Other MuGraphic.ModifierLambda
p2Patkowski P2HydrogenHindePatkowski
p2Patkowski P2HydrogenHindePatkowskiAtomic
P2PenetrableBond etomica.potential
Potential with a well having a finite potential on either side.
P2PenetrableBond(Space) P2PenetrableBond
P2PenetrableBond(Space, double, double, boolean) P2PenetrableBond
P2PenetrableSphere etomica.potential
Basic penetrable-sphere potential.
P2PenetrableSphere(Space) P2PenetrableSphere
Constructor with default values of unity for core diameter and core energy.
P2PenetrableSphere(Space, double, double) P2PenetrableSphere
P2PenetrableSquareWell etomica.potential
Square-well potential with a penetrable core.
P2PenetrableSquareWell(Space) P2PenetrableSquareWell
P2PenetrableSquareWell(Space, double, double, double, boolean) P2PenetrableSquareWell
P2PotentialGroupBuilder etomica.potential
Creates a two-body potential group using model parameters for 1 or 2 species.
P2PotentialGroupBuilder() P2PotentialGroupBuilder
P2PotentialGroupBuilder(Space, P2PotentialGroupBuilder.ModelParams, P2PotentialGroupBuilder.ModelParams) P2PotentialGroupBuilder
P2PotentialGroupBuilder.ModelParams etomica.potential
p2pseudo NeighborListManagerColloid
P2QChem etomica.potential
This class requires a bash script called ./runQChem to load the appropriate Q-Chem module and run it.
P2QChem(Space) P2QChem
P2QChemInterpolated etomica.potential
Pair potential for argon interpolated from Q-Chem results.
P2QChemInterpolated(Space) P2QChemInterpolated
P2QChemInterpolated.DampingParams etomica.potential
P2ReactionFieldDipole etomica.potential
Potential to implement the reaction field treatment of electrostatic interactions.
P2ReactionFieldDipole(Space, IMoleculePositionDefinition) P2ReactionFieldDipole
P2ReactionFieldDipoleTruncated etomica.potential
P2ReactionFieldDipoleTruncated(Space, IMoleculePositionDefinition) P2ReactionFieldDipoleTruncated
P2ReactionFieldDipoleTruncated.P0ReactionField etomica.potential
A 0-body potential that should be added along with this potential.
P2RepRowley etomica.models.rowley
Purely repulsive potential from Rowley et al (2006) used for interactions between satellite sites, X.
P2RepRowley(Space) P2RepRowley
P2RepRowley(Space, double, double) P2RepRowley
P2RoughSphere etomica.potential
Basic hard-(rod/disk/sphere) potential, with surface roughness to couple rotation and translational motions.
P2RoughSphere(Space) P2RoughSphere
P2RoughSphere(Space, double, boolean) P2RoughSphere
p2S Sam
p2SCH2 Sam
p2SCH2t Sam
P2SemiclassicalAtomic etomica.potential
Effective semiclassical molecular potential using the approach of Takahashi and Imada
P2SemiclassicalAtomic(Space, IPotentialTorque, double) P2SemiclassicalAtomic
P2SemiclassicalAtomic.AtomInfo etomica.potential
P2SemiclassicalMolecular etomica.potential
Effective semiclassical molecular potential using the approach of
Takahashi and Imada
http://dx.doi.org/10.1143/JPSJ.53.3765
as described by Schenter
http://dx.doi.org/10.1063/1.1505441
P2SemiclassicalMolecular(Space, IPotentialMolecularTorque) P2SemiclassicalMolecular
P2SemiclassicalMolecular.MoleculeInfo etomica.potential
P2SemiclassicalMolecular.MoleculeInfoBrute etomica.potential
p2Soft Potential2SoftSphericalLSMulti
p2Soft Potential2SoftSphericalLSMultiLat
p2Soft Potential2SoftSphericalLS
P2SoftSphere etomica.potential
Soft-sphere interatomic potential.
P2SoftSphere(Space) P2SoftSphere
P2SoftSphere(Space, double, double, int) P2SoftSphere
P2SoftSphericalTruncated etomica.potential
Wraps a soft-spherical potential to apply a truncation to it.
P2SoftSphericalTruncated(Space, Potential2SoftSpherical, double) P2SoftSphericalTruncated
P2SoftSphericalTruncated.P0Lrc etomica.potential
Inner class that implements the long-range correction for this truncation scheme.
P2SoftSphericalTruncatedForceShifted etomica.potential
Soft-spherical potential class that shifts both the potential energy and the
force such that both are 0 at the cutoff.
P2SoftSphericalTruncatedForceShifted(Space, Potential2SoftSpherical, double) P2SoftSphericalTruncatedForceShifted
P2SoftSphericalTruncatedShifted etomica.potential
Wraps a soft-spherical potential to apply a truncation to it.
P2SoftSphericalTruncatedShifted(Space, Potential2SoftSpherical, double) P2SoftSphericalTruncatedShifted
P2SoftSphericalTruncatedSwitched etomica.potential
Wraps a soft-spherical potential to apply a truncation to it.
P2SoftSphericalTruncatedSwitched(Space, Potential2SoftSpherical, double) P2SoftSphericalTruncatedSwitched
P2SoftTruncated etomica.potential
Wraps a soft-spherical potential to apply a truncation to it.
P2SoftTruncated(Potential2Soft, double, Space) P2SoftTruncated
P2SpheroPolyhedron etomica.potential
P2SpheroPolyhedron(Space) P2SpheroPolyhedron
P2Spin etomica.spin.heisenberg
Magnetic spin potential, with an energy defined by
P2Spin etomica.spin.ising
Magnetic spin potential, with an energy defined by
P2Spin(Space) P2Spin
P2Spin(Space) P2Spin
P2Spin(Space, double) P2Spin
P2Spin(Space, double) P2Spin
P2SquareWell etomica.potential
Basic square-well potential.
P2SquareWell(Space) P2SquareWell
P2SquareWell(Space, double, double, double, boolean) P2SquareWell
P2SquareWellBonded etomica.modules.chainequilibrium
Similar to square-well potential, but considers and alters bonding states
with collisions.
P2SquareWellBonded etomica.modules.reactionequilibrium
Similar to square-well potential, but considers and alters bonding states
with collisions.
P2SquareWellBonded(Space, AtomLeafAgentManager<IAtom>, double, double, double, boolean) P2SquareWellBonded
P2SquareWellBonded(Space, AtomLeafAgentManager, double, double, double) P2SquareWellBonded
P2SquareWellBonded.RingResult etomica.modules.chainequilibrium
P2SquareWellBonding etomica.modules.catalysis
Basic square-well potential.
P2SquareWellBonding(Space, AtomLeafAgentManager, double, double, double, int, double, double, double) P2SquareWellBonding
P2SquareWellBondingCO etomica.modules.catalysis
Basic square-well potential.
P2SquareWellBondingCO(Space, AtomLeafAgentManager, double, double, double, int, double, double, double) P2SquareWellBondingCO
P2SquareWellMonomer etomica.modules.colloid
P2SquareWellMonomer(Space, AtomLeafAgentManager) P2SquareWellMonomer
P2SquareWellOneSide etomica.modules.mu
Basic square-well potential.
P2SquareWellOneSide(Space) P2SquareWellOneSide
P2SquareWellOneSide(Space, double, double, double, boolean) P2SquareWellOneSide
P2SquareWellRadical etomica.modules.chainequilibrium
Similar to square-well potential, but considers and alters bonding states
with collisions based on free radical reactions.
P2SquareWellRadical(Space, AtomLeafAgentManager, double, double, double, IRandom) P2SquareWellRadical
P2SquareWellRobust etomica.potential
Basic square-well potential.
P2SquareWellRobust(Space) P2SquareWellRobust
P2SquareWellRobust(Space, double, double, double, boolean) P2SquareWellRobust
P2SquareWellSurface etomica.modules.catalysis
Basic square-well potential.
P2SquareWellSurface(Space, AtomLeafAgentManager) P2SquareWellSurface
P2SquareWellSurface(Space, AtomLeafAgentManager, double, double, double, int) P2SquareWellSurface
p2St Sam
p2SulfurSurfaceLJ Sam
p2SurfaceBond Sam
p2Tail InterfacialSW
p2TailTail InterfacialSW
P2Tether etomica.potential
Potential that acts like a hard string connecting the centers of two atoms.
P2Tether(Space) P2Tether
P2Tether(Space, double, boolean) P2Tether
P2TriangleWell etomica.potential
Hard core with an attractive tail that goes to zero linearly with r.
P2TriangleWell(Space) P2TriangleWell
P2TriangleWell(Space, double, double, double) P2TriangleWell
p2Truncated VLESim
p2Truncated SimMappedRdf
p2Truncated MappedU
p2Truncated MappedVirialLJ
p2Truncated MappedVirialLJVGr
p2Truncated VLESim
P2Water3P etomica.models.water
3-point potential for water.
P2Water3P(Space, double, double, double, double) P2Water3P
P2Water3PSoft etomica.models.water
3-point potential for water that can calculate gradient and torque (for the
center of mass of the water molecule).
P2Water3PSoft(Space, double, double, double, double) P2Water3PSoft
P2Water4P etomica.models.water
4-point potential for water.
P2Water4P(Space, double, double, double, double, IMoleculePositionDefinition) P2Water4P
P2Water4PSoft etomica.models.water
3-point potential for water that can calculate gradient and torque (for the
center of mass of the water molecule).
P2Water4PSoft(Space, double, double, double, double, IMoleculePositionDefinition) P2Water4PSoft
P2Water4PSoft.AtomicTensorAtomicPair etomica.models.water
P2WaterDHS(Space, double, double) VirialB2WaterTIP4P_DHS_difference.P2WaterDHS
P2WaterPotentialsJankowski etomica.potential
P2WaterPotentialsJankowski(Space, int, int, double, IPotentialAtomic) P2WaterPotentialsJankowski
P2WaterSPC etomica.models.water
SPC potential for water.
P2WaterSPC(Space) P2WaterSPC
P2WaterSPCE etomica.models.water
SPC/E potential for water.
P2WaterSPCE(Space) P2WaterSPCE
P2WaterSPCSoft etomica.models.water
SPC potential for water.
P2WaterSPCSoft(Space) P2WaterSPCSoft
P2WaterSzalewicz etomica.models.water
Water potential as described by
http://dx.doi.org/10.1063/1.4875097
This class handles 2-body, 3-body and induction terms.
P2WaterSzalewicz(Space, int) P2WaterSzalewicz
P2WaterSzalewicz.Component etomica.models.water
P2WaterSzalewicz.P2H2OSC etomica.models.water
P2WaterTIP4P etomica.models.water
TIP4P potential for water.
P2WaterTIP4P(Space) P2WaterTIP4P
P2WaterTIP4P(Space, double) P2WaterTIP4P
P2WaterTIP4PHardCore etomica.models.water
4-point potential for water.
P2WaterTIP4PHardCore(Space, double, double, double, double, double) P2WaterTIP4PHardCore
P2WaterTIP4PSoft etomica.models.water
TIP4P potential for water.
P2WaterTIP4PSoft(Space, double, IMoleculePositionDefinition) P2WaterTIP4PSoft
P2WCA etomica.potential
Weeks-Chandler-Andersen potential.
P2WCA(Space) P2WCA
Constructs potential using default sigma and epsilon given by Default class.
P2WCA(Space, double, double) P2WCA
P2WCAP etomica.potential
LJ potential minus WCA.
P2WCAP(Space) P2WCAP
Constructs potential using default sigma and epsilon given by Default class.
P2WCAP(Space, double, double) P2WCAP
P2XOrder etomica.normalmode
Hard potential that enforces ordering of the x-coordinates of the
pairs.
P2XOrder(Space, Potential2HardSpherical) P2XOrder
P2Yukawa etomica.potential
Yukawa interatomic potential.
P2Yukawa(Space) P2Yukawa
P2Yukawa(Space, double, double) P2Yukawa
p3 MayerFunctionMolecularThreeBody
p3 MayerFunctionSphericalThreeBody
P3AdditiveQChem etomica.potential
P3AdditiveQChem() P3AdditiveQChem
P3AdditiveQChem.DampingParams etomica.potential
P3AxilrodTeller etomica.potential
Axilrod-Teller potential.
P3AxilrodTeller(Space, Map<AtomType, P3AxilrodTeller.MyAgent>) P3AxilrodTeller
P3AxilrodTeller.MyAgent etomica.potential
p3Bond Sam
P3BondAngle etomica.potential
Simple 3-body soft bond-angle potential
P3BondAngle(Space) P3BondAngle
P3BondAngleDreiding etomica.potential
Simple 3-body soft bond-angle for Dreiding potential
* U(theta) = gamma * [ cos(theta) - cos(theta_e)]^2
where gamma is the potential's energy parameter
theta_e is the equilibrium bond angle
P3BondAngleDreiding(Space, double, double) P3BondAngleDreiding
P3CPSNonAdditiveHe etomica.potential
Ab initio non-additive trimer potential for He developed by Cencek, Patkowski, and Szalewicz JCP 131 064105 2009.
P3CPSNonAdditiveHe(Space) P3CPSNonAdditiveHe
P3CPSNonAdditiveHe(Space, double) P3CPSNonAdditiveHe
P3CPSNonAdditiveHeLessSimplified etomica.potential
Ab initio non-additive trimer potential for He developed by Cencek, Patkowski, and Szalewicz JCP 131 064105 2009.
P3CPSNonAdditiveHeLessSimplified(Space) P3CPSNonAdditiveHeLessSimplified
P3CPSNonAdditiveHeOrig etomica.potential
Ab initio non-additive trimer potential for He developed by Cencek, Patkowski, and Szalewicz JCP 131 064105 2009.
P3CPSNonAdditiveHeOrig(Space) P3CPSNonAdditiveHeOrig
P3CPSNonAdditiveHeSimplified etomica.potential
Simplified version of ab initio, non-additive trimer potential for He developed by Cencek, Patkowski, and Szalewicz JCP 131 064105 2009.
P3CPSNonAdditiveHeSimplified(Space) P3CPSNonAdditiveHeSimplified
P3GCPMAxilrodTeller(Space) PNCO2GCPM.P3GCPMAxilrodTeller
P3GCPMAxilrodTeller(Space) PNGCPM.P3GCPMAxilrodTeller
P3HydrogenATM etomica.potential
P3HydrogenATM(Space) P3HydrogenATM
P3HydrogenATM.P3HydrogenAtomic etomica.potential
P3HydrogenAtomic(Space) P3HydrogenATM.P3HydrogenAtomic
P3HydrogenGarberoglioMolecular etomica.potential
P3HydrogenGarberoglioMolecular(Space) P3HydrogenGarberoglioMolecular
P3HydrogenManzhos etomica.potential
P3HydrogenManzhos(Space) P3HydrogenManzhos
P3HydrogenManzhos.P3HydrogenManzhosMolecular etomica.potential
P3HydrogenManzhosMolecular(Space) P3HydrogenManzhos.P3HydrogenManzhosMolecular
P3Induction etomica.potential
3-body induction potential based on form used by Oakley and Wheatley.
P3Induction(Space, Map<AtomType, P3Induction.MyAgent>) P3Induction
P3Induction.MyAgent etomica.potential
p3N2HellmannA VirialN2.VirialN2Param
p3N2HellmannA VirialN2PI.VirialN2Param
P3NitrogenHellmannNonAdditive etomica.potential
P3NitrogenHellmannNonAdditive(Space) P3NitrogenHellmannNonAdditive
p3ParametersFile VirialH2PI.VirialH2PIParam
P3QChem etomica.potential
P3QChem() P3QChem
P3QChem.DampingParams etomica.potential
p4BondCCCC Sam
p4BondCCCS Sam
P4BondTorsion etomica.potential
Torsion potential.
P4BondTorsion(Space, double, double, double, double) P4BondTorsion
P4BondTorsionAlkaneXCCH etomica.potential
slight modification from P4BondTorsion class(change energyAtAngle method)
Siepmann's Alkane TraPPE-EH model, XCCH torsion potential, X can be H or C, H is for H on CH3 only
U(torsion) = Cx * (1 -cos(3phi)); C(C):854K, C(H):717K
P4BondTorsionAlkaneXCCH(Space, double, double, double, double) P4BondTorsionAlkaneXCCH
P4BondTorsionOPLS etomica.potential
OPLS Torsion potential.
P4BondTorsionOPLS(Space, double, double, double, double) P4BondTorsionOPLS
P4TorsionDreiding etomica.potential
Simple 4-body soft bond-angle for Dreiding potential
U(phi) = (1/2) * Vjk * {1 - cos [njk (phi - phiEq)]}
where Vjk is the rotation barrier (always +ve) [unit Kelvin]
njk is the periodicity (an integer)
phiEq is the equilibrium dihedral angle [unit radians]
P4TorsionDreiding(Space, double, double, int) P4TorsionDreiding
pac AkimaSplineSmoother
PadeApproximation etomica.math.numerical
Class to approximate a power series with rational function (Pade Approximation)
Pade[K/L] = A_K/ C_L = B_M
with Kth, Lth and Mth order, where K + L = M
a0 + a1*x + a2*x^2 + ...
PadeApproximation(double[], int, int) PadeApproximation
PadeApproximation.VirialParam etomica.math.numerical
paint() ClusterPanel
paint() Plot
Classes which inherit from Plot must define this method.
paint(Graphics) DisplayCanvas
paint(Graphics) Plot
paint(Graphics) Grabber.ImagePanel
paintComponent(Graphics) EtomicaPlot
pair BiasVolume2SiteAceticAcid
pair BiasVolumeAceticAcid
pair ANIntergroupExchange
pair ApiIndexList
pair ApiInnerVariable
pair ApiIntergroup
pair PotentialCalculationMappedEnergy
pair PotentialCalculationMappedVirial
pair PotentialCalculationMappedVirialV
pair PNCO2GCPM
pair PNGCPM
pair CalcAnalytical2ndDerivativeNitrogen
pair MCMoveMoleculeCoupledInitPert
pair MCMoveMoleculeCoupledSuperBox
pair PNWaterGCPM
pair PNWaterGCPMReactionField
pair MpiInnerVariable
pair PotentialMasterCellMixed
pair NeighborListManagerSlantyMolecular
pair NeighborListManagerSlanty
pair MCMoveAtomCoupled
pair MCMoveAtomCoupledBennet
pair MCMoveAtomCoupledUmbrella
pair MCMoveAtomSuperBox
pair MCMoveMoleculeCoupled
pair PotentialNonAdditiveDifference
pair MeterMappedAveragingVSumPair
pair MCMoveClusterPolyhedraChain
pair MCMoveClusterPolyhedraTree
pairAB MCMoveMoleculeCoupledSuperBox
pairAB MCMoveRotateMolecule3DSuperBox
pairAB MCMoveAtomSuperBox
pairAgents PNGCPM
pairDone PotentialCommonAtomic
pairDone PotentialGroupPI
pairedAtom1 P2HardSphereCavity
pairedAtom2 P2HardSphereCavity
pairForce(IAtom, IAtom) P2Water4PSoft
pairId(int, int, int) VirialDiagrams
Returns the pair ID for the given indices (id0, id1, id2)
pairMatrix HarmonicAlphaNitrogenModelPairMolecule
pairMatrix HarmonicAlphaNitrogenModelPairMoleculeSequential
pairMatrix HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2
pairMatrix HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
pairMatrix HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
pairMatrix HarmonicBetaNitrogenModelPairMoleculeSequential
pairMatrix HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
pairMatrix HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2
pairMatrix HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
pairMatrix HarmonicBetaNitrogenModelPairMoleculeSequentialLS
pairMatrix HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
pairMatrix HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
pairOnly VirialH2PI.VirialH2PIParam
pairOnly VirialHePI_PotentialCorrection.VirialHePIParam
pairOnly VirialHePI.VirialHePIParam
pairOnly VirialHePISysErr.VirialHePIParam
pairOnly VirialHePIXCEven.VirialHePIParam
pairOnly VirialHePIXCOdd.VirialHePIParam
pairOnly VirialN2.VirialN2Param
pairOnly VirialN2PI.VirialN2Param
pairOnly VirialO2.VirialO2Param
pairOnly VirialO2PI.VirialO2Param
pairPolarization PNGCPM
pairPolarization PNWaterGCPM
pairPotential MCMoveMoleculeCoupledInitPert
pairPotential MCMoveAtomCoupled
pairPotential MCMoveMoleculeCoupled
pairPotentialIndex MCMoveAtomCoupled
pairSigma MCMoveClusterAtomHSChainMix
pairSigma MCMoveClusterAtomHSTreeMix
pairSum MeterVirialEBinMultiThreaded.MyDataCov
pairValues ClusterWheatleyMultibodyDerivatives
pairValues ClusterWheatleyMultibodyDerivativesBD
pairWell P2HardSphereCavity
PALETTE_ALTLOC StaticConstants
PALETTE_AMINO StaticConstants
PALETTE_CHAIN StaticConstants
PALETTE_CPK StaticConstants
PALETTE_ENERGY StaticConstants
PALETTE_FIXEDTEMP StaticConstants
PALETTE_FORMAL_CHARGE StaticConstants
PALETTE_GROUP StaticConstants
PALETTE_INSERTION StaticConstants
PALETTE_JMOL StaticConstants
PALETTE_MOLECULE StaticConstants
PALETTE_MONOMER StaticConstants
PALETTE_NONE StaticConstants
PALETTE_PARTIAL_CHARGE StaticConstants
PALETTE_POLYMER StaticConstants
PALETTE_PROPERTY StaticConstants
PALETTE_RASMOL StaticConstants
PALETTE_SHAPELY StaticConstants
PALETTE_STRAIGHTNESS StaticConstants
PALETTE_STRUCTURE StaticConstants
PALETTE_SURFACE StaticConstants
PALETTE_TEMP StaticConstants
PALETTE_TYPE StaticConstants
PALETTE_VARIABLE StaticConstants
PALETTE_VOLATILE StaticConstants
panel DeviceBox
Displayed panel that holds the label and value
(not yet used; meant to implement to make lightweight display)
panel DisplayPlot
panel DisplayTable
panel DisplayTextBox
Displayed panel that holds the label and value
(not yet used; meant to implement to make lightweight display)
panel AkimaSplineSmootherApp
panel ReactionEquilibrium
PanelMainFrame etomica.virial.GUI.containers
PanelMainFrame(int, int) PanelMainFrame
panelParentGroup DisplayTextBoxesCAE
parab P2WaterPotentialsJankowski
PARALLEL MeterCorrelation.CorrelationType
Parallelepiped etomica.math.geometry
A polyhedron composed of three pairs of rectangular faces placed opposite
each other and joined at arbitrary angles.
Parallelepiped(Space) Parallelepiped
Default constructor makes a cube of unit size
Parallelepiped(Space, Vector, Vector, Vector) Parallelepiped
Constructs a parallelepiped with the given edge vectors.
Parallelogram etomica.math.geometry
A quadrilateral with opposite sides parallel
.
Parallelogram(Space) Parallelogram
Default constructor makes a square of unit size
Parallelogram(Space, Vector, Vector) Parallelogram
Constructs a parallelogram with the given edge vectors.
Parallelotope etomica.math.geometry
Polytope having parallel faces, and which can be specified via a set of edge vectors.
param FitTanh
param P2WaterPotentialsJankowski
param FitTanh
Param() CH4NVT.Param
Param() DHS_NVT.Param
Param() DLJ_NVT_1site.Param
Param() DHS_NVT.Param
Param() DLJ_NVT_1site.Param
Param() TIP4P_NVT.Param
Param() Heisenberg.Param
Param() Heisenberg3Pair.Param
Param() HeisenbergPair.Param
PARAM_ALL MaxIsomorph
Parameters instance which does not filter out any graph property.
PARAM_ROOTY MaxIsomorph
ParameterBase etomica.util
Base class for all parameter wrapper implementations.
ParameterBase() ParameterBase
parameterGraphic() DevicePlotPoints
Returns the panel that contains the parameter sliders.
ParameterParser etomica.util
parameters MinimizeBetaNitrogenLatticeParameter
parameters MinimizeBetaNitrogenLatticeParameterFromFile
parameters MinimizeBetaNitrogenLatticeParameterLSFromFile
parameters MinimizeBetaNitrogenTranslationDOF
Parameters etomica.graph.operations
parametersB P2NitrogenHellmann
parametersB P3NitrogenHellmannNonAdditive
params UnaryChain.ChainParameters
params P2WaterSzalewicz
params P3CPSNonAdditiveHeLessSimplified
params P3CPSNonAdditiveHeSimplified
Params() EFSTungsten.Params
Params() HarmonicCrystalSsFccNxy.Params
params3 P2WaterSzalewicz
paramsManager P3AxilrodTeller
paramsManager P3Induction
paramsMap ConstructionParams
parent Atom
parentColor StrainColorScheme
parentGroup ApiIndexList
ParmedParser etomica.parser
Class that generates
ParmedStructure objects by invoking
the
ParmEd library and serializing its
Structure object using JSON.
ParmedParser() ParmedParser
ParmedStructure etomica.parser
Class that contains the data from a
ParmEd Structure,
and has methods to load this data into various
etomica components.
parse(Readable) SpeciesFileParser
parse(String) ParserImpl
parse(String) Parser
parse(String, ParsePosition) ScientificFormat
Parse out a number from the given text and return it as a Long if
possible; otherwise, return it as a Double.
parseARGB(String) Main.ColorOptionHandler
Parse the input value, which should be in the following
format: a.r.g.b where a, r, g and b are integer values,
in decimal notation, between 0 and 255.
parseArgs(String[]) ParseArgs
Parses each argument and attempts to match it with a field from
parameterWrapper and sets the field to the value from the next argument.
parseArgs(String[], boolean) ParseArgs
ParseArgs etomica.util
Class that handles parsing of commandline arguments.
ParseArgs() ParseArgs
ParseArgs(ParameterBase) ParseArgs
parseAsDecimal(String, ParsePosition) ScientificFormat
parse the input string, interpreting it as regular decimal format.
parseAsExponential(String, ParsePosition) ScientificFormat
parse the input string, interpreting it as exponential format.
parseAsFlexible(String, ParsePosition) ScientificFormat
parse the input string, interpreting it as either regular decimal
format or exponential format.
parseFloatArray(String) Parser
parseFloatArray2d(String) Parser
parseFloatArray3d(String) Parser
parseFloatArrayBsData(String[], BitSet, float[]) Parser
parseFloatArrayData(String[], float[]) Parser
parses a string array for floats.
parseFloatArrayDataN(String[], float[], int) Parser
parses a string array for floats.
parseFloatArrayFromMatchAndField(String, BitSet, int, int, int[], int, int, float[], int) Parser
the major lifter here.
parseFloatArrayNext(String, int[]) Parser
parseFloatNext(String, int[]) Parser
parseFloatRange(String, int, int[]) Parser
parseFloatStr(String) Parser
parseFloatStrict(String) Parser
parseGromacs(File, File) ParmedParser
Parses the given
Gromacs .top and .gro files
using the
ParmEd python library.
parseGromacsResourceFiles(String, String) ParmedParser
Convenience method to parse gromacs files located in the etomica-core/src/main/resources directory.
parseInt(String) Parser
parseIntNext(String, int[]) Parser
parseIntRadix(String, int) Parser
parseIntRange(String, int, int[]) Parser
parsePath(String) SpeciesFileParser
Parser org.jmol.util
Parser etomica.graph.engine
Parser() Parser
Parser.Assignment etomica.graph.engine
Parser.BinaryOp etomica.graph.engine
Parser.BinaryOpByte etomica.graph.engine
Parser.Command etomica.graph.engine
Parser.CommandPropertyValue etomica.graph.engine
Parser.CommandValue etomica.graph.engine
Parser.CommandVariable etomica.graph.engine
Parser.CommandVariableValue etomica.graph.engine
Parser.Constructor etomica.graph.engine
Parser.ConstructorColored etomica.graph.engine
Parser.ConstructorMono etomica.graph.engine
Parser.Expression etomica.graph.engine
Parser.ParserException etomica.graph.engine
Parser.Property etomica.graph.engine
Parser.Statement etomica.graph.engine
Parser.StrictExpression etomica.graph.engine
Parser.UnaryOp etomica.graph.engine
Parser.UnaryOpByte etomica.graph.engine
Parser.UnaryOpByteMap etomica.graph.engine
Parser.UnaryOpColor etomica.graph.engine
Parser.UnaryOpThreeColor etomica.graph.engine
Parser.UnaryOpTwoByte etomica.graph.engine
Parser.Value etomica.graph.engine
Parser.Variable etomica.graph.engine
parseRect(String) Main.RectangleOptionHandler
ParserException(String) Parser.ParserException
ParserException(String, Throwable) Parser.ParserException
ParserImpl etomica.graph.engine.impl
ParserImpl() ParserImpl
ParserLAMMPS etomica.parser
ParserLAMMPS() ParserLAMMPS
ParserLAMMPS.Options etomica.parser
ParserLAMMPS.Stuff etomica.parser
ParserLAMMPS.Truncation etomica.parser
parsers ParameterBase
parseStringInfestedFloatArray(String, BitSet, float[]) Parser
parses a "dirty" string for floats.
parseToken(String) Parser
parseTokenNext(String, int[]) Parser
parseTokenRange(String, int, int[]) Parser
parseTrimmed(String) Parser
parseTrimmedAt(String, int) Parser
parseTrimmedRange(String, int, int) Parser
PARTIAL_CHARGE EnumPalette
PARTIAL_CHARGE_COLIX_BLUE JmolConstants
PARTIAL_CHARGE_COLIX_RED JmolConstants
PARTIAL_CHARGE_COLIX_WHITE JmolConstants
PARTIAL_CHARGE_RANGE_SIZE JmolConstants
partialcharge Token
partialdots Token
particleCounters ANIntragroupExchange
particles ANIntragroupExchange
PartitionedIterator etomica.graph.iterators
PartitionedIterator(Map<Character, Byte>, Map<Character, Byte>) PartitionedIterator
partitions ClusterSinglyConnected
partitionsA ClusterWheatleyPartitionScreening
partitionsC ClusterWheatleyPartitionScreening
PartitionsP etomica.veos.bigdecimal
Number of partitions.
PartitionsP() PartitionsP
Default constructor initializing a list of partitions up to 7.
partnerColor ColorSchemeColliders
Color applied to the upList atom of the colliding pair
partners ApiIndexList
partners P1ImageHarmonic
pascal() P2O2Bartolomei
Pascal etomica.units
The Pascal unit of pressure, equal to 1 N/m^2.
path Token
pathforallfiles Token
pause Token
pause() Controller
PAUSE StatusAction.Status
pbuf Graphics3D
pbufT Graphics3D
pBW LJMC
pBW LJMD
pc ActionMinimizeEnergy
pc MeterPressureTensor
pc MeterRDFPC
pc DataSourceEnergies
pc MeterWallForce
pc MeterPUCut
pc MeterPUCutLS
pc MeterMappedRdf
pc MeterMappedU
pc MeterMappedVirial
pc MeterMappedVirialV
pc MaterialFracture
pc MeterLoad
pc MeterStress
pc PistonCylinderGraphic
pc MeterOsmoticPressure
pc MeterWallPressure
pc MeterEnergyMeanField
pc MeterMeanField
pCalc(double, double) Ushcats
pCalc(int, double[], double) QSeries
Computes the pressure via dlnQ/dV based on the volume series for Q given by coeffQ.
pcCSsum MeterEnergyMeanField
pcCSsum MeterMappedAveragingCorrelation
pcCSsum MeterMappedAveragingVSum
pcCvij MeterEnergyMeanField
pcDADv2 MeterPUCut
pcDADv2 MeterPUCutLS
pcDUDW DataSourceEnergies
pCenter MeterDDP
pCenter MeterDP
pcExtra MeterEnergyMeanField
pcForce MeterMappedRdf
pcForce MeterMappedU
pcForce MeterMappedVirial
pcForce MeterMappedVirialV
pcForce MeterMeanForce
pcForce SurfaceTensionMapped
pcForceSum MeterDADB
pcForceSum MeterSolidPropsLJ
PCJS VirialHePI.PotentialChoice
PCKLJS VirialHePI.PotentialChoice
PCopy etomica.graph.operations
PCopy() PCopy
pCore MCMoveClusterAtomSQWChain
pCore MCMoveClusterAtomSQWTree
pcPhiIJ MeterMappedAveragingVSum
pCross HSNPT
pData DataClusterer
pdbaddhydrogens Token
pdbgetheader Token
pdbsequential Token
PDBWriter etomica.action
Action that dumps a box's configuration to an PDB file.
PDBWriter() PDBWriter
PDBWriter(Box) PDBWriter
PDF DestinationType
PDF_CODE DestinationType
PDF_EXTENSION DestinationType
PDF_STR DestinationType
PE(double) IData
Plus-equals (+=) operation, adding given value to all values in data.
PE(double) DataDouble
Plus-equals (+=) operation.
PE(double) DataDoubleArray
Plus-equals (+=) operation.
PE(double) DataDoubleBDArray
Plus-equals (+=) operation.
PE(double) DataGroup
PE(double) DataTensor
Plus-equals (+=) operation.
PE(double) DataVector
Plus-equals (+=) operation.
PE(double) Tensor
"Plus equals" (+=) operation, adding the given value to each element of this tensor
PE(double) Vector
Plus-equals (+=) operation, causing a constant value to be added to all
components of this vector.
PE(double) Tensor1D
PE(double) Vector1D
PE(double) Tensor2D
PE(double) Vector2D
PE(double) Tensor3D
PE(double) Vector3D
PE(double) TensorND
PE(double) VectorND
PE(int, int, double) Tensor
"Plus equals" (+=) operation, performed on a single element of this tensor.
PE(int, int, double) Tensor1D
PE(int, int, double) Tensor2D
PE(int, int, double) Tensor3D
PE(int, int, double) TensorND
PE(IData) IData
Plus-equals (+=) operation.
PE(IData) DataDouble
Plus-equals (+=) operation.
PE(IData) DataDoubleArray
Plus-equals (+=) operation.
PE(IData) DataDoubleBDArray
Plus-equals (+=) operation.
PE(IData) DataGroup
PE(IData) DataTensor
Plus-equals (+=) operation.
PE(IData) DataVector
Plus-equals (+=) operation.
PE(Quaternion) Quaternion
Adds the input Quaternion components to its components.
PE(Tensor) Tensor
"Plus equals" (+=) operation, adding the elements of the given tensor to the
respective elements of this tensor
PE(Tensor) Tensor1D
PE(Tensor) Tensor2D
PE(Tensor) Tensor3D
PE(Tensor) TensorND
PE(Vector) Vector
Plus-equals (+=) operation.
PE(Vector) Vector1D
PE(Vector) Vector2D
PE(Vector) Vector3D
PE(Vector) VectorND
PE(IBigValue) BigValue
Plus-equals (+=) operation.
PE(IBigValue) IBigValue
Plus-equals (+=) operation.
PE(IBigValue) MyBigDecimal
Plus-equals (+=) operation.
PEa1Tt1(double, Tensor) Tensor
"Plus equals" (+=) operation based on a scalar and tensor.
PEa1Tt1(double, Tensor) Tensor1D
PEa1Tt1(double, Tensor) Tensor2D
PEa1Tt1(double, Tensor) Tensor3D
PEa1Tt1(double, Tensor) TensorND
PEa1Tv1(double, Vector) Vector
Increments (+=) components by (a1 * v1)
PEa1Tv1(double, Vector) Vector1D
PEa1Tv1(double, Vector) Vector2D
PEa1Tv1(double, Vector) Vector3D
PEa1Tv1(double, Vector) VectorND
PEa1Tv1(double, IBigValue) BigValue
Plus-equals (+=) a1 times v1.
PEa1Tv1(double, IBigValue) IBigValue
Plus-equals (+=) a1 times v1.
PEa1Tv1(double, IBigValue) MyBigDecimal
Plus-equals (+=) a1 times v1.
peek() RectangularLattice.Iterator
peek() RectangularLatticeNbrIterator
Returns the next iterate without advancing the iterator.
peek() SiteIterator
Returns the next iterate without advancing the iterator.
percent Token
Percent etomica.units
Decimal representation of something that represents the fractional
amount of a whole (e.g., mole fraction) as a percentage value typically
between 0 and 100.
percentvdwatom Token
PercolationByImmFrac() DataSourcePercolation.PercolationByImmFrac
percP DataSourcePercolation
PercusYevick etomica.virial
Calculates the Percus-Yevick (PY) virial coefficients of second to Mth order for any spherically-symmetric Mayer function, fr.
PercusYevick() PercusYevick
PercusYevick1QC etomica.virial
Computes the Percus-Yevick compressibility-route approximation to the
first quantum correction of Bn, where the first quantum correction is
as defined Kim and Henderson (1968,1966).
PercusYevick1QC() PercusYevick1QC
periodicity Mpi1ACell
periodicity MpiAACell
periodicity Api1ASite
PermutationDegenerateIterator etomica.math.discrete
Iterator that returns unique permutations of an array of integers, with
degeneracy such that some of the integers may appear more than once in the array.
PermutationDegenerateIterator(int) PermutationDegenerateIterator
Constructs instance whose iterates are int[] of length n.
PermutationIterator etomica.math.discrete
Iterator that returns different permutations of a sequence of integers when
called in successive iterations.
PermutationIterator etomica.virial.cluster
PermutationIterator(int) PermutationIterator
PermutationIterator(int[]) PermutationIterator
permutations ClusterBonds
Permutator etomica.graph.model
perParticleFrequency MCMoveBox
Flag indicating whether nominal frequency is interpreted as a
perParticleFrequency, or as a full frequency.
PERPENDICULAR MeterCorrelation.CorrelationType
perspective(int, float) G3DSys
Handles perspective based on depth and diameter.
perspectivedepth Token
perspectivemodel Token
pEst SimOverlapSoftSphereTP.SimOverlapParam
PETA Prefix
PEv1v2(Vector, Vector) Tensor
"Plus equals" (+=) operation with a dyad argument.
PEv1v2(Vector, Vector) Tensor1D
PEv1v2(Vector, Vector) Tensor2D
PEv1v2(Vector, Vector) Tensor3D
PEv1v2(Vector, Vector) TensorND
pFast LjMd3D.LjMd3DParams
pFF LJMC
pFF LJMD
pFull LjMd3D.LjMd3DParams
pFull PotentialNonAdditiveDifference
phaseAngles MeterStructureFactor
phaseAngles NormalModesVariable
phi MeterMappedAveragingSum.MoleculeAgent
phi MoleculeAgent
phi PotentialCalculationMoleculeAgentSum
phi PotentialCalculationPair
phi Token
phi() MeterMappedAveragingSum.MoleculeAgent
phi() MoleculeAgent
phi2Sum MeterTiltRotationStdev
phiData MeterDihedralAngle
phiEq P4TorsionDreiding
phiIJsum MeterMappedAveragingVSum
phiSlider SamGraphic
phiSum MeterTiltRotationStdev
phongexponent Token
phongExponent Shader
pi ColorSchemeScaledOverlap
pi(BigInteger) Prime
return the count of primes <= n
pi(MathContext) BigDecimalMath
Euler's constant.
pi32 SimLattice
picking Token
pickingspinrate Token
pickingstyle Token
picklabel Token
PICO Prefix
Picosecond etomica.units
Simulation unit of time.
pidOf(Object) EnumPalette
PINK Colix
PistonCylinder etomica.modules.pistoncylinder
Simple hard-sphere MD in piston-cylinder apparatus
PistonCylinder(int) PistonCylinder
PistonCylinderGraphic etomica.modules.pistoncylinder
PistonCylinderGraphic(PistonCylinder, Space) PistonCylinderGraphic
Creates a PistonCylinder graphic instance.
PistonCylinderGraphic.Applet etomica.modules.pistoncylinder
PistonCylinderGraphic.ModifierAtomDiameter etomica.modules.pistoncylinder
PistonCylinderGraphic.ModifierPistonDensity etomica.modules.pistoncylinder
PistonPlane etomica.modules.pistoncylinder
Wrap a P1HardMovingBoundary and make it look like a Plane.
PistonPlane(Space, P1HardMovingBoundary) PistonPlane
pistonPotential MeterRDFCylinder
pistonPotential PistonCylinder
pistonPotential PistonPlane
pistonUpdateRequested() IntegratorHardPiston
pivot MCMoveGeometricCluster
pivot MCMoveGeometricClusterRestrictedGE
pixel DisplayCanvas
Pixel etomica.units
Unit converting between simulation unit of length and pixels rendered in an
image.
Pixel() Pixel
Constructs with default of 10 pixels per Angstrom.
Pixel(double) Pixel
Constructor for Pixel.
pixelUnitToMillimeter SVGConverter
Millimeters Per Pixel
pixelX Grabber.CornerData
pixelY Grabber.CornerData
pj ColorSchemeScaledOverlap
pkl MCMoveClusterRingPartialRegrow
pkl MCMoveClusterRingRegrow
pkl MCMoveClusterRingRegrowExchange
PLANCK_H Constants
Planck's constant, in simulation units.
plane Token
Plane etomica.math.geometry
Class describing a plane occupying a 3-dimensional space.
Plane(Plane) Plane
Constructs a new Plane as a copy of the given one.
Plane(Space) Plane
Default constructor returns the y-z plane.
Plane(Space, double, double, double, double) Plane
Constructs a Plane satisfying the equation a x + b y + c z + d = 0
PLat MeterSolidProps
PLat MeterSolidPropsLJ
Platform org.jmol.awt
Platform() Platform
play Token
playDumb MCMoveIDBiasAction
playrev Token
plm(int, int, double) P2O2Bartolomei
plmrb(double[][], double, int) P2HydrogenPatkowski
plmrb(double[][], double, int) P2HydrogenPatkowskiAtomic
plot DisplayPlot
plot StatisticsMCGraphic.HistoryPlotBits
plot LJMD2D
Plot etomica.modules.clustergenerator
Used from comphys.graphic.plot
A class which makes plotting a little more convenient than using
Java's Graphics methods.
Plot() Plot
Constructor sets default size of the plot
Plot(Color, int, int) Plot
plot3d Token
plotAction AkimaSplineSmootherApp
plotAction AkimaSplineSmootherDyApp
PlotAction(int) AkimaSplineSmootherApp.PlotAction
PlotAction(int) AkimaSplineSmootherDyApp.PlotAction
plotBox(double, double, double, double) Plot
plotD PistonCylinderGraphic
plotImage(int, int, int, Image, Graphics3D, short, int, int) GData
plotImage(int, int, int, Object, Graphics3D, short, int, int) Graphics3D
plotImagePixel(int, int, int, int, int, int) Graphics3D
plotLine(double, double, double, double) Plot
plotP PistonCylinderGraphic
plotPanel SimulationPanel
plotPixelClippedP3i(Point3i) Graphics3D
plotRDF PistonCylinderGraphic
plots VirialRowleyAlcohol
plotsPane PistonCylinderGraphic
plotString(String, double, double) Plot
plotStringCenter(String, double, double) Plot
plotT PistonCylinderGraphic
plotText(int, int, int, int, int, String, JmolFont, Graphics3D) Graphics3D
plotText(int, int, int, int, int, String, JmolFont, Graphics3D) GData
plus(Complex) Complex
Addition of Complex numbers (doesn't change this Complex number).
plus(Rational) Rational
Returns a new Rational instance, which is the result of adding the given
Rational to this Rational.
pmesh Token
pN2HellmannA VirialN2PI.VirialN2Param
pNA MayerFunctionNonAdditiveFull
PNCO2GCPM etomica.models.co2
GCPM CO2 potential class (GCPCDO).
PNCO2GCPM(Space) PNCO2GCPM
PNCO2GCPM(Space, int) PNCO2GCPM
PNCO2GCPM.Component etomica.models.co2
PNCO2GCPM.P3GCPMAxilrodTeller etomica.models.co2
PNG DestinationType
PNG_CODE DestinationType
PNG_EXTENSION DestinationType
PNG_STR DestinationType
PNGCPM etomica.models.co2
Generic GCPM potential class, capable of handling both CO2 and water.
PNGCPM(Space, Map<AtomType, PNGCPM.GCPMAgent>, int) PNGCPM
PNGCPM(Space, Map<AtomType, PNGCPM.GCPMAgent>, int, int) PNGCPM
PNGCPM.Component etomica.models.co2
PNGCPM.GCPMAgent etomica.models.co2
PNGCPM.P3GCPMAxilrodTeller etomica.models.co2
PNGCPM.PNGCPMCached etomica.models.co2
PNGCPMCached() PNGCPM.PNGCPMCached
PNGCPMX etomica.models.co2
GCPM potential that allows combining parameters to be adjusted.
PNGCPMX(Space, Map<AtomType, PNGCPM.GCPMAgent>, int, double, double, double) PNGCPMX
PNGCPMX(Space, Map<AtomType, PNGCPM.GCPMAgent>, int, double, double, double, int) PNGCPMX
PNWaterGCPM etomica.models.water
GCPM Water potential class.
PNWaterGCPM(Space) PNWaterGCPM
PNWaterGCPM.Component etomica.models.water
PNWaterGCPM.PNWaterGCPMCached etomica.models.water
PNWaterGCPMCached() PNWaterGCPM.PNWaterGCPMCached
PNWaterGCPMReactionField etomica.models.water
GCPM Water potential class including Reaction Field Method.
PNWaterGCPMReactionField(Space) PNWaterGCPMReactionField
PNWaterGCPMThreeSite etomica.models.water
GCPM Water potential with three association site for Wertheim approach.
PNWaterGCPMThreeSite(Space, double, boolean) PNWaterGCPMThreeSite
PNWaterGCPMThreeSite(Space, double, boolean, boolean) PNWaterGCPMThreeSite
pochhammer(BigDecimal, int) BigDecimalMath
Pochhammer's function.
Pochhammer(int) Rational
Compute pochhammer's symbol (this)_n.
Pochhammer(BigInteger) Rational
Compute Pochhammer's symbol (this)_n.
point Token
Point etomica.math.geometry
A zero-dimensional polytope, a mathematical point in space.
Point(Space) Point
Point(Space, Vector) Point
Point3f org.jmol.util
A 3 element point that is represented by single precision floating point
x,y,z coordinates.
Point3f() Point3f
Point3fi org.jmol.util
the Point3fi class allows storage of critical information involving
an atom, picked bond, or measurement point, including:
xyz position
screen position
screen radius (-1 for a simple point)
index (for atoms or for an associated bond that has be picked)
associated modelIndex (for measurement points)
Point3fi() Point3fi
Point3i org.jmol.util
A 3 element point that is represented by signed integer x,y,z coordinates.
Point3i() Point3i
Point4f org.jmol.util
A 4 element point that is represented by single precision floating point
x,y,z,w coordinates.
Point4f() Point4f
Constructs and initializes a Point4f to (0,0,0,0).
pointCharges ConformationEthanol
pointCharges ConformationMethanol
pointCharges DimerApproach
pointCharges VirialRowleyAlcohol
pointCount() ClusterDiagramTree
pointCount() ClusterAbstract
Number of points in the cluster.
pointCount() ClusterBonds
pointCount() ClusterChainHS
pointCount() ClusterChainSoft
pointCount() ClusterConstant
pointCount() ClusterCoupledFlipped
pointCount() ClusterCoupledFlippedMultivalue
pointCount() ClusterCoupledFlippedPartial
pointCount() ClusterDifference
pointCount() ClusterExchange
pointCount() ClusterMultiToSingle
pointCount() ClusterMultivalueUmbrella
pointCount() ClusterSinglyConnected
pointCount() ClusterSum
pointCount() ClusterSumHS
pointCount() ClusterSumNonAdditiveTrimerEnergy
pointCount() ClusterSumPolarizable
pointCount() ClusterSumPolarizableWertheimProduct
pointCount() ClusterSumPolarizableWertheimProduct4Pt
pointCount() ClusterSumPolarizableWertheimProduct4PtFinal
pointCount() ClusterTree
pointCount() ClusterWeightAbs
pointCount() ClusterWeightSumWall
pointCount() ClusterWeightUmbrella
pointCount() ClusterWheatleyExtendSW
pointCount() ClusterWheatleyHS
pointCount() ClusterWheatleyMultibodyDerivatives.ClusterRetrievePrimes
pointCount() ClusterWheatleyMultibodyDerivativesBD.ClusterRetrievePrimes
pointCount() ClusterWheatleyPartitionScreening
pointCount() ClusterWheatleyPT.ClusterRetrieveOrders
pointCount() ClusterWheatleyPT.ClusterRetrievePrimesBD
pointCount() ClusterWheatleyPT
pointCount() ClusterWheatleySoft
pointCount() ClusterWheatleySoftBD
pointCount() ClusterWheatleySoftDerivatives.ClusterRetrievePrimes
pointCount() ClusterWheatleySoftDerivatives.ClusterRetrievePrimesBD
pointCount() ClusterWheatleySoftDerivatives
pointCount() ClusterWheatleySoftDerivativesBD.ClusterRetrievePrimes
pointCount() ClusterWheatleySoftDerivativesBD
pointCount() VirialH2OGCPMD.Clusterfoo
pointgroupdistancetolerance Token
pointgrouplineartolerance Token
PointsToggler() MyApplet.PointsToggler
Poise etomica.units
The Poise unit of viscosity, equal to 1 gram/(cm-sec).
pol P2WaterSzalewicz
polar VirialTraPPE.TraPPEParams
polE1 P2WaterSzalewicz
polSite P3Induction.MyAgent
PolydisperseHS etomica.polydisperseHS
Three-dimensional hard-sphere molecular dynamics simulation, using
neighbor listing.
PolydisperseHS(PolydisperseHS.HSPolyParam) PolydisperseHS
Makes a simulation according to the specified parameters.
PolydisperseHS.HSPolyParam etomica.polydisperseHS
Polygon etomica.math.geometry
Representation of a mathematical polygon, a 2-dimensional polytope.
Polygon(LineSegment[]) Polygon
Constructs a polygon using the given edges for its sides.
Polygon(Space, int) Polygon
Constructs a polygon with the given number of sides arranged in a closed loop.
polygonColixes MeshSurface
polygonCount MeshSurface
polygonCount0 MeshSurface
PolygonGeneral etomica.math.geometry
TODO To change the template for this generated type comment go to Window -
Preferences - Java - Code Style - Code Templates
PolygonGeneral(LineSegment[]) PolygonGeneral
PolygonGeneral(Space, int) PolygonGeneral
polygonIndexes MeshSurface
polyhedra Token
Polyhedron etomica.math.geometry
Representation of a mathematical polyhedron, a 3-dimensional polytope.
Polyhedron(Polygon[]) Polyhedron
Constructs a polyhedron with the given faces for its sides.
PolyhedronGeneral etomica.math.geometry
Representation of a mathematical polyhedron, a 3-dimensional polytope.
PolyhedronGeneral(Polygon[]) PolyhedronGeneral
polymer Token
POLYMER EnumPalette
polymerlength Token
polymerList CriterionTether3
PolymerParam() StarPolymerMC.PolymerParam
PolymerParam() StarPolymerMD.PolymerParam
polymerSpecies CriterionTether3
PolynomialFit etomica.math.numerical
Class that performs a polynomial fit to x,y data, optionally taking weights
associated with each data point.
PolynomialFit() PolynomialFit
PolynomialFit.FitResult etomica.math.numerical
polySigma PolydisperseHS.HSPolyParam
polytope DisplayPolytope
Polytope etomica.math.geometry
Representation of a mathematical polytope, which is a finite region of space
enclosed by a finite number of hyperplanes.
Polytope(Polytope[]) Polytope
Constructs a polytope of dimension D from the D-1 finite "planes" that
constitute it.
populate(AtomArrayList, IAtom, boolean) AssociationHelperBranched
populate(AtomArrayList, IAtom, IAtom, boolean) AssociationHelperDouble
populate(MoleculeArrayList, IMolecule, boolean) AssociationHelperMolecule
populateArrays(int, boolean) DataOverlapCaching
populateArrays(int, boolean) DataOverlap
populateBonds(Graph, List<ClusterBonds>, List<Double>, boolean) VirialDiagramsPT
populateEFBonds(Graph, ArrayList<ClusterBonds>, boolean) MayerIonicDiagram1qbond
populateEFBonds(Graph, ArrayList<ClusterBonds>, boolean) MayerIonicDiagram2qbonds
populateEFBonds(Graph, ArrayList<ClusterBonds>, boolean) MayerIonicDiagram4qbonds
populateEFBonds(Graph, ArrayList<ClusterBonds>, boolean) WertheimDiagrams2SiteRho
populateEFBonds(Graph, ArrayList<ClusterBonds>, boolean) WertheimDiagrams3SiteRho
populateEFBonds(Graph, List<ClusterBonds>, List<Double>, boolean) VirialDiagrams
populateEFBonds(Graph, List<ClusterBonds>, List<Double>, int, int, boolean, boolean, int) VirialDiagramsMix2
populateEFdfdTBonds(Graph, ArrayList<ClusterBonds>, boolean) VirialDiagrams
populateEFdfdTdf2dT2Bonds(Graph, ArrayList<ClusterBonds>, boolean) VirialDiagrams
populateList(AtomArrayList) MCMoveAtomMonomer
populateList(AtomArrayList) MCMoveAtomSmer
populateList(AtomArrayList) MCMoveBiasUB
populateList(AtomArrayList) MCMoveRotateAssociated
populateList(AtomArrayList) MCMoveSmer
populateList(AtomArrayList) MCMoveSmerRotate
populateList(AtomArrayList, IAtom) MCMoveVolumeAssociated
populateList(AtomArrayList, IAtom, boolean) AssociationHelperBranched
populateList(AtomArrayList, IAtom, boolean) AssociationHelperDouble
populateList(AtomArrayList, IAtom, boolean) AssociationHelperSingle
populateList(AtomArrayList, IAtom, boolean) IAssociationHelper
Populates smerList with all atoms in the smer that contains atom.
populateList(MoleculeArrayList, IMolecule, boolean) AssociationHelperMolecule
populateList(MoleculeArrayList, IMolecule, boolean) IAssociationHelperMolecule
Populates smerList with all molecules in the smer that contains molecule.
populateVDWDiameters(DiameterHashByElement) DiameterHashByElement
Populates the given instance with diameters based on atomic radii
(taken from various sources).
PopupListener(JPopupMenu) DisplayPlot.PopupListener
popupMenu DisplayPlot.PopupListener
poreCenter DCVGCMD
poreCenter DCVGCMD
pos P2CO2Hellmann
pos CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
pos CalcNumerical2ndDerivativeNitrogen
pos MCMoveRotateMoleculePhiTheta
pos MeterPlaneSlip
pos P2NitrogenHellmann
pos P3HydrogenGarberoglioMolecular
pos P3NitrogenHellmannNonAdditive
posA P2CO2Hellmann
posB P2CO2Hellmann
position Atom
position MeterProfileByAtoms
position MeterProfileByVolume
position Polytope
position LatticeSumCrystalMolecular
position MoleculeOriented
position MeterDisplacementMoleculeRMS
position(IMolecule) IMoleculePositionDefinition
Returns the defined position for the given molecule.
position(IMolecule) MoleculePositionCOM
position(IMolecule) MoleculePositionFirstAtom
position(IMolecule) MoleculePositionGeometricCenter
position(IMolecule) MoleculePositionGeometricCenterAlkaneEH
position(IMolecule) MoleculePositionGeometricCenterPBC
positionDefinition ConfigurationLattice
positionDefinition MeterProfileByVolume
positionDefinition IntegratorRigidMatrixIterative.BoxImposePbcMolecule
positionDefinition MCMoveRotateMolecule3D
positionDefinition FindPairMoleculeIndex
positionDefinition FindPairMoleculeIndexBetaN2
positionDefinition MCMoveRotateMolecule3DConstraint
positionDefinition MCMoveRotateMolecule3DFixedAngle
positionDefinition MCMoveRotateMolecule3DN2AveCosThetaConstraint
positionDefinition MCMoveRotateMolecule3DSuperBox
positionDefinition P2Water4P
positionDefinition ConfigurationMembrane
positionDefinition ConfigurationMembraneWater
positionDefinition MeterFlux
positionDefinition Sam
positionDefinition BoxAgentSourceCellManager
positionDefinition BoxAgentSourceCellManagerMolecular
positionDefinition NeighborCellManagerMolecular
positionDefinition NeighborCellManager
positionDefinition CoordinateDefinitionMolecule.MoleculeSiteSource
positionDefinition CoordinateDefinitionMolecule
positionDefinition CoordinateDefinitionMoleculeVolumeFluctuation.MoleculeSiteSource
positionDefinition CoordinateDefinitionMoleculeVolumeFluctuation
positionDefinition P2MoleculeTruncated
positionDefinition P2ReactionFieldDipole
positionDefinition P2ReactionFieldDipoleTruncated
positionDefinition PotentialGroupSoft
positionDefinition BoxCluster
positionDefinition ClusterCoupledFlipped
positionDefinition ClusterCoupledFlippedMultivalue
positionDefinition ClusterCoupledFlippedPartial
positionDefinition CoordinatePairMoleculeSet
positionDefinition MCMoveClusterTorsionAlkaneEH
positionDefinition MCMoveClusterTorsionMulti
positionDefinition(IMolecule) MCMoveVolumeAssociatedMolecule
positions SimDimerLJadatom
positions CoordinatePairLeafSet
positionSelectedAtoms MCMoveClusterWiggleAlkaneEH
positionSource MeterProfile
positionSource MeterWidomInsertion
positionSource MCMoveInsertDelete
positionSource MCMoveMoleculeExchange
positionSource MeterWidomInsertionCorrection
positionSource MeterWidomInsertionP
positionSource MCMoveGeometricCluster
positionSource MCMoveGeometricClusterRestrictedGE
positionVector CoordinateDefinitionNitrogen
positionVector LatticeSumCrystalMolecular
postAction SimulationRestart
postAction ConfigFromFileLAMMPS.ModifierConfiguration
posVec P2WaterPotentialsJankowski
posVecToAtoms(Vector[], Vector[]) P2WaterPotentialsJankowski
pot PotentialCommonAtomic
poten() P2WaterPotentialsJankowski
potential TestAceticAcidMC3D_NPT
potential SimGCPMWaterMCNPT
potential SimGCPMWaterMCNVT
potential TestIGAssociationMC3D_NPT_DoubleSites
potential TestLJAssociationMC3D_NPT_DoubleSites
potential TestLJAssociationMC3D_NPT
potential TestLJAssociationMC3D_NVTOld
potential HSMDCavity
The hard-sphere potential governing the interactions.
potential HSMDWidom
The hard-sphere potential governing the interactions.
potential MeterEnergy
potential MeterPotentialEnergy
potential SimFe
potential SimIdealGas
potential SimLJ
potential MCMove
potential LjMC3D
potential LjMd3D
potential MeterPotentialEnergyCutoff
potential CalcAnalytical2ndDerivativeNitrogen
potential CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
potential CalcNumerical2ndDerivativeNitrogen
potential HarmonicAlphaNitrogenModel
potential HarmonicAlphaNitrogenModelDecomposed
potential HarmonicAlphaNitrogenModelPairMolecule
potential HarmonicAlphaNitrogenModelPairMoleculeSequential
potential HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2
potential HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
potential HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
potential HarmonicBetaNitrogenModel
potential HarmonicBetaNitrogenModelDecomposed
potential HarmonicBetaNitrogenModelPairMoleculeSequential
potential HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
potential HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2
potential HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
potential HarmonicBetaNitrogenModelPairMoleculeSequentialLS
potential HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
potential HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
potential MCMoveMoleculeCoupledSuperBox
potential MinimizationBetaNitrogenModel
potential MinimizationBetaNitrogenModelLS
potential MinimizeBetaNitrogenLatticeParameterLSFromFile
potential MinimizeGammaNitrogenLatticeParameter
potential SimOverlapAlphaN2TP
potential SimOverlapBetaN2RPScaling
potential SimOverlapBetaN2TP
potential SimOverlapDisorderedAlphaN2RPScaling
potential SimOverlapDisorderedAlphaN2TP
potential SimulationAlphaNitrogenModel
potential SimulationBetaNitrogenModel
potential SimulationBetaNitrogenModelTest
potential SimulationGammaNitrogenModel
potential DCVGCMD
potential SimGlass.GlassParams
potential ReverseOsmosisGraphic.ModifierAtomDiameter
potential ReverseOsmosisGraphic.ModifierEpsilon
potential ReverseOsmosisWaterGraphic.ModifierAtomDiameter
potential ReverseOsmosisWaterGraphic.ModifierEpsilon
potential LJVacancyMin
potential MCMoveAtomSuperBox
potential MeterAPIPotentialEnergy
potential HSNPT2DSim
potential SimHSMDVacancy
potential SimLJHTTISuper
potential SimLJHTTISuperHCP
potential SimLJHTTISuperHCP2
potential SimLJHTTISuperSFMD
potential SimLJVacancy
potential AshtonWildingLJ
potential PolydisperseHS
The hard-sphere potential governing the interactions.
potential P2MoleculeSoftTruncatedSwitched
potential P2MoleculeTruncated
potential P2ReactionFieldDipoleTruncated.P0ReactionField
potential P2SoftSphericalTruncated
potential P2SoftSphericalTruncatedSwitched
potential PotentialGroup.PotentialLinker
potential PotentialMaster.PotentialLinker
potential ChainHSMD3D
potential GEMCWithRotation
potential HSMD3D
The hard-sphere potential governing the interactions.
potential HSMD3DNoNbr
potential LJMD2D
potential LJMD3D
potential LJMD3DNbr
potential SoftSphere3d
potential SWMD2D
potential SWMD3D
potential Heisenberg
potential Heisenberg3Pair
potential HeisenbergPair
potential Ising
potential TestLJGCMC3D
potential TestLJMC3D
potential TestLJMD3D
potential MayerGeneralAtomic
potential TestLJAssociationMC3D_NPT
potential VirialHeD.VirialParam
potential VirialHeNonAdditiveD.VirialParam
Potential etomica.potential
Superclass for all Potential classes, which define how the atoms in the
system interact with each other.
Potential(int, Space) Potential
General constructor for a potential instance
Potential0 etomica.potential
Potential that does not depend on any atom positions.
Potential0(Space) Potential0
Potential0Lrc etomica.potential
Zero-body potential implementing the long-range correction
that compensates for truncation of the potential.
Potential0Lrc(Space, AtomType[], IPotentialAtomic) Potential0Lrc
potential1 DCVGCMD
potential1 AshtonWildingOsmoticVirial
potential1 AshtonWildingVirial
potential1 GCRestrictedGibbsHS
potential1 GCWidomInsertHS
potential1 NVTWidomInsertLJ
Potential1 etomica.potential
Potential acting on a single atom or atom group.
Potential1(Space) Potential1
Potential1.Intramolecular etomica.potential
Marker interface indicating that a one-body potential is an intramolecular
potential, and not, e.g., a potential of interaction with an external field.
potential11 ReverseOsmosis
potential11 HSMC2D
potential11 HSMD2D
potential12 ReverseOsmosis
potential12 AshtonWildingOsmoticVirial
potential12 GCRestrictedGibbsHS
potential12 GCWidomInsertHS
potential12 NVTWidomInsertLJ
potential12 HSMC2D
potential12 HSMD2D
potential2 AshtonWildingOsmoticVirial
potential2 GCRestrictedGibbsHS
potential2 GCWidomInsertHS
potential2 NVTWidomInsertLJ
Potential2 etomica.potential
Potential acting on 2 atoms or molecules.
Potential2(Space) Potential2
Constructs potential with given space.
potential22 ReverseOsmosis
potential22 HSMC2D
potential22 HSMD2D
Potential2HardSpherical etomica.potential
Methods for a hard (impulsive), spherically-symmetric pair potential.
Potential2HardSpherical(Space) Potential2HardSpherical
Potential2Soft etomica.potential
Methods for properties obtained for a soft, differentiable pair potential.
Potential2SoftSpherical etomica.potential
Methods for a soft (non-impulsive), spherically-symmetric pair potential.
Potential2SoftSpherical(Space) Potential2SoftSpherical
Potential2SoftSphericalLS etomica.potential
Methods for a soft (non-impulsive), spherically-symmetric pair potential.
Potential2SoftSphericalLS(Space, double, double[], Potential2Soft) Potential2SoftSphericalLS
Potential2SoftSphericalLSMulti etomica.liquidLJ
Methods for a soft (non-impulsive), spherically-symmetric pair potential.
Potential2SoftSphericalLSMulti(Space, double[], Potential2Soft) Potential2SoftSphericalLSMulti
Potential2SoftSphericalLSMultiLat etomica.liquidLJ
Class for spherical pair potential that computes lattice sums for various
truncations.
Potential2SoftSphericalLSMultiLat(Space, double[], Potential2Soft, CoordinateDefinition) Potential2SoftSphericalLSMultiLat
Potential2SoftSphericalLSMultiLat.ReturnValue etomica.liquidLJ
Potential2SoftSphericalLSMultiLatSlanty etomica.liquidLJ
Methods for a soft (non-impulsive), spherically-symmetric pair potential.
Potential2SoftSphericalLSMultiLatSlanty(Space, double[], Potential2Soft, CoordinateDefinition, int[]) Potential2SoftSphericalLSMultiLatSlanty
Potential2Spherical etomica.potential
interface for spherical 2-body potentials
potentialA MultiharmonicMC
potentialA MultiharmonicMC
potentialA MultiharmonicMC
potentialAA MCMoveRotateMolecule3DSuperBox
potentialAA Mu
potentialAA OsmosisSim
potentialAB Mu
potentialAB OsmosisSim
potentialAddedNotify(IPotentialAtomic, PotentialGroup) PotentialMasterHybrid
potentialAddedNotify(IPotentialAtomic, PotentialGroup) PotentialMasterNbr
potentialAddedNotify(IPotentialAtomic, PotentialGroup) PotentialMaster
Notifies the PotentialMaster that the sub-potential has been added to
the given PotentialGroup, which is associated (but not necessarily held
by) this PotentialMaster.
potentialAgentManager PotentialMasterMonatomic
PotentialArray etomica.potential
Instances of this class are created by AtomType classes to
store the list of potentials and criteria that apply to
the atoms of that type.
PotentialArray() PotentialArray
PotentialArrayByType etomica.potential
This class stores an array of Potentials and remembers the "other" IAtomType
that the IPotential applies to.
PotentialArrayByType() PotentialArrayByType
PotentialArrayMolecular etomica.potential
Instances of this class are created by MoleculeType classes to
store the list of potentials and criteria that apply to
the molecules of that type.
PotentialArrayMolecular() PotentialArrayMolecular
potentialAtomic PotentialMolecularMonatomic
PotentialAtomicSum etomica.potential
Atomic potential class that simply sums up contributions from multiple
(atomic) potentials.
PotentialAtomicSum(IPotentialAtomic[]) PotentialAtomicSum
potentialAtt MayerPTAtt
potentialB MultiharmonicMC
potentialB MultiharmonicMC
potentialB MultiharmonicMC
potentialBB Mu
potentialBB OsmosisSim
PotentialCalculation etomica.potential
Class defining a particular action to be performed on a set of atoms using an
arbitrary potential.
PotentialCalculationCSsum(double[], double[]) MeterEnergyMeanField.PotentialCalculationCSsum
PotentialCalculationDUDW etomica.freeenergy.npath
Potential calculation whose sole purpose in life is to invoke getDUDW
Created by andrew on 5/8/17.
PotentialCalculationDUDW() PotentialCalculationDUDW
PotentialCalculationEFSSP etomica.normalmode
PotentialCalculationEFSSP(Space, Box, CoordinateDefinition, double, double, boolean) PotentialCalculationEFSSP
PotentialCalculationEnergies() DataSourceEnergies.PotentialCalculationEnergies
PotentialCalculationEnergiesEAM(P2EAM) DataSourceEnergies.PotentialCalculationEnergiesEAM
PotentialCalculationEnergySum etomica.potential
Evaluates the energy summed over all iterated atoms.
PotentialCalculationEnergySum() PotentialCalculationEnergySum
PotentialCalculationEnergySumBigDecimal etomica.potential
Mimics original PotentialEnergySum calculation, but uses a BigDecimal
representation for the sum.
PotentialCalculationEnergySumBigDecimal(int) PotentialCalculationEnergySumBigDecimal
PotentialCalculationEnergySumCutoff etomica.liquidLJ
Evaluates the energy summed over all iterated atoms.
PotentialCalculationEnergySumCutoff(Space, double[]) PotentialCalculationEnergySumCutoff
PotentialCalculationEnergySumEAM etomica.eam
Evaluate the energy for the EAM model using the P2EAM potential.
PotentialCalculationEnergySumEAM(P2EAM) PotentialCalculationEnergySumEAM
PotentialCalculationForcePressureSum etomica.potential
Sums the force on each iterated atom and adds it to the integrator agent
associated with the atom.
PotentialCalculationForcePressureSum(Space) PotentialCalculationForcePressureSum
PotentialCalculationForcePressureSumGB etomica.dimer
Sums the force on each iterated atom and adds it to the integrator agent
associated with the atom.
PotentialCalculationForcePressureSumGB(Space, Box) PotentialCalculationForcePressureSumGB
PotentialCalculationForceStress etomica.modules.materialfracture
PotentialCalculationForceStress(Space) PotentialCalculationForceStress
PotentialCalculationForceSum etomica.potential
Sums the force on each iterated atom and adds it to the integrator agent
associated with the atom.
PotentialCalculationForceSum() PotentialCalculationForceSum
PotentialCalculationForceSumGlass etomica.modules.glass
PotentialCalculationForceSumGlass(Box) PotentialCalculationForceSumGlass
PotentialCalculationForceSumWall etomica.modules.sam
PotentialCalculationForceSumWall(P1WCAWall) PotentialCalculationForceSumWall
PotentialCalculationForceSumWallForce etomica.modules.rosmosis
Sums the force and torque on each iterated atom or molecule and adds it to
the agent associated with the atom.
PotentialCalculationForceSumWallForce(IPotential) PotentialCalculationForceSumWallForce
PotentialCalculationFreeEnergy etomica.spin.heisenberg
Anx expressions for computing v_E and v_EE in the mapping.
PotentialCalculationFreeEnergy(Space, double, double, double, AtomLeafAgentManager<MoleculeAgent>) PotentialCalculationFreeEnergy
PotentialCalculationFSum etomica.potential
PotentialCalculationFSum etomica.spin.heisenberg
PotentialCalculationFSum(Space, double, double, double) PotentialCalculationFSum
PotentialCalculationFSum(Space, double, double, double) PotentialCalculationFSum
PotentialCalculationHeisenberg etomica.spin.heisenberg
Anx expressions for computing v_E and v_EE in the mapping.
PotentialCalculationHeisenberg(Space, double, double, double, int, AtomLeafAgentManager<MoleculeAgent>) PotentialCalculationHeisenberg
PotentialCalculationHyperVirialSum etomica.potential
Evaluates the hypervirial summed over all iterated atoms.
PotentialCalculationHyperVirialSum() PotentialCalculationHyperVirialSum
PotentialCalculationLJSP etomica.normalmode
PotentialCalculationLJSP(Space, Box, CoordinateDefinition, double, double, double, double, double) PotentialCalculationLJSP
PotentialCalculationMappedEnergy etomica.mappedvirial
PotentialCalculation that implements mapped-averaged framework (to get the energy).
PotentialCalculationMappedEnergy(Space, Box, int, AtomLeafAgentManager<Vector>) PotentialCalculationMappedEnergy
PotentialCalculationMappedRdf etomica.mappedRdf
PotentialCalculationMappedRdf(double, Space, Box, int, AtomLeafAgentManager<Vector>) PotentialCalculationMappedRdf
PotentialCalculationMappedVirial etomica.mappedvirial
PotentialCalculation that implements mapped-averaged virial (to get the
pressure).
PotentialCalculationMappedVirial(Space, Box, int, AtomLeafAgentManager<Vector>) PotentialCalculationMappedVirial
PotentialCalculationMappedVirialV etomica.mappedvirial
PotentialCalculation that implements mapped-averaged virial (to get the
pressure).
PotentialCalculationMappedVirialV(Space, Box, int, AtomLeafAgentManager<Vector>) PotentialCalculationMappedVirialV
PotentialCalculationMappedVirialV.UShift etomica.mappedvirial
PotentialCalculationMappedVirialV.USine etomica.mappedvirial
PotentialCalculationMappedVirialV.VFunc etomica.mappedvirial
PotentialCalculationMeanField etomica.spin.heisenberg
Potential Calculation for mean field
PotentialCalculationMeanField(Space, double, Box) PotentialCalculationMeanField
PotentialCalculationMolecular etomica.potential
Class defining a particular action to be performed on a set of atoms using an
arbitrary potential.
PotentialCalculationMolecularVirialSum etomica.potential
Evaluates the virial summed over all iterated molecules.
PotentialCalculationMolecularVirialSum() PotentialCalculationMolecularVirialSum
PotentialCalculationMoleculeAgentSum etomica.spin.heisenberg
Anx expressions for computing v_E and v_EE in the mapping.
PotentialCalculationMoleculeAgentSum(Space, double, double, double, int, AtomLeafAgentManager<MoleculeAgent>) PotentialCalculationMoleculeAgentSum
PotentialCalculationMoleculeAgentSumMinusIdeal etomica.spin.heisenberg
Anx expressions for computing v_E and v_EE in the mapping.
PotentialCalculationMoleculeAgentSumMinusIdeal(Space, double, double, double, int, AtomLeafAgentManager<MoleculeAgent>) PotentialCalculationMoleculeAgentSumMinusIdeal
PotentialCalculationMoleculeAgentSumMinusIdealPair etomica.spin.heisenberg
Anx expressions for computing v_E and v_EE in the mapping.
PotentialCalculationMoleculeAgentSumMinusIdealPair(Space, double, double, double, int, AtomLeafAgentManager<MoleculeAgent>) PotentialCalculationMoleculeAgentSumMinusIdealPair
PotentialCalculationMoleculeAgentSumPair etomica.spin.heisenberg
Anx expressions for computing v_E and v_EE in the mapping.
PotentialCalculationMoleculeAgentSumPair(Space, double, double, double, int, AtomLeafAgentManager<MoleculeAgent>) PotentialCalculationMoleculeAgentSumPair
PotentialCalculationPair etomica.spin.heisenberg
Any eypressions for computing v_E and v_EE in the mapping.
PotentialCalculationPair(Space, double, double, double, int, AtomLeafAgentManager<MoleculeAgent>) PotentialCalculationPair
PotentialCalculationPhiSum etomica.potential
PotentialCalculationPhiSum etomica.spin.heisenberg
PotentialCalculationPhiSum() PotentialCalculationPhiSum
PotentialCalculationPhiSum(Space) PotentialCalculationPhiSum
PotentialCalculationPhiSumHeisenberg etomica.potential
PotentialCalculationPhiSumHeisenberg(Space) PotentialCalculationPhiSumHeisenberg
PotentialCalculationPressureTensor etomica.potential
Calculates the pressure tensor by calculating the force on each atom, along
with including the kinetic portion (from the velocities or an Integrator).
PotentialCalculationPressureTensor(Space) PotentialCalculationPressureTensor
PotentialCalculationRDF etomica.data.meter
PotentialCalculation that simply does the work of collecting an RDF.
PotentialCalculationRDF(Space, Box) PotentialCalculationRDF
PotentialCalculationSolidSuper etomica.normalmode
Sums the force on each iterated atom and adds it to the integrator agent
associated with the atom.
PotentialCalculationSolidSuper(Space, CoordinateDefinition) PotentialCalculationSolidSuper
PotentialCalculationSolidSuperCut etomica.normalmode
Sums the force on each iterated atom and adds it to the integrator agent
associated with the atom.
PotentialCalculationSolidSuperCut(Space, CoordinateDefinition, double[]) PotentialCalculationSolidSuperCut
PotentialCalculationSolidSuperCutLS etomica.normalmode
Sums the force on each iterated atom and adds it to the integrator agent
associated with the atom.
PotentialCalculationSolidSuperCutLS(Space, CoordinateDefinition, double[]) PotentialCalculationSolidSuperCutLS
PotentialCalculationSumCutoff etomica.liquidLJ
Evaluates the energy summed over all iterated atoms.
PotentialCalculationSumCutoff(Space, double[]) PotentialCalculationSumCutoff
PotentialCalculationSumCutoffLS etomica.liquidLJ
Evaluates the energy summed over all iterated atoms.
PotentialCalculationSumCutoffLS() PotentialCalculationSumCutoffLS
PotentialCalculationSumquare etomica.spin.heisenberg
Anx expressions for computing v_E and v_EE in the mapping.
PotentialCalculationSumquare(Space, double) PotentialCalculationSumquare
PotentialCalculationTorqueSum etomica.potential
Sums the force and torque on each iterated atom or molecule and adds it to
the agent associated with the atom.
PotentialCalculationTorqueSum() PotentialCalculationTorqueSum
PotentialCalculationTorqueSumWallForce etomica.modules.rosmosis
Sums the force and torque on each iterated atom or molecule and adds it to
the agent associated with the atom.
PotentialCalculationTorqueSumWallForce(IPotential) PotentialCalculationTorqueSumWallForce
PotentialCalculationVirialSum etomica.potential
Evaluates the virial summed over all iterated atoms.
PotentialCalculationVirialSum() PotentialCalculationVirialSum
PotentialCalculationVSum etomica.spin.heisenberg
PotentialCalculationVSum() PotentialCalculationVSum
PotentialCalculationWallForce() MeterWallForce.PotentialCalculationWallForce
potentialCC Catalysis
potentialChoice SimGlass
potentialChoice BnPYCHe.BnPYHeParams
potentialChoice VirialHePI.VirialHePIParam
potentialChoice VirialLJOrC.VirialLJrParam
potentialChooser InsertionGraphic
potentialChooser PistonCylinderGraphic
potentialChooser SwmdGraphic
potentialChooserListener InsertionGraphic
potentialChooserListener MuGraphic
potentialChooserListener PistonCylinderGraphic
potentialChooserListener SwmdGraphic
potentialCO Catalysis
PotentialCommonAtomic etomica.virial
PotentialCommonAtomic(IPotentialAtomic) PotentialCommonAtomic
potentialCS Catalysis
potentialCS P2SquareWellBondingCO
PotentialCuLREP etomica.eam
PotentialCuLREP(Space) PotentialCuLREP
PotentialDepletion etomica.osmoticvirial
PotentialDepletion(Space, String) PotentialDepletion
PotentialDLPOLY etomica.potential
PotentialDLPOLY(Space) PotentialDLPOLY
PotentialEAM etomica.eam
EAM (Embedded Atom Method) potential
PotentialEAM(Space, double, double, double, double, double, double) PotentialEAM
PotentialEAM_LS etomica.eam
EAM (Embedded Atom Potential) potential with a lattice sum
PotentialEAM_LS(CoordinateDefinition, Space, double, double, double, double, double, double, Vector[]) PotentialEAM_LS
PotentialEFS etomica.eam
EFS (Extended Finnis-Sinclair) potential
PotentialEFS(Space, double, double, double, double, double, double, double, double, double) PotentialEFS
PotentialEmul etomica.potential
PotentialEmul class invokes the emul external program to compute energies
between molecules.
PotentialEmul(Space, String) PotentialEmul
PotentialEmul(Space, String, double) PotentialEmul
PotentialEmul(Space, String, int, double) PotentialEmul
PotentialEmulCached etomica.virial
Potential class whose sole purpose is to remember previously calculated
energies and return them if no change has been made to the configuration.
PotentialEmulCached(Space, String, double, int) PotentialEmulCached
PotentialEmulCached(Space, String, int) PotentialEmulCached
PotentialEmulCached(Space, String, int, double, int) PotentialEmulCached
potentialES ClathrateHarmonicFE
potentialES MinimizationTIP4P
potentialES ProtonDisorderGenerator
potentialFene StarPolymerMC
potentialFene StarPolymerMD
potentialFull MayerSphericalPTAtt
potentialGhost Insertion
potentialGroup VirialTraPPE.TraPPEParams
PotentialGroup etomica.potential
Collection of potentials that act between the atoms contained in
one or more groups of atoms.
PotentialGroup(int) PotentialGroup
Makes a potential group defined on the position of nBody atom or atom groups.
PotentialGroup(int, Space) PotentialGroup
PotentialGroup.PotentialLinker etomica.potential
PotentialGroup3PI etomica.virial
PotentialGroup that calculates the energy between PI molecules triplets.
PotentialGroup3PI(int) PotentialGroup3PI
PotentialGroup3PI.PotentialGroup3PISkip etomica.virial
PotentialGroup3PISkip(int) PotentialGroup3PI.PotentialGroup3PISkip
PotentialGroupHybrid etomica.nbr
A PotentialGroup class to work with PotentialMasterHybrid.
PotentialGroupHybrid(int) PotentialGroupHybrid
PotentialGroupNbr etomica.nbr
PotentialGroupNbr(int) PotentialGroupNbr
PotentialGroupPI etomica.virial
PotentialGroup that calculates the energy between PI molecule pairs.
PotentialGroupPI(int) PotentialGroupPI
PotentialGroupPI.PotentialGroupPISkip etomica.virial
PotentialGroupPISkip(int) PotentialGroupPI.PotentialGroupPISkip
PotentialGroupSoft etomica.potential
include virial and gradient for a molecular potential
PotentialGroupSoft(int, Space, double) PotentialGroupSoft
PotentialHard etomica.potential
Interface for hard potentials, having impulsive forces.
potentialHS InsertionGraphic
potentialHS PistonCylinderGraphic
potentialHS SwmdGraphic
potentialIdeal PistonCylinderGraphic
potentialIdeal SwmdGraphic
potentialLevel VirialH2PI.VirialH2PIParam
potentialLevel VirialH2PISimple.VirialH2PISimpleParam
potentialLevel VirialN2.VirialN2Param
potentialLevel VirialO2.VirialO2Param
PotentialLinker(IPotentialAtomic, AtomsetIteratorBasisDependent, AtomType[], PotentialGroup.PotentialLinker) PotentialGroup.PotentialLinker
PotentialLinker(IPotentialMolecular, MoleculesetIteratorPDT, ISpecies[]) PotentialMaster.PotentialLinker
potentialList PotentialMaster
potentialLJ ClathrateHarmonicFE
potentialLJ ProtonDisorderGenerator
potentialLJClCl ReverseOsmosisWater
potentialLJLS ClathrateHarmonicFE
potentialLJLS MinimizationTIP4P
potentialLJNaCl ReverseOsmosisWater
potentialLJNaNa ReverseOsmosisWater
potentialLJOCl ReverseOsmosisWater
potentialLJONa ReverseOsmosisWater
potentialM1 ReverseOsmosis
potentialM2 ReverseOsmosis
potentialMaster ActionMinimizeEnergy
potentialMaster CH4NVT
potentialMaster DHS_NVT
potentialMaster DLJ_NVT_1site
potentialMaster MCMoveDimer
potentialMaster MCMoveDimerRotate
potentialMaster MCMoveSmer
potentialMaster MCMoveSmerRotate
potentialMaster HSMDCavity
potentialMaster HSMDWidom
potentialMaster MeterDipoleSumSquaredMappedAverage
potentialMaster MeterHyperVirial
potentialMaster MeterPressure
potentialMaster MeterPressureTensor
potentialMaster MeterRDFPC
potentialMaster DHS_NVT
potentialMaster DLJ_NVT_1site
potentialMaster TIP4P_NVT
potentialMaster SimDimerLJadatom
potentialMaster EFSTungsten
potentialMaster DataSourceEnergies
potentialMaster SimFe
potentialMaster IntegratorBox
potentialMaster MCMoveDimer
potentialMaster MCMoveDimerRotate
potentialMaster MCMoveInsertDeleteLatticeVacancy
potentialMaster MCMoveInsertDeleteVacancy
potentialMaster LJMD
potentialMaster MeterWallForce
potentialMaster SimKMCLJadatom
potentialMaster MeterPU
potentialMaster MeterPUCut
potentialMaster MeterPUCutLS
potentialMaster MeterMappedRdf
potentialMaster MeterMappedU
potentialMaster MeterMappedVirial
potentialMaster MeterMappedVirialV
potentialMaster MeterMeanForce
potentialMaster CalcGradientDifferentiable
potentialMaster LJmuVT
potentialMaster LJNPT
potentialMaster LJNVT
potentialMaster ClathrateHarmonicFE
potentialMaster MinimizationTIP4P
potentialMaster ProtonDisorderGenerator
potentialMaster HarmonicAlphaNitrogenModel
potentialMaster HarmonicAlphaNitrogenModelDecomposed
potentialMaster HarmonicAlphaNitrogenModelPairMolecule
potentialMaster HarmonicAlphaNitrogenModelPairMoleculeSequential
potentialMaster HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2
potentialMaster HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
potentialMaster HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
potentialMaster HarmonicBetaNitrogenModel
potentialMaster HarmonicBetaNitrogenModelDecomposed
potentialMaster HarmonicBetaNitrogenModelPairMoleculeSequential
potentialMaster HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
potentialMaster HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2
potentialMaster HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
potentialMaster HarmonicBetaNitrogenModelPairMoleculeSequentialLS
potentialMaster HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
potentialMaster HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
potentialMaster MeterTargetRPMolecule
potentialMaster MeterTargetTPMolecule
potentialMaster MinimizationBetaNitrogenModel
potentialMaster MinimizeBetaNitrogenLatticeParameter
potentialMaster MinimizeBetaNitrogenLatticeParameterFromFile
potentialMaster MinimizeBetaNitrogenTranslationDOF
potentialMaster MinimizeGammaNitrogenLatticeParameter
potentialMaster SimOverlapAlphaN2TP
potentialMaster SimOverlapBetaN2RPScaling
potentialMaster SimOverlapBetaN2TP
potentialMaster SimOverlapDisorderedAlphaN2RPScaling
potentialMaster SimOverlapDisorderedAlphaN2TP
potentialMaster SimulationAlphaNitrogenModel
potentialMaster SimulationBetaNitrogenModel
potentialMaster SimulationBetaNitrogenModelTest
potentialMaster SimulationGammaNitrogenModel
potentialMaster DimerApproach
potentialMaster TestEwaldTIP4PWater
potentialMaster ConfigurationCatalysis
potentialMaster ChainEquilibriumSim
potentialMaster FreeRadicalPolymerizationSim
potentialMaster ColloidSim
potentialMaster DropletAtomic
potentialMaster P1MagicWall
potentialMaster ConfigurationSAM
potentialMaster Sam
potentialMaster SelfAssemblySim
potentialMaster MeterPressure2
potentialMaster BoxAgentSourceCellManagerListMolecular
potentialMaster NeighborCellManagerListMolecular
potentialMaster NeighborListManagerMolecular.MoleculePotential1ListSource
potentialMaster NeighborListManagerMolecular
potentialMaster PotentialMasterListMolecular.NeighborListAgentSourceMolecular
potentialMaster NeighborListAgentSource
potentialMaster NeighborListManager.AtomPotential1ListSource
potentialMaster NeighborListManager
potentialMaster HessianDB
potentialMaster HSDimerNPT
potentialMaster HSNPT
potentialMaster HTTPSoftSphereSim
potentialMaster LatticeSumMolecularCrystal
potentialMaster LJVacancyMin
potentialMaster MeterBoltzmannHTTP
potentialMaster MeterDADB
potentialMaster MeterDDP
potentialMaster MeterDP
potentialMaster MeterSolidDA
potentialMaster MeterSolidDACut
potentialMaster MeterSolidProps
potentialMaster MeterSolidPropsLJ
potentialMaster MeterTargetTP
potentialMaster MinimizeHCP
potentialMaster NormalModesMolecular
potentialMaster HSNPT2DSim
potentialMaster SimCalcSLJ
potentialMaster SimCalcSSoftSphere2D
potentialMaster SimCalcSSoftSphereFCC
potentialMaster SimCalcSSoftSphereFCCSuperBox
potentialMaster SimEinStep1
potentialMaster SimEinStep1HCP
potentialMaster SimEinStep2
potentialMaster SimEinStep2HCP
potentialMaster SimFluidSoftSphere
potentialMaster SimLJHTTISuper
potentialMaster SimLJHTTISuperHCP
potentialMaster SimLJHTTISuperHCP2
potentialMaster SimLJHTTISuperSFMD
potentialMaster SimLJVacancy
potentialMaster SimOverlapSoftSphereDP
potentialMaster SimOverlapSoftSphereEin
potentialMaster SimOverlapSoftSphereEinHarm
potentialMaster SimOverlapSoftSphereTP
potentialMaster SimOverlapSoftSphereTPHCP
potentialMaster SimOverlapSoftSphereTPSlantedBox
potentialMaster SimUmbrellaSoftSphere
potentialMaster PolydisperseHS
potentialMaster P2SquareWellRobust
potentialMaster PotentialGroup
potentialMaster HSMD3D
potentialMaster LJMC3D
potentialMaster LJMC3DDimer
potentialMaster SoftSphere3d
potentialMaster Heisenberg
potentialMaster MeterEnergyMeanField
potentialMaster MeterMappedAveraging
potentialMaster MeterMappedAveragingCorrelation
potentialMaster MeterMappedAveragingCV
potentialMaster MeterMappedAveragingFreeEnergy
potentialMaster MeterMappedAveragingPairExcess
potentialMaster MeterMappedAveragingSum
potentialMaster MeterMappedAveragingVSum
potentialMaster MeterMeanField
potentialMaster MeterPairSum
potentialMaster Ising
potentialMaster MCMoveClusterRotateArm
potentialMaster StarPolymerMC
potentialMaster StarPolymerMD
potentialMaster LJMC
potentialMaster SurfaceTensionMapped
PotentialMaster etomica.potential
Manager of all potentials in simulation.
PotentialMaster() PotentialMaster
PotentialMaster(IteratorFactory) PotentialMaster
PotentialMaster.AtomIterator0 etomica.potential
PotentialMaster.MoleculeIterator0 etomica.potential
PotentialMaster.PotentialLinker etomica.potential
potentialMasterA MultiharmonicMC
potentialMasterB MultiharmonicMC
potentialMasterCell SimIdealGas
potentialMasterCell SimLJ
potentialMasterCell LJMC
potentialMasterCell LjMC3D
potentialMasterCell PotentialGroupHybrid
PotentialMasterCell etomica.nbr.cell
A PotentialMaster for use with a Simulation where cell-listing of atoms and
their neighbors is appropriate.
PotentialMasterCell(Simulation, double, BoxAgentSourceCellManager) PotentialMasterCell
PotentialMasterCell(Simulation, double, Space) PotentialMasterCell
Constructs with null AtomPositionDefinition, which indicates the position
definition given with each atom's AtomType should be used.
PotentialMasterCell(Simulation, Space) PotentialMasterCell
Creates PotentialMasterCell with default (1.0) range.
PotentialMasterCellMixed etomica.nbr.cell
A PotentialMaster for use with mixtures having very different iteraction ranges.
PotentialMasterCellMixed(Simulation, double) PotentialMasterCellMixed
PotentialMasterCellMixed(Simulation, double, BoxAgentSourceCellManager) PotentialMasterCellMixed
potentialMasterDADv2 MeterPUCut
potentialMasterDADv2 MeterPUCutLS
potentialMasterDADv2 MeterSolidDACut
potentialMasterHarmonic SimEinStep1
potentialMasterHarmonic SimEinStep1HCP
potentialMasterHarmonic SimEinStep2
potentialMasterHarmonic SimEinStep2HCP
potentialMasterHarmonic SimOverlapSoftSphereEin
potentialMasterHarmonic SimOverlapSoftSphereEinHarm
PotentialMasterHybrid etomica.nbr
PotentialMaster that uses both neighbor-cell iteration and cell-list
iteration.
PotentialMasterHybrid(Simulation, double, Space) PotentialMasterHybrid
potentialMasterList LjMd3D
potentialMasterList PotentialGroupHybrid
potentialMasterList SimHSMDVacancy
PotentialMasterList etomica.nbr.list
PotentialMaster used to implement neighbor listing.
PotentialMasterList(Simulation, double, NeighborListAgentSource, Space) PotentialMasterList
PotentialMasterList(Simulation, double, Space) PotentialMasterList
PotentialMasterList(Simulation, Space) PotentialMasterList
Default constructor uses range of 1.0.
PotentialMasterListMolecular etomica.nbr.list.molecule
PotentialMaster used to implement neighbor listing.
PotentialMasterListMolecular(Simulation, double, IMoleculePositionDefinition, Space) PotentialMasterListMolecular
Constructs class using given position definition for all atom cell
assignments.
PotentialMasterListMolecular(Simulation, double, BoxAgentSourceCellManagerListMolecular, BoxAgentManager<? extends BoxCellManager>, PotentialMasterListMolecular.NeighborListAgentSourceMolecular, Space) PotentialMasterListMolecular
PotentialMasterListMolecular(Simulation, double, BoxAgentSourceCellManagerListMolecular, BoxAgentManager<? extends BoxCellManager>, Space) PotentialMasterListMolecular
PotentialMasterListMolecular(Simulation, double, BoxAgentSourceCellManagerListMolecular, Space) PotentialMasterListMolecular
PotentialMasterListMolecular(Simulation, double, Space) PotentialMasterListMolecular
Constructor specifying space and range for neighbor listing; uses null AtomPositionDefinition.
PotentialMasterListMolecular(Simulation, Space) PotentialMasterListMolecular
Default constructor uses range of 1.0.
PotentialMasterListMolecular.NeighborListAgentSourceMolecular etomica.nbr.list.molecule
potentialMasterLong LjMd3D
potentialMasterLongCut LjMd3D
PotentialMasterLrc etomica.potential
Collects potentials used for long-range correction.
PotentialMasterLrc() PotentialMasterLrc
potentialMasterMonatomic SimBennet
potentialMasterMonatomic SimHarmonicUmbrella
potentialMasterMonatomic SimTargetUmbrella
potentialMasterMonatomic SimUmbrella
PotentialMasterMonatomic etomica.potential
PotentialMaster suitable for monatomic molecules without using neighbor
lists and avoids PotentialMaster's performance problems.
PotentialMasterMonatomic(Simulation) PotentialMasterMonatomic
PotentialMasterNbr etomica.nbr
PotentialMasterNbr(Simulation) PotentialMasterNbr
PotentialMasterNbrMolecular etomica.nbr.molecule
PotentialMasterNbrMolecular(Simulation, BoxAgentManager.BoxAgentSource<? extends BoxCellManager>, BoxAgentManager<? extends BoxCellManager>) PotentialMasterNbrMolecular
potentialMasterRef SimOverlapBetaN2RP
potentialMasterRef SimOverlapSoftSphereSoftness
PotentialMasterSite etomica.nbr.site
PotentialMasterSite(Simulation, int) PotentialMasterSite
PotentialMasterSite(Simulation, int, Space) PotentialMasterSite
Invokes superclass constructor, specifying IteratorFactoryCell
for generating molecule iterators.
potentialMasterTarg SimOverlapBetaN2RP
potentialMasterTarg SimOverlapSoftSphereSoftness
potentialMasterTarget SimOverlapNitrogenModel
potentialMasterTarget SimOverlap
potentialMasterTarget SimOverlapSoftSphere
potentialMasterTarget SimOverlapSoftSphereHCP
potentialMasterTarget SimOverlapSoftSphereReweighting
potentialMasterTarget SimOverlapSSnxy
potentialMCl ReverseOsmosisWater
potentialMM ReverseOsmosis
potentialMM ReverseOsmosisWater
potentialMM ZeoliteSimulation
The hard-sphere potential governing the interactions.
potentialMNa ReverseOsmosisWater
potentialMO ReverseOsmosisWater
PotentialMolecular etomica.potential
Superclass for all Potential classes, which define how the atoms in the
system interact with each other.
PotentialMolecular(int, Space) PotentialMolecular
General constructor for a potential instance
potentialMolecularInterNonBondedUnlike CollectionPotentialMolecularUnlike
PotentialMolecularMonatomic etomica.potential
Intermolecular potential that wraps an atomic potential.
PotentialMolecularMonatomic(Space, IPotentialAtomic) PotentialMolecularMonatomic
PotentialMolecularSoft etomica.potential
Methods for properties obtained for a soft, differentiable pair potential.
PotentialMolecularSum etomica.potential
Molecular potential class that simply sums up contributions from multiple
(molecular) potentials.
PotentialMolecularSum(IPotentialMolecular[]) PotentialMolecularSum
potentialN EFSTungsten
PotentialN etomica.potential
PotentialN(Space) PotentialN
Constructor for PotentialN.
PotentialNonAdditive etomica.virial
Potential class which computes non-additive energies from potentials
that return the full energies for various-sized groups of molecules.
PotentialNonAdditive(IPotentialMolecular[]) PotentialNonAdditive
PotentialNonAdditive(IPotentialMolecular[], int[]) PotentialNonAdditive
PotentialNonAdditive.PotentialNonAdditiveNB etomica.virial
PotentialNonAdditiveDifference etomica.potential
PotentialNonAdditiveDifference(Space, IPotentialMolecular, IPotentialMolecular) PotentialNonAdditiveDifference
PotentialNonAdditiveNB(int) PotentialNonAdditive.PotentialNonAdditiveNB
potentialOO Catalysis
potentialOS Catalysis
potentialPlus MayerSphericalPlus
PotentialPolarizable etomica.potential
Interface for a polarizable potential.
potentialQClCl ReverseOsmosisWater
potentialQHCl ReverseOsmosisWater
potentialQHNa ReverseOsmosisWater
potentialQNaCl ReverseOsmosisWater
potentialQNaNa ReverseOsmosisWater
potentialQOCl ReverseOsmosisWater
potentialQONa ReverseOsmosisWater
PotentialReactive etomica.potential
Interface for potentials that change the bond state of an atom.
PotentialReactive.BondChangeData etomica.potential
potentialRef MayerPTAtt
potentialRef MayerSphericalPTAtt
potentials MCMoveGeometricCluster
potentials MCMoveGeometricClusterRestrictedGE
potentials PotentialNonAdditive
potentials0body PotentialMasterNbr
PotentialSoft etomica.potential
Methods for properties obtained for a soft, differentiable pair potential.
potentialSW InsertionGraphic
potentialSW PistonCylinderGraphic
potentialSW SwmdGraphic
potentialTether PotentialCalculationForceSumWallForce
potentialTether PotentialCalculationTorqueSumWallForce
potentialTether ReverseOsmosis
potentialTether ReverseOsmosisWater
PotentialTruncated etomica.potential
Interface for a potential that is artificially truncated, and thus which can
provide a zero-body potential that (approximately) corrects for the
truncation.
potentialwall DCVGCMD
potentialwall DCVGCMD
potentialwall1 DCVGCMD
potentialwall1 DCVGCMD
potentialwallPorousA DCVGCMD
potentialwallPorousA1 DCVGCMD
potentialwallPorousB DCVGCMD
potentialwallPorousB1 DCVGCMD
potentialWater ReverseOsmosisWater
potentialWCA StarPolymerMC
potentialWCA StarPolymerMD
potentialWrapper Insertion
potentialWrapper PistonCylinder
potentialWrapper Swmd
potentot(double, double, double, double) P2HydrogenPatkowski
potentot(double, double, double, double) P2HydrogenPatkowskiAtomic
potparts(int, int, double, int, int, int[], int[]) P2WaterPotentialsJankowski
potparts_old(int, int, double, int, int, int[], int[]) P2WaterPotentialsJankowski
pots(double, double, double) P2WaterPotentialsJankowski
pow DataPumpListenerPow
pow DataPumpListenerPowStrict
pow MCMoveClusterAtomChainHSTail
pow(int) BigIntegerPoly
Raise to a positive power.
pow(int) Ifactor
Exponentiation with a positive integer.
pow(int) Rational
Power to an integer.
pow(Rational) Rational
Raise to a rational power.
pow(BigDecimal, BigDecimal) BigDecimalMath
Power function.
pow(BigInteger) Rational
Power to an integer.
Pow etomica.graph.operations
Pow() Pow
power() CGS
power() LJ
power() MKS
power() UnitSystem
power() UnitSystem.Sim
Power etomica.units.dimensions
Dimension for all power units.
powerD(double) Space
powerD(double) Space1D
powerD(double) Space2D
powerD(double) Space3D
powerD(int) Space
powerD(int) Space1D
powerD(int) Space2D
powerD(int) Space3D
PowParameters etomica.graph.operations
PowParameters(byte) PowParameters
powRound(BigDecimal, int) BigDecimalMath
Raise to an integer power and round.
powRound(BigDecimal, Rational) BigDecimalMath
Raise to a fractional power and round.
powRound(BigDecimal, BigInteger) BigDecimalMath
Raise to an integer power and round.
pPade VirialOptimizer
PREC Gamma
prec2err(double, int) BigDecimalMath
Convert a precision (relative error) to an absolute error.
precalcQ ClusterSumHS
precalcQ ClusterWheatleyHS
precalcQ ClusterWheatleyPartitionScreening
precision DataDoubleBDArray.DataInfoDoubleBDArray
precision DeviceBox
Integer specifying the number of significant figures to be displayed.
precision PotentialCalculationEnergySumBigDecimal
precision_s EwaldSumMolecules
precisionLimit ClusterWheatleyMultibodyBD
precisionLimit ClusterWheatleyMultibodyDerivativesBD
precisionLimit ClusterWheatleySoftDerivativesBD
predefinedArgbs Colix
predefinedGroup1Names JmolConstants
predefinedGroup3Names JmolConstants
predefinedStatic JmolConstants
predefinedVariable JmolConstants
predictor() IntegratorGear4
prefix() PrefixedUnit
Prefix etomica.units
Base class for all unit prefixes, such as kilo, micro, nano, etc.
prefixAllowed() CompoundUnit
prefixAllowed() PrefixedUnit
prefixAllowed() SimpleUnit
Some units (such as Angstroms) are not normally defined with a prefix
attached, and for such units this flag can be set to false to prohibit
the application of a prefix.
prefixAllowed() LJ.LJUnit
prefixAllowed() Unit
Indicates if the unit is appropriate for use with a prefix.
PrefixedUnit etomica.units
Implementation of the Unit interface formed from a base Unit (e.
PrefixedUnit(Prefix, Unit) PrefixedUnit
Constructs a PrefixedUnit using the given prefix and base.
PrefixedUnit(Unit) PrefixedUnit
Constructs a PrefixedUnit using the given base and a Null prefix
preMultiply(Quaternion) Quaternion
Returns the Quaternion r resulting from multiplying the input Quaternion preMultiplier to the current Quaternion q.
prepForGradient() P2EAM
pRes MeterSolidDA
preservestate Token
press() DeviceButton
Performs the button's action.
press() DeviceButtonSingle
Performs the button's action.
pressure TestAceticAcidMC3D_NPT.AceticAcidMCParam
pressure MeterEnthalpyVolume
pressure SimGCPMWaterMCNPT.GCPMWaterMCParam
pressure MCMoveVolumeAssociated
pressure MCMoveVolumeAssociatedMolecule
pressure TestIGAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
pressure TestLJAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
pressure TestLJAssociationMC3D_NPT.VirialAssociatingFluidParam
pressure TestLJAssociationMC3D_NVTOld.VirialAssociatingFluidParam
pressure MeterWidomInsertion
pressure MCMoveBoxSize
pressure MCMoveVolume
pressure MeterWidomInsertionP
pressure LJNPT.LJMCParams
pressure MCMoveVolumeN2
pressure DataSourceDensityFunction
pressure MeterExcessAdsorbed
pressure HSDimerNPT.HSMD3DParameters
pressure MCMoveVolumeMonoclinicScaled
pressure MCMoveVolumeSolid
pressure MCMoveVolumeSolidNPTMolecular
pressure ColorSchemeScaledOverlap
pressure DisplayBoxCanvas2DNpTScaling
pressure HSNPT2DSim
pressure HardSphereSolid.EOSParams
pressure TestLJAssociationMC3D_NPT.VirialAssociatingFluidParam
pressure() CGS
pressure() LJ
pressure() MKS
pressure() UnitSystem
pressure() UnitSystem.Sim
pressure(double) EOSSW
pressure(double) EOSSWPatel
pressure(double) VEOS3SW
Pressure etomica.units.dimensions
Dimension for (3D) pressure.
pressure0 LJNPT.LJMCParams
pressure2D() UnitSystem.Sim
Pressure2D etomica.units.dimensions
Simulation unit of (2D) pressure is (D-A/ps^2)/A = D/ps^2
pressureAverage HSMD2D_noNbr
pressureDisplayTextBox PistonCylinderGraphic
pressureFast MeterWidomInsertionCorrection
pressureFull MeterWidomInsertionCorrection
pressureHistory HSMD2D_noNbr
pressureMeter PistonCylinderGraphic
pressurePump HSMD2D_noNbr
PressureSink() DataClusterer.PressureSink
PressureSink() DataClusterWriter.PressureSink
pressureSlider PistonCylinderGraphic
pressureSliderPanel PistonCylinderGraphic
pressureTensor PotentialCalculationForcePressureSumGB
pressureTensor IntegratorRigidIterative
pressureTensor IntegratorRigidMatrixIterative
pressureTensor IntegratorVelocityVerlet
pressureTensor IntegratorVerlet
pressureTensor IntegratorDroplet
pressureTensor PotentialCalculationForcePressureSum
pressureTensor PotentialCalculationPressureTensor
pressureTensor IntegratorVelocityVerletQuaternion
pretendBox MeterTargetRPMolecule
pretendBox MeterTargetTPMolecule
pretendBox MeterBoltzmannHTTP
pretendBox MeterDDP
pretendBox MeterDP
pretendBox MeterTargetTP
prev IndexIteratorIncreasing
prev Token
prevConfigIndex AtomSignalMobility
prevConfigIndex AtomSignalMotion
prevConfigIndex DataSourcePrevTime
previous FunctionChain.Link
previous TreeLinker
previousTensor OrientationCalcWater3P
previousTensor OrientationCalcWater4P
previousValue ModifierCells3D
previousValue ModifierXCells2D
previousValue ModifierYCells2D
prevprime(BigInteger) Prime
return the largest prime smaller than n
prevSampleIndex MeterCorrelation
pRigid P2WaterPotentialsJankowski
primaryCoordDef MeterBoltzmannRotPerturb
primaryCoordDef MeterRotPerturbMolecule
Prime etomica.veos.bigdecimal
Prime numbers.
Prime() Prime
Default constructor initializing a list of primes up to 17.
primeexp Ifactor
primitive BravaisLattice
primitive MinimizationBetaNitrogenModel
primitive MinimizationBetaNitrogenModelLS
primitive MinimizeBetaNitrogenLatticeParameter
primitive MinimizeBetaNitrogenLatticeParameterFromFile
primitive MinimizeBetaNitrogenLatticeParameterLSFromFile
primitive MinimizeBetaNitrogenTranslationDOF
primitive SimOverlapAlphaN2TP
primitive SimOverlapBetaN2RPScaling
primitive SimOverlapBetaN2TP
primitive SimOverlapDisorderedAlphaN2RPScaling
primitive SimOverlapDisorderedAlphaN2TP
primitive SimOverlapNitrogenModel
primitive SimulationAlphaNitrogenModel
primitive SimulationBetaNitrogenModel
primitive SimulationBetaNitrogenModelTest
primitive SimulationGammaNitrogenModel
primitive CoordinateDefinition
primitive HessianDB
primitive LJVacancyMin
primitive NormalModeAnalysisDisplay1D
primitive NormalModeAnalysisDisplay2D
primitive NormalModeAnalysisDisplay3D
primitive NormalModes2D
primitive NormalModes3D
primitive NormalModesMolecular
primitive SimBennet
primitive SimCalcJ
primitive SimCalcS
primitive SimCalcSLJ
primitive SimCalcSMorse
primitive SimCalcSSoftSphere2D
primitive SimCalcSSoftSphereFCC
primitive SimCalcSSoftSphereFCCSuperBox
primitive SimEinStep1
primitive SimEinStep1HCP
primitive SimEinStep2
primitive SimEinStep2HCP
primitive SimHarmonic
primitive SimHarmonicUmbrella
primitive SimLJHTTISuper
primitive SimLJHTTISuperHCP
primitive SimLJHTTISuperHCP2
primitive SimLJHTTISuperSFMD
primitive SimModesJ
primitive SimOverlap
primitive SimOverlapLJ
primitive SimOverlapLJModule
primitive SimOverlapSoftSphere
primitive SimOverlapSoftSphereDP
primitive SimOverlapSoftSphereEin
primitive SimOverlapSoftSphereEinHarm
primitive SimOverlapSoftSphereHCP
primitive SimOverlapSoftSphereReweighting
primitive SimOverlapSoftSphereSoftness
primitive SimOverlapSoftSphereSuperBox
primitive SimOverlapSoftSphereTP
primitive SimOverlapSoftSphereTPHCP
primitive SimOverlapSoftSphereTPSlantedBox
primitive SimOverlapSSnxy
primitive SimTarget
primitive SimTargetUmbrella
primitive SimUmbrella
primitive SimUmbrellaSoftSphere
primitive WaveVectorFactory2D
primitive WaveVectorFactoryFcc
primitive WaveVectorFactorySimple
Primitive etomica.lattice.crystal
Collection of primitive elements that specify or are determined
by the structure of a Bravais lattice.
Primitive(Space) Primitive
This constructor is called directly when a Primitive is constructing
its reciprocal primitive.
PrimitiveBcc etomica.lattice.crystal
Primitive group for a body-centered-cubic system.
PrimitiveBcc(Space) PrimitiveBcc
PrimitiveBcc(Space, double) PrimitiveBcc
PrimitiveCubic etomica.lattice.crystal
Primitive group for a cubic system.
PrimitiveCubic(Space) PrimitiveCubic
PrimitiveCubic(Space, double) PrimitiveCubic
PrimitiveFcc etomica.lattice.crystal
Primitive group for a face-centered-cubic system.
PrimitiveFcc(Space) PrimitiveFcc
PrimitiveFcc(Space, double) PrimitiveFcc
PrimitiveGeneral etomica.lattice.crystal
Primitive defined simply by its vectors.
PrimitiveGeneral(Space, Vector[]) PrimitiveGeneral
PrimitiveHCP4 etomica.lattice.crystal
Orthorhombic primitive cell for an HCP system.
PrimitiveHCP4(Space) PrimitiveHCP4
PrimitiveHCP4(Space, double) PrimitiveHCP4
PrimitiveHexagonal etomica.lattice.crystal
Primitive group for a hexagonal system.
PrimitiveHexagonal(Space) PrimitiveHexagonal
PrimitiveHexagonal(Space, double, double) PrimitiveHexagonal
PrimitiveHexagonal.PrimitiveHexagonalReciprocal etomica.lattice.crystal
PrimitiveHexagonal2D etomica.lattice.crystal
Primitive group for a 2D hexagonal system.
PrimitiveHexagonal2D(Space) PrimitiveHexagonal2D
PrimitiveHexagonal2D(Space, double) PrimitiveHexagonal2D
PrimitiveHexagonal2D.PrimitiveHexagonal2DReciprocal etomica.lattice.crystal
PrimitiveHexagonal2DReciprocal(Space, double) PrimitiveHexagonal2D.PrimitiveHexagonal2DReciprocal
PrimitiveHexagonalReciprocal(Space, double, double) PrimitiveHexagonal.PrimitiveHexagonalReciprocal
PrimitiveMonoclinic etomica.lattice.crystal
Primitive group for a monoclinic system.
PrimitiveMonoclinic(Space) PrimitiveMonoclinic
PrimitiveMonoclinic(Space, double, double, double, double) PrimitiveMonoclinic
PrimitiveMonoclinic.PrimitiveMonoclinicReciprocal etomica.lattice.crystal
PrimitiveMonoclinicReciprocal(Space, double, double, double, double) PrimitiveMonoclinic.PrimitiveMonoclinicReciprocal
PrimitiveOrthorhombic etomica.lattice.crystal
Primitive group for an orthorhombic system.
PrimitiveOrthorhombic(Space) PrimitiveOrthorhombic
PrimitiveOrthorhombic(Space, double, double, double) PrimitiveOrthorhombic
PrimitiveOrthorhombicHexagonal etomica.lattice.crystal
Primitive group for an orthorhombic system.
PrimitiveOrthorhombicHexagonal(Space, double) PrimitiveOrthorhombicHexagonal
PrimitiveTetragonal etomica.lattice.crystal
Primitive group for a tetragonal system.
PrimitiveTetragonal(Space) PrimitiveTetragonal
PrimitiveTetragonal(Space, double, double) PrimitiveTetragonal
PrimitiveTriclinic etomica.lattice.crystal
Primitive group for a triclinic system.
PrimitiveTriclinic(Space) PrimitiveTriclinic
PrimitiveTriclinic(Space, double, double, double, double, double, double) PrimitiveTriclinic
PrimitiveTrigonal etomica.lattice.crystal
Primitive group for a trigonal system.
PrimitiveTrigonal(Space) PrimitiveTrigonal
PrimitiveTrigonal(Space, double, double, double, double) PrimitiveTrigonal
primitiveUnitCell SimOverlapNitrogenModel
primitiveUnitCell HessianDB
primitiveUnitCell SimCalcSLJ
primitiveUnitCell SimCalcSSoftSphereFCC
primitiveUnitCell SimOverlapLJ
primitiveUnitCell SimOverlapSoftSphere
primitiveUnitCell SimOverlapSoftSphereHCP
primitiveUnitCell SimOverlapSoftSphereSoftness
primitiveUnitCell SimOverlapSoftSphereTPSlantedBox
primitiveUnitCell SimOverlapSSnxy
primitiveUnitCell SimUmbrellaSoftSphere
print P2HydrogenHindePatkowski
print P2HydrogenHindePatkowskiAtomic
print P2HydrogenPatkowski
print P2HydrogenPatkowskiAtomic
print() ClusterWheatleyPartitionScreening.FrequencyCounter
print(Parser.CommandVariable) Interpreter
printapalooza VirialRowleyAlcohol
printCheckData() ClusterWheatleySoftDerivatives
printed ClusterCoupledFlippedMultivalue
printFortranInput(IAtomList) P2WaterSzalewicz
Prints atom coordinates and euler angles in a format compatible with the CCpol fortran program
The orientations are taken from the given atoms.
printInConvertedUnits VirialN2.VirialN2Param
printInterval IntegratorRigidIterative
printInterval IntegratorRigidMatrixIterative
printInterval IntegratorVelocityVerletShake
printInterval IntegratorVelocityVerletQuaternion
printKeyAtomPositions() IntegratorDimerApproach
printResults(double) SimulationVirial
printResults(double) SimulationVirialOverlap2
printResults(double, String[]) SimulationVirialOverlap2
printStrands(List, int) FFTDecomposition
printStrands(List, int) IsFFT
printStrands(List, int) CalcFFT
printTargetHistogram() SimulationVirialOverlap2
Prints out the target histogram of maximum separation distances as
set up by setupTargetHistogram().
probabilityBins MCMoveClusterTorsionAlkaneEH
probabilityBins MCMoveClusterTorsionMulti
probabilityReverseMap MCMoveClusterTorsionAlkaneEH
probabilityReverseMap MCMoveClusterTorsionMulti
probe Token
proceedOnSourceTranscodingFailure(SVGConverterSource, File, String) DefaultSVGConverterController
Invoked when the rasterizer got an error while
transcoding the input source.
proceedOnSourceTranscodingFailure(SVGConverterSource, File, String) Main
proceedOnSourceTranscodingFailure(SVGConverterSource, File, String) SVGConverterController
Invoked when the rasterizer got an error while
transcoding the input source.
proceedWithComputedTask(Transcoder, Map, List, List) DefaultSVGConverterController
Invoked when the rasterizer has computed the
exact description of what it should do.
proceedWithComputedTask(Transcoder, Map, List, List) Main
proceedWithComputedTask(Transcoder, Map, List, List) SVGConverterController
Invoked when the rasterizer has computed the
exact description of what it should do.
proceedWithSourceTranscoding(SVGConverterSource, File) DefaultSVGConverterController
Invoked when the rasterizer is about to start transcoding
of a given source.
proceedWithSourceTranscoding(SVGConverterSource, File) Main
proceedWithSourceTranscoding(SVGConverterSource, File) SVGConverterController
Invoked when the rasterizer is about to start transcoding
of a given source.
processAtoms(IAtomList) P2WaterPotentialsJankowski
processData(int, long, double) DataSourceBlockAvgCor
processData(IData) DataProcessorCavity
processData(IData) DataProcessorErrorBar
processData(IData) DataProcessorGContactP
processData(IData) DataProcessorPContactG
processData(IData) DataProcessorWidomContact
processData(IData) AccumulatorAverageBootstrap
processData(IData) AccumulatorAverageCollapsingLog
processData(IData) DataAccumulator
Returns getData() every pushInterval times it is invoked, otherwise returns null
(thereby preventing transmission of data to the next DataSinks).
processData(IData) DataGroupFilter
Returns the output data that was established with a previous call to
processDataInfo.
processData(IData) DataLogger
Gives data to DataSink for writing
processData(IData) DataProcessor
Processes the input Data and returns Data for pushing to the next
DataSink.
processData(IData) DataProcessorChemicalPotential
processData(IData) DataProcessorFunction
Applies the function to all elements of the input data.
processData(IData) DataProcessorInterfacialTension
processData(IData) DataPump
Returns the given Data.
processData(IData) CastGroupOfTablesToDataTable
Converts data in given group to a DataDoubleArray as described in the
general comments for this class.
processData(IData) CastGroupToDoubleArray
Converts data in given group to a DataDoubleArray as described in the
general comments for this class.
processData(IData) CastToDouble
Extracts a double from the input data and returns it encapsulated in a
DataDouble.
processData(IData) CastToDoubleArray
Copies input Data to a DataDoubleArray and returns it (the DataDataDoubleArray).
processData(IData) CastToGroup
Processes the input Data to update the output DataGroup.
processData(IData) CastToTable
Copies input Data to a DataTable and returns it (the DataTable).
processData(IData) DataProcessorCvMD
processData(IData) DataProcessorReweight
processData(IData) DataProcessorReweightRatio
processData(IData) LjMd3D.DataProcessorCorrection
processData(IData) LjMd3D.DataProcessorReweight
processData(IData) DataProcessorXY
processData(IData) MolecularWeightAvg
processData(IData) MolecularWeightAvg2
processData(IData) DropletGraphic.DataProcessorTensorSplitter
processData(IData) GlassGraphic.DataProcessorTensorTrace
processData(IData) DataProcessorInterfacialTensionProfile
processData(IData) FitTanh
processData(IData) InterfacialSWGraphic.DataProcessorTensorSplitter
processData(IData) LjmdGraphic.DataProcessorTensorTrace
processData(IData) MuGraphic.DataProcessorMu
processData(IData) MuGraphic.DataSinkExcludeOverlap
processData(IData) DataProcessorBias
processData(IData) DataProcessorBounds
processData(IData) DataProcessorDyDLnx
processData(IData) DataProcessorVar
processData(IData) MultiharmonicGraphicMC.DataProcessAHT
processData(IData) NucleationGraphic.DataSinkExcludeOverlap
processData(IData) ReverseOsmosisGraphic.DataSinkExcludeOverlap
processData(IData) ReverseOsmosisWaterGraphic.DataSinkExcludeOverlap
processData(IData) SamGraphic.DataPipeStressStrain
processData(IData) AccumulatorMimicMu
processData(IData) DataProcessorBounds
processData(IData) DataProcessorMu
processData(IData) StatisticsMCGraphic.DataProcessorUndo
processData(IData) SwmdGraphic.DataSinkExcludeOverlap
processData(IData) BoltzmannProcessor
processData(IData) DataProcessorBoltzmannFactor
processData(IData) DataProcessorSum
processData(IData) DataProcessorSurfaceTension
processData(IData) FitTanh
processData(IData) SurfaceTensionMapped
processData(IData) DataProcessorVirialOverlap
take in v1/pi1, pi0/pi1, spit out v1/pi, overlap0, overlap1, overlap2...
processData(IData) VirialPolyhedra.DataProcessorR2
processData(IData) VirialPolyhedra2.DataProcessorR2
processDataInfo(IDataInfo) DataProcessorCavity
processDataInfo(IDataInfo) DataProcessorErrorBar
processDataInfo(IDataInfo) DataProcessorGContactP
processDataInfo(IDataInfo) DataProcessorPContactG
processDataInfo(IDataInfo) DataProcessorWidomContact
processDataInfo(IDataInfo) AccumulatorAverage
Prepares the accumulator for input data.
processDataInfo(IDataInfo) AccumulatorAverageBlockless
Prepares the accumulator for input data.
processDataInfo(IDataInfo) AccumulatorAverageBlocklessSlim
processDataInfo(IDataInfo) AccumulatorAverageBootstrap
processDataInfo(IDataInfo) AccumulatorAverageCollapsing
processDataInfo(IDataInfo) AccumulatorAverageCollapsingLog
processDataInfo(IDataInfo) AccumulatorAverageCovariance
processDataInfo(IDataInfo) AccumulatorAverageFixed
processDataInfo(IDataInfo) AccumulatorAverageFixedOutputFile
Prepares the accumulator for input data.
processDataInfo(IDataInfo) AccumulatorCounter
Does nothing.
processDataInfo(IDataInfo) AccumulatorHistogram
Sets up data and histograms, discarding any previous results.
processDataInfo(IDataInfo) AccumulatorHistory
Sets up data and histories, discarding any previous results.
processDataInfo(IDataInfo) AccumulatorRatioAverageCovariance
processDataInfo(IDataInfo) AccumulatorRatioAverageCovarianceFull
processDataInfo(IDataInfo) DataGroupFilter
Determines data that will be output, using the given DataInfo and
the index specification given at construction.
processDataInfo(IDataInfo) DataLogger
processDataInfo(IDataInfo) DataProcessor
Informs this DataProcessor of the DataInfo for the Data it will be
processing.
processDataInfo(IDataInfo) DataProcessorChemicalPotential
processDataInfo(IDataInfo) DataProcessorFunction
Returns a copy of the given dataInfo
processDataInfo(IDataInfo) DataProcessorInterfacialTension
processDataInfo(IDataInfo) DataPump
Returns the given DataInfo.
processDataInfo(IDataInfo) CastGroupOfTablesToDataTable
Prepares processor to handle Data.
processDataInfo(IDataInfo) CastGroupToDoubleArray
Prepares processor to handle Data.
processDataInfo(IDataInfo) CastToDouble
Prepares processor to handle Data.
processDataInfo(IDataInfo) CastToDoubleArray
Prepares processor to perform cast.
processDataInfo(IDataInfo) CastToGroup
processDataInfo(IDataInfo) CastToTable
Prepares processor to perform cast.
processDataInfo(IDataInfo) DataProcessorCvMD
processDataInfo(IDataInfo) DataProcessorReweight
processDataInfo(IDataInfo) DataProcessorReweightRatio
processDataInfo(IDataInfo) LjMd3D.DataProcessorCorrection
processDataInfo(IDataInfo) LjMd3D.DataProcessorReweight
processDataInfo(IDataInfo) DataProcessorXY
processDataInfo(IDataInfo) MolecularWeightAvg
processDataInfo(IDataInfo) MolecularWeightAvg2
processDataInfo(IDataInfo) DropletGraphic.DataProcessorTensorSplitter
processDataInfo(IDataInfo) AccumulatorAutocorrelationPTensor
processDataInfo(IDataInfo) AccumulatorAutocorrelationShearStress
processDataInfo(IDataInfo) GlassGraphic.DataProcessorTensorTrace
processDataInfo(IDataInfo) DataProcessorInterfacialTensionProfile
processDataInfo(IDataInfo) FitTanh
processDataInfo(IDataInfo) InterfacialSWGraphic.DataProcessorTensorSplitter
processDataInfo(IDataInfo) LjmdGraphic.DataProcessorTensorTrace
processDataInfo(IDataInfo) MuGraphic.DataProcessorMu
processDataInfo(IDataInfo) MuGraphic.DataSinkExcludeOverlap
processDataInfo(IDataInfo) DataProcessorBias
processDataInfo(IDataInfo) DataProcessorBounds
processDataInfo(IDataInfo) DataProcessorDyDLnx
processDataInfo(IDataInfo) DataProcessorVar
processDataInfo(IDataInfo) MultiharmonicGraphicMC.DataProcessAHT
processDataInfo(IDataInfo) NucleationGraphic.DataSinkExcludeOverlap
processDataInfo(IDataInfo) ReverseOsmosisGraphic.DataSinkExcludeOverlap
processDataInfo(IDataInfo) ReverseOsmosisWaterGraphic.DataSinkExcludeOverlap
processDataInfo(IDataInfo) SamGraphic.DataPipeStressStrain
processDataInfo(IDataInfo) DataProcessorBounds
processDataInfo(IDataInfo) DataProcessorMu
processDataInfo(IDataInfo) StatisticsMCGraphic.DataProcessorUndo
processDataInfo(IDataInfo) SwmdGraphic.DataSinkExcludeOverlap
processDataInfo(IDataInfo) BoltzmannProcessor
processDataInfo(IDataInfo) DataProcessorBoltzmannFactor
processDataInfo(IDataInfo) DataProcessorSum
processDataInfo(IDataInfo) DataProcessorSurfaceTension
processDataInfo(IDataInfo) FitTanh
processDataInfo(IDataInfo) SurfaceTensionMapped
processDataInfo(IDataInfo) DataProcessorVirialOverlap
processDataInfo(IDataInfo) VirialPolyhedra.DataProcessorR2
processDataInfo(IDataInfo) VirialPolyhedra2.DataProcessorR2
processReverseList() IntegratorHard
Recalculate collision times (up) for any atoms atoms in the "reverse"
list of atoms that thought they would collide with an atom that's
changed.
product AccumulatorAutocorrelationPTensor
product AccumulatorAutocorrelationShearStress
product(int[]) Standard
Prepares a set of bond pairs for a clusters
formed from a disconnected set of fully connected subclusters.
product(ClusterDiagram[]) ClusterOperations
Returns the product of all the given clusters.
product(ClusterDiagram[], ClusterDiagram[]) ClusterOperations
Returns an array of clusters formed from taking the product of each of the diagrams
of the first set with each of the diagrams of the second set.
product(ClusterDiagram, ClusterDiagram) ClusterOperations
Returns a new cluster that is the product of the given clusters.
product3D(Vector, Vector, Vector) P2SpheroPolyhedron
profile1 DCVGCMD
profile1 DCVGCMD
profile1pump DCVGCMD
profile1pump DCVGCMD
profile1TemperaturePump DCVGCMD
profile2 DCVGCMD
profile2 DCVGCMD
profile2pump DCVGCMD
profile2pump DCVGCMD
profile2TemperaturePump DCVGCMD
profileData DataSourceTensorVirialHardProfile
profileDataInfo DataSourceTensorVirialHardProfile
profileDim MeterProfile
Vector describing the orientation of the profile.
profileDim MeterProfileByAtoms
Vector describing the orientation of the profile.
profileDim MeterProfileByVolume
Vector describing the orientation of the profile.
profileDim DataProcessorInterfacialTensionProfile
profilePlot InterfacialSWGraphic
profileTemperature1 DCVGCMD
profileTemperature2 DCVGCMD
projectOntoAxis(Point3f, Point3f, Vector3f, Vector3f) Measure
prompt(String, String, String[], boolean) ApiPlatform
prompt(String, String, String[], boolean) Platform
prop MaxIsomorph.MaxIsomorphParameters
propane DCVGCMD
propene DCVGCMD
PROPERTIES BuildProperties
PropertiesResource etomica.server.resources
PropertiesResource(SimulationStore) PropertiesResource
property SetPropertyFilter
property DeviceSlider
Property being modulated
property DeviceSpinner
Property being modulated
property ModifierGeneral
property PropertyUpdate
property MeterVirialBDBinMultiThreaded
property MeterVirialBinMultiThreaded
property MeterVirialEBinMultiThreaded
property Token
Property etomica.graph.property
Property etomica.meta.properties
Created by kofke on 7/23/17.
PROPERTY EnumPalette
PROPERTY_ALL MaxIsomorph
propertyatomnumbercolumncount Token
propertyatomnumberfield Token
propertyChange(PropertyChangeEvent) PropertyText
Listen to update display if editor changes value in some other way.
propertyChange(PropertyChangeEvent) SoftSphereSolidEOSCalculator
Called when a field's "value" property changes.
propertycolorscheme Token
propertydatacolumncount Token
propertydatafield Token
propertyFilter AllIsomorphs.AllIsomorphsParameters
PropertyFilter etomica.graph.iterators.filters
PropertyFilter(GraphIterator, Property) PropertyFilter
PROPERTYFLAGS Token
PropertyImpl etomica.graph.engine.impl
PropertyImpl(String) PropertyImpl
PropertySerializer etomica.server.serializers
PropertySerializer(Class<Property>) PropertySerializer
PropertyText etomica.graphics
PropertyText(PropertyEditor) PropertyText
PropertyUpdate etomica.server.representations
PropertyUpdate() PropertyUpdate
PropertyUpdate(long, String, Object) PropertyUpdate
pRotConstraint MeterTargetRPMolecule
pRotConstraint SimOverlapAlphaN2TP
pRotConstraint SimOverlapBetaN2RPScaling
pRotConstraint SimOverlapDisorderedAlphaN2RPScaling
PRotConstraint etomica.models.nitrogen
PRotConstraint(Space, CoordinateDefinitionNitrogen, Box) PRotConstraint
protein Token
ProtonDisorderGenerator etomica.models.clathrates
Implementation of Buch's algorithm for proton disorder.
ProtonDisorderGenerator(Space, String, int, int[], double[], boolean, int, double, double) ProtonDisorderGenerator
ProtonDisorderGenerator.SimParams etomica.models.clathrates
pSat() EOSSW
Psat LJMD.LJMDParams
psi Token
psi(double) BigDecimalMath
Digamma function.
psi1x1 PotentialCalculationHeisenberg
psi1x1 PotentialCalculationVSum
psi1x11 PotentialCalculationHeisenberg
psi1x11 PotentialCalculationVSum
psi1x2 PotentialCalculationHeisenberg
psi1x2 PotentialCalculationVSum
psi1x22 PotentialCalculationHeisenberg
psi1x22 PotentialCalculationVSum
psi1y1 PotentialCalculationHeisenberg
psi1y1 PotentialCalculationVSum
psi1y11 PotentialCalculationHeisenberg
psi1y11 PotentialCalculationVSum
psi1y2 PotentialCalculationHeisenberg
psi1y2 PotentialCalculationVSum
psi1y22 PotentialCalculationHeisenberg
psi1y22 PotentialCalculationVSum
pSimData VirialOptimizer
psix1 PotentialCalculationHeisenberg
psix1 PotentialCalculationVSum
psix11 PotentialCalculationHeisenberg
psix11 PotentialCalculationVSum
psix111 PotentialCalculationHeisenberg
psix111 PotentialCalculationVSum
psix112 PotentialCalculationHeisenberg
psix112 PotentialCalculationVSum
psix12 PotentialCalculationHeisenberg
psix12 PotentialCalculationVSum
psix2 PotentialCalculationHeisenberg
psix2 PotentialCalculationVSum
psix22 PotentialCalculationHeisenberg
psix22 PotentialCalculationVSum
psix221 PotentialCalculationHeisenberg
psix221 PotentialCalculationVSum
psix222 PotentialCalculationHeisenberg
psix222 PotentialCalculationVSum
psiy1 PotentialCalculationHeisenberg
psiy1 PotentialCalculationVSum
psiy11 PotentialCalculationHeisenberg
psiy11 PotentialCalculationVSum
psiy111 PotentialCalculationHeisenberg
psiy111 PotentialCalculationVSum
psiy112 PotentialCalculationHeisenberg
psiy112 PotentialCalculationVSum
psiy12 PotentialCalculationHeisenberg
psiy12 PotentialCalculationVSum
psiy2 PotentialCalculationHeisenberg
psiy2 PotentialCalculationVSum
psiy22 PotentialCalculationHeisenberg
psiy22 PotentialCalculationVSum
psiy221 PotentialCalculationHeisenberg
psiy221 PotentialCalculationVSum
psiy222 PotentialCalculationHeisenberg
psiy222 PotentialCalculationVSum
pSoluteMM ReverseOsmosisWaterGraphic.ModifierSoluteCharge
pSolutePM ReverseOsmosisWaterGraphic.ModifierSoluteCharge
pSolutePP ReverseOsmosisWaterGraphic.ModifierSoluteCharge
pSpan MeterDDP
pSpan MeterDP
pSpan SimOverlapSoftSphereDP.SimOverlapParam
pSplitter DataSourceAvgPressure
pSplitter DataSourceAvgPressure2
pSplitter DataSourceMuRoot
pSplitter DataSourceMuRoot1
pSplitter DataSourceMuRootPMatch
pSplitter DataSourcePMu
pSplitter DataSourcePN
psuedoSinks DataSet
pSum DataClusterer
pSum DataClusterWriter
pSum HSNPT.MyAgent
pSum2 HSNPT.MyAgent
pt MaterialFracture
pt EnumVdw
pt4Value(ScriptVariable) ScriptVariable
pThermalize P1Wall
pTmp1 Potential2SoftSphericalLSMultiLat
pTmp1 PotentialCalculationSolidSuperCut
ptOrder VirialLJPT.VirialLJParam
pTruncated NormalModeAnalysisDisplay3D
pTruncatedAA SimCalcSSoftSphereFCCSuperBox
pTruncatedAB SimCalcSSoftSphereFCCSuperBox
ptValue(ScriptVariable) ScriptVariable
pTW LJMC
pTW LJMD
pU MayerENonGeneral
pullFactor MCMoveIDBiasAction
pump LJMD3D
pump LJMD3DNbr
pump Ising
pump TestLJMD3D
pumpRG ChainHSMD3D
pUnit NucleationGraphic
pUnit PistonCylinderGraphic
pUnit ReverseOsmosisGraphic
pUnit ReverseOsmosisWaterGraphic
pUnit SwmdGraphic
purine Token
PURPLE Colix
pushHistograms() AccumulatorAverageBootstrap
Constructs and pushes histograms to any histogram data sink.
pushInterval DataAccumulator
Accumulated data are pushed to the data sinks after every pushInterval calls
pushme ClusterCoupledFlippedMultivalue
pushme ClusterWheatleyMultibodyDerivatives
pushme ClusterWheatleySoft
pushme ClusterWheatleySoftBD
pushme ClusterWheatleySoftDerivatives
pushme ClusterWheatleySoftDerivativesBD
pushmeval ClusterWheatleyMultibodyDerivatives
pushmeval ClusterWheatleySoftDerivatives
pushR2 ClusterSumMultibody
pushR2 ClusterSumNonAdditiveTrimerEnergy
pushR2 ClusterSumPolarizable
pushR2 ClusterSumPolarizableWertheimProduct
pushR2 ClusterSumPolarizableWertheimProduct4Pt
pushR2 ClusterSumPolarizableWertheimProduct4PtFinal
put(int, int) Int2IntHash
put(int, V) IndexMap
put(Integer, V) IndexMap
put_rigid() P2WaterPotentialsJankowski
putAll(Map<? extends Integer, ? extends V>) IndexMap
putCount DataAccumulator
Counter that keeps track of the number of interval events
received since last call to updateSums
putData(int, double[][]) DataSinkBlockAveragerSFac.Sink
putData(int, double[][]) DataSourceCorrelation.Receiver
putData(int, double[][]) StructureFactorComponentCorrelation
putData(int, int, double[][]) DataSourceCorrelation
putData(int, IData, double[]) StructureFactorComponentCorrelation
putData(IData) DataProcessorWidomContact.GContactSink
putData(IData) DataArrayWriter
putData(IData) DataDistributer
putData(IData) DataDump
putData(IData) DataFork
Puts the given Data through into all DataSinks.
putData(IData) DataGroupSplitter
putData(IData) DataLogger
Performs the open/write/close file actions in accordance with the
settings of the Logger.
putData(IData) DataProcessor
Processes input Data and pushes it downstream if output Data and DataSink
are not null.
putData(IData) DataSet.DataSetSink
putData(IData) DataSinkConsole
Causes the given values to be written to the print stream.
putData(IData) DataSplitter
putData(IData) DataTableWriter
putData(IData) IDataSink
Gives data to DataSink for processing, display, or whatever it does.
putData(IData) DisplayTextBox
Sets the display text to reflect the desired value from the datasource.
putData(IData) DisplayTextBoxesCAE
putData(IData) AccumulatorPTensor
putData(IData) AccumulatorPTensor.TemperatureSink
putData(IData) DataClusterer.PressureSink
putData(IData) DataClusterer
putData(IData) DataClusterWriter.PressureSink
putData(IData) DataClusterWriter
putData(IData) DataSinkBlockAveragerSFac
putData(IData) DataSourceBlockAvgCor
putData(IData) DataSourceHisogram
putData(IData) DataSourceMSDcorP
putData(IData) DataSourcePMSDHistory
putData(IData) StructorFactorComponentExtractor
putData(IData) StructureFactorComponentCorrelation.Sink
putData(IData) AccumulatorOverlapAverageUa2
Add the given values to the sums and block sums
putData(IData) MultiharmonicGraphicMC.DataSinkReweightedDeltaU
putData(IData) DataAccCorrectedPusher
putData(IData) DataAccDiffCorrectedPusher
putData(IData) DataAccDifficultyPusher
putData(IData) DataAccPusher
putData(IData) DataAccSamplesPusher
putDataInfo(IDataInfo) DataProcessorWidomContact.GContactSink
putDataInfo(IDataInfo) AccumulatorAverageBlocklessSlim
Prepares the accumulator for input data.
putDataInfo(IDataInfo) AccumulatorAverageFixed
putDataInfo(IDataInfo) DataArrayWriter
putDataInfo(IDataInfo) DataDistributer
putDataInfo(IDataInfo) DataDump
putDataInfo(IDataInfo) DataFork
Puts the given DataInfo through into all DataSinks, inserting
a data caster before any sinks needing one.
putDataInfo(IDataInfo) DataGroupSplitter
putDataInfo(IDataInfo) DataProcessor
Invokes processDataInfo on the given DataInfo, and passes the returned
DataInfo to the dataSink (if not null).
putDataInfo(IDataInfo) DataSet.DataSetSink
putDataInfo(IDataInfo) DataSinkConsole
Causes the given DataInfo to be written to the print stream.
putDataInfo(IDataInfo) DataSplitter
putDataInfo(IDataInfo) DataTableWriter
putDataInfo(IDataInfo) IDataSink
Informs the DataSink of the type of Data it should expect to receive.
putDataInfo(IDataInfo) DisplayTextBox
putDataInfo(IDataInfo) DisplayTextBoxesCAE
putDataInfo(IDataInfo) AccumulatorPTensor
putDataInfo(IDataInfo) AccumulatorPTensor.TemperatureSink
putDataInfo(IDataInfo) DataClusterer.PressureSink
putDataInfo(IDataInfo) DataClusterer
putDataInfo(IDataInfo) DataClusterWriter.PressureSink
putDataInfo(IDataInfo) DataClusterWriter
putDataInfo(IDataInfo) DataSinkBlockAveragerSFac
putDataInfo(IDataInfo) DataSourceBlockAvgCor
putDataInfo(IDataInfo) DataSourceHisogram
putDataInfo(IDataInfo) DataSourceMSDcorP
putDataInfo(IDataInfo) DataSourcePMSDHistory
putDataInfo(IDataInfo) StructorFactorComponentExtractor
putDataInfo(IDataInfo) StructureFactorComponentCorrelation.Sink
putDataInfo(IDataInfo) AccumulatorOverlapAverageUa2
putDataInfo(IDataInfo) MultiharmonicGraphicMC.DataSinkReweightedDeltaU
putDataInfo(IDataInfo) AccumulatorMimicMu
putDataInfo(IDataInfo) DataAccPusher
putDataInfoInternal(IDataInfo) DataArrayWriter
putDataInfoInternal(IDataInfo) DataTableWriter
putDataInternal(IData) DataArrayWriter
putDataInternal(IData) DataTableWriter
putEdge(byte) Graph
putEdge(byte) GraphImpl
putEdge(byte, byte) Graph
putEdge(byte, byte) GraphImpl
putMSD(int, long, double) DataSourceCorMSD
putMSD(int, long, double) DataSourceHistogramMSD
putMSD(int, long, double) DataSourceMSD.MSDSink
putMSD(int, long, double) DataSourceMSDcorP
putMSD(int, long, double) DataSourcePMSDHistory
putValue(String, Object) Grabber.ActionCornerSetter
pvBox LatticeEditor
pvx10 PotentialCalculationMoleculeAgentSum
pvx10 PotentialCalculationPair
pvx11 PotentialCalculationMoleculeAgentSum
pvx11 PotentialCalculationPair
pvx20 PotentialCalculationMoleculeAgentSum
pvx20 PotentialCalculationPair
pvx21 PotentialCalculationMoleculeAgentSum
pvx21 PotentialCalculationPair
pvy10 PotentialCalculationMoleculeAgentSum
pvy10 PotentialCalculationPair
pvy11 PotentialCalculationMoleculeAgentSum
pvy11 PotentialCalculationPair
pvy20 PotentialCalculationMoleculeAgentSum
pvy20 PotentialCalculationPair
pvy21 PotentialCalculationMoleculeAgentSum
pvy21 PotentialCalculationPair
pWater TIP4P_NVT
pWell MCMoveClusterAtomSQWChain
pWell MCMoveClusterAtomSQWTree
pWertheim2Site WertheimDiagrams2SiteRho
Pwr2 TriangleData
PY ClusterOperations
PYGenerate(int, char) PYGenerator
Returns the graphs (at each order, up to n+2) in the PY approximation to c.
PYGenerator etomica.virial
PYGenerator() PYGenerator
PYGenerator.IteratorEF etomica.virial
pyrimidine Token
pzxySum Potential2SoftSphericalLSMultiLat.ReturnValue
pzxySum PotentialCalculationSolidSuperCut
Q
q PotentialCalculationMappedRdf
q PotentialCalculationMappedEnergy
q PotentialCalculationMappedVirial
q PotentialCalculationMappedVirialV
q P2CO2Hellmann
q P2Nitrogen
q DataSourceF
q DataSourceFOld
q DataSourceFs
q GCRestrictedGibbsHS.simParams
q GCWidomInsertHS.simParams
q P2NitrogenHellmann
q P3Induction.MyAgent
q P3NitrogenHellmannNonAdditive
q VirialHSMixture.VirialHSParam
q VirialHSMixtureOverlap.VirialHSParam
q(double, double, double) SimLattice
Q P2HePCKLJS
Q PotentialCalculationFSum
q_err EwaldSumMolecules
q0 Quaternion
q0 Quaternion
q1 Quaternion
q1 P2Electrostatic
q1 P2ElectrostaticWithHardCore
q1 Quaternion
q1Bond MayerIonicDiagram1qbond
q1Bond MayerIonicDiagram2qbonds
q1Bond MayerIonicDiagram4qbonds
q2 Quaternion
q2 P2Electrostatic
q2 P2ElectrostaticWithHardCore
q2 Quaternion
q2Bond MayerIonicDiagram2qbonds
q2Bond MayerIonicDiagram4qbonds
q3 Quaternion
q3 Quaternion
q3Bond MayerIonicDiagram4qbonds
q4Bond MayerIonicDiagram4qbonds
Q4sum DataSourceQ4
Q4sum2 DataSourceQ4
qA P2CO2Hellmann
qA P2NitrogenHellmann
qA P3NitrogenHellmannNonAdditive
qaa P2O2Bartolomei
qaaMRCI P2O2Bartolomei
qaaPT2 P2O2Bartolomei
qajmols P2O2Bartolomei
qajmolsMRCI P2O2Bartolomei
qajmolsPT2 P2O2Bartolomei
qajp1 P2O2Bartolomei
qajp1MRCI P2O2Bartolomei
qajp1PT2 P2O2Bartolomei
qajpn P2O2Bartolomei
qajpnMRCI P2O2Bartolomei
qajpnPT2 P2O2Bartolomei
qB P2CO2Hellmann
qB P2NitrogenHellmann
qB P3NitrogenHellmannNonAdditive
qbet P2O2Bartolomei
qbetMRCI P2O2Bartolomei
qbetPT2 P2O2Bartolomei
qCalc(double, int) Ushcats
Computes q, given as Q * N!/V^N, where Q is the configurational integral.
qCalc(int, double[]) QSeries
Computes Q * N!/V^N based on the volume series for Q given by qCalc.
QFH VirialHePCKLJS.VirialParam
QFH VirialHePCKLJSCHNCCorrection.VirialLJParam
QFH VirialHePCKLJSPYCorrection.VirialLJParam
QFH VirialHePCKLJSTempDeriv.VirialParam
qH P2WaterTIP4P
QH P2WaterSPCE
Qi IntegratorHarmonic
QO P2WaterSPCE
qp PotentialCalculationMappedRdf
qp PotentialCalculationMappedEnergy
qp_q PotentialCalculationMappedEnergy
qq P2Electrostatic
qq P2ElectrostaticWithHardCore
Qr IntegratorHarmonic
QSeries etomica.veos
Fluid properties based on direct expansion of the canonical partition function Q in terms
of irreducible cluster integrals beta.
QSeries(BetaSource) QSeries
qSite P3Induction.MyAgent
qsqv P2SpheroPolyhedron
qu PotentialCalculationMappedVirial
qu PotentialCalculationMappedVirialV
quadId(int, int, int, int, int) VirialDiagrams
Returns the quad ID for the given indices (id0, id1, id2, id3) and given
number of molecules (n).
quadId(int, int, int, int, int) VirialDiagramsPT
Returns the quad ID for the given indices (id0, id1, id2, id3) and given
number of molecules (n).
Quadric org.jmol.util
Quadric(double[]) Quadric
Quadric(Vector3f[], float[], boolean) Quadric
quadStart VirialDiagrams
quadStart VirialDiagramsPT
quality SVGConverter
Output image quality.
quantity() CGS
quantity() LJ
quantity() MKS
quantity() UnitSystem
quantity() UnitSystem.Sim
Quantity etomica.units.dimensions
The dimension for the quantity of discrete things (e.g.
quat IntegratorVelocityVerletQuaternion.MoleculeAgent
quaternion AtomOrientedQuaternion
Quaternion etomica.math
Quaternion object , its properties and associated operations
Quaternion org.jmol.util
Quaternion() Quaternion
Quaternion(double[]) Quaternion
Constructs the Quaternion q = p[0] + p[1]*i + p[2]*j + p[3]*k
Quaternion(double, double[]) Quaternion
Constructs the Quaternion q = a + b[0]*i + b[1]*j + b[2]*k
Quaternion(double, double, double, double) Quaternion
Constructs the Quaternion q = a + b*i + c*j + d*k
Quaternion(double, Vector) Quaternion
Constructs the Quaternion q = a + b
Quaternion(Vector[]) Quaternion
Constructs the Quaternion q for an input basis vector array.
Quaternion(Vector, double) Quaternion
Constructs the unit Quaternion q = cos(angle/2) + axis*sin(angle/2)
Quaternion(OrientationFull3D) Quaternion
Constructs the Quaternion q for an input OrientationFull3D with two vectors.
Quaternion(Matrix) Quaternion
Constructs the Quaternion q given an input rotation matrix.
quaternionframe Token
quatVelocity IntegratorVelocityVerletQuaternion
quiet MeterVirialBDBinMultiThreaded
quiet MeterVirialBinMultiThreaded
quiet MeterVirialEBinMultiThreaded
quintId(int, int, int, int, int, int) VirialDiagrams
Returns the quint ID for the given indices (id0, id1, id2, id3, id4) and given
number of molecules (n).
quintId(int, int, int, int, int, int) VirialDiagramsPT
Returns the quint ID for the given indices (id0, id1, id2, id3, id4) and given
number of molecules (n).
quintStart VirialDiagrams
quintStart VirialDiagramsPT
quit() ConsoleContainer
quit() Launcher.ConsoleWindow
quit(Parser.Command) Interpreter
quitSearch() IntegratorDimerMin
Called after criteria is met in the rotateDimer method.
qx GlassProd.SimParams
R
r IntegratorDimerApproach
r MCMoveVolumeAssociated
r MCMoveVolumeAssociatedMolecule
r DataSourcePercolation
r DataSourcePercolation0
r DataSourceQ4
r ConfigurationPolymer
r IntegratorPolymer
r P1Sinusoidal
r VirialH2OGCPMD.Clusterfoo
R PotentialCalculationMappedRdf
r0 MCMoveDimerRotate
r0 MCMoveSmerRotate
r0 MeterWidomCavity
r0 PotentialCuLREP
r0 ConfigFromFileLAMMPS.ColorSchemeDeviation
r0 MCMoveDimerRotate
r0 MCMoveRotateMolecule3D
r0 MCMoveRotateMolecule3DConstraint
r0 MCMoveRotateMolecule3DFixedAngle
r0 MCMoveRotateMolecule3DN2AveCosThetaConstraint
r0 MCMoveRotateMolecule3DSuperBox
r0 IntegratorDroplet.MyAgent
r0 P2HydrogenHindePatkowski
r0 P2HydrogenHindePatkowskiAtomic
r0 P2WaterPotentialsJankowski
r0 MCMoveBondLength
r0 MCMoveClusterBondLength
r0 MCMoveClusterConformationMDTest
r0 MCMoveClusterRotateArm
r0 MCMoveRotateArm
r0 VirialCPSHeliumNonAdditiveClassical_Correction
r0 VirialCPSHeliumNonAdditiveClassical
R0 P2Nitrogen
R0 P2NitrogenAB
R0 P2NitrogenAnisotropic
R0 P2WaterSzalewicz
R0 P3HydrogenGarberoglioMolecular
r00 VirialH2PIBoltzmann.VirialHePIParam
r01Vec VirialCPSHeliumNonAdditiveClassical_Correction
r01Vec VirialCPSHeliumNonAdditiveClassical
r02Vec VirialCPSHeliumNonAdditiveClassical_Correction
r02Vec VirialCPSHeliumNonAdditiveClassical
r1 P3HydrogenATM
r1 VirialCPSHeliumNonAdditiveClassical_Correction
r1 VirialCPSHeliumNonAdditiveClassical
R1 PotentialEAM_LS
R1 P2Nitrogen
R1 P2NitrogenAB
R1 P2NitrogenAnisotropic
r12 P3AdditiveQChem.DampingParams
r12 P3QChem.DampingParams
r12Vec PotentialEmul
r12Vec VirialCPSHeliumNonAdditiveClassical_Correction
r12Vec VirialCPSHeliumNonAdditiveClassical
r12Vector PNWaterGCPMReactionField
r2 P2Nitrogen
r2 P2NitrogenAB
r2 P2NitrogenShellModel
r2 CriterionSimple
r2 CriterionSimpleMolecular
r2 P3HydrogenATM
r2 ClusterSumMultibody
r2 ClusterWheatleyMultibody
r2 ClusterWheatleyMultibodyBD
r2 ClusterWheatleyMultibodyDerivatives
r2 ClusterWheatleyMultibodyDerivativesBD
r2 ClusterWheatleyMultibodyMix
r2 CoordinatePairLeafSet
r2 CoordinatePairMoleculeSet
r2 VirialCPSHeliumNonAdditiveClassical_Correction
r2 VirialCPSHeliumNonAdditiveClassical
r2(Vector1D, Vector1D, Boundary) Space1D
Computes the square of the magnitude of the difference of two vectors, subject
to a nearest image transformation.
r2(Vector1D, Vector1D, Boundary, Vector1D) Space1D
Computes the square of the magnitude of the difference of two vectors, subject
to a nearest image transformation.
r2(Vector2D, Vector2D, Boundary) Space2D
Computes the square of the magnitude of the difference of two vectors, subject
to a nearest image transformation.
r2(Vector2D, Vector2D, Boundary, Vector2D) Space2D
Computes the square of the magnitude of the difference of two vectors, subject
to a nearest image transformation.
r2(Vector3D, Vector3D, Boundary) Space3D
Computes the square of the magnitude of the difference of two vectors, subject
to a nearest image transformation.
r2(Vector3D, Vector3D, Boundary, Vector3D) Space3D
Computes the square of the magnitude of the difference of two vectors, subject
to a nearest image transformation.
R2 PotentialEAM_LS
r2a P2CO2H2OWheatley.P2CO2H2OSC
r2ab P2CO2H2OWheatley.P2CO2H2OSC
r2b P2CO2H2OWheatley.P2CO2H2OSC
r2Core PotentialEmul
r2Cut PotentialCalculationSolidSuperCut
r2Cutoff P2MoleculeSoftTruncatedSwitched
r2Cutoff P2MoleculeTruncated
r2Cutoff P2SoftSphericalTruncated
r2Cutoff P2SoftSphericalTruncatedSwitched
r2Cutoff P2SoftTruncated
r2Cuts PotentialCalculationEnergySumCutoff
r2Cuts PotentialCalculationSumCutoff
r2d2udr2 PercusYevick1QC
r2Data P2QChemInterpolated
r2MaxSafe CriterionSimple
r2MaxSafe CriterionSimpleMolecular
r2Switch P2MoleculeSoftTruncatedSwitched
r2Switch P2SoftSphericalTruncatedSwitched
r3 P3HydrogenATM
R3 PotentialEAM_LS
rAB EwaldSummation
rac P1LepsHarmonic
rAccum MeterMeanSquareDisplacement
radau_f1_tst(Vector[]) P2WaterPotentialsJankowski
Radian etomica.units
Simulation unit for the measure of an angle.
radiansPerDegree Measure
radiansPerDegree JmolConstants
radicalColorMap ColorSchemeRadical
radioB MyApplet
radioB1 MyApplet
radius Hypersphere
radius Token
random AtomActionRandomizeVelocity
random AtomSourceRandomDimer
random AtomSourceRandomSmer
random ColorSchemeSmer
random ColorSchemeSmerByLength
random MCMoveDimer
random MCMoveDimerRotate
random MCMoveSmer
random MCMoveSmerRotate
random MoleculeSourceRandomDimer
random AtomSourceRandomLeaf
random AtomSourceRandomSpecies
random RandomPositionSourceDeformable
random RandomPositionSourceRectangular
random MeterWidomCavity
random P2HardSphereCavity
random ConfigurationLatticeRandom
random AccumulatorAverageBootstrap
random AccumulatorAverageCollapsingLog
random MCMoveAtomCoupled
random MCMoveAtomSwap
random IntegratorManagerMC
random IntegratorMC
random IntegratorMD
random MCMoveAtom
random MCMoveDimer
random MCMoveDimerRotate
random MCMoveInsertDelete
random MCMoveMolecule
random MCMoveVolume
random AkimaSplineSmoother
random CoordinateDefinitionNitrogen
random CoordinateDefinitionNitrogenSuperBox
random MCMoveMoleculeCoupledInitPert
random MCMoveMoleculeCoupledSuperBox
random MCMoveRotateMolecule3DSuperBox
random MeterDirectInitPert
random P1Wall
random ConfigurationLatticeFreeRadical
random P2SquareWellRadical
random ConfigurationColloid
random ConfigurationDroplet
random AtomTestRandom
random DataClusterer
random MCMoveSwap
random MCMoveMultiHarmonic
random ConfigurationPolymer
random MoleculeSourceRandomMolecule
random MCMoveAtomCoupled
random MCMoveAtomCoupledBennet
random MCMoveAtomCoupledUmbrella
random MCMoveAtomSuperBox
random MCMoveEinsteinCrystal
random MCMoveHarmonic
random MCMoveHarmonicStep
random MCMoveMoleculeCoupled
random MCMovePhaseAngle
random MCMoveSingleMode
random MCMoveVolumeMonoclinicScaled
random MCMoveVolumeSolidNPTMolecular
random MCMoveWV
random MCMoveGeometricCluster
random MCMoveGeometricClusterRestrictedGE
random Simulation
random MCMoveSpinCluster
random MCMoveSpinFlip
random ClusterDiagramTree
random ClusterCoupledFlippedMultivalue
random ClusterSumStickyEF
random ClusterWheatleySoft
random ClusterWheatleySoftDerivatives
random ConfigurationClusterAceticAcid
random ConfigurationClusterMove
random ConfigurationClusterWertheimGCPM
random ConfigurationClusterWertheimGCPM4Pt
random ConfigurationClusterWertheimGCPMDirectSampling
random MCMoveClusterAngleBend
random MCMoveClusterAngleBendAceticAcid
random MCMoveClusterReptateMulti
random MCMoveClusterRingPartialRegrow
random MCMoveClusterRingRegrow
random MCMoveClusterRingRegrowExchange
random MCMoveClusterRingScale
random MeterVirialBDBin
random MeterVirialBDBinMultiThreaded
random MeterVirialBinMultiThreaded
random MeterVirialEBinMultiThreaded
RANDOM VirialHSMixture.VirialHSParam
random1 IntegratorDimerRT
randomAtom0 MCMoveAtomSuperBox
randomAtom1 MCMoveAtomSuperBox
randomDirection(IRandom) Vector1D
randomizeDiagram() ClusterSumStickyEF
set the diagram used for calculating the value to a random one.
randomizeMomenta() IntegratorHard
Updates collision times appropriately after randomizing momenta
as part of the Andersen thermostat.
randomizeMomenta() IntegratorMD
Randomizes the velocities of all atoms in the box using values
chosen from a Maxwell-Boltzmann distribution, as in the Andersen
thermostat.
randomizeMomenta() IntegratorRigidIterative
randomizeMomenta() IntegratorRigidMatrixIterative
randomizeMomenta() IntegratorVerlet
Updates MrLast appropriately after randomizing momenta
as part of the Andersen thermostat.
randomizeMomenta() IntegratorFixedWall
randomizeMomenta() IntegratorVelocityVerletQuaternion
randomizeMomentum(IAtomKinetic) IntegratorHard
Updates collision time appropriately after randomizing momentum
as part of the Andersen thermostat.
randomizeMomentum(IAtomKinetic) IntegratorMD
Randomizes the velocities of the given atom using value
chosen from a Maxwell-Boltzmann distribution, as in the Andersen
thermostat.
randomizeMomentum(IAtomKinetic) IntegratorRigidIterative
randomizeMomentum(IAtomKinetic) IntegratorRigidMatrixIterative
randomizeMomentum(IAtomKinetic) IntegratorVerlet
Updates MrLast appropriately after randomizing momentum
as part of the Andersen thermostat.
randomizePositions() SimDimerLJadatom
randomizePositions() IntegratorKMC
randomizePositions() IntegratorKMCCluster
randomizePositions() SimKMCLJadatom
randomizer P1Wall
randomizeTotalKE() IntegratorHard
Updates collision times appropriately after randomizing momenta
as part of the Andersen scaling thermostat.
randomizeTotalKE() IntegratorMD
Scales all velocities so that the total kinetic energy matches a value selected at random for the
previously specified temperature.
randomJustChecking ClusterWheatleySoftDerivatives
randomLensPoint(double, Vector3D) MCMoveClusterAtomHSRing
Returns a randomly selected point from within the lens-shaped region of
overlap of two spheres of unit radius separated by a distance d.
randomLensPoint(Vector, Vector, Vector3D, Vector, double) MCMoveClusterAtomHSRing
Sets a given vector to a point chosen uniformly at random in the lens-shaped region
formed by the overlap of two spheres of unit radius located at the given positions r1 and r2.
randomLensPointInBox(Vector, Vector, Vector) MCMoveClusterAtomHSRing
RandomMersenneTwister etomica.util.random
Mersenne Twister RNG.
RandomMersenneTwister(int) RandomMersenneTwister
Creates a Mersenne Twister with the given seed.
RandomMersenneTwister(int[]) RandomMersenneTwister
Creates a Mersenne Twister with the given array of seeds.
randomMol0 MCMoveMoleculeCoupledSuperBox
randomMol1 MCMoveMoleculeCoupledSuperBox
randomNumber0 MCMoveAtomSuperBox
randomNumber1 MCMoveAtomSuperBox
RandomNumberGenerator etomica.util.random
Random number generator class.
RandomNumberGenerator() RandomNumberGenerator
RandomNumberGenerator(long) RandomNumberGenerator
RandomNumberGeneratorUnix etomica.util.random
Random number generator that takes random bits from files.
RandomNumberGeneratorUnix() RandomNumberGeneratorUnix
Create an RNG using /dev/urandom as a source of random bits.
RandomNumberGeneratorUnix(String) RandomNumberGeneratorUnix
Create an RNG using the given file as a source of random bits.
randomOrientation(Vector) MCMoveClusterPolyhedraChain
randomOrientation(Vector) MCMoveClusterPolyhedraTree
randomPosition() RandomPositionSource
Returns a random position with the previously set box's boundary.
randomPosition() RandomPositionSourceDeformable
randomPosition() RandomPositionSourceRectangular
randomPosition() BoundaryTruncatedOctahedron
RandomPositionSource etomica.box
Interface for an object which returns random positions within a box's
boundary.
RandomPositionSourceDeformable etomica.box
Implementation of RandomPositionSource that can handle
BoundaryDeformablePeriodic.
RandomPositionSourceDeformable(Space, IRandom) RandomPositionSourceDeformable
RandomPositionSourceRectangular etomica.box
RandomPositionSourceRectangular(Space, IRandom) RandomPositionSourceRectangular
randomRotation(IRandom, double) IOrientation
Perform a rotation by a random amount in the solid angle theta on the
present orientation.
randomRotation(IRandom, double) Orientation1D
Sets orientation randomly to be +1 or -1.
randomRotation(IRandom, double) Orientation2D
Applies a random rotation of angle selected uniformly within plus or minus tStep
from the current value.
randomRotation(IRandom, double) Orientation3D
Applies a random rotation of angle selected uniformly from 0 to tStep.
randomRotation(IRandom, double) OrientationFull3D
Applies a random rotation of angle selected uniformly from 0 to tStep.
randomSeeds GlassProd.SimParams
randomSeeds SimLJHTTISuper.SimOverlapParam
randomSeeds SimLJHTTISuperHCP.SimOverlapParam
randomSeeds SimLJHTTISuperHCP2.SimOverlapParam
randomSeeds SimLJHTTISuperSFMD.SimOverlapParam
randomSeeds VirialHSBinMultiThreaded.VirialHSBinParam
randomSeeds VirialLJDU.VirialLJParam
randomSeeds VirialSQWBinMultiThreaded.VirialHSBinParam
range ColorSchemeTemperature
range RectangularLatticeNbrIteratorSquare
range MyMCMove
range P1Wall
range P1Wall
range BoxAgentSourceCellManager
range BoxAgentSourceCellManagerMolecular
range NeighborCellManagerMolecular
range NeighborCellManager
range PotentialMasterListMolecular.NeighborListAgentSourceMolecular
range PotentialMasterListMolecular
range NeighborListAgentSource
range P2Ideal
range P2HSPolymer
range Token
RangeComparator() MeterVirialExternalFieldOverlapConfined.RangeComparator
rangedAgentManager PotentialMasterNbrMolecular
rangedPotentials PotentialMasterNbr
rangedPotentials1Body PotentialMasterNbr
RangePermutator etomica.graph.iterators
This is a facility class that iterates through (maxP1 - minP1 + 1) permutations one at
a time.
RangePermutator(int, int, int) RangePermutator
rangeselected Token
rasmol Token
RASMOL EnumPalette
RASMOL EnumVdw
RASTERIZER_SECURITY_POLICY Main
URL for Squiggle's security policy file
ratio AccumulatorRatioAverageCovariance
ratio AccumulatorRatioAverageCovarianceFull
ratio MultiharmonicGraphicMC.DataSinkReweightedDeltaU
RATIO AccumulatorRatioAverageCovariance
RATIO AccumulatorRatioAverageCovarianceFull
RATIO DataOverlap
RATIO_ERROR AccumulatorRatioAverageCovariance
RATIO_ERROR AccumulatorRatioAverageCovarianceFull
ratioError AccumulatorRatioAverageCovariance
ratioError AccumulatorRatioAverageCovarianceFull
ratioErrorStat DataVirialOverlap
ratioMaxN MCMoveIDBiasAction
Rational etomica.math
Class handling rational numbers (numerator / denominator), including
addition, multiplication and reducing (15/6 => 5/2).
Rational etomica.veos.bigdecimal
Fractions (rational numbers).
Rational() Rational
Rational() Rational
Default ctor, which represents the zero.
Rational(int) Rational
ctor from an integer.
Rational(int, int) Rational
Creates Rational instance with the given numerator and denominator.
Rational(int, int) Rational
ctor from a numerator and denominator.
Rational(String) Rational
ctor from a string representation.
Rational(String, int) Rational
ctor from a string representation in a specified base.
Rational(BigInteger) Rational
ctor from a numerator.
Rational(BigInteger, BigInteger) Rational
ctor from a numerator and denominator.
ratios MCMoveOverlapListener
ratioStat DataVirialOverlap
RAW_RGB Colix
rawData MeterCavityMapped
rawData MeterRDFMapped
rawData AccumulatorAverageBootstrap
rawData AccumulatorAverageCollapsingLog
rawData2 AccumulatorAverageBootstrap
rawData2 AccumulatorAverageCollapsingLog
rawData3 AccumulatorAverageBootstrap
rawData3 AccumulatorAverageCollapsingLog
rawDataBlockSize AccumulatorAverageBootstrap
rawDataBlockSize AccumulatorAverageCollapsingLog
rawDataInfo MeterCavityMapped
rawDataInfo MeterRDFMapped
RawDataWindowOpener(int, DisplayPlot) DisplayPlot.RawDataWindowOpener
rawSink MeterCavityMapped
rawSink MeterRDFMapped
rawTag MeterCavityMapped
rawTag MeterRDFMapped
rBond VirialDiagramsPT
rBound(double, int) DisplayBoxCanvasG3DSys
helper method that returns the position r if there are no bounds or
if r is inside the bounds or (if r is outside the bounds) returns the
position in the bounds nearest r.
rc SimLJ.LjMC3DParams
rc SimMappedRdf.LJMDParams
rc MappedU.LJMDParams
rc MappedVirialLJ.LJMDParams
rc MappedVirialLJVGr.LJMDParams
rc LJmuVT.LJMCParams
rc LJNPT.LJMCParams
rc LJNVT.LJMCParams
rc HarmonicCrystalSsFccNxy.Params
rc LJVacancyMin.SimOverlapParam
rc MinimizeHCP.SimOverlapParam
rc SimEinStep1.SimOverlapParam
rc SimEinStep1HCP.SimOverlapParam
rc SimEinStep2.SimOverlapParam
rc SimEinStep2HCP.SimOverlapParam
rc SimLJHTTISuper.SimOverlapParam
rc SimLJHTTISuperHCP.SimOverlapParam
rc SimLJHTTISuperHCP2.SimOverlapParam
rc SimLJHTTISuperSFMD.SimOverlapParam
rc SimLJVacancy.LJParams
rc SimOverlapSoftSphereDP.SimOverlapParam
rc SimOverlapSoftSphereEin.SimOverlapParam
rc SimOverlapSoftSphereEinHarm.SimOverlapParam
rc SimOverlapSoftSphereTP.SimOverlapParam
rc SimOverlapSoftSphereTPHCP.SimOverlapParam
rc SimOverlapSoftSphereTPSlantedBox.SimOverlapParam
rc ParserLAMMPS.Options
rC CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
rC CalcNumerical2ndDerivativeNitrogen
rC HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
rC HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
rC HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
rC HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
rC HarmonicBetaNitrogenModelPairMoleculeSequentialLS
rC HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
rC HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
rC MinimizationBetaNitrogenModelLS
rC P2Nitrogen
rC P2NitrogenAB
rC P2NitrogenAnisotropic
rC P2NitrogenShellModel
rc0 SimLJHTTISuper.SimOverlapParam
rc0 SimLJHTTISuperHCP.SimOverlapParam
rc0 SimLJHTTISuperHCP2.SimOverlapParam
rC1 PotentialCuLREP
rC1 PotentialEAM_LS
rC1 PotentialEAM
rc12 P2EAM
rC2 PotentialCuLREP
rC2 PotentialEAM_LS
rC2 PotentialEAM
rc22 P2EAM
rCc PotentialEFS
rCd PotentialEFS
RcData P2QChemInterpolated
rcforHandfinmap MeterMappedRdf
rcforHandfinmap PotentialCalculationMappedRdf
rcforHandfinmap SimMappedRdf.LJMDParams
rcLong LjMd3D.LjMd3DParams
rcMax0 SimLJHTTISuper.SimOverlapParam
rcMax0 SimLJHTTISuperHCP.SimOverlapParam
rcMax0 SimLJHTTISuperHCP2.SimOverlapParam
rcMax1 SimLJHTTISuper.SimOverlapParam
rcMax1 SimLJHTTISuperHCP.SimOverlapParam
rcMax1 SimLJHTTISuperHCP2.SimOverlapParam
rcond P2WaterPotentialsJankowski
rcScale SimOverlapAlphaN2TP.SimOverlapParam
rcScale SimOverlapBetaN2TP.SimOverlapParam
rcScale SimOverlapDisorderedAlphaN2TP.SimOverlapParam
rcShort LjMC3D.LjMC3DParams
rcShort LjMd3D.LjMd3DParams
rcShort LjMd3Dv2y.LjMd3DParams
rCut P2Water4P
rCut EwaldSumMolecules
rCut2 Potential2SoftSphericalLSMulti
rCut2 Potential2SoftSphericalLSMultiLat
rCut2 P2CO2EMP
rCut2 Potential2SoftSphericalLS
rCut2 ClusterWheatleyMultibody
rCut2 ClusterWheatleyMultibodyBD
rCut2 ClusterWheatleyMultibodyMix
rCut2 ClusterWheatleySoftDerivatives
rCut2 ClusterWheatleySoftDerivativesBD
rCutLJ ClathrateHarmonicFE.SimParams
rCutLJ MinimizationTIP4P.SimParams
rCutMax Potential2SoftSphericalLSMulti
rCutMax Potential2SoftSphericalLSMultiLat
rCutoff P2MoleculeSoftTruncatedSwitched
rCutoff P2MoleculeTruncated
rCutoff P2SoftSphericalTruncated
rCutoff P2SoftSphericalTruncatedSwitched
rCutoff P2SoftTruncated
rCutRealES ClathrateHarmonicFE.SimParams
rCutRealES MinimizationTIP4P.SimParams
rCutRealES ProtonDisorderGenerator.SimParams
rCutRealES EwaldSummation
rCutSquared EwaldSummation
rD MeterPressureTensor
rData MeterCavityMapped
rData MeterRDFMapped
rData MeterWidomCavity
rData MeterRDF
rData MeterRDFPC
rData MeterMappedRdf
rData CorrelationSelf2
rData MeterCorrelation
rData P2QChemInterpolated
rData MeterBondLength
rDataInfo MeterWidomCavity
rdfdr HypernettedChain
rdfdr PercusYevick
rdfInterval HSMDWidom.HSMDParam
rdfListener PistonCylinderGraphic
rdfPump PistonCylinderGraphic
rDistributionErrorHash CalcFFT
rDistributionHash CalcFFT
rdudr PercusYevick1QC
re P1HydrogenMielke
ReactionEquilibrium etomica.modules.reactionequilibrium
ReactionEquilibrium() ReactionEquilibrium
ReactionEquilibriumGraphic etomica.modules.reactionequilibrium
ReactionEquilibriumGraphic(ReactionEquilibrium, Space) ReactionEquilibriumGraphic
ReactionEquilibriumGraphic.Applet etomica.modules.reactionequilibrium
ReactionEquilibriumGraphic.MassEditor etomica.modules.reactionequilibrium
ReactionEquilibriumGraphic.MySpeciesEditor etomica.modules.reactionequilibrium
reactionField TestAceticAcidMC3D_NPT
reactionManagerCO Catalysis
ReactionManagerCO etomica.modules.catalysis
ReactionManagerCO(Catalysis) ReactionManagerCO
read(Parser.CommandVariableValue) Interpreter
read(String) ConsoleReader
read(String) Interpreter
readBlockData(String) AccumulatorAverageFixed
Reads block data from the given file.
readBoxRestart(BufferedReader, int) SimulationVirialOverlap2
ReadCluster etomica.modules.glass
ReadCluster() ReadCluster
ReadCluster.ReadClusterParams etomica.modules.glass
readClusterFile(DataClusterer, String, int) DataClusterReader
readClusterFile(String) DataClusterer
ReadClusterParams() ReadCluster.ReadClusterParams
readData(String[]) MeterVirialBDBin
readData(String[]) MeterVirialBDBinMultiThreaded
readData(String[]) MeterVirialBinMultiThreaded
readData(String[], int) MeterVirialEBinMultiThreaded
readData(String[], int, boolean) MeterVirialEBinMultiThreaded
readDataReBin(String[], int, int) MeterVirialEBinMultiThreaded
readdb(Parser.CommandValue) Interpreter
readDistribution(int, boolean) CalcFFT
ReaderIn etomica.eigenstuff
Reads in a file.
ReaderIn() ReaderIn
readFile(String, double[][]) AkimaSplineSmootherApp
readFile(String, double[][]) AkimaSplineSmootherDyApp
readFile(String, double[][]) AkimaSplineSmootherMain
readLine(PipedInputStream) ViewConsoleOutputBox
readMethod ModifierGeneral
readOutputFile() PotentialEmul
readParameters() ReadParameters
Reads each line from inputFileName and attempts to match it with a field
from parameterWrapper and sets the field to the value from the file.
ReadParameters etomica.util
This class reads input parameters from a file and assigns the values to the
fields of an object.
ReadParameters() ReadParameters
ReadParameters(String) ReadParameters
ReadParameters(String, ParameterBase) ReadParameters
readProcessData(String, int) MeterVirialEBinMultiThreaded
readResolve() DestinationType
readRestart(String, boolean) SimulationVirialOverlap2
readStateFromFile(BufferedReader) IntegratorOverlap
readWeights(String) MeterVirialBDBin
readWeights(String) MeterVirialBDBinMultiThreaded
readWeights(String) MeterVirialBinMultiThreaded
readWeights(String, int) MeterVirialEBinMultiThreaded
readWriteData(String[], String, int) MeterVirialEBinMultiThreaded
This method reads all input files in parallel and writes lines out to
the new file as the bin data is known to be complete.
ready B2Fit.FunctionMayerB2LJQ
ready() MeterStructureFactor.AtomSignalSource
ready() AtomSignalMobility
ready() AtomSignalMotion
ready() AtomSignalStress
real() Complex
Real part of this Complex number, the x-coordinate in rectangular coordinates.
reallocate() CorrelationSelf2
reallocate(int) DataSinkBlockAveragerSFac
reallocate(int) DataSourceAlpha2
reallocate(int) DataSourceBlockAvgCor
reallocate(int) DataSourceCorrelation
reallocate(int) DataSourceFs
reallocate(int) DataSourceMSD
reallocate(int) DataSourceMSDcorP
reallocate(int) DataSourcePercolation
reallocate(int) DataSourcePMSDHistory
reallocate(int) DataSourceQ4
reallocate(int) DataSourceStrings
reallocate(int) DataSourceVAC
reallocate(int) MeterCorrelation
reallocate(int) MeterGs
reallocate(int) StructureFactorComponentCorrelation
realT MeterHarmonicCoordinate
realT MeterHarmonicEnergy
realT MeterHarmonicSingleEnergy
realT MeterNormalMode
reblockData() AccumulatorAverageBootstrap
Reblock data from rawData2 into rawData3, then copy it back to rawData2
reblockData() AccumulatorAverageCollapsingLog
Reblock data from rawData2 into rawData3, then copy it back to rawData2
reblockData(int) AccumulatorAverageBootstrap
Brute-force reblock data from rawData into rawData2,
taking blocks of size n
reblockData(int) AccumulatorAverageCollapsingLog
Reblock data from rawData into rawData2, taking blocks of size n
Receiver(int) DataSourceCorrelation.Receiver
Reciprocal() Function.Reciprocal
reclaim(IAtom) ColorSchemeSmer
recomputeColumnHeaders() DisplayTable
Reconstruct the column headers array.
recomputeCriteriaRanges() PotentialMasterListMolecular
Recomputes the range for all criterion based on our own range.
recomputeMoveFrequencies() MCMoveManager
Recomputes all the move frequencies.
recomputeUnits() DisplayTable
Reconstruct the units array.
recomputeWeights() MeterVirialBDBin
recomputeWeights() MeterVirialBDBinMultiThreaded
recomputeWeights() MeterVirialBinMultiThreaded
recomputeWeights() MeterVirialEBinMultiThreaded
recomputeWeights(Map<IntSet, MeterVirialBDBinMultiThreaded.MyData>, long) MeterVirialBDBinMultiThreaded
recomputeWeights(Map<IntSet, MeterVirialBDBinMultiThreaded.MyData>, long, boolean) MeterVirialBDBinMultiThreaded
This method will read MyData.unscreenedCount and MyData.accumulator
and write to MyData.weight.
recomputeWeights(Map<IntSet, MeterVirialBinMultiThreaded.MyData>, long) MeterVirialBinMultiThreaded
recomputeWeights(Map<IntSet, MeterVirialBinMultiThreaded.MyData>, long, boolean) MeterVirialBinMultiThreaded
This method will read MyData.unscreenedCount and MyData.accumulator
and write to MyData.weight.
recomputeWeights(Map<IntSet, MeterVirialEBinMultiThreaded.MyData>, long, boolean, int) MeterVirialEBinMultiThreaded
This method will read MyData.unscreenedCount and MyData.accumulator
and write to MyData.weight.
recomputeWeights(Map<IntSet, MeterVirialEBinMultiThreaded.MyData>, long, int) MeterVirialEBinMultiThreaded
reconfig DropletGraphic.ModifierBoxSize
reconfig InterfacialSWGraphic.ModifierBoxSize
Rectangle etomica.math.geometry
A 2-dimensional geometric rectangle.
Rectangle(Space) Rectangle
Constructs a square rectangle of unit size.
Rectangle(Space, double, double) Rectangle
Constructs a rectangle with edge lengths having the given values.
RECTANGLE G3DSys
RectangleOptionHandler() Main.RectangleOptionHandler
Rectangular etomica.math.geometry
Interface for a polytope with shape that can be specified by the length
of D sides.
RectangularLattice etomica.lattice
Basic implementation of the AbstractLattice interface, providing construction
and access of sites for a lattice of arbitrary dimension.
RectangularLattice(int, SiteFactory) RectangularLattice
Constructs a lattice of the given dimension (D) with sites
made from the given factory.
RectangularLattice.Iterator etomica.lattice
Iterates over all sites of the lattice.
RectangularLatticeNbrIterator etomica.lattice
An abstract iterator that generates the neighboring sites of a given site.
RectangularLatticeNbrIterator(int) RectangularLatticeNbrIterator
Constructs iterator that needs to be configured before use.
RectangularLatticeNbrIteratorAdjacent etomica.lattice
Iterates over the neighbors of a site, where neighbors are those
sites immediately adjacent to it in each direction; this does not
include sites diagonal to the site.
RectangularLatticeNbrIteratorAdjacent(int) RectangularLatticeNbrIteratorAdjacent
RectangularLatticeNbrIteratorSquare etomica.lattice
Iterates over neighbors of a site, where neighbors are defined as
those sites lying in a rectangular region centered on the site.
RectangularLatticeNbrIteratorSquare(int) RectangularLatticeNbrIteratorSquare
recursiveTag(IAtom) MeterChainLength
recursiveTag(IAtom, int) AtomTestChainLength
recursiveTag(IAtom, int) ColorSchemeRadical
recursiveTag(IAtom, int) AtomTestChainLength
RED Colix
REDBLUE EnumStereoMode
redColorScheme HSNPT2DGraphic
REDCYAN EnumStereoMode
REDGREEN EnumStereoMode
redistributeForces(IMolecule, AtomLeafAgentManager<Vector>) IntegratorVelocityVerletShake.BondConstraints
redomove Token
reduce(long, long) CoefficientImpl
reduce(ArrayList<ClusterDiagram>) ClusterOperations
Sorts cluster diagrams (but # of connections) and combines any diagrams
that are identical, resulting in a diagram with a weight equal to the
sum of the original weights.
reducedTemp CalcFFT
ReeHoover etomica.graph.operations
This operation performs conversion from a set of biconnected graphs with f
edges to a set of diagrams of fully connected diagrams with e and f edges.
ReeHoover() ReeHoover
ReeHoover.ReeHooverParameters etomica.graph.operations
reeHooverCB MyApplet
ReeHooverMC etomica.virial.simulations
An implementation of MSMC with direct sampling for computation of
virial coefficients of hard spheres, in the spirit of Ree-Hoover Monte Carlo
(Ree & Hoover, 1964, Fifth and Sixth Virial Coefficients for Hard Spheres and
Hard Disks).
ReeHooverMC() ReeHooverMC
ReeHooverMC.VirialParam etomica.virial.simulations
Inner class for parameters
ReeHooverParameters(char) ReeHoover.ReeHooverParameters
ReeHooverToggler() MyApplet.ReeHooverToggler
ref DataProcessorReweightRatio
ref VirialPolymerOverlapMC.VirialHSParam
ref VirialPolymerOverlapWithMD.VirialHSParam
ref VirialPolymerOverlapWithMDB3.VirialHSParam
ref VirialHS.VirialHSParam
ref VirialHSBinMultiThreaded.SimulationWorker
ref VirialHSBinMultiThreaded.VirialHSBinParam
ref VirialHSMixture.VirialHSParam
ref VirialHSMixtureOverlap.VirialHSParam
ref VirialPolyhedra.VirialHSParam
ref VirialPolyhedra2.VirialHSParam
ref VirialSWWE.VirialSWWEParam
REF DataOverlap
refAccumulator DataSourceVirialOverlap
refAccumulator DataVirialOverlap
refAvg DataOverlap
refAvg DataVirialOverlap.FullResult
reference FeatureRequirement
referenceDataInterval SimOverlapModule
refErr DataVirialOverlap.FullResult
refFrac Virial7SiteRigidSF6.VirialSF6Param
refFrac VirialAlkaneSKS.VirialSiepmannSpheresParam
refFrac VirialAnthracene464.VirialAnthracene545Param
refFrac VirialAnthracene545.VirialAnthracene545Param
refFrac VirialAnthraceneTraPPE.VirialAnthraceneTraPPEParam
refFrac VirialB2WaterTIP4P_DHS_difference.VirialParam
refFrac VirialB3C1HSDipole.VirialParam
refFrac VirialB3C1TIP4Pwater.VirialParam
refFrac VirialB3C2HSDipole.VirialParam
refFrac VirialB3C2TIP4Pwater.VirialParam
refFrac VirialCH4AlkaneEHMix.VirialMixParam
refFrac VirialCO2.VirialCO2Param
refFrac VirialCO2AlkaneEHMix.VirialMixParam
refFrac VirialCO2AlkaneUAMix.VirialMixParam
refFrac VirialCO2anthracene464.VirialCO2anthracene545Param
refFrac VirialCO2anthracene545.VirialCO2anthracene545Param
refFrac VirialCO2AnthraceneTraPPE.VirialCO2AnthraceneTraPPEParam
refFrac VirialCO2CH4Mix.VirialMixParam
refFrac VirialCO2CH4UAMix.VirialMixParam
refFrac VirialCO2CH4UAMixWheatley.VirialMixParam
refFrac VirialCO2H2OGCPM.VirialParam
refFrac VirialCO2H2OGCPMX.VirialParam
refFrac VirialCO2H2OSC.VirialCO2SCParam
refFrac VirialCO2LJQ.VirialCO2LJQParam
refFrac VirialCO2N2Mix.VirialMixParam
refFrac VirialCO2NaphthaleneLJQ.VirialCO2NaphthaleneLJQParam
refFrac VirialCO2NaphthaleneTraPPE.VirialCO2TraPPEParam
refFrac VirialCO2PI.VirialH2PIParam
refFrac VirialCO2SKSMix.VirialCO2Param
refFrac VirialCO2TraPPE.VirialCO2TraPPEParam
refFrac VirialEmulNonAdditive.VirialParam
refFrac VirialH2O.VirialH2OParam
refFrac VirialH2OGCPMD.VirialParam
refFrac VirialH2PI.VirialH2PIParam
refFrac VirialH2PISimple.VirialH2PISimpleParam
refFrac VirialH2PYCorrection.VirialH2PYCParam
refFrac VirialHeD.VirialParam
refFrac VirialHeNonAdditive.VirialParam
refFrac VirialHeNonAdditiveD.VirialParam
refFrac VirialHeNonAdditiveWheatley.VirialParam
refFrac VirialHePI_PotentialCorrection.VirialHePIParam
refFrac VirialHePI.VirialHePIParam
refFrac VirialHePISysErr.VirialHePIParam
refFrac VirialHePIXCOdd.VirialHePIParam
refFrac VirialHePYCorrection.VirialHePYCParam
refFrac VirialHeSC.VirialHePYCParam
refFrac VirialHSMixtureOverlap.VirialHSParam
refFrac VirialHSOrC.VirialLJrParam
refFrac VirialLJ.VirialLJParam
refFrac VirialLJD.VirialLJParam
refFrac VirialLJDU.VirialLJParam
refFrac VirialLJOrC.VirialLJrParam
refFrac VirialLJOrICPYC.VirialLJrParam
refFrac VirialLJPT.VirialLJParam
refFrac VirialMethaneEH.VirialMethaneParam
refFrac VirialN2.VirialN2Param
refFrac VirialN2AlkaneEHMix.VirialMixParam
refFrac VirialN2AlkaneUAMix.VirialMixParam
refFrac VirialN2AlkaneUARigid.VirialMixParam
refFrac VirialN2CH4Mix.VirialMixParam
refFrac VirialN2CH4UAMix.VirialMixParam
refFrac VirialN2PI.VirialN2Param
refFrac VirialN2TraPPE.VirialN2Param
refFrac VirialNaphthaleneTraPPE.VirialNaphthaleneTraPPEParam
refFrac VirialO2.VirialO2Param
refFrac VirialO2PI.VirialO2Param
refFrac VirialPh464.VirialPh3site464Param
refFrac VirialPh545.VirialPh3site545Param
refFrac VirialPhenanthreneTraPPE.VirialPhenanthreneTraPPEParam
refFrac VirialSF6LJAlkaneUAMix.VirialMixParam
refFrac VirialTraPPE.VirialParam
refFreq VirialAlkane.VirialSiepmannSpheresParam
refFreq VirialAlkaneEHTest.VirialParam
refFreq VirialAlkaneFlex.VirialSiepmannSpheresParam
refFreq VirialAlkaneFull.VirialSiepmannSpheresParam
refFreq VirialSwsPT.VirialSiepmannSpheresParam
reflect() MeterSolidMirror
reflectionVector MCMoveSpinCluster
refPref SimOverlapBetaN2RP
refPref SimOverlapNitrogenModel
refPref MeterSamplingHarmonic
refPref MeterSamplingTarget
refPref MeterWorkBennetHarmonic
refPref MeterWorkBennetTarget
refPref MeterWorkHarmonicBennet
refPref MeterWorkHarmonicTargetandReweighting
refPref MeterWorkHarmonicUmbrella
refPref MeterWorkTargetBennet
refPref MeterWorkTargetHarmonicandReweighting
refPref MeterWorkTargetUmbrella
refPref MeterWorkUmbrellaHarmonic
refPref MeterWorkUmbrellaTarget
refPref SimBennet
refPref SimHarmonicUmbrella
refPref SimOverlap
refPref SimOverlapLJ
refPref SimOverlapLJModule
refPref SimOverlapSoftSphere
refPref SimOverlapSoftSphereHCP
refPref SimOverlapSoftSphereReweighting
refPref SimOverlapSoftSphereSoftness
refPref SimOverlapSoftSphereSuperBox
refPref SimOverlapSSnxy
refPref SimTargetUmbrella
refPref SimUmbrella
refPref SimUmbrellaSoftSphere
refPref SimulationVirialOverlap2
refPrefFileName VirialH2PISimple.VirialH2PISimpleParam
refPrefFileName VirialN2.VirialN2Param
refPrefFileName VirialN2PI.VirialN2Param
refresh() DevicePlotPoints
Instructs the plot to redisplay any plotted functions with the most
recent data.
refresh() G3DSys
For a thorough redraw of the display
refreshAtomAgentMgr() DisplayBoxCanvasG3DSys
refreshAtomAgentMgr() - sets the new atom manager based upon the box.
refreshing Token
refreshSize() DisplayBoxCanvas1D
refreshSize() DisplayBoxCanvas2D
refSum MeterOverlapSwitch
rejectme MCMoveBondLength
rejectNotify() MCMoveBiasUB
rejectNotify() MCMoveBiasUBMolecule
rejectNotify() MCMoveDimer
Method called by IntegratorMC in the event that the most recent trial move is
rejected.
rejectNotify() MCMoveDimerRotate
Method called by IntegratorMC in the event that the most recent trial move is
rejected.
rejectNotify() MCMoveRotateAssociated
rejectNotify() MCMoveSmer
Method called by IntegratorMC in the event that the most recent trial move is
rejected.
rejectNotify() MCMoveSmerRotate
Method called by IntegratorMC in the event that the most recent trial move is
rejected.
rejectNotify() MCMoveVolumeAssociated
rejectNotify() MCMoveVolumeAssociatedMolecule
rejectNotify() MyMCMove
rejectNotify() MCMoveAtomCoupled
Method called by IntegratorMC in the event that the most recent trial move is
rejected.
rejectNotify() MCMoveAtomSwap
Method called by IntegratorMC in the event that the most recent trial move is
rejected.
rejectNotify() MCMove
Method called by IntegratorMC in the event that the most recent trial
move is rejected.
rejectNotify() MCMoveAtom
rejectNotify() MCMoveBoxSize
rejectNotify() MCMoveDimer
Method called by IntegratorMC in the event that the most recent trial move is
rejected.
rejectNotify() MCMoveDimerRotate
Method called by IntegratorMC in the event that the most recent trial move is
rejected.
rejectNotify() MCMoveInsertDelete
rejectNotify() MCMoveInsertDeleteBiased
rejectNotify() MCMoveMolecule
rejectNotify() MCMoveMoleculeExchange
rejectNotify() MCMoveRotate
rejectNotify() MCMoveRotateMolecule3D
rejectNotify() MCMoveSemigrand
rejectNotify() MCMoveSwapConfiguration
Performs no action; nothing required when move rejected.
rejectNotify() MCMoveTorsionAceticAcid
rejectNotify() MCMoveVolume
rejectNotify() MCMoveVolumeExchange
rejectNotify() MCMoveWiggleAceticAcid
rejectNotify() MCMoveAtomNbr
rejectNotify() MCMoveMoleculeCoupledInitPert
rejectNotify() MCMoveMoleculeCoupledSuperBox
rejectNotify() MCMoveRotateMolecule3DConstraint
rejectNotify() MCMoveRotateMolecule3DN2AveCosThetaConstraint
rejectNotify() MCMoveRotateMolecule3DSuperBox
rejectNotify() MCMoveVolumeN2
rejectNotify() MyMCMove
rejectNotify() MCMoveSwap
rejectNotify() MCMoveMultiHarmonic
rejectNotify() MCMoveAtomCoupled
Method called by IntegratorMC in the event that the most recent trial move is
rejected.
rejectNotify() MCMoveAtomCoupledBennet
Method called by IntegratorMC in the event that the most recent trial move is
rejected.
rejectNotify() MCMoveAtomCoupledUmbrella
Method called by IntegratorMC in the event that the most recent trial move is
rejected.
rejectNotify() MCMoveAtomSuperBox
Method called by IntegratorMC in the event that the most recent trial move is
rejected.
rejectNotify() MCMoveEinsteinCrystal
rejectNotify() MCMoveHarmonic
rejectNotify() MCMoveHarmonicStep
rejectNotify() MCMoveMoleculeCoupled
rejectNotify() MCMovePhaseAngle
rejectNotify() MCMoveRotateMoleculePhiTheta
rejectNotify() MCMoveSingleMode
rejectNotify() MCMoveVolumeMonoclinic
rejectNotify() MCMoveVolumeMonoclinicAngle
rejectNotify() MCMoveVolumeMonoclinicScaled
rejectNotify() MCMoveVolumeSolid
rejectNotify() MCMoveVolumeSolidNPTMolecular
rejectNotify() MCMoveVolumeSolidNPTMolecularOriented
rejectNotify() MCMoveWV
rejectNotify() MCMoveGeometricCluster
rejectNotify() MCMoveGeometricClusterRestrictedGE
rejectNotify() MCMoveSpinCluster
rejectNotify() MCMoveSpinFlip
rejectNotify() MCMoveBondLength
rejectNotify() MCMoveClusterBondLength
rejectNotify() MCMoveClusterConformationMDTest
rejectNotify() MCMoveClusterMoleculeHSChain
rejectNotify() MCMoveClusterMoleculeHSChainB3
rejectNotify() MCMoveClusterRotateArm
rejectNotify() MCMoveRotateArm
rejectNotify() MCMoveWiggle
rejectNotify() BoxCluster
Informs the box that the trial was rejected so it will go back to
the old coordinate pairs.
rejectNotify() MCMoveChangeBondLength
rejectNotify() MCMoveClusterAngleBend
rejectNotify() MCMoveClusterAngleBendAceticAcid
rejectNotify() MCMoveClusterAtom
rejectNotify() MCMoveClusterAtomChainHSTail
rejectNotify() MCMoveClusterAtomDiscrete
rejectNotify() MCMoveClusterAtomHSChain
rejectNotify() MCMoveClusterAtomHSRing
rejectNotify() MCMoveClusterAtomHSTree
rejectNotify() MCMoveClusterAtomInBox
rejectNotify() MCMoveClusterAtomMulti
rejectNotify() MCMoveClusterAtomQ
rejectNotify() MCMoveClusterAtomRotateMulti
rejectNotify() MCMoveClusterDiagram
rejectNotify() MCMoveClusterMolecule
rejectNotify() MCMoveClusterMoleculeHSChain
rejectNotify() MCMoveClusterMoleculeMulti
rejectNotify() MCMoveClusterPolyhedraChain
rejectNotify() MCMoveClusterPolyhedraTree
rejectNotify() MCMoveClusterReptateMulti
rejectNotify() MCMoveClusterRingPartialRegrow
rejectNotify() MCMoveClusterRingRegrow
rejectNotify() MCMoveClusterRingRegrowExchange
rejectNotify() MCMoveClusterRingRegrowOrientation
rejectNotify() MCMoveClusterRingScale
rejectNotify() MCMoveClusterRotateCH3
rejectNotify() MCMoveClusterRotateMolecule3D
rejectNotify() MCMoveClusterRotateMoleculeMulti
rejectNotify() MCMoveClusterTorsionAceticAcid
rejectNotify() MCMoveClusterTorsionAlkaneEH
rejectNotify() MCMoveClusterTorsionMulti
rejectNotify() MCMoveClusterWiggleAceticAcid
rejectNotify() MCMoveClusterWiggleAlkaneEH
rejectNotify() MCMoveClusterWiggleMulti
rejectNotify() MCMoveSwapCluster
relabel FFTDecomposition
relabel IsFFT
relabel(Graph) IEGenerator
Relabel etomica.graph.operations
Relabel() Relabel
RelabelParameters etomica.graph.operations
RelabelParameters(byte[]) RelabelParameters
RelabelWertheim etomica.graph.operations
RelabelWertheim() RelabelWertheim
relax() OrientationFull3D
Normalizes both direction and secondaryDirection
relaxAction MCMoveClusterRotateMolecule3D
relaxInterval MCMoveClusterRotateMolecule3D
relaxMolecule(IMolecule) IntegratorVelocityVerletShake.BondConstraints
releaseAgent(E) BoxAgentManager.BoxAgentSource
Disconnects the given agent from its box and performs any actions needed to clean up
releaseAgent(E, AtomType) AtomTypeAgentManager.AgentSource
This informs the agent source that the agent is going away and that the agent source should disconnect the
agent from other elements.
releaseAgent(E, IAtom, Box) AtomLeafAgentManager.AgentSource
This informs the agent source that the agent is going away and that
the agent source should disconnect the agent from other elements.
releaseAgent(E, IMolecule) MoleculeAgentManager.MoleculeAgentSource
This informs the agent source that the agent is going away and that
the agent source should disconnect the agent from other elements
releaseAgent(E, ISpecies) SpeciesAgentManager.AgentSource
This informs the agent source that the agent is going away and that
the agent source should disconnect the agent from other elements.
releaseAgent(ActionMinimizeEnergy.MyForceTorque, IAtom, Box) ActionMinimizeEnergy
releaseAgent(ColorSchemeSmer.ColorAgent, IAtom, Box) ColorSchemeSmer
releaseAgent(MCMoveVolumeAssociated.Agent, IAtom, Box) MCMoveVolumeAssociated
releaseAgent(AtomArrayList, IAtom, Box) AssociationManager
releaseAgent(AtomArrayList, IAtom, Box) P2SquareWellRobust
releaseAgent(AtomLeafAgentManager<E>) BoxAgentSourceAtomManager
releaseAgent(IAtom[], IAtom, Box) ChainEquilibriumSim
releaseAgent(IAtom[], IAtom, Box) FreeRadicalPolymerizationSim
releaseAgent(IAtom, IAtom, Box) ReactionEquilibrium
releaseAgent(IntegratorGear4.Agent, IAtom, Box) IntegratorGear4
releaseAgent(IntegratorHard.Agent, IAtom, Box) IntegratorHard
releaseAgent(IntegratorRigidIterative.AtomForceAgent, IAtom, Box) IntegratorRigidIterative
releaseAgent(IntegratorVerlet.Agent, IAtom, Box) IntegratorVerlet
releaseAgent(InteractionTracker.CatalysisAgent, IAtom, Box) InteractionTracker
releaseAgent(AtomTestChainLength.LengthAgent, IAtom, Box) AtomTestChainLength
releaseAgent(ColorSchemeRadical.LengthAgent, IAtom, Box) ColorSchemeRadical
releaseAgent(MeterChainLength.AtomTag, IAtom, Box) MeterChainLength
releaseAgent(IntegratorDroplet.MyAgent, IAtom, Box) IntegratorDroplet
releaseAgent(AtomTestChainLength.LengthAgent, IAtom, Box) AtomTestChainLength
releaseAgent(MoleculeAgentManager<E>) BoxAgentSourceMoleculeManager
releaseAgent(Cell, IAtom, Box) NeighborCellManager
Removes the given atom from the cell.
releaseAgent(NeighborCellManagerMolecular) BoxAgentSourceCellManagerMolecular
releaseAgent(NeighborCellManager) BoxAgentSourceCellManager
releaseAgent(CriterionPositionWall.DoubleWrapper, IAtom, Box) CriterionPositionWall
releaseAgent(AtomNeighborLists, IAtom, Box) NeighborListManager
releaseAgent(AtomPotentialList, IAtom, Box) NeighborListManager.AtomPotential1ListSource
releaseAgent(NeighborListManagerMolecular) PotentialMasterListMolecular.NeighborListAgentSourceMolecular
releaseAgent(NeighborListManager) NeighborListAgentSource
releaseAgent(AtomSite, IAtom, Box) NeighborSiteManager
releaseAgent(HSNPT.MyAgent, IAtom, Box) HSNPT.ActionSummer
releaseAgent(EwaldSummation.MyCharge, IAtom, Box) MinimizationTIP4P.ChargeAgentSourceRPM
releaseAgent(EwaldSummation.MyCharge, IAtom, Box) ChargeAgentSourceTIP4PWater
releaseAgent(P2HardBondedList.BondArrayList, IAtom, Box) P2HardBondedList
releaseAgent(PotentialArrayByType, AtomType) PotentialMasterMonatomic
releaseAgent(Vector[], IMolecule) CoordinateDefinitionNitrogen.OrientationAgentSource
releaseAgent(Vector, IAtom, Box) IntegratorDimerRT
releaseAgent(Vector, IAtom, Box) IntegratorMD.VectorSource
releaseAgent(Vector, IAtom, Box) IntegratorVelocityVerlet
releaseAgent(Vector, IAtom, Box) MeterMappedRdf
releaseAgent(Vector, IAtom, Box) P1Tether
releaseAgent(Vector, IAtom, Box) CriterionSimple
releaseAgent(Vector, IAtom, Box) CoordinateDefinition.SiteSource
releaseAgent(Vector, IAtom, Box) PotentialCalculationMeanField
releaseAgent(Vector, IMolecule) MeterFlux
releaseAgent(Vector, IMolecule) CoordinateDefinitionMolecule.MoleculeSiteSource
releaseAgent(MeterDipoleMoment.ForceTorque, IAtom, Box) MeterDipoleMoment
releaseAgent(MeterMappedAveragingCorrelation.CorrelationAgent, IAtom, Box) MeterMappedAveragingCorrelation
releaseAgent(MeterMappedAveragingSum.MoleculeAgent, IAtom, Box) MeterMappedAveragingSum
releaseAgent(MeterMeanField.ForceTorque, IAtom, Box) MeterMeanField
releaseAgent(MoleculeAgent, IAtom, Box) MeterMappedAveraging
releaseAgent(MoleculeAgent, IAtom, Box) MeterMappedAveraging3Pair
releaseAgent(MoleculeAgent, IAtom, Box) MeterMappedAveragingFreeEnergy
releaseAgent(MoleculeAgent, IAtom, Box) MeterMappedAveragingPair
releaseAgent(MoleculeAgent, IAtom, Box) MeterMappedAveragingPairExcess
releaseAgent(MoleculeAgent, IAtom, Box) MeterMappedAveragingVSum
releaseAgent(MoleculeAgent, IAtom, Box) MeterMappedAveragingVSum3Pair
releaseAgent(MoleculeAgent, IAtom, Box) MeterMappedAveragingVSumPair
releaseAgent(Ball[], IAtom, Box) DisplayBoxCanvasG3DSys.OrientedAgentSource
releaseAgent(Ball, IAtom, Box) DisplayBoxCanvasG3DSys
releaseAgent(Color, IAtom, Box) ColorSchemeCollectiveAgent
releaseAgent(Color, IAtom, Box) ColorSchemeRandom
releaseAgent(Boolean, IAtom, Box) AtomTestLiquidAtomic
releaseAgent(Object, IMolecule) AssociationManagerMolecule
releaseAgent(Object, IMolecule) MCMoveVolumeAssociatedMolecule
releaseAgent(Object, IMolecule) MeterDipoleSumSquaredMappedAverage
releaseAgent(Object, IMolecule) ColorSchemeRandomByMolecule
releaseAgent(Object, IMolecule) IntegratorRigidIterative
releaseAgent(Object, IMolecule) IntegratorRigidMatrixIterative
releaseAgent(Object, IMolecule) CoordinateDefinitionNitrogenSuperBox.OrientationAgentSource
releaseAgent(Object, IMolecule) CriterionTether3
releaseAgent(Object, IMolecule) NeighborCellManagerMolecular
Removes the given atom from the cell.
releaseAgent(Object, IMolecule) NeighborListManagerMolecular.MoleculePotential1ListSource
releaseAgent(Object, IMolecule) NeighborListManagerMolecular
releaseAgent(Object, IMolecule) CriterionSimpleMolecular
releaseAgent(Object, IMolecule) CoordinateDefinitionMoleculeVolumeFluctuation.MoleculeSiteSource
releaseAgent(Object, IMolecule) IntegratorVelocityVerletQuaternion
releaseAgent(Object, ISpecies) IntegratorRigidIterative
releaseAgent(Object, ISpecies) IntegratorRigidMatrixIterative
releaseAgent(Object, ISpecies) IntegratorVelocityVerletShake
releaseAgent(Object, ISpecies) IntegratorVelocityVerletQuaternion
releaseBond(Object) DisplayBoxCanvasG3DSys
Removes the given bond from the graphical display.
releaseScreenImage() Graphics3D
releaseScreenImage() GData
remove() CartesianIterator
remove() CartesianPermutator
remove() ChainedIterator
remove() DefaultIterator
remove() DefaultPermutator
remove() EdgelessIterator
remove() GlobalFilter
remove() LocalFilter
remove() FixedEdgeCountIterator
remove() IteratorWrapper
remove() RangePermutator
remove() StoredIterator
remove() TreeLinker
Disconnects this linker from the linkers above and below it, and
puts them in sequence, repairing the hole.
remove() PYGenerator.IteratorEF
remove(int) AtomArrayList
This removes the atom at the given index and shifts the remaining atoms
back (maintaining the order).
remove(int) AtomPair
remove(int) AtomSetSinglet
remove(int) MoleculeArrayList
remove(int) MoleculePair
remove(int) MoleculeSetSinglet
remove(int) P2HardBondedList.BondArrayList
remove(int) IndexMap
remove(Device) SimulationGraphic
remove(Display) SimulationGraphic
remove(IFunction) FunctionChain
Removes the given function from the chain.
remove(TreeLinker) TreeList
remove(Object) AtomPair
remove(Object) AtomSetSinglet
remove(Object) GraphList
remove(Object) MoleculePair
remove(Object) MoleculeSetSinglet
remove(Object) IndexMap
removeAction(IAction) ActionGroup
Removes a specified action from the group.
removeAction(IAction) ActionGroupSeries
removeAll(Collection<?>) AtomPair
removeAll(Collection<?>) AtomSetSinglet
removeAll(Collection<?>) GraphList
removeAll(Collection<?>) MoleculePair
removeAll(Collection<?>) MoleculeSetSinglet
removeAllValueChangedListeners() DeviceBox
Removes all objects that are listening for a value changed event.
removeAndReplace(int) AtomArrayList
This removes the atom at the given index and replaces the hole with the
last atom.
removeAndReplace(int) MoleculeArrayList
removeAtom(IAtom) Cell
removeAtoms(double, Vector) SimDimerLJadatom
removeAtoms(double, Vector) SimKMCLJadatom
removeBox(Box) Simulation
Removes a Box to the simulation.
removeChildAtom(IAtom) Molecule
Removes the given child Atom from this AtomGroup.
removeCollisionListener(IntegratorHard.CollisionListener) IntegratorHard
De-registers an object from the list of collision listeners.
removeCountOfSpeciesSLMListener(int) ViewSpeciesSelection
removeData() ModelMoleculeListDisplayTable_new
removeData() ModelMoleculeListDisplayTable
removeData() ModelPotParamDisplayTable
removeDataListener(DataSetListener) DataSet
removeDataSink(IDataSink) DataFork
removeDataSink(IDataSink) DataPipeForked
Removes the specified data sink.
removeDataSink(IDataSink) DataProcessorForked
Removes the specified data sink.
removeDrawable(Drawable) DisplayBox
removeDrawable(Object) DisplayBox
removeFig(Figure) G3DSys
Removes the Figure to from associated FigureManager
removeIntegrator(Integrator) IntegratorManagerMC
Removes the given integrator from the list of integrators.
removeLine(LineSegment) DisplayBoxCanvasG3DSys
removeListener(BoxEventListener) BoxEventManager
removeListener(IntegratorListener) IntegratorEventManager
Removes the given listener from this event manager.
removeListener(IntegratorListener) IntegratorListenerGroupSeries
Removes the given listener from the group.
removeListener(INeighborListListener) NeighborListEventManager
removeListener(INeighborListListenerMolecular) NeighborListEventManagerMolecular
removeListener(SimulationListener) SimulationEventManager
removeListener(BoundaryEventListener) BoundaryEventManager
Removes the given listener from this event manager.
removeListener(IListener<E>) EventManager
Removes the given listener from this event manager.
removeMCMove(MCMove) MCMoveManager
Removes the given MCMove from the set of moves performed by the integrator and
recalculates move frequencies.
removeMolecule(IMolecule) Box
Removes the given molecule from this Box.
removeMolecule(IMolecule) CellMolecular
removeMoleculeListDisplayLSMListener() ViewSpeciesSelection
removeMoleculeListDisplayLSMListener() ViewSpeciesSelection
removeMoleculeListDisplayTMListener() ViewSpeciesSelection
removeMoleculeListDisplayTMListener() ViewSpeciesSelection
removeObject(T[], T) Arrays
Returns an array formed by removing the given object from the given array.
removeObjectByBox(Box) DisplayBoxCanvasG3DSys
removeOption(String) DeviceSelector
removeParser(ParameterParser) ParameterBase
removePlane(Plane) DisplayBoxCanvasG3DSys
removePotential(IPotential) PotentialArray
Removes the given potential and the associated criterion from the list
held by this type instance, and returns the index that was assigned to
it.
removePotential(IPotential) PotentialArrayByType
Removes the given potential and the associated criterion from the list
held by this type instance, and returns the index that was assigned to
it.
removePotential(IPotentialAtomic) PotentialMasterList
removePotential(IPotentialAtomic) PotentialGroupNbr
removePotential(IPotentialAtomic) PotentialMasterHybrid
removePotential(IPotentialAtomic) PotentialMasterNbr
removePotential(IPotentialAtomic) PotentialGroup
Removes given potential from the group.
removePotential(IPotentialAtomic) PotentialMaster
Removes given potential from the group.
removePotential(IPotentialAtomic) PotentialMasterMonatomic
removePotential(IPotentialMolecular) PotentialMasterListMolecular
removePotential(IPotentialMolecular) PotentialMasterNbrMolecular
removePotential(IPotentialMolecular) PotentialArrayMolecular
Removes the given potential and the associated criterion from the list
held by this type instance, and returns the index that was assigned to
it.
removePotential(IPotentialMolecular) PotentialMaster
Removes given potential from the group.
removePotentialJListListener() ViewSpeciesSelection
removePotentialJListListener() ViewSpeciesSelection
removePotParamDisplayLSMListener() ViewSpeciesSelection
removePotParamDisplayLSMListener() ViewSpeciesSelection
removePotParamDisplayTMListener() ViewSpeciesSelection
removePotParamDisplayTMListener() ViewSpeciesSelection
removePropertyChangeListener(PropertyChangeListener) Display
removePropertyChangeListener(PropertyChangeListener) Grabber.ActionCornerSetter
removeSeries(String) DisplayPlotXChart
removeSpecies() ArrayMoleculeDisplayList
removeSpecies(ISpecies) ConfigurationLatticeWithPlane
removeSpeciesAtIndex(int) ArrayMoleculeDisplayList
removeSpeciesJListListener() ViewSpeciesSelection
removeSpeciesJListListener() ViewSpeciesSelection
removeSpeciesMolecule(int) ModelSelectedSpecies
removeSpeciesNotify(ISpecies) Box
Notifies the Box that a Species has been removed.
removeValueChangedListener(DeviceBoxValueChangedListener) DeviceBox
Remove an object that is listening for the DeviceBox value to change
renderAllStrings(Object) Graphics3D
renderAllStrings(Object) GData
renderBackground(Graphics3D) Graphics3D
renderBackground(Graphics3D) GData
renderCrossHairs(int[], int, int, Point3f, float) Graphics3D
renderHermiteRibbon(boolean, boolean, int, Point3i, Point3i, Point3i, Point3i, Point3i, Point3i, Point3i, Point3i, int, int) HermiteRenderer
renderHermiteRope(boolean, int, int, int, int, Point3i, Point3i, Point3i, Point3i) HermiteRenderer
repaint() DisplayBox
Repaint the graphic associated with the display box.
repaint() DisplayCanvas
repaint() DisplayPolytope
repaint() PropertyText
repaint(Object) ApiPlatform
repaint(Object) Platform
REPAINT_INTERVAL MultiharmonicGraphicMC
REPAINT_INTERVAL MultiharmonicGraphicMC
REPAINT_INTERVAL MultiharmonicGraphicMC
REPAINT_INTERVAL MultiharmonicGraphicMC
repaintwaitms Token
replaceAllCharacter(String, String, char) TextFormat
Does a clean replace of any of the characters in str with chrTo
If strTo contains strFrom, then only a single pass is done.
replaceAllCharacters(String, String, String) TextFormat
Does a clean replace of any of the characters in str with strTo
If strTo contains strFrom, then only a single pass is done.
replaceQuotedStrings(String, List<String>, List<String>) TextFormat
replaceQuotedStrings(Vector, Vector, String, int) ScientificFormat
replaceStrings(String, List<String>, List<String>) TextFormat
replicate(Configuration, Box, int[], Space) ConfigurationFileBinary
Reads the configuration from the file and then replicates the
configuration reps times in each direction.
replicate(Configuration, Box, int[], Space) ConfigurationReplicate
Replicates the configuration from config within boxBig.
REPULSION_ATTRACTION PistonCylinderGraphic
REPULSION_ONLY PistonCylinderGraphic
requestFocusInWindow(Object) ApiPlatform
requestFocusInWindow(Object) Platform
Requirement etomica.compatibility
Requirement() Requirement
RequirementSet etomica.compatibility
rescale(Configuration, Box, double, Space) ConfigurationFileBinary
rescaleBox(double) SimFluidSoftSphere
rescaledCoords0 ConfigFromFileLAMMPS.ColorSchemeDeviation
rescalingToFitVolume ConfigurationLattice
reservoir MCMoveInsertDelete
reset() ANIntergroupCoupled
reset() ANIntergroupExchange
reset() ANIntragroupExchange
reset() ApiIndexList
Resets iterator to a state where hasNext is true, if atoms in pair are
not null.
reset() ApiInnerVariable
Resets the iterator, so that it is ready to go through all of its pairs.
reset() ApiInterArrayList
Sets iterator in condition to begin iteration.
reset() ApiIntergroup
reset() ApiIntergroupCoupled
reset() ApiIntergroupExchange
reset() ApiIntraArrayList
Sets iterator in condition to begin iteration.
reset() ApiIntragroup
Puts iterator in a state to begin iteration.
reset() AtomIteratorArrayList
Puts iterator in state ready to begin iteration.
reset() AtomIteratorArrayListAdjacent
Readies the iterator to begin iteration.
reset() AtomIteratorArrayListSimple
Puts iterator in state ready to begin iteration.
reset() AtomIteratorBasis
Puts iterator in a state ready to begin iteration.
reset() AtomIteratorBasisAdjustableStart
Puts iterator in a state ready to begin iteration.
reset() AtomIteratorNull
reset() AtomIteratorSinglet
Resets iterator to a state where hasNext is true.
reset() Atomset3IteratorIndexList
Resets iterator to a state where hasNext is true, if atoms in pair are
not null.
reset() Atomset4IteratorIndexList
Resets iterator to a state where hasNext is true, if atoms in pair are
not null.
reset() AtomsetIterator
Resets the iterator to loop through its iterates again.
reset() AtomsetIteratorAllLeafAtoms
reset() DataProcessorCavity
reset() MeterCavityMapped
Resets the data collected.
reset() MeterContactRatio
reset() MeterPairedFraction
reset() MeterPressureCollisionCount
reset() MeterRDFMapped
Resets the data collected.
reset() ConformationChain
Resets the vector instructions.
reset() ConformationChain2D
reset() ConformationChain3D
reset() ConformationChainZigZag
reset() ConformationChainZigZag2
reset() AccumulatorAverage
Resets all sums to zero.
reset() AccumulatorAverageBlockless
Resets all sums to zero.
reset() AccumulatorAverageBlocklessSlim
Resets all sums to zero.
reset() AccumulatorAverageBootstrap
Resets all sums to zero.
reset() AccumulatorAverageCollapsing
Resets all sums to zero.
reset() AccumulatorAverageCollapsingLog
Resets all sums to zero.
reset() AccumulatorAverageCollapsingLogAB
Resets all sums to zero.
reset() AccumulatorAverageCovariance
reset() AccumulatorAverageFixed
reset() AccumulatorAverageFixedOutputFile
Resets all sums to zero.
reset() AccumulatorCounter
Sets count to zero.
reset() AccumulatorHistogram
Zeros histograms, discarding any previous contributions.
reset() AccumulatorHistory
reset() AccumulatorRatioAverageCovariance
reset() AccumulatorRatioAverageCovarianceFull
reset() DataAccumulator
Clear accumulated values.
reset() DataArrayWriter
reset() DataLogger.DataWriter
Informs the DataSink that it will be writing the beginning of the
file so printing header information is appropriate.
reset() DataPumpListenerPow
reset() DataPumpListenerPowStrict
reset() DataSet
reset() DataTableWriter
reset() Histogram
resets all histogram values and counts to zero
reset() HistogramCollapsing
reset() HistogramDiscrete
reset() HistogramExpanding
reset() HistogramNotSoSimple
reset() HistogramReweightedData
reset() HistogramSimple
reset() History
Resets the History.
reset() HistoryCollapsing
Removes entire history, setting all values to NaN.
reset() HistoryCollapsingAverage
reset() HistoryComplete
Removes entire history, setting all values to NaN.
reset() HistoryScrolling
Removes entire history, setting all values to NaN.
reset() MeterDihedralAngle
Zero's out the G(phi) sum tracked by this meter.
reset() MeterMeanSquareDisplacement
Specifies the set of atoms that will be tracked to compute their MSD.
reset() MeterPressureByVolumeChange.DataSourceExp
reset() MeterPressureHard
reset() MeterProfile
reset() MeterProfileByAtoms
reset() MeterProfileByVolume
reset() MeterRDF
Zero's out the RDF sum tracked by this meter.
reset() MeterRDFPC
Zero's out the RDF sum tracked by this meter.
reset() PotentialCalculationRDF
Zero's out the RDF sum tracked by this meter.
reset() IntegratorDCVGCMD
reset() IntegratorDimerMin
reset() IntegratorDimerRT
reset() PotentialCalculationForcePressureSumGB
Zeros out the pressureTensor.
reset() P2EAM
reset() PotentialCalculationDUDW
reset() DeviceRunControls
reset() DeviceTrioControllerButton
Sets controller toggle button to read "Start"
reset() Integrator
Defines the actions taken by the integrator to reset itself, such as
required if a perturbation is applied to the simulated box (e.g.,
addition or deletion of a molecule).
reset() IntegratorBox
Performs superclass reset actions and recalculated currentPotentialEnergy
reset() IntegratorGear4
reset() IntegratorHard.CollisionHandlerUp
resets the "atom" held by this class, ensuring the method will
work even if (coincidentally) the atom is the same as the same
one as the last time the method was called.
reset() IntegratorHard
reset() IntegratorManagerMC
Causes recalculation of move frequencies and zero of selection counts for
moves.
reset() IntegratorMC
Causes recalculation of move frequencies and zero of selection counts for
moves.
reset() IntegratorMD
reset() IntegratorRigidIterative
reset() IntegratorRigidMatrixIterative
reset() IntegratorVelocityVerlet
reset() IntegratorVelocityVerletRattle
reset() IntegratorVelocityVerletShake
reset() IntegratorVerlet
reset() MCMoveInsertDeleteLatticeVacancy.AtomIteratorBruteForce
reset() MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbr
reset() MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbrCell
reset() MCMoveInsertDeleteLatticeVacancy
reset() MCMoveInsertDeleteVacancy
reset() MCMoveOverlapListener
reset() MCMoveTracker
reset() MeterWallForce.PotentialCalculationWallForce
Re-zeros the force vector.
reset() CellLattice.NeighborIterator
reset() IndexIterator
reset() IndexIteratorIncreasing
Resets the iterator.
reset() IndexIteratorRectangular
Puts iterator in a condition to begin iteration.
reset() IndexIteratorReflecting
reset() IndexIteratorTriangular
Sets iterator to begin returning iterates.
reset() IndexIteratorTriangularPermutations
reset() RectangularLattice.Iterator
reset() RectangularLatticeNbrIterator
Resets the iterator to loop through its iterates again.
reset() SiteIterator
Puts the iterator in a state ready to begin iteration.
reset() MeterMappedRdf
Zero's out the RDF sum tracked by this meter.
reset() PotentialCalculationMappedRdf
Zero's out the RDF sum tracked by this meter.
reset() PotentialCalculationMappedEnergy
reset() PotentialCalculationMappedVirial
reset() PotentialCalculationMappedVirialV
reset() CombinationIterator
reset() FixedSumIterator
Sets the iterator to begin iteration.
reset() PermutationDegenerateIterator
Readies the iterator for iteration.
reset() PermutationIterator
reset() MeterDensityDistribution
reset() MeterNormalizedCoord
Sets the tensor summation to 0.
reset() MeterNormalizedCoordBeta
Sets the tensor summation to 0.
reset() MeterOrientationDistribution
Sets the tensor summation to 0.
reset() MeterRotationDistributionGroup
Sets the tensor summation to 0.
reset() EOSSW
reset() EOSSWPatel
reset() IntegratorHybrid
reset() MeterProfileByVolumeAdsorption
reset() ModifierPMu
reset() VEOS3SW
reset() InteractionTracker
reset() MeterChainLength
reset() IntegratorDCVGCMD
reset() IntegratorDroplet
reset() AccumulatorAutocorrelationPTensor
reset() AccumulatorAutocorrelationShearStress
reset() AccumulatorPTensor
reset() ConfigurationStorage
reset() DataClusterer
reset() DataClusterWriter
reset() DataSourceCorrelation
reset() DataSourceF
reset() DataSourceFOld
reset() DataSourceFs
reset() DataSourceMSD
reset() DataSourcePercolation0
reset() DataSourceVAC
reset() MeterCorrelationSelf
reset() PotentialCalculationForceSumGlass
reset() StructureFactorComponentCorrelation
reset() InsertionGraphic.MeterWidom
reset() PotentialCalculationForceStress
reset() MeterMBAR
reset() AccumulatorOverlapAverageUa2
Resets all sums to zero
reset() MultiharmonicGraphicMC.DataSinkReweightedDeltaU
reset() IntegratorHardPiston
reset() MeterRDFCylinder
reset() PotentialCalculationForceSumWallForce
Re-zeros the force vectors.
reset() PotentialCalculationTorqueSumWallForce
Re-zeros the force vectors.
reset() PotentialCalculationForceSumWall
reset() B2Fit.FunctionMayerB2LJQ
reset() MoleculeIteratorAll
reset() MoleculeIteratorArrayList
Puts iterator in state ready to begin iteration.
reset() MoleculeIteratorArrayListSimple
Puts iterator in state ready to begin iteration.
reset() MoleculeIteratorMolecule
reset() MoleculeIteratorSinglet
Resets iterator to a state where hasNext is true.
reset() MpiInnerFixed
Resets the iterator, so that it is ready to go through all of its pairs.
reset() MpiInnerVariable
Resets the iterator, so that it is ready to go through all of its pairs.
reset() MpiInterArrayList
Sets iterator in condition to begin iteration.
reset() MpiInterspecies1A
reset() MpiInterspeciesAA
Sets iterator in condition to begin iteration.
reset() MpiIntraArrayList
Sets iterator in condition to begin iteration.
reset() MpiIntraspecies1A
reset() MpiIntraspeciesAA
Sets iterator in condition to begin iteration.
reset() MpiMolecule
Readies iterator for iteration.
reset() Api1ACell
reset() Mpi1ACell
reset() MpiAACell
reset() PotentialMasterCell
Reassign atoms to cell lists for all boxes.
reset() NeighborListManagerMolecular
For each box in the array, applies central image,
resets neighbors of all atoms, and sets up all neighbor
lists.
reset() PotentialMasterListMolecular
Recomputes the maximum potential range (which might change without this
class receiving notification) and readjust cell lists
reset() NeighborListManager
For each box in the array, applies central image,
resets neighbors of all atoms, and sets up all neighbor
lists.
reset() PotentialMasterList
Recomputes the maximum potential range (which might change without this
class receiving notification) and readjust cell lists
reset() Api1ASite
reset() HSNPT.ActionSummer
reset() IntegratorHardMDMC
reset() MeterNormalMode
Sets the tensor summation to 0.
reset() MeterTiltHistogram
reset() MeterTiltRotationHistogram
reset() PotentialCalculationEFSSP
Sets the virial sum to zero, typically to begin a new virial-sum calculation.
reset() PotentialCalculationLJSP
Sets the virial sum to zero, typically to begin a new virial-sum calculation.
reset() IntegratorOverlap
reset() PotentialCalculationForcePressureSum
Zeros out the pressureTensor.
reset() PotentialCalculationForceSum
Re-zeros the force vectors.
reset() PotentialCalculationTorqueSum
Re-zeros the force vectors.
reset() PotentialMaster.AtomIterator0
reset() PotentialMaster.MoleculeIterator0
reset() IntegratorVelocityVerletQuaternion
reset() RotationTensor
Sets tensor to a condition of no rotation.
reset() RotationTensor1D
reset() RotationTensor2D
reset() RotationTensor3D
reset() MeterEnergyMeanField.PotentialCalculationCSsum
reset() PotentialCalculationMeanField
reset() PotentialCalculationPhiSum
reset() PotentialCalculationVSum
reset() MeterBondLength
Zero's out the RDF sum tracked by this meter.
reset() TreeList
clear the tree by disconnecting everything from the head.
reset() ClusterDiagram
Resets the cluster to being fully connected except that root points
are not connected to each other.
reset() ClusterGenerator
Resets the cluster generator.
reset() PermutationIterator
reset() ModelAlkaneLengthSelection
reset() ModelSelectedSpecies
Reset to initial value.
reset() ModelSimulationEnvironment
reset() ModelSpeciesSelection
reset() ModelTemperatureAndSteps
reset() ViewSpeciesSelection
reset() ViewSpeciesSelection
reset() AccumulatorVirialOverlapSingleAverage
Resets all sums to zero
reset() DataSourceVirialOverlap
Convenience method that resets reference and target accumulators
reset() DataVirialOverlap
Convenience method that resets reference and target accumulators
reset() IntegratorOverlap
Deprecated.
reset() IndexIterator
Resets iteration; should be called before use
reset() BoxInfo
reset(long) CoordinatePairLeafSet
reset(long) CoordinatePairMoleculeSet
reset(long) CoordinatePairSet
Informs the CoordinatePairSet that the configuration has changed and that it
has a new ID
reset(IAtom) ColloidSim.CriterionNone
reset(IAtom) CriterionTether3
reset(IAtom) CriterionAdapter
Indicates to wrapped criterion that given atom's neighbor list has just
been updated, and that properties (e.g., record of atom's position) used
by needUpdate and unsafe() methods should be reset.
reset(IAtom) CriterionAll
Performs no action.
reset(IAtom) CriterionNone
Performs no action.
reset(IAtom) CriterionPositionWall
reset(IAtom) CriterionSimple
reset(IAtom) NeighborCriterion
Indicates to criterion that given atom's neighbor list has just been
updated, and that properties (e.g., record of atom's position)
used by needUpdate and unsafe() methods should be reset.
reset(IMolecule) CriterionAdapterMolecular
Indicates to wrapped criterion that given atom's neighbor list has just
been updated, and that properties (e.g., record of atom's position) used
by needUpdate and unsafe() methods should be reset.
reset(IMolecule) CriterionAllMolecular
Performs no action.
reset(IMolecule) CriterionSimpleMolecular
reset(IMolecule) NeighborCriterionMolecular
Indicates to criterion that given molecule's neighbor list has just been
updated, and that properties (e.g., record of molecule's position)
used by needUpdate and unsafe() methods should be reset.
RESET StatusAction.Status
resetAcceptance() IntegratorMDHarmonicMC
ResetAccumulators etomica.action
ResetAccumulators() ResetAccumulators
ResetAccumulatorsAveraged etomica.action
ResetAccumulatorsAveraged() ResetAccumulatorsAveraged
resetAction DeviceNSelector
resetAction ReactionEquilibriumGraphic
resetAction NormalModeAnalysisDisplay3DGraphic
resetAdjustStep() MCMoveStepTracker
Resets damped step adjustment.
resetAfterData MeterCavityMapped
resetAfterData MeterRDFMapped
resetAfterData MeterRDF
resetAxes() EtomicaPlot
Overrides a not-so-useful method in superclass
resetBonds() ChainEquilibriumSim
resetBonds() FreeRadicalPolymerizationSim
resetCollision() IntegratorHard.Agent
resets collision potential and partner.
resetCollisionFull() IntegratorHard.Agent
resets time, potential and partner.
resetData() MeterStructureFactor
resetHybridAcceptance() IntegratorMD
Zeros counters used to track acceptance fraction of HYBRID_MC thermostat.
resetNewMoleculePair() FindPairMoleculeIndex
resetNewMoleculePair() FindPairMoleculeIndexBetaN2
resetPiston() IntegratorHardPiston
resetRotation() GrainBoundaryTiltConfiguration
resetSelectionViewANew() ControllerSpeciesSelection
resetSlab() MeshSurface
resetStep0() DataSourceBlockAvgCor
resetStep0() DataSourceHisogram
resetStep0() DataSourceHistogramMSD
resetStep0() DataSourceMSDcorP
resetStep0() DataSourcePMSDHistory
resetStepCount() Integrator
This method resets the step counter.
resetStepCount() IntegratorHard
resetStepCount() IntegratorMD
resetStepCount() IntegratorHybrid
resetTest() AtomTestCollective
Informs the AtomTest that something in the system has changed (atom
positions, velocityies, etc) has changed and the status of the
atoms should be determined.
resetTest() AtomTestChainLength
resetTest() AtomTestLiquid
resetTest() AtomTestLiquidAtomic
resetTest() AtomTestChainLength
resetViewAfterSSSPException() ControllerSpeciesSelection
resetViewToDisplaySpecies1() ControllerSpeciesSelection
resetZoom() DisplayPlotXChart
resevoirMolecule MyMCMove
reshape(int, int) DisplayCanvas
Same as setSize, but included to implement DisplayCanvasInterface,
which has this for compatibility with OpenGL.
residual MeterWidomInsertionCorrection
residue Token
resizeData(int) AccumulatorAverageBootstrap
resizeData(int) AccumulatorAverageCollapsingLog
resizeData(int) AccumulatorAverageCollapsingLogAB
resizeDimer() IntegratorDimerRT
resizeGraphic() DevicePlotPoints
Returns the top level panel that the plot scale resizing components sit on.
resno Token
Resources etomica.util
RESOURCES Messages
The error messages bundle class name.
restart() ActivityIntegrate
restart() Activity
restartAction ReactionEquilibrium
restartCurrentActivity() Controller
restartFilename VirialLJDU.VirialLJParam
resume Token
retainAll(Collection<?>) AtomPair
retainAll(Collection<?>) AtomSetSinglet
retainAll(Collection<?>) GraphList
retainAll(Collection<?>) MoleculePair
retainAll(Collection<?>) MoleculeSetSinglet
returnMu DataSourcePMu
ReturnValue(int, Space) Potential2SoftSphericalLSMultiLat.ReturnValue
reverse Token
reverse(double[], double) SineTransform
ReverseOsmosis etomica.modules.rosmosis
Reverse osmosis simulation, based on simulation code by Sohail Murad.
ReverseOsmosis() ReverseOsmosis
ReverseOsmosisGraphic etomica.modules.rosmosis
Graphical and data collection bits for reverse osmosis simulation.
ReverseOsmosisGraphic(ReverseOsmosis, Space) ReverseOsmosisGraphic
ReverseOsmosisGraphic.Applet etomica.modules.rosmosis
ReverseOsmosisGraphic.DataSinkExcludeOverlap etomica.modules.rosmosis
ReverseOsmosisGraphic.ModifierAtomDiameter etomica.modules.rosmosis
ReverseOsmosisGraphic.ModifierEpsilon etomica.modules.rosmosis
ReverseOsmosisWater etomica.modules.rosmosis
Reverse osmosis simulation, based on simulation code by Sohail Murad.
ReverseOsmosisWater() ReverseOsmosisWater
ReverseOsmosisWaterGraphic etomica.modules.rosmosis
Graphical and data collection bits for reverse osmosis simulation.
ReverseOsmosisWaterGraphic(ReverseOsmosisWater) ReverseOsmosisWaterGraphic
ReverseOsmosisWaterGraphic.Applet etomica.modules.rosmosis
ReverseOsmosisWaterGraphic.DataSinkExcludeOverlap etomica.modules.rosmosis
ReverseOsmosisWaterGraphic.ModifierAtomDiameter etomica.modules.rosmosis
ReverseOsmosisWaterGraphic.ModifierEpsilon etomica.modules.rosmosis
ReverseOsmosisWaterGraphic.ModifierSoluteCharge etomica.modules.rosmosis
revertDiagram() ClusterSumStickyEF
set the diagram used for calculating the value to the ith diagram.
revertF() ClusterSumPolarizableWertheimProduct
revertF() ClusterSumPolarizableWertheimProduct4Pt
revertF() ClusterSumPolarizableWertheimProduct4PtFinal
revertF() ClusterTree
rewind Token
rFill(StringXBuilder, String, String) TextFormat
rfit P2O2Bartolomei
rfit0 P2O2Bartolomei
rfitMRCI P2O2Bartolomei
rfitPT2 P2O2Bartolomei
rgb(int, int, int) ColorUtil
Rgb16 org.jmol.util
Rgb16() Rgb16
rGraftMin2 P2SquareWellMonomer
RheologyGraphic etomica.modules.rheology
Module for "Macromolecular dynamics related to rheological properties
through Brownian dynamics simulations", designed by Lewis Wedgewood.
RheologyGraphic(SimulationRheology) RheologyGraphic
RheologyGraphic.Applet etomica.modules.rheology
rho P2EAM
rho VirialOptimizer
rho HarmonicCrystalSsFccNxy.Params
rho HSDimerNPT.HSMD3DParameters
rho HSNPT.HSMD3DParameters
rho SimOverlapSoftSphereDP.SimOverlapParam
rho MayerIonicDiagram1qbond
rho MayerIonicDiagram2qbonds
rho MayerIonicDiagram4qbonds
rho VirialDiagrams
rho VirialDiagramsPT
rho WertheimDiagrams2SiteRho
rho WertheimDiagrams3SiteRho
rho0 HardSphereSolid
rho0 WertheimDiagrams2SiteRho
rho0 WertheimDiagrams3SiteRho
rho0point SingleAssociationSiteFluid.VirialAssociatingFluidParam
rho0point SingleAssociationSiteFluid2.VirialAssociatingFluidParam
rho0point SingleAssociationSiteFluid2Pt.VirialAssociatingFluidParam
rho0point SingleAssociationSiteFluid3Pt.VirialAssociatingFluidParam
rho0point SingleAssociationSiteFluid4Points.VirialAssociatingFluidParam
rho0point SingleAssociationSiteFluid4Pt.VirialAssociatingFluidParam
rho0point VirialAssociatingFluid.VirialAssociatingFluidParam
rho0point VirialAssociatingFluid4points.VirialAssociatingFluidParam
rho1 WertheimDiagrams3SiteRho
rhoA DecorateWertheim2SiteRho.DecorateWertheimParameters2Site
rhoA DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
rhoA DecorateWertheimNaphthalene2Rho.DecorateNaphthalene2Site
rhoA VirialDiagramsMix
rhoA VirialDiagramsMix2
rhoA WertheimDiagrams2SiteRho
rhoA WertheimDiagrams3SiteRho
rhoAB DecorateWertheim2SiteRho.DecorateWertheimParameters2Site
rhoAB DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
rhoAB DecorateWertheimNaphthalene2Rho.DecorateNaphthalene2Site
rhoAB WertheimDiagrams2SiteRho
rhoAB WertheimDiagrams3SiteRho
rhoAB0 WertheimDiagrams2SiteRho
rhoABC DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
rhoABC WertheimDiagrams3SiteRho
rhoAC DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
rhoAC WertheimDiagrams3SiteRho
rhoAlphaTrans FindTransitionTemperature
rhoB DecorateWertheim2SiteRho.DecorateWertheimParameters2Site
rhoB DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
rhoB DecorateWertheimNaphthalene2Rho.DecorateNaphthalene2Site
rhoB VirialDiagramsMix
rhoB VirialDiagramsMix2
rhoB WertheimDiagrams2SiteRho
rhoB WertheimDiagrams3SiteRho
rhoBC DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
rhoBC WertheimDiagrams3SiteRho
rhoBetaTrans FindTransitionTemperature
rhoc EOSSW
rhoC DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
rhoC WertheimDiagrams3SiteRho
rhoForPressure(double) EOSSW
rhoForPressure(double) EOSSWPatel
rhoForPressure(double) VEOS3SW
rhograd P2EAM
rhograd PotentialCuLREP
rhograd PotentialEAM_LS
rhograd PotentialEAM
rhograd PotentialEFS
rhopoint SingleAssociationSiteFluid.VirialAssociatingFluidParam
rhopoint SingleAssociationSiteFluid2.VirialAssociatingFluidParam
rhopoint SingleAssociationSiteFluid2Pt.VirialAssociatingFluidParam
rhopoint SingleAssociationSiteFluid3Pt.VirialAssociatingFluidParam
rhopoint SingleAssociationSiteFluid4Points.VirialAssociatingFluidParam
rhopoint SingleAssociationSiteFluid4Pt.VirialAssociatingFluidParam
rhopoint VirialAssociatingFluid.VirialAssociatingFluidParam
rhopoint VirialAssociatingFluid4points.VirialAssociatingFluidParam
rHSCore P2WaterPotentialsJankowski
ri P2CO2Hellmann
ri P2WaterSzalewicz.P2H2OSC
ri P3Induction
ribbon Token
ribbonaspectratio Token
ribbonborder Token
right Token
RIGHT DisplayBox
RIGHT DisplayPolytope
rightAngle Primitive
rightDifference(Quaternion) Quaternion
RIGID VirialHePI.FlexApproach
RIGID VirialHePISysErr.FlexApproach
rij PNCO2GCPM.P3GCPMAxilrodTeller
rij PNGCPM.P3GCPMAxilrodTeller
rij PotentialCalculationEFSSP
rij PotentialCalculationLJSP
rij P3Induction
Rij PotentialCalculationEFSSP
Rij PotentialCalculationLJSP
rijVector PNCO2GCPM
rijVector PNGCPM
rijVector PNWaterGCPM
rijVector PNWaterGCPMReactionField
rik PNCO2GCPM.P3GCPMAxilrodTeller
rik PNGCPM.P3GCPMAxilrodTeller
rik P3Induction
rIndices PermutationIterator
ring(int) Standard
Returns a ring of bonds, {{0,1},{1,2},...{n-2,n-1},{n-1,0}}
Ring etomica.virial.cluster
Ring(int) Ring
Constructor for Ring.
RING_CHAIN_TREES VirialHS.VirialHSParam
RING_CHAIN_TREES VirialHSMixture.VirialHSParam
RING_CHAIN_TREES VirialPolyhedra.VirialHSParam
RING_CHAIN_TREES VirialSWWE.VirialSWWEParam
RING_TREE VirialHS.VirialHSParam
RING_TREE VirialHSMixture.VirialHSParam
RING_TREE VirialPolyhedra.VirialHSParam
RING_TREE VirialSWWE.VirialSWWEParam
ring0 ModifierTPI
ring1 ModifierTPI
ringFrac ClusterChainHS
ringFrac VirialHS.VirialHSParam
ringFrac VirialHSBinMultiThreaded.SimulationWorker
ringFrac VirialHSBinMultiThreaded.VirialHSBinParam
ringFrac VirialPolyhedra.VirialHSParam
ringFrac VirialSQWBinMultiThreaded.SimulationWorker
ringFrac VirialSQWBinMultiThreaded.VirialHSBinParam
ringFrac VirialSWWE.VirialSWWEParam
ringHS(int) Standard
Return integral for ring of hard spheres of size nPoints
ringResult P2SquareWellBonded
RingResult() P2SquareWellBonded.RingResult
rings VirialHePIXCOdd.VirialHePIParam
RINGS VirialHS.VirialHSParam
RINGS VirialHSMixture.VirialHSParam
RINGS VirialPolyhedra.VirialHSParam
RINGS VirialSWWE.VirialSWWEParam
rj P2CO2Hellmann
rj P2WaterSzalewicz.P2H2OSC
rj P2SemiclassicalMolecular.MoleculeInfoBrute
rj P3Induction
rjk PNCO2GCPM.P3GCPMAxilrodTeller
rjk PNGCPM.P3GCPMAxilrodTeller
rjrj P2SemiclassicalMolecular.MoleculeInfoBrute
rk P3Induction
rkl P2NitrogenAnisotropic
rLast MeterMeanSquareDisplacement
rm ElementChemical
rm ElementSimple
rm() AtomType
rm() Element
rm() ElementChemical
rm() ElementSimple
rm() IElement
rmax BnPCJSDHe.BnPCJSDHeParams
rmax BnPYCHe.BnPYHeParams
rMax MeterDihedralAngle
rMax DisplayBoxCanvasG3DSys
rMaxRDF PolydisperseHS.HSPolyParam
rMaxSafe CriterionPositionWall
rMin DisplayBoxCanvasG3DSys
rMin P2HydrogenHindePatkowskiAtomic
rMin P2HydrogenPatkowski
rMin P2HydrogenPatkowskiAtomic
rMin P2O2Bartolomei
rMrLast IntegratorVerlet.Agent
rmsdFile SimFe.LjMC3DParams
rna Token
rNbr ConfigFromFileLAMMPS.ColorSchemeDeviation
rocket Token
rocketbarrels Token
rOM ConformationWaterTIP4P
root(int) Ifactor
Pulling the r-th root.
root(int, BigDecimal) BigDecimalMath
The integer root.
root(BigInteger) Rational
r-th root.
rootD(double) Space
rootD(double) Space1D
rootD(double) Space2D
Returns the square root of the given value, a^(1/D), which is a^(1/2).
rootD(double) Space3D
Returns the cube root of the given value, a^(1/D) which is a^(1/3).
rootDeg(BigInteger) BigIntegerPoly
Compute the order of the root r.
rootPointsSpecial MetadataImpl
rot P2WaterSzalewicz.P2H2OSC
rot0 P2CO2H2OWheatley
rot0 P2CO2Hellmann.P2CO2SC
rot0 P2NitrogenHellmann.P2N2QFH
rot1 P2CO2H2OWheatley
rot1 P2CO2Hellmann.P2CO2SC
rot1 P2NitrogenHellmann.P2N2QFH
rotate IntegratorDimerMin
rotate IntegratorDimerRT
rotate SimOverlapAlphaN2TP
rotate SimOverlapBetaN2TP
rotate SimOverlapDisorderedAlphaN2TP
rotate Token
rotate(Matrix4f) Quadric
rotateBy(double) IOrientation2D
Rotate the orientation by the amount dt (radians) in the
counter-clockwise direction.
rotateBy(double) Orientation2D
Rotates orientation around the given axis by the given value.
rotateBy(double, double, Vector, Vector) P2NitrogenHellmann
rotateBy(double, Vector) IOrientation3D
Rotate the orientation by the amount dt (radians) about the given axis.
rotateBy(double, Vector) Orientation3D
Rotates orientation by the given value about the given axis.
rotateBy(double, Vector) OrientationFull3D
Rotates orientation by the given value about the given axis.
rotateByX(float) G3DSys
Rotate the display around the x axis
rotateByXY(float, float) G3DSys
Rotate the display around the x and y axes
rotateByY(float) G3DSys
Rotate the display around the y axis
rotateByZ(float) G3DSys
Rotate the display around the z axis
rotateDimerNewton() IntegratorDimerMin
Rotates the dimer in potential energy hyperspace and aligns it with the surface's lowest
curvature mode.
rotateDimerNewton() IntegratorDimerRT
Rotates the dimer in potential energy hyperspace and aligns it with the surface's lowest
curvature mode.
rotateMolecule CH4NVT
rotateMolecule DHS_NVT
rotateMolecule DLJ_NVT_1site
rotateMolecule DHS_NVT
rotateMolecule DLJ_NVT_1site
rotateMolecule TIP4P_NVT
rotateOrientation(OrientationFull3D) Quaternion
Rotates the input orientation by using the Quaternion rotation operator L(v) = qvq*.
rotatePhi MCMoveRotateMoleculePhiTheta
rotateTensor MCMoveClusterRotateCH3
rotateTensor MCMoveClusterWiggleAlkaneEH
rotateToHome() G3DSys
Remove all rotation (and translation) and return to the home position
rotateToX(float) TransformManager
rotateToY(float) TransformManager
rotateToZ(float) TransformManager
rotateVector(Vector) Quaternion
Rotates the input vector by using the Quaternion rotation operator L(v) = qvq*.
rotation MCMoveRotateMolecule3DConstraint
rotation MCMoveRotateMolecule3DFixedAngle
rotation TestRotationVector
rotation Token
rotationAxis FindBetaN2AngleFromParameter
rotationAxis MCMoveRotateMolecule3DConstraint
rotationAxis MCMoveRotateMolecule3DFixedAngle
rotationAxis TestRotationVector
rotationAxis MCMoveClusterRotateMoleculeMulti
rotationradius Token
rotationTensor BiasVolume2SiteAceticAcid
rotationTensor BiasVolumeAceticAcid
rotationTensor MCMoveBiasUBMolecule
rotationTensor MCMoveDimerRotate
rotationTensor MCMoveSmerRotate
rotationTensor MeterKineticEnergyRigid
rotationTensor IntegratorRigidIterative
rotationTensor IntegratorRigidMatrixIterative
rotationTensor MCMoveDimerRotate
rotationTensor MCMoveRotateMolecule3D
rotationTensor CoordinateDefinitionNitrogen
rotationTensor CoordinateDefinitionNitrogenSuperBox
rotationTensor MCMoveRotateMolecule3DConstraint
rotationTensor MCMoveRotateMolecule3DFixedAngle
rotationTensor MCMoveRotateMolecule3DN2AveCosThetaConstraint
rotationTensor MCMoveRotateMolecule3DSuperBox
rotationTensor OrientationCalcWater3P
rotationTensor OrientationCalcWater4P
rotationTensor MCMoveVolumeSolidNPTMolecularOriented
rotationTensor IntegratorVelocityVerletQuaternion
rotationTensor OrientationFull3D
rotationTensor MCMoveClusterConformationMDTest
rotationTensor MCMoveClusterRotateArm
rotationTensor MCMoveRotateArm
RotationTensor etomica.space
A tensor intended for use to perform rotations in space.
RotationTensor1D etomica.space1d
Rotation tensor in 1D either flips orientation or keeps it unchanged.
RotationTensor1D() RotationTensor1D
Default is identity tensor that performs no rotation (flip).
RotationTensor2D etomica.space2d
RotationTensor2D() RotationTensor2D
rotationTensor3D P2Water4PSoft
RotationTensor3D etomica.space3d
RotationTensor3D() RotationTensor3D
rotationTolerance IntegratorRigidMatrixIterative
rotCounter IntegratorDimerMin
rotCounter IntegratorDimerRT
rotDim CoordinateDefinitionNitrogen
rotNum IntegratorDimerRT
rotX(float) Matrix3f
Sets the value of this matrix to a rotation matrix about the x axis by the
passed angle.
rotX(float) Matrix4f
Sets the value of this matrix to a rotation matrix about the x axis by the
passed angle.
rotY(float) Matrix3f
Sets the value of this matrix to a rotation matrix about the y axis by the
passed angle.
rotY(float) Matrix4f
Sets the value of this matrix to a rotation matrix about the y axis by the
passed angle.
rotZ(float) Matrix3f
Sets the value of this matrix to a rotation matrix about the z axis by the
passed angle.
rotZ(float) Matrix4f
Sets the value of this matrix to a rotation matrix about the z axis by the
passed angle.
round(double) FastFourierTransform
roundInt(int) GData
JavaScript won't really have an integer here after integer division.
route IntegratorDimerApproach
routeParams IntegratorDimerApproach
rowHeaders DataTable.DataInfoTable
rowHeaders DataTable.DataInfoTableFactory
rowLabelColumnHeader DisplayTable
rowLabels DisplayTable
rows() BenchBox.IVecSys
rows() BenchBox.VectorSystem
rp IntegratorDroplet.MyAgent
rPermutations ClusterBonds
Rpol P2WaterSzalewicz
rPow MCMoveClusterAtomDiscrete
rPow VirialHSOrC.VirialLJrParam
rPow VirialLJOrC.VirialLJrParam
rPow VirialLJOrICPYC.VirialLJrParam
Rpow P3CPSNonAdditiveHe
Rpow P3CPSNonAdditiveHeLessSimplified
Rpow P3CPSNonAdditiveHeSimplified
Rq PNWaterGCPMReactionField
rr P2HydrogenPatkowski
rr P2HydrogenPatkowskiAtomic
rr0Tensor P2CO2H2OWheatley.P2CO2H2OSC
rr0Tensor P2CO2Hellmann.P2CO2SC
rr0Tensor P2WaterSzalewicz.P2H2OSC
rr0Tensor P2NitrogenHellmann.P2N2QFH
rr1Tensor P2CO2H2OWheatley.P2CO2H2OSC
rr1Tensor P2CO2Hellmann.P2CO2SC
rr1Tensor P2WaterSzalewicz.P2H2OSC
rr1Tensor P2NitrogenHellmann.P2N2QFH
rRand MCMoveHarmonic
rrlong P2HydrogenPatkowski
rrlong P2HydrogenPatkowskiAtomic
rrounded BoundaryTruncatedOctahedron
rScale CoordinateDefinitionMolecule
rScale CoordinateDefinitionMoleculeVolumeFluctuation
rScaled Rgb16
rTag MeterWidomCavity
rTag CorrelationSelf2
rTensor0 P2CO2H2OWheatley.P2CO2H2OSC
rTensor0 P2CO2Hellmann.P2CO2SC
rTensor0 P2WaterSzalewicz.P2H2OSC
rTensor0 P2NitrogenHellmann.P2N2QFH
rTensor1 P2CO2H2OWheatley.P2CO2H2OSC
rTensor1 P2CO2Hellmann.P2CO2SC
rTensor1 P2WaterSzalewicz.P2H2OSC
rTensor1 P2NitrogenHellmann.P2N2QFH
rTmp P2WaterSzalewicz
rTrial MCMoveClusterRingPartialRegrow
rTrial MCMoveClusterRingRegrow
rTrial MCMoveClusterRingRegrowExchange
run() Launcher.ConsoleWindowRunnable
run() ViewConsoleOutputBox
run() VirialHSBinMultiThreaded.SimulationWorker
run() VirialSQWBinMultiThreaded.SimulationWorker
run(Parser.CommandValue) Interpreter
run(EtomicaServerConfig, Environment) EtomicaServer
runActivity(Controller.ControllerHandle) ActivityIntegrate
runActivity(Controller.ControllerHandle) Activity
runActivityBlocking(Activity) Controller
Runs an activity to completion on the current thread.
runEmul() PotentialEmul
runGraphic(SimulationVirialOverlap2, int) SimulationRunner
runName VirialHSBinMultiThreaded.SimulationWorker
runName VirialHSBinMultiThreaded.VirialHSBinParam
runName VirialSQWBinMultiRecalcW.VirialHSParam
runName VirialSQWBinMultiThreaded.SimulationWorker
runName VirialSQWBinMultiThreaded.VirialHSBinParam
runName VirialSQWRecalcSmallMem.VirialHSParam
running MyApplet
runQChem() P2QChem
runSimulation(ModelSimulationEnvironment, ArrayList<ICollectionPotential>) SimulationRunner
runVirial(VirialExternalFieldConfinedOverlap.VirialExternalFieldParam) VirialExternalFieldConfinedOverlap
runVirial(VirialExternalFieldConfinedOverlapRho.VirialExternalFieldParam) VirialExternalFieldConfinedOverlapRho
runVirial(VirialExternalFieldConfinedOverlapSW.VirialExternalFieldParam) VirialExternalFieldConfinedOverlapSW
runVirial(VirialExternalFieldOverlapRho.VirialExternalFieldParam) VirialExternalFieldOverlapRho
runVirial(VirialLJ.VirialLJParam) VirialLJ
runVirial(VirialLJD.VirialLJParam) VirialLJD
runVirial(VirialLJDU.VirialLJParam) VirialLJDU
runVirial(VirialLJPT.VirialLJParam) VirialLJPT
runVirial(VirialLJSeries.VirialLJParam) VirialLJSeries
runVirial(VirialSW.VirialSWParam) VirialSW
rv Potential2SoftSphericalLSMultiLat
rv P2SemiclassicalMolecular.MoleculeInfoBrute
Rvdw P2QChemInterpolated
RvdwF P2QChemInterpolated.DampingParams
RvdwF P2QChemInterpolated
RvdwF P3AdditiveQChem.DampingParams
RvdwF P3QChem.DampingParams
rwList PotentialDepletion
RYDBERG_R Constants
Rydberg's constant, in Angstroms.
rzero P1LepsHarmonic
S
s P2WaterTIP4P
s IntegratorPolymer
s P2O2Bartolomei
s MayerIonicDiagram1qbond
s MayerIonicDiagram2qbonds
s MayerIonicDiagram4qbonds
s VirialO2.VirialO2Param
s VirialO2PI.VirialO2Param
s Line
S1DHR(int, double, int) NormalModes1DHR
Returns the analytical result for the S matrix (just a scalar in this
case) for the 1D HR system with PBC
S2 P2WaterSzalewicz
S2fit(double, double, double, double, double, double, double) P2WaterSzalewicz
S3 P2WaterSzalewicz
sa P2WaterPotentialsJankowski
saa P2O2Bartolomei
saaMRCI P2O2Bartolomei
saaPT2 P2O2Bartolomei
saddle IntegratorDimerMin
saddle SimDimerLJadatom
saddleEnergy IntegratorDimerRT
saddleFine SimDimerLJadatom
saddleFound IntegratorDimerRT
saddleT IntegratorDimerRT
safeHandleOption(String[], SVGConverter) Main.AbstractOptionHandler
safeHandleOption(String[], SVGConverter) Main.NoValueOptionHandler
safeHandleOption(String[], SVGConverter) Main.SingleValueOptionHandler
safetl P2WaterPotentialsJankowski
safeTruncate(float, int) TextFormat
safetyFactor CriterionPositionWall
safetyFactor CriterionSimple
safetyFactor CriterionSimpleMolecular
sajmols P2O2Bartolomei
sajmolsMRCI P2O2Bartolomei
sajmolsPT2 P2O2Bartolomei
sajp1 P2O2Bartolomei
sajp1MRCI P2O2Bartolomei
sajp1PT2 P2O2Bartolomei
sajpn P2O2Bartolomei
sajpnMRCI P2O2Bartolomei
sajpnPT2 P2O2Bartolomei
Sam etomica.modules.sam
Self-assembled monolayer module.
Sam() Sam
SamGraphic etomica.modules.sam
SamGraphic(Sam) SamGraphic
SamGraphic.ActionMoveWall etomica.modules.sam
SamGraphic.Applet etomica.modules.sam
SamGraphic.DataPipeStressStrain etomica.modules.sam
SamGraphic.ModifierWallPosition etomica.modules.sam
sample ProtonDisorderGenerator.SimParams
sampleCluster BoxCluster
sampleCluster SimulationVirial
sampleClusters SimulationVirialOverlap2
sampleCount MeterVirialBDBinMultiThreaded.MyData
sampleCount MeterVirialBinMultiThreaded.MyData
sampleCount MeterVirialEBinMultiThreaded.MyData
sanityCheckBC AccumulatorAverageFixed
sasurface Token
satisfies(Requirement) FeatureSet
save Token
save(Parser.CommandValue) Interpreter
savedBlockData AccumulatorAverageFixed
savedData AccumulatorAutocorrelationPTensor
savedData AccumulatorAutocorrelationShearStress
savedSeed RandomMersenneTwister
savedSeedArray RandomMersenneTwister
savedSteps ConfigurationStorage
savedTimes ConfigurationStorage
saveproteinstructurestate Token
saveValues ViewAlkaneLengthSelection
sb P2WaterPotentialsJankowski
sbet P2O2Bartolomei
sbetMRCI P2O2Bartolomei
sbetPT2 P2O2Bartolomei
scale DisplayBox
Factor used to scale the size of the image.
scale DisplayPolytope
Factor used to scale the size of the image.
scale SimOverlapNitrogenModel.SimOverlapParam
scale MCMoveClusterRingScale
scale Quadric
scale(float) Quadric
scale(float) Tuple3f
Sets the value of this tuple to the scalar multiplication of itself.
scale(float) Tuple4f
Sets the value of this tuple to the scalar multiplication of itself.
scaleAdd(float, Tuple3f) Tuple3f
Sets the value of this tuple to the scalar multiplication of itself and
then adds tuple t1 (this = s*this + t1).
scaleAdd(int, Tuple3i, Tuple3i) Tuple3i
Sets the value of this tuple to the scalar multiplication of tuple t1 plus
tuple t2 (this = s*t1 + t2).
scaleAdd2(float, Tuple3f, Tuple3f) Tuple3f
Sets the value of this tuple to the scalar multiplication of tuple t1 and
then adds tuple t2 (this = s*t1 + t2).
scaleangstromsperinch Token
scaleAtoms(double) MCMoveVolumeAssociated
scaleAtoms(double) MCMoveVolumeAssociatedMolecule
scaleBox(Point3f[], float) BoxInfo
scaleBy(double) LatticeCubicBcc
Rescales the lattice by the given factor.
scaleBy(double) LatticeCubicDiamond
Rescales the lattice by the given factor.
scaleBy(double) LatticeCubicFcc
Rescales the lattice by the given factor.
scaleBy(double) LatticeCubicSimple
Rescales the lattice by the given factor.
scaleBy(double) LatticeHcp
Rescales the lattice by the given factor.
scaleBy(double) LatticeHcp4
Rescales the lattice by the given factor.
scaleBy(double) LatticeOrthorhombicHexagonal
Rescales the lattice by the given factor.
scaledCoords0 ConfigFromFileLAMMPS.ColorSchemeDeviation
scaleFitToScreen() G3DSys
scaleMomenta() IntegratorHard
Updates collision times appropriately after scaling momenta.
scaleMomenta() IntegratorMD
Crude method to enforce constant-temperature constraint, by
scaling momenta of all atoms by a constant factor so that
box adheres to setpoint temperature.
scaleMomenta() IntegratorRigidIterative
scaleMomenta() IntegratorRigidMatrixIterative
scaleMomenta() IntegratorVelocityVerletQuaternion
scaleMomenta(Vector) IntegratorMD
scalePixelsPerAngstrom TransformManager
scalePrec(BigComplex, int) BigDecimalMath
Append decimal zeros to the value.
scalePrec(BigDecimal, int) BigDecimalMath
Append decimal zeros to the value.
scalePrec(BigDecimal, MathContext) BigDecimalMath
Boost the precision by appending decimal zeros to the value.
scaleSetSize(int, int) DisplayBoxCanvas1D
Sets the size of the display to a new value and scales the image so that
the box fits in the canvas in the same proportion as before.
scaleSetSize(int, int) DisplayBoxCanvas2D
Sets the size of the display to a new value and scales the image so that
the box fits in the canvas in the same proportion as before.
scaleSetSize(int, int) DisplayBoxCanvasG3DSys
Sets the size of the display to a new value and scales the image so that
the box fits in the canvas in the same proportion as before.
scaleSetSize(int, int) DisplayPolytopeCanvas2D
Sets the size of the display to a new value and scales the image so that
the box fits in the canvas in the same proportion as before.
scaleSetSize(int, int) DisplayPolytopeCanvasG3DSys
Sets the size of the display to a new value and scales the image so that
the box fits in the canvas in the same proportion as before.
scaleSize(double) Primitive
Scales (multiplies) the size of each primitive vector by the given value.
scaleSize(double) PrimitiveBcc
Multiplies the size of the current vectors by the given value.
scaleSize(double) PrimitiveCubic
scaleSize(double) PrimitiveFcc
Multiplies the size of the current vectors by the given value.
scaleSize(double) PrimitiveGeneral
scaleSize(double) PrimitiveHexagonal
scaleSize(double) PrimitiveHexagonal2D
scaleSize(double) PrimitiveMonoclinic
scaleSize(double) PrimitiveOrthorhombic
scaleSize(double) PrimitiveOrthorhombicHexagonal
scaleSize(double) PrimitiveTetragonal
scaleSize(double) PrimitiveTriclinic
scaleSize(double) PrimitiveTrigonal
scaleSlider PistonCylinderGraphic
scaleVector BoxInflate
scaleVector MCMoveVolumeMonoclinic
scaleVector MCMoveVolumeMonoclinicScaled
scBeads VirialN2PI.VirialN2Param
scf P2QChemInterpolated
scf P3AdditiveQChem.DampingParams
scfAtoms ClusterSumPolarizable
scfAtoms ClusterSumPolarizableWertheimProduct
scfAtoms ClusterSumPolarizableWertheimProduct4Pt
scfAtoms ClusterSumPolarizableWertheimProduct4PtFinal
ScientificFormat etomica.util
a formatter that uses a format suitable for numeric values in a
scientific context.
ScientificFormat() ScientificFormat
Create a ScientificFormat using the default pattern and symbols
for the default locale.
ScientificFormat(String) ScientificFormat
Creates a ScientificFormat using a given pattern
ScientificFormat(Locale) ScientificFormat
Create a ScientificFormat using the default pattern for the
given locale.
ScientificFormat(Locale, String) ScientificFormat
Creates a ScientificFormat using a given pattern for the specified
locale
scoreGreaterThan(int[]) ClusterDiagram
Determines if the cluster's current configuration has a score greater
than the given score.
screenDiameter Point3fi
screened ClusterWheatleyHS
screened ClusterWheatleyPartitionScreening
screenSpace(Point3f, Point3i) G3DSys
Converts molspace point p (in Angstroms) to a point on the display
in pixels.
screenx Token
screenX Point3fi
screenxyz Token
screeny Token
screenY Point3fi
screenz Token
screenZ Point3fi
SCRIPT_EDITOR_IGNORE JmolConstants
scriptCommand Token
scriptqueue Token
scriptreportinglevel Token
ScriptVariable org.jmol.script
ScriptVariable(int) ScriptVariable
ScriptVariable.Sort org.jmol.script
ScriptVariableInt org.jmol.script
ScriptVariableInt(int) ScriptVariableInt
SearchState etomica.graph.isomorphism
secDerXr CalcAnalytical2ndDerivativeNitrogen
secDerXr P2Nitrogen
Second etomica.units
secondaryBox MeterBoltzmannRotPerturb
secondaryBox MeterRotPerturbMolecule
secondaryCoordDef MeterBoltzmannRotPerturb
secondaryCoordDef MeterRotPerturbMolecule
secondaryDirection ConfigurationOrientedFile
secondaryDirection OrientationFull3D
secondAxis BiasVolume2SiteAceticAcid
secondAxis BiasVolumeAceticAcid
secondBox MCMoveVolumeExchange
secondder PotentialCuLREP
secondder PotentialEAM_LS
secondder PotentialEAM
secondder PotentialEFS
secondder(IAtomList) PotentialCuLREP
secondder(IAtomList) PotentialEAM
secondder(IAtomList) PotentialEFS
secondDerivative P2Water4PSoft
secondDerivative EwaldSummation
secondDerivative P2HSDipole
secondDerivative P2LJDipole
secondDerivative P2ReactionFieldDipole
secondDerivative P2Spin
secondDerivative(IAtomList) IPotentialAtomicSecondDerivative
secondDerivative(IAtomList) P2Spin
compute the secondDerivative array of pair energy w.r.t theta1 or theta2
i.e d^2u/dtheta1_dtheta1 d^2u/dtheta1_dtheta2 and d^2u/dtheta2_dtheta2
theta1 is the angle between x axis and atom1's orientation etc.
secondDerivative(IAtom, IAtom) EwaldSummation
secondDerivative(IMoleculeList) P2Nitrogen
secondDerivative(IMoleculeList) P2Water4PSoft
secondDerivative(IMoleculeList) IPotentialMolecularSecondDerivative
secondDerivative(IMoleculeList) P2HSDipole
secondDerivative(IMoleculeList) P2LJDipole
secondDerivative(IMoleculeList) P2ReactionFieldDipole
secondDerivativeSum MeterDipoleSumSquaredMappedAverage
secondDerivativeSum PotentialCalculationPhiSum
secondDerivativeSum PotentialCalculationPhiSumHeisenberg
secondDerivativeSum MeterMappedAveraging
secondDerivativeSum MeterMappedAveraging3Pair
secondDerivativeSum MeterMappedAveragingFreeEnergy
secondDerivativeSum MeterMappedAveragingPair
secondDerivativeSum MeterMappedAveragingPairExcess
secondDerivativeSum MeterMappedAveragingSum
secondDerivativeSum MeterMappedAveragingVSum
secondDerivativeSum MeterMappedAveragingVSum3Pair
secondDerivativeSum MeterMappedAveragingVSumPair
secondDerivativeSumIdeal MeterMappedAveraging
secondDerivativeSumIdeal MeterMappedAveraging3Pair
secondDerivativeSumIdeal MeterMappedAveragingFreeEnergy
secondDerivativeSumIdeal MeterMappedAveragingPair
secondDerivativeSumIdeal MeterMappedAveragingPairExcess
secondDerivativeSumIdeal MeterMappedAveragingVSum
secondDerivativeSumIdeal MeterMappedAveragingVSum3Pair
secondDerivativeSumIdeal MeterMappedAveragingVSumPair
secondDerivativeXr(IMoleculeList) P2Nitrogen
secondDerivativeXrRotRot(IMoleculeList) P2Nitrogen
securityOff SVGConverter
Controls whether scripts should be run securely or not
seed VirialH2OGCPMD.VirialParam
seed VirialHeD.VirialParam
seed VirialHeNonAdditiveD.VirialParam
seed VirialRowleyAlcohol.VirialParam
seed VirialTraPPE.VirialParam
SEED_COUNT MeshSurface
seeds Simulation
seen(byte) AbstractTraversal
seenAll() AbstractTraversal
seenArrays DataOverlapCaching
seenParams DataOverlapCaching
segment CoordinateDefinitionNitrogenSuperBox
segmentList FFTDecomposition
selectallmodels Token
selected Token
selectedAtoms MCMoveWiggleAceticAcid
selectedAtoms MCMoveWiggle
selectedAtoms MCMoveClusterRotateCH3
selectedAtoms MCMoveClusterWiggleAceticAcid
selectedAtoms MCMoveClusterWiggleAlkaneEH
selectedAtoms MCMoveClusterWiggleMulti
selectedfloat Token
selectedMolecules MCMoveClusterTorsionAceticAcid
selectedMolecules MCMoveClusterTorsionAlkaneEH
selectedMolecules MCMoveClusterTorsionMulti
selecthetero Token
selecthydrogen Token
selectionForKey(char, ComboBoxModel) DimensionedDoubleEditor
Implementation of KeySelectionManager interface that uses key press to
select a unit prefix (instead of selecting a combo box item).
selectionhalos Token
selectItemTok(Token) ScriptVariable
selectItemTok(Token, int) ScriptVariable
selectItemVar(ScriptVariable) ScriptVariable
selectItemVar2(ScriptVariable, int) ScriptVariable
selectMolecules() MCMoveClusterReptateMulti
selectMolecules() MCMoveClusterTorsionAlkaneEH
selectMolecules() MCMoveClusterTorsionMulti
selectMove() MCMoveManager
Selects a MCMove instance from among those added to the integrator, with
probability in proportion to the frequency value assigned to the move.
SelfAssemblyGraphic etomica.modules.selfassembly
SelfAssemblyGraphic(SelfAssemblySim) SelfAssemblyGraphic
SelfAssemblySim etomica.modules.selfassembly
SelfAssemblySim(Space) SelfAssemblySim
selfELJ MinimizationTIP4P
semiClassical VirialHeNonAdditive.VirialParam
semiClassical VirialHeNonAdditiveWheatley.VirialParam
semiClassical VirialHePI.VirialHePIParam
semiClassical VirialHePISysErr.VirialHePIParam
semiClassical VirialHePYCorrection.VirialHePYCParam
semiClassical VirialHeSC.VirialHePYCParam
sep P2WaterSzalewicz
separationProbability(int, double) MCMoveClusterAtomHSRing
Normalized probability for the separation of the centers of two spheres located at the
end of a chain of (n+1) overlapping spheres.
seq MCMoveClusterMoleculeHSChain
seq MCMoveClusterMoleculeHSChainB3
seq MCMoveClusterAtomHSChain
seq MCMoveClusterAtomHSRing
seq MCMoveClusterMoleculeHSChain
seq MCMoveClusterPolyhedraChain
sequence Token
serial EllipseDisplayAction
serialize(IData, JsonGenerator, SerializerProvider) DataSerializer
serialize(Property, JsonGenerator, SerializerProvider) PropertySerializer
serialize(Wrapper<?>, JsonGenerator, SerializerProvider) WrapperSerializer
serialize(Vector, JsonGenerator, SerializerProvider) VectorSerializer
serialVersionUID DimerApproach
set(float, float, float) Tuple3f
Sets the value of this tuple to the specified xyz coordinates.
set(float, float, float, float) Tuple4f
Sets the value of this tuple to the specified xyzw coordinates.
set(int) Euler
Compute a coefficient in the internal table.
set(int) BitSet
Sets the bit at the specified index to true.
set(int, int) BigIntegerPoly
Set a polynomial coefficient.
set(int, int, int) Tuple3i
Sets the value of this tuple to to the specified x, y, and z coordinates.
set(int, IAtom) AtomArrayList
set(int, IAtom) AtomPair
set(int, IAtom) AtomSetSinglet
set(int, IMolecule) MoleculeArrayList
set(int, IMolecule) MoleculePair
set(int, IMolecule) MoleculeSetSinglet
set(int, Rational) Bernoulli
Set a coefficient in the internal table.
set(int, BigInteger) BigIntegerPoly
Set a polynomial coefficient.
set(Parser.CommandPropertyValue) Interpreter
set(ScriptVariable, boolean) ScriptVariable
creates a NEW version of the variable
set(Quaternion) Quaternion
set_sites(Vector[]) P2WaterPotentialsJankowski
set_sites_itypea P2WaterPotentialsJankowski
set_sites_sa P2WaterPotentialsJankowski
set_sites_sitea P2WaterPotentialsJankowski
set2(Point3f, Point3i) Point3fi
set4(float, float, float, float) AxisAngle4f
Sets the value of this axis angle to the specified x,y,z,angle.
setA() P3CPSNonAdditiveHe
setA() P3CPSNonAdditiveHeOrig
setA(double) IntegratorPolymer
setA(double) P2Exp6
setA(double) P2ModifiedMorse
setA(double) P2Morse
setA(float[]) Matrix3f
Sets the values in this Matrix3f equal to the row-major array parameter
(ie, the first four elements of the array will be copied into the first row
of this matrix, etc.).
setA(float[]) Matrix4f
Sets the values in this Matrix4f equal to the row-major array parameter
(ie, the first four elements of the array will be copied into the first row
of this matrix, etc.).
setA(float[]) Tuple3f
Sets the value of this tuple from the 3 values specified in the array.
setA(int, double) P2HeSimplified
Sets the ith parameter value
u = A0 * exp(-A1*r) - A2/r^6 - A3/r^X
where X = 10 if useC10 is true, X=8 otherwise
setAA(AxisAngle4f) AxisAngle4f
Sets the value of this axis angle to the value of axis angle t1.
setAA(AxisAngle4f) Matrix3f
Sets the value of this matrix to the matrix conversion of the single
precision axis and angle argument.
setAA(AxisAngle4f) Matrix4f
Sets the value of this matrix to the matrix conversion of the single
precision axis and angle argument.
setAA(AxisAngle4f) Quaternion
setABC(int) MeshSurface
setAcceptanceTarget(double) MCMoveStepTracker
Sets the desired rate of acceptance (as a fraction between 0 and 1
inclusive) of trials of this move.
setAccumulator(AccumulatorAverage) DisplayTextBoxesCAE
Specifies the accumulator that generates the displayed values.
setAccumulator(AccumulatorAverageCollapsingLog) DataProcessorBounds
setAccumulator(AccumulatorAverageCollapsingLog) DataProcessorVar
setAccumulator(IDataSink) SimulationVirial
setAccumulator(AccumulatorVirialOverlapSingleAverage, int) SimOverlapBetaN2RP
setAccumulator(AccumulatorVirialOverlapSingleAverage, int) SimOverlapNitrogenModel
setAccumulator(AccumulatorVirialOverlapSingleAverage, int) SimOverlap
setAccumulator(AccumulatorVirialOverlapSingleAverage, int) SimOverlapLJ
setAccumulator(AccumulatorVirialOverlapSingleAverage, int) SimOverlapSoftSphere
setAccumulator(AccumulatorVirialOverlapSingleAverage, int) SimOverlapSoftSphereEinHarm
setAccumulator(AccumulatorVirialOverlapSingleAverage, int) SimOverlapSoftSphereHCP
setAccumulator(AccumulatorVirialOverlapSingleAverage, int) SimOverlapSoftSphereReweighting
setAccumulator(AccumulatorVirialOverlapSingleAverage, int) SimOverlapSoftSphereSoftness
setAccumulator(AccumulatorVirialOverlapSingleAverage, int) SimOverlapSoftSphereSuperBox
setAccumulator(AccumulatorVirialOverlapSingleAverage, int) SimOverlapSSnxy
setAccumulatorBlockSize(long) SimulationVirial
setAccumulatorBlockSize(long) SimulationVirialOverlap2
setAccumulators(AccumulatorAverageCollapsingLog[]) MultiharmonicGraphicMC.DataSourceBias
setAccumulatorUpdateInterval(int) DataTableAverages
Sets the interval for updates to the accumulators feeding this table.
setAction(IAction) DeviceButton
Defines the action to be performed when the button is pressed.
setAction(IAction) DeviceButtonSingle
Defines the action to be performed when the button is pressed.
setActive(boolean) DataAccumulator
setActive(int, boolean, boolean) P1HardBoundary
setActiveLevel(int, boolean) Logger
Changes the activation state for a logging level.
setAddAnotherSpecies(JButton) ViewSpeciesSelection
setAddPotential(JButton) ViewSpeciesSelection
setAddPotential(JButton) ViewSpeciesSelection
setAddSameSpecies(JButton) ViewSpeciesSelection
setAddSpecies(JButton) ViewSpeciesSelection
setAddSpecies1(JButton) ViewSpeciesSelection
setAddSpecies2(JButton) ViewSpeciesSelection
setAddSpecies3(JButton) ViewSpeciesSelection
setAdiabatic() DeviceThermoSlider
Set the Adiabatic button to its selected state.
setAdiabatic() DeviceThermoSliderGEMC
Set the Adiabatic button to its selected state.
setAdjustInterval(long) MCMoveStepTracker
Sets the interval between steps size adjustments.
setAdjustInterval(long) IntegratorOverlap
Sets how frequently the appropriate reference vs.
setAdjustStepFraction(boolean) IntegratorOverlap
Sets whether to adjust the number of relative number of steps for each
sub-integrator.
setAdjustStepFreq(boolean) IntegratorOverlap
Deprecated.
Sets whether to adjust the number of relative number of steps for each
sub-integrator.
setAdjustStepSize(double) MCMoveStepTracker
Sets the step adjustment size.
setAelement(ElementSimple) SimpleElementForSimilarSpecies
setAgent(AtomType, E) AtomTypeAgentManager
Sets the agent associated with the given atom type to be the given agent.
setAgent(IAtom, E) AtomLeafAgentManager
Sets the agent associated with the given atom to be the given agent.
setAgent(Box, E) BoxAgentManager
Associates an Agent with a Box.
setAgent(IMolecule, E) MoleculeAgentManager
Sets the agent associated with the given atom to be the given agent.
setAgent(ISpecies, E) SpeciesAgentManager
Sets the agent associated with the given atom type to be the given
agent.
setAgentManager(AtomLeafAgentManager) PotentialCalculationTorqueSumWallForce
setAgentManager(AtomLeafAgentManager) PotentialCalculationPhiSum
setAgentManager(AtomLeafAgentManager) PotentialCalculationVSum
setAgentManager(AtomLeafAgentManager<?>) PotentialCalculationTorqueSum
setAgentManager(AtomLeafAgentManager<AtomPotentialList>) NeighborListManager.AtomPotential1ListSource
setAgentManager(AtomLeafAgentManager<Vector>) PotentialCalculationForceSum
setAggressiveAdjustStepFraction(boolean) IntegratorOverlap
Sets whether to use "aggressive" adjustment.
setAlertMessage(String) ModelAlertMsgDialog
setAlertMsgBoxController(ControllerAlertMsgBox) ControllerSpeciesSelection
setAlertMsgBoxSpeciesRemoval(ViewAlertMsgBoxSpeciesRemoval) ViewSpeciesSelection
setAlign(int, int) DisplayBox
setAlign(int, int) DisplayPolytope
setAlkaneIndex(int) MolecularModelSKS_SpeciesAlkane
setAlkaneIndex(int) MolecularModelTRAPPE_SpeciesAlkane
setAlkaneLength(int, int) ModelAlkaneLengthSelection
setAlkaneLengthSelectionDM(ModelAlkaneLengthSelection) ControllerAlkaneLengthSelection
setAlkaneLengthSelectionView(ViewAlkaneLengthSelection, int) ControllerAlkaneLengthSelection
setAll(int) BitSetUtil
setAllEVal() DeviceEigenvaluesSlider
Set the "All eigenvalues" button to its selected state.
setAllowedScriptTypes(String) SVGConverter
Sets the set of allowed script types (i.e., the set of possible
values for the type attribute in the <script> element),
as a comma separated list of allowed values.
setAllowEqualElements(boolean) IndexIteratorTriangular
Sets flag indicating whether iterates may have elements that are equal to one another.
setAllPermutations(boolean) ClusterGenerator
Set whether to generate all permutations.
setAllPermutations(boolean) VirialDiagrams
setAllPermutations(boolean) VirialDiagramsPT
setAllUnits(Unit) DisplayTable
Sets the units of all columns to the given unit.
setAllWV() DeviceWaveVectorSlider
Set the "All Wave Vectors" button to its selected state.
setAlpha() P3CPSNonAdditiveHe
setAlpha() P3CPSNonAdditiveHeOrig
setAlpha(double) PrimitiveTrigonal
setAlpha(double) MultiharmonicGraphicMC.DataSourceAlphaFE
setAlpha(double) MultiharmonicGraphicMC.DataSourceBias
setAlpha(double) MeterUmbrella
setAlpha(double) EwaldSummation
setAlpha(double) P2Dreiding
setAlpha(double) P2Exp6Buckingham
setAlpha(double[]) MeterTargetRPMolecule
setAlpha(double[]) MeterTargetTPMolecule
setAlpha(double[]) MeterOverlapSwitch
setAlpha(double[]) MeterTargetTP
setAlpha(double[], double[]) MeterMBAR
sets the range of parameter values used for Bennets method.
setAlpha(double, double) SimOverlapModule
setAlphaCenter(double, double) SimOverlapSoftSphereEinHarm
setAlphaEin(double) MCMoveEinsteinCrystal
Sets the Einstein spring constant
u = alpha * r^2
setAlphaEin(double) MCMoveHarmonicEin
Sets the Einstein spring constant
setAlphaFac(double) MeterUmbrella
setAlphaRange(double, double) MeterOverlap
sets the range of parameter values used for Bennets method.
setAlphaSpan(double) MeterTargetRPMolecule
setAlphaSpan(double) MeterTargetTPMolecule
setAlphaSpan(double) MeterOverlapSwitch
setAlphaSpan(double) MeterTargetTP
setAlternateStylesheet(String) SVGConverter
Sets the alternateStyleSheet value.
setAlterSimEnv(JButton) ViewSpeciesSelection
setAlterSimEnv(JButton) ViewSpeciesSelection
setAlwaysScaleRandomizedMomenta(boolean) IntegratorMD
Configure thermostat to always scale randomized momenta to match the set
temperature
setAmbientPercent(int) GData
fractional distance from black for ambient color
setAmplitude(double) P2Fene
setAndIncrement(Rgb16, Rgb16) Rgb16
setAngle(double) MeterTargetRPMolecule
setAngle(double) P3BondAngle
Sets the nominal bond angle (in radians)
setAngle(double) P3BondAngleDreiding
Sets the nominal bond angle (in radians)
setAngle(double) P3CPSNonAdditiveHeOrig
Sets the nominal bond angle (in radians)
setAngle(int, double) ConformationChainLinear
setAngle(int, double) ConformationLinear
setAngleAlpha(double) PrimitiveTriclinic
setAngleBeta(double) PrimitiveMonoclinic
setAngleBeta(double) PrimitiveTriclinic
setAngleGamma(double) PrimitiveTriclinic
setAngles(double[]) Primitive
Sets the angles between the primitive vector to the corresponding
values in the given array.
setAngles(double[]) P2WaterPotentialsJankowski
setAngles(double, double, double) AtomActionRotateBy
setAnharmonicConstant(double) P2Anharmonic
setAppending(boolean) DataLogger
Overwrite or attach the data to the file.
setApplyToMolecules(boolean) BoxImposePbc
Sets a flag indicating whether periodic boundaries are applied to the
molecules (true), or to the atoms (false).
setApproximation(int) ClusterOperations
setArea(Rectangle2D) SVGConverter
Sets the area as a Rectangle.
setArray(double[][]) MyEigenvalueDecomposition
setArrayList(AtomArrayList) AtomToAtomSetFixed
setArrayList(MoleculeArrayList) MoleculeToMoleculeSetFixed
setArrayListPotentialCollection(ArrayList<ICollectionPotential>) ModelSimulationConstructor
setArrayShape(int[]) DataDoubleArray.DataInfoDoubleArrayFactory
Sets the array shape.
setArrayShape(int[]) DataDoubleBDArray.DataInfoDoubleBDArrayFactory
Sets the array shape.
setAsCube(double) BoundaryDeformablePeriodic
Sets the shape of the boundary to a cube with edges equal to the given value.
setAspect(float) Ellipse
setAsRectangular(Vector) BoundaryDeformablePeriodic
Sets the shape of the boundary as a rectangular parallelepiped (or
parallelogram) with edge lengths given by the elements of the given
vector.
setAssociationManager(AssociationManager) AtomSourceRandomDimer
setAssociationManager(AssociationManager) AtomSourceRandomMonomer
setAssociationManager(AssociationManager) AtomSourceRandomSmer
setAssociationManager(AssociationManager) MCMoveAtomDimer
setAssociationManager(AssociationManager) MCMoveAtomMonomer
setAssociationManager(AssociationManager) MCMoveAtomNoSmer
setAssociationManager(AssociationManager) MCMoveAtomSmer
setAssociationManager(AssociationManager) MCMoveBiasUB
setAssociationManager(AssociationManager) MCMoveDimer
setAssociationManager(AssociationManager) MCMoveDimerRotate
setAssociationManager(AssociationManager) MCMoveRotateAssociated
setAssociationManager(AssociationManager) MCMoveRotateNoSmer
setAssociationManager(AssociationManager) MCMoveSmer
setAssociationManager(AssociationManager) MCMoveSmerRotate
setAssociationManager(AssociationManager) MCMoveVolumeAssociated
setAssociationManager(AssociationManager) MeterDimerMoleFraction
setAssociationManager(AssociationManagerMolecule) MoleculeSourceRandomDimer
setAssociationManager(AssociationManagerMolecule) MoleculeSourceRandomMonomer
setAssociationManager(AssociationManagerMolecule, IAssociationHelperMolecule) MCMoveBiasUBMolecule
setAssociationManager(AssociationManagerMolecule, IAssociationHelperMolecule) MCMoveMoleculeMonomer
setAssociationManager(AssociationManagerMolecule, IAssociationHelperMolecule) MCMoveMoleculeRotateAssociated
setAssociationManager(AssociationManagerMolecule, IAssociationHelperMolecule) MCMoveMoleculeSmer
setAssociationManager(AssociationManagerMolecule, IAssociationHelperMolecule) MCMoveVolumeAssociatedMolecule
setAsText(String) DimensionedDoubleEditor
Sets the value, interpreted as being in the editor's units, from a text string.
setAtom(IAtom) AtomIteratorArrayList
Sets the first atom for iteration.
setAtom(IAtom) AtomIteratorArrayListAdjacent
Sets the first atom for iteration.
setAtom(IAtom) AtomIteratorAtomDependent
setAtom(IAtom) AtomIteratorSinglet
Defines atom returned by iterator and leaves iterator unset.
setAtom(IAtom) ColorSchemeNeighbor
setAtom(IAtom) ColorSchemeNeighborCell
setAtom(IAtom) IntegratorHard.CollisionHandlerUp
sets the atom whose collision time is to be calculated
setAtom(IAtom) MCMoveInsertDeleteLatticeVacancy.AtomIteratorBruteForce
setAtom(IAtom) MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbr
setAtom(IAtom) MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbrCell
setAtom(IAtom) AtomSite
setAtomAgentManager(Box, AtomLeafAgentManager<? extends Vector>) P1HarmonicSite
setAtomInfo(AtomType, P2SemiclassicalAtomic.AtomInfo) P2SemiclassicalAtomic
setAtomNumber(int) MeterElongation
setAtomNumber(int) MeterStrain
setAtomPositionDefinition(IMoleculePositionDefinition) MoleculeActionTranslateTo
setAtomPositionDefinition(IMoleculePositionDefinition) MCMoveMoleculeExchange
setAtomPositionDefinition(IMoleculePositionDefinition) MCMoveSemigrand
setAtoms(IAtom[]) AtomListFromArray
Copies the atoms in the given array to the wrapped, final array of atoms.
setAtoms(IAtomList) AtomListFromArray
Copies the atoms in the given atom set to the wrapped array of atoms.
setAtoms(IAtomList) MeterStructureFactor
setAtoms(IAtom, IAtom) DataSourceAtomDistance
setAtomSource(AtomSource) MCMoveDimer
setAtomSource(AtomSource) MCMoveDimerRotate
setAtomSource(AtomSource) MCMoveSmer
setAtomSource(AtomSource) MCMoveSmerRotate
setAtomSource(AtomSource) MCMoveAtomCoupled
setAtomSource(AtomSource) MCMoveAtomSwap
setAtomSource(AtomSource) MCMoveAtom
setAtomSource(AtomSource) MCMoveDimer
setAtomSource(AtomSource) MCMoveDimerRotate
setAtomSource(AtomSource) MCMoveAtomCoupled
setAtomSource(AtomSource) MCMoveAtomCoupledBennet
setAtomSource(AtomSource) MCMoveAtomCoupledUmbrella
setAtomSource(AtomSource) MCMoveClusterAtomQ
setAtomTestDoDisplay(AtomTest) DisplayBox
Mutator method for the atom filter that determines which atoms
are displayed.
setAtomType(AtomType) MeterRDF
setAtomType(AtomType) MeterWallForce.PotentialCalculationWallForce
setAtomType(AtomType) CorrelationSelf2
setAtomType(AtomType) DataSourceFs
setAtomType(AtomType) DataSourceVAC
setAtomType(AtomType) MeterCorrelationSelf
setAtomTypeFactor(AtomType, double) MeterStructureFactor.AtomSignalSourceByType
Sets the given atom type to have the given form factor
https://en.wikipedia.org/wiki/Structure_factor
setAtomTypes(AtomType) MeterGs
setAtomTypes(AtomType, AtomType) MeterRDF
setAtomTypes(AtomType, AtomType) MeterCorrelation
setAutoScale(boolean) DevicePlotPoints
setAvgDef(boolean) DataSourceFE
setAxial(int, double) RotationTensor
setAxial(int, double) RotationTensor1D
setAxial(int, double) RotationTensor2D
setAxial(int, double) RotationTensor3D
Sets tensor for rotation about the indicated axis (0=x,1=y,2=z) by
the given angle.
setAxis(int) ColorSchemeDirection
setB(double) IntegratorPolymer
setB(double) P1Sinusoidal
setB(double) P2Exp6
setBackgroundArgb(int) GData
sets background color to the specified argb value
setBackgroundColor(Color) SVGConverter
Sets the backgroundColor value.
setBackgroundColor(Color) DisplayBoxCanvasG3DSys
Sets the background color of the display box canvas.
setBackgroundColor(Color) DisplayPolytopeCanvasG3DSys
Sets the background color of the display box canvas.
setBackgroundImage(Object) GData
setBackgroundTransparent(boolean) Graphics3D
setBackgroundTransparent(boolean) GData
setBarrier(double) P2SquareWellBonding
setBarrier(double) P2SquareWellBondingCO
setBarrier(double) P2SquareWellBonded
setBasis(IMoleculeList) ANIntergroupCoupled
Specifies the basis, which identifies the molecules subject to
iteration.
setBasis(IMoleculeList) ANIntergroupExchange
Specifies the basis, which identifies the molecules subject to
iteration.
setBasis(IMoleculeList) ANIntragroupExchange
Specifies the basis, which identifies the molecules subject to
iteration.
setBasis(IMoleculeList) ApiIndexList
setBasis(IMoleculeList) ApiIntergroup
Specifies the basis, which identifies the atoms subject to iteration.
setBasis(IMoleculeList) ApiIntergroupExchange
setBasis(IMoleculeList) ApiIntragroup
Specifies the parent atom of the iterates.
setBasis(IMoleculeList) AtomIteratorBasis
Sets the basis for iteration, such that the childList atoms of the given
atom will be subject to iteration (within any specifications given by a
prior or subsequent call to setTarget).
setBasis(IMoleculeList) AtomIteratorBasisAdjustableStart
Sets the basis for iteration, such that the childList atoms of the given
atom will be subject to iteration (within any specifications given by a
prior or subsequent call to setTarget).
setBasis(IMoleculeList) Atomset3IteratorIndexList
setBasis(IMoleculeList) Atomset4IteratorIndexList
setBasis(IMoleculeList) AtomsetIteratorAllLeafAtoms
setBasis(IMoleculeList) AtomsetIteratorBasisDependent
Identifies the atoms that form the basis for iteration, such that
the childList atoms of those given will form the iterates.
setBasis(IMoleculeList) MoleculesetIteratorBasisDependent
setBasis(IMoleculeList) PotentialMaster.AtomIterator0
setBasisMolecules(Basis) ConfigurationSAM
setBasisSurface(Basis) ConfigurationSAM
setBbcage(float) BoxInfo
setBDAccFrac(double, IRandom) ClusterCoupledFlippedMultivalue
setBDAccFrac(double, IRandom) ClusterWheatleySoft
Directs this cluster to only compute p fraction of the time when the
value is too small (below tol).
setBDAccFrac(double, IRandom) ClusterWheatleySoftDerivatives
Directs this cluster to only compute p fraction of the time when the
value is too small (below tol).
setBennetParam(double, double) AccumulatorOverlapAverageUa2
sets the range of parameter values used for Bennets method.
setBennetParam(double, double) AccumulatorVirialOverlapSingleAverage
sets the range of parameter values used for Bennets method.
setBennetParam(double, double) DataProcessorVirialOverlap
sets the range of parameter values used for Bennets method.
setBeta(double) PrimitiveTrigonal
setBeta(double) P4TorsionDreiding
setBeta3() P3CPSNonAdditiveHeOrig
setBeta4211() P3CPSNonAdditiveHeOrig
setBeta4220() P3CPSNonAdditiveHeOrig
setBetaPhase(boolean) MeterTargetTPMolecule
setBetaPositionAndOrientation(IMoleculeList) CoordinateDefinitionNitrogen
setBGColor(Color) G3DSys
Change the background color of the G3D display
setBiasCubeDimensions(double) BiasVolumeCube
setBiasCubeDimensions(Vector) BiasVolumeCube
setBiasSphereInnerRadius(double) BiasVolume2SiteAceticAcid
setBiasSphereInnerRadius(double) BiasVolumeAceticAcid
setBiasSphereInnerRadius(double) BiasVolumeSphere
setBiasSphereInnerRadius(double) BiasVolumeSphereOriented
setBiasSphereInnerRadius(double) BiasVolumeSphereOrientedDoubleSites
setBiasSphereRadius(double) BiasVolume2SiteAceticAcid
setBiasSphereRadius(double) BiasVolumeAceticAcid
setBiasSphereRadius(double) BiasVolumeSphere
setBiasSphereRadius(double) BiasVolumeSphereOriented
setBiasSphereRadius(double) BiasVolumeSphereOrientedDoubleSites
setBiasVolume(BiasVolume2SiteAceticAcid) P2AceticAcidTwoSite
setBiasVolume(BiasVolume2SiteAceticAcid) P2HardAssociationRefAceticAcidTwoSite
setBigStep(int) ConfigurationStoragePumper
setBinSize(double) DataSourceTensorVirialHardProfile
setBit(int) Bitmap
setBit(int) BitmapOfLong
The highest order bit is at bit 0 of bitmap, and the lowest order bit is at bit
bitSize() - 1 of bitmap.
setBit(int) BitmapOfLongVector
The highest order bit is at bit 0 of bitmap[0], and the lowest order bit is at bit
bitSize() - 1 of bitmap[size()-1].
setBits(boolean) Bitmap
setBits(boolean) AbstractBitmap
setBits(boolean) BitmapOfLong
TIME = O(1).
setBits(boolean) BitmapOfLongVector
setBits(int, int) BitSet
Sets the bits from the specified fromIndex (inclusive) to the
specified toIndex (exclusive) to true.
setBitSize(int) BitmapOfLong
setBitSize(int) BitmapOfLongVector
setBitTo(int, boolean) BitSet
Sets the bit at the specified index to the specified value.
setBlockDataSink(IDataSink) AccumulatorAverageFixed
Allows individual block data to be passed to a data sink.
setBlockSize(long) AccumulatorAverage
Sets the size of the block used to group data for error analysis.
setBlockSize(long) AccumulatorAverageCollapsing
Sets the size of the block used to group data for error analysis.
setBondConstraints(ISpecies, int[][], double[]) IntegratorVelocityVerletShake
setBondDelta(double) P2HardBond
Sets the bond extension factor (max = length * (1+delta))
setBondDelta(double) P2PenetrableBond
Sets the bond extension factor (max = length * (1+delta))
setBonded(boolean) CriterionBondedSimple
setBonded(boolean, IAtom, IAtom, double) P2HardBondedList
Adds/removes the pair of atoms to/from each other's bonded list.
setBondedSurfaceAtoms(IMolecule, IAtomList) CriterionTether3
setBondFac(double) P2HardSphereMC
setBondFac(double) P2SquareWellMonomer
setBondL(double) MolecularModelEMP2_SpeciesCO2
setBondL(double) MolecularModelSKS_SpeciesAlkane
setBondL(double) MolecularModelSPCE_SpeciesH2O
setBondL(double) MolecularModelTRAPPE_SpeciesAlkane
setBondL(double) MolecularModelTrappe_SpeciesCO2
setBondLength(double) AtomHydrogen
setBondLength(double) ConformationChainLinear
setBondLength(double) ConformationLinear
setBondLength(double) P2Dreiding
setBondLength(double) P2HardBond
Setter method for the bond length
setBondLength(double) P2PenetrableBond
Setter method for the bond length
setBondLength(double) MolecularModel2CLJQ_SpeciesCO2
setBondLength(double) MolecularModel2CLJQ_SpeciesEthane
setBondLength(double) MolecularModel2CLJQ_SpeciesLJ
setBondLength(double) MCMoveClusterReptateMulti
setBondLength(double) MCMoveClusterTorsionAlkaneEH
setBondLength(double) MCMoveClusterTorsionMulti
setBondLengths(double[]) P2WaterPotentialsJankowski
setBonds(int[]) ClusterTreeNode
setBonds(int[][]) ClusterCollapsedTreeNode
setBondType(int) P2HardAssociationGCPMReference
setBondType(int) PNWaterGCPMThreeSite
setBondType(int) Bond
setBoolean(boolean) ModifierBoolean
Sets the modified value to the given boolean.
setBorderAlignment(int) DeviceSlider
setBorderAlignment(int) DeviceSpinner
setBorderBackground(Color) DeviceBox
setBoundaries(int, double[], int[]) MeterFlux
setBoundaryFrameColor(Color) DisplayBoxCanvasG3DSys
Sets the color of the box boundary.
setBoundaryFrameColor(Color) DisplayPolytopeCanvasG3DSys
Sets the color of the box boundary.
setBoundaryPadding(double) ConfigurationLattice
setBoundaryVectors(double[]) G3DSys
Sets the boundary vectors to be used for calculating image shells
setBoundaryVectors(double[]) ImageShell
setBoundaryVectorsIterator(IndexIterator) G3DSys
Sets the index iterator to use for calculating image shells
setBoundaryVectorsIterator(IndexIterator) ImageShell
setBoundaryWall(boolean) CriterionPositionWall
Sets whether the walls are at the box boundaries or not.
setBoundBox(Point3f, Point3f, boolean, float) BoxInfo
setBoundingBox(float, float, float, float, float, float) G3DSys
Set the min and maximum coordinates for the model.
setBoundingBox(Vector, Vector) DisplayBoxCanvasG3DSys
Sets the display bounding box.
setBounds(int, int, int, int) DisplayBoxCanvas1D
setBounds(int, int, int, int) DisplayBoxCanvas2D
setBounds(int, int, int, int) DisplayBoxCanvasG3DSys
setBounds(int, int, int, int) DisplayPolytope
setBounds(int, int, int, int) DisplayPolytopeCanvas2D
setBounds(int, int, int, int) DisplayPolytopeCanvasG3DSys
setBox(Box) BoxAction
Specifies the Box that will be subject to the action, upon subsequent call to actionPerformed()
setBox(Box) BoxActionAdapter
setBox(Box) BoxQuench
setBox(Box) PDBWriter
setBox(Box) WriteConfiguration
Sets the box whose atom coordinates get written to the file.
setBox(Box) WriteConfigurationBinary
Sets the box whose atom coordinates get written to the file.
setBox(Box) WriteConfigurationDLPOLY
Sets the box whose atom coordinates get written to the file.
setBox(Box) WriteConfigurationP2DLPOLY
Sets the box whose atom coordinates get written to the file.
setBox(Box) AtomSourceRandomDimer
setBox(Box) AtomSourceRandomSmer
setBox(Box) BiasVolume2SiteAceticAcid
setBox(Box) BiasVolumeAceticAcid
setBox(Box) BiasVolumeCube
setBox(Box) BiasVolumeSphere
setBox(Box) BiasVolumeSphereOriented
setBox(Box) BiasVolumeSphereOrientedDoubleSites
setBox(Box) MCMoveBiasUB
setBox(Box) MCMoveBiasUBMolecule
setBox(Box) MCMoveDimer
setBox(Box) MCMoveDimerRotate
setBox(Box) MCMoveRotateAssociated
setBox(Box) MCMoveSmer
setBox(Box) MCMoveSmerRotate
setBox(Box) MCMoveVolumeAssociated
setBox(Box) MCMoveVolumeAssociatedMolecule
setBox(Box) MeterDimerMoleFraction
setBox(Box) MoleculeSourceRandomDimer
setBox(Box) AtomSource
sets the Box the source should pull Atoms from.
setBox(Box) AtomSourceRandomLeaf
setBox(Box) AtomSourceRandomSpecies
setBox(Box) ApiLeafAtoms
Conditions iterator to return all leaf-atom pairs from the given box.
setBox(Box) AtomIteratorLeafAtoms
Configures iterator to form its iterates from the leaf atoms of the given
box.
setBox(Box) AtomsetIteratorBoxDependent
Sets the Box to pull iterates from
setBox(Box) RandomPositionSource
Notifies the RandomPositionSource of the box from which random positions
should be taken from.
setBox(Box) RandomPositionSourceDeformable
setBox(Box) RandomPositionSourceRectangular
setBox(Box) DataProcessorInterfacialTension
setBox(Box) DataSourcePositioned
setBox(Box) DataSourcePositionedBoltzmannFactor
setBox(Box) MeterAvgBondLength
setBox(Box) MeterDihedralAngle
setBox(Box) MeterDipoleSumSquared1site
setBox(Box) MeterDipoleSumSquaredTIP4PWater
setBox(Box) MeterHyperVirial
setBox(Box) MeterKineticEnergyRigid
Sets the box to the given box.
setBox(Box) MeterMoleculeTemperature
setBox(Box) MeterMoleFraction
setBox(Box) MeterMomentumCOM
setBox(Box) MeterNMolecules
setBox(Box) MeterPositionCOM
setBox(Box) MeterPotentialEnergy
setBox(Box) MeterPressure
setBox(Box) MeterPressureTensor
Sets the integrator associated with this instance.
setBox(Box) MeterProfile
setBox(Box) MeterProfileByAtoms
setBox(Box) MeterProfileByVolume
setBox(Box) MeterRadiusGyration
setBox(Box) MeterRDF
setBox(Box) MeterRDFPC
setBox(Box) MeterTensorVelocity
setBox(Box) MeterVolume
setBox(Box) MeterWidomInsertion
setBox(Box) PotentialCalculationRDF
setBox(Box) MeterFlux
setBox(Box) MyMCMove
setBox(Box) P2EAM
setBox(Box) PotentialCuLREP
setBox(Box) PotentialEAM_LS
setBox(Box) PotentialEAM
setBox(Box) PotentialEFS
setBox(Box) DataSourceEnergies
setBox(Box) MCMoveAtomCoupled
setBox(Box) MCMoveAtomSwap
setBox(Box) P1ImageHarmonic
setBox(Box) DeviceNSelector
setBox(Box) DisplayBox
Specifies the box for this display.
setBox(Box) IntegratorBox
setBox(Box) MCMoveAtom
setBox(Box) MCMoveBox
Sets the box on which this move acts.
setBox(Box) MCMoveBoxSize
setBox(Box) MCMoveDimer
setBox(Box) MCMoveDimerRotate
setBox(Box) MCMoveInsertDelete
setBox(Box) MCMoveInsertDeleteBiased
setBox(Box) MCMoveInsertDeleteLatticeVacancy
setBox(Box) MCMoveManager
Invokes superclass method and informs all MCMoves about the new box.
setBox(Box) MCMoveMolecule
setBox(Box) MCMoveRotate
setBox(Box) MCMoveSemigrand
Extends the superclass method to initialize the exchange-set species agents for the box.
setBox(Box) MCMoveVolume
setBox(Box) MeterPotentialEnergyCutoff
setBox(Box) MeterPU
setBox(Box) MeterPUCut
setBox(Box) MeterPUCutLS
setBox(Box) MeterWidomInsertionCorrection
setBox(Box) MeterWidomInsertionP
setBox(Box) Potential2SoftSphericalLSMulti
setBox(Box) Potential2SoftSphericalLSMultiLat
setBox(Box) Potential2SoftSphericalLSMultiLatSlanty
setBox(Box) PotentialCalculationEnergySumCutoff
setBox(Box) PotentialCalculationSumCutoff
setBox(Box) MeterMappedRdf
setBox(Box) PotentialCalculationMappedRdf
setBox(Box) P2CO2H2OWheatley.P2CO2H2OSC
setBox(Box) P2CO2H2OWheatley.P2CO2H2OSCTI
setBox(Box) P2CO2H2OWheatley
setBox(Box) P2CO2Hellmann.P2CO2SC
setBox(Box) P2CO2Hellmann
setBox(Box) PNCO2GCPM.P3GCPMAxilrodTeller
setBox(Box) PNCO2GCPM
setBox(Box) PNGCPM.P3GCPMAxilrodTeller
setBox(Box) PNGCPM.PNGCPMCached
setBox(Box) PNGCPM
setBox(Box) MCMoveMoleculeCoupledInitPert
setBox(Box) MCMoveMoleculeCoupledSuperBox
setBox(Box) MCMoveVolumeN2
setBox(Box) P0LatticeEnergyCorrec
setBox(Box) P2Nitrogen
setBox(Box) P2NitrogenAB
setBox(Box) P2NitrogenAnisotropic
setBox(Box) P2NitrogenShellModel
setBox(Box) PRotConstraint
setBox(Box) P2AceticAcidTwoSite
setBox(Box) P2HardAssociationRefAceticAcidTwoSite
setBox(Box) P2Water3P
setBox(Box) P2Water4P
setBox(Box) P2WaterSzalewicz.P2H2OSC
setBox(Box) P2WaterSzalewicz
setBox(Box) P2WaterTIP4PHardCore
setBox(Box) PNWaterGCPM.PNWaterGCPMCached
setBox(Box) PNWaterGCPM
setBox(Box) PNWaterGCPMReactionField
setBox(Box) MeterExcessAdsorbed
setBox(Box) MyMCMove
setBox(Box) P1Wall
setBox(Box) P2SquareWellBonding
setBox(Box) AtomTestChainLength
setBox(Box) ColorSchemeRadical
setBox(Box) MeterChainLength
setBox(Box) P2SquareWellBonded
setBox(Box) ColloidSim.CriterionNone
setBox(Box) MeterEnd2End
setBox(Box) P1Wall
setBox(Box) MeterFlux
setBox(Box) MyMCMove
setBox(Box) MeterDeformation
setBox(Box) P1Smash
setBox(Box) MCMoveSwap
setBox(Box) DataProcessorInterfacialTensionProfile
setBox(Box) MeterOrientation
setBox(Box) MeterElongation
setBox(Box) MeterStrain
setBox(Box) MeterStress
setBox(Box) P1Tension
setBox(Box) StrainColorScheme
setBox(Box) P1MagicWall
setBox(Box) MCMoveMultiHarmonic
setBox(Box) MeterFreeEnergy
setBox(Box) MeterDimerFraction
setBox(Box) MeterEndToEnd
setBox(Box) MeterNormalStress
setBox(Box) MeterViscosity
setBox(Box) MeterFlux
setBox(Box) CriterionTether3
setBox(Box) MeterTilt
setBox(Box) MeterWallPressure
setBox(Box) P1Sinusoidal
setBox(Box) AtomTestChainLength
setBox(Box) MeterPressure2
setBox(Box) MoleculeIteratorAll
Sets the box containing the molecules for iteration.
setBox(Box) MoleculeIteratorAllMolecules
Sets the box having the molecules to be returned as iterates.
setBox(Box) MoleculeIteratorMolecule
Sets the box containing the molecules for iteration.
setBox(Box) MoleculesetIteratorBoxDependent
Sets the Box to pull iterates from
setBox(Box) MpiInterspecies1A
Configures iterator to return molecules from the set species in the given
box.
setBox(Box) MpiInterspeciesAA
Configures iterator to return molecules from the set species in the given
box.
setBox(Box) MpiIntraspecies1A
Configures iterator to return molecules from the set species in the given
box.
setBox(Box) MpiIntraspeciesAA
Configures iterator to return molecules from the set species in the given
box.
setBox(Box) MpiMolecule
Specifies the box from which iterates are taken.
setBox(Box) MoleculeSource
sets the Box the source should pull Atoms from.
setBox(Box) MoleculeSourceRandomMolecule
setBox(Box) MoleculeToMoleculeListSpecies
setBox(Box) Mpi1ACell
setBox(Box) CriterionAdapter
Specifies to the wrapped criterion the box where the criterion is being
applied.
setBox(Box) CriterionAll
Performs no action.
setBox(Box) CriterionNone
Performs no action.
setBox(Box) CriterionPositionWall
setBox(Box) CriterionSimple
setBox(Box) CriterionAdapterMolecular
Specifies to the wrapped criterion the box where the criterion is being
applied.
setBox(Box) CriterionAllMolecular
Performs no action.
setBox(Box) CriterionSimpleMolecular
setBox(Box) NeighborCriterionMolecular
Specifies the box where the criterion is being applied.
setBox(Box) NeighborCriterion
Specifies the box where the criterion is being applied.
setBox(Box) Api1ASite
setBox(Box) DeviceCellNum3DSlider
setBox(Box) DeviceCellNumXYSlider
setBox(Box) MCMoveAtomCoupled
setBox(Box) MCMoveAtomCoupledBennet
setBox(Box) MCMoveAtomCoupledUmbrella
setBox(Box) MCMoveAtomSuperBox
setBox(Box) MCMoveHarmonic
setBox(Box) MCMoveHarmonicStep
setBox(Box) MCMoveMoleculeCoupled
setBox(Box) MCMoveRotateMoleculePhiTheta
setBox(Box) MCMoveSingleMode
setBox(Box) MCMoveVolumeMonoclinic
setBox(Box) MCMoveVolumeMonoclinicAngle
setBox(Box) MCMoveVolumeMonoclinicScaled
setBox(Box) MCMoveVolumeSolid
setBox(Box) MCMoveVolumeSolidNPTMolecular
setBox(Box) MCMoveWV
setBox(Box) MeterAPIPotentialEnergy
setBox(Box) MeterHarmonicSingleEnergy
setBox(Box) MeterNormalMode
Sets the box, and should be called while the Atoms are in
their lattice positions.
setBox(Box) MeterOverlapSwitch
setBox(Box) MeterPhiDeviation
setBox(Box) MeterPlaneSlip
setBox(Box) MeterThetaDeviation
setBox(Box) MeterTilt
setBox(Box) MeterTiltHistogram
setBox(Box) MeterTiltRotation
setBox(Box) MeterTiltRotationHistogram
setBox(Box) MeterTiltRotationStdev
setBox(Box) P1ConstraintNbr
setBox(Box) P1ConstraintNbrHcp
setBox(Box) P2XOrder
setBox(Box) PotentialCalculationSolidSuper
setBox(Box) PotentialCalculationSolidSuperCut
setBox(Box) SimEinStep2.MeterPotentialEnergyComposite
setBox(Box) SimEinStep2HCP.MeterPotentialEnergyComposite
setBox(Box) SimOverlapSoftSphereEin.MeterPotentialEnergyComposite
setBox(Box) SimOverlapSoftSphereEinHarm.MeterPotentialEnergyComposite
setBox(Box) MCMoveGeometricCluster
setBox(Box) PotentialDepletion
setBox(Box) P2HardSpherePoly
setBox(Box) EwaldSummation.P2EwaldReal
setBox(Box) EwaldSummation
setBox(Box) EwaldSumMolecules
setBox(Box) IPotential
Informs the potential of the box on which it acts so that it can
properly consider the boundaries.
setBox(Box) P1ExternalField
setBox(Box) P1HardBoundary
setBox(Box) P1HarmonicSite
setBox(Box) P1HydrogenMielke
setBox(Box) P22CLJmuQ
setBox(Box) P22CLJQ
setBox(Box) P2CO2EMP
setBox(Box) P2DiscreteFeynmanHibbs
setBox(Box) P2DLPOLY
setBox(Box) P2EffectiveFeynmanHibbs
setBox(Box) P2HardAssociationCone
setBox(Box) P2HardAssociationConeDoubleSites
setBox(Box) P2HardAssociationConeFourSites
setBox(Box) P2HardAssociationConeFourSitesSW
setBox(Box) P2HardAssociationConeOneSite
setBox(Box) P2HardAssociationConeReference
setBox(Box) P2HardAssociationConeReferenceFourSites
setBox(Box) P2HardAssociationConeSW
setBox(Box) P2HardBondedList
setBox(Box) P2HardWrapper
setBox(Box) P2HC2Yukawa
setBox(Box) P2HePCKLJS.P2HeQFH
setBox(Box) P2HePCKLJS.P2HeTI
setBox(Box) P2HeSimplified.P2HeQFH
setBox(Box) P2HeSimplified.P2HeTI
setBox(Box) P2HSDipole
setBox(Box) P2HydrogenHinde
setBox(Box) P2HydrogenHindeAtomic
setBox(Box) P2HydrogenHindePatkowski
setBox(Box) P2HydrogenHindePatkowskiAtomic
setBox(Box) P2HydrogenPatkowski
setBox(Box) P2HydrogenPatkowskiAtomic
setBox(Box) P2Ideal
Does nothing.
setBox(Box) P2LJDipole
setBox(Box) P2LJQ
setBox(Box) P2LJQQ
setBox(Box) P2MoleculeMonatomic
setBox(Box) P2MoleculeSoftTruncatedSwitched
setBox(Box) P2MoleculeTruncated
setBox(Box) P2NitrogenHellmann.P2N2QFH
setBox(Box) P2NitrogenHellmann
setBox(Box) P2O2Bartolomei.P2O2TI
setBox(Box) P2O2Bartolomei
setBox(Box) P2QChem
setBox(Box) P2ReactionFieldDipole
setBox(Box) P2ReactionFieldDipoleTruncated.P0ReactionField
setBox(Box) P2ReactionFieldDipoleTruncated
setBox(Box) P2SemiclassicalAtomic
setBox(Box) P2SemiclassicalMolecular
setBox(Box) P2SoftSphericalTruncated
setBox(Box) P2SoftSphericalTruncatedSwitched
setBox(Box) P2SoftTruncated
setBox(Box) P2SpheroPolyhedron
setBox(Box) P2SquareWellRobust
setBox(Box) P2TriangleWell
setBox(Box) P2WaterPotentialsJankowski
setBox(Box) P2WCAP
setBox(Box) P3AxilrodTeller
setBox(Box) P3BondAngle
setBox(Box) P3BondAngleDreiding
setBox(Box) P3CPSNonAdditiveHe
setBox(Box) P3CPSNonAdditiveHeLessSimplified
setBox(Box) P3CPSNonAdditiveHeOrig
setBox(Box) P3CPSNonAdditiveHeSimplified
setBox(Box) P3HydrogenATM
setBox(Box) P3HydrogenManzhos
setBox(Box) P3Induction
setBox(Box) P3NitrogenHellmannNonAdditive
setBox(Box) P4BondTorsion
setBox(Box) P4BondTorsionAlkaneXCCH
setBox(Box) P4TorsionDreiding
setBox(Box) Potential
Informs the potential of the box on which it acts.
setBox(Box) Potential0Lrc
setBox(Box) Potential1
setBox(Box) Potential2HardSpherical
setBox(Box) Potential2SoftSpherical
setBox(Box) Potential2SoftSphericalLS
setBox(Box) PotentialAtomicSum
setBox(Box) PotentialCalculationPressureTensor
setBox(Box) PotentialDLPOLY
setBox(Box) PotentialEmul
setBox(Box) PotentialGroup
setBox(Box) PotentialMaster.MoleculeIterator0
setBox(Box) PotentialMolecular
Informs the potential of the box on which it acts.
setBox(Box) PotentialMolecularMonatomic
setBox(Box) PotentialMolecularSum
setBox(Box) PotentialNonAdditiveDifference
setBox(Box) P2LJDipole
setBox(Box) Boundary
Sets the box that holds the boundary.
setBox(Box) MCMoveSpinCluster
setBox(Box) MeterSpinMSquare
setBox(Box) P2Spin
does nothing
setBox(Box) MCMoveSpinFlip
setBox(Box) MeterSpin
setBox(Box) P2Spin
setBox(Box) MCMoveBondLength
setBox(Box) MCMoveClusterBondLength
setBox(Box) MCMoveClusterRotateArm
setBox(Box) MCMoveRotateArm
setBox(Box) MCMoveWiggle
setBox(Box) P2HSPolymer
setBox(Box) ClusterSumIC.FR2
setBox(Box) MayerD2FDT2Spherical
setBox(Box) MayerDFDTSpherical
setBox(Box) MayerDFQFHDTSpherical
setBox(Box) MayerEGeneral
setBox(Box) MayerEHardSphere
setBox(Box) MayerENonGeneral
setBox(Box) MayerESpherical
setBox(Box) MayerFunction
setBox(Box) MayerFunctionMolecularThreeBody
setBox(Box) MayerFunctionNonAdditive
setBox(Box) MayerFunctionNonAdditiveFull
setBox(Box) MayerFunctionProductGeneral
setBox(Box) MayerFunctionSphericalThreeBody
setBox(Box) MayerFunctionSum
setBox(Box) MayerFunctionSumGeneral
setBox(Box) MayerFunctionTemperature
setBox(Box) MayerFunctionThreeBody
setBox(Box) MayerGeneral
setBox(Box) MayerGeneralAtomic
setBox(Box) MayerGeneralSpherical
setBox(Box) MayerHardSphere
setBox(Box) MayerHSMixture
setBox(Box) MayerPTAtt
setBox(Box) MayerPUGeneral
setBox(Box) MayerSphericalPlus
setBox(Box) MayerSphericalPTAtt
setBox(Box) MayerSSSeries
setBox(Box) MayerWell
setBox(Box) MayerXSpherical
setBox(Box) MCMoveChangeBondLength
setBox(Box) MCMoveClusterAngleBend
setBox(Box) MCMoveClusterAngleBendAceticAcid
setBox(Box) MCMoveClusterAtom
setBox(Box) MCMoveClusterAtomDiscrete
setBox(Box) MCMoveClusterAtomHSRing
setBox(Box) MCMoveClusterAtomHSTree
setBox(Box) MCMoveClusterAtomMulti
setBox(Box) MCMoveClusterAtomQ
setBox(Box) MCMoveClusterAtomRotateMulti
setBox(Box) MCMoveClusterDiagram
setBox(Box) MCMoveClusterMoleculeMulti
setBox(Box) MCMoveClusterPolyhedraTree
setBox(Box) MCMoveClusterReptateMulti
setBox(Box) MCMoveClusterRingPartialRegrow
setBox(Box) MCMoveClusterRingRegrow
setBox(Box) MCMoveClusterRingRegrowExchange
setBox(Box) MCMoveClusterRingRegrowOrientation
setBox(Box) MCMoveClusterRingScale
setBox(Box) MCMoveClusterRotateCH3
setBox(Box) MCMoveClusterRotateMoleculeMulti
setBox(Box) MCMoveClusterTorsionAlkaneEH
setBox(Box) MCMoveClusterTorsionMulti
setBox(Box) MCMoveClusterWiggleAceticAcid
setBox(Box) MCMoveClusterWiggleAlkaneEH
setBox(Box) MCMoveClusterWiggleMulti
setBox(Box) MuFGeneral
setBox(Box) MuGeneral
setBox(Box) P1IntraLambda
setBox(Box) PotentialCommonAtomic
setBox(Box) PotentialEmulCached
setBox(Box) PotentialGroup3PI.PotentialGroup3PISkip
setBox(Box) PotentialGroup3PI
setBox(Box) PotentialGroupPI.PotentialGroupPISkip
setBox(Box) PotentialGroupPI
setBox(Box) PotentialNonAdditive.PotentialNonAdditiveNB
setBox(Box) PotentialNonAdditive
setBox(Box) VirialB2WaterTIP4P_DHS_difference.MuDeltaEBond
setBox(Box) VirialB2WaterTIP4P_DHS_difference.P2WaterDHS
setBox(Box) VirialB3C1TIP4Pwater.MuFBond
setBox(Box) VirialB3C2TIP4Pwater.fPlusBetaEU
setBox(Box) VirialB3C2TIP4Pwater.MuProduct
setBox(BoxCluster) ClusterWeightSumWall.DataSourceClusterWall
setBox(BoxCluster) MeterSamplingWeight
setBox(BoxCluster) MeterVirial
setBox(BoxCluster) MeterVirialBD
setBox(BoxCluster) MeterVirialBDBin
setBox(BoxCluster) MeterVirialBDBinMultiThreaded
setBox(BoxCluster) MeterVirialBinMultiThreaded
setBox(BoxCluster) MeterVirialEBinMultiThreaded
setBox(BoxCluster) MeterVirialExternalField
setBox(BoxCluster) MeterVirialExternalFieldConfined
setBox(BoxCluster) MeterVirialExternalFieldOverlapConfined
setBox(BoxCluster) MeterVirialExternalFieldOverlapConfinedRho
setBox(BoxCluster) MeterVirialExternalFieldOverlapConfinedSW
setBox(BoxCluster) MeterVirialExternalFieldOverlapRho
setBox(BoxCluster) MeterVirialExternalFieldRho
setBox(BoxCluster) MeterVirialExternalFieldSW
setBox(BoxCluster) MeterVirialIC
setBox(BoxCluster) MeterVirialSWWE
setBoxCanvas(DisplayCanvas) DisplayBox
setBoxForCriteria(Box) PotentialMasterNbr
Sets the box for all NeighborCriterions
setBoxForPotentials(Box) PotentialMasterNbr
Sets the box for all ranged potentials
setBoxIndex(int) MeterMBAR
setBoxLength(double) SimulationVirial
setBoxLengths(double, double) SimulationVirialOverlap2
setBoxSize(Box, int[]) GrainBoundaryTiltConfiguration
Resizes simulation box to preserve periodic boundary conditions after rotation of lattice.
setBoxSize(Vector) Boundary
Scales the boundary dimensions such that the boundary's would be
inscribed within a rectangle of the of the given size.
setBoxSize(Vector) BoundaryDeformablePeriodic
Scales each boundary edge so that its length equals the corresponding value
in the given vector.
setBoxSize(Vector) BoundaryRectangular
Sets the size and shape of the rectangular boundary.
setBoxSize(Vector) BoundaryTruncatedOctahedron
setBPRes(double[]) MeterSolidDACut
setBXX(double) P2RepRowley
setC(double) P2Exp6
setC(double, double) MinimizeHCP
setCaching(boolean) ClusterSum
setCaching(boolean) ClusterSumPolarizable
setCaching(boolean) ClusterSumPolarizableWertheimProduct4Pt
setCaching(boolean) ClusterSumPolarizableWertheimProduct4PtFinal
setCapacity(int) AtomNeighborLists
Sets the number of up and down lists maintained by this instance.
setCapacity(int) AtomPotentialList
setCapacity(int) MoleculeNeighborLists
Sets the number of up and down lists maintained by this instance.
setCapacity(int) MoleculePotentialList
setCellDensity(double) HarmonicCrystalSsFccNxy
setCellRange(int) NeighborCellManagerMolecular
Sets the cell range to the given value.
setCellRange(int) NeighborCellManager
Sets the cell range to the given value.
setCellRange(int) PotentialMasterCell
setCellRange(int) PotentialMasterListMolecular
setCellRange(int) PotentialMasterList
setCellRange(int) PotentialMasterHybrid
setCellRange(int) PotentialMasterSite
setCellSize(double, double) P1Sinusoidal
setCellSizeX(double) ConfigurationCatalysis
setCellSizeX(double) ConfigurationSAM
setCellSizeZ(double) ConfigurationCatalysis
setCellSizeZ(double) ConfigurationSAM
setCenterOfRotation(Point3f) G3DSys
Set the molecule space location around which rotation occurs
setCH2element(ElementSimple) SimpleElementForSimilarSpecies
setCH3element(ElementSimple) SimpleElementForSimilarSpecies
setChainLength(int) ColloidSim
setChainLength(int) ConfigurationColloid
setChainLength(int) MeterEnd2End
setChainLength(int) NeighborListManagerColloid
setChainLength(int) P2HardSphereMC
setChainLength(int) P2SquareWellMonomer
setChainLength(int) SimulationRheology
setChainLength(int) Sam
setChainPhi(int, double) Sam
setChainPsi(double) Sam
setChainTheta(double) Sam
setCharge(double, int) MolecularModelEMP2_SpeciesCO2
setCharge(double, int) MolecularModelSPCE_SpeciesH2O
setCharge(double, int) MolecularModelTrappe_SpeciesCO2
setCharge1(double) P2Electrostatic
Sets the charge on the first type of atom.
setCharge1(double) P2ElectrostaticWithHardCore
Sets the charge on the first type of atom.
setCharge2(double) P2Electrostatic
Sets the charge on the second type of atom.
setCharge2(double) P2ElectrostaticWithHardCore
Sets the charge on the second type of atom.
setCloseFileEachTime(boolean) DataLogger
Close the file and open a new one at each time INTERVAL.
setCloseWindow(JButton) ViewAlertMsgBox
setCloseWindow(JButton) ViewAlkaneLengthSelection
setClusterFileOut(String) DataClusterer
setClusterNeighborDistance(double) DataClusterer
setColix(short) Graphics3D
sets current color from colix color index
setColix(short) GData
setColix(short) MeshSurface
setColixBack(short) MeshSurface
setCollapseOnReset(boolean) HistoryComplete
Sets a flag that determines if the history is collapsed (to 100 data
points) when reset is called.
setCollision(double, IAtomKinetic, PotentialHard) IntegratorHard.Agent
Sets parameters associated with next two-body collision of this atom with another atom.
setCollisionDiameter(double) P2HardSphere
Accessor method for collision diameter
setCollisionRadius(double) MeterOsmoticPressure
Sets the collision radius used to calculate accessible "area"
assuming that the relevant hard "boundaries" form right-angles with
other hard boundaries.
setCollisionRadius(double) P1HardWall
Distance from the center of the sphere to the boundary at collision.
setCollisionRadius(double) P1HardBoundary
Distance from the center of the sphere to the boundary at collision.
setCollisionRadius(double) P1HardMovingBoundary
Distance from the center of the sphere to the boundary at collision.
setColloidMonomerBondManager(AtomLeafAgentManager) ConfigurationColloid
setColloidSigma(double) ColloidSim
setColor(char) Edge
setColor(char) EdgeImpl
setColor(char) NodeImpl
setColor(char) Node
setColor(int) Graphics3D
setColor(int) GData
setColor(short) Axes
set the color of the figure
setColor(short) Ball
set the color of the figure
setColor(short) Box
set the color of the figure
setColor(short) Ellipse
set the color of the figure
setColor(short) Line
set the color of the figure
setColor(short) Triangle
set the color of the figure
setColor(AtomType, int, Color) ColorSchemeStepWise
Sets atoms of the given type and number of bonds to be the given color.
setColor(AtomType, Color) ColorSchemeByType
setColor(String) Plot
setColorIn(Color) ColorSchemePlane
Color for atoms that are in the plane.
setColorOut(Color) ColorSchemePlane
Color for atoms that are out of the plane.
setColors(Color[]) DisplayPlotXChart
setColorScheme(ConfigFromFileLAMMPS.ColorSchemeDeviation) ConfigFromFileLAMMPS.ModifierConfiguration
setColorScheme(ColorScheme) DisplayBox
Mutator method for the color scheme used for this display
setColumn(int, float[]) Matrix4f
Sets the specified column of this matrix4f to the four values provided.
setColumn(int, float, float, float) Matrix3f
Sets the specified column of this matrix3d to the three values provided.
setColumn4(int, float, float, float, float) Matrix4f
Sets the specified column of this matrix4f to the four values provided.
setColumnA(int, float[]) Matrix3f
Sets the specified column of this matrix3d to the four values provided.
setColumnHeader(DataTag[], String) DisplayTable
setColumnInfoFactories(DataDoubleArray.DataInfoDoubleArrayFactory[]) DataTable.DataInfoTableFactory
Sets the DataInfoFactories for the columns
setColumnNames(String[]) DeviceTableModelGeneric
setColumnV(int, Vector3f) Matrix3f
Sets the specified column of this matrix3d to the vector provided.
setCombinationProbability(double) P2SquareWellRadical
Sets the probability that two radicals will bond instead of becoming
unreactive.
setComponent(int) CalcGradientDifferentiable
setComponent(int, int, double) Tensor
setComponent(int, int, double) Tensor1D
setComponent(int, int, double) Tensor2D
setComponent(int, int, double) Tensor3D
setComponent(int, int, double) TensorND
setComponent(PNCO2GCPM.Component) PNCO2GCPM
setComponent(PNGCPM.Component) PNGCPM
setComponent(P2WaterSzalewicz.Component) P2WaterSzalewicz
setComponent(PNWaterGCPM.Component) PNWaterGCPM
setComponent(Object) DeviceSlider
setComponent(Object) DeviceSpinner
setComponentValues(String[][]) MolecularModelLJQ_SpeciesLJ
setConfigDLPOLY(WriteConfigurationDLPOLY) PotentialDLPOLY
setConfigIndex(int) AtomTestDeviation
setConfigIndex(int) ColorSchemeDeviation
setConfigIndex(int) ColorSchemeDirection
setConfigIndex(int) DisplayBoxCanvas2DGlass
setConfigIndex(int) DisplayBoxCanvas3DGlass
setConfigIndex(int) DisplayBoxCanvasGlass
setConfigIndex(int) MeterGs
setConfigP2DLPOLY(WriteConfigurationP2DLPOLY) P2DLPOLY
setConfigStorage(ConfigurationStorage) AtomTestDeviation
setConfigStorage(ConfigurationStorage) ColorSchemeDeviation
setConfigStorage(ConfigurationStorage) ColorSchemeDirection
setConfigStorage(ConfigurationStorage) DataSourcePrevTime
setConfigStorage(ConfigurationStorage) DisplayBoxCanvas2DGlass
setConfigStorage(ConfigurationStorage) DisplayBoxCanvas3DGlass
setConfigStorage(ConfigurationStorage) DisplayBoxCanvasGlass
setConfiguration(Configuration) SimulationRestart
setConfiguration(Configuration) CoordinateDefinitionNitrogen
setConfiguration(Configuration) CoordinateDefinitionNitrogenSuperBox
setConfiguration(Configuration) CoordinateDefinitionHSDimer
setConfName(String) WriteConfiguration
Sets the configuration name.
setConfName(String) WriteConfigurationBinary
Sets the configuration name.
setConfName(String) WriteConfigurationDLPOLY
Sets the configuration name.
setConfName(String) WriteConfigurationP2DLPOLY
Sets the configuration name.
setConformation(int, ConformationChainZigZag) ConfigurationSAM
setConformationsList(ArrayList<List<Vector>>) MCMoveClusterConformationMDTest
setConstrainScriptOrigin(boolean) SVGConverter
Sets whether scripts should only be loaded from the same
location as the documents referencing them.
setConstraint(P1ConstraintNbr) MeterBoltzmannHTTP
setConstraint(P1ConstraintNbr) MeterDDP
setConstraint(P1ConstraintNbr) MeterDP
setConstraint(P1ConstraintNbr) MeterTargetTP
setConstraint(IPotentialAtomic) MCMoveAtomCoupled
setConstraintAngle(double) MeterDirectInitPert
setConstraintAngle(double) PRotConstraint
setConstraintMap(int[]) MCMoveClusterMoleculeMulti
setConstraintMap(int[]) MCMoveClusterRotateMoleculeMulti
setConstructorObject(Integer) ModelSpeciesSelection
setContainingCubeEdgeLength(double) TruncatedOctahedron
Sets the size of the truncated octahedron in terms of the edge length of
a cube that would contain it.
setController(Controller) Device
setController(Controller) DeviceThermoSlider
Set the temperature slider controller.
setController(Controller) DeviceCellNum3DSlider
Set the n- Cell # slider controller.
setController(Controller) DeviceCellNumXYSlider
Set the x- and y- Cell # slider controller.
setController(Controller) DeviceWaveVectorSlider
Set the wavevector # slider controller.
setCoordinateDefinition(CoordinateDefinition) CalcJacobian
setCoordinateDefinition(CoordinateDefinition) MCMoveAtomCoupledBennet
setCoordinateDefinition(CoordinateDefinition) MCMoveAtomCoupledUmbrella
setCoordinateDefinition(CoordinateDefinition) MCMoveEinsteinCrystal
setCoordinateDefinition(CoordinateDefinition) MCMoveHarmonic
setCoordinateDefinition(CoordinateDefinition) MCMoveHarmonicStep
setCoordinateDefinition(CoordinateDefinition) MCMoveSingleMode
setCoordinateDefinition(CoordinateDefinition) MeterDDP
setCoordinateDefinition(CoordinateDefinition) MeterDP
setCoordinateDefinition(CoordinateDefinition) MeterNormalMode
Sets the object that defines the real-space generalized coordinates.
setCoreDiameter(double) P2SquareWellBonding
Accessor method for core diameter.
setCoreDiameter(double) P2SquareWellBondingCO
Accessor method for core diameter.
setCoreDiameter(double) P2SquareWellSurface
Accessor method for core diameter.
setCoreDiameter(double) P2SquareWellOneSide
Accessor method for core diameter.
setCoreDiameter(double) P2DoubleWell
Accessor method for core diameter.
setCoreDiameter(double) P2PenetrableSphere
Mutator method for core diameter.
setCoreDiameter(double) P2PenetrableSquareWell
Accessor method for core diameter.
setCoreDiameter(double) P2SquareWell
Accessor method for core diameter.
setCoreDiameter(double) P2SquareWellRobust
Accessor method for core diameter.
setCoreDiameter(double) P2TriangleWell
setCoreDiameterSquared(double) P2PenetrableSquareWell
setCountOfMoleculesStrings(String[]) ModelSpeciesSelection
setCountOfSpeciesSLM(SpinnerListModel, int) ViewSpeciesSelection
setCountOfSpeciesSLMListener(ChangeListener[]) ViewSpeciesSelection
setCountSpecies(int, int) ModelSimulationEnvironment
setCoupling(double) P2Spin
set the coupling parameter J
setCoupling(double) P2Spin
setCriterion(AtomType, AtomType, NeighborCriterion) PotentialMasterNbr
Sets the criterion associated with the given pair of atom types, overriding
the default provided by the PotentialMasterList.
setCriterion(IPotentialMolecular, NeighborCriterionMolecular) PotentialMasterListMolecular
Sets the criterion associated with the given potential, overriding the
default provided by the PotentialMasterList.
setCriterion(IPotentialMolecular, NeighborCriterionMolecular) PotentialArrayMolecular
Sets the criterion associated with the given potential
setCriterion(IPotential, NeighborCriterion) PotentialArray
Sets the criterion associated with the given potential
setCriterion1Body(IPotentialAtomic, AtomType, NeighborCriterion) PotentialMasterNbr
Sets the criterion associated with the given 1-body potential, overriding
the default provided by the PotentialMasterList.
setCSPotential(P2SquareWellSurface) P2SquareWellBondingCO
setCubicSize(double) PrimitiveBcc
Sets the length of all primitive vectors to the given value.
setCubicSize(double) PrimitiveFcc
Sets the length of all primitive vectors to the given value.
setCubicSize(double) PrimitiveTrigonal
Sets the length of all primitive vectors to the given value.
setCursor(int, Object) ApiPlatform
setCursor(int, Object) Platform
setCutoff(double) MeterStructureFactor
Sets the wave vector cutoff.
setCutoff(double) AtomTestLiquid
setCutoff(double, double) P2EAM
setCutOffDistance(double) PNWaterGCPMReactionField
setCutoffFactorLJ(double) P2HardAssociationCone
Accessor method for Lennard-Jones cutoff distance; divided by sigma
setCutoffFactorLJ(double) P2HardAssociationConeDoubleSites
Accessor method for Lennard-Jones cutoff distance; divided by sigma
setCutoffFactorLJ(double) P2HardAssociationConeFourSites
Accessor method for Lennard-Jones cutoff distance; divided by sigma
setCutoffFactorLJ(double) P2HardAssociationConeFourSitesSW
Accessor method for Lennard-Jones cutoff distance; divided by sigma
setCutoffFactorLJ(double) P2HardAssociationConeOneSite
Accessor method for Lennard-Jones cutoff distance; divided by sigma
setCutoffFactorLJ(double) P2HardAssociationConeSW
Accessor method for Lennard-Jones cutoff distance; divided by sigma
setCutoffRatio(double) P2MoleculeTruncated
setCutoffRatio(double) P2ReactionFieldDipoleTruncated
setCVector(Vector) BoxInflateAnisotropic
setCXX(double) P2RepRowley
setD(float) Ball
set the molspace diameter of the figure, when applicable
setD(float) Bond
set the molspace diameter of the figure, when applicable
setD(float) Ellipse
set the molspace diameter of the figure, when applicable
setD2dfac(double) AkimaSplineSmoother
sets weight given to minimizing discontinuities in the 2nd derivative
(at data points)
setD2fac(double) AkimaSplineSmoother
sets weight given to minimizing the 2nd derivative
setD3dfac(double) AkimaSplineSmoother
setD3fac(double) AkimaSplineSmoother
sets weight given to minimizing the 3nd derivative
setDampingParams(int, int, double, int, boolean) P2QChemInterpolated
The energy u.
setData(double[]) FastFourierTransform
For passing only one set of data - assumes passing all reals
setData(double[], boolean) FastFourierTransform
For passing only all reals (true) or all imaginaries (false)
setData(double[], double[]) FastFourierTransform
Saves the two passed arrays of doubles into this class, real and
imaginary in order to transform.
setData(int, double) DataCollector
setData(IData) DataAndInfo
setDataInfo(IDataInfo) DataAndInfo
setDataResetAction(SimulationDataAction) SimulationRestart
setDataSink(int, IDataSink) DataDistributer
Sets the DataSink for the ith output stream (corresponding to the ith
numerical value coming in).
setDataSink(int, IDataSink) DataGroupSplitter
Sets the DataSink for the ith output stream (corresponding to the ith
numerical value coming in).
setDataSink(int, IDataSink) DataSplitter
Sets the DataSink for the ith output stream (corresponding to the ith
numerical value coming in).
setDataSink(IDataSink) DataFork
Sets the given DataSink as the only one connected to this DataFork.
setDataSink(IDataSink) DataLogger
setDataSink(IDataSink) DataPipe
Sets the DataSink that will receive data from this DataPipe.
setDataSink(IDataSink) DataProcessor
Sets the sink receiving the data.
setDataSink(IDataSink) DataProcessorForked
setDataSinkFactory(DataSplitter.IDataSinkFactory) DataSplitter
setDataSinks(IDataSink[]) DataFork
setDataSinks(IDataSink[]) DataPipeForked
Sets the list of DataSinks that receive the Data entering this DataFork.
setDataSinks(IDataSink[]) DataProcessorForked
setDataSource(DataSourceMolecular) MeterProfileByAtoms
Accessor method for the meter that defines the profiled quantity.
setDataSource(DataSourceMolecular) MeterProfileByVolume
Accessor method for the meter that defines the profiled quantity.
setDataSource(DataSourcePositioned) MeterProfile
Accessor method for the meter that defines the profiled quantity.
setDataSourceMuRoot(DataSourceMuRoot) DataSourceAvgPressure2
setDecimalMode() ScientificFormat
setDecimalSeparatorAlwaysShown(boolean) ScientificFormat
setDecimalSliderLabelTable(Hashtable) DecimalSlider
setDecimalSliderMajorTickSpacing(double) DecimalSlider
setDecimalSliderMaximum(double) DecimalSlider
setDecimalSliderMinimum(double) DecimalSlider
setDecimalSliderMinorTickSpacing(double) DecimalSlider
setDecimalSliderValue(double) DecimalSlider
setDefaultColor(Color) ColorScheme
setDefaultDaDef(double) MCMoveIDBiasAction
setDefaultFontFamily(String) SVGConverter
Sets the defaultFontFamily value.
setDefaultLabel(String) DisplayTextBox
Sets label to the given value if it was not previously set.
setDefaultRotation() G3DSys
Rescales slab and depth after image shell mode is toggled
or the number of layers changed.
setDefaultUnit(Unit) DisplayPlotXChart
setDeformation(double) ConfigurationDroplet
setDegeneracy(int[]) PermutationDegenerateIterator
Invokes setDegeneracy(degeneracy, degeneracy.length), thus using all elements of given array.
setDegeneracy(int[], int) PermutationDegenerateIterator
Sets parameter that describes number of duplicate elements in the
iterates.
setDelayExponent(double) DeviceDelaySlider
setDeltaCut(double) ClusterSumNonAdditiveTrimerEnergy
setDeltaCut(double) ClusterSumPolarizable
setDeltaCut(double) ClusterSumPolarizableWertheimProduct
setDeltaCut(double) ClusterSumPolarizableWertheimProduct4Pt
setDeltaCut(double) ClusterSumPolarizableWertheimProduct4PtFinal
setDeltaTmax(int) MSDProcessor
Allows for a new value of deltaTmax.
setDeltaX(double) HistogramExpanding
setDenominator(int) Coefficient
setDenominator(int) CoefficientImpl
setDensity(double) Box
Uses BoxInflate to adjust the volume to the specified density.
setDensityProfileDump(IDataSource) DataProcessorChemicalPotential
setDepth(double) DisplayBoxCanvasG3DSys
Set depth percentage
setDepth(double) DisplayPolytopeCanvasG3DSys
Set depth percentage
setDepth(int) GData
clipping from the front and the back
setDepthPercent(float) G3DSys
setDescription(JTextArea) ViewSpeciesSelection
setDescription(JTextArea) ViewSpeciesSelection
setDestination(Vector) MoleculeActionTranslateTo
setDestinationType(DestinationType) SVGConverter
Sets the destinationType attribute value.
setDiagram(int) ClusterSumStickyEF
setDiagramSampling(boolean) ClusterDiagramTree
setDiameter(AtomType, double) DiameterHashByType
setDiameter(String, double) DiameterHashByElement
setDiameter(String, double) DiameterHashByElementType
setDiameterHash(DiameterHash) DisplayBox
Sets the DiameterHash used by this DisplayBox.
setDielectric(double) P2ReactionFieldDipole
setDielectric(double) P2ReactionFieldDipoleTruncated
Sets the dielectric constant of the fluid surrounding the cavity.
setDiffusePercent(int) GData
df in I = df * (N dot L) + sf * (R dot V)^p
setDim(Dimension) UnitGraphics
setDimension(Dimension) DataInfoFactory
Sets the dimension
setDimension(Dimension) IDataInfoFactory
Sets the dimension
setDimensions(int, int, int, int, int, int, double, double, double, double, double, double) GrainBoundaryConfiguration
setDimensions(Tensor) BoundaryDeformablePeriodic
Sets the boundary tensor to equal the given tensor.
setDimensions(Vector) CellLattice
setDims(int[]) MeterNormalStress
setDimx(int) NormalModeAnalysisDisplay2D
setDimy(int) NormalModeAnalysisDisplay2D
setDipole(double) P2HSDipole
setDipole(double) P2LJDipole
setDipoleMomentSquare(double) P2LJDipole
setDipoleSource(DipoleSource) MeterDipoleSumSquaredMappedAverage
setDipoleSource(DipoleSource) P1ExternalField
setDipoleSource(DipoleSource) P2ReactionFieldDipole
setDipoleSource(DipoleSource) P2ReactionFieldDipoleTruncated
Sets the dipole source used by this object should use.
setDipoleSource(DipoleSource) PotentialCalculationFSum
setDipoleSource(DipoleSource) PotentialCalculationPhiSum
setDipoleSource(DipoleSource) PotentialCalculationFSum
setDipoleStrength(double) DipoleSourceWater
Sets the strength (magnitude) of the dipole.
setDirection(IteratorDirective.Direction) ApiIntragroup
Specifies the direction, which applies only if iterating pairs
with a target atom; otherwise, if all pairs from group are indicated,
direction is ignored.
setDirection(IteratorDirective.Direction) AtomsetIteratorDirectable
setDirection(IteratorDirective.Direction) MCMoveInsertDeleteLatticeVacancy.AtomIteratorBruteForce
setDirection(IteratorDirective.Direction) MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbr
setDirection(IteratorDirective.Direction) MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbrCell
setDirection(IteratorDirective.Direction) RectangularLatticeNbrIterator
Sets the iterator to return only up-list neighbors or down-list neighbors.
setDirection(IteratorDirective.Direction) MoleculeIteratorAll
Has no effect, but is included as part of the AtomsetIteratorPDT interface.
setDirection(IteratorDirective.Direction) MoleculeIteratorMolecule
Has no effect, but is included as part of the AtomsetIteratorPDT interface.
setDirection(IteratorDirective.Direction) MpiInterspecies1A
Indicates allowed direction for iteration, relative to specified target
atom.
setDirection(IteratorDirective.Direction) MpiIntraspecies1A
Specifies the direction, which applies only if iterating pairs
with a target atom; otherwise, if all pairs from group are indicated,
direction is ignored.
setDirection(IteratorDirective.Direction) MpiMolecule
Specifies the direction from which partners of a target atoms
are taken to form iterates.
setDirection(IteratorDirective.Direction) Api1ACell
Indicates allowed direction for iteration, relative to specified target
atom.
setDirection(IteratorDirective.Direction) Mpi1ACell
Indicates allowed direction for iteration, relative to specified target
atom.
setDirection(IteratorDirective.Direction) Api1ASite
Indicates allowed direction for iteration, relative to specified target
atom.
setDirection(IteratorDirective.Direction) IteratorDirective
setDirection(IteratorDirective.Direction) PotentialMaster.MoleculeIterator0
setDirection(Vector) IOrientation
Sets this orientation to point in the given direction.
setDirection(Vector) Orientation1D
setDirection(Vector) Orientation2D
setDirection(Vector) Orientation3D
Sets this orientation to point in the given direction.
setDirection(Vector) OrientationFull3D
Sets this orientation to point in the given direction.
setDirection(Vector) P1MagneticField
setDirections(Vector, Vector) IOrientationFull3D
Sets the orientation's primary and secondary direction to be the given
directions.
setDirections(Vector, Vector) OrientationFull3D
setDisp(boolean) P2QChemInterpolated
setDisplayDensity(double) ColorSchemeScaledOverlap
setDisplayDensity(double) DisplayBoxCanvas2DNpTScaling
setDisplayDensity(double) HSNPT2DGraphic
setDistanceToOrigin(double) Plane
Sets perpendicular distance from the plane to the origin.
setDoAbs(boolean) ClusterWeightAbs
Sets the cluster to actually return the |value| (as default) or just value.
setDoAdjustOnTime(boolean) IntegratorOverlap
If true, causes the integrator to optimize how much each system runs
based on the wall clock time needed to run steps in each system.
setDoApplyPBC(boolean) WriteConfiguration
Directs the writer to apply periodic boundary conditions or not (true
by default).
setDoApplyPBC(boolean) WriteConfigurationBinary
Directs the writer to apply periodic boundary conditions or not (true
by default).
setDoApplyPBC(boolean) WriteConfigurationDLPOLY
Directs the writer to apply periodic boundary conditions or not (true
by default).
setDoApplyPBC(boolean) WriteConfigurationP2DLPOLY
Directs the writer to apply periodic boundary conditions or not (true
by default).
setDoApplyPBC(boolean) NeighborCellManagerMolecular
setDoApplyPBC(boolean) NeighborCellManager
setDoApplyPBC(boolean) NeighborListManagerMolecular
setDoApplyPBC(boolean) NeighborListManager
setDoAveraging(boolean) HistogramNotSoSimple
turns "averaging" on or off.
setDoCaching(boolean) ClusterWheatleySoft
setDoCaching(boolean) ClusterWheatleySoftBD
setDoCaching(boolean) ClusterWheatleySoftDerivatives
setDoCaching(boolean) ClusterWheatleySoftDerivativesBD
setDoClear(boolean) DisplayPlot
setDoConfigButton(boolean) PistonCylinderGraphic
Enable the config (and velocity) buttons.
setDoCov(boolean) MeterVirialEBinMultiThreaded
setDodebug(boolean) PNWaterGCPMReactionField
setDoDensityInput(boolean) PistonCylinderGraphic
Enable the RDF plot.
setDoDisconnectedMatching(boolean) VirialDiagrams
setDoDisconnectedMatching(boolean) VirialDiagramsMix2
setDoDisconnectedMatching(boolean) VirialDiagramsPT
setDoDouble(boolean) MeterNormalStress
setDoDrawLines(DataTag[], boolean) DisplayPlot
Sets the data set corresponding to the given tags to be have the data
points connected with lines or not.
setDoDrawLines(DataTag[], boolean) DisplayPlotXChart
setDoEnforceBounds(boolean) DataSourceUniform
setDoExchange(boolean) VirialDiagrams
setDoExchange(boolean) VirialDiagramsPT
setDoExchange(boolean[]) MCMoveChangeBondLength
setDoExchange(boolean[]) MCMoveClusterRingRegrowOrientation
setDoExchangeCondensing(boolean) VirialDiagrams
Turn on replacement of exchanged groups of nodes with a single node (of
a different color)
setDoExchangeCondensing(boolean) VirialDiagramsPT
Turn on replacement of exchanged groups of nodes with a single node (of
a different color)
setDoExchangeF(boolean) VirialDiagrams
Turn on replacement of eBonds with bonds that represent a single fBond
between an exchange group and another molecule (or another exchange
group).
setDoExchangeF(boolean) VirialDiagramsPT
Turn on replacement of eBonds with bonds that represent a single fBond
between an exchange group and another molecule (or another exchange
group).
setDoExcludeBogusConfigs(boolean) MeterVirialBDBinMultiThreaded
setDoExcludeBogusConfigs(boolean) MeterVirialBinMultiThreaded
setDoExcludeNonNeighbors(boolean) MCMoveMoleculeCoupledInitPert
Configures the move to not explicitly calculate the potential for atom
pairs that are not neighbors (as determined by the potentialMaster).
setDoExcludeNonNeighbors(boolean) MCMoveAtomCoupled
Configures the move to not explicitly calculate the potential for atom
pairs that are not neighbors (as determined by the potentialMaster).
setDoExcludeNonNeighbors(boolean) MCMoveMoleculeCoupled
Configures the move to not explicitly calculate the potential for atom
pairs that are not neighbors (as determined by the potentialMaster).
setDoExp(boolean) VirialDiagramsPT
setDoFastButton(boolean) PistonCylinderGraphic
setDoHB(boolean) VirialDiagrams
Enable construction of diagrams from the Hellmann-Bich formulation
setDoHB(boolean) VirialDiagramsPT
Enable construction of diagrams from the Hellmann-Bich formulation
setDoImposePBC(boolean) MCMoveClusterAtomMulti
setDoIncludeCoefficients(boolean) GraphMap
setDoKeepEBonds(boolean) VirialDiagrams
setDoKeepEBonds(boolean) VirialDiagramsMix
setDoKeepEBonds(boolean) VirialDiagramsMix2
setDoKeepEBonds(boolean) VirialDiagramsPT
setDoLegend(boolean) DisplayPlot
Mutator for flag determining if a legend is to be shown.
setDoLegend(boolean) DisplayPlotXChart
setDoMinimalBC(boolean) VirialDiagrams
setDoMinimalBC(boolean) VirialDiagramsMix
setDoMinimalBC(boolean) VirialDiagramsPT
setDoMinimalMulti(boolean) VirialDiagrams
Only include graphs with nonadditive bonds.
setDoMinimalMulti(boolean) VirialDiagramsMix
setDoMinimalMulti(boolean) VirialDiagramsPT
setDoMobileOnly(boolean) AtomTestDeviation
setDoMultiFromPair(boolean) VirialDiagrams
setDoMultiFromPair(boolean) VirialDiagramsPT
setDoNegativeExchange(boolean) VirialDiagrams
setDoNegativeExchange(boolean) VirialDiagramsPT
setDoNMoleculeSlider(boolean) PistonCylinderGraphic
Enable the # of molecules slider.
setDoNonEquilibrium(boolean) PotentialCalculationPressureTensor
setDoPBC(boolean) BoundaryDeformablePeriodicSwitch
setDoPBC(boolean) BoundaryRectangularPeriodicSwitch
setDoPrevious(boolean) ConfigFromFileLAMMPS.ModifierConfiguration
setDoRDF(boolean) PistonCylinderGraphic
Enable the RDF plot.
setDoReeHoover(boolean) MayerIonicDiagram1qbond
setDoReeHoover(boolean) MayerIonicDiagram2qbonds
setDoReeHoover(boolean) MayerIonicDiagram4qbonds
setDoReeHoover(boolean) VirialDiagrams
setDoReeHoover(boolean) VirialDiagramsMix
setDoReeHoover(boolean) VirialDiagramsMix2
setDoReeHoover(boolean) VirialDiagramsPT
setDoReeHoover(boolean) WertheimDiagrams3SiteRho
setDoResetFilter(boolean) ColorSchemeLiquidVapor
setDoScaling(boolean) MeterTargetRPMolecule
setDoSecondDerivative(boolean) PotentialCalculationSolidSuper
setDoShortcut(boolean) MayerIonicDiagram1qbond
setDoShortcut(boolean) MayerIonicDiagram2qbonds
setDoShortcut(boolean) MayerIonicDiagram4qbonds
setDoShortcut(boolean) VirialDiagrams
setDoShortcut(boolean) VirialDiagramsMix
setDoShortcut(boolean) VirialDiagramsMix2
setDoShortcut(boolean) VirialDiagramsPT
setDoShortcut(boolean) WertheimDiagrams2SiteRho
setDoShortcut(boolean) WertheimDiagrams3SiteRho
setDoShowCorrelation(boolean) DisplayTextBoxesCAE
setDoShowCurrent(boolean) DisplayTextBoxesCAE
setDoSubtractAvg(double) AtomSignalKineticEnergy
setDoThermalizeMembrane(boolean, ISpecies, IRandom) IntegratorDCVGCMD
setDoTotal(boolean) ClusterWheatleyMultibody
setDoTotal(boolean) ClusterWheatleyMultibodyBD
setDoVelocity(boolean) ConfigurationStorage
setDoWiggle(boolean) SimulationVirial
setDoWiggle(boolean) SimulationVirialOverlap2
setDrawable(boolean) Figure
setDrawable(boolean) ImageShell
setDrawBoundary(int) DisplayCanvas
setDrawBoundaryType(int) ImageShell
Sets the boundary drawing style
setDrawDisplacement(boolean) DisplayBoxCanvas2DGlass
setDrawDisplacement(boolean) DisplayBoxCanvas3DGlass
setDrawDisplacement(boolean) DisplayBoxCanvasGlass
setDrawingHeight(int) DisplayBox
Set the height of the drawing area (only relevant for 1D)
setDrawingThickness(int) P1HardBoundary
setDrawNumbersOfBlack(boolean) MyApplet.Starter
setDrawNumbersOfWhite(boolean) MyApplet.Starter
setDrawOverflow(boolean) DisplayBox
setDrawPoints(boolean) MyApplet.Starter
setDrString(double) ColorSchemeDeviation
setDst(File) SVGConverter
When converting a single source, dst can be a file.
setDSVO(DataSourceVirialOverlap) IntegratorOverlap
Deprecated.
Sets the DataSource that retrieves data from both boxs and provides
information to the integrator about their progress.
setDumpIndex(int) GlassGraphic.MeterFromDumps
setDv(double) P2Cohesion
setDynamic(boolean) SpeciesBuilder
setEdgeLength(double) Cube
setEdgeLength(double) Square
setEdgeLength(double) TruncatedOctahedron
Specifies the common length of all edges of the truncated octahedron.
setEdgeLengths(double, double) Rectangle
setEdgeLengths(double, double, double) Cuboid
Sets the lengths of all edges of the cuboid.
setEdgeLengths(Vector) Cuboid
Sets the three edge lengths of the cuboid, taking
each element of the given vector for the length of
the corresponding cuboid edge.
setEdgeLengths(Vector) LineSegment
Sets the length equal to the element of the (presumably 1D) vector.
setEdgeLengths(Vector) Rectangle
Sets the two edge lengths of the rectangle, taking
each element of the given vector for the length of
the corresponding rectangle edge.
setEdgeLengths(Vector) Rectangular
Specifies the D edge lengths needed to describe the shape
of the polytope.
setEdgeVector(int, Vector) BoundaryDeformablePeriodic
setEdgeVectors(Vector[]) Parallelepiped
Sets the lengths and directions of all edges of the parellelepiped.
setEdgeVectors(Vector[]) Parallelogram
Sets the lengths and directions of all edges of the parellelepiped.
setEdgeVectors(Vector[]) Parallelotope
Specifies the polytope via an array of edge vectors.
setEdgeVectors(Vector[]) BoundaryDeformablePeriodic
setEditable(boolean) DeviceBox
setEditValues(boolean) DeviceSlider
setEditValues(boolean) DeviceThermoSlider
Set whether the temperature text box should be editable.
setEditValues(boolean) DeviceThermoSliderGEMC
Set whether the temperature text box should be editable.
setEditValues(boolean) DeviceCellNumXYSlider
Set whether the x- and y-Cell # text box should be editable.
setEditValues(boolean) DeviceEigenvaluesSlider
Set whether the eigenvalue # text box should be editable.
setEditValues(boolean) DeviceWaveVectorSlider
Set whether the wavevector # text box should be editable.
setEditVariables(JButton) ViewSpeciesSelection
setEditVariables(JButton) ViewSpeciesSelection
setEigenvectors(double[]) MeterHarmonicCoordinate
setEigenvectors(double[][][]) MeterHarmonicEnergy
setEigenvectors(double[][][]) MeterHarmonicSingleEnergy
setEigenVectors(double[][]) MCMoveHarmonicStep
Informs the move of the eigenvectors for the k=0 wave vector.
setEigenVectors(double[][][]) IntegratorHarmonic
setEigenVectors(double[][][]) MCMoveHarmonic
setEigenVectors(double[][][]) MCMoveSingleMode
Informs the move of the eigenvectors for the selected wave vector.
setElement(int, int, float) Matrix3f
Sets the specified element of this matrix3d to the value provided.
setElement(int, int, float) Matrix4f
Sets the specified element of this matrix4f to the value provided.
setEllipsoidMatrix(Vector3f[], float[], Vector3f, Matrix3f) Quadric
setEnabled(boolean) DeviceNSelector
setEnabled(boolean) DeviceSlider
Sets the deivce's slider and textfield to be enabled or not.
setEnabled(boolean) AccumulatorPTensor
setEnabled(boolean) ConfigurationStorage
setEnabled(boolean) DataSourceBlockAvgCor
setEnabled(boolean) DataSourceHisogram
setEnabled(boolean) DataSourceHistogramMSD
setEnabled(boolean) DataSourceMSDcorP
setEnabled(boolean) DataSourcePMSDHistory
setEnabled(boolean) PotentialMaster
Permits enabling/disabling of all potentials.
setEnabled(boolean) PotentialMasterLrc
setEnabled(boolean) Grabber.ActionCornerSetter
setEnabled(boolean) Grabber.DefaultMouseListener
setEnabled(IPotentialAtomic, boolean) PotentialGroup
Indicates that the specified potential should not contribute to potential
calculations.
setEnabled(IPotentialAtomic, boolean) PotentialMaster
Indicates that the specified potential should not contribute to potential
calculations.
setEnabled(IPotentialMolecular, boolean) PotentialMaster
Indicates that the specified potential should not contribute to potential
calculations.
setEnablePBC(boolean) P2Nitrogen
setEnd(float, float, float) Line
setEnd(Point3f) Line
setEnergyBase(double) BoltzmannProcessor
setEnergyFac(double) MeterWidomInsertionCorrection
setEnergyFactor(double) MCMoveClusterRingPartialRegrow
setEnergyFactor(double) MCMoveClusterRingRegrow
sets the harmonic bond "energy" factor
The probability of the bond have length x is proportional to exp(-factor*x^2)
(there is no temperature involved here)
setEnergyFactor(double) MCMoveClusterRingRegrowExchange
sets the harmonic bond "energy" factor
The probability of the bond to have length x is proportional to exp(-factor*x^2)
(there is no temperature involved here)
setEnergyFactor(double) MCMoveClusterRingScale
setEnergyMeter(MeterPotentialEnergy) MeterWidomInsertion
setEnergyMeter(MeterPotentialEnergy) MeterWidomInsertionP
setEnergyMeter(MeterPotentialEnergy, MeterPotentialEnergy) MeterWidomInsertionCorrection
setEpsilon(double) P1WCAWall
setEpsilon(double) EOSSW
setEpsilon(double) P1Wall
setEpsilon(double) P2SquareWellBonding
Accessor method for depth of well
setEpsilon(double) P2SquareWellBondingCO
Accessor method for depth of well
setEpsilon(double) P2SquareWellSurface
Accessor method for depth of well
setEpsilon(double) P1Wall
setEpsilon(double) P1WCAPorousWall
setEpsilon(double) P1WCAWall
setEpsilon(double) P2Cohesion
setEpsilon(double) P2SquareWellOneSide
Accessor method for depth of well
setEpsilon(double) P1Tether
setEpsilon(double) P1WCAWall
setEpsilon(double) VLESim
setEpsilon(double) P22CLJQ
setEpsilon(double) P2Exp6Buckingham
setEpsilon(double) P2HardAssociation
Accessor method for depth of well.
setEpsilon(double) P2HardAssociationCone
Accessor method for depth of well
setEpsilon(double) P2HardAssociationConeDoubleSites
Accessor method for depth of well
setEpsilon(double) P2HardAssociationConeFourSites
Accessor method for depth of well
setEpsilon(double) P2HardAssociationConeFourSitesSW
Accessor method for depth of well
setEpsilon(double) P2HardAssociationConeOneSite
Accessor method for depth of well
setEpsilon(double) P2HardAssociationConeSW
Accessor method for depth of well
setEpsilon(double) P2HC2Yukawa
Mutator methods for size and energy parameters.
setEpsilon(double) P2LennardJones
Mutator method for Lennard-Jones energy parameter
setEpsilon(double) P2LennardJonesDreiding
Mutator method for Lennard-Jones energy parameter
setEpsilon(double) P2LJDipole
setEpsilon(double) P2LJQ
setEpsilon(double) P2LJQQ
setEpsilon(double) P2ModifiedMorse
setEpsilon(double) P2Morse
setEpsilon(double) P2PenetrableSphere
Accessor method for height of core.
setEpsilon(double) P2PenetrableSquareWell
Mutator method for depth of well.
setEpsilon(double) P2SoftSphere
Mutator method for soft-sphere energy parameter
setEpsilon(double) P2SquareWell
Accessor method for depth of well
setEpsilon(double) P2SquareWellRobust
Accessor method for depth of well
setEpsilon(double) P2TriangleWell
setEpsilon(double) P2WCA
Mutator method for the energy parameter
setEpsilon(double) P2WCAP
Mutator method for the energy parameter
setEpsilon(double) P3BondAngle
Sets the characteristic energy of the potential
setEpsilon(double) P3CPSNonAdditiveHeOrig
Sets the characteristic energy of the potential
setEpsilon(double) P2LJDipole
setEpsilon(double) LJ
setEpsilon(double, int) MolecularModel2CLJQ_SpeciesCO2
setEpsilon(double, int) MolecularModel2CLJQ_SpeciesEthane
setEpsilon(double, int) MolecularModel2CLJQ_SpeciesLJ
setEpsilon(double, int) MolecularModelEMP2_SpeciesCO2
setEpsilon(double, int) MolecularModelLJ_SpeciesLJ
setEpsilon(double, int) MolecularModelLJQ_SpeciesLJ
setEpsilon(double, int) MolecularModelSKS_SpeciesAlkane
setEpsilon(double, int) MolecularModelSPCE_SpeciesH2O
setEpsilon(double, int) MolecularModelTRAPPE_SpeciesAlkane
setEpsilon(double, int) MolecularModelTrappe_SpeciesCO2
setEpsilonBonding(double) P2SquareWellBonding
setEpsilonBonding(double) P2SquareWellBondingCO
setEpsilonCore(double) P2DoubleWell
Accessor method for depth of well
setEpsilonCore(double) P2PenetrableSquareWell
Sets height of penetrable core.
setEpsilonWell(double) P2DoubleWell
setEpsInner(double) P2PenetrableBond
setEpsOuter(double) P2PenetrableBond
setEquilibrating(boolean) MCMoveManager
setErrMulti(double) P2HePCKLJS
setEthanolParams(int) EthanolRouteParams
setEValNum(int) DeviceEigenvaluesSlider
Set the current value for the eigenvalue # slider/text box.
setEValNum(int) IntegratorHarmonic
setEventInterval(int) Integrator
Sets value of interval between successive firing of integrator interval events.
setExcludeArticulationPair(boolean) ClusterGenerator
Set whether to exclude clusters having an articulation pair.
setExcludeArticulationPoint(boolean) ClusterGenerator
Set whether to exclude clusters having an articulation point.
setExcludeNodalPoint(boolean) ClusterGenerator
Set whether to exclude clusters having a nodal point.
setExecuteOnload(boolean) SVGConverter
Sets whether or not scripts attached to the DOM using 'onload'
event attribute must be executed before rasterizing.
setExp(int) MayerSSSeries
Sets the HS diameter.
setExpGroupingSize(int) ScientificFormat
setExpMaximumIntegerDigits(int) ScientificFormat
setExpMinimumIntegerDigits(int) ScientificFormat
setExpNegativePrefix(String) ScientificFormat
setExpNegativeSuffix(String) ScientificFormat
setExponentialMode() ScientificFormat
setExpPositivePrefix(String) ScientificFormat
setExpPositiveSuffix(String) ScientificFormat
setExpPSpan(double) MeterDDP
setExpPSpan(double) MeterDP
setExternalField(Vector) P1ExternalField
setExtraTargetClusters(ClusterAbstract[]) SimulationVirialOverlap2
setFac(double) DiameterHashGlass
setFactory(SimulationRunner) ModelSimulationConstructor
setFalseLabel(String) ActionToggle
Specifies the button's label when the toggle is set to false.
setFalseLabel(String) DeviceToggleButton
Specifies the button's label when the toggle is set to false.
setFalseLabel(String) DeviceToggleRadioButtons
Specifies the button's label when the toggle is set to false.
setFile(File) PDBWriter
Sets the file to write to.
setFile(File) XYZWriter
Sets the file to write to.
setFile(String) AccumulatorAverageFixedOutputFile
setFile(String) AccumulatorVirialOverlapSingleAverage
setFilename(String) WriteS
setFileName(String) PDBWriter
Sets the file name to write to.
setFileName(String) WriteConfiguration
setFileName(String) WriteConfigurationBinary
setFileName(String) XYZWriter
Sets the file name to write to.
setFileName(String) DataLogger
Define the name of the output file.
setFileName(String) IntegratorDimerMin
Set's the filename of the output of this integrator.
setFileName(String) IntegratorDimerRT
Set's the filename of the output of this integrator.
setFileName(String) NormalModesMolecular
setFileName(String) NormalModesPotential
setFileWriter(FileWriter) DataArrayWriter
setFileWriter(FileWriter) DataLogger.DataWriter
Sets the FileWriter to be used for actual file I/O.
setFileWriter(FileWriter) DataTableWriter
setFilter(Predicate<IAtom>) MeterDeformation
setFitToWindow(boolean) DisplayTable
If true, columns will be squeezed so table fits to window; if false,
table will exceed window size, and to view full width must be placed in a
scroll pane.
setFixedCOM(boolean) MCMoveEinsteinCrystal
setFixedDaDef(double) MCMoveIDBiasAction
setFixedDeltaU(double) CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
setFixedDeltaU(double) CalcNumerical2ndDerivative
setFixedDeltaU(double) CalcNumerical2ndDerivativeNitrogen
setFixedDeltaU(double) FiniteDifferenceDerivativeCGNitrogenBeta
setFixedOrientation(boolean) MCMoveChangeBondLength
setFixedSpecies(ISpecies) GrainBoundaryTiltConfiguration
setFixedWall(FixedWall) IntegratorFixedWall
setFlexCancelOnly(boolean) VirialDiagrams
This method only effects the graphs returned by getMSMCGraphs
setFlexCancelOnly(boolean) VirialDiagramsPT
This method only effects the graphs returned by getMSMCGraphs
setFlexibleMode() ScientificFormat
setFlipDisplacement(boolean) DisplayBoxCanvas2DGlass
setFlipDisplacement(boolean) DisplayBoxCanvas3DGlass
setFlipDisplacement(boolean) DisplayBoxCanvasGlass
setFlipped(boolean) DiameterHashGlass
setFluctuationFactor(double) HSNPT.ColorSchemeDisplacement
setFluidNbrDistance(double) MCMoveInsertDeleteLatticeVacancy
setFont(JmolFont) Graphics3D
setFont(JmolFont) GData
setFontFid(byte) Graphics3D
setFontFid(byte) GData
setForce(double) P1HardMovingBoundary
setForceconstant(double) MolecularModelSKS_SpeciesAlkane
setForceconstant(double) MolecularModelTRAPPE_SpeciesAlkane
setForceInBox(boolean) MCMoveClusterAtomHSChain
setForceInBox(boolean) MCMoveClusterAtomHSTree
setForceSum(PotentialCalculationForceSum) IntegratorVelocityVerlet
setForceSum(PotentialCalculationForceSum) IntegratorVelocityVerletShake
setFrac(double) MCMoveHarmonicEin
Sets the fraction of the systems energy from the normal mode
contribution.
setFrac(double) MeterBoltzmannHarmonic
Sets the fraction that the system is coupled to measured energy.
setFrac(double) MeterBoltzmannTarget
setFrac(double) SimOverlapSoftSphereEin.MeterPotentialEnergyComposite
setFrac(double) SimOverlapSoftSphereEinHarm.MeterPotentialEnergyComposite
setFraction(double) AtomTestRandom
setFrameProperties() AppFrameMixtureBuilder
setFreeRadicalColor(AtomType, Color) ColorSchemeRadical
setFrequency(MCMove, double) MCMoveManager
Sets the trial frequency for the given move to the given frequency.
setFugacityFraction(double[]) MCMoveSemigrand
Specifies the fugacity fractions for the set of species that can participate in
an exchange move.
setFullBondColor(AtomType, Color) ColorSchemeRadical
setFullColor(AtomType, Color) ColorSchemeRadical
setFunction(FunctionInvertible) ModifierFunctionWrapper
setFunction(IFunction) DataSourceFunction
setG(double) P1Smash
setG1(Graph) AbstractSearchState
setG2(Graph) AbstractSearchState
setGamma(double) PrimitiveTrigonal
setGamma(double) P3BondAngleDreiding
Sets the characteristic energy of the potential
setGammaPositionAndOrientation(IMoleculeList) CoordinateDefinitionNitrogenSuperBox
setGBplane(int[]) GrainBoundaryTiltConfiguration
Allows a user to specify a plane for GB
setGlobal() ScriptVariable
setGlobalMoveInterval(double) IntegratorManagerMC
Sets the average interval between box-swap trials.
setGoal(int) AbstractTraversal
setGreyscaleMode(boolean) GData
controls greyscale rendering
setGroupingSize(int) ScientificFormat
setGroupingUsed(boolean) ScientificFormat
setH(double) FiniteDifferenceDerivative
setH(double) P1MagneticField
setHandledByCells(ISpecies, boolean) PotentialMasterCellMixed
Indicates that the given species is handled by cell lists.
setHardCoreDiamterSq(double) P22CLJmuQ
setHardCoreDiamterSq(double) P22CLJQ
setHardCoreDiamterSq(double) P2LJQ
setHardCoreDiamterSq(double) P2LJDipole
setHarmonicFudge(double) NormalModes
Set the fudge factor applied to frequencies.
setHarmonicFudge(double) NormalModes1DHR
setHarmonicFudge(double) NormalModes2D
setHarmonicFudge(double) NormalModes3D
setHarmonicFudge(double) NormalModesFromFile
setHarmonicFudge(double) NormalModesMolecular
setHarmonicFudge(double) NormalModesPotential
setHarmonicFudge(double) NormalModesSoftSpherical
setHarmonicWV(int) MCMoveSingleMode
The harmonic wavevector and all wavevectors with higher numbers are not
able to be changed by this MCMove.
setHashMapAtomsetIterator(HashMap<String[], AtomsetIteratorBasisDependent>) CollectionPotentialAtomicLike
setHashMapAtomTypeLikePairs(HashMap<String[], AtomType[]>) CollectionPotentialAtomicLike
setHashMapAtomTypesUnlikePairs(HashMap<String[], AtomType[]>) CollectionPotentialAtomicUnlike
setHashMapPotentialIntraBonded(HashMap<String[], IPotential>) CollectionPotentialAtomicLike
setHashMapPotentialNonBonded() CollectionPotentialAtomicLike
setHashMapPotentialNonBonded() CollectionPotentialAtomicUnlike
setHashMapPotentialNonBonded(HashMap<String[], IPotential>) HashMapPotentialNonBonded
setHeight(float) SVGConverter
In less than or equal to zero, the height is not
constrained on the output image.
setHello(String) EtomicaServerConfig
setHexagonal(boolean) MeterElongation
setHexagonal(boolean) MeterStrain
setHexagonal(boolean) StrainColorScheme
setHistogram(Histogram) AccumulatorHistogram
setHistogramFactory(AccumulatorAverageBootstrap.HistogramFactory) AccumulatorAverageBootstrap
setHistogramming(boolean) ClusterDiagramTree
setHistogramSink(int, IDataSink) AccumulatorAverageBootstrap
Sets the sink that will receive histograms for a block when pushHistograms is called.
setHistory(History) AccumulatorHistory
setHistoryLength(int) History
Sets the number of data points to be tracked by the History.
setHistoryLength(int) HistoryCollapsing
Sets the number of values kept in the history.
setHistoryLength(int) HistoryComplete
Sets the number of values kept in the history.
setHistoryLength(int) HistoryScrolling
Sets the number of values kept in the history.
setId(int) ArrayMoleculeDisplayList
setID(int) Figure
Set the ID of the figure.
setIdentity() Matrix3f
Sets this Matrix3f to identity.
setIdentity() Matrix4f
Sets this Matrix4f to identity.
setIgnoredAtomType(AtomType) MeterChainLength
setIgnoreOverlap(boolean) ActivityIntegrate
setIgnoreOverlap(boolean) IntegratorReset
setIgnoreOverlap(boolean) SimulationRestart
setIgnoreOverlap(boolean) ZeoliteSimStart
setIgnoreReferenceAvg(boolean) DataVirialOverlap
Directs this class to ignore the reference average when deciding how
much time to spend on each system.
setImage(Image) Grabber.ImagePanel
setImageShells(int) DisplayBox
Changes the value of image shells, and increases/decreases scale accordingly.
setImmFracs(double[]) DataSourcePercolation0
setImportantAtoms() IntegratorDimerApproach
setIncludeACInError(boolean) AccumulatorAverage
Include correction to the uncertainty from block correlation function as
prescribed in
Kolafa, Jiri(1986) 'Autocorrelations and subseries averages in Monte
Carlo Simulations', Molecular Physics (59) 1035
setIncludeAdiabatic(boolean) DeviceThermoSelector
setIncludeHeader(boolean) DataArrayWriter
Directs the writer to include column headers or not
setIncludeHeader(boolean) DataTableWriter
Directs the writer to include column headers or not
setIncludeLrc(boolean) MeterHyperVirial
Sets flag indicating whether calculated energy should include
long-range correction for potential truncation (true) or not (false).
setIncludeLrc(boolean) MeterPotentialEnergy
Sets flag indicating whether calculated energy should include
long-range correction for potential truncation (true) or not (false).
setIncludeLrc(boolean) MeterPressure
Sets flag indicating whether calculated energy should include
long-range correction for potential truncation (true) or not (false).
setIncludeLrc(boolean) MeterPressureMolecular
Sets flag indicating whether calculated energy should include
long-range correction for potential truncation (true) or not (false).
setIncludeLrc(boolean) MeterPressureTensor
Sets flag indicating whether calculated energy should include
long-range correction for potential truncation (true) or not (false).
setIncludeLrc(boolean) MeterPU
Sets flag indicating whether calculated energy should include
long-range correction for potential truncation (true) or not (false).
setIncludeLrc(boolean) MeterPressure2
Sets flag indicating whether calculated energy should include
long-range correction for potential truncation (true) or not (false).
setIncludeLrc(boolean) MeterPressureSuperBox
Sets flag indicating whether calculated energy should include
long-range correction for potential truncation (true) or not (false).
setIncludeLrc(boolean) SimEinStep2.MeterPotentialEnergyComposite
setIncludeLrc(boolean) SimEinStep2HCP.MeterPotentialEnergyComposite
setIncludeLrc(boolean) SimOverlapSoftSphereEin.MeterPotentialEnergyComposite
setIncludeLrc(boolean) SimOverlapSoftSphereEinHarm.MeterPotentialEnergyComposite
setIncludeLrc(boolean) IteratorDirective
Sets flag indicating if lrc potentials (long-range correction) should be
included.
setIndex(int) Atom
setIndex(int) AtomType
Informs the IAtomType what its index should be.
setIndex(int) IAtom
Informs the IAtom of its index within the atoms of its parent molecule.
setIndex(int) Box
Informs the Box what its index is.
setIndex(int) IMolecule
Informs the IMolecule of its index.
setIndex(int) Molecule
setIndex(int) ISpecies
Informs the ISpecies what its index should be.
setIndex(int) SpeciesGeneral
setIndex(int) SpeciesGeneralMutable
setIndexed(int) SVGConverter
Tells the PNG encoder to reduce the image to 256 colors, so the
PNG file is indexed.
setIndexSelectedSpecies(int) ExceptionDoNotRemoveSpecies
setInflateDimensions(boolean[]) MeterPressureByVolumeChange
For anisotropic volume change, indicates dimension in which volume is perturbed.
setInflater(BoxInflate) MCMoveVolume
setInflater(BoxInflate) MCMoveVolumeMonoclinic
setInflater(BoxInflate) MCMoveVolumeMonoclinicScaled
setInflater(BoxInflate) MCMoveVolumeSolidNPTMolecular
setInitialStateConditions(double, double) IntegratorKMC
setInitialStateConditions(double, double) IntegratorKMCCluster
setInitVolume(Vector) CoordinateDefinitionMolecule
setInitVolume(Vector) CoordinateDefinitionMoleculeVolumeFluctuation
setInnerIterator(GraphIterator) CartesianIterator
setInnerList(IAtomList) ApiInterArrayList
Sets the list that will be used to generate the pairs.
setInnerList(IMoleculeList) MpiInterArrayList
Sets the list that will be used to generate the pairs.
setInnerPermutator(DefaultPermutator) CartesianPermutator
setInnerWellCutoffFactor(double) P2HardAssociationConeFourSitesSW
setInnerWellCutoffFactor(double) P2HardAssociationConeSW
setInputData(double[], double[]) AkimaSpline
setInputData(double[], double[], double[]) AkimaSplineSmoother
setInputData(double[], double[], double[]) AkimaSplineSmootherDy
setInputData(double[], double[], double[], double[]) AkimaSplineSmootherDy
Set the nominal values for x and y and uncertainty in y (ey).
setInputFileName(String) ReadParameters
Sets the fileName to read the parameters from.
setInputFileName(String) WriteParameters
Sets the fileName to read the parameters from.
setInsertionDistances(double[]) MeterWidomCavity
setInt(int) Rgb16
setInteger(boolean) DeviceBox
Sets a flag indicating if the value should be displayed as an integer.
setIntegerDisplay(boolean) DisplayTextBox
setIntegrator(Integrator) IntegratorAction
setIntegrator(Integrator) IntegratorActionAdapter
setIntegrator(Integrator) DataSourceCountSteps
setIntegrator(IntegratorBox) DataProcessorChemicalPotential
setIntegrator(IntegratorBox) DataSourcePositionedBoltzmannFactor
Sets the integrator.
setIntegrator(IntegratorBox) MeterPotentialEnergyFromIntegrator
setIntegrator(IntegratorBox) MeterPressure
Sets the integrator associated with this instance.
setIntegrator(IntegratorBox) MeterPressureByVolumeChange
Sets the integrator associated with this instance.
setIntegrator(IntegratorBox) MeterPressureMolecular
Sets the integrator associated with this instance.
setIntegrator(IntegratorBox) MeterWidomInsertion
Sets the integrator associated with this class.
setIntegrator(IntegratorBox) DeviceThermoSelector
setIntegrator(IntegratorBox) MeterWidomInsertionP
Sets the integrator associated with this class.
setIntegrator(IntegratorBox) MeterFlux
setIntegrator(IntegratorBox) MeterPressureSuperBox
Sets the integrator associated with this instance.
setIntegrator(IntegratorBox) PotentialCalculationPressureTensor
Sets an integrator to use a source for the temperature to compute the
kinetic portion of the pressure.
setIntegrator(IntegratorHard) DataSourceCountCollisions
setIntegrator(IntegratorHard) DataSourceTensorVirialHard
Informs meter of the integrator for its box, and zeros elapsed-time counter
setIntegrator(IntegratorHard) MeterPressureHardTensor
setIntegrator(IntegratorHard) DataSourceWallPressureCatalysis
Registers meter as a collisionListener to the integrator, and sets up
a DataSourceTimer to keep track of elapsed time of integrator.
setIntegrator(IntegratorHard) DataSourceTensorVirialHardProfile
setIntegrator(IntegratorHard) DataSourceWallPressureMu
Registers meter as a collisionListener to the integrator, and sets up
a DataSourceTimer to keep track of elapsed time of integrator.
setIntegrator(IntegratorMD) MeterKineticEnergyFromIntegrator
setIntegrator(IntegratorVelocityVerlet) MeterPressureTensorFromIntegrator
setIntegrator(IntegratorVelocityVerlet) DataProcessorCvMD
setIntegrator(IntegratorPolymer) MeterNormalStress
setIntegrator(IntegratorPolymer) MeterViscosity
setIntegrator(IntegratorHarmonic) DeviceWaveVectorSlider
Sets the integrator for the device.
setIntegratorMC(IntegratorMC, int) IntegratorMD
A Monte Carlo integrator is employed with this MD integrator when performing hybrid MD/MC
sampling.
setIntegratorOverlap(IntegratorOverlap) SimOverlapModule
setIntegrators(IntegratorMC, IntegratorMD, IRandom) IntegratorDCVGCMD
setIntegrators(IntegratorMC, IntegratorMD, IRandom) IntegratorDCVGCMD
setInteractionRange(double) CriterionPositionWall
Informs the criterion of the interaction range of the wall potential.
setInteractionRange(double) CriterionSimple
setInteractionRange(double) CriterionSimpleMolecular
setIntercepts(double, double, double) Plane
Reorients and positions the plane so that its intercepts with the
x-, y-, and z-axes are the given values, respectively.
setInteriorColor(Color) ColorSchemeDropletSurface
setInterval(int) IntegratorListenerAction
setInterval(int) IntegratorListenerGroupSeries
setInterval(int) DataSourceHisogram
setInterval(int) DataSourceHistogramMSD
setInterval(int) DataSourcePMSDHistory
setInterval(int) MSDCoordWriter.AfterPBC
setInterval(long) DataPumpListener
setIntraMolecularCriterion(NeighborCriterion) CriterionInterMolecular
Configures to use the given criterion for intramolecular pairs.
setIntraMolecularOnly(boolean) CriterionInterMolecular
setInverseNormixes() Normix
setIs256() CoordinateDefinitionLeafSuperBox
setIs864() CoordinateDefinitionLeafSuperBox
setIsAlpha() CoordinateDefinitionNitrogen
setIsAlpha() CoordinateDefinitionNitrogenSuperBox
setIsAppend(boolean) XYZWriter
setIsBeta() CoordinateDefinitionNitrogen
setIsBetaHCP() CoordinateDefinitionNitrogen
setIsBetaLatticeSum() CoordinateDefinitionNitrogen
setIsDoLatticeSum() CoordinateDefinitionNitrogen
setIsFluctuationFromAvg(boolean) HSNPT.ColorSchemeDisplacement
setIsGamma() CoordinateDefinitionNitrogen
setIsGamma() CoordinateDefinitionNitrogenSuperBox
setIsInteracting(boolean, int) AtomPotentialList
Sets whether the atom is interacting or not with the potential corresponding to the given index.
setIsInteracting(boolean, int) MoleculePotentialList
Sets whether the molecule is interacting or not with the potential
corresponding to the given index.
setIsothermal() DeviceThermoSlider
Set the Isothermal button to its selected state.
setIsothermal() DeviceThermoSliderGEMC
Set the Isothermal button to its selected state.
setIsothermal(boolean) IntegratorDCVGCMD
setIsothermal(boolean) IntegratorBox
setIsothermal(boolean) IntegratorMD
setIsothermal(boolean) IntegratorHybrid
setIsothermal(boolean) IntegratorDCVGCMD
setIsothermalButtonsVisibility(boolean) DeviceThermoSlider
setIsothermalButtonsVisibility(boolean) DeviceThermoSliderGEMC
setIsString(boolean) ColorSchemeDeviation
setIsUpperBound(boolean) DataProcessorBounds
setIterator(AtomIterator) DataSourceRmsVelocity
Sets the iterator defining the atoms for which the RMS velocity is
calculated.
setIterator(AtomIterator) VelocityWriter
setIterator(AtomIterator) MSDCoordWriter.AfterPBC
setIterator(AtomIterator) MSDCoordWriter
setIterator(AtomIteratorBoxDependent) MeterLocalDensity
setIterator(AtomIteratorBoxDependent) MeterLocalMoleFraction
setIterator(AtomIteratorBoxDependent) MeterMeanSquareDisplacement
setIterator(MoleculeIteratorAllMolecules) MeterRadiusGyration
Mutator method for the iterator that generates the atom pairs used to
tabulate the ROG.
setJSpinnerCountOfSpecies1(JSpinner, int) ViewSpeciesSelection
setK(Vector) LatticeSum
setK(Vector) LatticeSumCrystal
setK(Vector) LatticeSumCrystalMolecular
setKappa(double) P2Yukawa
Mutator methods for size and energy parameters.
setKinetic(DataSourceScalar) MeterEnergy
setKineticEnergyMeter(DataSourceScalar) MeterTemperature
setLabel(String) DataInfoFactory
Sets the label
setLabel(String) IDataInfoFactory
Sets the label
setLabel(String) DeviceBox
Sets the value of a descriptive label using the given string.
setLabel(String) DeviceButton
Sets the value of a descriptive label using the given string.
setLabel(String) DeviceButtonGroup
Sets the label for the group of radio buttons
setLabel(String) DeviceSelector
setLabel(String) DeviceSlider
Sets the value of a descriptive label using the given string.
setLabel(String) DeviceSpinner
Sets the value of a descriptive label using the given string.
setLabel(String) Display
Accessor method of the label describing the display.
setLabel(String) DisplayTextBox
Sets the value of a descriptive label using the given string.
setLabel(String) DisplayTextBoxesCAE
setLabel(String) ModifierGeneral
setLabel(String) DeviceButtonSingle
Sets the value of a descriptive label using the given string.
setLabelPosition(Constants.CompassDirection) DeviceBox
setLabelPosition(Constants.CompassDirection) DisplayTextBox
setLabelPosition(Constants.CompassDirection) DisplayTextBoxesCAE
setLabelType(DeviceBox.LabelType) DeviceBox
Sets the label type to "border" or "string".
setLabelType(DisplayTextBox.LabelType) DisplayTextBox
setLabelType(DisplayTextBox.LabelType) DisplayTextBoxesCAE
setLambda(double) EOSSW
setLambda(double) P2SquareWellBonding
Accessor method for well-diameter multiplier.
setLambda(double) P2SquareWellBondingCO
Accessor method for well-diameter multiplier.
setLambda(double) P2SquareWellSurface
Accessor method for well-diameter multiplier.
setLambda(double) P2SquareWellOneSide
Accessor method for well-diameter multiplier.
setLambda(double) SimEinStep2.MeterPotentialEnergyComposite
setLambda(double) SimEinStep2HCP.MeterPotentialEnergyComposite
setLambda(double) P2DoubleWell
Accessor method for well-diameter multiplier.
setLambda(double) P2PenetrableSquareWell
Accessor method for well-diameter multiplier.
setLambda(double) P2SquareWell
Accessor method for well-diameter multiplier.
setLambda(double) P2SquareWellRobust
Accessor method for well-diameter multiplier.
setLambda(double) P2TriangleWell
setLanguage(String) SVGConverter
Sets the user language.
setLattice(CellLattice) MpiAACell
setLattice(FiniteLattice) ColorSchemeCell
setLattice(FiniteLattice) CellLattice.NeighborIterator
setLattice(FiniteLattice) RectangularLattice.Iterator
setLattice(FiniteLattice) RectangularLatticeNbrIterator
Sets the lattice from which the iterates are given.
setLattice(FiniteLattice) RectangularLatticeNbrIteratorSquare
setLattice(FiniteLattice) SiteIterator
Sets the lattice having the sites to be given by this iterator.
setLattice(SpaceLattice) LatticeSum
setLattice(Vector[], Vector[]) ConfigFromFileLAMMPS.ColorSchemeDeviation
setLatticeBox(Box) MCMoveVolumeMonoclinicScaled
setLatticeBox(Box) MCMoveVolumeSolidNPTMolecular
setLatticeConstant(double) CubicLattice
Sets the size of the unit cell, the length of each edge.
setLatticeConstant(double) LatticeCubicBcc
The lattice constant is the size of the cubic primitive vectors
of the lattice underlying this crystal.
setLatticeConstant(double) LatticeCubicDiamond
The lattice constant is the size of the cubic primitive vectors
of the lattice underlying this crystal.
setLatticeConstant(double) LatticeCubicFcc
The lattice constant is the size of the cubic primitive vectors
of the lattice underlying this crystal.
setLatticeConstant(double) LatticeCubicSimple
The lattice constant is the size of the cubic primitive vectors.
setLatticeCorrec(double) MCMoveVolumeN2
setLatticeEnergy(double) MeterRotPerturbMolecule
setLatticeEnergy(double) MeterTargetRPMolecule
setLatticeEnergy(double) MeterTargetTPMolecule
setLatticeEnergy(double) MCMoveAtomCoupledBennet
setLatticeEnergy(double) MCMoveAtomCoupledUmbrella
setLatticeEnergy(double) MeterBoltzmannHarmonic
setLatticeEnergy(double) MeterBoltzmannHTTP
setLatticeEnergy(double) MeterBoltzmannTarget
setLatticeEnergy(double) MeterDADB
setLatticeEnergy(double) MeterDirectSamplingHarmonic
setLatticeEnergy(double) MeterDirectSamplingTarget
setLatticeEnergy(double) MeterOverlapSwitch
setLatticeEnergy(double) MeterTargetTP
setLatticeEnergy(double) MeterWorkBennetHarmonic
setLatticeEnergy(double) MeterWorkBennetTarget
setLatticeEnergy(double) MeterWorkHarmonicBennet
setLatticeEnergy(double) MeterWorkHarmonicPhaseSpace
setLatticeEnergy(double) MeterWorkHarmonicTargetandReweighting
setLatticeEnergy(double) MeterWorkHarmonicUmbrella
setLatticeEnergy(double) MeterWorkTargetBennet
setLatticeEnergy(double) MeterWorkTargetHarmonicandReweighting
setLatticeEnergy(double) MeterWorkTargetPhaseSpace
setLatticeEnergy(double) MeterWorkTargetUmbrella
setLatticeEnergy(double) SimOverlapLJModule.APIPotentialTarget
setLayers(int) ImageShell
Sets the number of image shell layers to use
setLeafIndex(int) Atom
setLeafIndex(int) IAtom
Sets the atom's global index to the give value.
setLegend(DataTag[], String) DisplayPlot
setLegend(DataTag[], String) DisplayPlotXChart
setLength(double) LineSegment
Sets the length of the segment to the given value, keeping
its orientation and the position of its midpoint fixed.
setLength(int) DataCollector
setLength(int) StringXBuilder
setLengthAlkaneChain(int, int) ModelSimulationEnvironment
setLengthFactor(double) ColorSchemeDeviation
setLinPSpan(double) MeterDDP
setLinPSpan(double) MeterDP
setLiquidColor(Color) ColorSchemeLiquidVapor
setLiquidFilter(AtomTest) P2Cohesion
setList(IAtomList) ApiIntraArrayList
Sets the list that will be used to generate the pairs.
setList(IAtomList) AtomIteratorArrayListSimple
Sets the list for iteration.
setList(IMoleculeList) MoleculeIteratorArrayListSimple
Sets the list for iteration.
setList(IMoleculeList) MpiIntraArrayList
Sets the list that will be used to generate the pairs.
setLnBias(int, double) MCMoveInsertDeleteBiased
setLnBias(int, double) MCMoveInsertDeleteLatticeVacancy
setLocale(Locale) Messages
Implements Localizable.setLocale(Locale).
setLocalVisitor(TraversalVisitor) AbstractTraversal
setLog2StepStart(int) DataSourcePercolation
setLogger(LoggerInterface) Logger
Replaces the current logger implementation by a new one.
setLogLevel(int) Logger
Activates all logging levels up through a given level.
setLongWall(int, boolean, boolean) P1HardBoundary
setM(Matrix3f) AxisAngle4f
Sets the value of this axis-angle to the rotational component of the passed
matrix.
setM(Matrix3f) Matrix3f
Sets the value of this matrix to the double value of the Matrix3f argument.
setM(Matrix3f) Quaternion
setM(Matrix4f) Matrix4f
Sets the value of this matrix to a copy of the passed matrix m1.
setM3(Matrix3f) Matrix4f
Sets the rotational component (upper 3x3) of this matrix to the matrix
values in the single precision Matrix3f argument; the other elements of
this matrix are initialized as if this were an identity matrix (ie, affine
matrix with no translational component).
setMacrostateManager(MacrostateManager) IntegratorTMMC
setMakeLrc(boolean) P2SoftSphericalTruncated
setMakeReeHover(boolean) ClusterGenerator
Set whether to generate Ree-Hoover diagrams.
setMappingCut(double) MeterCavityMapped
setMappingCut(double) MeterRDFMapped
setMass(double) ElementSimple
Sets mass of this element and updates reciprocal mass accordingly.
setMass(double) P1HardMovingBoundary
setMass(double) P2DiscreteFeynmanHibbs
Sets the mass; we assume the reduced mass is m/2 (correct for particles
with identical mass).
setMass(double) P2EffectiveFeynmanHibbs
Sets the mass; we assume the reduced mass is m/2 (correct for particles
with identical mass).
setMass(double) MaxwellBoltzmann.Distribution
setMass(double) LJ
setMax(int) IndexIteratorIncreasing
Sets a new maximum for iteration.
setMaxAdjustInterval(long) MCMoveStepTracker
The step size is adjusted every adjustInterval trials.
setMaxBlocks(int) AccumulatorAverageCollapsing
Changes the maximum number of blocks.
setMaxBonds(int) AssociationHelperBranched
setMaxBonds(int) AssociationHelperMolecule
setMaxClusterDistance(double) DataClusterer
setmaxCosPhi(double) BiasVolume2SiteAceticAcid
setmaxCosPhi(double) BiasVolumeAceticAcid
setmaxCosTheta(double) BiasVolume2SiteAceticAcid
setmaxCosTheta(double) BiasVolumeAceticAcid
setMaxDistance(double) MCMoveInsertDeleteLatticeVacancy
setMaxDistance(double) MCMoveInsertDeleteVacancy
setMaxDr(double) DataSourceQ4
setMaxElement(int) IndexIteratorTriangular
Sets the largest allow value for any element to have.
setMaxElement(int) LatticeSum
Specifies the largest index element that will be included in the lattice sum.
setMaxElementMin(int) IndexIteratorTriangular
setMaxHeight(float) SVGConverter
If less than or equal to zero, the maximum height
does not have any effect on the output image.
setMaximum(double) DeviceSlider
Sets maximum value of slider; should be called after
any calls to setPrecision.
setMaximum(double) DeviceSpinner
Sets maximum value of slider
setMaximum(double) DeviceThermoSlider
Set the maximum value for the temperature.
setMaximum(double) DeviceThermoSliderGEMC
Set the maximum value for the temperature.
setMaximum(int) DeviceCellNum3DSlider
Set the maximum value for the N-Cell #.
setMaximum(int) DeviceCellNumXYSlider
Set the maximum value for the x- and y-Cell #.
setMaximum(int) DeviceEigenvaluesSlider
Set the maximum value for the eigenvalue #.
setMaximum(int) DeviceWaveVectorSlider
Set the maximum value for the wavevector #.
setMaximumFractionDigits(int) ScientificFormat
setMaximumIntegerDigits(int) ScientificFormat
setMaximumSeparation(double) P2Fene
Accessor method for harmonic energy parameter
setMaxIndex(int) HardRods
setMaxIndex(int) VanderWaals
setMaxInsertDistance(double) MCMoveInsertDeleteLatticeVacancy
setMaxInsertDistance(double) MCMoveInsertDeleteVacancy
setMaxIterations(int) IntegratorRigidIterative
setMaxIterations(int) IntegratorRigidMatrixIterative
setMaxIterations(int) IntegratorVelocityVerletShake
setMaxIterations(int) DataClusterer
setMaxIterations(int) FitTanh
setMaxIterations(int) FitTanh
setMaxLatticeShell(int) LatticeSumCrystal
Specifies the largest index element that will be included in the lattice sum.
setMaxLatticeShell(int) LatticeSumCrystalMolecular
Specifies the largest index element that will be included in the lattice sum.
setMaxLatticeShell(int) HarmonicCrystal
setMaxLatticeShell(int) HarmonicCrystalSsFccNxy
setMaxLatticeShell(int) NormalModesPotential
setMaxLength(int) MCMoveAtomMonomer
setMaxLength(int) MCMoveAtomSmer
setMaxLength(int) MCMoveBiasUB
setMaxLength(int) MCMoveRotateAssociated
setMaxNbrsVapor(int) AtomTestLiquidAtomic
setMaxNumBlocks(int) AccumulatorAverageBootstrap
Sets the maximum number of blocks of raw data to be 1<
setMaxPhi(double) MCMoveRotateMoleculePhiTheta
setMaxPhi(double) MCMoveVolumeSolidNPTMolecularOriented
setMaxSample(double) AccumulatorAverageCollapsingLogAB
setMaxSleep(int) DeviceDelaySlider
setMaxSteps(long) ActionIntegrate
Mutator method for the number of doStep steps to be
performed by this integrator after it is started.
setMaxSteps(long) ActivityIntegrate
setMaxWidth(float) SVGConverter
If less than or equal to zero, the maximum width
does not have any effect on the output image.
setMaxWidth(int) ScientificFormat
the the maximum width of the decimal format.
setMCMove(MCMoveStepDependent) MCMoveStepTracker
setMCMoveClusterTorsionMulti(MCMoveClusterTorsionMulti[]) CollectionPotentialAtomicLike
setMCMoveInsertDelete(MyMCMove, MyMCMove) IntegratorHybrid
setMCMoves(MCMove[]) MCMoveManager
Sets moves in given array to be integrator's set of moves, deleting any
existing moves.
setMDStepRepetitions(int) IntegratorDCVGCMD
setMDStepRepetitions(int) IntegratorHybrid
setMDStepRepetitions(int) IntegratorDCVGCMD
setMediaType(String) SVGConverter
Sets the mediaType value.
setMembraneDim(int) ConfigurationMembrane
setMembraneDim(int) ConfigurationMembraneWater
setMembraneThickness(double) ConfigurationMembraneWater
setMembraneThicknessPerLayer(double) ConfigurationMembrane
setMembraneWidth(int) ConfigurationMembrane
setMembraneWidth(int) ConfigurationMembraneWater
setMeter(IDataSource) SimulationVirial
setMeter(MeterNormalMode) WriteS
setMeterPotentialEnergy(DataSourceScalar) IntegratorBox
setMeterTemperature(MeterTemperature) IntegratorMD
Sets the temperature meter used to calculate temperature for
velocity rescaling.
setMethanolParams(int) MethanolRouteParams
setMillerIndex(int, int) LatticePlane
Sets the i-th Miller index to h, keeping the others fixed.
setMillerIndices(int[]) LatticePlane
Sets the plane to the orientation specified by the given Miller indices
applied to the current primitive.
setMinAdjustStep(double) MCMoveStepTracker
When the step size is adjusted, it is adjusted by adjustStep.
setMinBondedAtomDistance(double) AssociationHelperBranched
setMinBondedAtomDistance(double) AssociationHelperDouble
setMinBondedMoleculeDistance(double) AssociationHelperMolecule
setMinConfigIndex(int) MeterGs
setMinDistance(double) MCMoveInsertDeleteVacancy
setMinDistance(double) AtomTestDeviation
setMinimum(double) DeviceSlider
Sets minimum value of slider; should be called after
any calls to setPrecision.
setMinimum(double) DeviceSpinner
Sets minimum value of spinner
setMinimum(double) DeviceThermoSlider
Set the minimum value for the temperature.
setMinimum(double) DeviceThermoSliderGEMC
Set the minimum value for the temperature.
setMinimum(int) DeviceCellNum3DSlider
Set the minimum value for the N-Cell #.
setMinimum(int) DeviceCellNumXYSlider
Set the minimum value for the x- and y-Cell #.
setMinimum(int) DeviceEigenvaluesSlider
Set the minimum value for the eigenvalue #.
setMinimum(int) DeviceWaveVectorSlider
Set the minimum value for the wavevector #.
setMinimumFractionDigits(int) ScientificFormat
setMinimumIntegerDigits(int) ScientificFormat
setMinInterval(int) DataSourceBlockAvgCor
setMinInterval(int) StructureFactorComponentCorrelation
setMinMax(int, int) MCMoveInsertDeleteBiased
setMinPrevSample(int) MeterCorrelation
setMinRadicalSites(int) P2SquareWellSurface
setMobileSpecies(ISpecies) GrainBoundaryTiltConfiguration
setModelSelectedSpecies(ModelSelectedSpecies) AppModelMixtureBuilder
setModelSpeciesSelection(ModelSpeciesSelection) AppModelMixtureBuilder
setModeNum(int[]) MCMoveHarmonic
setModes(int[]) MCMoveHarmonicStep
Sets the indices of the harmonic modes of the k=0 wave vector which
should be sampled.
setModifier(Modifier) DeviceBox
Specifies the modifier that receives the edit.
setModifier(Modifier) DeviceNSelector
setModifier(Modifier) DeviceSlider
setModifier(Modifier) DeviceSpinner
setModifier(Modifier) DeviceThermoSlider
Set the temperature modifier object.
setModifier(Modifier) DeviceThermoSliderGEMC
Set the temperature modifier object.
setModifier(Modifier) DeviceEigenvaluesSlider
Set the eigenvalue # modifier object.
setModifier(Modifier) DeviceWaveVectorSlider
Set the wavevector # modifier object.
setModifier(ModifierBoolean) ActionToggle
Specifies the boolean modifier that is set between true and false by the
action.
setModifier(ModifierBoolean) DeviceCheckBox
Returns the boolean modifier set by this button.
setModifier(ModifierBoolean) DeviceToggleRadioButtons
Returns the boolean modifier set by this button.
setModifier(ModifierBoolean, String, String) DeviceToggleButton
setMolecule(IMolecule) MoleculeIteratorArrayList
Sets the first atom for iteration.
setMolecule(IMolecule) MoleculeIteratorMoleculeDependent
setMolecule(IMolecule) MoleculeIteratorSinglet
Defines atom returned by iterator and leaves iterator unset.
setMolecule(IMolecule, IMolecule) WriteConfigurationP2DLPOLY
setMoleculeAgentManager(MoleculeAgentManager) PotentialCalculationTorqueSumWallForce
setMoleculeAgentManager(MoleculeAgentManager) PotentialCalculationTorqueSum
setMoleculeInfo(ISpecies, P2SemiclassicalMolecular.MoleculeInfo) P2SemiclassicalMolecular
setMoleculeListDisplayLSM(ListSelectionModel) ViewSpeciesSelection
setMoleculeListDisplayLSM(ListSelectionModel) ViewSpeciesSelection
setMoleculeListDisplayString(ArrayList<String>) ModelSpeciesSelection
setMoleculeListDisplayTable(JTable) ViewSpeciesSelection
setMoleculeListDisplayTable(JTable) ViewSpeciesSelection
setMoleculeListDisplayTM(ModelMoleculeListDisplayTable_new) ViewSpeciesSelection
setMoleculeListDisplayTM(ModelMoleculeListDisplayTable_new) ViewSpeciesSelection
setMoleculeListDisplayTMListener(TableModelListener) ViewSpeciesSelection
setMoleculeListDisplayTMListener(TableModelListener) ViewSpeciesSelection
setMoleculeLists(IMoleculeList[]) AtomSetAllMolecules
Configures this list based on the given array of lists.
setMoleculeOffset(Vector) ConfigurationCatalysis
setMoleculeOffset(Vector) ConfigurationSAM
setMoleculeOriented(boolean) SpeciesBuilder
setMoleculePosition(IMoleculePositionDefinition) CriterionSimpleMolecular
setMolecules() IntegratorDimerApproach
setMoleculeSource(MoleculeSource) MCMoveMolecule
setMoleculeSource(MoleculeSource) MCMoveMoleculeExchange
Sets the AtomSource this class uses to pick molecules to delete.
setMoleculeSource(MoleculeSource) MCMoveClusterAngleBend
setMoleculeSource(MoleculeSource) MCMoveClusterAngleBendAceticAcid
setMoment(double) VLESim
setMoment(double, int) MolecularModel2CLJQ_SpeciesCO2
setMoment(double, int) MolecularModel2CLJQ_SpeciesEthane
setMoment(double, int) MolecularModel2CLJQ_SpeciesLJ
setMomentOfInertia(Vector) SpeciesBuilder
setMomentSquare(double, int) MolecularModelLJQ_SpeciesLJ
setMonomerColor(Color) ColorSchemeSmer
Sets the color used for all dimers.
setMonomerMonomerBondManager(AtomLeafAgentManager) ConfigurationColloid
setMovable(boolean) DisplayCanvas
setMovable(boolean) DisplayPolytope
setMovableAtoms(double, Vector) SimDimerLJadatom
setMovableAtoms(double, Vector) SimKMCLJadatom
setMove(MCMove) DataSourceAcceptanceRatio
Sets the move for which the acceptance ratio is reported.
setMoveManager(MCMoveManager) IntegratorManagerMC
setMoveManager(MCMoveManager) IntegratorMC
setMu(double) MCMoveIDBiasAction
Sets a nominal bias for states that have not yet been visited.
setMu(double) MCMoveInsertDelete
Mutator method for the chemical potential of the insertion/deletion species.
setMu(double) MCMoveInsertDeleteBiased
setMu(double) DataSourceAvgPressure
setMu(double) DataSourceFEHistogram
setMu(double) DataSourceImposedFEFit
setMu(double) DataSourceImposedFEHistogram
setMu(double) DataSourcePMu
setMu(double, double) IntegratorDCVGCMD
setMV(Matrix3f, Vector3f) Matrix4f
Initializes a Matrix4f from the rotation matrix
and translation.
setN(int) NormalModeAnalysisDisplay3D
setN(int) P4TorsionDreiding
setN(int) Ushcats
setNA(int) SelfAssemblySim
setName(String) MeterDihedralAngle
setName(String) MeterMomentumCOM
setName(String) MeterPositionCOM
setName(String) MeterRDF
setName(String) MeterRDFPC
setName(String) MeterTensorVelocity
setName(String) MeterMappedRdf
setName(String) MeterDimerFraction
setName(String) MeterHarmonicSingleEnergy
setName(String) MeterNormalMode
setName(String) MeterBondLength
setName(String) ScriptVariable
setNB(int) SelfAssemblySim
setNB1(int) SelfAssemblySim
setNB2(int) SelfAssemblySim
setNBins(int) AccumulatorHistogram
Sets the number of bins in each histogram.
setNBins(int) Histogram
Sets the number of bins used by the Histogram.
setNBins(int) HistogramDiscrete
setNBins(int) HistogramExpanding
Sets the number of bins to n.
setNBins(int) HistogramNotSoSimple
setNBins(int) HistogramReweightedData
setNBins(int) HistogramSimple
setNbrDistance(double) MCMoveAtomSwap
setNbrMax(double) AtomNbrClusterer
setNbrMax(double) ColorSchemeCluster
setNbrMax(double) DataSourcePercolation
setNbrMax(double) DataSourcePercolation0
setNbrMax(double) ColorSchemeCluster
setNCellModifier(Modifier) DeviceCellNum3DSlider
Set the n-Cell # modifier object.
setNCellNum(int) DeviceCellNum3DSlider
Set the current value for the N-Cell # slider/text box.
setNCellNum(int) NormalModes3D
setNCells(int[]) NormalModeAnalysisDisplay2D
setNCells(int[]) NormalModeAnalysisDisplay3D
setNCellsX(int) ConfigurationCatalysis
setNCellsX(int) ConfigurationSAM
setNCellsZ(int) ConfigurationCatalysis
setNCellsZ(int) ConfigurationSAM
setNCrossLinkersAcid(int) ChainEquilibriumSim
setNDiAcid(int) ChainEquilibriumSim
setNDiol(int) ChainEquilibriumSim
setNegativePrefix(String) ScientificFormat
setNegativeSuffix(String) ScientificFormat
setNeighborDistance(double) CellLattice.NeighborIterator
Defines neighbors to be all cells that are within the given distance
from a central cell.
setNeighborRange(double) RectangularLattice
setNeighborRange(double) CriterionPositionWall
Sets the neighbor range of the criterion.
setNeighborRange(double) CriterionSimple
setNeighborRange(double) CriterionSimpleMolecular
setNewWindowParametersForExport() GData
setNGraft(int) ConfigurationColloid
setNInsert(int) MeterWidomCavity
Number of Widom insertions attempted with each call to currentValue
setNInsert(int) MeterWidomInsertion
Number of Widom insertions attempted with each call to currentValue
setNInsert(int) MeterWidomInsertionCorrection
Number of Widom insertions attempted with each call to currentValue
setNInsert(int) MeterWidomInsertionP
Number of Widom insertions attempted with each call to currentValue
setNMajor(int) DeviceSlider
setNMajor(int) DeviceThermoSliderGEMC
setNMax(int) AccumulatorAutocorrelationPTensor
setNMax(int) AccumulatorAutocorrelationShearStress
setNMaxReweight(int) MCMoveIDBiasAction
setNMinor(int) DeviceSlider
setNMolecules(ISpecies, int) Box
Sets the number of molecules in this box of the given Species to n.
setNMonoAcid(int) ChainEquilibriumSim
setNMonoOl(int) ChainEquilibriumSim
setNo72B2B3NonAdd(boolean) ClusterSumNonAdditiveTrimerEnergy
setNoisyAdjustment(boolean) MCMoveStepTracker
setNoisySurfaceShade(Point3i, Point3i, Point3i) Graphics3D
used by CartoonRenderer (DNA surface) and GeoSurfaceRenderer (face) to
assign a noisy shade to the surface it will render
setNoisySurfaceShade(Point3i, Point3i, Point3i) GData
setNominalFluctuation(double) HSNPT.ColorSchemeDisplacement
setNominalReference(IMoleculeList) CoordinateDefinitionNitrogen
setNominalTheta(double) MCMoveVolumeSolidNPTMolecularOriented
setNominalTheta(double) MeterThetaDeviation
setNoOfSpheres(JTextField) ViewAlkaneLengthSelection
setNoOfSteps(int) ModelSimulationEnvironment
setNoOfSteps(int) ModelTemperatureAndSteps
setNormalizeByN(boolean) MeterStructureFactor
Normalizing by N will produce a structure factor that is insensitive to
finite-size effects if there is no long-range order.
setNormalModes(NormalModes) MCMoveAtomCoupledBennet
setNormalModes(NormalModes) MCMoveAtomCoupledUmbrella
setNormalPoint(Vector, Vector) Plane
Defines the plane via a normal vector (1st argument) and
a point (2nd argument).
setNormalVector(Vector) Plane
Sets the orientation of the plane to be normal to the given vector.
setnPoints(int[]) ModelSimulationEnvironment
setNPoints(int) P2DiscreteFeynmanHibbs
setnReactCO(int) ReactionManagerCO
setNRows(int) DataTable.DataInfoTableFactory
Sets the number of rows.
setNSliderPostAction(IAction) DeviceCellNum3DSlider
Set the post slider value changed action.
setNSpheres(int) MolecularModelSKS_SpeciesAlkane
setNSpheres(int) MolecularModelTRAPPE_SpeciesAlkane
setNthSpeciesAdded(int) ModelSelectedSpecies
setNthSpeciesSelectedIndex(int) ModelSpeciesSelection
setNullPotential(PotentialHard) IntegratorHard.Agent
setNullPotential(PotentialHard, AtomType) IntegratorHard
Sets the "null" potential for the given AtomType.
setNullRegionMethod(int) P3CPSNonAdditiveHe
setNullRegionMethod(int) P3CPSNonAdditiveHeLessSimplified
setNullRegionMethod(int) P3CPSNonAdditiveHeSimplified
setNumAlpha(int) MeterTargetRPMolecule
setNumAlpha(int) MeterTargetTPMolecule
setNumAlpha(int) MeterMBAR
setNumAlpha(int) AccumulatorOverlapAverageUa2
setNumAlpha(int) MeterOverlapSwitch
setNumAlpha(int) MeterTargetTP
setNumAlpha(int) SimOverlapSoftSphereEinHarm
setNumAlpha(int) MeterOverlap
setNumAlpha(int) AccumulatorVirialOverlapSingleAverage
setNumAlpha(int) DataProcessorVirialOverlap
setNumAlpha(int) SimulationVirialOverlap2
Sets the number of alpha values used for the production stage of the
simulation.
setNumBDCheckBins(int) ClusterWheatleySoftDerivatives
setNumBeads(int) MCMoveClusterRingPartialRegrow
setNumber(double) StrainColorScheme
setNumBoxes(int) IntegratorPT.BoxTracker
Specifies the number of boxes that are tracked.
setNumClusters(int) DataClusterer
setNumCO(int) ConfigurationCatalysis
setNumCollapseBins(int) HistoryCollapsing
Sets the number of "collapse" bins.
setNumDigitColumns(int) DisplayTable
setNumerator(int) Coefficient
setNumerator(int) CoefficientImpl
setNumFactors(int) Graph
setNumFactors(int) GraphImpl
setNumGraft(int) ColloidSim
setNumInnerSteps(int) IntegratorImageMultistepMD
setNumMembraneLayers(int) ConfigurationMembrane
setNumMembraneLayers(int) ConfigurationMembraneWater
setNumO2(int) ConfigurationCatalysis
setNumP(int) MeterDDP
setNumP(int) MeterDP
setNumRawDataDoubles(int) AccumulatorAverageBootstrap
Sets the number of times the random block generation method is used.
setNumRawDataDoubles(int) AccumulatorAverageCollapsingLog
Sets the number of times the random block generation method is used.
setNumSubSteps(int) IntegratorOverlap
Deprecated.
Sets the number of total number of integrator steps the sub-integrators
perform for every step of the overlap integrator.
setNumSubSteps(long) IntegratorOverlap
Sets the number of total number of integrator steps the sub-integrators
perform for every step of the overlap integrator.
setNumSurfaceSites(int) P2SquareWellBonding
setNumSurfaceSites(int) P2SquareWellBondingCO
setNumTrial(int) MCMoveClusterRingPartialRegrow
setNumTrial(int) MCMoveClusterRingRegrow
Sets the number of configurational bias trials
setNumTrial(int) MCMoveClusterRingRegrowExchange
Sets the number of configurational bias trials
setNumXCells(int) Sam
setNumZCells(int) Sam
setNValues(int) DataSourceUniform
Sets the number of uniformly spaced values.
setOelement(ElementSimple) SimpleElementForSimilarSpecies
setOffset(Vector) ConformationChainLinear
setOffset(Vector) ConformationLinear
setOffset(Vector) P1Sinusoidal
setOmegaSquared(double[][]) MCMoveHarmonic
setOmegaSquared(double[][]) MeterHarmonicEnergy
setOmegaSquared(double[][]) MeterHarmonicSingleEnergy
setOmegaSquared(double[][], double[]) IntegratorHarmonic
setOmegaSquared(double[][], double[]) MCMoveSingleMode
setOneEVal() DeviceEigenvaluesSlider
Set the "eigenvalues" button to its selected state.
setOneEVal(boolean) IntegratorHarmonic
setOneEValButtonsVisibility(boolean) DeviceEigenvaluesSlider
setOneWV() DeviceWaveVectorSlider
Set the "wave vector" button to its selected state.
setOneWV(boolean) IntegratorHarmonic
setOneWVButtonsVisibility(boolean) DeviceWaveVectorSlider
setOnlyConnected(boolean) ClusterGenerator
Set whether to only generate clusters that are singly-connected.
setOnlyDoublyConnected(boolean) ClusterGenerator
Set whether to only generate clusters that are doubly-connected.
setOrderBeta(int) VirialDiagramsPT
setOrientation(IMolecule, double[]) OrientationCalcWater3P
setOrientation(IMolecule, double[]) OrientationCalcWater4P
setOrientation(IMolecule, double[]) OrientationCalcQuaternion
setOrientation(IMolecule, IOrientationFull3D) OrientationCalcWater3P
setOrientation(IMolecule, IOrientationFull3D) OrientationCalcWater4P
setOrientation(IMolecule, IOrientationFull3D) OrientationCalc
Sets the orientation of the given molecule to be equal to the given
orientation.
setOrientation(IMolecule, IOrientationFull3D) OrientationCalcAtom
setOrientation(Vector) ConformationChainLinear
setOrientation(Vector) ConformationLinear
setOrientation(IOrientationFull3D) RotationTensor3D
setOrientationCalc(ISpecies, OrientationCalc) IntegratorRigidIterative
setOrientationCalc(ISpecies, OrientationCalc) IntegratorRigidMatrixIterative
setOrientationCalc(ISpecies, OrientationCalcQuaternion) IntegratorVelocityVerletQuaternion
setOrientationColor(Color) DisplayBoxCanvas2D
setOrientationLength(double) DisplayBoxCanvas2D
Sets the length of the drawn orientation line as a fraction of diameter
setOrientations(Vector[][], double[], CoordinateDefinitionHSDimer.IntegerFunction) CoordinateDefinitionHSDimer
setOrientationSites(AtomTypeOriented, DisplayBoxCanvasG3DSys.OrientedSite[]) DisplayBoxCanvasG3DSys
setOrientationVectorAlpha(Space) CoordinateDefinitionNitrogen
setOrientationVectorAlpha(Space) CoordinateDefinitionNitrogenSuperBox
setOrientationVectorBeta(Space) CoordinateDefinitionNitrogen
setOrientationVectorBetaInitial(Space) CoordinateDefinitionNitrogen
setOrientationVectorBetaLatticeSum(Space, double, double[][]) CoordinateDefinitionNitrogen
setOrientationVectorGamma(Space) CoordinateDefinitionNitrogen
setOrientationVectorGamma(Space) CoordinateDefinitionNitrogenSuperBox
setOrigin(Vector) LatticePlane
Sets the origin from which the position of the atom is measured.
setOriginShift(int, int) DisplayBox
Amount (in pixels) of a simple shift (translation) applied in determing origin.
setOrtho(boolean, boolean) IntegratorDimerRT
Set's the Dimer search's orthogonality criteria.
setOtherAngles(double[]) MeterTargetRPMolecule
setOtherDensities(double[]) MeterDDP
setOtherDensities(double[]) MeterDP
setOtherSwitchFrac(double[]) MeterOverlapSwitch
setOtherTemperature(double) MeterBoltzmannHTTP
setOtherTemperatures(double[]) MeterTargetTPMolecule
setOtherTemperatures(double[]) MeterTargetTP
setOut(PrintStream) DataSinkConsole
Sets the output print stream where data is written.
setOuterGraph(Graph) CartesianIterator
setOuterIterator(GraphIterator) CartesianIterator
setOuterList(IAtomList) ApiInterArrayList
Sets the list that will be used to generate the pairs.
setOuterList(IMoleculeList) MpiInterArrayList
Sets the list that will be used to generate the pairs.
setOuterPermutation(byte[]) CartesianPermutator
setOuterPermutator(DefaultPermutator) CartesianPermutator
setOverlapSplitter(DataSplitter) MultiharmonicGraphicMC.DataSourceAlphaFE
setOverwrite(boolean) WriteS
setP1(P1ImageHarmonic) MCMoveAtomCoupled
setP1Harmonic(P1ImageHarmonic) IntegratorImageHarmonicMD
setP1Harmonic(P1ImageHarmonic) IntegratorImageMultistepMD
setP1Harmonic(P1ImageHarmonic) IntegratorMDHarmonicMC
setPaddingSigma(double) DisplayBox
Sets the amount of padding added around the edge of the drawing area.
setPaintInterval(Box, int) SimulationGraphic
setPaintInterval()
setParameter(String, String) IMolecularModel_SpeciesFactory
setParameter(String, String) MolecularModel2CLJQ_SpeciesCO2
setParameter(String, String) MolecularModel2CLJQ_SpeciesEthane
setParameter(String, String) MolecularModel2CLJQ_SpeciesLJ
setParameter(String, String) MolecularModelEMP2_SpeciesCO2
setParameter(String, String) MolecularModelLJ_SpeciesLJ
setParameter(String, String) MolecularModelLJQ_SpeciesLJ
setParameter(String, String) MolecularModelSKS_SpeciesAlkane
setParameter(String, String) MolecularModelSPCE_SpeciesH2O
setParameter(String, String) MolecularModelTRAPPE_SpeciesAlkane
setParameter(String, String) MolecularModelTrappe_SpeciesCO2
setParameterLimits(String, double, double) DevicePlotPoints
Sets the minimum and maximum allowable values for a function parameter.
setParameters(double) P2HC2Yukawa
Parameter calculation method.
setParameters(double) P3CPSNonAdditiveHeSimplified
setParameters(String) P3CPSNonAdditiveHeLessSimplified
setParameters(String) P3CPSNonAdditiveHeSimplified
setParameterWrapper(ParameterBase) ParseArgs
Sets the parameterWrapper
setParameterWrapper(ParameterBase) ReadParameters
Sets the parameterWrapper
setParameterWrapper(ParameterBase) WriteParameters
Sets the parameterWrapper
setParams() BnJHBVArgon_Analytic
setParent(IMolecule) Atom
Informs the Atom that the given AtomGroup is its parent.
setParent(IMolecule) IAtom
Informs the Atom that the given IMolecule is its parent.
setParseIntegerOnly(boolean) ScientificFormat
setPartner(int, int) P1ImageHarmonic
setPass2(boolean) Graphics3D
setPass2(boolean) GData
setPbcEnforcer(BoxImposePbc) NeighborListManagerMolecular
setPCenter(double[]) MeterDDP
setPCenter(double[]) MeterDP
setPeriodicity(boolean[]) RectangularLattice
setPeriodicity(boolean[]) RectangularLatticeNbrIterator
setPerpendicularTo(Vector) Vector3D
setPerspectiveDepth(boolean) G3DSys
setPhi(double) P4TorsionDreiding
setPhongExponent(int) GData
p in I = df * (N dot L) + sf * (R dot V)^p
setPistonPotential(P1HardMovingBoundary) BoundaryPistonCylinder
setPixelUnit(Pixel) DisplayBox
Sets unit for conversion between simulation units and display pixels.
setPixelUnit(Pixel) DisplayCanvas
Sets unit for conversion between simulation units and display pixels.
setPixelUnit(Pixel) DisplayPolytope
Sets unit for conversion between simulation units and display pixels.
setPixelUnitToMillimeter(float) SVGConverter
Sets the millimeters per pixel constant.
setPlaneColor(Color) DisplayBoxCanvasG3DSys
Sets the color of the plane.
setPlayDumb(boolean) MCMoveIDBiasAction
With "play dumb" on, the bias will simply try to produce a flat
histogram based on previously-measured free energy differences
(no fitting or defect free energy will be used).
setPolygonCount(int) MeshSurface
setPolytope(Polytope) DisplayPolytope
Specifies the polytope for this display.
setPolytopeCanvas(DisplayCanvas) DisplayPolytope
setPoreCenters(Vector[]) P1WCAPorousWall
setPoreDim(int) BoundaryRectangularPore
Sets the periodic dimension to that indicated by the given value
(0 is x-dimension, 1 is y-dimension, etc.).
setPoreRadius(double) P1WCAPorousWall
setPosition(double) LatticePlane
Sets to the position of the i-th plane from the one through the origin.
setPosition(IAtom, String) ConfigurationFile
setPosition(IAtom, String) ConfigurationOrientedFile
setPosition(Vector) Hypersphere
setPosition(Vector) Polytope
Sets the position of the geometric center of the polytope.
setPosition(Vector) Shape
Sets the position of the shape, which typically represents some central
point within it.
setPositionDefinition(IMoleculePositionDefinition) BoxImposePbc
setPositionDefinition(IMoleculePositionDefinition) MeterProfileByAtoms
setPositionDefinition(IMoleculePositionDefinition) MeterProfileByVolume
setPositionDefinition(IMoleculePositionDefinition) MCMoveRotateMolecule3D
setPositionDefinition(IMoleculePositionDefinition) CoordinateDefinitionMolecule
setPositionDefinition(IMoleculePositionDefinition) CoordinateDefinitionMoleculeVolumeFluctuation
setPositionDefinition(IMoleculePositionDefinition) BoxCluster
setPositionDefinition(IMoleculePositionDefinition) CoordinatePairMoleculeSet
setPositionSource(RandomPositionSource) MeterProfile
Sets a new RandomPositionSource for this meter to use.
setPositionSource(RandomPositionSource) MeterWidomInsertion
Sets a new RandomPositionSource for this meter to use.
setPositionSource(RandomPositionSource) MCMoveInsertDelete
Sets a new RandomPositionSource for this move to use.
setPositionSource(RandomPositionSource) MCMoveMoleculeExchange
Sets a new RandomPositionSource for this move to use.
setPositionSource(RandomPositionSource) MeterWidomInsertionCorrection
Sets a new RandomPositionSource for this meter to use.
setPositionSource(RandomPositionSource) MeterWidomInsertionP
Sets a new RandomPositionSource for this meter to use.
setPositivePrefix(String) ScientificFormat
setPositiveSuffix(String) ScientificFormat
setPostAction(IAction) SimulationRestart
setPostAction(IAction) ConfigFromFileLAMMPS.ModifierConfiguration
setPostAction(IAction) Device
Sets an action to be performed after the primary action executed
by the device.
setPotential(AtomType, AtomType, IPotentialAtomic) MCMoveGeometricCluster
Informs the move that p2 is the potential between type1 and type2.
setPotential(AtomType, AtomType, IPotentialAtomic) MCMoveGeometricClusterRestrictedGE
Informs the move that p2 is the potential between type1 and type2.
setPotential(DataSourceScalar) MeterEnergy
setPotential(IPotentialAtomic) MCMoveAtomCoupled
setPotential(IPotentialAtomic[]) MCMoveAtomCoupled
setPotential(IPotentialMolecular) MCMoveMoleculeCoupledInitPert
setPotential(IPotentialMolecular) MCMoveMoleculeCoupledSuperBox
setPotential(IPotentialMolecular) MCMoveRotateMolecule3DSuperBox
setPotential(IPotentialMolecular) MCMoveMoleculeCoupled
setPotential(P1HardMovingBoundary) MeterRDFCylinder
setPotential(Potential2) MCMoveAtomSuperBox
setPotential(Potential2SoftSpherical) PotentialCalculationMappedRdf
setPotential(Potential2SoftSpherical) NormalModesPotential
setPotential(Potential2SoftSpherical) NormalModesSoftSpherical
setPotential(String) InsertionGraphic
setPotential(String) PistonCylinderGraphic
setPotential(String) SwmdGraphic
setPotentialCalculation(DataSourceEnergies.PotentialCalculationEnergies) DataSourceEnergies
setPotentialCalculation(PotentialCalculationEnergySum) MeterPotentialEnergy
setPotentialCollectionFactory(ICollectionPotential) ModelSimulationConstructor
setPotentialGroupInterNonBondedLike(PotentialGroup) CollectionPotentialAtomicLike
setPotentialGroupInterNonBondedUnlike(PotentialGroup) CollectionPotentialAtomicUnlike
setPotentialGroupIntraBonded(PotentialGroup) CollectionPotentialAtomicLike
setPotentialHard(boolean) PotentialMaster
setPotentialIntraBondedTorsion(IPotentialAtomic) CollectionPotentialAtomicLike
setPotentialJList(JList) ViewSpeciesSelection
setPotentialJList(JList) ViewSpeciesSelection
setPotentialJListListener(ListSelectionListener) ViewSpeciesSelection
setPotentialJListListener(ListSelectionListener) ViewSpeciesSelection
setPotentialList(Class[]) ModelSpeciesSelection
setPotentialListDisplayLSM(ListSelectionModel) ViewSpeciesSelection
setPotentialListDisplayLSM(ListSelectionModel) ViewSpeciesSelection
setPotentialMaster(PotentialMasterListMolecular) BoxAgentSourceCellManagerListMolecular
setPotentialMaster(PotentialMasterListMolecular) NeighborCellManagerListMolecular
setPotentialMaster(PotentialMasterListMolecular) PotentialMasterListMolecular.NeighborListAgentSourceMolecular
setPotentialMaster(PotentialMasterList) NeighborListAgentSource
setPotentialMaster(PotentialMasterList, AtomType[]) P2SquareWellRobust
Informs the square-well class what the potential master is (if neighbor
listing is used) and the types of atoms interacting with this potential.
setPotentialMaster(PotentialMaster) MeterHyperVirial
setPotentialMaster(PotentialMaster) MeterPressure
setPotentialMaster(PotentialMaster) MeterPU
setPotentialMaster(PotentialMaster) MeterPUCut
setPotentialMaster(PotentialMaster) MeterPUCutLS
setPotentialMaster(PotentialMaster) MeterPressure2
Sets the integrator associated with this instance.
setPotentialMaster(PotentialMaster) PotentialGroupHybrid
setPotentialMaster(PotentialMaster) PotentialGroup
setPotentialMaster(PotentialMaster) ClusterSumExternalField
setPotentialMasterDADv2(PotentialMaster) MeterPUCut
setPotentialMasterDADv2(PotentialMaster) MeterPUCutLS
setPotentialMasterDADv2(PotentialMaster, double[]) MeterSolidDACut
setPotentialMC(IPotentialAtomic) NeighborListManagerColloid
setPotentialMolecularNonBondedLike(IPotentialMolecular) CollectionPotentialMolecularLike
setPotentialMolecularUnlike(IPotentialMolecular) CollectionPotentialMolecularUnlike
setPotentialParamAndValuesString(String[][]) ModelSpeciesSelection
setPotentialParamDispayTable(JTable) ViewSpeciesSelection
setPotentialParamDispayTable(JTable) ViewSpeciesSelection
setPotentialParamDisplayLSM(ListSelectionModel) ViewSpeciesSelection
setPotentialParamDisplayLSM(ListSelectionModel) ViewSpeciesSelection
setPotentialParamDisplayTM(ModelPotParamDisplayTable) ViewSpeciesSelection
setPotentialParamDisplayTM(ModelPotParamDisplayTable) ViewSpeciesSelection
setPotentialParamDisplayTMListener(TableModelListener) ViewSpeciesSelection
setPotentialParamDisplayTMListener(TableModelListener) ViewSpeciesSelection
setPotentialParamString(String[]) ModelSpeciesSelection
setPotentialPseudo(IPotentialAtomic) NeighborListManagerColloid
setPotentialRange(double) NeighborCellManagerMolecular
Sets the potential range to the given value.
setPotentialRange(double) NeighborCellManager
Sets the potential range to the given value.
setPotentialsClassList(Class[]) ModelSpeciesSelection
setPotentialsCollectionBuilder(BuilderCollectionPotential) ModelSimulationConstructor
setPotentialSites(String[]) MolecularModel2CLJQ_SpeciesLJ
setPotentialsSelectedIndex(int[]) ModelSpeciesSelection
setPotentialsSelectedIndex(int, int) ModelSpeciesSelection
setPreAction(IAction) Device
Sets an action to be performed before the primary action executed
by the device.
setPrecision(int) DataDoubleBDArray.DataInfoDoubleBDArrayFactory
setPrecision(int) DecimalSlider
Mutator method for precision of slider.
setPrecision(int) DeviceBox
Accessor method of the precision, which specifies the number of significant figures to be displayed.
setPrecision(int) DeviceSlider
setPrecision(int) DeviceThermoSlider
Set the precision of the scrollbar.
setPrecision(int) DisplayTable
Accessor method of the precision, which specifies the number of
significant figures to be displayed.
setPrecision(int) DisplayTextBox
Accessor method of the precision, which specifies the number of significant figures to be displayed.
setPrecision(int) DisplayTextBoxesCAE
Accessor method of the precision, which specifies the number of significant figures to be displayed.
setPrecision(int) DeviceThermoSliderGEMC
Set the precision of the scrollbar.
setPrecision(int) PotentialCalculationEnergySumBigDecimal
setPrecisionLimit(int) ClusterWheatleyMultibodyBD
setPrecisionLimit(int) ClusterWheatleyMultibodyDerivativesBD
setPrecisionLimit(int) ClusterWheatleySoftDerivativesBD
setPrefactor(double) ClusterDiagramTree
setPreferredSize(int, int) DeviceTable
Set the preferred size attribute of the scrolled window the table
sits on.
setPrefix(Prefix) PrefixedUnit
Changes prefix to given instance if prefixAllowed flag is true.
setPRes(double) MeterSolidDA
setPressure(double) MCMoveVolumeAssociated
setPressure(double) MCMoveVolumeAssociatedMolecule
setPressure(double) MeterWidomInsertion
setPressure(double) MCMoveVolume
setPressure(double) MeterWidomInsertionP
setPressure(double) MCMoveVolumeN2
setPressure(double) DataSourceDensityFunction
setPressure(double) MeterExcessAdsorbed
setPressure(double) MCMoveVolumeMonoclinicScaled
setPressure(double) MCMoveVolumeSolid
setPressure(double) MCMoveVolumeSolidNPTMolecular
setPressure(double) ColorSchemeScaledOverlap
setPressure(double) DisplayBoxCanvas2DNpTScaling
setPressure(double) HSNPT2DGraphic
setPressure(double) P1HardMovingBoundary
setPressure(double, double, IFunction) MeterWidomInsertionCorrection
setPrevConfig(int) AtomSignalMobility
setPrevConfig(int) AtomSignalMotion
setPrevConfigIndex(int) DataSourcePrevTime
setPrevSampleIndex(int) MeterCorrelation
setPrevStep(int) ConfigurationStoragePumper
setPrevX(float) DisplayCanvas
setPrevY(float) DisplayCanvas
setPrimitive(Primitive) BravaisLattice
Sets the primitive for this lattice to the one given, and
updates the site positions.
setPrimitive(Primitive) LatticePlane
setPrimitive(Primitive) NormalModesSoftSpherical
setProfileDim(int) MeterProfile
Accessor method for vector describing the direction along which the profile is measured.
setProfileDim(int) MeterProfileByAtoms
Accessor method for vector describing the direction along which the profile is measured.
setProfileDim(int) MeterProfileByVolume
Accessor method for vector describing the direction along which the profile is measured.
setProfileDim(int) DataProcessorInterfacialTensionProfile
setProperty(String) DeviceSlider
setProperty(String) DeviceSpinner
setProperty(String, String) Environment
setProperty(String, String) EnvironmentImpl
SetPropertyFilter etomica.graph.operations
SetPropertyFilter(Property) SetPropertyFilter
setPT2(boolean) P2O2Bartolomei
setPullFactor(double) MCMoveIDBiasAction
setPushInterval(long) DataAccumulator
Accumulated data are pushed to the data sinks after every pushInterval calls
to putData.
setQ(double) Charge
setQ(Vector) DataSourceFs
setQuadrupolarMomentSquare(double) P22CLJQ
setQuadrupolarMomentSquare(double) P2LJQ
setQuadrupolarMomentSquare(double) P2LJQQ
setQuality(float) SVGConverter
Sets the JPEG encoding quality.
setQuaternions(double[]) RotationTensor3D
setQuiet(boolean) NeighborListManagerMolecular
Sets the quiet flag, indicating if unsafe-neighbor conditions should generate
an error message (would not want this if atoms were inserted in a MC
move, for example).
setQuiet(boolean) NeighborListManager
Sets the quiet flag, indicating if unsafe-neighbor conditions should generate
an error message (would not want this if atoms were inserted in a MC
move, for example).
setQuiet(boolean) MeterVirialBDBinMultiThreaded
setQuiet(boolean) MeterVirialBinMultiThreaded
setQuiet(boolean) MeterVirialEBinMultiThreaded
setR0(double) P2Harmonic
Sets the the separation at which potential is at its minimum.
setr2d2udr2(double[]) PercusYevick1QC
setRadicalColor(AtomType, Color) ColorSchemeRadical
setRadioGroupPostAction(IAction) DeviceThermoSlider
Sets an action to be performed after a isothermal/adiabatic button is
pressed and the integrator's isothermality has been set.
setRadius(double) Hypersphere
setRadius(double) P1SoftBoundary
Sets the radius.
setRandom(IRandom) Simulation
Set the simulation's random number generator to the given one.
setRandom(IRandom) ClusterDiagramTree
setRandomCube(IRandom) Vector
Assigns each component to (its own) random value between -0.5 and + 0.5.
setRandomCube(IRandom) Vector1D
setRandomCube(IRandom) Vector2D
setRandomCube(IRandom) Vector3D
setRandomCube(IRandom) VectorND
setRandomInSphere(IRandom) Vector
Assigns this vector to equal a point chosen randomly in the volume
of a unit sphere.
setRandomInSphere(IRandom) Vector1D
setRandomInSphere(IRandom) Vector2D
setRandomInSphere(IRandom) Vector3D
setRandomInSphere(IRandom) VectorND
setRandomNumberGenerator(IRandom) AtomSourceRandomDimer
setRandomNumberGenerator(IRandom) AtomSourceRandomSmer
setRandomNumberGenerator(IRandom) MoleculeSourceRandomDimer
setRandomNumberGenerator(IRandom) AtomSourceRandomLeaf
Sets the random number generator used to pick atoms
setRandomNumberGenerator(IRandom) AtomSourceRandomSpecies
Sets the random number generator used to pick atoms
setRandomNumberGenerator(IRandom) MoleculeSourceRandomMolecule
Sets the random number generator used to pick molecules
setRandomSphere(IRandom) Vector
Assigns this vector to equal a point chosen randomly on the
surface of a unit sphere.
setRandomSphere(IRandom) Vector1D
setRandomSphere(IRandom) Vector2D
setRandomSphere(IRandom) Vector3D
Creating a random unit vector on unit sphere Uses only two random number
generator at a time
Based on M.P.
setRandomSphere(IRandom) VectorND
Creating a random unit vector on unit sphere Uses only two random number
generator at a time
Based on M.P.
setRange(double) PotentialEAM_LS
setRange(double) PotentialEAM
setRange(double) PotentialEFS
setRange(double) P2Nitrogen
setRange(double) P1Wall
setRange(double) P1Wall
setRange(double) BoxAgentSourceCellManager
setRange(double) BoxAgentSourceCellManagerMolecular
setRange(double) PotentialMasterCell
setRange(double) NeighborListManagerMolecular
Sets the interaction range, which affects the cell-list neighbor iteration
used to generate candidate neighbors for neighbor listing.
setRange(double) PotentialMasterListMolecular.NeighborListAgentSourceMolecular
setRange(double) PotentialMasterListMolecular
Sets the range that determines how far to look for neighbors.
setRange(double) NeighborListAgentSource
setRange(double) NeighborListManager
Sets the interaction range, which affects the cell-list neighbor iteration
used to generate candidate neighbors for neighbor listing.
setRange(double) PotentialMasterList
Sets the range that determines how far to look for neighbors.
setRange(double) PotentialMasterHybrid
setRange(double) P2CO2EMP
setRange(double) P2Ideal
setRange(double) P2ReactionFieldDipole
setRange(double) P2ReactionFieldDipoleTruncated
setRange(double, double) PotentialCuLREP
setRange(double, double) MeterProfileByVolumeAdsorption
setRange(int[]) RectangularLatticeNbrIteratorSquare
Sets the range used to define the neighboring sites.
setRange(int, double, double) MeterExcessAdsorbed
setRatio(double, double) MinimizeGammaNitrogenLatticeParameter
setRawData(AccumulatorAverageBlockless.AllData) AccumulatorAverageBlockless
setRawData(AccumulatorAverageBlockless.AllData) AccumulatorAverageBlocklessSlim
setRawSink(IDataSink) MeterCavityMapped
setRawSink(IDataSink) MeterRDFMapped
setRCut(double) EwaldSummation
Sets a new value of rCutRealES
This will not alter values of alpha or nRealShells!
setRCut(double) ClusterWheatleyMultibody
setRCut(double) ClusterWheatleyMultibodyBD
setRCut(double) ClusterWheatleySoftDerivatives
setRCut(double) ClusterWheatleySoftDerivativesBD
setrdfdr(double[]) HypernettedChain
setrdfdr(double[]) PercusYevick
setrdudr(double[]) PercusYevick1QC
setRe(double) P2ModifiedMorse
setRe(double) P2Morse
setReader(ConsoleReader) Console
setReader(ConsoleReader) ConsoleUI
setRef(Quaternion) Quaternion
setRefAvg(DataOverlap.DataSourceOverlapAvg) DataOverlap
setReferenceDataInterval(int) SimOverlapModule
setReferenceFracSource(IntegratorOverlap.ReferenceFracSource) IntegratorOverlap
Sets the DataSource that retrieves data from both boxes and provides
information to the integrator about their progress, which is used to
decide how much to sample each system.
setReflecting(boolean[]) IndexIteratorReflecting
Indicates the indexes of the elements that are subject to reflection.
setRefPref(double) SimOverlapNitrogenModel
setRefPref(double) MeterSamplingHarmonic
setRefPref(double) MeterSamplingTarget
setRefPref(double) MeterWorkBennetHarmonic
setRefPref(double) MeterWorkBennetTarget
setRefPref(double) MeterWorkHarmonicBennet
setRefPref(double) MeterWorkHarmonicUmbrella
setRefPref(double) MeterWorkTargetBennet
setRefPref(double) MeterWorkTargetUmbrella
setRefPref(double) MeterWorkUmbrellaHarmonic
setRefPref(double) MeterWorkUmbrellaTarget
setRefPref(double) SimBennet
setRefPref(double) SimHarmonicUmbrella
setRefPref(double) SimOverlap
setRefPref(double) SimOverlapLJ
setRefPref(double) SimOverlapSoftSphere
setRefPref(double) SimOverlapSoftSphereHCP
setRefPref(double) SimOverlapSoftSphereReweighting
setRefPref(double) SimOverlapSoftSphereSuperBox
setRefPref(double) SimOverlapSSnxy
setRefPref(double) SimTargetUmbrella
setRefPref(double) SimUmbrella
setRefPref(double) SimUmbrellaSoftSphere
setRefPref(double) SimulationVirialOverlap2
setRefPref(double, double) SimOverlapBetaN2RP
setRefPref(double, double) SimOverlapNitrogenModel
setRefPref(double, double) SimOverlap
setRefPref(double, double) SimOverlapLJ
setRefPref(double, double) SimOverlapSoftSphere
setRefPref(double, double) SimOverlapSoftSphereHCP
setRefPref(double, double) SimOverlapSoftSphereReweighting
setRefPref(double, double) SimOverlapSoftSphereSoftness
setRefPref(double, double) SimOverlapSoftSphereSuperBox
setRefPref(double, double) SimOverlapSSnxy
setRefPref(double, double) SimulationVirialOverlap2
setRefStepFraction(double) IntegratorOverlap
setRejectable(boolean) MCMoveHarmonic
setRelaxAction(MoleculeAction) MCMoveClusterRotateMolecule3D
setRelaxAction(MoleculeAction) MCMoveClusterRotateMoleculeMulti
setRemove(JButton) ViewSpeciesSelection
setRemoveSpecies1(JButton) ViewSpeciesSelection
setRemoveSpecies2(JButton) ViewSpeciesSelection
setRemoveSpecies3(JButton) ViewSpeciesSelection
setRemoveSpeciesAfterAlertFlag(boolean) ModelSpeciesSelection
setRepaintInterval(int) PistonCylinderGraphic
setRescalingToFitVolume(boolean) ConfigurationLattice
Sets the resizeLatticeToFitVolume flag, which if true indicates that the
primitive vectors should be resized to fit the dimensions of the box.
setReset(JButton) ViewSpeciesSelection
setReset(JButton) ViewSpeciesSelection
setResetAction(IAction) DeviceNSelector
setResetAfterData(boolean) MeterCavityMapped
setResetAfterData(boolean) MeterRDFMapped
setResidual(boolean) MeterWidomInsertion
Sets flag specifying if full or residual chemical potential is computed
Default is true (only residual is computed)
setResidual(boolean) MeterWidomInsertionCorrection
setResizable(boolean) DisplayCanvas
setResizable(boolean) DisplayPolytope
setResizeOnNewBox(boolean) DisplayBox
Set the flag indicating whether the graphic should resize from its
currently displayed size when a new box is set.
setRgb(Rgb16) Rgb16
setRGraftMin(double) P2SquareWellMonomer
setRho(double) PNWaterGCPMReactionField
setRm(double) P2Exp6Buckingham
setRmax(double) MeterDihedralAngle
setRmax(double) P2Exp6Buckingham
setRotationAxis(Vector, double) RotationTensor3D
Sets the tensor for rotation about the axis v by an angle theta.
setRotationBOTTOM(int, double) GrainBoundaryTiltConfiguration
setRotationMatrix(Matrix3f) Graphics3D
setRotationScale(Matrix3f) Matrix4f
Replaces the upper 3x3 matrix values of this matrix with the values in the
matrix m1.
setRotationTOP(int, double) GrainBoundaryTiltConfiguration
Sets tensor for rotation about the indicated axis (0=x,1=y,2=z) by
the given angle.
setRotNum(int) IntegratorDimerRT
setRoute(boolean) HypernettedChain
setRoute(boolean) PercusYevick
setRoute(int) IntegratorDimerApproach
setRouteParams(double[][]) IntegratorDimerApproach
setRow(int, float[]) Matrix4f
Sets the specified row of this matrix4f to the four values provided.
setRow(int, float, float, float) Matrix3f
Sets the specified row of this matrix3d to the three values provided.
setRowA(int, float[]) Matrix3f
Sets the specified row of this matrix3d to the four values provided.
setRowHeaders(String[]) DataTable.DataInfoTableFactory
Sets the row headers.
setRowLabelColumnHeader(String) DisplayTable
Sets the header of the row-label column.
setRowLabels(String[]) DisplayTable
Sets values for descriptive text for each row (as defined before
transpose).
setRowV(int, Vector3f) Matrix3f
Sets the specified row of this matrix3d to the Vector provided.
setRPow(double) MCMoveClusterAtomDiscrete
setRun(JButton) ViewSpeciesSelection
setRun(JButton) ViewSpeciesSelection
setS(int) P2O2Bartolomei
setSafetyFactor(double) CriterionPositionWall
Sets the safety factor (between 0 and 1.0) that determines when the
criterion thinks it needs an update.
setSafetyFactor(double) CriterionSimple
setSafetyFactor(double) PotentialMasterListMolecular
Sets the safety factor.
setSafetyFactor(double) PotentialMasterList
Sets the safety factor.
setSafetyFactor(double) CriterionSimpleMolecular
setSameFileEachTime(boolean) DataLogger
Write to the same file at each time INTERVAL, and close the file at the
end of the simulation.
setSampleClusters(ClusterWeight[]) SimulationVirialOverlap2
setSampledSwitchFrac(double) MeterOverlapSwitch
setSampleInterval(int) ConfigurationStorage
setSaveValues(JButton) ViewAlkaneLengthSelection
setScale(double) BoxInflate
Sets the scale defining the amount of inflation.
setScale(double) DisplayBox
setScale(double) DisplayPolytope
setScale(float) Matrix3f
Sets the value of this matrix to a scale matrix with the passed scale
amount.
setSCF(boolean) P2QChemInterpolated
setSearchLimit(int) IntegratorKMC
setSecurityOff(boolean) SVGConverter
Sets whether or not scripts should be run securely
setSeed(int) RandomMersenneTwister
Configures the RNG with the given seed.
setSeedArray(int[]) RandomMersenneTwister
Configures the RNG with an array of seeds
setSeeds(int[]) SimulationVirial
setSeen(int) AbstractTraversal
setSelected(int) DeviceButtonGroup
Selects ith radio button.
setSelected(int) DeviceSelector
Sets the i-th item (counting from 0) in the list as the one currently selected.
setSelected(int) DeviceThermoSelector
Sets the i-th item (counting from 0) in the list as the one currently selected.
setSelected(String) DeviceButtonGroup
Selects the button with the given label.
setSelectedFloats(float, BitSet, float[]) Parser
setSelectedSpecies(IMolecularModel_SpeciesFactory) ModelSpeciesSelection
setSelectedValue(int, ScriptVariable) ScriptVariable
setSfacPlotSink(IDataSink) ConfigFromFileLAMMPS.ModifierConfiguration
setShakeTolerance(double) IntegratorVelocityVerletShake
setShape(Polytope) MeterLocalDensity
setShape(Polytope) MeterLocalMoleFraction
Sets the subvolume shape for the mole fraction calculation.
setShape(String) DeviceTrioControllerButton
Sets display shape of the device.
setShapeOrigin(Vector) MeterLocalMoleFraction
Sets the origin of the subvolume (Polytopes typically have their center
at 0).
setShearRateNumber(double) IntegratorPolymer
setShift(Vector) WriteConfigurationInterfacial
setShiftX(float) DisplayCanvas
setShiftY(float) DisplayCanvas
setShowBorder(boolean) DeviceSlider
setShowBorder(boolean) DeviceSpinner
setShowBoundary(boolean) DisplayBox
Set the flag indicating if the boundary should be drawn.
setShowEValvalues(boolean) DeviceEigenvaluesSlider
Set whether the eigenvalue # text box should be displayed.
setShowingColumnHeaders(boolean) DisplayTable
setShowingRowLabels(boolean) DisplayTable
Mutator method for whether table should include a column of "x" values.
setShowingUnits(boolean) DisplayTable
Flag indicating whether a units suffix applied to the column headers (or
row labels, if transposing).
setShowSlider(boolean) DeviceSlider
setShowValues(boolean) DeviceSlider
setShowValues(boolean) DeviceThermoSlider
Set whether the temperature text box should be displayed.
setShowValues(boolean) DeviceThermoSliderGEMC
Set whether the temperature text box should be displayed.
setShowValues(boolean) DeviceCellNumXYSlider
Set whether the x- and y-Cell # text box should be displayed.
setShowValues(boolean) DeviceWaveVectorSlider
Set whether the wavevector # text box should be displayed.
setSigma(double) P1WCAWall
Sets the radius.
setSigma(double) ColorSchemeOverlap
setSigma(double) EOSSW
setSigma(double) P1Wall
setSigma(double) P1Wall
setSigma(double) P1WCAPorousWall
Sets the radius.
setSigma(double) P1WCAWall
Sets the radius.
setSigma(double) P1WCAWall
Sets the radius.
setSigma(double) VLESim
setSigma(double) P1HardPeriodic
setSigma(double) P22CLJQ
setSigma(double) P2ElectrostaticWithHardCore
setSigma(double) P2HardAssociationCone
Accessor method for Lennard-Jones size parameter
setSigma(double) P2HardAssociationConeDoubleSites
Accessor method for Lennard-Jones size parameter
setSigma(double) P2HardAssociationConeFourSites
Accessor method for Lennard-Jones size parameter
setSigma(double) P2HardAssociationConeFourSitesSW
Accessor method for Lennard-Jones size parameter
setSigma(double) P2HardAssociationConeOneSite
Accessor method for Lennard-Jones size parameter
setSigma(double) P2HardAssociationConeReference
Accessor method for Lennard-Jones size parameter
setSigma(double) P2HardAssociationConeReferenceFourSites
Accessor method for Lennard-Jones size parameter
setSigma(double) P2HardAssociationConeSW
Accessor method for Lennard-Jones size parameter
setSigma(double) P2HC2Yukawa
setSigma(double) P2HSDipole
setSigma(double) P2LennardJones
Mutator method for Lennard-Jones size parameter.
setSigma(double) P2LennardJonesDreiding
Mutator method for Lennard-Jones size parameter.
setSigma(double) P2LJDipole
setSigma(double) P2LJQ
setSigma(double) P2LJQQ
setSigma(double) P2SoftSphere
Mutator method for soft sphere size parameter.
setSigma(double) P2WCA
Mutator method for Lennard-Jones size parameter.
setSigma(double) P2WCAP
Mutator method for Lennard-Jones size parameter.
setSigma(double) P2LJDipole
setSigma(double) LJ
setSigma(double) MayerEHardSphere
Sets the HS diameter.
setSigma(double) MayerHardSphere
Sets the HS diameter.
setSigma(double, int) MolecularModel2CLJQ_SpeciesCO2
setSigma(double, int) MolecularModel2CLJQ_SpeciesEthane
setSigma(double, int) MolecularModel2CLJQ_SpeciesLJ
setSigma(double, int) MolecularModelEMP2_SpeciesCO2
setSigma(double, int) MolecularModelLJ_SpeciesLJ
setSigma(double, int) MolecularModelLJQ_SpeciesLJ
setSigma(double, int) MolecularModelSKS_SpeciesAlkane
setSigma(double, int) MolecularModelSPCE_SpeciesH2O
setSigma(double, int) MolecularModelTRAPPE_SpeciesAlkane
setSigma(double, int) MolecularModelTrappe_SpeciesCO2
setSigmaColloid(double) ConfigurationColloid
setSigmaHSRef(double) MolecularModel2CLJQ_SpeciesCO2
setSigmaHSRef(double) MolecularModel2CLJQ_SpeciesEthane
setSigmaHSRef(double) MolecularModel2CLJQ_SpeciesLJ
setSigmaHSRef(double) MolecularModelEMP2_SpeciesCO2
setSigmaHSRef(double) MolecularModelLJ_SpeciesLJ
setSigmaHSRef(double) MolecularModelLJQ_SpeciesLJ
setSigmaHSRef(double) MolecularModelSKS_SpeciesAlkane
setSigmaHSRef(double) MolecularModelSPCE_SpeciesH2O
setSigmaHSRef(double) MolecularModelTRAPPE_SpeciesAlkane
setSigmaHSRef(double) MolecularModelTrappe_SpeciesCO2
setSigmaHSRef(double, int) ModelSimulationEnvironment
setSigmaHSRefField(JTextField, int) ViewSimEnvironmentSelection
setSigmaMonomer(double) ConfigurationColloid
setSimEnvController(ControllerSimEnvironmentSelection) ControllerSpeciesSelection
setSite(int[]) RectangularLatticeNbrIterator
Identifies the site whose neighbors will be given on iteration.
setSite(String) EnumSiteName
setSiteFactor(double) HSNPT.ColorSchemeDisplacement
setSitesOnSpecies(String[]) ModelSpeciesSelection
setSize(double[]) Primitive
Sets the length of each primitive vector to the corresponding
value in the given array.
setSize(int) IndexIteratorRectangular
Sets range of all indexes to the given value
Indices returned vary from 0 to size-1
setSize(int) Quadric
setSize(int[]) FiniteLattice
Sets the array size, defined as described in the getSize method.
setSize(int[]) IndexIteratorRectangular
Sets the individual ranges for the elements of the returned
array.
setSize(int[]) IndexIteratorSizable
Specifies maximum index in each dimension (for dimension
i, maximum index is size[i]-1).
setSize(int[]) RectangularLattice
Sets the number lattice size (specified via the largest index in each dimension), and
rebuilds the all sites using the site factory.
setSize(int[]) IndexIterator
Sets the size of each dimension; in general they should all be the
same size.
setSize(int, int) DeviceTable
Set the size attribute of the scrolled window the table sits on.
setSize(int, int) DisplayPlot
Sets the drawn size of the plot
setSize(int, int) DisplayPlotXChart
setSize(int, int) DisplayPolytope
setSize(int, int) Plot
Sets width and height of plot in pixels.
setSizeA(double) PrimitiveMonoclinic
setSizeA(double) PrimitiveOrthorhombic
setSizeA(double) PrimitiveOrthorhombicHexagonal
Sets A to the given value and B to 2.0/sqrt(3.0)*A
setSizeA(double) PrimitiveTriclinic
setSizeAB(double) PrimitiveHexagonal
setSizeAB(double) PrimitiveHexagonal2D
setSizeAB(double) PrimitiveTetragonal
setSizeABC(double) PrimitiveCubic
Sets the length of all primitive vectors to the given value.
setSizeB(double) PrimitiveMonoclinic
setSizeB(double) PrimitiveOrthorhombic
setSizeB(double) PrimitiveTriclinic
setSizeC(double) PrimitiveHexagonal
setSizeC(double) PrimitiveMonoclinic
setSizeC(double) PrimitiveOrthorhombic
setSizeC(double) PrimitiveTetragonal
setSizeC(double) PrimitiveTriclinic
setSlab(double) DisplayBoxCanvasG3DSys
Set slab percentage
setSlab(double) DisplayPolytopeCanvasG3DSys
Set slab percentage
setSlab(int) GData
clipping from the front and the back
setSlab(BitSet, BitSet, String, String, float) MeshSurface
setSlabEnabled(boolean) TransformManager
Enable/disable slab and depth
setSlabPercent(float) G3DSys
setSleepPeriod(double) Controller
setSliderMajorValues(int) DeviceThermoSlider
Set the number of "major" values that should be shown on the
temperature slider.
setSliderMajorValues(int) DeviceThermoSliderGEMC
Set the number of "major" values that should be shown on the
temperature slider.
setSliderMajorValues(int) DeviceCellNum3DSlider
Set the number of "major" values that should be shown on the
n- CellNum slider.
setSliderMajorValues(int) DeviceCellNumXYSlider
Set the number of "major" values that should be shown on the
x- and y- CellNum slider.
setSliderMajorValues(int) DeviceEigenvaluesSlider
Set the number of "major" values that should be shown on the
eigenvalue slider.
setSliderMajorValues(int) DeviceWaveVectorSlider
Set the number of "major" values that should be shown on the
temperature slider.
setSliderMinorValues(int) DeviceThermoSlider
setSliderPostAction(IAction) DeviceThermoSlider
Set the post slider value changed action.
setSliderPostAction(IAction) DeviceThermoSliderGEMC
Set the post slider value changed action.
setSliderPostAction(IAction) DeviceEigenvaluesSlider
Set the post slider value changed action.
setSliderPostAction(IAction) DeviceWaveVectorSlider
Set the post slider value changed action.
setSliderTextboxesEditable(boolean) DevicePlotPoints
setSliderValueShape(String) DeviceSlider
setSliderVerticalOrientation(boolean) DeviceSlider
setSlitDim(int) BoundaryRectangularSlit
Sets the non-periodic dimension to that indicated by the given value
(0 is x-dimension, 1 is y-dimension, etc.).
setSmoothedY(double[]) AkimaSplineSmoother
setSnapshotTime(float) SVGConverter
Sets the document time to seek to before rasterizing.
setSoluteMoleFraction(double) ConfigurationMembrane
setSoluteMoleFraction(double) ConfigurationMembraneWater
setSolutionChamberDensity(double) ConfigurationMembrane
setSolutionChamberDensity(double) ConfigurationMembraneWater
setSolventChamberDensity(double) ConfigurationMembrane
setSolventChamberDensity(double) ConfigurationMembraneWater
setSolventThermoFrac(double) P2SquareWellBonded
Sets the fraction of well energy that is gained by an atom pair when
they hop in their well.
setSolventThermoFrac(double) P2SquareWellRadical
Sets the fraction of well energy that is gained by an atom pair when
they hop in their well.
setSources(String[]) SVGConverter
Sets the list of individual SVG sources.
setSpace(Space) DataTensor.DataInfoTensorFactory
Sets the Space
setSpace(Space) DataVector.DataInfoVectorFactory
Sets the Space
setSpacePosition(double) LatticePlane
Sets the position of the plane to be the given distance from the
origin in the direction of the normal.
setSpecies(ISpecies) AtomSourceRandomSpecies
setSpecies(ISpecies) AtomType
Informs the atom type what species contains the atom types.
setSpecies(ISpecies) MeterWidomCavity
Sets the species, takes a prototype molecule, and gets handle to
appropriate species agent in box
setSpecies(ISpecies) DataSourcePositionedBoltzmannFactor
Sets the ISpecies for which the chemical potential is to be measured.
setSpecies(ISpecies) MeterDensity
setSpecies(ISpecies) MeterLocalMoleFraction
Accessor method to set which species mole-fraction or molar-density is averaged
To set to total number density, invoke with static ALL_SPECIES field as argument
setSpecies(ISpecies) MeterMoleculeTemperature
setSpecies(ISpecies) MeterMoleFraction
setSpecies(ISpecies) MeterNMolecules
setSpecies(ISpecies) MeterProfileByAtoms
setSpecies(ISpecies) MeterProfileByVolume
setSpecies(ISpecies) MeterWidomInsertion
Sets the species, takes a prototype molecule, and gets handle to
appropriate species agent in box
setSpecies(ISpecies) MyMCMove
setSpecies(ISpecies) DeviceNSelector
setSpecies(ISpecies) MCMoveInsertDelete
setSpecies(ISpecies) WriteConfigurationInterfacial
setSpecies(ISpecies) MeterWidomInsertionCorrection
Sets the species, takes a prototype molecule, and gets handle to
appropriate species agent in box
setSpecies(ISpecies) MeterWidomInsertionP
Sets the species, takes a prototype molecule, and gets handle to
appropriate species agent in box
setSpecies(ISpecies) MCMoveVolumeN2
setSpecies(ISpecies) P0LatticeEnergyCorrec
setSpecies(ISpecies) MyMCMove
setSpecies(ISpecies) MyMCMove
setSpecies(ISpecies) DeviceCellNum3DSlider
setSpecies(ISpecies) DeviceCellNumXYSlider
setSpecies(ISpecies) MCMoveBondLength
setSpecies(ISpecies) MCMoveClusterBondLength
setSpecies(ISpecies) MCMoveClusterRotateArm
setSpecies(ISpecies) MCMoveRotateArm
setSpecies(ISpecies) MCMoveWiggle
setSpecies(ISpecies) MCMoveClusterAngleBend
setSpecies(ISpecies) MCMoveClusterAngleBendAceticAcid
setSpecies(ISpecies) MCMoveClusterRotateCH3
setSpecies(ISpecies) MCMoveClusterTorsionAlkaneEH
setSpecies(ISpecies) MCMoveClusterTorsionMulti
setSpecies(ISpecies) MCMoveClusterWiggleAceticAcid
setSpecies(ISpecies) MCMoveClusterWiggleAlkaneEH
setSpecies(ISpecies) MCMoveClusterWiggleMulti
setSpecies(ISpecies[]) MCMoveSemigrand
Mutator method for the set of species that can participate in an exchange move.
setSpecies(ISpecies[]) MeterConversion
setSpecies(ISpecies[]) MeterFlux
setSpecies(ISpecies, double, IPotentialMolecular) MyMCMove
setSpecies(ISpecies, int) ModelSelectedSpecies
setSpecies(ISpecies, ISpecies) CoordinateDefinitionNitrogenSuperBox
setSpecies(ISpecies, ISpecies) ConfigurationLatticeFreeRadical
setSpecies(ISpecies, ISpecies) CoordinateDefinitionLeafSuperBox
setSpecies(SpeciesGeneral) SpeciesGeneralMutable
setSpecies1(ISpecies) ConfigurationZincblende
setSpecies1AtomicFlag(boolean) BuilderCollectionPotential
setSpecies2(ISpecies) ConfigurationZincblende
setSpecies2AtomicFlag(boolean) BuilderCollectionPotential
setSpeciesA(ISpecies) MeterDimerFraction
setSpeciesA(ISpecies, ISpecies) GrainBoundaryConfiguration
setSpeciesAllocation(ISpecies, float) ConfigurationLatticeWithPlane
Sets the initial allocation of the species on the left side
of the plane.
setSpeciesAlreadyAdded(boolean, int) ModelSpeciesSelection
setSpeciesB(ISpecies, ISpecies) GrainBoundaryConfiguration
setSpeciesColloid(ISpecies) NeighborListManagerColloid
setSpeciesCount1(JTextField) ViewSpeciesSelection
setSpeciesCount2(JTextField) ViewSpeciesSelection
setSpeciesCount3(JTextField) ViewSpeciesSelection
setSpeciesDataModel(IMolecularModel_SpeciesFactory, int) ModelSelectedSpecies
setSpeciesDM(ModelSelectedSpecies) ControllerAlkaneLengthSelection
setSpeciesID(int) MolecularModel2CLJQ_SpeciesCO2
setSpeciesID(int) MolecularModel2CLJQ_SpeciesEthane
setSpeciesID(int) MolecularModel2CLJQ_SpeciesLJ
setSpeciesIdentifier(String, int) ModelSpeciesSelection
setSpeciesIndex(int) CollectionPotentialAtomicLike
setSpeciesIndex(int) CollectionPotentialMolecularLike
setSpeciesIndex(int[]) CollectionPotentialAtomicUnlike
setSpeciesIndex(int[]) CollectionPotentialMolecularUnlike
setSpeciesIndex(int, int) CollectionPotentialAtomicUnlike
setSpeciesIndex(int, int) CollectionPotentialMolecularUnlike
setSpeciesInteractionIndex(int[][]) ModelSelectedSpecies
setSpeciesJList(JList) ViewSpeciesSelection
setSpeciesJList(JList) ViewSpeciesSelection
setSpeciesJListListener(ListSelectionListener) ViewSpeciesSelection
setSpeciesJListListener(ListSelectionListener) ViewSpeciesSelection
setSpeciesListDisplayLSM(ListSelectionModel) ViewSpeciesSelection
setSpeciesListDisplayLSM(ListSelectionModel) ViewSpeciesSelection
setSpeciesMembrane(ISpecies) ConfigurationMembrane
setSpeciesMembrane(ISpecies) ConfigurationMembraneWater
setSpeciesMoleculeCount(int, int) ModelSelectedSpecies
setSpeciesMonomer(ISpecies) NeighborListManagerColloid
setSpeciesRemovalMsgBox(JOptionPane) ViewSpeciesSelection
setSpeciesSelectedIndex(int[]) ModelSpeciesSelection
setSpeciesSelectedIndex(int, int) ModelSpeciesSelection
setSpeciesSelectionChanged(boolean) ModelSpeciesSelection
setSpeciesSelectionDM(ModelSpeciesSelection) ModelAlertMsgDialog
setSpeciesSolute(ISpecies) ConfigurationMembrane
setSpeciesSolute1(ISpecies) ConfigurationMembraneWater
setSpeciesSolute2(ISpecies) ConfigurationMembraneWater
setSpeciesSolvent(ISpecies) ConfigurationMembrane
setSpeciesSolvent(ISpecies) ConfigurationMembraneWater
setSpeciesSpheres(SpeciesGeneral[]) ConfigurationLatticeTube
setSpeciesTube(SpeciesGeneral) ConfigurationLatticeTube
setSpecular(boolean) GData
setSpecularExponent(int) GData
log_2(p) in I = df * (N dot L) + sf * (R dot V)^p for faster calculation of
shades
setSpecularPercent(int) GData
sf in I = df * (N dot L) + sf * (R dot V)^p not a percent of anything,
really
setSpecularPower(int) GData
fractional distance to white for specular dot
setSpiffiness(int) MultiharmonicGraphicMC.DataSourceAlphaChi
setSpinnerPanel(JPanel) ViewSpeciesSelection
setSpringConstant(double) P1Tension
setSpringConstant(double) P1Harmonic
setSpringConstant(double) P1HarmonicSite
setSpringConstant(double) P2Anharmonic
Accessor method for harmonic energy parameter
setSpringConstant(double) P2Harmonic
Accessor method for harmonic energy parameter
setStart(float, float, float) Line
setStart(Object) DataStreamAction
setStartAtom(int) MCMoveClusterAtomMulti
setStartConnection(int) ClusterGenerator
setStartMolecule(int) MCMoveClusterMoleculeMulti
setState(boolean) DeviceCheckBox
Sets the button to the given state.
setState(boolean) DeviceToggleButton
Toggles the button to the given state.
setState(boolean) DeviceToggleRadioButtons
Sets the button to the given state.
setStationary(boolean) P1HardMovingBoundary
setStatus(StatusAction.Status) StatusAction
setStepFactor(double) P2DiscreteFeynmanHibbs
setStepFreq0(double) IntegratorOverlap
Deprecated.
setStepSize(double) MCMoveBoxStep
setStepSize(double) MCMoveStep
setStepSize(double) MCMoveStepDependent
Sets the step size of the move.
setStepSizeMax(double) MCMoveBoxStep
setStepSizeMax(double) MCMoveStep
setStepSizeMax(double) MCMoveStepDependent
Sets the maximum allowable step size.
setStepSizeMin(double) MCMoveBoxStep
setStepSizeMin(double) MCMoveStep
setStepSizeMin(double) MCMoveStepDependent
Returns the maximum allowable steps size.
setStiffness(double, double) MCMoveClusterRingRegrowOrientation
Set PI harmonic spring stiffness for given temperature and atomic mass.
setStiffness(double, P1IntraMolecular) MCMoveChangeBondLength
setStopConnection(int) ClusterGenerator
setStopSimulation(boolean) ModelSimulationEnvironment
setStreamAction(DataStreamAction) SimulationDataAction
setSubDataInfo(IDataInfo[]) DataGroup.DataInfoGroupFactory
setSubtractComb(boolean) DataSourceFE
If true, the free energy differences will not include the combinatoric
contributions (they will be the free energy of defect formation).
setSulfurType(AtomType) IntegratorVelocityVerletSAM
setSum(int) FixedSumIterator
Specifies the target sum that defines the iterates.
setSuppressBoxLengthWarning(boolean) NeighborCellManager
setSurfaceColor(Color) ColorSchemeDropletSurface
setSurfaceDimension(int) DataProcessorInterfacialTension
Sets the dimension of the surfaces.
setSurfaceYOffset(double) ConfigurationCatalysis
setSurfaceYOffset(double) ConfigurationSAM
setSwitch(boolean) PRotConstraint
setSwitchFac(double) P2MoleculeSoftTruncatedSwitched
setSwitchFac(double) P2SoftSphericalTruncatedSwitched
setSystemSigmaHSRef(double) ModelSimulationEnvironment
setT(Tuple3f) Tuple3f
Sets the value of this tuple to the value of the Tuple3f argument.
setT(Tuple3i) Tuple3i
Sets the value of this tuple to the value of tuple t1.
setT1(double) HTTPSoftSphereApplet
setT2(double) HTTPSoftSphereApplet
setTA(Tuple3f, float) Quaternion
q = (cos(theta/2), sin(theta/2) * n)
setTableColumnNames(String[]) DevicePlotPoints
Sets the column headers to the given strings and fires an event
indicating the column headers have been changed.
setTableUpdateInterval(int) DataTableAverages
Sets the interval for updating the table.
setTags(DataTag[]) DataInfoFactory
setTags(DataTag[]) IDataInfoFactory
Sets the factory's tags to those in the given array.
setTarget(IAtom) ANIntergroupCoupled
setTarget(IAtom) ANIntergroupExchange
setTarget(IAtom) ANIntragroupExchange
setTarget(IAtom) ApiIndexList
setTarget(IAtom) ApiIntergroup
Specifies a target atom, which should appear in all iterates.
setTarget(IAtom) ApiIntragroup
setTarget(IAtom) AtomIteratorBasis
Method to specify a target atom.
setTarget(IAtom) AtomIteratorBasisAdjustableStart
Method to specify a target atom.
setTarget(IAtom) Atomset3IteratorIndexList
setTarget(IAtom) Atomset4IteratorIndexList
setTarget(IAtom) AtomsetIteratorAllLeafAtoms
Sets the target of iteration...
setTarget(IAtom) AtomsetIteratorTargetable
setTarget(IAtom) MeterPotentialEnergy
setTarget(IAtom) Api1ACell
Sets the target molecule with which all pairs are formed.
setTarget(IAtom) Api1ASite
Sets the target molecule with which all pairs are formed.
setTarget(IAtom) SimEinStep2.MeterPotentialEnergyComposite
setTarget(IAtom) SimEinStep2HCP.MeterPotentialEnergyComposite
setTarget(IAtom) SimOverlapSoftSphereEin.MeterPotentialEnergyComposite
setTarget(IAtom) SimOverlapSoftSphereEinHarm.MeterPotentialEnergyComposite
setTarget(IAtom) PotentialMaster.AtomIterator0
setTarget(IMolecule) MeterPotentialEnergy
setTarget(IMolecule) MoleculeIteratorAll
Sets the target of iteration...
setTarget(IMolecule) MoleculeIteratorMolecule
Specifies molecule returned by this iterator, as the one containing
the given target atom.
setTarget(IMolecule) MoleculesetIteratorTargetable
setTarget(IMolecule) MpiInterspecies1A
Sets the target molecule with which all pairs are formed.
setTarget(IMolecule) MpiIntraspecies1A
Sets the target molecule with which all pairs are formed.
setTarget(IMolecule) MpiMolecule
Sets target atoms and determines the pair iterator according to the value
of targetAtom.
setTarget(IMolecule) Mpi1ACell
Sets the target molecule with which all pairs are formed.
setTarget(IMolecule) SimEinStep2.MeterPotentialEnergyComposite
setTarget(IMolecule) SimEinStep2HCP.MeterPotentialEnergyComposite
setTarget(IMolecule) SimOverlapSoftSphereEin.MeterPotentialEnergyComposite
setTarget(IMolecule) SimOverlapSoftSphereEinHarm.MeterPotentialEnergyComposite
setTarget(IMolecule) PotentialMaster.MoleculeIterator0
setTargetAtom(IAtom) IPotential0Lrc
Informs the potential of a target atom.
setTargetAtom(IAtom) IteratorDirective
setTargetAtom(IAtom) P2ReactionFieldDipoleTruncated.P0ReactionField
setTargetAtom(IAtom) Potential0Lrc
setTargetAvg(DataOverlap.DataSourceOverlapAvg) DataOverlap
setTargetDataInterval(int) SimOverlapModule
setTargetDensity(double) BoxInflate
Sets the action to change the box dimensions isotropically to achieve
the given density.
setTargetMolecule(IMolecule) IPotential0Lrc
Informs the potential of a target atom.
setTargetMolecule(IMolecule) IPotential0MoleculeLrc
Informs the potential of a target atom.
setTargetMolecule(IMolecule) IteratorDirective
setTargetMolecule(IMolecule) P2ReactionFieldDipoleTruncated.P0ReactionField
setTargetMolecule(IMolecule) Potential0Lrc
setTemperature(double) AtomActionRandomizeVelocity
setTemperature(double) BoxQuench
Sets the quench temperature.
setTemperature(double) BoxRandomizeMomenta
setTemperature(double) BoxScaleMomenta
setTemperature(double) MeterHyperVirial
setTemperature(double) MeterPressure
setTemperature(double) MeterPressureTensor
setTemperature(double) MeterWidomInsertion
setTemperature(double) IntegratorDCVGCMD
setTemperature(double) DeviceThermoSlider
Set the current value for the temperature slider/text box.
setTemperature(double) DeviceThermoSliderGEMC
Set the current value for the temperature slider/text box.
setTemperature(double) IntegratorBox
setTemperature(double) IntegratorHard
setTemperature(double) IntegratorManagerMC
Sets the temperature for this integrator if that's relevant
setTemperature(double) IntegratorMD
setTemperature(double) MCMoveOverlapListener
setTemperature(double) MeterPU
setTemperature(double) MeterPUCut
setTemperature(double) MeterPUCutLS
setTemperature(double) MeterWidomInsertionCorrection
setTemperature(double) MeterWidomInsertionP
setTemperature(double) PotentialCalculationMappedRdf
setTemperature(double) MeterTargetRPMolecule
setTemperature(double) MeterTargetTPMolecule
setTemperature(double) PNWaterGCPMReactionField
setTemperature(double) EOSSW
setTemperature(double) IntegratorHybrid
setTemperature(double) IntegratorDCVGCMD
setTemperature(double) BoltzmannProcessor
setTemperature(double) DataProcessorBoltzmannFactor
setTemperature(double) IntegratorHarmonic
setTemperature(double) MCMoveAtomCoupledBennet
setTemperature(double) MCMoveAtomCoupledUmbrella
setTemperature(double) MCMoveEinsteinCrystal
setTemperature(double) MCMoveHarmonic
setTemperature(double) MCMoveSingleMode
setTemperature(double) MCMoveVolumeMonoclinicScaled
Sets the temperature being sampled.
setTemperature(double) MCMoveVolumeSolid
Sets the temperature being sampled.
setTemperature(double) MCMoveVolumeSolidNPTMolecular
Sets the temperature being sampled.
setTemperature(double) MeterBoltzmannHarmonic
setTemperature(double) MeterBoltzmannHTTP
setTemperature(double) MeterBoltzmannTarget
setTemperature(double) MeterDDP
setTemperature(double) MeterDirectSamplingHarmonic
setTemperature(double) MeterDP
setTemperature(double) MeterOverlapSwitch
setTemperature(double) MeterSolidDA
setTemperature(double) MeterSolidDACut
setTemperature(double) MeterSolidMirror
setTemperature(double) MeterTargetTP
setTemperature(double) MeterWorkHarmonicBennet
setTemperature(double) MeterWorkHarmonicPhaseSpace
setTemperature(double) MeterWorkHarmonicTargetandReweighting
setTemperature(double) NormalModes
Set the temperature used for calculating omega-squared.
setTemperature(double) NormalModes1DHR
setTemperature(double) NormalModes2D
setTemperature(double) NormalModes3D
setTemperature(double) NormalModesFromFile
setTemperature(double) NormalModesMolecular
setTemperature(double) NormalModesPotential
setTemperature(double) NormalModesSoftSpherical
setTemperature(double) WriteS
setTemperature(double) MCMoveGeometricClusterRestrictedGE
setTemperature(double) P2DiscreteFeynmanHibbs
setTemperature(double) P2EffectiveFeynmanHibbs
setTemperature(double) P2LJDipole
Sets the temperature used for Boltzmann-weighting of the orientational
average energy used in u(double) and integral(double)
setTemperature(double) P2LJQ
Sets the temperature used for Boltzmann-weighting of the orientational
average energy used in u(double) and integral(double)
setTemperature(double) P2LJQQ
Sets the temperature used for Boltzmann-weighting of the orientational
average energy used in u(double) and integral(double)
setTemperature(double) P2SemiclassicalAtomic
setTemperature(double) P2SemiclassicalMolecular
setTemperature(double) PotentialCalculationPressureTensor
setTemperature(double) MaxwellBoltzmann.Distribution
setTemperature(double) VanderWaals
setTemperature(double) ClusterAbstract
setTemperature(double) ClusterChainHS
setTemperature(double) ClusterChainSoft
setTemperature(double) ClusterConstant
setTemperature(double) ClusterCoupledFlipped
setTemperature(double) ClusterCoupledFlippedMultivalue
setTemperature(double) ClusterCoupledFlippedPartial
setTemperature(double) ClusterDifference
setTemperature(double) ClusterExchange
setTemperature(double) ClusterMultiToSingle
setTemperature(double) ClusterMultivalueUmbrella
setTemperature(double) ClusterSinglyConnected
setTemperature(double) ClusterSum
setTemperature(double) ClusterSumHS
setTemperature(double) ClusterSumNonAdditiveTrimerEnergy
setTemperature(double) ClusterSumPolarizable
setTemperature(double) ClusterSumPolarizableWertheimProduct
setTemperature(double) ClusterSumPolarizableWertheimProduct4Pt
setTemperature(double) ClusterSumPolarizableWertheimProduct4PtFinal
setTemperature(double) ClusterTree
setTemperature(double) ClusterWeightAbs
setTemperature(double) ClusterWeightSumWall
setTemperature(double) ClusterWeightUmbrella
setTemperature(double) ClusterWheatleyExtendSW
setTemperature(double) ClusterWheatleyHS
setTemperature(double) ClusterWheatleyMultibody
setTemperature(double) ClusterWheatleyMultibodyDerivatives.ClusterRetrievePrimes
setTemperature(double) ClusterWheatleyMultibodyDerivatives
setTemperature(double) ClusterWheatleyMultibodyDerivativesBD.ClusterRetrievePrimes
setTemperature(double) ClusterWheatleyMultibodyDerivativesBD
setTemperature(double) ClusterWheatleyPartitionScreening
setTemperature(double) ClusterWheatleyPT.ClusterRetrieveOrders
setTemperature(double) ClusterWheatleyPT.ClusterRetrievePrimesBD
setTemperature(double) ClusterWheatleyPT
setTemperature(double) ClusterWheatleySoft
setTemperature(double) ClusterWheatleySoftBD
setTemperature(double) ClusterWheatleySoftDerivatives.ClusterRetrievePrimes
setTemperature(double) ClusterWheatleySoftDerivatives.ClusterRetrievePrimesBD
setTemperature(double) ClusterWheatleySoftDerivatives
setTemperature(double) ClusterWheatleySoftDerivativesBD.ClusterRetrievePrimes
setTemperature(double) ClusterWheatleySoftDerivativesBD
setTemperature(double) ModelSimulationEnvironment
setTemperature(double) ModelTemperatureAndSteps
setTemperature(double) MCMoveChangeBondLength
setTemperature(double) MCMoveClusterTorsionAlkaneEH
setTemperature(double) MCMoveClusterTorsionMulti
setTemperature(double) VirialH2OGCPMD.Clusterfoo
setTemperature(double, P2SoftSphericalTruncated) PotentialCalculationMappedVirialV
setTemperature(double, Potential2SoftSpherical) PotentialCalculationMappedEnergy
setTemperature(double, Potential2SoftSpherical) PotentialCalculationMappedVirial
setTemperatures(double[]) DeviceThermoSelector
setTempZSlab(int) Graphics3D
setTetherLength(double) P2Tether
Accessor method for the tether distance
setTextBackground(Color) DeviceBox
setThermalize(IntegratorBox, double, IRandom) P1Wall
setThermostat(IntegratorMD.ThermostatType) IntegratorMD
Sets the type of thermostat used by the integrator for isothermal sampling.
setThermostatInterval(int) IntegratorMD
Sets the number of integrator steps between thermostat
actions (for thermostats such as velocity scaling and Andersen).
setThermostatNoDrift(boolean) IntegratorMD
Configures the thermostat to remove any net momenta imparted
to the system after use of the thermostat.
setTheta(double) BiasVolumeSphereOriented
Accessor method for angle (in radians) describing width of cone.
setTheta(double) BiasVolumeSphereOrientedDoubleSites
Accessor method for angle (in radians) describing width of cone.
setTheta(double) P2HardAssociationGCPMReference
Accessor method for angle (in radians) describing width of cone.
setTheta(double) PNWaterGCPMThreeSite
Accessor method for angle (in radians) describing width of cone.
setTheta(double) P2HardAssociationCone
Accessor method for angle (in radians) describing width of cone.
setTheta(double) P2HardAssociationConeDoubleSites
Accessor method for angle (in radians) describing width of cone.
setTheta(double) P2HardAssociationConeFourSites
Accessor method for angle (in radians) describing width of cone.
setTheta(double) P2HardAssociationConeFourSitesSW
Accessor method for angle (in radians) describing width of cone.
setTheta(double) P2HardAssociationConeOneSite
Accessor method for angle (in radians) describing width of cone.
setTheta(double) P2HardAssociationConeReference
Accessor method for angle (in radians) describing width of cone.
setTheta(double) P2HardAssociationConeReferenceFourSites
Accessor method for angle (in radians) describing width of cone.
setTheta(double) P2HardAssociationConeSW
Accessor method for angle (in radians) describing width of cone.
setTheta(double) MolecularModelSKS_SpeciesAlkane
setTheta(double) MolecularModelTRAPPE_SpeciesAlkane
setThetaFrac(double) MCMoveVolumeSolidNPTMolecularOriented
setThickness(double) P1HardMovingBoundary
setTHigh(double) ColorSchemeTemperature
setThreePoints(Vector, Vector, Vector) Plane
Defines the plane by specifying three points that lie in it.
setThreshold(double) ConfigFromFileLAMMPS.AtomTestDeviation
setTilt(double) AkimaSplineSmootherApp.PlotAction
setTilt(double) AkimaSplineSmootherDyApp.PlotAction
setTimeData() DataSourceCorrelation
setTimeData() StructureFactorComponentCorrelation
setTimeDataSource(DataSourceScalar) AccumulatorHistory
Sets the DataSource used for the "time" component of the history.
setTimeStep(double) IntegratorGear4
setTimeStep(double) IntegratorMD
setTimeStep(double) IntegratorVerlet
setTimeStep(double) IntegratorPolymer
setTitle(String) DeviceTable
Set the title of the border surrounding the table.
setTitle(String) DeviceToggleRadioButtons
setTitle(String) DisplayPlotXChart
setTLow(double) ColorSchemeTemperature
setToCenter(Vector) Plane
Sets the given vector to be the point in the plane closest to the origin.
setToInitialPosition() CalcNumerical2ndDerivative
setToInitialPosition(double[]) FiniteDifferenceDerivativeCGNitrogenBeta
setToInitialPosition(int[]) CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
setToInitialPosition(int[]) CalcNumerical2ndDerivativeNitrogen
setToInPlaneSquare(double, Vector[]) Plane
inPlaneSquare with square centered on point in plane closest to origin.
setToInPlaneSquare(Vector, double, Vector[]) Plane
Returns four points as the vertices of a square of size d centered on x0.
setToInPlaneVectors(Vector[]) Plane
Computes and returns two unit vectors perpendicular to each other and in the plane.
setTolerance(double) ActionMinimizeEnergy
setTolerance(double) LatticePlane
setTolerance(double) FitTanh
setTolerance(double) FitTanh
setTolerance(double) ClusterWheatleyMultibody
setTolerance(double) ClusterWheatleyMultibodyDerivatives
setTolerance(double) ClusterWheatleySoftDerivatives
setTolerance(double) ClusterWheatleySoftDerivativesMix
setToNearestPoint(Vector, Vector) Plane
Determines the point in the plane closest to the point x0 (first argument).
setToNormalVector(Vector) Plane
Sets the given vector to be a unit normal vector to the plane and returns it.
setTopPadding(double) ConfigurationLammps
setTorqueSum(PotentialCalculationTorqueSum) IntegratorRigidIterative
setTorsionpotentiala0(double) MolecularModelSKS_SpeciesAlkane
setTorsionpotentiala0(double) MolecularModelTRAPPE_SpeciesAlkane
setTorsionpotentiala1(double) MolecularModelSKS_SpeciesAlkane
setTorsionpotentiala1(double) MolecularModelTRAPPE_SpeciesAlkane
setTorsionpotentiala2(double) MolecularModelSKS_SpeciesAlkane
setTorsionpotentiala2(double) MolecularModelTRAPPE_SpeciesAlkane
setTorsionpotentiala3(double) MolecularModelSKS_SpeciesAlkane
setTorsionpotentiala3(double) MolecularModelTRAPPE_SpeciesAlkane
setToU(double[], Vector) TestRotationVector
setToU(int, double, double) MCMoveRotateMolecule3DFixedAngle
setToU(IMoleculeList, double[]) CoordinateDefinitionNitrogen
setToU(IMoleculeList, double[]) CoordinateDefinitionNitrogenSuperBox
setToU(IMoleculeList, double[]) CoordinateDefinition
Set all the molecules in a cell to a position and orientation that corresponds to the
given generalized coordinate.
setToU(IMoleculeList, double[]) CoordinateDefinitionHSDimer
setToU(IMoleculeList, double[]) CoordinateDefinitionLeaf
Sets the position of the atom to be its lattice position plus the offset u
setToU(IMoleculeList, double[]) CoordinateDefinitionMolecule
setToU(IMoleculeList, double[]) CoordinateDefinitionMoleculeVolumeFluctuation
setToUMoleculei(int, double[]) CoordinateDefinitionNitrogen
setToUMoleculei(int, double[]) CoordinateDefinitionHSDimer
setTracker(MCMoveTracker) MCMove
setTransformationTensor(Tensor) AtomActionTransformed
setTransformationTensor(Tensor) AtomActionTransformed
setTransformFunction(IFunction) AccumulatorAverageBootstrap
setTranslation(Vector3f) Matrix4f
Modifies the translational components of this matrix to the values of the
Vector3f argument; the other values of this matrix are not modified.
setTranslationVector(Vector) AtomActionTranslateBy
setTranslucentCoverOnly(boolean) Graphics3D
setTransparentCursor(Object) ApiPlatform
setTransparentCursor(Object) Platform
setTransposed(boolean) DisplayTable
If fillHorizontal is true, each data set fills a row; if false, data are
arranged to fill columns.
setTRatio(double) MeterVirialBDBin
setTRatio(double) MeterVirialBDBinMultiThreaded
setTRatio(double) MeterVirialBinMultiThreaded
setTRatio(double) MeterVirialEBinMultiThreaded
setTrimThreshold(float) AtomArrayList
setTrimThreshold(float) MoleculeArrayList
setTrueLabel(String) ActionToggle
Specifies the button's label when the toggle is set to true.
setTrueLabel(String) DeviceToggleButton
Specifies the button's label when the toggle is set to true.
setTrueLabel(String) DeviceToggleRadioButtons
Specifies the button's label when the toggle is set to true.
setTruncation(double) PotentialGroupSoft
setTruncationRadius(double) P2MoleculeSoftTruncatedSwitched
Mutator method for the radial cutoff distance.
setTruncationRadius(double) P2MoleculeTruncated
Mutator method for the radial cutoff distance.
setTruncationRadius(double) P2SoftSphericalTruncated
Mutator method for the radial cutoff distance.
setTruncationRadius(double) P2SoftSphericalTruncatedForceShifted
Mutator method for the radial cutoff distance.
setTruncationRadius(double) P2SoftSphericalTruncatedShifted
Mutator method for the radial cutoff distance.
setTruncationRadius(double) P2SoftSphericalTruncatedSwitched
Mutator method for the radial cutoff distance.
setTruncationRadius(double) P2SoftTruncated
Mutator method for the radial cutoff distance.
setTruncationRadius(double) P2LJDipole
Mutator method for the radial cutoff distance.
setTruncationRadius(double) BoundaryDeformablePeriodic
setTSelement(ElementSimple) SimpleElementForSimilarSpecies
setTunable(boolean) MCMoveStepTracker
Sets a flag to indicate whether tuning of the move is to be performed
Tuning adjust the step size or other property of the move with the aim of
achieving a trial acceptance rate that is near to some target value.
setType(char) Edge
setType(char) EdgeImpl
setType(char) NodeImpl
setType(char) Node
setTypeMax(DataSourceUniform.LimitType) DataSourceUniform
Mutator method for the type of the right limit.
setTypeMin(DataSourceUniform.LimitType) DataSourceUniform
Mutator method for the type of the left limit.
setULatFunction(Function) MCMoveVolumeMonoclinicScaled
Sets a function that returns the lattice energy for a given density.
setULatFunction(Function) MCMoveVolumeSolid
Sets a function that returns the lattice energy for a given density.
setULatFunction(Function) MCMoveVolumeSolidNPTMolecular
Sets a function that returns the lattice energy for a given density.
setULatFunction(Function) MeterDDP
Sets a function that returns the lattice energy for a given density.
setULatFunction(Function) MeterDP
Sets a function that returns the lattice energy for a given density.
setULatTruncFunction(Function) MCMoveVolumeSolid
Sets a function that returns the lattice energy for a given density
using the same truncation as the potentials in the system.
setUnit(DataTag[], Unit) DisplayPlot
setUnit(DataTag[], Unit) DisplayPlotXChart
setUnit(DataTag[], Unit) DisplayTable
setUnit(PrefixedUnit) DeviceThermoSelector
Override superclass setUnit method to update label when unit is changed
setUnit(Unit) Device
setUnit(Unit) DeviceBox
Accessor method to set the physical units of the displayed value.
setUnit(Unit) DeviceSlider
Override superclass setUnit method to update label when unit is changed
setUnit(Unit) DeviceSpinner
Override superclass setUnit method to update label when unit is changed
setUnit(Unit) DeviceThermoSlider
Set the unit of temperature.
setUnit(Unit) DisplayPlot
setUnit(Unit) DisplayPlotXChart
setUnit(Unit) DisplayTextBox
Accessor method to set the physical units of the displayed value.
setUnit(Unit) DisplayTextBoxesCAE
setUnit(Unit) DeviceThermoSliderGEMC
Set the unit of temperature.
setUnit(String, Unit) DisplayPlotXChart
setUntransformHistograms(boolean) AccumulatorAverageBootstrap
setup() IntegratorDCVGCMD
setup() IntegratorDimerMin
setup() IntegratorDimerRT
Takes in a current configuration of atoms (Rc) and creates a dimer of their positions (R1 and R2).
setup() IntegratorEnergyMap
setup() Integrator
Perform initialization.
setup() IntegratorManagerMC
setup() IntegratorMD
setup() IntegratorKMC
setup() IntegratorKMCCluster
setup() IntegratorHybrid
setup() IntegratorDCVGCMD
setup() BenchSimCatalysis
setup() DataProcessorVirialOverlap
setup(byte, Graph, TraversalVisitor) AbstractTraversal
setup(Box, PotentialMaster, IMoleculeList, Space) CalcVibrationalModes
setup(Graph, TraversalVisitor) AbstractTraversal
setup(Graph, TraversalVisitor) Biconnected
setUp() BenchApiAACell
setUp() BenchBox
setUp() BenchNbrUpdates
setUp() BenchSimDCVGCMD
setUp() BenchSimHSMD3D
setUp() BenchSimLammpsLJ
setUp() BenchSimLJGCMC3D
setUp() BenchSimLJMC3D
setUp() BenchSimLJMD3D
setUp() BenchSimSurfacetensionLJMC
setUp() BenchSimSWChain
setUp() BenchSimVirialLJ
setUp() BenchVector
setUp() BenchVector3D
setUp() BenchSimVirialH2OGCPMD
setupActiveAtoms() MyMCMove
setupActiveAtoms() MyMCMove
setupActiveAtoms() MyMCMove
setupData() DataSourceRmsVelocity
Creates the data object (a DataFunction) to be returned by getData().
setupData(int) MeterChainLength
Creates the data object (a DataFunction) to be returned by getData().
setupData(String, Dimension) DataSourceFunction
Recalculates the y values from the current x values.
setUpdateInterval(int) DisplayTimer
Sets the period for updating the display.
setUpdateInterval(int) NeighborListManagerMolecular
Sets the interval for which neighbor update checks are performed.
setUpdateInterval(int) NeighborListManager
Sets the interval for which neighbor update checks are performed.
setUpdatingOnAnyChange(boolean) DataSet
Describes protocol for firing table events that notify of column data
changes.
setupIterators() ApiIntergroup
setupProfileData() DataSourceTensorVirialHardProfile
setupTargetHistogram(long) SimulationVirialOverlap2
Sets up a histogram for the target system that measures how often
maximum separation distances are visited.
setupVirial(VirialLJ.VirialLJParam) BenchSimVirialLJ
setuReactCO(double) ReactionManagerCO
setuReactCORev(double) ReactionManagerCO
setUseNbrLists(boolean) PotentialMasterHybrid
setUseNumberLocalization(boolean) TextFormat
setUsePermutations(boolean) ClusterBonds
Sets the usePermutations flag.
setUserStylesheet(String) SVGConverter
Sets the user stylesheet.
setUseSurfaceOnly(boolean) P2Cohesion
setUSplitter(DataDistributer) DataSourceMuRoot
setVA(Vector3f, float) AxisAngle4f
Sets the value of this AxisAngle4f to the specified axis and angle.
setValidate(boolean) SVGConverter
Defines whether or not input sources should be validated in
the conversion process
setValue(double) ConfigFromFileLAMMPS.ModifierConfiguration
setValue(double) DeviceSlider
setValue(double) DeviceSpinner
setValue(double) DimensionedDoubleEditor
Sets the value to the given value, which is taken to be in simulation units.
setValue(double) Modifier
Sets the value of the property.
setValue(double) ModifierFunctionWrapper
Applies function to given value before setting modified property.
setValue(double) ModifierGeneral
setValue(double) ModifierNMolecule
setValue(double) ModifierPMu
setValue(double) ColloidGraphic.WallRangeModifier
setValue(double) LatticeEditor.NModifier
setValue(double) IntegratorDCVGCMD.Mu1Modulator
setValue(double) IntegratorDCVGCMD.Mu2Modulator
setValue(double) DropletGraphic.ModifierBoxSize
setValue(double) InterfacialSWGraphic.ModifierBoxSize
setValue(double) MuGraphic.ModifierAtomDiameter
setValue(double) MuGraphic.ModifierEpsilon
setValue(double) MuGraphic.ModifierLambda
setValue(double) NucleationGraphic.ModifierDensity
setValue(double) ModifierPistonPressure
setValue(double) PistonCylinderGraphic.ModifierAtomDiameter
setValue(double) PistonCylinderGraphic.ModifierPistonDensity
setValue(double) ReverseOsmosisGraphic.ModifierAtomDiameter
setValue(double) ReverseOsmosisGraphic.ModifierEpsilon
setValue(double) ReverseOsmosisWaterGraphic.ModifierAtomDiameter
setValue(double) ReverseOsmosisWaterGraphic.ModifierEpsilon
setValue(double) ReverseOsmosisWaterGraphic.ModifierSoluteCharge
setValue(double) SamGraphic.ModifierWallPosition
setValue(double) SwmdGraphic.ModifierAtomDiameter
setValue(double) ModifierCells3D
setValue(double) ModifierXCells2D
setValue(double) ModifierYCells2D
setValue(double) ModifierTPI
setValue(int) DeviceBoxValueChangedEvent
Set the value of a DeviceBoxValueChangedEvent (should be the value of the text box)
setValue(Object) DimensionedDoubleEditor
Sets the value to the given value, which is taken to be in simulation units.
setValue(Object, Field, String) ParameterParser
Sets obj's field to appropriate value based on the given string, if this
parser is appropriate for the given field, or throws an exception if
it's not.
setValue(Field, String) ParameterBase
setValueAt(Object, int, int) DeviceTableModelGeneric
Set the value in the given table cell.
setValueAt(Object, int, int) ModelMoleculeListDisplayTable_new
setValueAt(Object, int, int) ModelMoleculeListDisplayTable
setValueAt(Object, int, int) ModelPotParamDisplayTable
setValueForAction(boolean) ModifyBooleanAction
Stores the new value to be set by the wrapped modifier.
setValueForAction(double) ModifyAction
Stores the new value to be set by the wrapped modifier.
setVaporColor(Color) ColorSchemeLiquidVapor
setVariable(String, Set<Graph>) Environment
setVariable(String, Set<Graph>) EnvironmentImpl
setVCut(double) PotentialCalculationMappedRdf
setVCut(double) PotentialCalculationMappedEnergy
setVCut(double) PotentialCalculationMappedVirial
setVCut(double) PotentialCalculationMappedVirialV
setVCut(double) PotentialCalculationMappedVirialV.UShift
setVCut(double) PotentialCalculationMappedVirialV.USine
setVectorScale(Vector) BoxInflate
Sets the scale defining the amount of inflation for each dimension.
setVertex1(Vector) LineSegment
setVertex2(Vector) LineSegment
setVFunc(PotentialCalculationMappedVirialV.VFunc) PotentialCalculationMappedVirialV
setViewSpeciesSelection(ViewSpeciesSelection) AppViewMixtureBuilder
setVisible(boolean) ClusterViewer
setVisible(boolean) AboutBoxWindow
setVolFluctuation(boolean) MeterNormalizedCoord
setVolume(double) PotentialCalculationMappedRdf
Sets volume to an arbitrary value (instead of the box volume).
setVolume(double) PotentialCalculationMappedEnergy
Sets volume to an arbitrary value (instead of the box volume).
setVolume(double) PotentialCalculationMappedVirial
Sets volume to an arbitrary value (instead of the box volume).
setVolume(double) PotentialCalculationMappedVirialV
Sets volume to an arbitrary value (instead of the box volume).
setVolumeBias(IFunction) MCMoveVolume
setVZero(double) P2Yukawa
setW(double) P1ImageHarmonic
setWallDim(int) P1WCAWall
setWallDim(int) P1WCAWall
setWallDim(int) P1WCAWall
setWallDim(int) CriterionPositionWall
Sets the orientation of the wall to be perpendicular to the given dimension
setWallPosition(double) P1WCAWall
setWallPosition(double) CriterionPositionWall
Sets the position of the wall.
setWallPosition(double) P1HardMovingBoundary
setWallVelocity(double) P1HardMovingBoundary
setWaveVec(Vector[]) MeterStructureFactor
setWaveVector(Vector) MeterHarmonicCoordinate
setWaveVectorCoefficients(double[]) IntegratorHarmonic
setWaveVectorCoefficients(double[]) MCMoveHarmonic
setWaveVectorCoefficients(double[]) MCMoveSingleMode
setWaveVectorFactory(WaveVectorFactory) CalcJacobian
Sets the object that defines the normal-coordinate wave vectors.
setWaveVectorFactory(WaveVectorFactory) MeterNormalMode
Sets the object that defines the normal-coordinate wave vectors.
setWaveVectorFactory(WaveVectorFactory) WriteS
setWaveVectorNum(int) DeviceWaveVectorSlider
Set the current value for the wavevector # slider/text box.
setWaveVectorNum(int) IntegratorHarmonic
setWaveVectors(Vector[]) IntegratorHarmonic
setWaveVectors(Vector[]) MCMoveHarmonic
setWaveVectors(Vector[]) MCMoveSingleMode
Set the wave vectors used by the move.
setWaveVectors(Vector[], double[]) MeterHarmonicEnergy
setWaveVectors(Vector[], double[]) MeterHarmonicSingleEnergy
setWeight(double) MeterVirialBDBin
setWeight(double) MeterVirialBDBinMultiThreaded
setWeight(double) MeterVirialBinMultiThreaded
setWeight(double) MeterVirialEBinMultiThreaded
setWeight(Rational) ClusterDiagram
setWeightCoefficients(double[]) ClusterMultivalueUmbrella
setWeightCoefficients(double[]) ClusterWeightUmbrella
setWeightUpdateInterval(int) IntegratorTMMC
Sets the number of doStep calls between updating of weights.
setWellCutoffFactor(double) P2HardAssociationCone
Accessor method for attractive-well diameter divided by sigma;
setWellCutoffFactor(double) P2HardAssociationConeDoubleSites
Accessor method for attractive-well diameter divided by sigma;
setWellCutoffFactor(double) P2HardAssociationConeFourSites
Accessor method for attractive-well diameter divided by sigma;
setWellCutoffFactor(double) P2HardAssociationConeFourSitesSW
Accessor method for attractive-well diameter divided by sigma;
setWellCutoffFactor(double) P2HardAssociationConeOneSite
Accessor method for attractive-well diameter divided by sigma;
setWellCutoffFactor(double) P2HardAssociationConeSW
Accessor method for attractive-well diameter divided by sigma;
setWellDiameter(double) P2HardAssociation
Accessor for well-diameter.
setWellEpsilon(double) P2HardAssociationCone
Accessor method for attractive-well depth parameter.
setWellEpsilon(double) P2HardAssociationConeDoubleSites
Accessor method for attractive-well depth parameter.
setWellEpsilon(double) P2HardAssociationConeFourSites
Accessor method for attractive-well depth parameter.
setWellEpsilon(double) P2HardAssociationConeFourSitesSW
Accessor method for attractive-well depth parameter.
setWellEpsilon(double) P2HardAssociationConeOneSite
Accessor method for attractive-well depth parameter.
setWellEpsilon(double) P2HardAssociationConeSW
Accessor method for attractive-well depth parameter.
setWidth(float) SVGConverter
In less than or equal to zero, the width is not
constrained on the output image.
setWidthHeight(boolean) GData
setWindow(double, double, double, double) Plot
Sets up a mapping from physical units to pixel units.
setWindowParameters(int, int, boolean) Graphics3D
setWindowParameters(int, int, boolean) GData
setWireFrame(boolean) ImageShell
setWithReplacement(boolean) AccumulatorAverageBootstrap
setWrappedPotential(IPotentialAtomic) P2MoleculeMonatomic
setWrappedPotential(PotentialHard) P2HardWrapper
setWriteBlocks(String) AccumulatorAverageFixed
Configures the accumulator to write block data to the given file.
setWriteInterval(int) DataLogger
Define how many number of interval events received between writings to
file.
setWriteInterval(int) VelocityWriter
Equates intervalAction method variable to variable passed in from simulation class
setWriteInterval(int) MSDCoordWriter
Equates intervalAction method variable to variable passed in from simulation class
setWriteOnFinish(IDataSource) DataLogger
setWriteOnInterval(boolean) DataLogger
setWriteRestart(String, boolean) SimulationVirialOverlap2
setWriteScale(boolean) DisplayCanvas
setWriteVelocity(boolean) WriteConfigurationDLPOLY
setWriteVelocity(boolean) WriteConfigurationP2DLPOLY
setX(double, double, int) MeterPressureByVolumeChange
setX(float) Ball
set the x molspace position of the figure
setX(float) Ellipse
set the x molspace position of the figure
setX(int, double) Vector
Sets the i-th component of the vector to the given value d.
setX(int, double) Vector1D
setX(int, double) Vector2D
setX(int, double) Vector3D
setX(int, double) VectorND
setX0(Vector) P1Harmonic
setXCellModifier(Modifier) DeviceCellNumXYSlider
Set the x-Cell # modifier object.
setXCellNum(int) DeviceCellNumXYSlider
Set the current value for the xCell # slider/text box.
setXComp() DeviceCellNumXYSlider
Set the "x-axis" button to its selected state.
setXDataSource(DataSourceIndependent) DataFunction.DataInfoFunctionFactory
Sets array of independent DataInfo.
setXFlipped(boolean) G3DSys
setXLabel(String) DisplayPlot
setXLabel(String) DisplayPlotXChart
setXLog(boolean) DisplayPlotXChart
setXMax(double) DataSourceUniform
Mutator method for the right limit of the range.
setXMin(double) DataSourceUniform
Mutator method for the left limit of the range.
setXRange(double, double) DisplayPlotXChart
setXRange(double, double, int) MCMoveAtomInRegion
Defines the region atoms must be selected from.
setXRange(DoubleRange) Histogram
Sets the range of x values used in the histogram (min and max).
setXRange(DoubleRange) HistogramCollapsing
setXRange(DoubleRange) HistogramDiscrete
setXRange(DoubleRange) HistogramExpanding
setXRange(DoubleRange) HistogramNotSoSimple
setXRange(DoubleRange) HistogramReweightedData
setXRange(DoubleRange) HistogramSimple
setXRot(float) DisplayCanvas
setXScale(double, double, double) DevicePlotPoints
Sets the minimum and maximum X-axis limits on the function display
sliders.
setXSliderPostAction(IAction) DeviceCellNumXYSlider
Set the post slider value changed action.
setXUnit(Unit) DisplayPlot
Extend superclass method to update label with change of unit.
setXUnit(Unit) DisplayPlotXChart
setXYZChange() MCMoveVolumeN2
setY(float) Ball
set the y molspace position of the figure
setY(float) Ellipse
set the y molspace position of the figure
setYCellModifier(Modifier) DeviceCellNumXYSlider
Set the y-Cell # modifier object.
setYCellNum(int) DeviceCellNumXYSlider
Set the current value for the yCell # slider/text box.
setYComp() DeviceCellNumXYSlider
Set the "y-axis" button to its selected state.
setYesButton(JButton) ViewAlertMsgBoxSpeciesRemoval
setYFlipped(boolean) G3DSys
setYLabel(String) DisplayPlotXChart
setYLog(boolean) DisplayPlotXChart
setYRange(double, double) DisplayPlotXChart
setYRot(float) DisplayCanvas
setYScale(double, double, double) DevicePlotPoints
Sets the minimum and maximum Y-axis limits on the function display
sliders.
setYSliderPostAction(IAction) DeviceCellNumXYSlider
setZ(double) P1WCAPorousWall
setZ(float) Ball
set the z molspace position of the figure
setZ(float) Ellipse
set the z molspace position of the figure
setZ1(double) P2ModifiedMorse
setZ2(double) P2ModifiedMorse
setZ3() P3CPSNonAdditiveHeOrig
setZ4211() P3CPSNonAdditiveHeOrig
setZ4220() P3CPSNonAdditiveHeOrig
setZero() Matrix3f
Sets this matrix to all zeros.
setZero() Matrix4f
Sets this matrix to all zeros.
setZeroForce(boolean) P1ImageHarmonic
setZFraction(double) MyMCMove
Sets the zFraction, the fraction of the box volume into which atoms are
inserted or deleted.
setZFraction(double) MyMCMove
Sets the zFraction, the fraction of the box volume into which atoms are
inserted or deleted.
setZFraction(double, double) MyMCMove
Sets the zFraction, the fraction of the box volume into which atoms are
inserted or deleted.
setZoom(float) DisplayCanvas
setZShade(boolean, int, int, int) Graphics3D
setZShade(boolean, int, int, int) GData
SFacButtonAction(List<MeterStructureFactor.AtomSignalSourceByType>, AccumulatorAverageFixed, AtomType, double) GlassGraphic.SFacButtonAction
sfacData ConfigFromFileLAMMPS.ModifierConfiguration
sfacDataInfo ConfigFromFileLAMMPS.ModifierConfiguration
sfacMinInterval GlassProd.SimParams
sfacPlotSink ConfigFromFileLAMMPS.ModifierConfiguration
shadeIndexLast Shader
shadeIndexMax Shader
shadeIndexNoisyLimit Shader
shadeIndexNormal Shader
Shader org.jmol.util
All static functions.
Shader() Shader
shakeAgentManager IntegratorVelocityVerletShake
shakeTol IntegratorVelocityVerletShake
shape HarmonicCrystalSsFccNxy.Params
shape SimOverlapSSnxy.SimOverlapParam
shape Boundary
shape VirialPolyhedra2.VirialHSParam
shape Token
Shape etomica.math.geometry
Interface for an object that defines a closed region of space.
SHAPE_AXES JmolConstants
SHAPE_BACKBONE JmolConstants
SHAPE_BALLS JmolConstants
SHAPE_BBCAGE JmolConstants
SHAPE_CARTOON JmolConstants
SHAPE_CONTACT JmolConstants
SHAPE_DIPOLES JmolConstants
SHAPE_DOTS JmolConstants
SHAPE_DRAW JmolConstants
SHAPE_ECHO JmolConstants
SHAPE_ELLIPSOIDS JmolConstants
SHAPE_FRANK JmolConstants
SHAPE_GEOSURFACE JmolConstants
SHAPE_HALOS JmolConstants
SHAPE_HOVER JmolConstants
SHAPE_HSTICKS JmolConstants
SHAPE_ISOSURFACE JmolConstants
SHAPE_LABELS JmolConstants
SHAPE_LCAOCARTOON JmolConstants
SHAPE_MAX JmolConstants
SHAPE_MAX_HAS_ID JmolConstants
SHAPE_MAX_MESH_COLLECTION JmolConstants
SHAPE_MAX_SECONDARY JmolConstants
SHAPE_MAX_SIZE_ZERO_ON_RESTRICT JmolConstants
SHAPE_MAX_SPECIAL JmolConstants
SHAPE_MAX_SURFACE JmolConstants
SHAPE_MEASURES JmolConstants
SHAPE_MESHRIBBON JmolConstants
SHAPE_MIN_HAS_ID JmolConstants
SHAPE_MIN_MESH_COLLECTION JmolConstants
SHAPE_MIN_SECONDARY JmolConstants
SHAPE_MIN_SPECIAL JmolConstants
SHAPE_MIN_SURFACE JmolConstants
SHAPE_MO JmolConstants
SHAPE_PLOT3D JmolConstants
SHAPE_PMESH JmolConstants
SHAPE_POLYHEDRA JmolConstants
SHAPE_RIBBONS JmolConstants
SHAPE_ROCKETS JmolConstants
SHAPE_SSSTICKS JmolConstants
SHAPE_STARS JmolConstants
SHAPE_STICKS JmolConstants
SHAPE_STRANDS JmolConstants
SHAPE_STRUTS JmolConstants
SHAPE_TRACE JmolConstants
SHAPE_UCCAGE JmolConstants
SHAPE_VECTORS JmolConstants
shapeClassBases JmolConstants
ShapeData() ShapeParser.ShapeData
SHAPELY EnumPalette
ShapeParser etomica.virial.simulations
ShapeParser() ShapeParser
ShapeParser.ShapeData etomica.virial.simulations
shapes VirialPolyhedra.VirialHSParam
shapeTokenIndex(int) JmolConstants
shareData VirialHSBinMultiThreaded.VirialHSBinParam
shareData VirialSQWBinMultiThreaded.VirialHSBinParam
shearBox RheologyGraphic
shearRate IntegratorPolymer
sheet Token
sheetsmoothing Token
shift ConfigurationLammps
shift WriteConfigurationInterfacial
shift MeterDensityDistribution
shift PNCO2GCPM
shift PNGCPM
shift P2Nitrogen
shift P2NitrogenAB
shift P2NitrogenAnisotropic
shift P2NitrogenShellModel
shift P2Water3P
shift P2Water4P
shift PNWaterGCPM
shift PNWaterGCPMReactionField
shift P2CO2EMP
shift P2SoftSphericalTruncatedShifted
shift BoundaryTruncatedOctahedron
shift0 BoundaryRectangular
shift0 BoundaryTruncatedOctahedron
shifted SimLJVacancy.LJParams
SHIFTED ParserLAMMPS.Truncation
shiftMomenta() IntegratorMD
Subtracts velocity from all atoms such that the new net momentum of
the whole system is zero.
shiftMomenta() IntegratorRigidIterative
shiftMomenta() IntegratorRigidMatrixIterative
shiftMomenta() IntegratorVelocityVerletQuaternion
showaxes Token
showboundbox Token
showfrank Token
showhiddenselectionhalos Token
showhydrogens Token
showingColumnHeaders DisplayTable
showingRowLabels DisplayTable
showingUnits DisplayTable
showkeystrokes Token
showmeasurements Token
showmultiplebonds Token
shownavigationpointalways Token
showNumMoleculesPlots VLE.VLEParams
showNumMoleculesPlots SWVLE
showNumMoleculesPlots VLE
showPointInput(boolean) DevicePlotPoints
Sets the visibility of the data point input table.
showReport(SimulationVirialOverlap2, double) SimulationRunner
showScale(boolean) DevicePlotPoints
Sets the visibility of the plot axis limit sliders.
showscript Token
showtiming Token
showunitcell Token
sidechain Token
sig ClusterWheatleyHS.AllSigs
sig ClusterWheatleyPartitionScreening
sig2 ColorSchemeOverlap
sig2 P2HardSphere
Square of collisionDiameter
sigBox PistonCylinderGraphic
sigBox ReverseOsmosisGraphic
sigBox ReverseOsmosisWaterGraphic
sigBox SwmdGraphic
sigCounter ClusterWheatleyPartitionScreening
sigma DataProcessorCavity
sigma MeterCavityMapped
sigma MeterContactRatio
sigma MeterRDFMapped
sigma DCVGCMD
sigma P1WCAWall
sigma VLESim
sigma PNGCPM.GCPMAgent
sigma P2Water3P
sigma P2Water4P
sigma P2WaterTIP4PHardCore
sigma PNWaterGCPM
sigma PNWaterGCPMReactionField
sigma EOSSW
sigma P1Wall
sigma P1Wall
sigma P1WCAWall
sigma DropletAtomic
sigma PistonCylinderGraphic
sigma P1WCAWall
sigma SwmdGraphic
sigma VLESim
sigma SoftSphereSolidEOS
sigma SoftSphereSolidEOSCalculator
sigma P1HardPeriodic
sigma P2ElectrostaticWithHardCore
sigma P2HePCJS
sigma P2PotentialGroupBuilder.ModelParams
sigma P3CPSNonAdditiveHe
sigma ConformationStarPolymerGraft
sigma MCMoveClusterMoleculeHSChain
sigma MCMoveClusterMoleculeHSChainB3
sigma LJ
sigma BnPYCHe.BnPYHeParams
sigma MCMoveClusterAtomChainHSTail
sigma MCMoveClusterAtomHSChain
sigma MCMoveClusterAtomHSRing
sigma MCMoveClusterAtomHSTree
sigma MCMoveClusterMoleculeHSChain
sigma MCMoveClusterPolyhedraChain
sigma MCMoveClusterPolyhedraTree
sigma Virial2CLJmuQ.Virial2CLJQParam
sigma Virial2CLJQ.Virial2CLJQParam
sigma VirialB2WaterTIP4P_DHS_difference.P2WaterDHS
sigma VirialHeNonAdditiveWheatley.VirialParam
sigma VirialTraPPE.TraPPEParams
sigma() Ifactor
Sum of the divisors of the number.
sigma(double) P2HePCJS
sigma(double) P3HydrogenManzhos
sigma(int) BigIntegerMath
Evaluate sigma(n).
sigma(int) Ifactor
Sum of the k-th powers of divisors of the number.
sigma(BigInteger) BigIntegerMath
Evaluate sigma(n).
SIGMA EnumPotentialParamDescription
SIGMA P2WaterSPCE
sigma_AD(double) P2HePCJS
sigma_BO(double) P2HePCJS
sigma_QED(double) P2HePCJS
sigma_REL(double) P2HePCJS
sigma0point DoubleAssociationSitesFluid2Pt.VirialAssociatingFluidParam
sigma0point DoubleAssociationSitesFluid3Pt.VirialAssociatingFluidParam
sigma0point DoubleAssociationSitesFluid4Pt.VirialAssociatingFluidParam
sigma0point FourAssociationSitesFluid2Pt.VirialAssociatingFluidParam
sigma2 P2Water3P
sigma2 P2Water4P
sigma2 P2WaterTIP4PHardCore
sigma2 P1WCAWall
sigma2 HSNPT.HSMD3DParameters
sigma2 NVTWidomInsertLJ.simParams
sigma2 MayerHSMixture
sigma2 MayerWell
sigmaA VirialN2TraPPE.VirialN2Param
sigmaABpoint DoubleAssociationSitesFluid2Pt.VirialAssociatingFluidParam
sigmaABpoint DoubleAssociationSitesFluid3Pt.VirialAssociatingFluidParam
sigmaABpoint DoubleAssociationSitesFluid4Pt.VirialAssociatingFluidParam
sigmaABpoint FourAssociationSitesFluid2Pt.VirialAssociatingFluidParam
sigmaAll PNCO2GCPM
sigmaApoint DoubleAssociationSitesFluid2Pt.VirialAssociatingFluidParam
sigmaApoint DoubleAssociationSitesFluid3Pt.VirialAssociatingFluidParam
sigmaApoint DoubleAssociationSitesFluid4Pt.VirialAssociatingFluidParam
sigmaApoint FourAssociationSitesFluid2Pt.VirialAssociatingFluidParam
sigmaB SimGlass
sigmaBpoint DoubleAssociationSitesFluid2Pt.VirialAssociatingFluidParam
sigmaBpoint DoubleAssociationSitesFluid3Pt.VirialAssociatingFluidParam
sigmaBpoint DoubleAssociationSitesFluid4Pt.VirialAssociatingFluidParam
sigmaBpoint FourAssociationSitesFluid2Pt.VirialAssociatingFluidParam
sigmaC PNCO2GCPM
sigmaC P2CO2EMP
sigmaC2 P2CO2EMP
sigmaCH2 Sam
sigmaCH2 VirialCO2AlkaneUAMix.VirialMixParam
sigmaCH2 VirialN2AlkaneUAMix.VirialMixParam
sigmaCH2 VirialN2AlkaneUARigid.VirialMixParam
sigmaCH2 VirialSF6LJAlkaneUAMix.VirialMixParam
sigmaCH3 VirialCO2AlkaneUAMix.VirialMixParam
sigmaCH3 VirialN2AlkaneUAMix.VirialMixParam
sigmaCH3 VirialN2AlkaneUARigid.VirialMixParam
sigmaCH3 VirialSF6LJAlkaneUAMix.VirialMixParam
sigmaCO P2CO2EMP
sigmaCO2 P2CO2EMP
sigmaColloid ConfigurationColloid
sigmaH PNWaterGCPM
sigmaH PNWaterGCPMReactionField
sigmaHC P2HePCKLJS
sigmaHC2 P2HeSimplified
sigmaHS DHS_NVT.Param
sigmaHS VirialB3C1HSDipole.VirialParam
sigmaHS VirialB3C2HSDipole.VirialParam
sigmaHS2 VirialB2WaterTIP4P_DHS_difference.P2WaterDHS
sigmaHSRef Wertheim2SiteAceticAcid.WertheimParam
sigmaHSRef WertheimGCPM3PtEBondDecomp.VirialAssociatingFluidParam
sigmaHSRef WertheimGCPM3PtThreeSite.VirialAssociatingFluidParam
sigmaHSRef WertheimGCPM4PtEBondDecomp.WertheimAssociatingFluidParam
sigmaHSRef WertheimGCPM4PtEBondDecompFinal.VirialAssociatingFluidParam
sigmaHSRef WertheimGCPM4PtThreeSite.VirialAssociatingFluidParam
sigmaHSRef BnFlexibleContributionTraPPEUAMethanol.VirialParam
sigmaHSRef DoubleAssociationSitesFluid2Pt.VirialAssociatingFluidParam
sigmaHSRef DoubleAssociationSitesFluid3Pt.VirialAssociatingFluidParam
sigmaHSRef DoubleAssociationSitesFluid4Pt.VirialAssociatingFluidParam
sigmaHSRef FourAssociationSitesFluid2Pt.VirialAssociatingFluidParam
sigmaHSRef ReeHooverMC.VirialParam
sigmaHSRef SingleAssociationSiteFluid.VirialAssociatingFluidParam
sigmaHSRef SingleAssociationSiteFluid2.VirialAssociatingFluidParam
sigmaHSRef SingleAssociationSiteFluid2Pt.VirialAssociatingFluidParam
sigmaHSRef SingleAssociationSiteFluid3Pt.VirialAssociatingFluidParam
sigmaHSRef SingleAssociationSiteFluid4Points.VirialAssociatingFluidParam
sigmaHSRef SingleAssociationSiteFluid4Pt.VirialAssociatingFluidParam
sigmaHSRef SingleAssociationSiteFluidGraph.VirialAssociatingFluidParam
sigmaHSRef Virial2CLJmuQ.Virial2CLJQParam
sigmaHSRef Virial2CLJQ.Virial2CLJQParam
sigmaHSRef Virial7SiteRigidSF6.VirialSF6Param
sigmaHSRef VirialAceticAcid.VirialParam
sigmaHSRef VirialAceticAcidFlex.VirialParam
sigmaHSRef VirialAnthracene464.VirialAnthracene545Param
sigmaHSRef VirialAnthracene545.VirialAnthracene545Param
sigmaHSRef VirialAnthraceneTraPPE.VirialAnthraceneTraPPEParam
sigmaHSRef VirialAssociatingFluid.VirialAssociatingFluidParam
sigmaHSRef VirialAssociatingFluid4points.VirialAssociatingFluidParam
sigmaHSRef VirialB2WaterTIP4P_DHS_difference.VirialParam
sigmaHSRef VirialB3C1HSDipole.VirialParam
sigmaHSRef VirialB3C1TIP4Pwater.VirialParam
sigmaHSRef VirialB3C2HSDipole.VirialParam
sigmaHSRef VirialB3C2TIP4Pwater.VirialParam
sigmaHSRef VirialCO2.VirialCO2Param
sigmaHSRef VirialCO2AlkaneUAMix.VirialMixParam
sigmaHSRef VirialCO2anthracene464.VirialCO2anthracene545Param
sigmaHSRef VirialCO2anthracene545.VirialCO2anthracene545Param
sigmaHSRef VirialCO2AnthraceneTraPPE.VirialCO2AnthraceneTraPPEParam
sigmaHSRef VirialCO2CH4Mix.VirialMixParam
sigmaHSRef VirialCO2CH4UAMix.VirialMixParam
sigmaHSRef VirialCO2CH4UAMixWheatley.VirialMixParam
sigmaHSRef VirialCO2H2OGCPM.VirialParam
sigmaHSRef VirialCO2H2OGCPMX.VirialParam
sigmaHSRef VirialCO2H2OSC.VirialCO2SCParam
sigmaHSRef VirialCO2LJQ.VirialCO2LJQParam
sigmaHSRef VirialCO2N2Mix.VirialMixParam
sigmaHSRef VirialCO2NaphthaleneLJQ.VirialCO2NaphthaleneLJQParam
sigmaHSRef VirialCO2NaphthaleneTraPPE.VirialCO2TraPPEParam
sigmaHSRef VirialCO2PI.VirialH2PIParam
sigmaHSRef VirialCO2SKSMix.VirialCO2Param
sigmaHSRef VirialCO2TraPPE.VirialCO2TraPPEParam
sigmaHSRef VirialCPSHeliumNonAdditive.VirialParam
sigmaHSRef VirialCPSHeliumNonAdditiveClassical_Correction.VirialParam
sigmaHSRef VirialCPSHeliumNonAdditiveClassical.VirialParam
sigmaHSRef VirialEmulNonAdditive.VirialParam
sigmaHSRef VirialH2O.VirialH2OParam
sigmaHSRef VirialH2OGCPMD.VirialParam
sigmaHSRef VirialH2PI.VirialH2PIParam
sigmaHSRef VirialH2PISimple.VirialH2PISimpleParam
sigmaHSRef VirialH2PYCorrection.VirialH2PYCParam
sigmaHSRef VirialHardAssociationCone.VirialLJParam
sigmaHSRef VirialHardAssociationConeDoubleSites.VirialLJParam
sigmaHSRef VirialHeD.VirialParam
sigmaHSRef VirialHeNonAdditive.VirialParam
sigmaHSRef VirialHeNonAdditiveD.VirialParam
sigmaHSRef VirialHeNonAdditiveWheatley.VirialParam
sigmaHSRef VirialHePCKLJS.VirialParam
sigmaHSRef VirialHePCKLJSCHNCCorrection.VirialLJParam
sigmaHSRef VirialHePCKLJSPYCorrection.VirialLJParam
sigmaHSRef VirialHePCKLJSTempDeriv.VirialParam
sigmaHSRef VirialHePI_PotentialCorrection.VirialHePIParam
sigmaHSRef VirialHePI.VirialHePIParam
sigmaHSRef VirialHePISysErr.VirialHePIParam
sigmaHSRef VirialHePIXCOdd.VirialHePIParam
sigmaHSRef VirialHePYCorrection.VirialHePYCParam
sigmaHSRef VirialHeSC.VirialHePYCParam
sigmaHSRef VirialLJ.VirialLJParam
sigmaHSRef VirialLJBridge.VirialLJParam
sigmaHSRef VirialLJCHNCCorrection.VirialLJParam
sigmaHSRef VirialLJD.VirialLJParam
sigmaHSRef VirialLJDU.VirialLJParam
sigmaHSRef VirialLJMultiOverlap.VirialMixParam
sigmaHSRef VirialLJPT.VirialLJParam
sigmaHSRef VirialLJPYCorrection.VirialLJParam
sigmaHSRef VirialLJSeries.VirialLJParam
sigmaHSRef VirialMethaneEH.VirialMethaneParam
sigmaHSRef VirialN2.VirialN2Param
sigmaHSRef VirialN2AlkaneUAMix.VirialMixParam
sigmaHSRef VirialN2AlkaneUARigid.VirialMixParam
sigmaHSRef VirialN2CH4Mix.VirialMixParam
sigmaHSRef VirialN2CH4UAMix.VirialMixParam
sigmaHSRef VirialN2PI.VirialN2Param
sigmaHSRef VirialN2TraPPE.VirialN2Param
sigmaHSRef VirialNaphthaleneTraPPE.VirialNaphthaleneTraPPEParam
sigmaHSRef VirialO2.VirialO2Param
sigmaHSRef VirialO2PI.VirialO2Param
sigmaHSRef VirialPh464.VirialPh3site464Param
sigmaHSRef VirialPh545.VirialPh3site545Param
sigmaHSRef VirialPhenanthreneTraPPE.VirialPhenanthreneTraPPEParam
sigmaHSRef VirialSF6LJAlkaneUAMix.VirialMixParam
sigmaHSRef VirialSW.VirialSWParam
sigmaHSRef VirialSwsPT.VirialSiepmannSpheresParam
sigmaHSRef VirialTraPPE.VirialParam
SIGMAHSREF EnumPotentialParamDescription
sigmak(BigInteger, int) BigIntegerMath
Evaluate sigma_k(n).
sigmaLJ DLJ_NVT_1site.Param
sigmaLJ DLJ_NVT_1site.Param
sigmaLJ TIP4P_NVT
sigmaM PNWaterGCPM
sigmaM PNWaterGCPMReactionField
sigmaMembrane ReverseOsmosisGraphic
sigmaMonomer ConfigurationColloid
sigmaN VirialN2TraPPE.VirialN2Param
sigmaO PNCO2GCPM
sigmaO P2CO2EMP
sigmaO2 P2CO2EMP
sigmaOC VirialRowleyAlcohol
sigmaOH VirialRowleyAlcohol
sigmaRatio PolydisperseHS.HSPolyParam
sigmas P2HardSpherePoly
sigmaSF6 VirialSF6LJAlkaneUAMix.VirialMixParam
sigmaSolute ReverseOsmosisGraphic
sigmaSolvent ReverseOsmosisGraphic
signal MeterStructureFactor.AtomSignalSourceByType
signal(IAtom) MeterStructureFactor.AtomSignalSource
signal(IAtom) MeterStructureFactor.AtomSignalSourceByType
signal(IAtom) AtomSignalKineticEnergy
signal(IAtom) AtomSignalMobility
signal(IAtom) AtomSignalMotion
signal(IAtom) AtomSignalStress
signalSource MeterStructureFactor
signalSources GlassGraphic.SFacButtonAction
signature() Atom
Returns a string of digits that uniquely identifies this atom.
signature() Molecule
Returns a string of digits that uniquely identifies this atom.
signature() Dimension
The signature is the exponents of each of the base dimensions forming the
given dimension.
signatureMaker GlobalFilter
SignatureMaker() GlobalFilter.SignatureMaker
signum() BigSurd
The sign: 1 if the number is >0, 0 if ==0, -1 if <0
signum() BigSurdVec
Sign function.
signum() Rational
The sign: 1 if the number is >0, 0 if ==0, -1 if <0
Silver etomica.chem.elements
Class for the Silver element.
Silver(String) Silver
Silver(String, double) Silver
SILVER Colix
sim MCMoveVolumeAssociatedMolecule
sim AtomTypeAgentManager
sim BoxAgentSourceMoleculeManager
sim MeterKineticEnergyRigid
sim MeterTemperature
sim IntegratorDimerMin
sim IntegratorDimerRT
sim DisplayBox
sim IntegratorRigidIterative
sim IntegratorRigidMatrixIterative
sim AdsorptionGraphic
sim CatalysisGraphic
sim ConfigurationCatalysis
sim ReactionManagerCO
sim ChainEquilibriumGraphic
sim FreeRadicalPolymerizationGraphic
sim ColloidGraphic
sim CrystalViewer
sim DropletAtomicGraphic
sim DropletGraphic
sim LJMCGraphic
sim GlassGraphic
sim InsertionGraphic
sim InterfacialSWGraphic
sim LjmdGraphic
sim MuGraphic
sim MultiharmonicGraphicMC
sim MultiharmonicGraphic
sim MultiharmonicGraphicMC
sim MultiharmonicGraphicMC
sim MultiharmonicGraphicMC
sim NucleationGraphic
sim Osmosis
sim ReactionEquilibriumGraphic
sim ConfigurationMembrane
sim ConfigurationMembraneWater
sim MeterFlux
sim ReverseOsmosisGraphic
sim ReverseOsmosisWaterGraphic
sim ConfigurationSAM
sim CriterionTether3
sim SamGraphic.DataPipeStressStrain
sim SelfAssemblyGraphic
sim StatisticsMCGraphic
sim SwmdGraphic
sim BoxAgentSourceCellManagerMolecular
sim NeighborCellManagerMolecular
sim CoordinateDefinitionMolecule
sim CoordinateDefinitionMoleculeVolumeFluctuation
sim HTTPSoftSphereApplet
sim NormalModeAnalysisDisplay1DGraphic
sim NormalModeAnalysisDisplay2DGraphic
sim NormalModeAnalysisDisplay3DGraphic
sim HSNPT2DGraphic
sim IntegratorVelocityVerletQuaternion
Sim() UnitSystem.Sim
SIM UnitSystem
Instance of simulation units, the unit system used for internal calculations.
SIM_CONTEXT_CLASSES Construction
SIM_UNIT Angle
SIM_UNIT Area
SIM_UNIT Charge
Simulation unit of charge.
SIM_UNIT Current
Simulation unit of electrical current.
SIM_UNIT Dipole
SIM_UNIT ElectricPotential
Simulation unit of charge.
SIM_UNIT Energy
The simulation unit of energy is D-A^2/ps^2.
SIM_UNIT Force
SIM_UNIT Fraction
The simulation unit is the Decimal.
SIM_UNIT Frequency
The simulation unit is 1/ps = 1/(10^-12 s) = 10^12/s = 1 THz.
SIM_UNIT Length
Simulation unit for length is the angstrom.
SIM_UNIT LuminousIntensity
The Candela unit.
SIM_UNIT Mass
The simulation unit is the Dalton.
SIM_UNIT Momentum
The simulation unit is A/ps.
SIM_UNIT Power
The simulation unit of power is D-A^2/ps^3.
SIM_UNIT Pressure
Simulation unit of pressure is (D-A/ps^2)/A^2 = D/(A-ps^2).
SIM_UNIT Pressure2D
SIM_UNIT Quantity
Simulation unit is Count.
SIM_UNIT Temperature
The simulation unit for temperature, which as kT has dimensions
of energy and is D-A^2/ps^2.
SIM_UNIT Time
Simulation unit for time is the picosecond.
SIM_UNIT Velocity
The simulation unit is A/ps.
SIM_UNIT Viscosity
The simulation unit is Dalton/(A-ps).
SIM_UNIT Volume
Simulation unit of volume is cubic Angstroms.
SIM_UNIT Wavenumber
The simulation unit is 1/A
SimBennet etomica.normalmode
Simulation to sample Bennet's Overlap Region
SimBennet(Space, int, double, double, String, int) SimBennet
SimBennet.SimBennetParam etomica.normalmode
SimBennetParam() SimBennet.SimBennetParam
SimBennetParam() SimHarmonicUmbrella.SimBennetParam
SimBennetParam() SimTargetUmbrella.SimBennetParam
SimBennetParam() SimUmbrella.SimBennetParam
SimBennetParam() SimUmbrellaSoftSphere.SimBennetParam
SimCalcJ etomica.normalmode
Simulation class of hard spheres in 1D or 3D that calculates the dq/dx
Jacobian.
SimCalcJ(Space, int) SimCalcJ
SimCalcS etomica.normalmode
MD simulation of hard spheres in 1D or 3D with tabulation of the
collective-coordinate S-matrix.
SimCalcS(Space, int, double) SimCalcS
SimCalcSLJ etomica.normalmode
MD simulation of hard spheres in 1D or 3D with tabulation of the
collective-coordinate S-matrix.
SimCalcSLJ(Space, int, double, double) SimCalcSLJ
SimCalcSMorse etomica.normalmode
MC simulation of Morse model in 3D with tabulation of the
collective-coordinate S-matrix.
SimCalcSMorse(Space, int, double, double) SimCalcSMorse
SimCalcSSoftSphere2D etomica.normalmode
MC simulation of FCC soft-sphere model in 2D with tabulation of the
collective-coordinate S-matrix.
SimCalcSSoftSphere2D(Space, int, int[], double, int) SimCalcSSoftSphere2D
SimCalcSSoftSphereFCC etomica.normalmode
MC simulation of FCC soft-sphere model in 3D with tabulation of the
collective-coordinate S-matrix.
SimCalcSSoftSphereFCC(Space, int, double, double, int) SimCalcSSoftSphereFCC
SimCalcSSoftSphereFCCSuperBox etomica.normalmode
MC simulation of FCC soft-sphere model in 3D with tabulation of the
collective-coordinate S-matrix.
SimCalcSSoftSphereFCCSuperBox(Space, int, double, double, int) SimCalcSSoftSphereFCCSuperBox
SimClassInfo etomica.server.representations
SimClassInfo(String, String) SimClassInfo
SimDimerLJadatom etomica.dimer
Simulation using Henkelman's Dimer method to find a saddle point for
an adatom on a surface, modeled with LJ.
SimDimerLJadatom() SimDimerLJadatom
SimDirectBetaN2RP etomica.models.nitrogen
Direct Sampling for Rotational Perturbation
SimDirectBetaN2RP(Space, int, double, double, double[]) SimDirectBetaN2RP
SimDirectBetaN2RP.SimOverlapParam etomica.models.nitrogen
Inner class for parameters understood by the SimOverlapBetaN2RP constructor
SimDirectBetaN2RPAngleToNoAngle etomica.models.nitrogen
Direct Sampling for Rotational Perturbation
from NO rotational energy to constraint-angle rotational energy
SimDirectBetaN2RPAngleToNoAngle(Space, int, double, double, double, long) SimDirectBetaN2RPAngleToNoAngle
SimDirectBetaN2RPInitPert etomica.models.nitrogen
Direct Sampling for Rotational Perturbation
from NO rotational energy to constraint-angle rotational energy
SimDirectBetaN2RPInitPert(Space, int, double, double, double, long) SimDirectBetaN2RPInitPert
SimDirectDisorderedAlphaN2RPInitPert etomica.models.nitrogen
Direct Sampling for Rotational Perturbation
from NO rotational energy to constraint-angle rotational energy
SimDirectDisorderedAlphaN2RPInitPert(Space, int, double, double, double, long) SimDirectDisorderedAlphaN2RPInitPert
SimEinStep1 etomica.normalmode
Simulation that samples a composite energy function (soft sphere and
Einstein crystal) and perturbs into overlap regions shared by systems with
more or less soft sphere contributions.
SimEinStep1(Space, int, double, double, double, int, double, boolean) SimEinStep1
SimEinStep1.SimOverlapParam etomica.normalmode
Inner class for parameters understood by the HSMD3D constructor
SimEinStep1HCP etomica.normalmode
Simulation that samples a composite energy function (soft sphere and
Einstein crystal) and perturbs into overlap regions shared by systems with
more or less soft sphere contributions.
SimEinStep1HCP(Space, int, double, double, double, int, double, double) SimEinStep1HCP
SimEinStep1HCP.SimOverlapParam etomica.normalmode
Inner class for parameters understood by the HSMD3D constructor
SimEinStep2 etomica.normalmode
Simulation that samples a composite energy function (soft sphere and
Einstein crystal) and perturbs into overlap regions shared by systems with
more or less soft sphere contributions.
SimEinStep2(Space, int, double, double, double, int, double, boolean) SimEinStep2
SimEinStep2.MeterPotentialEnergyComposite etomica.normalmode
SimEinStep2.SimOverlapParam etomica.normalmode
Inner class for parameters understood by the HSMD3D constructor
SimEinStep2HCP etomica.normalmode
Simulation that samples a composite energy function (soft sphere and
Einstein crystal) and perturbs into overlap regions shared by systems with
more or less soft sphere contributions.
SimEinStep2HCP(Space, int, double, double, double, int, double, double) SimEinStep2HCP
SimEinStep2HCP.MeterPotentialEnergyComposite etomica.normalmode
SimEinStep2HCP.SimOverlapParam etomica.normalmode
Inner class for parameters understood by the HSMD3D constructor
SimFe etomica.freeenergy.npath
SimFe(SimFe.Crystal, int, double, double, double, int, int, boolean, boolean, double) SimFe
SimFe.LjMC3DParams etomica.freeenergy.npath
SimFluidSoftSphere etomica.normalmode
MC simulation of soft-sphere fluid model
SimFluidSoftSphere(Space, int, double, double, int) SimFluidSoftSphere
SimGCPMWaterMCNPT etomica.association.GCPMWater
GCPM Water Monte Carlo NPT simulation in 3D.
SimGCPMWaterMCNPT(int, double, double, double, long) SimGCPMWaterMCNPT
SimGCPMWaterMCNPT.GCPMWaterMCParam etomica.association.GCPMWater
SimGCPMWaterMCNVT etomica.association.GCPMWater
GCPM Water Monte Carlo NPT simulation in 3D.
SimGCPMWaterMCNVT(int, double, double, long) SimGCPMWaterMCNVT
SimGCPMWaterMCNVT.GCPMWaterMCParam etomica.association.GCPMWater
SimGlass etomica.modules.glass
SimGlass(int, int, int, double, double, boolean, SimGlass.PotentialChoice, double) SimGlass
SimGlass(int, int, int, double, double, boolean, SimGlass.PotentialChoice, double, int[]) SimGlass
SimGlass.GlassParams etomica.modules.glass
SimGlass.PotentialChoice etomica.modules.glass
simGraphic MuGraphic.ModifierAtomDiameter
SimHarmonic etomica.normalmode
Simulation to sample harmonic potential
SimHarmonic(Space, int, double, String, double) SimHarmonic
SimHarmonicUmbrella etomica.normalmode
Simulation to sample harmonic system and perturbing into
the umbrella sampling region
SimHarmonicUmbrella(Space, int, double, double, String, int) SimHarmonicUmbrella
SimHarmonicUmbrella.SimBennetParam etomica.normalmode
SimHSMDVacancy etomica.normalmode
Simple Lennard-Jones molecular dynamics simulation in 3D
SimHSMDVacancy(int, double, double, int, int, double) SimHSMDVacancy
SimHSMDVacancy.HSMDVParams etomica.normalmode
SimIdealGas etomica.freeenergy.npath
Simple Lennard-Jones molecular dynamics simulation in 3D
SimIdealGas(int, double, double, double, int) SimIdealGas
SimIdealGas.LjMC3DParams etomica.freeenergy.npath
SimKMCLJadatom etomica.kmc
Simulation using Henkelman's Dimer method to find a saddle point for
an adatom on a surface, modeled with LJ.
SimKMCLJadatom() SimKMCLJadatom
SimLattice etomica.freeenergy.npath
Simple Lennard-Jones molecular dynamics simulation in 3D
SimLattice(int, double, double, double, int) SimLattice
SimLattice.LjMC3DParams etomica.freeenergy.npath
SimLJ etomica.freeenergy.npath
Simple Lennard-Jones molecular dynamics simulation in 3D
SimLJ(int, double, double, double, double, int) SimLJ
SimLJ.LjMC3DParams etomica.freeenergy.npath
SimLJHTTISuper etomica.normalmode
SimLJHTTISuper(Space, int, double, double, double, boolean, int[]) SimLJHTTISuper
SimLJHTTISuper.SimOverlapParam etomica.normalmode
Inner class for parameters understood by the HSMD3D constructor
SimLJHTTISuperHCP etomica.normalmode
Mapped averaging for LJ HCP with 2-atom basis.
SimLJHTTISuperHCP(Space, int, double, double, double, double, boolean, int[]) SimLJHTTISuperHCP
SimLJHTTISuperHCP.SimOverlapParam etomica.normalmode
Inner class for parameters understood by the HSMD3D constructor
SimLJHTTISuperHCP2 etomica.normalmode
SimLJHTTISuperHCP2(Space, int, double, double, double, double, boolean, int[]) SimLJHTTISuperHCP2
SimLJHTTISuperHCP2.SimOverlapParam etomica.normalmode
Inner class for parameters understood by the HSMD3D constructor
SimLJHTTISuperSFMD etomica.normalmode
SimLJHTTISuperSFMD(Space, int, double, double, double, int[]) SimLJHTTISuperSFMD
SimLJHTTISuperSFMD.SimOverlapParam etomica.normalmode
Inner class for parameters understood by the HSMD3D constructor
SimLJVacancy etomica.normalmode
Simple Lennard-Jones molecular dynamics simulation in 3D
SimLJVacancy(int, double, double, double, int, double, boolean, boolean) SimLJVacancy
SimLJVacancy.Applet etomica.normalmode
SimLJVacancy.LJParams etomica.normalmode
SimMappedRdf etomica.mappedRdf
Calculates pair distribution using histograms and mapped averaging
SimMappedRdf(Space, int, double, double, double) SimMappedRdf
SimMappedRdf.LJMDParams etomica.mappedRdf
simModel Wrapper
SimModesJ etomica.normalmode
Simulation class of hard spheres in 1D or 3D that calculates the dq/dx
Jacobian.
SimModesJ(Space, int) SimModesJ
SimOverlap etomica.normalmode
Simulation to run sampling with the hard sphere potential, but measuring
the harmonic potential based on normal mode data from a previous simulation.
SimOverlap(Space, int, double, double, String, double) SimOverlap
SimOverlap.SimOverlapParam etomica.normalmode
Inner class for parameters understood by the HSMD3D constructor
SimOverlapAlphaN2TP etomica.models.nitrogen
Temperature-perturbation simulation for alpha-phase Nitrogen
SimOverlapAlphaN2TP(Space, int[], double, double, double[], double[], int, double, long, double, double, boolean) SimOverlapAlphaN2TP
SimOverlapAlphaN2TP.SimOverlapParam etomica.models.nitrogen
Inner class for parameters understood by the HSMD3D constructor
SimOverlapBetaN2RP etomica.models.nitrogen
SimOverlapBetaN2RP(Space, int, double, double, double[], double, double, int) SimOverlapBetaN2RP
SimOverlapBetaN2RP.SimOverlapParam etomica.models.nitrogen
Inner class for parameters understood by the SimOverlapBetaN2RP constructor
SimOverlapBetaN2RPScaling etomica.models.nitrogen
rotational-perturbation simulation for beta-phase Nitrogen with angle scaling
however, one can set parameter "doScaling" to FALSE if scaling not desirable
SimOverlapBetaN2RPScaling(Space, int, double, double, double[], double[], int, double, long, double, boolean) SimOverlapBetaN2RPScaling
SimOverlapBetaN2RPScaling.SimOverlapParam etomica.models.nitrogen
Inner class for parameters understood by the SimOverlapBetaN2TP constructor
SimOverlapBetaN2TP etomica.models.nitrogen
Temperature-perturbation simulation for beta-phase Nitrogen
SimOverlapBetaN2TP(Space, int, double, double, double[], double[], int, double, long, boolean, boolean, double) SimOverlapBetaN2TP
SimOverlapBetaN2TP.SimOverlapParam etomica.models.nitrogen
Inner class for parameters understood by the SimOverlapBetaN2TP constructor
SimOverlapDisorderedAlphaN2RPScaling etomica.models.nitrogen
rotational-perturbation simulation for beta-phase Nitrogen with angle scaling
however, one can set parameter "doScaling" to FALSE if scaling not desirable
SimOverlapDisorderedAlphaN2RPScaling(Space, int, double, double, double[], double[], int, double, long, double, boolean) SimOverlapDisorderedAlphaN2RPScaling
SimOverlapDisorderedAlphaN2RPScaling.SimOverlapParam etomica.models.nitrogen
Inner class for parameters understood by the SimOverlapBetaN2TP constructor
SimOverlapDisorderedAlphaN2TP etomica.models.nitrogen
Temperature-perturbation simulation for disordered alpha-phase Nitrogen
SimOverlapDisorderedAlphaN2TP(Space, int, double, double, double[], double[], int, double, long, boolean, boolean, double) SimOverlapDisorderedAlphaN2TP
SimOverlapDisorderedAlphaN2TP.SimOverlapParam etomica.models.nitrogen
Inner class for parameters understood by the SimOverlapBetaN2TP constructor
SimOverlapLJ etomica.normalmode
Simulation to run sampling with the LJ potential, but measuring
the harmonic potential based on normal mode data from a previous simulation.
SimOverlapLJ(Space, int, double, double, double) SimOverlapLJ
SimOverlapLJ.SimOverlapParam etomica.normalmode
Inner class for parameters understood by the HSMD3D constructor
SimOverlapLJModule etomica.normalmode
Main method that constructs an overlap sampling module to calculate the free
energy difference between a harmonic system and a lennard jones solid.
SimOverlapLJModule() SimOverlapLJModule
SimOverlapLJModule.APIPotentialReference etomica.normalmode
SimOverlapLJModule.APIPotentialTarget etomica.normalmode
SimOverlapLJModule.MeterPotentialEnergyDifference etomica.normalmode
SimOverlapLJModule.SimOverlapParam etomica.normalmode
Inner class for parameters understood by the HSMD3D constructor
SimOverlapModule etomica.normalmode
Overlap sampling "module" to calculate free energy difference.
SimOverlapModule(Box, Box, Integrator, Integrator, IAPIPotential, IAPIPotential, double) SimOverlapModule
SimOverlapNitrogenModel etomica.models.nitrogen
Simulation to run sampling with the nitrogen model to find the free energy difference
between the harmonic reference system and the target system
The Bennett's Overlapping Sampling Simulation
- used to check for the computation time
SimOverlapNitrogenModel(Space, int, double, String, double) SimOverlapNitrogenModel
SimOverlapNitrogenModel.SimOverlapParam etomica.models.nitrogen
Inner class for parameters understood by the HSMD3D constructor
SimOverlapParam() SimDirectBetaN2RP.SimOverlapParam
SimOverlapParam() SimOverlapAlphaN2TP.SimOverlapParam
SimOverlapParam() SimOverlapBetaN2RP.SimOverlapParam
SimOverlapParam() SimOverlapBetaN2RPScaling.SimOverlapParam
SimOverlapParam() SimOverlapBetaN2TP.SimOverlapParam
SimOverlapParam() SimOverlapDisorderedAlphaN2RPScaling.SimOverlapParam
SimOverlapParam() SimOverlapDisorderedAlphaN2TP.SimOverlapParam
SimOverlapParam() SimOverlapNitrogenModel.SimOverlapParam
SimOverlapParam() LJVacancyMin.SimOverlapParam
SimOverlapParam() MinimizeHCP.SimOverlapParam
SimOverlapParam() SimEinStep1.SimOverlapParam
SimOverlapParam() SimEinStep1HCP.SimOverlapParam
SimOverlapParam() SimEinStep2.SimOverlapParam
SimOverlapParam() SimEinStep2HCP.SimOverlapParam
SimOverlapParam() SimLJHTTISuper.SimOverlapParam
SimOverlapParam() SimLJHTTISuperHCP.SimOverlapParam
SimOverlapParam() SimLJHTTISuperHCP2.SimOverlapParam
SimOverlapParam() SimLJHTTISuperSFMD.SimOverlapParam
SimOverlapParam() SimOverlap.SimOverlapParam
SimOverlapParam() SimOverlapLJ.SimOverlapParam
SimOverlapParam() SimOverlapLJModule.SimOverlapParam
SimOverlapParam() SimOverlapSoftSphere.SimOverlapParam
SimOverlapParam() SimOverlapSoftSphereDP.SimOverlapParam
SimOverlapParam() SimOverlapSoftSphereEin.SimOverlapParam
SimOverlapParam() SimOverlapSoftSphereEinHarm.SimOverlapParam
SimOverlapParam() SimOverlapSoftSphereHCP.SimOverlapParam
SimOverlapParam() SimOverlapSoftSphereReweighting.SimOverlapParam
SimOverlapParam() SimOverlapSoftSphereSoftness.SimOverlapParam
SimOverlapParam() SimOverlapSoftSphereSuperBox.SimOverlapParam
SimOverlapParam() SimOverlapSoftSphereTP.SimOverlapParam
SimOverlapParam() SimOverlapSoftSphereTPHCP.SimOverlapParam
SimOverlapParam() SimOverlapSoftSphereTPSlantedBox.SimOverlapParam
SimOverlapParam() SimOverlapSSnxy.SimOverlapParam
SimOverlapSoftSphere etomica.normalmode
Simulation to run sampling with the hard sphere potential, but measuring
the harmonic potential based on normal mode data from a previous simulation.
SimOverlapSoftSphere(Space, int, double, double, String, double, int) SimOverlapSoftSphere
SimOverlapSoftSphere.SimOverlapParam etomica.normalmode
Inner class for parameters understood by the HSMD3D constructor
SimOverlapSoftSphereDP etomica.normalmode
Simulation to run density perturbation for soft spheres.
SimOverlapSoftSphereDP(Space, int, boolean, double, double, double[], double[], int, int, double, long, double) SimOverlapSoftSphereDP
SimOverlapSoftSphereDP.SimOverlapParam etomica.normalmode
Inner class for parameters understood by the HSMD3D constructor
SimOverlapSoftSphereEin etomica.normalmode
Simulation that samples a composite energy function (soft sphere and
Einstein crystal) and perturbs into overlap regions shared by systems with
more or less soft sphere contributions.
SimOverlapSoftSphereEin(Space, int, double, boolean, double, double, double, double[], double[], int, int, double, long, double) SimOverlapSoftSphereEin
SimOverlapSoftSphereEin.MeterPotentialEnergyComposite etomica.normalmode
SimOverlapSoftSphereEin.SimOverlapParam etomica.normalmode
Inner class for parameters understood by the HSMD3D constructor
SimOverlapSoftSphereEinHarm etomica.normalmode
Overlap sampling simulation whose target system has a composite energy
function (soft sphere and Einstein crystal) and whose reference system is
defined by (harmonically coupled) normal modes and Einstein crystal.
SimOverlapSoftSphereEinHarm(Space, int, double, boolean, double, double, double, int, double) SimOverlapSoftSphereEinHarm
SimOverlapSoftSphereEinHarm.MeterPotentialEnergyComposite etomica.normalmode
SimOverlapSoftSphereEinHarm.SimOverlapParam etomica.normalmode
Inner class for parameters understood by the HSMD3D constructor
SimOverlapSoftSphereHCP etomica.normalmode
Simulation to run sampling with the soft-sphere potential, but measuring
the harmonic potential based on normal mode data from a previous simulation.
SimOverlapSoftSphereHCP(Space, int, double, double, String, double, int) SimOverlapSoftSphereHCP
SimOverlapSoftSphereHCP.SimOverlapParam etomica.normalmode
Inner class for parameters understood by the HSMD3D constructor
SimOverlapSoftSphereReweighting etomica.normalmode
Simulation to run sampling with the hard sphere potential, but measuring
the harmonic potential based on normal mode data from a previous simulation.
SimOverlapSoftSphereReweighting(Space, int, double, double, String, double, int) SimOverlapSoftSphereReweighting
SimOverlapSoftSphereReweighting.SimOverlapParam etomica.normalmode
Inner class for parameters understood by the HSMD3D constructor
SimOverlapSoftSphereSoftness etomica.normalmode
Conduct Bennett's Overlap Sampling to quantify the free-energy difference
between soft-sphere model with different softness
Soft-Sphere potential: U = epsilon*(sigma/r)^n
where n is the exponent, s = 1/n (where s is softness)
epsilon and sigma is set to 1
SimOverlapSoftSphereSoftness(Space, int, double, double, double, int[], double, double, int) SimOverlapSoftSphereSoftness
SimOverlapSoftSphereSoftness.SimOverlapParam etomica.normalmode
Inner class for parameters understood by the HSMD3D constructor
SimOverlapSoftSphereSuperBox etomica.normalmode
Simulation to run sampling with the hard sphere potential, but measuring
the harmonic potential based on normal mode data from a previous simulation.
SimOverlapSoftSphereSuperBox(Space, int, double, double, String, double, int) SimOverlapSoftSphereSuperBox
SimOverlapSoftSphereSuperBox.SimOverlapParam etomica.normalmode
Inner class for parameters understood by the HSMD3D constructor
SimOverlapSoftSphereTP etomica.normalmode
Simulation to run sampling with the hard sphere potential, but measuring
the harmonic potential based on normal mode data from a previous simulation.
SimOverlapSoftSphereTP(Space, int, boolean, boolean, double, double, double[], double[], int, int, double, long, double) SimOverlapSoftSphereTP
SimOverlapSoftSphereTP.SimOverlapParam etomica.normalmode
Inner class for parameters understood by the HSMD3D constructor
SimOverlapSoftSphereTPHCP etomica.normalmode
The original Bennett's Overlapping Sampling Simulation
- used to check for the computation time
SimOverlapSoftSphereTPHCP(Space, int, double, double, double[], double[], int, int, double, long, double) SimOverlapSoftSphereTPHCP
SimOverlapSoftSphereTPHCP.SimOverlapParam etomica.normalmode
Inner class for parameters understood by the HSMD3D constructor
SimOverlapSoftSphereTPSlantedBox etomica.normalmode
Simulation to run sampling with the hard sphere potential, but measuring
the harmonic potential based on normal mode data from a previous simulation.
SimOverlapSoftSphereTPSlantedBox(Space, int, double, double, double[], double[], int, int, double, long, double) SimOverlapSoftSphereTPSlantedBox
SimOverlapSoftSphereTPSlantedBox.SimOverlapParam etomica.normalmode
Inner class for parameters understood by the HSMD3D constructor
SimOverlapSSnxy etomica.normalmode
Simulation to run sampling with the hard sphere potential, but measuring
the harmonic potential based on normal mode data from a previous simulation.
SimOverlapSSnxy(Space, int, double, double, String, double, int, int[]) SimOverlapSSnxy
SimOverlapSSnxy.SimOverlapParam etomica.normalmode
Inner class for parameters understood by the HSMD3D constructor
SimOverlapTPSSParams() HTTPSoftSphereApplet.SimOverlapTPSSParams
simParams() AshtonWildingLJ.simParams
simParams() AshtonWildingOsmoticVirial.simParams
simParams() AshtonWildingVirial.simParams
simParams() GCRestrictedGibbsHS.simParams
simParams() GCWidomInsertHS.simParams
simParams() NVTWidomInsertLJ.simParams
SimParams() ClathrateHarmonicFE.SimParams
SimParams() MinimizationTIP4P.SimParams
SimParams() ProtonDisorderGenerator.SimParams
SimParams() GlassClustering.SimParams
SimParams() GlassProd.SimParams
SimParams() LJMC3D.SimParams
SimParams() LJMC3DDimer.SimParams
SimParams() TestHSMD3D.SimParams
SimParams() TestLJGCMC3D.SimParams
SimParams() TestLJMC3D.SimParams
SimParams() TestLJMD3D.SimParams
SimParams() TestSWChain.SimParams
simple(String) AtomType
simple(String, double) AtomType
Convenience factory method for creating an AtomType with a one-off ElementSimple.
Simple() ColorScheme.Simple
Simple(Color) ColorScheme.Simple
SimpleElementForSimilarSpecies etomica.virial.GUI.components
simpleFromSim(Simulation) AtomType
simpleReplace(String, String, String) TextFormat
Does a clean replace of strFrom in str with strTo
If strTo contains strFrom, then only a single pass is done.
SimpleUnit etomica.units
Superclass for all base unit classes.
SimpleUnit(Dimension, double, String, String, boolean) SimpleUnit
simplifiedP3NonAdd VirialCPSHeliumNonAdditiveClassical_Correction.VirialParam
simplifiedP3NonAdd VirialCPSHeliumNonAdditiveClassical.VirialParam
simplify() Rational
Simplify the rational.
simplify() BigIntegerPoly
Simplify the representation.
SimTarget etomica.normalmode
Simulation to run sampling with the hard sphere potential, but measuring
the harmonic potential based on normal mode data from a previous simulation.
SimTarget(Space, int, double) SimTarget
SimTargetUmbrella etomica.normalmode
Simulation to sample target system and perturbing into
the umbrella sampling region
SimTargetUmbrella(Space, int, double, double, String, int) SimTargetUmbrella
SimTargetUmbrella.SimBennetParam etomica.normalmode
simulation SimulationGraphic
simulation ColorSchemeStepWise
simulation PotentialMasterNbrMolecular
simulation PotentialMasterNbr
Simulation etomica.simulation
The main class that organizes the elements of a molecular simulation.
Simulation(Space) Simulation
Creates a new simulation using the given space
SimulationAlphaNitrogenModel etomica.models.nitrogen
Simulation class for nitrogen molecules
alpha-N2 crystal Structure
SimulationAlphaNitrogenModel(Space, int[], double, double) SimulationAlphaNitrogenModel
SimulationBetaNitrogenModel etomica.models.nitrogen
Simulation class for nitrogen molecules
beta-N2 crystal Structure
SimulationBetaNitrogenModel(Space, int, double, double) SimulationBetaNitrogenModel
SimulationBetaNitrogenModelTest etomica.models.nitrogen
Simulation class for nitrogen molecules
beta-N2 crystal Structure
SimulationBetaNitrogenModelTest(Space, int[], double, double, double) SimulationBetaNitrogenModelTest
simulationBoxAdded(Simulation, Box) BoxAgentManager
simulationBoxAdded(Simulation, Box) SimulationListener
simulationBoxRemoved(Simulation, Box) BoxAgentManager
simulationBoxRemoved(Simulation, Box) SimulationListener
SimulationConstructor etomica.server.representations
SimulationConstructor() SimulationConstructor
SimulationContainer etomica.simulation
TODO To change the template for this generated type comment go to
Window - Preferences - Java - Code Style - Code Templates
SimulationDataAction etomica.action
Action that performs a call to the reset() method of a set
of accumulators, as specified via a list of AccumulatorManager
instances.
SimulationDataAction(DataStreamAction) SimulationDataAction
SimulationEventManager etomica.simulation
SimulationEventManager(Simulation) SimulationEventManager
SimulationGammaNitrogenModel etomica.models.nitrogen
Simulation class for nitrogen molecules
gamma-N2 crystal Structure
SimulationGammaNitrogenModel(Space, int, double, double) SimulationGammaNitrogenModel
SimulationGraphic etomica.graphics
General class for graphical presentation of the elements of a molecular simulation.
SimulationGraphic(Simulation) SimulationGraphic
SimulationGraphic(Simulation, int) SimulationGraphic
SimulationGraphic(Simulation, int, String) SimulationGraphic
SimulationGraphic(Simulation, int, String, int) SimulationGraphic
SimulationGraphic(Simulation, String) SimulationGraphic
SimulationGraphic(Simulation, String, int) SimulationGraphic
SimulationListener etomica.simulation
SimulationModel etomica.meta
SimulationModel(Simulation) SimulationModel
SimulationPanel etomica.graphics
Main panel used to display the graphical elements of a simulation.
SimulationPanel() SimulationPanel
SimulationPanel(String) SimulationPanel
SimulationResource etomica.server.resources
SimulationResource(SimulationStore, DataStreamStore) SimulationResource
SimulationRestart etomica.action
Action that invokes reset method of all registered simulation elements,
effectively initializing the entire simulation.
SimulationRestart(Simulation) SimulationRestart
SimulationRheology etomica.modules.rheology
Simulation for rheology module.
SimulationRheology(Space) SimulationRheology
SimulationRunner etomica.virial.GUI.components
SimulationRunner(ModelSelectedSpecies) SimulationRunner
SimulationsIndexResource etomica.server.resources
SimulationsIndexResource(ComponentIndex<Simulation>, SimulationStore) SimulationsIndexResource
SimulationStore etomica.server.dao
SimulationStore() SimulationStore
SimulationVirial etomica.virial.simulations
Generic simulation using Mayer sampling to evaluate cluster integrals
SimulationVirial(Space, ISpecies[], int[], double, ClusterWeight, ClusterAbstract, ClusterAbstract[]) SimulationVirial
SimulationVirial(Space, ISpecies, double, ClusterWeight, ClusterAbstract, ClusterAbstract[]) SimulationVirial
SimulationVirial(Space, ISpecies, double, ClusterWeight, ClusterAbstract, ClusterAbstract[], boolean) SimulationVirial
SimulationVirial(Space, ISpecies, double, ClusterWeight, ClusterAbstract, ClusterAbstract[], boolean, int[]) SimulationVirial
SimulationVirial(Space, SpeciesFactory, double, ClusterWeight, ClusterAbstract, ClusterAbstract[]) SimulationVirial
Constructor for simulation to determine the ratio between reference and target Clusters
SimulationVirial(Space, SpeciesFactory, double, ClusterWeight, ClusterAbstract, ClusterAbstract[], boolean) SimulationVirial
SimulationVirialDiagram etomica.virial.simulations
Virial simulation using diagram sampling.
SimulationVirialDiagram(Space, SpeciesFactory, double, ClusterWeight, ClusterAbstract, ClusterAbstract[]) SimulationVirialDiagram
SimulationVirialOverlap2 etomica.virial.simulations
Simulation implementing the overlap-sampling approach to evaluating a cluster
diagram.
SimulationVirialOverlap2(Space, ISpecies[], int[], double, ClusterAbstract[], ClusterAbstract[], ClusterWeight[], boolean) SimulationVirialOverlap2
SimulationVirialOverlap2(Space, ISpecies[], int[], double, ClusterAbstract[], ClusterWeight[], boolean) SimulationVirialOverlap2
SimulationVirialOverlap2(Space, ISpecies[], int[], double, ClusterAbstract, ClusterAbstract) SimulationVirialOverlap2
This constructor will create your simulation class, but you may call
set methods before using it.
SimulationVirialOverlap2(Space, ISpecies, double, ClusterAbstract[], ClusterWeight[], boolean) SimulationVirialOverlap2
SimulationVirialOverlap2(Space, ISpecies, double, ClusterAbstract, ClusterAbstract) SimulationVirialOverlap2
SimulationVirialOverlap2(Space, ISpecies, double, ClusterAbstract, ClusterAbstract, boolean) SimulationVirialOverlap2
SimulationVirialOverlap2(Space, ISpecies, int, double, ClusterAbstract, ClusterAbstract) SimulationVirialOverlap2
This constructor will create your simulation class, but you may call
set methods before using it.
SimulationVirialUmbrella etomica.virial.simulations
Simulation implementing the umbrella-sampling approach to evaluating a cluster
diagram.
SimulationVirialUmbrella(Space, double, ClusterAbstract, ClusterAbstract[]) SimulationVirialUmbrella
SimulationVirialUmbrella(Space, SpeciesFactory, double, ClusterAbstract, ClusterAbstract[]) SimulationVirialUmbrella
SimulationWorker(int, int, int, MayerFunction, MayerFunction, int, double, double, double, long, Space, String, double, Map<IntSet, MeterVirialBDBinMultiThreaded.MyData>, double, long[], boolean, int[], boolean) VirialHSBinMultiThreaded.SimulationWorker
SimulationWorker(int, int, MayerFunction, MayerFunction, MayerFunction, double, double, double, double, long, Space, String, double, Map<IntSet, MeterVirialEBinMultiThreaded.MyData>, double, long[], boolean, int[], boolean, double) VirialSQWBinMultiThreaded.SimulationWorker
SimulationWrapper etomica.meta.wrappers
Specialized wrapper for Simulations.
SimulationWrapper(Simulation, SimulationModel, boolean) SimulationWrapper
SimUmbrella etomica.normalmode
Simulation to sample Umbrella Sampling
SimUmbrella(Space, int, double, double, String, int) SimUmbrella
SimUmbrella.SimBennetParam etomica.normalmode
SimUmbrellaSoftSphere etomica.normalmode
Simulation to sample Umbrella Overlap Sampling
The original Umbrella Sampling Simulation
- used to check for the computation time
SimUmbrellaSoftSphere(Space, int, double, double, String, int) SimUmbrellaSoftSphere
SimUmbrellaSoftSphere.SimBennetParam etomica.normalmode
sin() Complex
Sine of this Complex number (doesn't change this Complex number).
sin(BigDecimal) BigDecimalMath
Trigonometric sine.
sin2tiMtj1 MeterMappedAveragingCV
sin2tiMtjtk1 MeterMappedAveragingCV
sincoscosInt(double, double) FunctionCosIntegral
Integral of sin(t) cos(t) Exp(b cos(t)) for t from 0 to x, accurate to within 0.01% for all b > 0 and -2Pi < x < 2Pi.
sincosInt(double, double) FunctionCosIntegral
Integral of sin(t) Exp(b cos(t)) for t from 0 to x, accurate to within 0.01% for all b > 0 and -2Pi < x < 2Pi.
sindtheta MeterMeanField
sinDtheta IntegratorDimerMin
SineTransform etomica.math.numerical
3D Fourier transforms of a function, f, simplify to 1D sine transforms of the auxiliary function F(r) = r*f(r)
when f is spherically symmetric.
SineTransform() SineTransform
sinGamma PrimitiveHexagonal
sinGamma PrimitiveHexagonal2D
singleAction MCMoveMoleculeCoupledInitPert
singleAction MCMoveMoleculeCoupledSuperBox
singleAction MCMoveMoleculeCoupled
SingleAssociationSiteFluid etomica.virial.simulations
SingleAssociationSiteFluid() SingleAssociationSiteFluid
SingleAssociationSiteFluid.VirialAssociatingFluidParam etomica.virial.simulations
SingleAssociationSiteFluid2 etomica.virial.simulations
repulsive potential: Lennard-Jones potential
attractive potential: short-handed square well potential
Wertheim's single attraction-site model
SingleAssociationSiteFluid2() SingleAssociationSiteFluid2
SingleAssociationSiteFluid2.VirialAssociatingFluidParam etomica.virial.simulations
SingleAssociationSiteFluid2Pt etomica.virial.simulations
repulsive potential: Lennard-Jones potential
attractive potential: short-handed square well potential
Wertheim's single attraction-site model
2points and 3 points diagram calculation
SingleAssociationSiteFluid2Pt() SingleAssociationSiteFluid2Pt
SingleAssociationSiteFluid2Pt.VirialAssociatingFluidParam etomica.virial.simulations
SingleAssociationSiteFluid3Pt etomica.virial.simulations
repulsive potential: Lennard-Jones potential
attractive potential: short-handed square well potential
Wertheim's single attraction-site model
2points and 3 points diagram calculation
SingleAssociationSiteFluid3Pt() SingleAssociationSiteFluid3Pt
SingleAssociationSiteFluid3Pt.VirialAssociatingFluidParam etomica.virial.simulations
SingleAssociationSiteFluid4Points etomica.virial.simulations
SingleAssociationSiteFluid4Points() SingleAssociationSiteFluid4Points
SingleAssociationSiteFluid4Points.VirialAssociatingFluidParam etomica.virial.simulations
SingleAssociationSiteFluid4Pt etomica.virial.simulations
repulsive potential: Lennard-Jones potential
attractive potential: short-handed square well potential
Wertheim's double attraction-site model
4points diagram calculation
SingleAssociationSiteFluid4Pt() SingleAssociationSiteFluid4Pt
SingleAssociationSiteFluid4Pt.VirialAssociatingFluidParam etomica.virial.simulations
SingleAssociationSiteFluidGraph etomica.virial.simulations
repulsive potential: Lennard-Jones potential
attractive potential: short-handed square well potential
Wertheim's single attraction-site model
SingleAssociationSiteFluidGraph() SingleAssociationSiteFluidGraph
SingleAssociationSiteFluidGraph.VirialAssociatingFluidParam etomica.virial.simulations
SingleDipole etomica.rotation
SingleDipole() SingleDipole
SingleDipole.Applet etomica.rotation
SingleDumbellRattle etomica.rotation
SingleDumbellRattle() SingleDumbellRattle
SingleDumbellRattle.Applet etomica.rotation
SingleDumbellShake etomica.rotation
SingleDumbellShake() SingleDumbellShake
SingleDumbellShake.Applet etomica.rotation
singleSample MeterRDF
singlet MCMoveAtomSwap
singlet MCMoveInsertDeleteLatticeVacancy.AtomIteratorBruteForce
singletId(int, int) VirialDiagrams
SingleValueOptionHandler() Main.SingleValueOptionHandler
SingleWater etomica.rotation
SingleWater() SingleWater
SingleWater.Applet etomica.rotation
SingleWaterMatrix etomica.rotation
SingleWaterMatrix() SingleWaterMatrix
SingleWaterMatrix.Applet etomica.rotation
SingleWaterRattle etomica.rotation
SingleWaterRattle() SingleWaterRattle
SingleWaterRattle.Applet etomica.rotation
SingleWaterShake etomica.rotation
SingleWaterShake() SingleWaterShake
SingleWaterShake.Applet etomica.rotation
sinh() Complex
Hyperbolic sine of this Complex number
(doesn't change this Complex number).
sinh(BigDecimal) BigDecimalMath
The hyperbolic sine.
sink NormalModeAnalysisDisplay1DGraphic
sink NormalModeAnalysisDisplay2DGraphic
Sink(int, MeterStructureFactor) StructureFactorComponentCorrelation.Sink
sink0 AkimaSplineSmootherApp
sink0 AkimaSplineSmootherDyApp
sinkDy AkimaSplineSmootherApp
sinkDy AkimaSplineSmootherDyApp
sinkDy2 AkimaSplineSmootherApp
sinkDy2 AkimaSplineSmootherDyApp
sinkDy3 AkimaSplineSmootherDyApp
sinkEigen NormalModeAnalysisDisplay3DGraphic
sinkEy AkimaSplineSmootherApp
sinkEy AkimaSplineSmootherDyApp
sinkrj EwaldSummation
sinks DataSinkBlockAveragerSFac
sinkSmoothed AkimaSplineSmootherApp
sinkSmoothed AkimaSplineSmootherDyApp
sinkTrue AkimaSplineSmootherDyApp
sinkTrueEy AkimaSplineSmootherDyApp
sinkWV NormalModeAnalysisDisplay3DGraphic
sint0 MeterMeanField
sinTheta P3CPSNonAdditiveHe
sinTheta P3CPSNonAdditiveHeLessSimplified
sintiMtj1 MeterMappedAveragingCV
sintiMtj2 MeterMappedAveragingCV
sintiMtj3 MeterMappedAveragingCV
sinusoidalB Sam
site Token
site(int[]) ConfigurationLattice.MyLattice
Returns the same instance of Vector with each call.
site(int[]) AbstractLattice
Returns the site specified by the given index.
site(int[]) BravaisLattice
Calculates and returns a vector that is the spatial position given
by adding together the primitive vectors, each multiplied by the corresponding
integer index given by the array argument.
site(int[]) BravaisLatticeCrystal
Returns a Vector instance giving the location of the referenced site.
site(int[]) RectangularLattice
Returns the instance of the object associated with the given index.
site(int[]) SpaceLattice
site(Vector) CellLattice
Returns the cell in which the given point lies.
siteat P2WaterPotentialsJankowski
sitebt P2WaterPotentialsJankowski
siteDisplacement FindPairMoleculeIndex
siteDisplacement FindPairMoleculeIndexBetaN2
siteDoubles P2WaterSzalewicz
siteFactor HSNPT.ColorSchemeDisplacement
siteFactory RectangularLattice
SiteFactory etomica.lattice
Interface for a class that generates the sites populating a lattice.
siteID P2CO2Hellmann
siteID P2NitrogenHellmann
siteID P3NitrogenHellmannNonAdditive
SiteIterator etomica.lattice
Interface for objects that iterate over some or all of the
sites of a lattice.
siteManager CoordinateDefinition
sitePos P2CO2H2OWheatley
sitePos P2WaterSzalewicz
sitePos3 P2WaterSzalewicz
sitePosA P2NitrogenHellmann
sitePosA P3NitrogenHellmannNonAdditive
sitePosB P2NitrogenHellmann
sitePosB P3NitrogenHellmannNonAdditive
sites RectangularLattice
sites P2WaterSzalewicz
sites() FiniteLattice
Returns an array containing all the sites in the lattice.
sites() RectangularLattice
sitesCO2L P2CO2H2OWheatley
sitesHH P2CO2H2OWheatley
sitesOH P2CO2H2OWheatley
SiteSource(Space) CoordinateDefinition.SiteSource
sixId(int, int, int, int, int, int, int) VirialDiagrams
Returns the six-molecule ID for the given indices (id0, id1, id2, id3, id4, id5)
and given number of molecules (n).
sixId(int, int, int, int, int, int, int) VirialDiagramsPT
Returns the six-molecule ID for the given indices (id0, id1, id2, id3, id4, id5)
and given number of molecules (n).
sixStart VirialDiagrams
sixStart VirialDiagramsPT
size Primitive
size RectangularLattice
size LatticeEditor
size DropletGraphic.ModifierBoxSize
size InterfacialSWGraphic.ModifierBoxSize
size StarPolymerMC.PolymerParam
size StarPolymerMD.PolymerParam
size() AtomArrayList
size() AtomListFromArray
Returns the length of the wrapped array.
size() AtomPair
size() AtomSetSinglet
size() IAtomList
size() ANIntergroupCoupled
size() ANIntergroupExchange
size() ANIntragroupExchange
size() ApiIndexList
size() ApiInnerVariable
Returns the number of pairs given by this iterator.
size() ApiInterArrayList
Returns the number of iterates, which is list.size*(list.size-1)/2
size() ApiIntergroup
Returns the number of pairs given by this iterator.
size() ApiIntergroupCoupled
Returns the number of pairs given by this iterator.
size() ApiIntergroupExchange
Returns the number of pairs given by this iterator.
size() ApiIntraArrayList
Returns the number of iterates, which is list.size*(list.size-1)/2
size() ApiIntragroup
Returns the number of atom pairs the iterator will return if
reset and iterated in its present state.
size() AtomIteratorArrayList
Returns the number of iterates that would be given by this iterator
if reset with the current list.
size() AtomIteratorArrayListAdjacent
Returns the number of iterates that iterator would give
if reset and iterated in its current condition.
size() AtomIteratorArrayListSimple
Returns the number of iterates that would be given by this iterator
if reset with the current list.
size() AtomIteratorBasisFilteredType
size() AtomIteratorBasisFilteredType2
size() AtomIteratorLeafFilteredType
size() AtomIteratorNull
size() AtomIteratorSinglet
returns 1 if atom is not null, 0 if atom is null.
size() Atomset3IteratorIndexList
size() Atomset4IteratorIndexList
size() AtomsetIterator
The number of iterates returned by this iterator in its current state.
size() AtomsetIteratorAllLeafAtoms
Returns the number of iterates given by this iterator, if iterated after
a call to reset().
size() AtomSetAllMolecules
size() GraphList
size() BitmapOfLongVector
size() RelabelParameters
size() MCMoveInsertDeleteLatticeVacancy.AtomIteratorBruteForce
size() MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbr
size() MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbrCell
size() RectangularLattice.Iterator
size() RectangularLatticeNbrIterator
The number of iterates returned by this iterator in its current state.
size() SiteIterator
Returns the number of iterates that this iterator would give
if reset.
size() ApiFilteredCylinder
size() IMoleculeList
size() MoleculeIteratorAll
Returns the number of iterates given by this iterator, if iterated after
a call to reset().
size() MoleculeIteratorArrayList
Returns the number of iterates that would be given by this iterator
if reset with the current list.
size() MoleculeIteratorArrayListSimple
Returns the number of iterates that would be given by this iterator
if reset with the current list.
size() MoleculeIteratorSinglet
returns 1 if atom is not null, 0 if atom is null.
size() MpiInnerFixed
Returns the number of pairs given by this iterator.
size() MpiInnerVariable
Returns the number of pairs given by this iterator.
size() MpiInterArrayList
Returns the number of iterates, which is list.size*(list.size-1)/2
size() MpiInterspecies1A
size() MpiInterspeciesAA
Returns the number of iterates, which is list.size*(list.size-1)/2
size() MpiIntraArrayList
Returns the number of iterates, which is list.size*(list.size-1)/2
size() MpiIntraspecies1A
Returns the number of atom pairs the iterator will return if
reset and iterated in its present state.
size() MpiIntraspeciesAA
Returns the number of iterates, which is list.size*(list.size-1)/2
size() MpiMolecule
Returns the number of iterates that would be given
when iterating after reset.
size() MoleculeArrayList
size() MoleculePair
size() MoleculeSetSinglet
size() Api1ACell
Returns the number of atom pairs the iterator will return if
reset and iterated in its present state.
size() Mpi1ACell
Returns the number of atom pairs the iterator will return if
reset and iterated in its present state.
size() MpiAACell
Returns the number of atom pairs the iterator will return if reset and
iterated in its present state.
size() Api1ASite
Returns the number of atom pairs the iterator will return if
reset and iterated in its present state.
size() P2HardBondedList.BondArrayList
size() PotentialMaster.AtomIterator0
size() PotentialMaster.MoleculeIterator0
size() IndexMap
size() BigIntegerPoly
Count of coefficients.
size() BitSet
Returns the number of bits of space actually in use by this BitSet
to represent bit values.
sizeCellX Sam
sizeCellZ Sam
sizeOf(Token) ScriptVariable
sizeOfArray() AtomArrayList
sizeOfArray() MoleculeArrayList
sizePanel LatticeEditor
sizeRatio AshtonWildingOsmoticVirial.simParams
skew AccumulatorAverageBootstrap
skew AccumulatorAverageCollapsingLog
SKEW MultiharmonicGraphicMC.DataSourceAlphaFE
SKEW MultiharmonicGraphicMC.DataSourceBias
skip AtomNbrClusterer
skipNow StructureFactorComponentCorrelation
slab Token
slab GData
slabBrillouin(Point3f[]) MeshSurface
slabbyatom Token
slabbymolecule Token
slabColix MeshSurface
slabenabled Token
slabMeshType MeshSurface
slabOptions MeshSurface
slabPolygons(Object[], boolean) MeshSurface
slabPolygonsList(List<Object[]>, boolean) MeshSurface
slabrange Token
slabValue TransformManager
slanty SimEinStep1.SimOverlapParam
slanty SimEinStep2.SimOverlapParam
slanty SimOverlapSoftSphereDP.SimOverlapParam
slanty SimOverlapSoftSphereEin.SimOverlapParam
slanty SimOverlapSoftSphereEinHarm.SimOverlapParam
slanty SimOverlapSoftSphereTP.SimOverlapParam
slider DeviceSlider
Subclass of Swing slider displayed to screen
located in utility package
slider(double, double, String, int, P2SquareWell) SelfAssemblyGraphic
sliderA RheologyGraphic
sliders(int, int, String, P2SquareWellBonded) ChainEquilibriumGraphic
sliders(int, int, String, P2SquareWellBonded) FreeRadicalPolymerizationGraphic
sliders(int, int, String, P2SquareWellRadical[]) FreeRadicalPolymerizationGraphic
smallmoleculemaxatoms Token
smartaromatic Token
smerList ColorSchemeSmer.ColorAgent
smerList ColorSchemeSmer
smerList ColorSchemeSmerByLength
smerList MCMoveAtomMonomer
smerList MCMoveAtomSmer
smerList MCMoveBiasUB
smerList MCMoveBiasUBMolecule
smerList MCMoveMoleculeMonomer
smerList MCMoveMoleculeRotateAssociated
smerList MCMoveMoleculeSmer
smerList MCMoveRotateAssociated
smerList MCMoveSmer
smerList MCMoveSmerRotate
smerList MCMoveVolumeAssociated
smerList MCMoveVolumeAssociatedMolecule
smiles2dimageformat Token
smilesurlformat Token
snapshotAnaglyphChannelBytes() Graphics3D
snapshotAnaglyphChannelBytes() GData
snapshotTime SVGConverter
Document time to seek to.
so2 NormalModeAnalysisDisplay3DGraphic
Sodium etomica.chem.elements
Class for the Sodium element.
Sodium(String) Sodium
Sodium(String, double) Sodium
SoftBDcount ClusterWheatleySoftDerivatives
SoftSphere3d etomica.simulation.prototypes
Simple soft-sphere Monte Carlo simulation in 3D.
SoftSphere3d() SoftSphere3d
SoftSphere3d(double, int, double) SoftSphere3d
SoftSphereSolidEOS etomica.normalmode
Soft-Sphere Solid Equation of State
for n = 12, 9 and 6
Reference: Tan, Schultz and Kofke, J Chem.
SoftSphereSolidEOS() SoftSphereSolidEOS
SoftSphereSolidEOSCalculator etomica.normalmode
SoftSphereSolidEOSCalculator() SoftSphereSolidEOSCalculator
solute MCMoveGeometricCluster
solute MCMoveGeometricClusterRestrictedGE
soluteChamberDensitySlider ReverseOsmosisGraphic
soluteChamberDensitySlider ReverseOsmosisWaterGraphic
soluteChargeSlider ReverseOsmosisWaterGraphic
soluteMoleFraction ConfigurationMembrane
soluteMoleFraction ConfigurationMembraneWater
soluteMoleFractionSlider ReverseOsmosisGraphic
soluteMoleFractionSlider ReverseOsmosisWaterGraphic
solutionChamberDensity ConfigurationMembrane
solutionChamberDensity ConfigurationMembraneWater
solve(BigInteger[][], BigInteger[]) BigIntegerMath
Solve a linear system of equations.
solveCoefficients() PadeApproximation
solvent Token
solventChamberDensity ConfigurationMembrane
solventChamberDensity ConfigurationMembraneWater
solventChamberDensitySlider ReverseOsmosisGraphic
solventChamberDensitySlider ReverseOsmosisWaterGraphic
solventprobe Token
solventproberadius Token
solventThermoFrac P2SquareWellBonded
solventThermoFrac P2SquareWellRadical
sort Graphics3D
sort() GraphList
sort() ClusterDiagram
Sorts list of connections for each node in the diagram such that
mConnections[i][j] < mConnections[i][k] for k > j.
sort(int[], int) FactorFFT
Sort(int) ScriptVariable.Sort
sortConnections(ClusterDiagram) ClusterOperations
sortDiagrams(ClusterDiagram[]) ClusterOperations
Sorts diagrams in order from most bonds to fewest bonds
sorted GraphList
sortedItem(List<String>, int) ArrayUtil
sortKey TreeLinker
sortOrReverse(int) ScriptVariable
sources SVGConverter
Sources files or URLs
SOUTH Constants.CompassDirection
space ActionMinimizeEnergy
space ConformationAlkaneEH
space ConformationMethane
space BiasVolume
space BiasVolumeMolecule
space MCMoveBiasUBMolecule
space MCMoveDimer
space MCMoveDimerRotate
space MCMoveSmer
space MCMoveSmerRotate
space ConfigurationLattice
space ConformationChain
space ConformationChainLinear
space ConformationLinear
space ConformationWater
space DataProcessorInterfacialTension
space DataSourceAtomDistance
space MeterDihedralAngle
space MeterDipoleSumSquaredMappedAverage
space MeterRDF
space MeterRDFPC
space MeterStructureFactor
space DataTensor.DataInfoTensor
space DataTensor.DataInfoTensorFactory
space DataVector.DataInfoVector
space DataVector.DataInfoVectorFactory
space MCMoveAtomCoupled
space MCMoveAtomSwap
space DisplayBoxCanvas2D
space SimulationGraphic
space IntegratorBox
space IntegratorMD.VectorSource
space MCMoveAtom
space MCMoveBoxSize
space MCMoveDimer
space MCMoveDimerRotate
space MCMoveInsertDeleteLatticeVacancy
space MCMoveMolecule
space MCMoveWiggleAceticAcid
space ConfigurationLammps
space MeterWallForce
space Primitive
space MeterMappedRdf
space PotentialCalculationMappedRdf
space MeterMappedU
space MeterMappedVirial
space MeterMappedVirialV
space MeterMeanForce
space PotentialCalculationMappedEnergy
space PotentialCalculationMappedVirial
space PotentialCalculationMappedVirialV
space Quaternion
space ConformationCO2
space P2CO2H2OWheatley
space P2CO2Hellmann
space CalcAnalytical2ndDerivativeNitrogen
space ConformationNitrogen
space ConformationNitrogenShellModel
space HarmonicAlphaNitrogenModel
space HarmonicAlphaNitrogenModelDecomposed
space HarmonicAlphaNitrogenModelPairMolecule
space HarmonicAlphaNitrogenModelPairMoleculeSequential
space HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2
space HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
space HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
space HarmonicBetaNitrogenModel
space HarmonicBetaNitrogenModelDecomposed
space HarmonicBetaNitrogenModelPairMoleculeSequential
space HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
space HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2
space HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
space HarmonicBetaNitrogenModelPairMoleculeSequentialLS
space HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
space HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
space MinimizationBetaNitrogenModel
space MinimizationBetaNitrogenModelLS
space MinimizeBetaNitrogenLatticeParameter
space MinimizeBetaNitrogenLatticeParameterFromFile
space MinimizeBetaNitrogenLatticeParameterLSFromFile
space MinimizeBetaNitrogenTranslationDOF
space MinimizeGammaNitrogenLatticeParameter
space SimulationAlphaNitrogenModel
space SimulationBetaNitrogenModel
space SimulationBetaNitrogenModelTest
space SimulationGammaNitrogenModel
space TestRotationVector
space ConformationAceticAcid
space ConformationEthanol
space ConformationMethanol
space ConfigurationFileTIP4P
space ConformationWater3P
space ConformationWaterGCPM
space ConformationWaterTIP4P
space P2WaterSzalewicz
space ConfigurationCatalysis
space DataSourceWallPressureCatalysis
space ConfigurationColloid
space ConformationTube
space DataSourcePercolation
space DataSourcePercolation0
space P1Tension
space DataSourceWallPressureMu
space ConfigurationSAM
space P1Sinusoidal
space BoxAgentSourceCellManagerMolecular
space NeighborCellManagerMolecular
space CriterionSimple
space PotentialMasterListMolecular.NeighborListAgentSourceMolecular
space PotentialMasterListMolecular
space CriterionSimpleMolecular
space ConformationHSDimer
space CoordinateDefinition
space HSNPT.ActionSummer
space LatticeSumMolecularCrystal
space MCMovePhaseAngle
space MCMoveWV
space MeterDADB
space MeterSolidProps
space MeterSolidPropsLJ
space NormalModes2D
space NormalModes3D
space NormalModesMolecular
space NormalModesPotential
space PotentialCalculationLJSP
space PotentialCalculationSolidSuper
space PotentialCalculationSolidSuperCut
space WaveVectorFactorySimple
space ParserLAMMPS.Options
space EwaldSummation
space EwaldSumMolecules
space P2HardWrapper
space P2NitrogenHellmann
space P2O2Bartolomei
space P2SemiclassicalAtomic
space P2SemiclassicalMolecular
space P2WaterPotentialsJankowski
space P3AxilrodTeller
space P3Induction
space P3NitrogenHellmannNonAdditive
space Potential
space PotentialCalculationPressureTensor
space PotentialMolecular
space Simulation
space Boundary
space MCMoveSpinCluster
space MeterMappedAveraging
space MeterMappedAveraging3Pair
space MeterMappedAveragingCorrelation
space MeterMappedAveragingCV
space MeterMappedAveragingFreeEnergy
space MeterMappedAveragingPair
space MeterMappedAveragingPairExcess
space MeterMappedAveragingSum
space MeterMappedAveragingVSum
space MeterMappedAveragingVSum3Pair
space MeterMappedAveragingVSumPair
space MeterPairSum
space PotentialCalculationMeanField
space ConformationStarPolymerGraft
space MCMoveBondLength
space MCMoveClusterBondLength
space MCMoveClusterRotateArm
space MCMoveRotateArm
space MCMoveWiggle
space MeterBondLength
space SurfaceTensionMapped
space BoxCluster
space ClusterCoupledFlipped
space ClusterCoupledFlippedMultivalue
space ClusterCoupledFlippedPartial
space ConfigurationCluster
space Conformation7SiteRigidSF6
space ConformationAnthracene3site
space ConformationAnthraceneTraPPE
space ConformationNaphthaleneTraPPE
space ConformationPh3site
space ConformationPhenanthreneTraPPE
space MCMoveClusterAngleBend
space MCMoveClusterAngleBendAceticAcid
space MCMoveClusterRingPartialRegrow
space MCMoveClusterRingRegrow
space MCMoveClusterRingRegrowExchange
space MCMoveClusterRingScale
space MCMoveClusterRotateCH3
space MCMoveClusterWiggleAceticAcid
space MCMoveClusterWiggleAlkaneEH
space MCMoveClusterWiggleMulti
space VirialHSBinMultiThreaded.SimulationWorker
space VirialSQWBinMultiThreaded.SimulationWorker
Space etomica.space
Superclass for all Space instances.
Space() Space
Space1D etomica.space1d
Factory and methods appropriate to a 1-dimensional space.
Space2D etomica.space2d
Factory and methods appropriate to a 2-dimensional space.
Space3D etomica.space3d
Factory and methods appropriate to a 3-dimensional space.
spacefill Token
SpaceLattice etomica.lattice
Marker interface indicating that AbstractLattice.site(int[]) returns an
IVector instance.
spanningVectors MeshSurface
spec_alternate Token
spec_atom Token
spec_chain Token
spec_model Token
spec_name_pattern Token
spec_resid Token
spec_seqcode Token
spec_seqcode_range Token
SPECIAL_COLIX_MAX Colix
SpecialFunctions etomica.math
Static-method library of various functions
specialposition Token
specialRef Wertheim2SiteAceticAcid.WertheimParam
species DHS_NVT
species DLJ_NVT_1site
species TestAceticAcidMC3D_NPT
species SimGCPMWaterMCNPT
species SimGCPMWaterMCNVT
species TestIGAssociationMC3D_NPT_DoubleSites
species TestLJAssociationMC3D_NPT_DoubleSites
species TestLJAssociationMC3D_NPT
species TestLJAssociationMC3D_NVTOld
species AtomSourceRandomSpecies
species AtomType
species BoxMoleculeCountEvent
species HSMDCavity
The single hard-sphere species.
species HSMDWidom
The single hard-sphere species.
species ConfigurationZincblende
species MeterProfileByAtoms
species MeterProfileByVolume
species DHS_NVT
species DLJ_NVT_1site
species TIP4P_NVT
species SimFe
species SimIdealGas
species SimLattice
species SimLJ
species DeviceNSelector
species VLESim
species MCMoveInsertDelete
species ConfigurationLammps
species FixedWall
species WriteConfigurationInterfacial
species LjMC3D
species LjMd3D
species SimMappedRdf
species MappedU
species MappedVirialLJ
species MappedVirialLJVGr
species LJmuVT
species LJNPT
species LJNVT
species ClathrateHarmonicFE
species MinimizationTIP4P
species ProtonDisorderGenerator
species HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2
species HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
species HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
species MeterTargetRPMolecule
species MeterTargetTPMolecule
species MinimizationBetaNitrogenModel
species MinimizationBetaNitrogenModelLS
species MinimizeBetaNitrogenLatticeParameter
species MinimizeBetaNitrogenLatticeParameterFromFile
species MinimizeBetaNitrogenLatticeParameterLSFromFile
species MinimizeBetaNitrogenTranslationDOF
species MinimizeGammaNitrogenLatticeParameter
species SimDirectBetaN2RP
species SimOverlapAlphaN2TP
species SimOverlapBetaN2RPScaling
species SimOverlapBetaN2TP
species SimOverlapDisorderedAlphaN2RPScaling
species SimOverlapDisorderedAlphaN2TP
species SimOverlapNitrogenModel
species SimulationAlphaNitrogenModel
species SimulationBetaNitrogenModel
species SimulationBetaNitrogenModelTest
species SimulationGammaNitrogenModel
species DimerApproach
species TestEwaldTIP4PWater
species ModifierNMolecule
species MeterExcessAdsorbed
species MeterConversion
species ColloidSim
species ConfigurationColloid
species CrystalViewer
species LatticeEditor
species Droplet
species DropletAtomic
species LJMC
species Insertion
species InterfacialSW
species Ljmd
species MaterialFracture
species MeterDensitySides
species MuGraphic.ModifierAtomDiameter
species MultiharmonicMC
species MultiharmonicMC
species MultiharmonicMC
species SWVLESim
species PistonCylinder
species SimulationRheology
species MeterFlux
species P1Tether
species ReverseOsmosisGraphic.ModifierAtomDiameter
species ReverseOsmosisWaterGraphic.ModifierAtomDiameter
species MeterTilt
species Sam
species Swmd
species VLESim
species MoleculeIteratorAll
species Molecule
species MoleculeToMoleculeListSpecies
species DeviceCellNum3DSlider
species DeviceCellNumXYSlider
species HSDimerNPT
species HSNPT
species HTTPSoftSphereSim
species LJVacancyMin
species MeterBoltzmannHTTP
species MeterDDP
species MeterDP
species MeterPlaneSlip
species MeterTargetTP
species MeterTilt
species MeterTiltHistogram
species MeterTiltRotation
species MeterTiltRotationHistogram
species MeterTiltRotationStdev
species ModifierCells3D
species ModifierXCells2D
species ModifierYCells2D
species NormalModeAnalysisDisplay1D
species NormalModeAnalysisDisplay2D
species NormalModeAnalysisDisplay3D
species NormalModesMolecular
species SimBennet
species SimFluidSoftSphere
species SimHarmonic
species SimHarmonicUmbrella
species SimHSMDVacancy
species SimLJHTTISuper
species SimLJHTTISuperHCP
species SimLJHTTISuperHCP2
species SimLJHTTISuperSFMD
species SimLJVacancy
species SimTargetUmbrella
species SimUmbrella
species SimUmbrellaSoftSphere
species ParserLAMMPS.Stuff
species PolydisperseHS
The single hard-sphere species.
species ChainHSMD3D
species GEMCWithRotation
species HSMC2D
species HSMD2D_noNbr
species HSMD3D
The single hard-sphere species.
species HSMD3DNoNbr
species LJMD2D
species LJMD3D
species LJMD3DNbr
species SoftSphere3d
species SWMD2D
species SWMD3D
species MCMoveBondLength
species MCMoveClusterBondLength
species MCMoveClusterRotateArm
species MCMoveRotateArm
species MCMoveWiggle
species StarPolymerMC
species StarPolymerMD
species LJMC
species TestHSMD3D
species TestLJGCMC3D
species TestLJMC3D
species TestLJMD3D
species MCMoveClusterAngleBend
species MCMoveClusterAngleBendAceticAcid
species MCMoveClusterRotateCH3
species MCMoveClusterTorsionAlkaneEH
species MCMoveClusterTorsionMulti
species MCMoveClusterWiggleAceticAcid
species MCMoveClusterWiggleAlkaneEH
species MCMoveClusterWiggleMulti
species SimulationVirial
species SimulationVirialOverlap2
species TestLJAssociationMC3D_NPT
species VirialTraPPE.TraPPEParams
species ZeoliteSimulation
The single hard-sphere species.
species() Simulation
Convenience method to return the first (and often only) ISpecies
in the simulation.
species1 DCVGCMD
species1 HSNPT2DSim
species1 AshtonWildingLJ
species1 AshtonWildingOsmoticVirial
species1 AshtonWildingVirial
species1 GCRestrictedGibbsHS
species1 GCWidomInsertHS
species1 NVTWidomInsertLJ
species1 HSMD2D
SPECIES1_INDEX Debug
species2 DCVGCMD
species2 AshtonWildingOsmoticVirial
species2 GCRestrictedGibbsHS
species2 GCWidomInsertHS
species2 NVTWidomInsertLJ
species2 HSMC2D
species2 HSMD2D
species2 TestHSMD3D
SPECIES2_INDEX Debug
Species7SiteRigidSF6 etomica.virial
Species SF6, 7 sites, LJ, rigid, no partial charge
Reference: Samios, Molecular force field investigation for sulfur hexafluoride: A computer simulation study
Species7SiteRigidSF6() Species7SiteRigidSF6
speciesA CoordinateDefinitionNitrogenSuperBox
speciesA Adsorption
speciesA ChainEquilibriumSim
speciesA FreeRadicalPolymerizationSim
speciesA MCMoveSwap
speciesA SimGlass
speciesA Mu
speciesA ReactionEquilibrium
speciesA SelfAssemblySim
speciesA CoordinateDefinitionLeafSuperBox
speciesA SimCalcSSoftSphereFCCSuperBox
SpeciesAceticAcid etomica.models.OPLS
Species for OPLS acetic acid
SpeciesAceticAcid() SpeciesAceticAcid
speciesAgentManager PotentialMasterNbrMolecular
SpeciesAgentManager E > - Class in etomica.species
AtomTypeAgentManager acts on behalf of client classes (an AgentSource) to
manage agents in every AtomType in a box.
SpeciesAgentManager(SpeciesAgentManager.AgentSource<E>, Simulation) SpeciesAgentManager
SpeciesAgentManager.AgentSource E > - Interface in etomica.species
Interface for an object that wants an agent associated with each
AtomType in a Simulation.
SpeciesAlkane etomica.virial
SpeciesAlkane() SpeciesAlkane
SpeciesAlkaneEH etomica.AlkaneEH
Species for TraPPE-Explicit hydrogen,Siepmann
SpeciesAlkaneEH() SpeciesAlkaneEH
SpeciesAnthracene3site464 etomica.virial
Species Anthracene molecule
rigid , LJ potential, no charge, this model is very similar to 3site 545 model, only the weight of the sites are different
reference: Iwai, monte carlo sim of Naphthalene, phenathlene,anthracene in SCF 1998
* @author shu
March, 7, 2011
SpeciesAnthracene3site464() SpeciesAnthracene3site464
SpeciesAnthracene3site545 etomica.virial
Species Anthracene molecule
rigid , LJ potential, no charge, 3 site model.each benzene ring is a site
reference: Iwai, monte carlo sim of Naphthalene, phenathlene,anthracene in SCF 1998
* @author shu
March, 7, 2011
SpeciesAnthracene3site545() SpeciesAnthracene3site545
speciesB CoordinateDefinitionNitrogenSuperBox
speciesB Adsorption
speciesB ChainEquilibriumSim
speciesB FreeRadicalPolymerizationSim
speciesB MCMoveSwap
speciesB SimGlass
speciesB Mu
speciesB ReactionEquilibrium
speciesB SelfAssemblySim
speciesB CoordinateDefinitionLeafSuperBox
speciesB SimCalcSSoftSphereFCCSuperBox
speciesBottomWall LJMC
speciesBottomWall LJMD
SpeciesBuilder etomica.species
SpeciesBuilder(Space) SpeciesBuilder
speciesC Catalysis
speciesC ConfigurationCatalysis
speciesC DataSourceWallPressureCatalysis
speciesC MeterDensityCO
speciesC MeterDensityCO2
speciesCH4 CH4NVT
speciesChlorine ReverseOsmosisWater
speciesColloid ColloidSim
speciesColloid ConfigurationColloid
speciesColloid NeighborListManagerColloid
SpeciesEthanol etomica.models.rowley
Species for ethanol with satellite site (Rowley et al 2006).
SpeciesEthanol() SpeciesEthanol
SpeciesFactory etomica.virial
SpeciesFactoryMethanol etomica.models.traPPE
SpeciesFactory that makes methanol.
SpeciesFactoryMethanol() SpeciesFactoryMethanol
SpeciesFactorySpheres etomica.virial
SpeciesFactory that makes SpeciesSpheresMono
SpeciesFactorySpheres() SpeciesFactorySpheres
SpeciesFactoryWaterGCPM etomica.virial
SpeciesFactory that makes SpeciesWater
SpeciesFactoryWaterGCPM() SpeciesFactoryWaterGCPM
SpeciesFileParser etomica.species
SpeciesFileParser() SpeciesFileParser
speciesFluid LJMC
speciesFluid LJMD
SpeciesGeneral etomica.species
SpeciesGeneral(AtomType[], IConformation, String[], int[][], boolean, boolean, Vector, Space, SpeciesGeneral.AtomFactory) SpeciesGeneral
SpeciesGeneral.AtomFactory etomica.species
SpeciesGeneralMutable etomica.species
SpeciesGeneralMutable(SpeciesGeneral) SpeciesGeneralMutable
speciesGhost Insertion
SpeciesHSDimer etomica.normalmode
Species hard-sphere dimer molecule
SpeciesHSDimer() SpeciesHSDimer
speciesIndex CollectionPotentialAtomicUnlike
speciesIndex CollectionPotentialMolecularUnlike
speciesInitiator ConfigurationLatticeFreeRadical
speciesMembrane ConfigurationMembrane
speciesMembrane ConfigurationMembraneWater
speciesMembrane ReverseOsmosis
speciesMembrane ReverseOsmosisWater
SpeciesMethane etomica.AlkaneEH
Species for methane with explicit hydrogen
Bond angle = 109.5 -- not exactly, conformation is changed!!!
SpeciesMethane() SpeciesMethane
SpeciesMethanol etomica.models.rowley
Species for methanol with satellite site (Rowley et al 2006).
SpeciesMethanol etomica.models.traPPE
Species for methanol with satellite site (Rowley et al 2006).
SpeciesMethanol() SpeciesMethanol
SpeciesMethanol() SpeciesMethanol
speciesMolecules ConfigurationSAM
speciesMonomer ConfigurationLatticeFreeRadical
speciesMonomer NeighborListManagerColloid
speciesMonomer P2HardSphereMC
SpeciesN2 etomica.models.nitrogen
Species nitrogen molecule
with 4-points charges
SpeciesN2() SpeciesN2
SpeciesN2ShellModel etomica.models.nitrogen
Species nitrogen molecule (shell model)
Reference: Fabianski R.
SpeciesN2ShellModel() SpeciesN2ShellModel
speciesO ProtonDisorderGenerator
speciesO Catalysis
speciesO ConfigurationCatalysis
speciesO DataSourceWallPressureCatalysis
speciesO MeterDensityO2
SpeciesPh3site464 etomica.virial
Species Phenanthrene molecule
rigid , LJ potential, no charge, 3 site model.each benzene ring is a site, 464 model
reference: Iwai, monte carlo sim of Naphthalene, phenathlene,anthracene in SCF 1998
SpeciesPh3site464() SpeciesPh3site464
SpeciesPh3site545 etomica.virial
Species Phenanthrene molecule
rigid , LJ potential, no charge, 3 site model.each benzene ring is a site
reference: Iwai, monte carlo sim of Naphthalene, phenathlene,anthracene in SCF 1998
SpeciesPh3site545() SpeciesPh3site545
SpeciesPolyhedron etomica.species
Species in which molecules are made of a single atom of type SpheroPolyhedron
SpeciesPolyhedron() SpeciesPolyhedron
SpeciesPolymerMono etomica.starpolymer
Species in which molecules are each made of a single spherical atom.
SpeciesPolymerMono() SpeciesPolymerMono
speciesSodium ReverseOsmosisWater
speciesSolute OsmosisSim
speciesSolute ConfigurationMembrane
speciesSolute ReverseOsmosis
speciesSolute1 ConfigurationMembraneWater
speciesSolute2 ConfigurationMembraneWater
speciesSolvent OsmosisSim
speciesSolvent ConfigurationMembrane
speciesSolvent ConfigurationMembraneWater
speciesSolvent ReverseOsmosis
speciesSolvent ReverseOsmosisWater
speciesSpheres ConfigurationLatticeTube
SpeciesSpheresRotating etomica.species
Species in which molecules are made of a single atom of type OrientedSphere
SpeciesSpheresRotating() SpeciesSpheresRotating
SpeciesSpheresRotatingMolecule etomica.species
Species in which molecules are made of a single atom.
SpeciesSpheresRotatingMolecule() SpeciesSpheresRotatingMolecule
speciesSurface Catalysis
speciesSurface ConfigurationCatalysis
speciesSurface InteractionTracker
speciesSurface ConfigurationSAM
speciesSurface Sam
speciesTopWall LJMC
speciesTopWall LJMD
SpeciesTraPPEAnthracene etomica.virial
Species Anthracene molecule
this is for TraPPE, the Anthracene is rigid , LJ potential, 10 interaction site
reference: TraPPE 4, UA description of linear and branched alkanes and alkylbenzenes, Siepmann
modified from Species Anthracene molecule class
SpeciesTraPPEAnthracene() SpeciesTraPPEAnthracene
SpeciesTraPPECO2 etomica.models.co2
Species CO2 molecule
this is for TraPPE, the CO2 is rigid , LJ potential + QQ
SpeciesTraPPECO2() SpeciesTraPPECO2
SpeciesTraPPENaphthalene etomica.virial
Species Naphthalene molecule
this is for TraPPE, the Naphthalene is rigid , LJ potential
reference: TraPPE 4, UA description of linear and branched alkanes and alkylbenzenes, Siepmann
SpeciesTraPPENaphthalene() SpeciesTraPPENaphthalene
SpeciesTraPPEPhenanthrene etomica.virial
Species Phenanthrene molecule
this is for TraPPE, the Phenanthrene is rigid , LJ potential
reference: TraPPE 4, UA description of linear and branched alkanes and alkylbenzenes, Siepmann
modified from species of phenanthrene C14H10
SpeciesTraPPEPhenanthrene() SpeciesTraPPEPhenanthrene
speciesTube ConfigurationLatticeTube
speciesTube DCVGCMD
SpeciesWater3P etomica.models.water
Species for 3-point water molecule.
SpeciesWater3P() SpeciesWater3P
SpeciesWater4P etomica.models.water
Species for 4-point water molecule.
SpeciesWater4P() SpeciesWater4P
SpeciesWater4PCOM etomica.models.water
Species for 4-point water molecule.
SpeciesWater4PCOM() SpeciesWater4PCOM
specular Token
specularexponent Token
specularExponent Shader
specularFactor Shader
specularOn Shader
specularpercent Token
specularPercent Shader
specularpower Token
specularPower Shader
sphere Token
Sphere etomica.math.geometry
A sphere in 3D.
Sphere() Sphere
Creates sphere with unit radius
Sphere(double) Sphere
Creates sphere of the given radius.
sphereArea(double) Space
The surface "area" of the "sphere" defined in the D-dimensional space.
sphereArea(double) Space1D
sphereArea(double) Space2D
Returns 2 PI r.
sphereArea(double) Space3D
sphereMean(Quaternion[], float[], float) Quaternion
SphereRenderer org.jmol.g3d
Implements high performance rendering of shaded spheres.
sphereShadeIndexes Shader
sphereShadingCalculated Shader
sphereShapeCache Shader
sphereVolume(double) Space
The "volume" of the "sphere" defined in the D-dimensional space.
sphereVolume(double) Space1D
sphereVolume(double) Space2D
Returns PI r^2.
sphereVolume(double) Space3D
spiffiness MultiharmonicGraphicMC.DataSourceAlphaChi
spine Token
spinfps Token
spinner DeviceSpinner
Actual JSpinner
SpinnerListener() DeviceSpinner.SpinnerListener
spinnerModel DeviceSpinner
Actual spinner model
spins Heisenberg
spins Heisenberg3Pair
spins HeisenbergPair
spins MeterMeanField
spins Ising
spinx Token
spiny Token
spinz Token
spline MCMoveOverlapListener
spline DataVirialOverlap
spline(double[], double, double) P2O2Bartolomei
splineC10 P2QChemInterpolated
splineC6 P2QChemInterpolated
splineC8 P2QChemInterpolated
splineRatio P2QChemInterpolated
splineRc P2QChemInterpolated
splineUSCF P2QChemInterpolated
splint(double[], double[], double) P2O2Bartolomei
split(String, char) TextFormat
Split etomica.graph.operations
Split() Split
splitChars(String, String) TextFormat
proper splitting, even for Java 1.3 -- if the text ends in the run,
no new line is appended.
SplitGraph etomica.graph.operations
Split a disconnected graph into multiple graphs.
SplitGraph() SplitGraph
splitGrapher ComponentSubst
SplitOne etomica.graph.operations
Performs the substitution 1=a+b.
SplitOne() SplitOne
SplitOne.SplitOneParameters etomica.graph.operations
splitOneBC PYGenerator.IteratorEF
SplitOneBiconnected etomica.graph.operations
Performs the substitution 1=a+b within each biconnected component.
SplitOneBiconnected() SplitOneBiconnected
SplitOneBiconnected.SplitOneParametersBC etomica.graph.operations
splitOneParameters PYGenerator.IteratorEF
SplitOneParameters(char, char) SplitOne.SplitOneParameters
SplitOneParametersBC(char, char, char) SplitOneBiconnected.SplitOneParametersBC
SplitParameters etomica.graph.operations
SplitParameters(char, char, char) SplitParameters
SplitParameters(char, char, char, Property) SplitParameters
splitSets(Set<Graph>, int) DecorateWertheim3SiteRho
splitter MultiharmonicGraphicMC.DataSourceAlphaFE
splitter DataOverlap.DataSourceOverlapAvgCollapsingSplit
splitterA MultiharmonicGraphicMC
splitterB MultiharmonicGraphicMC
spring LJMD.LJMDParams
spring P1Wall
spring SimEinStep1.SimOverlapParam
spring SimEinStep1HCP.SimOverlapParam
spring SimEinStep2.SimOverlapParam
spring SimEinStep2HCP.SimOverlapParam
spring SimOverlapSoftSphereEin.SimOverlapParam
spring SimOverlapSoftSphereEinHarm.SimOverlapParam
springPosition LJMD.LJMDParams
springPosition P1Wall
sprintf(String, String, Object[]) TextFormat
sprintf emulation uses (almost) c++ standard string formats 's' string 'i'
or 'd' integer 'f' float/decimal 'p' point3f 'q' quaternion/plane/axisangle
' with added "i" in addition to the insipid "d" (digits?)
sprintf(String, ScriptVariable) ScriptVariable
sprintfArray(ScriptVariable[]) ScriptVariable
sprintf accepts arguments from the format() function
First argument is a format string.
sqdt IntegratorPolymer
sqr() BigSurd
Compute the square.
sqr() BigSurdVec
Compute the square.
sqrt() Complex
Complex square root (doesn't change this complex number).
sqrt(BigDecimal) BigDecimalMath
The square root.
sqrt(BigDecimal, MathContext) BigDecimalMath
The square root.
Sqrt() Function.Sqrt
sqrt2 HardSphere
sqrt2 HardSphereSolid
sqrt3a ConformationAnthraceneTraPPE
sqrt3a ConformationPhenanthreneTraPPE
sqrt3ofhalfofthebondlength ConformationNaphthaleneTraPPE
sqrtCOtau PNCO2GCPM
sqrtHMsigmas PNWaterGCPM
sqrtHMsigmas PNWaterGCPMReactionField
sqrtPI EwaldSummation
sqrtPiCCtau PNCO2GCPM
sqrtPiCOtau PNCO2GCPM
sqrtPiHMsigmas PNWaterGCPM
sqrtPiHMsigmas PNWaterGCPMReactionField
sqrtPiMMsigmas PNWaterGCPM
sqrtPiMMsigmas PNWaterGCPMReactionField
Square etomica.math.geometry
A 2-dimensional geometric square.
Square(Space) Square
Constructs a square of unit size.
Square(Space, double) Square
Constructs a square with edge length having the given value.
squared() Vector
Returns the square magnitude of this vector, e.g., x^2 + y^2 for D = 2.
squared() Vector1D
squared() Vector2D
squared() Vector3D
squared() VectorND
sqv P2SpheroPolyhedron
ss AkimaSplineSmoother
ss LJVacancyMin.SimOverlapParam
ss SimLJHTTISuper.SimOverlapParam
ss SimLJHTTISuperHCP.SimOverlapParam
ss SimLJHTTISuperHCP2.SimOverlapParam
ss SimLJVacancy.LJParams
SS SimGlass.PotentialChoice
SS VirialHSOrC.PotentialChoice
SS VirialLJOrC.PotentialChoice
ssbond Token
ssbondsbackbone Token
ssInit AkimaSplineSmootherDy
sSum DataSourceF
sSum DataSourceFOld
Standard etomica.virial.cluster
STANDARD_DEVIATION AccumulatorAverage
STANDARD_DEVIATION AccumulatorAverageBlockless
STANDARD_DEVIATION AccumulatorAverageBlocklessSlim
standardDeviation AccumulatorAverage
standardDeviation AccumulatorAverageBlockless
standardLensPoint MCMoveClusterAtomHSRing
standardLevel Geodesic
3 levels, 0 through 3
star Token
StarPolymerMC etomica.starpolymer
StarPolymerMC(int, int) StarPolymerMC
StarPolymerMC.PolymerParam etomica.starpolymer
StarPolymerMD etomica.starpolymer
StarPolymerMD(int, int, double, double, boolean) StarPolymerMD
StarPolymerMD.PolymerParam etomica.starpolymer
start Line
start() Controller
start() ChainedIterator
START StatusAction.Status
START Debug
what step of the integrator debugging should start from.
startAtom MCMoveBondLength
startAtom MCMoveClusterBondLength
startAtom MCMoveClusterRotateArm
startAtom MCMoveRotateArm
startAtom MCMoveClusterAtomMulti
startAtom0 ApiIntergroupExchange
startAtom1 ApiIntergroupExchange
startBeadHalfs VirialH2PI.VirialH2PIParam
starter MyApplet
Starter() MyApplet.Starter
startMolecule MCMoveClusterMoleculeMulti
startOrtho IntegratorDimerRT
startRotate(float, float) DisplayCanvas
startRotation(int, int) G3DSys
startTimer(String) Logger
startWithDim(Dimension) UnitGraphics
statChoices() AccumulatorAverage
statChoices() AccumulatorAverageBlockless
statChoices() AccumulatorAverageBlocklessSlim
statChoices() AccumulatorAverageCovariance
Statcoulomb etomica.units
The statcoulomb unit of electrical charge, which is the
standard unit of charge in the CGS unit system.
state(int) MacrostateManager
Returns the value of the macrostate variable corresponding to the given index.
stateChanged(ChangeEvent) DeviceBox
calls doUpdate method.
stateChanged(ChangeEvent) DeviceSpinner.SpinnerListener
stateChanged(ChangeEvent) DisplayTextBox
calls doUpdate method.
stateIndex(Box) MacrostateManager
Returns an index identifying the current macrostate occupied by the box.
StaticConstants org.jmol.constant
StaticConstants() StaticConstants
StatisticsMCGraphic etomica.modules.statistics
StatisticsMCGraphic(LJMC, int) StatisticsMCGraphic
StatisticsMCGraphic.DataProcessorUndo etomica.modules.statistics
StatisticsMCGraphic.HistoryPlotBits etomica.modules.statistics
StatisticsMCGraphic.MyFunctionInvertible etomica.modules.statistics
StatisticsMCGraphic.StatsParams etomica.modules.statistics
StatsParams() StatisticsMCGraphic.StatsParams
StatType(String, int) AccumulatorAverage.StatType
StatType(String, int) AccumulatorAverageBlockless.StatType
StatType(String, int) AccumulatorAverageBlocklessSlim.StatType
status(byte) AbstractTraversal
STATUS_ARTICULATION_POINT Traversal
STATUS_START_BICOMPONENT Traversal
STATUS_START_COMPONENT Traversal
STATUS_VISITED_ALL Traversal
STATUS_VISITED_BICOMPONENT Traversal
STATUS_VISITED_COMPONENT Traversal
STATUS_VISITED_NODE Traversal
StatusAction etomica.server.representations
StatusAction() StatusAction
StatusAction.Status etomica.server.representations
statusreporting Token
stddev Token
stdev AccumulatorAverageBootstrap
stdev AccumulatorAverageCollapsingLog
STDEV MultiharmonicGraphicMC.DataSourceAlphaFE
STDEV MultiharmonicGraphicMC.DataSourceBias
STDEV2 MultiharmonicGraphicMC.DataSourceBias
SteepestDescent etomica.math.numerical
SteepestDescent(FunctionMultiDimensionalDifferentiable) SteepestDescent
step0 DataSourceBlockAvgCor
step0 DataSourceHisogram
step0 DataSourceHistogramMSD
step0 DataSourceMSDcorP
step0 DataSourcePMSDHistory
stepcount ClusterWheatleySoftDerivatives
stepCount ActionIntegrate
stepCount DataPumpListenerPow
stepCount Integrator
stepCount ConfigurationStorage
stepCount Debug
Provides step count to other pieces of code that want to know the step
count.
stepFactor P2DiscreteFeynmanHibbs
stepFinished() IntegratorEventManager
stepFrac IntegratorOverlap
stepLength IntegratorDimerMin
steps CH4NVT.Param
steps DHS_NVT.Param
steps DLJ_NVT_1site.Param
steps HSMDCavity.CavityParam
steps HSMDWidom.HSMDParam
steps DHS_NVT.Param
steps DLJ_NVT_1site.Param
steps TIP4P_NVT.Param
steps SimFe.LjMC3DParams
steps SimIdealGas.LjMC3DParams
steps SimLJ.LjMC3DParams
steps LJMC.LjMC3DParams
steps LJMD.LJMDParams
steps LjMC3D.LjMC3DParams
steps LjMd3D.LjMd3DParams
steps LjMd3Dv2y.LjMd3DParams
steps SimHSMDVacancy.HSMDVParams
steps SimLJVacancy.LJParams
steps LJMC3D.SimParams
steps LJMC3DDimer.SimParams
steps Heisenberg.Param
steps Heisenberg3Pair.Param
steps HeisenbergPair.Param
steps VirialHSBinMultiThreaded.SimulationWorker
steps VirialSQWBinMultiThreaded.SimulationWorker
STEPS EnumPotentialParamDescription
stepSize MCMoveBoxStep
stepSize MCMoveStep
stepSizeMax MCMoveBoxStep
stepSizeMax MCMoveStep
stepSizeMin MCMoveBoxStep
stepSizeMin MCMoveStep
stepSizeRotation SimGCPMWaterMCNPT.GCPMWaterMCParam
stepSizeRotation SimGCPMWaterMCNVT.GCPMWaterMCParam
stepSizeTranslation SimGCPMWaterMCNPT.GCPMWaterMCParam
stepSizeTranslation SimGCPMWaterMCNVT.GCPMWaterMCParam
stepSizeVolume SimGCPMWaterMCNPT.GCPMWaterMCParam
stepsPerBlock VirialCPSHeliumNonAdditiveClassical_Correction.VirialParam
stepsPerBlock VirialCPSHeliumNonAdditiveClassical.VirialParam
stepsPerBlock VirialHePCKLJS.VirialParam
stepsPerBlock VirialHePCKLJSCHNCCorrection.VirialLJParam
stepsPerBlock VirialHePCKLJSPYCorrection.VirialLJParam
stepsPerBlock VirialHePI_PotentialCorrection.VirialHePIParam
stepsPerBlock VirialHePIXCOdd.VirialHePIParam
stepsPerBlock VirialLJCHNCCorrection.VirialLJParam
stepsPerBlock VirialLJPYCorrection.VirialLJParam
stepStarted() IntegratorEventManager
stereodegrees Token
stillOnPolymer0 ANIntergroupExchange
stokeslet(double) IntegratorDroplet
STOP Debug
what step of the integrator should the simulation bail
set this to prevent Etomica from running for a long time while
outputting debugging information (potentially filling up the disk)
stopNow MyApplet
stopper MyApplet
Stopper() MyApplet.Stopper
stopRotate() DisplayBoxCanvasG3DSys
stopRotate() DisplayCanvas
stopRotate() DisplayPolytopeCanvasG3DSys
stopRotation() G3DSys
stopSimulation ModelSimulationEnvironment
storageType ConfigurationStorage
storeAngularMomentum IntegratorRigidIterative
StoredIterator etomica.graph.iterators
StoredIterator(byte) StoredIterator
straightness Token
STRAIGHTNESS EnumPalette
StrainColorScheme etomica.modules.materialfracture
StrainColorScheme() StrainColorScheme
strandcount Token
strandcountformeshribbon Token
strandcountforstrands Token
strands FFTDecomposition
strands IsFFT
strands Token
streamOut(OutputStream) GraphMap
stressSource AtomSignalStress
string Token
STRING DeviceBox.LabelType
STRING DisplayTextBox.LabelType
stringBuilder DisplayTable
StringFeature etomica.compatibility
StringFeature(String, String) StringFeature
stringiWV NormalModeAnalysisDisplay3DGraphic
stringOmega2 NormalModeAnalysisDisplay3DGraphic
strings DataSourceStrings
Strings etomica.util
Non-instantiable class providing a few static methods for String manipulation.
stringToDim(String) UnitFilter
stringToUnit(String) UnitFilter
stringToUnitSystem(String) UnitFilter
stringWidth(String) JmolFont
stringWV NormalModeAnalysisDisplay1DGraphic
stringWV NormalModeAnalysisDisplay2DGraphic
StringXBuilder org.jmol.util
Interesting thing here is that JavaScript is 3x faster than Java in handling strings.
StringXBuilder() StringXBuilder
strparam Token
strproperty Token
strTol2 DataSourceStrings
strucFac DataSourceF
strucFac DataSourceFOld
strucid Token
strucno Token
struct MeterStructureFactor
StructorFactorComponentExtractor etomica.modules.glass
This takes structure factor as data and extracts the sin/cos components
(using the phase angles) and sends them to a DataSourceCorrelation.
StructorFactorComponentExtractor(MeterStructureFactor[], int, DataSourceCorrelation) StructorFactorComponentExtractor
structure Token
structure(String) SimulationResource
STRUCTURE EnumPalette
StructureFactorComponentCorrelation etomica.modules.glass
StructureFactorComponentCorrelation(int[], ConfigurationStorage) StructureFactorComponentCorrelation
StructureFactorComponentCorrelation(int, ConfigurationStorage) StructureFactorComponentCorrelation
StructureFactorComponentCorrelation.Meter etomica.modules.glass
StructureFactorComponentCorrelation.Sink etomica.modules.glass
strutdefaultradius Token
strutlengthmaximum Token
struts Token
strutsmultiple Token
strutspacing Token
Stuff(PotentialGroup, PotentialGroup, ISpecies) ParserLAMMPS.Stuff
stx3leval(double, double, double) P2O2Bartolomei
sub(Matrix3f) Matrix3f
Sets the value of this matrix to the matrix difference of itself and matrix
m1 (this = this - m1).
sub(Matrix4f) Matrix4f
Sets the value of this matrix to the matrix difference of itself and matrix
m1 (this = this - m1).
sub(Tuple3f) Tuple3f
Sets the value of this tuple to the vector difference of itself and tuple
t1 (this = this - t1).
Sub etomica.graph.operations
Sub() Sub
sub2(Tuple3f, Tuple3f) Tuple3f
Sets the value of this tuple to the vector difference of tuple t1 and t2
(this = t1 - t2).
subBox MeterDensityDistribution
subClusterValues ClusterSumIC
subCriterion CriterionAdapter
subCriterion CriterionAdapterMolecular
subData MeterDensityDistribution
subDataInfo DataGroup.DataInfoGroup
subDataInfo DataGroup.DataInfoGroupFactory
submitActionInterrupt(IAction) Controller
Submit an Action which will be executed on the Activity thread before its next step.
subst BiComponentSubst.BiComponentSubstParameters
subst ComponentSubst.ComponentSubstParameters
substMinMulti(Graph) VirialDiagrams
substring(int) StringXBuilder
substring2(int, int) StringXBuilder
substructure Token
substSet PYGenerator.IteratorEF
subtract(int) Rational
Subtract an integer.
subtract(BigIntegerPoly) BigIntegerPoly
Subtract another polynomial
subtract(BigSurd) BigSurdVec
Subtract another number.
subtract(BigSurdVec) BigSurdVec
Subtract another number.
subtract(Rational) Rational
Subtract another fraction.
subtract(BigInteger) Rational
Subtract an integer.
subtractApprox VirialHeNonAdditive.VirialParam
subtractApprox VirialHeNonAdditiveWheatley.VirialParam
subtractApprox VirialHePISysErr.VirialHePIParam
subtractApprox VirialHePIXCEven.VirialHePIParam
subtractApprox VirialHePIXCOdd.VirialHePIParam
subtractApprox VirialHePYCorrection.VirialHePYCParam
subtractApprox VirialHeSC.VirialHePYCParam
subtractErr VirialHePISysErr.VirialHePIParam
subtractHalf VirialHePI.VirialHePIParam
subtractHalf VirialHePISysErr.VirialHePIParam
subtractHalf VirialHePIXCEven.VirialHePIParam
subtractHalf VirialHePIXCOdd.VirialHePIParam
subtractPotential VirialHePI.VirialHePIParam
subtractRound(BigComplex, BigComplex) BigDecimalMath
Subtract and round according to the larger of the two ulp's.
subtractRound(BigDecimal, BigDecimal) BigDecimalMath
Subtract and round according to the larger of the two ulp's.
subtractWhat VirialCO2PI.VirialH2PIParam
subtractWhat VirialH2PI.VirialH2PIParam
Sulfur etomica.chem.elements
Class for the Sulfur element.
Sulfur(String) Sulfur
Sulfur(String, double) Sulfur
sulfurType IntegratorVelocityVerletSAM
sum AccumulatorAverageBlockless.AllData
sum AccumulatorAverageBlockless
sum AccumulatorAverageBlocklessSlim
sum AccumulatorAverageFixedOutputFile
sum HistogramSimple
sum PotentialCalculationEnergySumEAM
sum PotentialCalculationDUDW
sum MeterWallForce.PotentialCalculationWallForce
sum PotentialCalculationMappedRdf
sum PotentialCalculationMappedEnergy
sum PotentialCalculationMappedVirial
sum PotentialCalculationMappedVirialV
sum AccumulatorAutocorrelationPTensor
sum AccumulatorAutocorrelationShearStress
sum InsertionGraphic.MeterWidom
sum MultiharmonicGraphicMC.DataSinkReweightedDeltaU
sum PotentialCalculationEnergySum
sum PotentialCalculationEnergySumBigDecimal
sum PotentialCalculationSumquare
sum MeterVirialBDBinMultiThreaded.MyData
sum MeterVirialBinMultiThreaded.MyData
sum MeterVirialEBinMultiThreaded.MyData
sum Token
sum() EwaldSumMolecules
sum(ClusterDiagram[], ClusterDiagram[]) ClusterOperations
Generates the set of diagrams obtained by adding the second set to the first set.
Sum etomica.graph.operations
Sum() Sum
sum_separate PotentialCalculationMappedEnergy
sum1 DataSourceEnergies.PotentialCalculationEnergies
sum1 Potential2SoftSphericalLSMultiLat.ReturnValue
sum1 PotentialCalculationSolidSuperCut
sum2 DataSourceEnergies.PotentialCalculationEnergies
sum2 StructureFactorComponentCorrelation
sum2 MeterVirialBDBinMultiThreaded.MyData
sum2 MeterVirialBinMultiThreaded.MyData
sum2 MeterVirialEBinMultiThreaded.MyData
sum2 Token
sumBlockSquare AccumulatorAverageFixedOutputFile
sumCheck MeterMBAR
sumDelete MCMoveOverlapListener
sumInsert MCMoveOverlapListener
summary(Parser.CommandVariable) Interpreter
summer HSNPT.ColorSchemeDisplacement
summer NormalModesMolecular
sumP2 AccumulatorPTensor
sumP4 AccumulatorPTensor
sums AccumulatorAverageBootstrap
sums AccumulatorAverageCollapsingLog
sums HistogramNotSoSimple
sums HistogramReweightedData
sums Potential2SoftSphericalLSMulti
sums PotentialCalculationEnergySumCutoff
sums PotentialCalculationSumCutoffLS
sumSqD2 AkimaSplineSmoother
sumSqD2D AkimaSplineSmoother
sumSqD3 AkimaSplineSmoother
sumSqD3D AkimaSplineSmoother
sumSqDy AkimaSplineSmoother
sumSquare AccumulatorAverageBlockless.AllData
sumSquare AccumulatorAverageBlockless
sumSquare AccumulatorAverageBlocklessSlim
sumSquare AccumulatorAverageFixed
sumSquare AccumulatorAverageFixedOutputFile
sumWeights MultiharmonicGraphicMC.DataSinkReweightedDeltaU
SuperImposeGraphs(Graph, Graph) IEGenerator
support Display
suppressAction DeviceSlider
suppressBoxLengthWarning NeighborCellManager
suppressMakeAgent P2SquareWellRobust
surface Token
SURFACE EnumPalette
surfaceColor ColorSchemeDropletSurface
surfaceCursor CriterionTether3
surfaceDim DataProcessorInterfacialTension
surfacedistance Token
surfacePosition SamGraphic.ModifierWallPosition
surfaceSet MeshSurface
SurfaceTensionMapped etomica.surfacetension
DataProcessor that adds in mapped average contributions to the surface
tension.
SurfaceTensionMapped(Space, Box, ISpecies, PotentialMaster) SurfaceTensionMapped
surfaceType CriterionTether3
surfactant InterfacialSW
surfactantProfileMeter InterfacialSWGraphic
surfactantProfilePump InterfacialSWGraphic
sv P2SpheroPolyhedron
sValue(Token) ScriptVariable
SVG_EXTENSION SVGConverter
SVG file extension
SVG_EXTENSION SVGConverter.SVGFileFilter
SVG_EXTENSION SVGConverterURLSource
SVG file extension
SVGConverter etomica.graph.view.rasterizer
This application can be used to convert SVG images to raster images.
SVGConverter() SVGConverter
SVGConverter(SVGConverterController) SVGConverter
SVGConverter.SVGFileFilter etomica.graph.view.rasterizer
Convenience class to filter svg files
SVGConverterController etomica.graph.view.rasterizer
Interface for controlling some aspectes of the
SVGConverter operation.
SVGConverterDocumentSource etomica.graph.view.rasterizer
SVGConverterDocumentSource(SVGDocument) SVGConverterDocumentSource
SVGConverterException etomica.graph.view.rasterizer
Describes an error condition in SVGConverter
SVGConverterException(String) SVGConverterException
SVGConverterException(String, boolean) SVGConverterException
SVGConverterException(String, Object[]) SVGConverterException
SVGConverterException(String, Object[], boolean) SVGConverterException
SVGConverterFileSource etomica.graph.view.rasterizer
Describes a file source for the SVGConverter
SVGConverterFileSource(File) SVGConverterFileSource
SVGConverterFileSource(File, String) SVGConverterFileSource
SVGConverterSource etomica.graph.view.rasterizer
Interface used to handle both Files and URLs in the
SVGConverter
SVGConverterURLSource etomica.graph.view.rasterizer
SVGConverterURLSource(String) SVGConverterURLSource
SVGFileFilter() SVGConverter.SVGFileFilter
SVGZ_EXTENSION SVGConverterURLSource
swap SimFe.LjMC3DParams
swap(int, int) ClusterDiagram
Swaps point1 and point2.
swap(Object[], int, int) ArrayUtil
swap0n(byte) VirialDiagrams
swap0n(byte) VirialDiagramsPT
swap0n(byte, int, int, boolean) VirialDiagramsMix2
swapAllAndCompare(boolean, ClusterDiagram, int[]) ClusterGenerator
SwapFactory() MCMoveSwapConfiguration.SwapFactory
SwapFactory() MCMoveSwapCluster.SwapFactory
swapInt(int[], int, int) ArrayUtil
swapMove SimGlass
swappedBoxes() IntegratorPT.MCMoveSwap
swappedBoxes() MCMoveSwapConfiguration
Implementation of MCMoveSwap interface
swappedBoxes() MCMoveSwapCluster
Implementation of MCMoveSwap interface
sweepRadius AtomTypeSpheroPolyhedron
SWITCHED ParserLAMMPS.Truncation
switchFac P2MoleculeSoftTruncatedSwitched
switchFac P2SoftSphericalTruncatedSwitched
Swmd etomica.modules.swmd
Swmd(Space) Swmd
SWMD2D etomica.simulation.prototypes
Simple square-well molecular dynamics simulation in 2D
SWMD2D() SWMD2D
SWMD3D etomica.simulation.prototypes
Simple square-well molecular dynamics simulation in 3D
SWMD3D() SWMD3D
SwmdGraphic etomica.modules.swmd
SwmdGraphic(Swmd, Space) SwmdGraphic
SwmdGraphic.Applet etomica.modules.swmd
SwmdGraphic.DataSinkExcludeOverlap etomica.modules.swmd
SwmdGraphic.ModifierAtomDiameter etomica.modules.swmd
SWVLE etomica.modules.nucleation
SWVLE(SWVLESim, Space) SWVLE
SWVLESim etomica.modules.nucleation
SWVLESim(int) SWVLESim
sx1 P1LepsHarmonic
sx2 P1LepsHarmonic
sy1 P1LepsHarmonic
sy2 P1LepsHarmonic
symbol Element
symbol Token
symbol() CompoundUnit
symbol() Prefix
Symbol used to show that prefix is part of the unit.
symbol() PrefixedUnit
symbol() SimpleUnit
symbol() LJ.LJUnit
symbol() Unit
Returns the symbol of unit, such as "g" for grams.
symmetry Token
symop Token
syncmouse Token
syncscript Token
SZ_INT BitmapUtils
SZ_LONG Bitmap
T
t ConfigFromFileLAMMPS.ColorSchemeDeviation
t AkimaSpline
t AkimaSplineSmoother
t MeterDipoleMoment.ForceTorque
t MeterMeanField.ForceTorque
t ClusterPY
T SimFe.LjMC3DParams
T SimIdealGas.LjMC3DParams
T SimLattice.LjMC3DParams
T SimLJ.LjMC3DParams
T LJMC.LjMC3DParams
T LJMD.LJMDParams
T LjMC3D.LjMC3DParams
T HarmonicCrystalSsFccNxy.Params
T BnPCJSDHe.BnPCJSDHeParams
T BnPYCHe.BnPYHeParams
T1ij PotentialCalculationEFSSP
T1ij PotentialCalculationLJSP
T1ik PotentialCalculationEFSSP
T2ij PotentialCalculationLJSP
T3ij PotentialCalculationLJSP
ta P2CO2H2OWheatley.P2CO2H2OSCTI
taa P2O2Bartolomei
taaMRCI P2O2Bartolomei
taaPT2 P2O2Bartolomei
TABBED_PANE SimulationGraphic
tabbedPane SimulationPanel
tableModel() DisplayTable
tableRowCountChanged(DataSinkTable) DataTableListener
Method called to indicate that the number of rows in the
table has changed.
tableRowCountChanged(DataSinkTable) DisplayTable
Part of the DataTableListener interface.
tableRowHeadersChanged(DataSinkTable) DataTableListener
Method called to indicate that the row headers in the table have
changed.
tableRowHeadersChanged(DataSinkTable) DisplayTable
tag MeterEnthalpyVolume
tag MeterCavityMapped
tag MeterRDFMapped
tag MeterWidomCavity
tag DataDistributer
tag DataDump
tag DataFork
tag DataGroupSplitter
tag DataProcessor
tag DataSourceFunction
tag DataSourceGroup
tag DataSourceIndependentSimple
tag DataSourcePositionedBoltzmannFactor
tag DataSourceRmsVelocity
tag DataSourceScalar
tag DataSourceTensorVirialHard
tag DataSourceUniform
tag DataSplitter
tag HistogramDataSource
tag MeterDihedralAngle
tag MeterDipoleSumSquaredMappedAverage
tag MeterHyperVirial
tag MeterMomentumCOM
tag MeterPositionCOM
tag MeterPressureByVolumeChange.DataSourceExp
tag MeterPressureHardTensor
tag MeterPressureTensor
tag MeterPressureTensorFromIntegrator
tag MeterProfile
tag MeterProfileByAtoms
tag MeterProfileByVolume
tag MeterRDF
tag MeterRDFPC
tag MeterStructureFactor
tag MeterTensorVelocity
tag DataSourceEnergies
tag MeterPotentialEnergyCutoff
tag MeterPU
tag MeterPUCut
tag MeterPUCutLS
tag MeterWidomInsertionCorrection
tag MeterMappedRdf
tag MeterMeanForce
tag MeterBoltzmann
tag MeterBoltzmannRotPerturb
tag MeterTargetRPMolecule
tag MeterTargetTPMolecule
tag DataSourceDensityFunction
tag DataSourceWallPressureCatalysis
tag MeterChainLength
tag MeterDeformation
tag AccumulatorPTensor
tag CorrelationSelf2
tag DataSourceAlpha2
tag DataSourceCorrelation
tag DataSourceF
tag DataSourceFOld
tag DataSourceFs
tag DataSourceHisogram
tag DataSourceHistogramMSD
tag DataSourceMSD
tag DataSourceMSDcorP
tag DataSourcePercolation
tag DataSourcePercolation0
tag DataSourcePMSDHistory
tag DataSourceQ4
tag DataSourceStrings
tag DataSourceVAC
tag MeterCorrelation
tag MeterCorrelationSelf
tag MeterGs
tag StructureFactorComponentCorrelation
tag DataSourceTensorVirialHardProfile.DataSourceVirialProfile
tag MeterOrientation
tag DataSourceWallPressureMu
tag MeterMBAR
tag MultiharmonicGraphicMC.DataSourceAlphaFE
tag MultiharmonicGraphicMC.DataSourceFunctionRaw
tag MeterUmbrella
tag MeterFlux
tag MeterOsmoticPressure
tag MeterTilt
tag DataCollector
tag DataSourceFE
tag DataSourceFEHistogram
tag DataSourceImposedFEFit
tag DataSourceImposedFEHistogram
tag DataSourcePMu
tag DataSourcePN
tag MeterBoltzmann
tag MeterBoltzmannHarmonic
tag MeterBoltzmannHTTP
tag MeterBoltzmannTarget
tag MeterDADB
tag MeterDDP
tag MeterDirectSamplingHarmonic
tag MeterDirectSamplingTarget
tag MeterDP
tag MeterOverlapSwitch
tag MeterPlaneSlip
tag MeterSamplingHarmonic
tag MeterSamplingTarget
tag MeterSolidDA
tag MeterSolidDACut
tag MeterSolidMirror
tag MeterSolidProps
tag MeterSolidPropsLJ
tag MeterTargetTP
tag MeterTilt
tag MeterTiltHistogram
tag MeterTiltRotation
tag MeterTiltRotationStdev
tag MeterWorkBennetHarmonic
tag MeterWorkBennetTarget
tag MeterWorkHarmonicBennet
tag MeterWorkHarmonicPhaseSpace
tag MeterWorkHarmonicTargetandReweighting
tag MeterWorkHarmonicUmbrella
tag MeterWorkTargetBennet
tag MeterWorkTargetHarmonicandReweighting
tag MeterWorkTargetPhaseSpace
tag MeterWorkTargetUmbrella
tag MeterWorkUmbrellaHarmonic
tag MeterWorkUmbrellaTarget
tag MeterOverlap
tag MeterDipoleMoment
tag MeterEnergyMeanField
tag MeterMappedAveraging
tag MeterMappedAveraging3Pair
tag MeterMappedAveragingCorrelation
tag MeterMappedAveragingCV
tag MeterMappedAveragingFreeEnergy
tag MeterMappedAveragingPair
tag MeterMappedAveragingPairExcess
tag MeterMappedAveragingSum
tag MeterMappedAveragingVSum
tag MeterMappedAveragingVSum3Pair
tag MeterMappedAveragingVSumPair
tag MeterMeanField
tag MeterBondLength
tagged MeterChainLength.AtomTag
tagManager MeterChainLength
tags DataInfoFactory
tags DataTagBag
tags DataProcessorBounds
tailType InterfacialSW
tajmols P2O2Bartolomei
tajmolsMRCI P2O2Bartolomei
tajmolsPT2 P2O2Bartolomei
tajp1 P2O2Bartolomei
tajp1MRCI P2O2Bartolomei
tajp1PT2 P2O2Bartolomei
tajpn P2O2Bartolomei
tajpnMRCI P2O2Bartolomei
tajpnPT2 P2O2Bartolomei
takeStep(Vector[], Vector[], double) ActionMinimizeEnergy
tan() Complex
Tangent of this Complex number (doesn't change this Complex number).
tan(BigDecimal) BigDecimalMath
The trigonometric tangent.
tangledMolecules MCMoveClusterRingPartialRegrow
tangledMolecules MCMoveClusterRingRegrow
tangledMolecules MCMoveClusterRingScale
tanh(BigDecimal) BigDecimalMath
The hyperbolic tangent.
taperOrder P2MoleculeSoftTruncatedSwitched
taperOrder P2SoftSphericalTruncatedSwitched
target ApiIndexList
TARGET DataOverlap
targetAcc HSDimerNPT.HSMD3DParameters
targetAccumulator DataSourceVirialOverlap
targetAccumulator DataVirialOverlap
targetAction DeviceButton
targetAction DeviceButtonGroup
targetAction DeviceSlider
targetAction DeviceSpinner
targetAction DeviceButtonSingle
targetAtom ApiIntergroup
targetAtom P2ReactionFieldDipoleTruncated.P0ReactionField
targetAvg DataOverlap
targetAvg DataVirialOverlap.FullResult
targetCluster MeterVirialBDBin
targetCluster MeterVirialBDBinMultiThreaded
targetCluster MeterVirialBinMultiThreaded
targetCluster MeterVirialEBinMultiThreaded
targetCluster MeterVirialIC
targetCluster ModifierTPI
targetDataInterval SimOverlapModule
targetErr DataVirialOverlap.FullResult
targetIndex MCMoveInsertDeleteLatticeVacancy.AtomIteratorBruteForce
targetMolecule CriterionTether3
targetSum MeterOverlapSwitch
targetTemp VirialSQWBinMultiThreaded.SimulationWorker
targetTemp VirialSQWBinMultiThreaded.VirialHSBinParam
targHist SimulationVirialOverlap2
targPiHist SimulationVirialOverlap2
tau PNGCPM.GCPMAgent
tau P2Water4PSoft
tauAll PNCO2GCPM
tauC PNCO2GCPM
tauO PNCO2GCPM
tb P2CO2H2OWheatley.P2CO2H2OSCTI
tbet P2O2Bartolomei
tbetMRCI P2O2Bartolomei
tbetPT2 P2O2Bartolomei
Tc EOSSW
tCompute(double[][], double[][], int, int, double) OrnsteinZernike
tData AccumulatorAutocorrelationPTensor
tData AccumulatorAutocorrelationShearStress
tData DataSourceAlpha2
tData DataSourceBlockAvgCor
tData DataSourceCorrelation
tData DataSourceF
tData DataSourceFOld
tData DataSourceFs
tData DataSourceMSD
tData DataSourceMSDcorP
tData DataSourcePercolation
tData DataSourcePercolation0
tData DataSourceQ4
tData DataSourceStrings
tData DataSourceVAC
tData MeterCorrelationSelf
tData StructureFactorComponentCorrelation
tDataInfo AccumulatorAutocorrelationPTensor
tDataInfo AccumulatorAutocorrelationShearStress
tDataInfo DataSourceAlpha2
tDataInfo DataSourceBlockAvgCor
tDataInfo DataSourceCorrelation
tDataInfo DataSourceF
tDataInfo DataSourceFOld
tDataInfo DataSourceFs
tDataInfo DataSourceMSD
tDataInfo DataSourceMSDcorP
tDataInfo DataSourcePercolation
tDataInfo DataSourcePercolation0
tDataInfo DataSourceQ4
tDataInfo DataSourceStrings
tDataInfo DataSourceVAC
tDataInfo MeterCorrelationSelf
tDataInfo StructureFactorComponentCorrelation
tdr CorrelationSelf2
TE(double) IData
Times-equals (*=) operation, multiplying all values in data by given
value.
TE(double) DataDouble
Times-equals (*=) operation.
TE(double) DataDoubleArray
Times-equals (*=) operation.
TE(double) DataDoubleBDArray
Times-equals (*=) operation.
TE(double) DataGroup
TE(double) DataTensor
Times-equals (*=) operation.
TE(double) DataVector
Times-equals (*=) operation.
TE(double) Quaternion
Multiplies all the components of the Quaternion q by the given scalar
TE(double) Tensor
"Times equals" (*=) operation, replaces each element of this tensor by its current value times the given scalar
TE(double) Vector
Multiplies all components by a constant.
TE(double) Tensor1D
TE(double) Vector1D
TE(double) Tensor2D
TE(double) Vector2D
TE(double) Tensor3D
TE(double) Vector3D
TE(double) TensorND
TE(double) VectorND
TE(double) BigValue
Times-equals (*=).
TE(double) IBigValue
Times-equals (*=).
TE(double) MyBigDecimal
Times-equals (*=).
TE(IData) IData
Times-equals (*=) operation.
TE(IData) DataDouble
Times-equals (*=) operation.
TE(IData) DataDoubleArray
Times-equals (*=) operation.
TE(IData) DataDoubleBDArray
Times-equals (*=) operation.
TE(IData) DataGroup
TE(IData) DataTensor
Times-equals (*=) operation.
TE(IData) DataVector
Times-equals (*=) operation.
TE(Tensor) Tensor
"Times equals" (*=) operation, as matrix multiplication.
TE(Tensor) Tensor1D
TE(Tensor) Tensor2D
TE(Tensor) Tensor3D
TE(Tensor) TensorND
TE(Vector) Vector
Times-equals (*=) operation.
TE(Vector) Vector1D
TE(Vector) Vector2D
TE(Vector) Vector3D
TE(Vector) VectorND
TE(IBigValue) BigValue
Times-equals (*=) operation.
TE(IBigValue) IBigValue
Times-equals (*=) operation.
TE(IBigValue) MyBigDecimal
Times-equals (*=) operation.
TEAL Colix
tearDown() BenchApiAACell
TEln(double) BigValue
Times-equals (*=) operation, multiplying by a value given as its logarithm.
temp IntegratorVelocityVerletShake
temp BoundaryDeformablePeriodicSwitch
temp AshtonWildingLJ.simParams
temp NVTWidomInsertLJ.simParams
temp Orientation3D
TEMP EnumPalette
TEMP EnumVdw
temp2 Orientation3D
tempAngularVelocity IntegratorRigidIterative
tempAngularVelocity IntegratorRigidMatrixIterative
tempAxesTensor IntegratorRigidMatrixIterative
temperature BoxQuench
temperature BoxRandomizeMomenta
temperature BoxScaleMomenta
temperature DHS_NVT.Param
temperature DLJ_NVT_1site.Param
temperature TestAceticAcidMC3D_NPT.AceticAcidMCParam
temperature Wertheim2SiteAceticAcid.WertheimParam
temperature SimGCPMWaterMCNPT.GCPMWaterMCParam
temperature WertheimGCPM3PtEBondDecomp.VirialAssociatingFluidParam
temperature WertheimGCPM3PtThreeSite.VirialAssociatingFluidParam
temperature WertheimGCPM4PtEBondDecomp.WertheimAssociatingFluidParam
temperature WertheimGCPM4PtEBondDecompFinal.VirialAssociatingFluidParam
temperature WertheimGCPM4PtThreeSite.VirialAssociatingFluidParam
temperature WertheimGCPM4PtThreeSiteEDecompDirectSampling.VirialAssociatingFluidParam
temperature TestIGAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
temperature TestLJAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
temperature TestLJAssociationMC3D_NPT.VirialAssociatingFluidParam
temperature TestLJAssociationMC3D_NVTOld.VirialAssociatingFluidParam
temperature MeterHyperVirial
temperature MeterPressure
temperature MeterWidomInsertion
temperature MyMCMove
temperature DHS_NVT.Param
temperature DLJ_NVT_1site.Param
temperature EFSTungsten.Params
temperature VLESim
temperature IntegratorBox
temperature IntegratorManagerMC
temperature MCMoveOverlapListener
temperature LjMd3D.LjMd3DParams
temperature MeterPU
temperature MeterPUCut
temperature MeterPUCutLS
temperature MeterWidomInsertionCorrection
temperature MeterWidomInsertionP
temperature SimMappedRdf.LJMDParams
temperature MappedU.LJMDParams
temperature MappedVirialLJ.LJMDParams
temperature MappedVirialLJVGr.LJMDParams
temperature LJmuVT.LJMCParams
temperature LJNPT.LJMCParams
temperature LJNVT.LJMCParams
temperature ClathrateHarmonicFE.SimParams
temperature P2CO2H2OWheatley.P2CO2H2OSCTI
temperature P2CO2Hellmann.P2CO2SC
temperature MeterTargetRPMolecule
temperature MeterTargetTPMolecule
temperature SimDirectBetaN2RP.SimOverlapParam
temperature SimOverlapAlphaN2TP.SimOverlapParam
temperature SimOverlapBetaN2RP.SimOverlapParam
temperature SimOverlapBetaN2RPScaling.SimOverlapParam
temperature SimOverlapBetaN2TP.SimOverlapParam
temperature SimOverlapDisorderedAlphaN2RPScaling.SimOverlapParam
temperature SimOverlapDisorderedAlphaN2TP.SimOverlapParam
temperature SimOverlapNitrogenModel.SimOverlapParam
temperature P2WaterSzalewicz.P2H2OSC
temperature EOSSW
temperature AccumulatorPTensor
temperature SimGlass.GlassParams
temperature MeterMBAR
temperature MeterUmbrella
temperature SWVLESim
temperature VLESim
temperature DataProcessorBoltzmannFactor
temperature IntegratorHarmonic
temperature MCMoveAtomCoupledBennet
temperature MCMoveAtomCoupledUmbrella
temperature MCMoveEinsteinCrystal
temperature MCMoveHarmonic
temperature MCMoveSingleMode
temperature MCMoveVolumeMonoclinicScaled
temperature MCMoveVolumeSolid
temperature MCMoveVolumeSolidNPTMolecular
temperature MeterBoltzmannHarmonic
temperature MeterBoltzmannHTTP
temperature MeterBoltzmannTarget
temperature MeterDADB
temperature MeterDDP
temperature MeterDirectSamplingHarmonic
temperature MeterDP
temperature MeterOverlapSwitch
temperature MeterSolidDA
temperature MeterSolidDACut
temperature MeterSolidMirror
temperature MeterSolidProps
temperature MeterSolidPropsLJ
temperature MeterTargetTP
temperature MeterWorkHarmonicBennet
temperature MeterWorkHarmonicPhaseSpace
temperature MeterWorkHarmonicTargetandReweighting
temperature NormalModeAnalysisDisplay1D
temperature NormalModeAnalysisDisplay2D
temperature NormalModeAnalysisDisplay3D
temperature NormalModes1DHR
temperature NormalModes2D
temperature NormalModes3D
temperature PotentialCalculationEFSSP
temperature PotentialCalculationLJSP
temperature SimBennet.SimBennetParam
temperature SimEinStep1.SimOverlapParam
temperature SimEinStep1HCP.SimOverlapParam
temperature SimEinStep2.SimOverlapParam
temperature SimEinStep2HCP.SimOverlapParam
temperature SimHarmonicUmbrella.SimBennetParam
temperature SimLJHTTISuper.SimOverlapParam
temperature SimLJHTTISuperHCP.SimOverlapParam
temperature SimLJHTTISuperHCP2.SimOverlapParam
temperature SimLJHTTISuperSFMD.SimOverlapParam
temperature SimLJVacancy.LJParams
temperature SimOverlap.SimOverlapParam
temperature SimOverlapLJ.SimOverlapParam
temperature SimOverlapLJModule.SimOverlapParam
temperature SimOverlapSoftSphere.SimOverlapParam
temperature SimOverlapSoftSphereDP.SimOverlapParam
temperature SimOverlapSoftSphereEin.SimOverlapParam
temperature SimOverlapSoftSphereEinHarm.SimOverlapParam
temperature SimOverlapSoftSphereHCP.SimOverlapParam
temperature SimOverlapSoftSphereReweighting.SimOverlapParam
temperature SimOverlapSoftSphereSoftness.SimOverlapParam
temperature SimOverlapSoftSphereSuperBox.SimOverlapParam
temperature SimOverlapSoftSphereTP.SimOverlapParam
temperature SimOverlapSoftSphereTPHCP.SimOverlapParam
temperature SimOverlapSoftSphereTPSlantedBox.SimOverlapParam
temperature SimOverlapSSnxy.SimOverlapParam
temperature SimTargetUmbrella.SimBennetParam
temperature SimUmbrella.SimBennetParam
temperature SimUmbrellaSoftSphere.SimBennetParam
temperature WriteS
temperature MCMoveGeometricClusterRestrictedGE
temperature MeterOverlap
temperature EwaldSumMolecules
temperature P2DiscreteFeynmanHibbs
temperature P2EffectiveFeynmanHibbs
temperature P2HePCKLJS.P2HeQFH
temperature P2HePCKLJS.P2HeTI
temperature P2HeSimplified.P2HeQFH
temperature P2HeSimplified.P2HeTI
temperature P2LJDipole
temperature P2LJQ
temperature P2LJQQ
temperature P2NitrogenHellmann.P2N2QFH
temperature P2O2Bartolomei.P2O2TI
temperature P2SemiclassicalAtomic
temperature P2SemiclassicalMolecular
temperature PotentialCalculationPressureTensor
temperature LJMC3D.SimParams
temperature Heisenberg.Param
temperature Heisenberg3Pair.Param
temperature HeisenbergPair.Param
temperature MeterMappedAveraging
temperature MeterMappedAveraging3Pair
temperature MeterMappedAveragingCorrelation
temperature MeterMappedAveragingCV
temperature MeterMappedAveragingFreeEnergy
temperature MeterMappedAveragingPair
temperature MeterMappedAveragingPairExcess
temperature MeterMappedAveragingSum
temperature MeterMappedAveragingVSum
temperature MeterMappedAveragingVSum3Pair
temperature MeterMappedAveragingVSumPair
temperature MeterMeanField
temperature MeterPairSum
temperature VirialPolymerOverlapMC.VirialHSParam
temperature LJMC.LJMCParams
temperature ModelTemperatureAndSteps
temperature BnFlexibleContributionTraPPEUAMethanol.VirialParam
temperature DirectSamplingTargetQCArReferenceAzizAr.VirialLJParam
temperature DoubleAssociationSitesFluid2Pt.VirialAssociatingFluidParam
temperature DoubleAssociationSitesFluid3Pt.VirialAssociatingFluidParam
temperature DoubleAssociationSitesFluid4Pt.VirialAssociatingFluidParam
temperature FourAssociationSitesFluid2Pt.VirialAssociatingFluidParam
temperature LJTSRefLJ.VirialLJParam
temperature SimulationVirial
temperature SimulationVirialOverlap2
temperature SingleAssociationSiteFluid.VirialAssociatingFluidParam
temperature SingleAssociationSiteFluid2.VirialAssociatingFluidParam
temperature SingleAssociationSiteFluid2Pt.VirialAssociatingFluidParam
temperature SingleAssociationSiteFluid3Pt.VirialAssociatingFluidParam
temperature SingleAssociationSiteFluid4Points.VirialAssociatingFluidParam
temperature SingleAssociationSiteFluid4Pt.VirialAssociatingFluidParam
temperature SingleAssociationSiteFluidGraph.VirialAssociatingFluidParam
temperature TestLJAssociationMC3D_NPT.VirialAssociatingFluidParam
temperature Virial2CLJmuQ.Virial2CLJQParam
temperature Virial2CLJQ.Virial2CLJQParam
temperature Virial7SiteRigidSF6.VirialSF6Param
temperature VirialAceticAcid.VirialParam
temperature VirialAceticAcidFlex.VirialParam
temperature VirialAlkane.VirialSiepmannSpheresParam
temperature VirialAlkaneEHTest.VirialParam
temperature VirialAlkaneFlex.VirialSiepmannSpheresParam
temperature VirialAlkaneFull.VirialSiepmannSpheresParam
temperature VirialAlkaneMix_Kong.VirialAlkaneMixParam
temperature VirialAlkaneMix.VirialAlkaneMixParam
temperature VirialAlkaneMix2_Kong.VirialAlkaneMixParam
temperature VirialAlkaneMix2.VirialAlkaneMixParam
temperature VirialAlkaneSKS.VirialSiepmannSpheresParam
temperature VirialAnthracene464.VirialAnthracene545Param
temperature VirialAnthracene545.VirialAnthracene545Param
temperature VirialAnthraceneTraPPE.VirialAnthraceneTraPPEParam
temperature VirialAssociatingFluid.VirialAssociatingFluidParam
temperature VirialAssociatingFluid4points.VirialAssociatingFluidParam
temperature VirialB3C1HSDipole.VirialParam
temperature VirialB3C2HSDipole.VirialParam
temperature VirialCH4AlkaneEHMix.VirialMixParam
temperature VirialCO2.VirialCO2Param
temperature VirialCO2AlkaneEHMix.VirialMixParam
temperature VirialCO2AlkaneUAMix.VirialMixParam
temperature VirialCO2anthracene464.VirialCO2anthracene545Param
temperature VirialCO2anthracene545.VirialCO2anthracene545Param
temperature VirialCO2AnthraceneTraPPE.VirialCO2AnthraceneTraPPEParam
temperature VirialCO2CH4Mix.VirialMixParam
temperature VirialCO2CH4UAMix.VirialMixParam
temperature VirialCO2CH4UAMixWheatley.VirialMixParam
temperature VirialCO2H2OGCPM.VirialParam
temperature VirialCO2H2OGCPMX.VirialParam
temperature VirialCO2H2OSC.VirialCO2SCParam
temperature VirialCO2LJQ.VirialCO2LJQParam
temperature VirialCO2N2Mix.VirialMixParam
temperature VirialCO2NaphthaleneLJQ.VirialCO2NaphthaleneLJQParam
temperature VirialCO2NaphthaleneTraPPE.VirialCO2TraPPEParam
temperature VirialCO2PI.VirialH2PIParam
temperature VirialCO2SKSMix.VirialCO2Param
temperature VirialCO2TraPPE.VirialCO2TraPPEParam
temperature VirialCPSHeliumNonAdditive.VirialParam
temperature VirialCPSHeliumNonAdditiveClassical_Correction.VirialParam
temperature VirialCPSHeliumNonAdditiveClassical.VirialParam
temperature VirialEmulNonAdditive.VirialParam
temperature VirialExternalFieldConfinedOverlap.VirialExternalFieldParam
temperature VirialExternalFieldConfinedOverlapRho.VirialExternalFieldParam
temperature VirialExternalFieldConfinedOverlapSW.VirialExternalFieldParam
temperature VirialExternalFieldOverlapRho.VirialExternalFieldParam
temperature VirialGCPM.VirialGCPMParam
temperature VirialH2OGCPMD.VirialParam
temperature VirialH2PI.VirialH2PIParam
temperature VirialH2PIBoltzmann.VirialHePIParam
temperature VirialH2PIXC.VirialHePIParam
temperature VirialH2PYCorrection.VirialH2PYCParam
temperature VirialHardAssociationCone.VirialLJParam
temperature VirialHardAssociationConeDoubleSites.VirialLJParam
temperature VirialHeD.VirialParam
temperature VirialHeNonAdditive.VirialParam
temperature VirialHeNonAdditiveD.VirialParam
temperature VirialHeNonAdditiveWheatley.VirialParam
temperature VirialHePCKLJS.VirialParam
temperature VirialHePCKLJSCHNCCorrection.VirialLJParam
temperature VirialHePCKLJSPYCorrection.VirialLJParam
temperature VirialHePCKLJSTempDeriv.VirialParam
temperature VirialHePI_PotentialCorrection.VirialHePIParam
temperature VirialHePI.VirialHePIParam
temperature VirialHePISysErr.VirialHePIParam
temperature VirialHePIXC.VirialHePIParam
temperature VirialHePIXCEven.VirialHePIParam
temperature VirialHePIXCOdd.VirialHePIParam
temperature VirialHePYCorrection.VirialHePYCParam
temperature VirialHeSC.VirialHePYCParam
temperature VirialHSOrC.VirialLJrParam
temperature VirialLJ.VirialLJParam
temperature VirialLJBridge.VirialLJParam
temperature VirialLJCHNCCorrection.VirialLJParam
temperature VirialLJD.VirialLJParam
temperature VirialLJDU.VirialLJParam
temperature VirialLJMultiOverlap.VirialMixParam
temperature VirialLJOrC.VirialLJrParam
temperature VirialLJOrICPYC.VirialLJrParam
temperature VirialLJPT.VirialLJParam
temperature VirialLJPYCorrection.VirialLJParam
temperature VirialMethaneEH.VirialMethaneParam
temperature VirialN2AlkaneEHMix.VirialMixParam
temperature VirialN2AlkaneUAMix.VirialMixParam
temperature VirialN2AlkaneUARigid.VirialMixParam
temperature VirialN2CH4Mix.VirialMixParam
temperature VirialN2CH4UAMix.VirialMixParam
temperature VirialN2TraPPE.VirialN2Param
temperature VirialNaphthaleneTraPPE.VirialNaphthaleneTraPPEParam
temperature VirialPh464.VirialPh3site464Param
temperature VirialPh545.VirialPh3site545Param
temperature VirialPhenanthreneTraPPE.VirialPhenanthreneTraPPEParam
temperature VirialRowleyAlcohol.VirialParam
temperature VirialSF6LJAlkaneUAMix.VirialMixParam
temperature VirialSW.VirialSWParam
temperature VirialTraPPE.VirialParam
temperature VirialTraPPEAlcohol.VirialParam
temperature Token
temperature() CGS
temperature() LJ
temperature() MKS
temperature() UnitSystem.Sim
temperature() UnitSystem
Temperature etomica.units.dimensions
The temperature dimension.
TEMPERATURE EnumPotentialParamDescription
temperature0 LJNVT.LJMCParams
temperature1 DCVGCMD
temperature2 DCVGCMD
temperatureAverage HSMD2D_noNbr
temperatureDisplayTextBox PistonCylinderGraphic
temperatureHistory HSMD2D_noNbr
temperatureK CH4NVT.Param
temperatureK SimGCPMWaterMCNVT.GCPMWaterMCParam
temperatureK TIP4P_NVT.Param
temperatureK VLESim.GEMCParams
temperatureK LJMC3DDimer.SimParams
temperatureK VirialB2WaterTIP4P_DHS_difference.VirialParam
temperatureK VirialB3C1TIP4Pwater.VirialParam
temperatureK VirialB3C2TIP4Pwater.VirialParam
temperatureK VirialH2O.VirialH2OParam
temperatureK VirialH2PISimple.VirialH2PISimpleParam
temperatureK VirialN2.VirialN2Param
temperatureK VirialN2PI.VirialN2Param
temperatureK VirialO2.VirialO2Param
temperatureK VirialO2PI.VirialO2Param
temperatureMelt GlassClustering.SimParams
temperatureMelt GlassProd.SimParams
temperaturePanel DeviceThermoSlider
temperaturePump HSMD2D_noNbr
TemperatureSink() AccumulatorPTensor.TemperatureSink
temperatureSlider DeviceThermoSlider
temperatureVec IntegratorMD
tempImage BoundaryRectangularPeriodic
tempImage BoundaryRectangularPore
tempImage BoundaryRectangularSlit
template2 VirialEmulNonAdditive.VirialParam
template3 VirialEmulNonAdditive.VirialParam
templateName PotentialEmul
tempOrientA FindPairMoleculeIndex
tempOrientA FindPairMoleculeIndexBetaN2
tempOrientation IntegratorRigidIterative
tempOrientation IntegratorRigidMatrixIterative
tempOrientB FindPairMoleculeIndex
tempOrientB FindPairMoleculeIndexBetaN2
tempQuat IntegratorVelocityVerletQuaternion
tempRotationTensor IntegratorRigidIterative
tempSet B3ForSphericallySymmetricU.DampingParams
tempSlider AdsorptionGraphic
tempSlider CatalysisGraphic
tempSlider InsertionGraphic
tempSlider MuGraphic
tempSlider NucleationGraphic
tempSlider ReverseOsmosisGraphic
tempSlider ReverseOsmosisWaterGraphic
tempSlider SwmdGraphic
tempTens BoxInflateDeformable
tempTensInv BoxInflateDeformable
tempTensorkk EwaldSummation
tempU MCMoveMoleculeCoupledInitPert
tempVec FindPairMoleculeIndex
tempVec FindPairMoleculeIndexBetaN2
tempX HistoryScrolling
tempY HistoryScrolling
tensor CoordinateDefinitionNitrogen
tensor CoordinateDefinitionNitrogenSuperBox
tensor MCMoveRotateMolecule3DConstraint
tensor MCMoveRotateMolecule3DFixedAngle
tensor TestRotationVector
Tensor etomica.space
Interface for a second-order tensor.
Tensor1D etomica.space1d
Implementation of a tensor for a 1-dimensional space.
Tensor1D() Tensor1D
Default constructor sets tensor element to zero.
Tensor1D(double) Tensor1D
Tensor2D etomica.space2d
Implementation of a tensor for a 2-dimensional space.
Tensor2D() Tensor2D
Default constructor sets all tensor elements to zero.
Tensor2D(double[][]) Tensor2D
Constructs tensor with elements set by the given array.
Tensor3D etomica.space3d
Tensor3D() Tensor3D
Default constructor sets all elements to zero.
Tensor3D(double[][]) Tensor3D
Constructs tensor with elements set by the given array.
TensorND etomica.spaceNd
Implementation of the 2nd-rank tensor class for arbitrary dimension.
TensorND(double[][]) TensorND
Constructs and initializes tensor to the values given in an array.
TensorND(int) TensorND
Constructs tensor with specified dimension
tensorTrans CalcAnalytical2ndDerivativeNitrogen
tensorWork P2Nitrogen
TERA Prefix
test PotentialCuLREP
test(IAtom) AtomTest
Returns true if atom passes the test.
test(IAtom) ConfigFromFileLAMMPS.AtomTestDeviation
test(IAtom) LatticePlane
test(IAtom) AtomTestChainLength
test(IAtom) AtomTestLiquid
test(IAtom) AtomTestLiquidAtomic
test(IAtom) AtomTestDeviation
test(IAtom) AtomTestRandom
test(IAtom) AtomTestChainLength
TestAceticAcidMC3D_NPT etomica.association.AceticAcid
OPLS Acetic Acid Monte Carlo NPT simulation in 3D.
TestAceticAcidMC3D_NPT(int, double, double, double, long) TestAceticAcidMC3D_NPT
TestAceticAcidMC3D_NPT.AceticAcidMCParam etomica.association.AceticAcid
testBit(int) Bitmap
testBit(int) BitmapOfLong
TIME = O(1).
testBit(int) BitmapOfLongVector
TestEwaldTIP4PWater etomica.models.water
testflag1 Token
testflag2 Token
testflag3 Token
testflag4 Token
TestHSMD3D etomica.tests
Simple hard-sphere molecular dynamics simulation in 3D.
TestHSMD3D(Space, int, Configuration) TestHSMD3D
TestHSMD3D.SimParams etomica.tests
TestIGAssociationMC3D_NPT_DoubleSites etomica.association
Simple ideal gas + S-W Association Monte Carlo NPT simulation in 3D.
TestIGAssociationMC3D_NPT_DoubleSites(int, double, double, double, double, double, int, boolean, long) TestIGAssociationMC3D_NPT_DoubleSites
TestIGAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam etomica.association
TestLammpsLJ etomica.tests
Simulation that attempts to replicate a LAMMPS benchmark.
TestLammpsLJ() TestLammpsLJ
TestLJAssociationMC3D_NPT etomica.association
Simple Lennard-Jones + S-W Association Monte Carlo NPT simulation in 3D.
TestLJAssociationMC3D_NPT etomica.virial.simulations
Simple Lennard-Jones + S-W Association Monte Carlo NPT simulation in 3D.
TestLJAssociationMC3D_NPT(int, double, double, double, double, long) TestLJAssociationMC3D_NPT
TestLJAssociationMC3D_NPT(int, double, double, double, double, long) TestLJAssociationMC3D_NPT
TestLJAssociationMC3D_NPT_DoubleSites etomica.association
Simple Lennard-Jones + S-W Association Monte Carlo NPT simulation in 3D.
TestLJAssociationMC3D_NPT_DoubleSites(int, double, double, double, double, double, int, boolean, long) TestLJAssociationMC3D_NPT_DoubleSites
TestLJAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam etomica.association
TestLJAssociationMC3D_NPT.VirialAssociatingFluidParam etomica.association
TestLJAssociationMC3D_NPT.VirialAssociatingFluidParam etomica.virial.simulations
TestLJAssociationMC3D_NVTOld etomica.association
Simple Lennard-Jones + S-W Association Monte Carlo NPT simulation in 3D.
TestLJAssociationMC3D_NVTOld(int, double, double, double, double, long) TestLJAssociationMC3D_NVTOld
TestLJAssociationMC3D_NVTOld.VirialAssociatingFluidParam etomica.association
TestLJGCMC3D etomica.tests
Grand Canonical Lennard-Jones Monte Carlo simulation in 3D.
TestLJGCMC3D(int, int, Configuration) TestLJGCMC3D
TestLJGCMC3D.SimParams etomica.tests
TestLJMC3D etomica.tests
Simple Lennard-Jones Monte Carlo simulation in 3D.
TestLJMC3D(int, Configuration) TestLJMC3D
TestLJMC3D.SimParams etomica.tests
TestLJMD3D etomica.tests
Simple Lennard-Jones molecular dynamics simulation in 3D
TestLJMD3D(int, Configuration) TestLJMD3D
TestLJMD3D.SimParams etomica.tests
testMolecule MeterWidomCavity
testMolecule DataSourcePositionedBoltzmannFactor
testMolecule MCMoveInsertDelete
testMoleculeIndex MyMCMove
testMoleculeIndex MyMCMove
testMoleculeIndex MyMCMove
testOrthoCurvature(Vector[], Vector[]) IntegratorDimerRT
Checks the curvature value at dimer orientation along a vector orthogonal to
lowest curvature mode's (lcm) vector with the lcm's unit vector.
testPair(Graph, byte, byte, List) FFTDecomposition
testPair(Graph, byte, byte, List<Integer>) IsFFT
TestRotationVector etomica.models.nitrogen
TestRotationVector() TestRotationVector
TestSWChain etomica.tests
Simple square-well chain simulation.
TestSWChain(Space, int, double, Configuration) TestSWChain
TestSWChain.SimParams etomica.tests
testTransformVector(Vector) BoundaryDeformablePeriodic
We test the given vector (v) to see if 0.5*v would be transformed by any
of our existing transformVectors.
tetherBox ReverseOsmosisGraphic
tetherBox ReverseOsmosisWaterGraphic
tetraNum MeterDihedralAngle
textAreaForBonds MyApplet
tExternal MeterCavityMapped
tExternal MeterPairedFraction
tExternal MeterRDFMapped
textField DeviceBox
Object for displaying the value as a text field
textField DeviceSlider
To show the values of slider
TextFormat org.jmol.util
TextFormat() TextFormat
thermalButtons DeviceThermoSlider
thermometer DCVGCMD
thermometer ChainEquilibriumSim
thermometer DCVGCMD
thermometer PistonCylinderGraphic
thermometer ReactionEquilibrium
thermometer SelfAssemblySim
thermostat IntegratorMD
thermostatActions IntegratorHardMDMC
thermostatCount IntegratorMD
thermostatInterval SimFe.LjMC3DParams
thermostatInterval IntegratorMD
thermostatNoDrift IntegratorMD
thermostatting IntegratorMD
theta EnumPotentialParamDescription
theta HSDimerNPT
theta P2QChemInterpolated
theta MCMoveClusterRotateMoleculeMulti
theta Token
THETA IntegratorDimerMin
THETA IntegratorDimerRT
theta0 MeterMeanField
thetaDot MeterMeanField
thetaFrac HSDimerNPT.HSMD3DParameters
thetaFrac MCMoveVolumeSolidNPTMolecularOriented
thetaSlider SamGraphic
THETAstar IntegratorDimerMin
THETAstar IntegratorDimerRT
THETAstarstar IntegratorDimerRT
thirdAxis BiasVolume2SiteAceticAcid
thirdAxis BiasVolumeAceticAcid
thirdterm PotentialCalculationMappedRdf
thisBox(Box) Debug
Checks whether the given box is of debugging interest
THREE_BODY P2WaterSzalewicz.Component
threej(int, int, int, int, int, int) P2O2Bartolomei
threesqrt3a ConformationAnthraceneTraPPE
threesqrt3a ConformationPhenanthreneTraPPE
threshold ConfigFromFileLAMMPS.AtomTestDeviation
thresholdS ConfigFromFileLAMMPS.ConfigFromFileLAMMPSParam
ti P2CO2H2OWheatley.P2CO2H2OSCTI
TIFF DestinationType
TIFF_CODE DestinationType
TIFF_EXTENSION DestinationType
TIFF_STR DestinationType
Tij PNCO2GCPM
Tij PNWaterGCPM
Tij PNWaterGCPMReactionField
tilt AkimaSplineSmootherApp.PlotAction
tilt AkimaSplineSmootherDyApp.PlotAction
time Biconnected
time() CGS
time() LJ
time() MKS
time() UnitSystem.Sim
time() UnitSystem
Time etomica.units.dimensions
Dimension for all units of time.
timeBD ClusterWheatleySoft
timeBD ClusterWheatleySoftDerivatives
TIMEDBALL G3DSys
TimeOptionHandler() Main.TimeOptionHandler
timer DisplayTimer
times(Complex) Complex
Complex multiplication (doesn't change this Complex number).
times(Rational) Rational
Returns a new Rational instance, which is the result of multiplying this
Rational by the given Rational.
timestep PolydisperseHS.HSPolyParam
timeStep SimFe.LjMC3DParams
timeStep IntegratorMD
timlim P2WaterPotentialsJankowski
Tin etomica.chem.elements
Class for the Tin element.
Tin(String) Tin
Tin(String, double) Tin
tInternal MeterCavityMapped
tInternal MeterPairedFraction
tInternal MeterRDFMapped
TIP4P_NVT etomica.dielectric
Canonical ensemble Monte Carlo simulation (NVT)
dielectric constant (epsilon)
TIP4P water
TIP4P_NVT(Space, int, double, double, double, double) TIP4P_NVT
TIP4P_NVT.DipoleSourceTIP4PWater etomica.dielectric
TIP4P_NVT.Param etomica.dielectric
tKelvin P2WaterPotentialsJankowski
tmp MCMoveSwap
tmp MeterCorrelation
tmp MeterGs
tmp DataOverlap
tmp MeterMappedAveraging
tmp MeterMappedAveragingFreeEnergy
tmp MeterMappedAveragingVSum
tmpAtomicTensor3 LatticeSumMolecularCrystal
tmpDrr P2Water4PSoft
tmpDrr1 LatticeSumMolecularCrystal
tmpSecondD P2Water4PSoft
tmpTensor P2Water4PSoft
toArray() AtomArrayList
toArray() AtomPair
toArray() AtomSetSinglet
toArray() GraphList
toArray() MoleculeArrayList
toArray() MoleculePair
toArray() MoleculeSetSinglet
toArray() Tensor
Returns tensor in a new array, writing elements row-wise.
toArray() Vector
toArray() Tensor1D
toArray() Tensor2D
Returns tensor in an array, writing rowwise, i.e., in order xx, xy, yx, yy.
toArray() Tensor3D
Returns tensor in a new array, writing elements row-wise, i.e.: xx, xy, xz, yx, yy, yz, zx, zy, zz;
toArray() TensorND
toArray() ScriptVariable
toArray(T[]) GraphList
toAtomLeafArray() AtomArrayList
toAxisAngle4f() Quaternion
toBytes(int, int) StringXBuilder
simple byte conversion not allowing for unicode.
toCanonical BoxInfo
toE(ClusterDiagram) ClusterOperations
Returns an array of cluster diagrams with all e-bonds representing
the same sum of diagrams as the given f-bond cluster.
toE(ClusterDiagram[]) ClusterOperations
Returns an array of cluster diagrams with all e-bonds representing
the same sum of diagrams as the given f-bond clusters.
toFString(int) Rational
Return a string in floating point format.
toggle() Controller
toggle() DeviceCheckBox
Toggles the state of the button (true to false, false to true).
toggleAction DeviceToggleButton
toggleInPlace(BitSet, BitSet) BitSetUtil
a perhaps curious method:
b is a reference set, perhaps all atoms in a certain molecule a is the
working set, perhaps representing all displayed atoms
For each set bit in b: a) if a is also set, then clear a's bit UNLESS b) if
a is not set, then add to a all set bits of b
Thus, if a equals b --> clear all if a is a subset of b, then --> b if b is
a subset of a, then --> a not b if a only intersects with b, then --> a or
b if a does not intersect with b, then a or b
In "toggle" mode, when you click on any atom of the molecule, you want
either:
(a) all the atoms in the molecule to be displayed if not all are already
displayed, or
(b) the whole molecule to be hidden if all the atoms of the molecule are
already displayed.
toIfactor(int) Factorial
Compute the factorial of the non-negative integer.
toInt() DestinationType
toJSON(String, Object) Escape
tok Token
tokAttr(int, int) Token
tokAttrOr(int, int, int) Token
Token org.jmol.script
Token() Token
Token(int) Token
tokenAnd Token
tokenAND Token
tokenAndFALSE Token
tokenComma Token
tokenConnected Token
tokenExpressionBegin Token
tokenExpressionEnd Token
tokenLeftParen Token
tokenOpIf Token
tokenOr Token
tokenOrTRUE Token
tokenRightParen Token
tol BnPCJSDHe.BnPCJSDHeParams
tol BnPYCHe.BnPYHeParams
tol ClusterCoupledFlippedMultivalue
tol ClusterWheatleyPT
tol ClusterWheatleySoft
tol ClusterWheatleySoftBD
tol ClusterWheatleySoftDerivatives
tol ClusterWheatleySoftDerivativesBD
tol VirialH2OGCPMD.VirialParam
tolerance ActionMinimizeEnergy
tolerance HistogramDiscrete
tolerance FindTransitionTemperature
tolerance MinimizeBetaNitrogenTranslationDOF
tolerance FitTanh
tolerance SoftSphereSolidEOS
tolerance FitTanh
tolf P2WaterPotentialsJankowski
tolr P2WaterPotentialsJankowski
toMoleculeArray() MoleculeArrayList
toNumberString() Bitmap
Returns a string for the integer represented by this bitmap
toNumberString() AbstractBitmap
toolbar SimulationPanel
toolbarPanel SimulationPanel
TOP DisplayBox
TOP DisplayPolytope
TOP Gamma
toPattern() ScientificFormat
TOPEXP Gamma
toPixels() Pixel
toPoint4f() Quaternion
topPadding ConfigurationLammps
toPString() BigIntegerPoly
Print as a polyomial in x.
topWall MeterWallForce
toRational() BigSurd
Convert to a rational value if possible
toRatPoly() BigIntegerPoly
Translate into a RatPoly copy.
toReadable(String, Object) Escape
torque ActionMinimizeEnergy.MyForceTorque
torque IntegratorRigidIterative.MoleculeAgent
torque P2CO2H2OWheatley
torque P2CO2Hellmann
torque P2Nitrogen
torque P2Water3PSoft
torque P2Water4PSoft
torque P2HSDipole
torque P2LJDipole
torque IntegratorVelocityVerletQuaternion.MoleculeAgent
torque P2LJDipole
torque MeterMappedAveragingCorrelation.CorrelationAgent
torque MeterMappedAveragingSum.MoleculeAgent
torque MoleculeAgent
torque P2Spin
torque() ActionMinimizeEnergy.MyForceTorque
torque() Integrator.Torquable
torque() IntegratorRigidIterative.MoleculeAgent
torque() MeterDipoleMoment.ForceTorque
torque() MeterMappedAveragingCorrelation.CorrelationAgent
torque() MeterMappedAveragingSum.MoleculeAgent
torque() MeterMeanField.ForceTorque
torque() MoleculeAgent
torqueAgentManager MeterMeanField
torqueSum MeterDipoleSumSquaredMappedAverage
torqueSum IntegratorRigidIterative
torqueSum IntegratorRigidMatrixIterative
torqueSum ReverseOsmosisWater
torqueSum MeterMappedAveraging
torqueSum MeterMappedAveraging3Pair
torqueSum MeterMappedAveragingCorrelation
torqueSum MeterMappedAveragingFreeEnergy
torqueSum MeterMappedAveragingPair
torqueSum MeterMappedAveragingPairExcess
torqueSum MeterMappedAveragingSum
torqueSum MeterMappedAveragingVSum
torqueSum MeterMappedAveragingVSum3Pair
torqueSum MeterMappedAveragingVSumPair
torqueSum MeterMeanField
torsionPotential MCMoveClusterTorsionAlkaneEH
torsionPotential MCMoveClusterTorsionMulti
toSim(double) CompoundUnit
toSim(double) PrefixedUnit
Takes the given value in class units (considering prefix) and converts it to simulation units.
toSim(double) SimpleUnit
Takes the given value in class units and converts it to simulation units.
toSim(double) LJ.LJUnit
toSim(double) Unit
Takes the given value in class units (considering prefix) and converts it to simulation units.
toSpherical(Vector, double[]) CoordinateConverter
toString() Atom
Returns a string formed by concatenating the signature of this atom
to a string that identifies it as a species master, species agent,
molecule, group, or (leaf) atom.
toString() AtomArrayList
toString() AtomListFromArray
toString() AtomPair
toString() AtomSetSinglet
toString() AtomType
toString() Box
toString() AccumulatorAverage.StatType
toString() AccumulatorAverageBlockless.StatType
toString() AccumulatorAverageBlocklessSlim.StatType
toString() DataAccumulator
toString() DataInfo
Returns "label (dimension)", where label and dimension are the values
held by this instance.
toString() IDataInfo
Returns "label (dimension)", where label and dimension are the values
held by this instance.
toString() DataDouble
Returns a string formed from the dataInfo label and this value.
toString() DataDoubleArray
Returns a string formed from the dataInfo label and the array values.
toString() DataDoubleBDArray
Returns a string formed from the dataInfo label and the array values.
toString() DataGroup
Returns a string formed from the encapsulated data objects.
toString() DataTensor
Returns a string formed from the dataInfo label and the tensor values.
toString() DataVector
Returns a string formed from the dataInfo label and the vector values.
toString() NodePair
toString() GraphList
toString() AbstractBitmap
toString() CoefficientImpl
toString() EdgeImpl
toString() GraphImpl
toString() MetadataImpl
toString() NodeImpl
toString() DestinationType
toString() SVGConverterFileSource
toString() SVGConverterURLSource
toString() Display
Overrides the Object class toString method to have it return the output
of getName
toString() IntegratorHard.Agent
toString() MCMove
toString() MCMoveBox
toString() PrimitiveBcc
toString() PrimitiveCubic
toString() PrimitiveFcc
toString() PrimitiveHexagonal
toString() PrimitiveHexagonal2D
toString() PrimitiveMonoclinic
toString() PrimitiveOrthorhombic
toString() PrimitiveOrthorhombicHexagonal
toString() PrimitiveTetragonal
toString() PrimitiveTriclinic
toString() PrimitiveTrigonal
toString() LatticeCubicBcc
Returns "Bcc".
toString() LatticeCubicDiamond
Returns "Diamond".
toString() LatticeCubicFcc
Returns "Fcc".
toString() LatticeCubicSimple
Returns "Simple cubic".
toString() LatticeHcp
toString() LatticeHcp4
toString() LatticeOrthorhombicHexagonal
Returns "OrthorhombicHexagonal".
toString() Complex
String representation of this Complex number.
toString() DoubleRange
Returns String of the form [min,max]
toString() Point
toString() Polytope
toString() Quaternion
Returns the string representation of the Quaternion q
toString() Rational
toString() EtomicaModuleInfo
toString() NucleationGraphic.ModifierDensity
toString() ModifierPistonPressure
toString() PistonCylinderGraphic.ModifierAtomDiameter
toString() ReverseOsmosisGraphic.ModifierAtomDiameter
toString() ReverseOsmosisWaterGraphic.ModifierAtomDiameter
toString() SwmdGraphic.ModifierAtomDiameter
toString() Molecule
Returns a string formed by concatenating the signature of this atom
to a string that identifies it as a molecule.
toString() MoleculePair
toString() MoleculeSetSinglet
toString() MCMoveRotateMoleculePhiTheta
toString() Vector1D
toString() Tensor2D
toString() Vector2D
toString() Tensor3D
toString() Vector3D
toString() TensorND
toString() VectorND
toString() SpeciesGeneral
toString() SpeciesGeneralMutable
toString() Dimension
toString() Prefix
toString() PrefixedUnit
toString() SimpleUnit
toString() Constants.CompassDirection
toString() TreeLinker
toString() BigComplex
Human-readable Fortran-type display
toString() BigIntegerPoly
Print as a comma-separated list of coefficients.
toString() BigSurd
Return a string in the format (number/denom)*()^(1/2).
toString() BigSurdVec
Return a string in the format (number/denom)*()^(1/2).
toString() Ifactor
Convert to printable format
toString() Rational
Return a string in the format number/denom.
toString() ClusterDiagram
toString() ClusterBonds
toString() IntSet
toString() MCMoveClusterAtomQ
toString() ScriptVariable
toString() Token
toString() AxisAngle4f
Returns a string that contains the values of this AxisAngle4f.
toString() BitSet
Returns a string representation of this bit set.
toString() Matrix3f
Returns a string that contains the values of this Matrix3f.
toString() Matrix4f
Returns a string that contains the values of this Matrix4f.
toString() Quadric
toString() Quaternion
Java axisAngle / plane / Point4f format
all have the format {x y z w}
so we go with that here as well
toString() Rgb16
toString() StringXBuilder
toString() Tuple3f
Returns a string that contains the values of this Tuple3f.
toString() Tuple3i
Returns a string that contains the values of this Tuple3i.
toString() Tuple4f
Returns a string that contains the values of this Tuple4f.
toString(String[]) Main
toString(MathContext) BigComplex
Human-readable Fortran-type display
toStringArray(Object[]) Strings
Takes an array of objects and converts them to an array of strings,
with each string given by the object's toString method.
toSVG(int) Graph
toSVG(int) GraphImpl
tot ClusterICPYC
total Match
total MeterConversion
total ClusterWheatleyHS
total ClusterWheatleyPartitionScreening
total VirialCPSHeliumNonAdditiveClassical.VirialParam
TOTAL CorrelationSelf2.CorrelationType
TOTAL MeterCorrelation.CorrelationType
TOTAL MeterCorrelationSelf.CorrelationType
totalAvg AccumulatorAverageCollapsing
totalBlockAvg AccumulatorAverageCollapsing
totalBlockVarSum AccumulatorAverageCollapsing
totalBondCount DataClusterer
totalCollisions DataProcessorCavity
totalCollisions MeterCavityMapped
totalCollisions MeterContactRatio
totalCollisions MeterRDFMapped
totalCount HistogramDiscrete
totalCount MCMoveClusterAtomHSRing
totalCount MeterVirialBDBin
totalCount MeterVirialBDBinMultiThreaded
totalCount MeterVirialBinMultiThreaded
totalCount MeterVirialEBinMultiThreaded
totalCount VirialHSBinMultiThreaded.SimulationWorker
totalCount VirialSQWBinMultiThreaded.SimulationWorker
totalDeleteCandidateTimes MCMoveInsertDeleteLatticeVacancy
totalDeleteCandidateTimes MCMoveInsertDeleteVacancy
totalMass PNWaterGCPM
totalMass PNWaterGCPMReactionField
totalMolecules MayerFunctionThreeBody
totalNCluster MyApplet
totalSteps DataPumpListenerPow
totalSum HistogramNotSoSimple
totalSumSquare AccumulatorAverageCollapsing
totalVarSum AccumulatorAverageCollapsing
totcount ClusterCoupledFlippedMultivalue
totcount ClusterWheatleyMultibodyDerivatives
totcount ClusterWheatleySoftDerivatives
totCount ClusterWheatleySoft
totNumSteps IntegratorOverlap
totPCore MCMoveClusterAtomChainHSTail
totSqErr AkimaSplineSmoother
totTime IntegratorOverlap
toWriteFile AccumulatorAverageFixedOutputFile
Tprod(Vector, Vector, Vector, double) P2WaterSzalewicz
Calculate the vector V resulting from the action
of the dipole propagator tensor T_ij on U
Ri, Rj - position vectors of molecules i and j, respectively
rij = |Ri - Rj|^(-3)
trace Token
trace() Tensor
trace() Tensor1D
trace() Tensor2D
trace() Tensor3D
trace() TensorND
tracealpha Token
tracker ConformationChain2D
trajectory Token
transcode(SVGConverterSource, File, Transcoder) SVGConverter
Converts the input image to the result image.
transform() FastFourierTransform
Forward Transformation of discrete data sets
transform(IMolecule, double) MCMoveClusterAngleBend
transform(IMolecule, double) MCMoveClusterAngleBendAceticAcid
transform(Vector) Tensor
Applies the given tensor transformation to this vector, replacing its
elements with the transformed values.
transform(Vector) Tensor1D
transform(Vector) Tensor2D
transform(Vector) Tensor3D
transform(Vector) TensorND
transform(Point3f) Matrix4f
Transforms the point parameter with this Matrix4f and places the result
back into point.
transform(Tuple3f) Matrix3f
transform(Vector3f) Quaternion
transform2(Point3f, Point3f) Matrix4f
Transforms the point parameter with this Matrix4f and places the result
into pointOut.
transform2(Tuple3f, Tuple3f) Matrix3f
Transform the vector vec using this Matrix3f and place the result into
vecOut.
transform4(Tuple4f) Matrix4f
Transform the vector vec using this Matrix4f and place the result back into
vec.
transformFunction AccumulatorAverageBootstrap
TransformManager g3dsys.control
transformP2(Tuple3f, Tuple3f) Quaternion
transformPoints(List<Point3f>, Matrix4f, Point3f) Measure
transformPt(Point3f) Quaternion
transformT2(Tuple4f, Tuple4f) Matrix4f
Transform the vector vec using this Matrix4f and place the result into
vecOut.
transformV(Vector3f) Matrix4f
Transforms the normal parameter by this transform and places the value back
into normal.
transformV2(Vector3f, Vector3f) Matrix4f
Transforms the normal parameter by this Matrix4f and places the value into
normalOut.
transformVectors BoundaryDeformablePeriodic
translate Token
translateBy IntegratorRigidIterative
translateBy IntegratorRigidMatrixIterative.BoxImposePbcMolecule
translateBy IntegratorRigidMatrixIterative
translateBy CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
translateBy CalcNumerical2ndDerivativeNitrogen
translateBy CoordinateDefinitionNitrogen
translateBy HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
translateBy HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
translateBy HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
translateBy HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
translateBy HarmonicBetaNitrogenModelPairMoleculeSequentialLS
translateBy HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
translateBy HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
translateBy LatticeSumCrystalMolecular
translateBy MinimizationBetaNitrogenModelLS
translateBy IntegratorVelocityVerletQuaternion
translateDimerQuickmin() IntegratorDimerRT
Moves the dimer along the lowest curvature mode of the energy surface, Quickmin style.
translateMonomerB() IntegratorDimerApproach
translateTo MCMoveVolumeMonoclinicScaled
translateTo MCMoveVolumeSolidNPTMolecular
translateVector MCMoveBondLength
translateVector MCMoveClusterBondLength
translation Token
translation(double[], double[], double[], Box) ConfigurationClusterWertheimGCPM4Pt
translation(double[], double[], Box) ConfigurationClusterWertheimGCPM
translation2Mol(int, double[], Box) ConfigurationClusterAceticAcid
translation3Mol(double[], double[], Box) ConfigurationClusterAceticAcid
translationRandom(IMolecule, Box) ConfigurationClusterAceticAcid
translationTetramer(double[], double[], double[], Box) ConfigurationClusterWertheimGCPMDirectSampling
translationTrimer(double[], double[], Box) ConfigurationClusterWertheimGCPMDirectSampling
translationVector BoxInflateAnisotropic
translationVector IntegratorDimerApproach
translationVector MCMoveDimer
translationVector MCMoveSmer
translationVector MCMoveAtomCoupled
translationVector MCMoveAtom
translationVector MCMoveDimer
translationVector MCMoveDimerRotate
translationVector MCMoveAtomCoupled
translationVector MCMoveAtomCoupledBennet
translationVector MCMoveAtomCoupledUmbrella
translationVector MCMoveAtomSuperBox
translationVector() IntegratorDimerApproach
translationVectors MCMoveWiggleAceticAcid
translationVectors MCMoveWiggle
translationVectors MCMoveClusterAtomDiscrete
translationVectors MCMoveClusterAtomMulti
translationVectors MCMoveClusterMoleculeMulti
translationVectors MCMoveClusterRotateCH3
translationVectors MCMoveClusterWiggleAceticAcid
translationVectors MCMoveClusterWiggleAlkaneEH
translationVectors MCMoveClusterWiggleMulti
translator BoxInflate
translator IntegratorRigidIterative
translator IntegratorRigidMatrixIterative.BoxImposePbcMolecule
translator IntegratorRigidMatrixIterative
translator CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
translator CalcNumerical2ndDerivativeNitrogen
translator IntegratorVelocityVerletQuaternion
translucencyMask Graphics3D
translucent Token
TRANSLUCENT_50 Colix
TRANSLUCENT_MASK Colix
TRANSLUCENT_SCREENED Colix
TRANSLUCENT_SHIFT Colix
translucentCoverOnly Graphics3D
TRANSPARENT Colix
transpose() Tensor
Performs a transpose operation on this tensor, replacing each element ab by its counterpart element ba
transpose() Tensor1D
transpose() Tensor2D
transpose() Tensor3D
transpose() TensorND
transpose() Matrix3f
Sets the value of this matrix to its transpose.
transpose() Matrix4f
Sets the value of this matrix to its transpose.
transposed DisplayTable
transposeM(Matrix3f) Matrix3f
Sets the value of this matrix to the transpose of the argument matrix
TraPPEParams(Space, VirialTraPPE.ChemForm) VirialTraPPE.TraPPEParams
tRatio MeterVirialBDBin
tRatio MeterVirialBDBinMultiThreaded
tRatio MeterVirialBinMultiThreaded
tRatio MeterVirialEBinMultiThreaded
tRatio VirialHSBinMultiThreaded.SimulationWorker
tRatio VirialSQWBinMultiRecalcW.VirialHSParam
tRatio VirialSQWBinMultiThreaded.SimulationWorker
tRatio VirialSQWRecalcSmallMem.VirialHSParam
Traversal etomica.graph.traversal
This interface generalizes algorithms that traverse the nodes of a graph.
TraversalVisitor etomica.graph.traversal
traverseAll(Graph, TraversalVisitor) AbstractTraversal
The only reason to override this method is to change the node choice before
traversing each component, or to traverse more complex components such as
biconnected, K-connected, etc.
traverseAll(Graph, TraversalVisitor) BiconectedNodalPoint
A variation of BCTraversal that only traverses connected components starting with
field nodes.
traverseAll(Graph, TraversalVisitor) Biconnected
traverseAll(Graph, TraversalVisitor) Traversal
Traverses all components of the graph, starting at an arbitrary node for each
component, and returns the total number of components traversed.
traverseBCC(byte, Graph, boolean) Biconnected
traverseComponent(byte, Graph) AbstractTraversal
traverseComponent(byte, Graph) Biconnected
traverseComponent(byte, Graph) BreadthFirst
traverseComponent(byte, Graph) DepthFirst
traverseComponent(byte, Graph, TraversalVisitor) AbstractTraversal
There should be no reason to override this method.
traverseComponent(byte, Graph, TraversalVisitor) Traversal
Traverses a single component of the graph starting at the designated node.
TREE VirialPolymerOverlapMC.VirialHSParam
TREE VirialPolymerOverlapWithMD.VirialHSParam
TREE VirialPolymerOverlapWithMDB3.VirialHSParam
TREE VirialHS.VirialHSParam
TREE VirialHSBinMultiThreaded.VirialHSBinParam
TREE VirialHSMixture.VirialHSParam
TREE VirialPolyhedra.VirialHSParam
TREE VirialPolyhedra2.VirialHSParam
TREE VirialSWWE.VirialSWWEParam
TREE_CHAIN VirialHSBinMultiThreaded.VirialHSBinParam
TREE_CHAIN_RING VirialHSBinMultiThreaded.VirialHSBinParam
treeFrac VirialSWWE.VirialSWWEParam
TreeLinker etomica.util
Linker used in the binary tree TreeList.
TreeLinker(Object) TreeLinker
Constructor throws exception if given atom is null.
TreeList etomica.util
TreeList is a generic binary tree structure made up of TreeLinkers.
TreeList() TreeList
trialCount MCMoveClusterRotateMolecule3D
trialNotify() BoxCluster
Inform the box that a trial move has been made so it can update
the coordinate pairs.
trialP AkimaSplineSmoother
Triangle g3dsys.images
Class for drawing triangles (possibly making up a polygon)
Triangle(G3DSys, short, Point3f, Point3f, Point3f) Triangle
TriangleData org.jmol.util
TriangleData() TriangleData
triangles Token
triangleTable2 TriangleData
trim Token
trim(String, String) TextFormat
trimerPotential MCMoveSmer
trimerPotential MCMoveSmerRotate
trimToSize() AtomArrayList
trimToSize() MoleculeArrayList
tripletDone PotentialCommonAtomic
tripletDone PotentialGroup3PI
tripletId(int, int, int, int) VirialDiagrams
Returns the triplet ID for the given indices (id0, id1, id2) and given
number of molecules (n).
tripletId(int, int, int, int) VirialDiagramsPT
Returns the triplet ID for the given indices (id0, id1, id2) and given
number of molecules (n).
tripletStart VirialDiagrams
tripletStart VirialDiagramsPT
trueButton() DeviceToggleRadioButtons
trueDataSource DataProcessorBias
trueMultiP VirialDiagrams
trueMultiP VirialDiagramsPT
trueY AkimaSplineSmootherDyApp
trunc() Rational
Remove the fractional part.
trunc(int) BigIntegerPoly
Truncate polynomial degree.
TRUNCATED ParserLAMMPS.Truncation
TruncatedOctahedron etomica.math.geometry
A truncated octahedron is an Archimedean, space-filling polyhedron with 24
vertices, 36 edges, and 14 faces.
TruncatedOctahedron(Space) TruncatedOctahedron
Constructs a truncated octahedron with vertices defined in the embedded
space and with unit edge lengths.
TruncatedOctahedron(Space, double) TruncatedOctahedron
Constructs a truncated octahedron with vertices defined in the embedded
space and with edge lengths equal to the given value.
truncatedPotential Potential0Lrc
truncation CH4NVT.Param
truncation ParserLAMMPS.Options
truncation PotentialGroupSoft
truncationRadius TestIGAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
truncationRadius TestLJAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
truncationRadius NormalModeAnalysisDisplay3D
truncationRadius BoundaryDeformablePeriodic
trycmd Token
TSelement SimpleElementForSimilarSpecies
tStep LJMD.LJMDParams
tStep LjMd3D.LjMd3DParams
tStep SimGlass.GlassParams
tStep SimHSMDVacancy.HSMDVParams
tStepFac LjMd3Dv2y.LjMd3DParams
tt0Tensor P2CO2H2OWheatley.P2CO2H2OSC
tt0Tensor P2CO2Hellmann.P2CO2SC
tt0Tensor P2WaterSzalewicz.P2H2OSC
tt0Tensor P2NitrogenHellmann.P2N2QFH
tt1Tensor P2CO2Hellmann.P2CO2SC
tt1Tensor P2WaterSzalewicz.P2H2OSC
tt1Tensor P2NitrogenHellmann.P2N2QFH
tTag AccumulatorAutocorrelationPTensor
tTag AccumulatorAutocorrelationShearStress
tTag DataSourceAlpha2
tTag DataSourceBlockAvgCor
tTag DataSourceCorrelation
tTag DataSourceF
tTag DataSourceFOld
tTag DataSourceFs
tTag DataSourceMSD
tTag DataSourceMSDcorP
tTag DataSourcePercolation
tTag DataSourcePercolation0
tTag DataSourceQ4
tTag DataSourceStrings
tTag DataSourceVAC
tTag MeterCorrelationSelf
tTag StructureFactorComponentCorrelation
tTmp P2CO2H2OWheatley.P2CO2H2OSCTI
tttprod P2WaterPotentialsJankowski
TTTprod(Vector, Vector, Vector, double) P2WaterPotentialsJankowski
tunable MCMoveStepTracker
Tungsten etomica.chem.elements
Class for the Tungsten element.
Tungsten(String) Tungsten
Tungsten(String, double) Tungsten
tUnit NucleationGraphic
tUnit PistonCylinderGraphic
tUnit SwmdGraphic
Tunit PNCO2GCPM
Tunit PNWaterGCPM
Tunit PNWaterGCPMReactionField
Tuple3f org.jmol.util
A generic 3 element tuple that is represented by single precision floating
point x,y and z coordinates.
Tuple3f() Tuple3f
Tuple3i org.jmol.util
A 3-element tuple represented by signed integer x,y,z coordinates.
Tuple3i() Tuple3i
Constructs and initializes a Tuple3i to (0,0,0).
Tuple4f org.jmol.util
A generic 4 element tuple that is represented by single precision floating
point x,y,z and w coordinates.
Tuple4f() Tuple4f
Constructs and initializes a Tuple4f to (0,0,0,0).
tV2 BoundaryDeformablePeriodic
twicesqrt3ofhalfofthebondlength ConformationNaphthaleneTraPPE
TWO_BODY PNCO2GCPM.Component
TWO_BODY PNGCPM.Component
TWO_BODY P2WaterSzalewicz.Component
TWO_BODY PNWaterGCPM.Component
TWO_PI Constants
tWork P2Nitrogen
twosqrt3a ConformationAnthraceneTraPPE
twosqrt3a ConformationPhenanthreneTraPPE
type Atom
type CorrelationSelf2
type DataSourceF
type DataSourceFOld
type DataSourceFs
type DataSourceMSD
type DataSourceVAC
type GlassGraphic.SFacButtonAction
type MeterCorrelationSelf
type MeterGs
type Token
TYPE EnumPalette
TYPE_EDGE_ANY Metadata
TYPE_NODE_DEFAULT Metadata
TYPE_NODE_FIELD Metadata
TYPE_NODE_ROOT Metadata
type1 MeterRDF
type1 MeterCorrelation
type1 MeterRmin
type1 MeterRminSpecies
type1 MeterBondLength
type2 MeterRDF
type2 MeterCorrelation
type2 MeterRmin
type2 MeterRminSpecies
type2 MeterBondLength
typeA SelfAssemblySim
typeAgentManager IntegratorRigidIterative
typeAgentManager IntegratorRigidMatrixIterative
typeAgentManager IntegratorVelocityVerletQuaternion
typeB1 SelfAssemblySim
typeB2 SelfAssemblySim
typeIndex DataSourcePercolation.ImmFractionByTypeSource
typeManager PNGCPM
typeOf(ScriptVariable) ScriptVariable
types Potential0Lrc
types PotentialGroup.PotentialLinker
types PotentialMaster.PotentialLinker
U
u MinimizationBetaNitrogenModelLS
u TestRotationVector
u CoordinateDefinitionLeaf
u CoordinateDefinitionMolecule
u CoordinateDefinitionMoleculeVolumeFluctuation
u IntegratorHarmonic
u MCMoveHarmonic
u MCMoveHarmonicStep
u(double) P2RepRowley
The energy u.
u(double) P2SquareWellBondingCO
u(double) P2SquareWellSurface
Returns infinity if overlapping, -epsilon if otherwise less than well diameter, or zero if neither.
u(double) P2Cohesion
u(double) P2SquareWellOneSide
Returns infinity if overlapping, -epsilon if otherwise less than well diameter, or zero if neither.
u(double) P2XOrder
u(double) PotentialDepletion
u(double) P1HydrogenMielke
u(double) P1IntraMolecular
u(double) P2Anharmonic
u(double) P2ArgonAziz1993
The energy u.
u(double) P2ArgonSlavicekEtAl2003
The energy u.
u(double) P2ArgonTangAndToennies2003
The energy u.
u(double) P2DiscreteFeynmanHibbs.P2HeEmpericalQuantum
u(double) P2DiscreteFeynmanHibbs
u(double) P2DoubleWell
Returns infinity if overlapping, -epsilon if otherwise less than well diameter, or zero if neither.
u(double) P2Dreiding
harmonic oscillator
u(double) P2EffectiveFeynmanHibbs
u(double) P2Electrostatic
u(double) P2ElectrostaticWithHardCore
u(double) P2Exp6
The energy u
u(double) P2Exp6Buckingham
The energy u
u(double) P2Fene
u(double) P2HardAssociation
Returns -epsilon if less than well diameter, or zero otherwise.
u(double) P2HardAssociationConeDoubleSites
u(double) P2HardAssociationConeFourSites
u(double) P2HardAssociationConeOneSite
u(double) P2HardBond
Returns 0 if the bond is within the required distance, infinity if not.
u(double) P2HardSphere
Interaction energy of the pair.
u(double) P2Harmonic
u(double) P2HC2Yukawa
Energy method.
u(double) P2HePCJS
u(double) P2HePCKLJS.P2HeQFH
u(double) P2HePCKLJS.P2HeTI
u(double) P2HePCKLJS
The energy u.
u(double) P2HeSimplified.P2HeQFH
u(double) P2HeSimplified.P2HeTI
u(double) P2HeSimplified
The energy u.
u(double) P2HydrogenPatkowskiIso
u(double) P2Ideal
Returns zero.
u(double) P2LennardJones
The energy u.
u(double) P2LennardJonesDreiding
The energy u.
u(double) P2LJQ
u(double) P2LJQQ
u(double) P2ModifiedMorse
The energy u.
u(double) P2Morse
The energy u.
u(double) P2O2Bartolomei.P2O2TI
u(double) P2PenetrableBond
Returns 0 if the bond is within the required distance, infinity if not.
u(double) P2PenetrableSphere
Returns epsilon if overlapping, or zero if not.
u(double) P2PenetrableSquareWell
Returns infinity if overlapping, -epsilon if otherwise less than well diameter, or zero if neither.
u(double) P2QChemInterpolated
u(double) P2SoftSphere
The energy u.
u(double) P2SoftSphericalTruncated.P0Lrc
u(double) P2SoftSphericalTruncated
Returns the energy of the wrapped potential if the separation
is less than the cutoff value
u(double) P2SoftSphericalTruncatedForceShifted
u(double) P2SoftSphericalTruncatedShifted
Returns the energy of the wrapped potential if the separation
is less than the cutoff value
u(double) P2SoftTruncated
u(double) P2SquareWell
Returns infinity if overlapping, -epsilon if otherwise less than well diameter, or zero if neither.
u(double) P2SquareWellRobust
Returns infinity if overlapping, -epsilon if otherwise less than well diameter, or zero if neither.
u(double) P2Tether
Returns infinity if separation is greater than tether distance, zero otherwise
u(double) P2WCA
The energy u.
u(double) P2WCAP
The energy u.
u(double) P2Yukawa
Energy method.
u(double) Potential2HardSpherical
The pair energy u(r^2) with no truncation applied.
u(double) Potential2Spherical
The pair energy u(r^2) with no truncation applied.
u(double) P1IntraLambda
U_Con PotentialCalculationMoleculeAgentSumMinusIdealPair
U_Map PotentialCalculationFreeEnergy
U_Map PotentialCalculationMoleculeAgentSumMinusIdealPair
u0 P1IntraLambda
UAlpha(double, double) FindTransitionTemperature
uBeads PotentialGroup3PI
uBeads PotentialGroupPI
UBeta(double, double) FindTransitionTemperature
uBondCorr() EwaldSummation
uccageTickEdges BoxInfo
uCorrect MCMoveMoleculeCoupledSuperBox
uCorrect MCMoveRotateMolecule3DSuperBox
uCorrection(double) P2SoftSphericalTruncated.P0Lrc
Long-range correction to the energy.
UEE PotentialCalculationHeisenberg
UEE PotentialCalculationMoleculeAgentSum
UEE PotentialCalculationMoleculeAgentSumMinusIdealPair
UEE PotentialCalculationMoleculeAgentSumPair
UEE PotentialCalculationPair
UEEnow PotentialCalculationHeisenberg
UEEnow PotentialCalculationMoleculeAgentSum
UEEnow PotentialCalculationMoleculeAgentSumPair
uFac MeterWidomInsertionCorrection
uFcc(double, double) LennardJones
Total ensemble-averaged internal potential energy for the fcc solid.
uFourier() EwaldSummation
uFourier() EwaldSumMolecules
uHarmonicNew MCMoveAtomCoupledUmbrella
uHarmonicOld MCMoveAtomCoupledUmbrella
uijPol ClusterSumPolarizable
uijPol ClusterSumPolarizableWertheimProduct
uijPol ClusterSumPolarizableWertheimProduct4Pt
uijPol ClusterSumPolarizableWertheimProduct4PtFinal
uInt(double) P2RepRowley
Integral of the potential, used to evaluate corrections for potential truncation.
uInt(double) P2Cohesion
uInt(double) P2Anharmonic
Integral used for corrections to potential truncation.
uInt(double) P2ArgonAziz1993
Integral used for corrections to potential truncation.
uInt(double) P2ArgonSlavicekEtAl2003
Integral used for corrections to potential truncation.
uInt(double) P2ArgonTangAndToennies2003
Integral used for corrections to potential truncation.
uInt(double) P2DiscreteFeynmanHibbs.P2HeEmpericalQuantum
uInt(double) P2Dreiding
Integral used for corrections to potential truncation.
uInt(double) P2Electrostatic
uInt(double) P2ElectrostaticWithHardCore
uInt(double) P2Exp6
Integral used for corrections to potential truncation.
uInt(double) P2Exp6Buckingham
Integral used for corrections to potential truncation.
uInt(double) P2Fene
Integral used for corrections to potential truncation.
uInt(double) P2Harmonic
Integral used for corrections to potential truncation.
uInt(double) P2HC2Yukawa
Integral from rC to infinity.
uInt(double) P2HePCJS
Integral used for corrections to potential truncation.
uInt(double) P2HePCKLJS
Integral used for corrections to potential truncation.
uInt(double) P2HeSimplified
Integral used for corrections to potential truncation.
uInt(double) P2HydrogenPatkowskiIso
uInt(double) P2LennardJones
Integral used for corrections to potential truncation.
uInt(double) P2LennardJonesDreiding
Integral used for corrections to potential truncation.
uInt(double) P2LJQQ
uInt(double) P2ModifiedMorse
Integral used for corrections to potential truncation.
uInt(double) P2Morse
Integral used for corrections to potential truncation.
uInt(double) P2QChemInterpolated
Integral used for corrections to potential truncation.
uInt(double) P2SoftSphere
Integral used for corrections to potential truncation.
uInt(double) P2SoftSphericalTruncated
Returns the value of uInt for the wrapped potential.
uInt(double) P2WCA
Returns zero, since there is no long-range correction.
uInt(double) P2Yukawa
Integral from rC to infinity.
uInt(double) Potential2SoftSpherical
Integral of the potential, used to evaluate corrections for potential truncation.
uIntOverQ(double, double, double) SimLattice
uisString(String) Lister
ULat MeterSolidProps
ULat MeterSolidPropsLJ
ulat0 SoftSphereSolidEOS
ulat0 SoftSphereSolidEOSCalculator
uLat0 MCMoveVolumeMonoclinicScaled
Nominal function for lattice energy
uLat0 MCMoveVolumeSolid
Nominal function for lattice energy
uLat0 MCMoveVolumeSolidNPTMolecular
Nominal function for lattice energy
uLat0 MeterDDP
Nominal function for lattice energy
uLat0 MeterDP
Nominal function for lattice energy
uLatFunction MCMoveVolumeMonoclinicScaled
uLatFunction MCMoveVolumeSolid
uLatFunction MCMoveVolumeSolidNPTMolecular
uLatFunction MeterDDP
uLatFunction MeterDP
ulatMeasured MeterBoltzmann
ulatSampled MeterBoltzmann
uLatTruncFunction MCMoveVolumeSolid
ULLMAN_ALGORITHM SearchState
UllmanSearchState etomica.graph.isomorphism
UllmanSearchState(UllmanSearchState) UllmanSearchState
UllmanSearchState(Graph, Graph) UllmanSearchState
umax Plot
umin Plot
una PotentialNonAdditive
Unary etomica.graph.operations
UNARY_OP_EDIF Parser
UNARY_OP_EXP Parser
UNARY_OP_INT Parser
UNARY_OP_ISO Parser
UNARY_OP_NCOPY Parser
UNARY_OP_NDIF Parser
UNARY_OP_PCOPY Parser
UNARY_OP_POWER Parser
UNARY_OP_RELABEL Parser
UNARY_OP_SPLIT Parser
UnaryChain etomica.graph.operations
Facilitates a chain of unary operations.
UnaryChain(Unary, Unary) UnaryChain
UnaryChain.ChainParameters etomica.graph.operations
UnaryOpByteImpl etomica.graph.engine.impl
UnaryOpByteImpl(String, Parser.Expression, byte) UnaryOpByteImpl
UnaryOpByteMapImpl etomica.graph.engine.impl
UnaryOpByteMapImpl(String, Parser.Expression, Map<Byte, Byte>) UnaryOpByteMapImpl
UnaryOpColorImpl etomica.graph.engine.impl
UnaryOpColorImpl(String, Parser.Expression, char) UnaryOpColorImpl
UnaryOpImpl etomica.graph.engine.impl
UnaryOpImpl(String, Parser.Expression) UnaryOpImpl
UnaryOpThreeColorImpl etomica.graph.engine.impl
UnaryOpThreeColorImpl(String, Parser.Expression, char, char, char) UnaryOpThreeColorImpl
UnaryOpTwoByteImpl etomica.graph.engine.impl
UnaryOpTwoByteImpl(String, Parser.Expression, byte, byte) UnaryOpTwoByteImpl
unbond(IAtom, IAtom) P2SquareWellBonded
this function unbonds two atoms
Undefined etomica.units.dimensions
Undefined dimension used for quantities with undefined or unknown dimensions.
undisplayThread EllipseDisplayAction
undo Token
undo() BoxInflate
Reverses the action of the inflation by performing the
action with a scale given the by the reciprocal of the
current scale.
undo() BoxInflateAnisotropic
undo() Undoable
Causes the effect of most recent call to actionPerformed to be reversed.
Undoable etomica.action
Interface for an action that can be "undone", such that its effect
is reversed if the undo() method is invoked immediately after the
actionPerformed().
undomove Token
unescapeBitset(String) Escape
unEscapeBitSetArray(ArrayList<ScriptVariable>, boolean) ScriptVariable
unEscapeBitSetArray(BitSet) ScriptVariable
unescapeMatrix(String) Escape
unescapePoint(String) Escape
unescapePointOrBitsetAsVariable(Object) ScriptVariable
unescapePointOrBitsetOrMatrixOrArray(String) Escape
unescapeStringArray(String) Escape
unescapeUnicode(String) Escape
uNew MCMoveDimer
uNew MCMoveDimerRotate
uNew MCMoveSmer
uNew MCMoveSmerRotate
uNew MCMoveAtomCoupled
uNew MCMoveAtomSwap
uNew MCMoveAtom
uNew MCMoveDimer
uNew MCMoveDimerRotate
uNew MCMoveInsertDelete
uNew MCMoveMolecule
uNew MCMoveVolume
uNew MCMoveMoleculeCoupledInitPert
uNew MCMoveMoleculeCoupledSuperBox
uNew MCMoveSwap
uNew MCMoveMultiHarmonic
uNew MCMoveAtomCoupled
uNew MCMoveAtomCoupledBennet
uNew MCMoveAtomCoupledUmbrella
uNew MCMoveAtomSuperBox
uNew MCMoveMoleculeCoupled
uNew MCMoveVolumeMonoclinicScaled
uNew MCMoveVolumeSolidNPTMolecular
uNew MCMoveSpinFlip
uNew MCMoveClusterAngleBend
uNew MCMoveClusterAngleBendAceticAcid
uNew MCMoveClusterRingPartialRegrow
uNew MCMoveClusterRingScale
uNewPE MCMoveRotateMolecule3DSuperBox
Unfactor etomica.graph.operations
This operation will do the reverse of the Factor operation.
Unfactor() Unfactor
Union etomica.graph.operations
Union() Union
unit Device
unit DisplayTextBox
Physical units associated with the displayed value.
unit() PrefixedUnit
unit() EnumPotentialParamDescription
Unit etomica.units
Interface used to specify the physical units to be used when inputting or
outputting a quantity.
UNIT Ampere
Singleton instance of this unit.
UNIT Angstrom
Singleton instance of this unit
UNIT Bar
Singleton instance of this unit.
UNIT Barye
Singleton instance of this unit.
UNIT BohrRadius
Singleton instance of this unit.
UNIT Calorie
Singleton instance of this unit.
UNIT Candela
Singleton instance of this unit.
UNIT Coulomb
Singleton instance of this unit.
UNIT Count
Singleton instance of this unit
UNIT CubicCentimeter
Singleton instance of this unit.
UNIT CubicMeter
Singleton instance of this unit.
UNIT Dalton
Singleton instance of this unit.
UNIT Debye
Singleton instance of this unit.
UNIT Decimal
Singleton instance of this unit
UNIT Degree
Single instance of this unit.
UNIT Null
Unit for an otherwise unspecified dimensionless quantity.
UNIT Undefined
Unit for a quantity having undefined or unknown units.
UNIT Dyne
Singleton instance of this unit.
UNIT Electron
Singleton instance of this unit.
UNIT ElectronVolt
Singleton instance of this unit.
UNIT Erg
Singleton instance of this unit.
UNIT Gram
Singleton instance of this unit.
UNIT Hartree
Hartree unit of energy, corresponding to the approximate energy of
hydrogen in its ground state.
UNIT Hertz
Singleton instance of this class.
UNIT Joule
Singleton instance of this unit.
UNIT Kelvin
Singleton instance of this unit.
UNIT Liter
Singleton instance of this class.
UNIT Meter
Singleton instance of this unit.
UNIT Mole
Singleton instance of this unit.
UNIT Newton
Singleton instance of this unit.
UNIT Pascal
Singleton instance of this unit.
UNIT Percent
Singleton instance of this unit
UNIT Picosecond
Singleton instance of this unit.
UNIT Poise
Singleton instance of this unit.
UNIT Radian
Singleton instance of this unit.
UNIT Second
Singleton instance of this unit.
UNIT Statcoulomb
Convenience instance of this unit to permit unit to be assigned
without creating a new instance of it each time
UNIT Volt
Singleton instance of this unit.
UNIT Watt
Singleton instance of this unit.
unitAxisVectors JmolConstants
unitcell Token
unitCell() Primitive
Returns a the unit cell specified by this primitive.
unitCell() PrimitiveCubic
Returns a new Square (if primitive is 2D) or Cube (if 3D) with edges
given by the size of the primitive vectors.
unitCell() PrimitiveOrthorhombic
Returns a new Cuboid with edges of length given by the current
values of the primitive vectors.
unitCell() PrimitiveOrthorhombicHexagonal
Returns a new Cuboid with edges of length given by the current
values of the primitive vectors.
unitCell() PrimitiveTetragonal
Returns a new Cuboid with edges given by the lengths of the
primitive vectors.
unitcellcolor Token
unitCubePoints BoxInfo
UnitFilter etomica.units.gui
UnitFilter() UnitFilter
UnitGraphics etomica.units.gui
UnitGraphics() UnitGraphics
unitList DisplayPlot
UnitRatio etomica.units
Class for constructing units forms as ratios of other units.
UnitRatio(Unit, Unit) UnitRatio
Constructs the compound unit using conversion factors and labels from the
constituent units.
UnitRatio(Unit, Unit, String, String) UnitRatio
units DisplayTable
unitSelector() DimensionedDoubleEditor
Returns a combo box that can be used to select the unit.
unitString() Lister
UnitSystem etomica.units.systems
Specifies a system of units.
UnitSystem() UnitSystem
UnitSystem.Sim etomica.units.systems
System of units based on simulation units of Daltons, picoseconds, and Angstroms
unitSystemString() Lister
unitx Token
unitxyz Token
unity Token
unitz Token
UNKNOWN EnumPalette
UNMASK_CHANGEABLE_TRANSLUCENT Colix
unpause() Controller
unrangedPotentials PotentialMasterCellMixed
unsafe() ColloidSim.CriterionNone
unsafe() CriterionTether3
unsafe() CriterionAdapter
Indicates whether the atom has changed (e.g.
unsafe() CriterionAll
Always returns false, indicating that neighbor list never needs updating.
unsafe() CriterionNone
Always returns false, indicating that neighbor list never needs updating.
unsafe() CriterionPositionWall
unsafe() CriterionSimple
unsafe() CriterionAdapterMolecular
Indicates whether the atom has changed (e.g.
unsafe() CriterionAllMolecular
Always returns false, indicating that neighbor list never needs updating.
unsafe() CriterionSimpleMolecular
unsafe() NeighborCriterionMolecular
Indicates whether the molecule has changed (e.g.
unsafe() NeighborCriterion
Indicates whether the atom has changed (e.g.
unscaleAtoms(double) MCMoveVolumeAssociated
unscaleAtoms(double) MCMoveVolumeAssociatedMolecule
unscreenedCount MeterVirialBDBin
unscreenedCount MeterVirialBDBinMultiThreaded.MyData
unscreenedCount MeterVirialBinMultiThreaded.MyData
unscreenedCount MeterVirialEBinMultiThreaded.MyData
unseenNeighbor(byte, byte) AbstractTraversal
unset() ANIntergroupCoupled
unset() ANIntergroupExchange
unset() ANIntragroupExchange
unset() ApiIndexList
Sets iterator to a state where hasNext() returns false.
unset() ApiInnerVariable
Sets the iterator such that hasNext is false.
unset() ApiInterArrayList
Sets iterator such that hasNext is false.
unset() ApiIntergroup
Sets the iterator such that hasNext is false.
unset() ApiIntraArrayList
Sets iterator such that next is null.
unset() ApiIntragroup
unset() AtomIteratorArrayList
unset() AtomIteratorArrayListAdjacent
Puts iterator in a state where hasNext is false.
unset() AtomIteratorArrayListSimple
Puts iterator in state in which hasNext is false.
unset() AtomIteratorNull
unset() AtomIteratorSinglet
Sets iterator to a state where hasNext() returns false.
unset() Atomset3IteratorIndexList
Sets iterator to a state where hasNext() returns false.
unset() Atomset4IteratorIndexList
Sets iterator to a state where hasNext() returns false.
unset() AtomsetIterator
Puts iterator in a state in which hasNext() returns false.
unset() AtomsetIteratorAllLeafAtoms
unset() MCMoveInsertDeleteLatticeVacancy.AtomIteratorBruteForce
unset() MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbr
unset() MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbrCell
unset() RectangularLattice.Iterator
unset() RectangularLatticeNbrIterator
Puts iterator in a state in which hasNext() returns false.
unset() SiteIterator
Puts the iterator in a state such that hasNext is false.
unset() MoleculeIteratorAll
unset() MoleculeIteratorArrayList
unset() MoleculeIteratorArrayListSimple
Puts iterator in state in which hasNext is false.
unset() MoleculeIteratorSinglet
Sets iterator to a state where hasNext() returns false.
unset() MpiInnerFixed
Sets the iterator such that hasNext is false.
unset() MpiInnerVariable
Sets the iterator such that hasNext is false.
unset() MpiInterArrayList
Sets iterator such that hasNext is false.
unset() MpiInterspecies1A
unset() MpiInterspeciesAA
Sets iterator such that hasNext is false.
unset() MpiIntraArrayList
Sets iterator such that next is null.
unset() MpiIntraspecies1A
unset() MpiIntraspeciesAA
Sets iterator such that next is null.
unset() MpiMolecule
Sets iterator to state in which hasNext is false.
unset() Api1ACell
unset() Mpi1ACell
unset() MpiAACell
unset() Api1ASite
unset() PotentialMaster.AtomIterator0
unset() PotentialMaster.MoleculeIterator0
untransform(double[], double[], IFunction) AccumulatorAverageBootstrap
unwrap() MSDCoordWriter.AfterPBC
uOld MCMoveDimer
uOld MCMoveDimerRotate
uOld MCMoveSmer
uOld MCMoveSmerRotate
uOld MCMoveAtomCoupled
uOld MCMoveAtomSwap
uOld MCMoveAtom
uOld MCMoveDimer
uOld MCMoveDimerRotate
uOld MCMoveInsertDelete
uOld MCMoveMolecule
uOld MCMoveVolume
uOld MCMoveMoleculeCoupledInitPert
uOld MCMoveMoleculeCoupledSuperBox
uOld MCMoveSwap
uOld MCMoveMultiHarmonic
uOld MCMoveAtomCoupled
uOld MCMoveAtomCoupledBennet
uOld MCMoveAtomCoupledUmbrella
uOld MCMoveAtomSuperBox
uOld MCMoveHarmonic
uOld MCMoveHarmonicStep
uOld MCMoveMoleculeCoupled
uOld MCMoveSingleMode
uOld MCMoveVolumeMonoclinicScaled
uOld MCMoveVolumeSolidNPTMolecular
uOld MCMoveSpinFlip
uOld MCMoveClusterAngleBend
uOld MCMoveClusterAngleBendAceticAcid
uOld MCMoveClusterRingPartialRegrow
uOld MCMoveClusterRingScale
uOldPE MCMoveRotateMolecule3DSuperBox
UP IteratorDirective.Direction
uPair PotentialCommonAtomic
update() DataSourceFunction
Updates the wrapped Data and DataInfo for change to the xDataSource
update() Primitive
update() PrimitiveBcc
update() PrimitiveCubic
update() PrimitiveFcc
update() PrimitiveGeneral
update() PrimitiveHexagonal.PrimitiveHexagonalReciprocal
update() PrimitiveHexagonal
update() PrimitiveHexagonal2D.PrimitiveHexagonal2DReciprocal
update() PrimitiveHexagonal2D
update() PrimitiveMonoclinic.PrimitiveMonoclinicReciprocal
update() PrimitiveMonoclinic
update() PrimitiveOrthorhombic
update() PrimitiveOrthorhombicHexagonal
update() PrimitiveTetragonal
update() PrimitiveTriclinic
update() PrimitiveTrigonal
update() ClipPlaneEditor
update() LatticeEditor
update() SamGraphic.ModifierWallPosition
update() BoundaryDeformablePeriodic
update(double[][], DataDoubleArray.DataInfoDoubleArray[]) DataSourceIndependentSimple
update(double[], double[]) DataSourcePoints
update(double[], DataDoubleArray.DataInfoDoubleArray) DataSourceIndependentSimple
update(BravaisLattice) CrystalViewer
update(Graphics) Plot
update(Graphics) Grabber.ImagePanel
update(Set<Graph>) Viewer
update(Set<Graph>) ClusterViewer
updateAtom(IAtom) IntegratorHard
updates collision time for a single atom (and any atom that might a
collision with the atom)
updateAtom(IAtom) IntegratorHardPiston
updateAtoms(AtomPair) IntegratorHard
Updates collision times/partners for collider and partner, and
for atoms that were to collide with one of them.
updateBegin() Console
updateBegin() ConsoleUI
updateCell(IAtom) NeighborCellManager
updateConformation(int) Sam
updateCounts(boolean, double) MCMoveStepTracker
updateCounts(boolean, double) MCMoveTracker
Updates statistics regarding the acceptance rate of this move.
updateDataMap() DataSet
This updates the mapping between pseudo DataSinks and indices (used for
getData(int), etc.).
updateDimensions() BoundaryRectangular
updateDimensions() BoundaryRectangularPeriodic
updateDimensions() BoundaryRectangularPore
updateDimensions() BoundaryRectangularSlit
updateDone() Console
updateDone() ConsoleUI
updateDrawType() ImageShell
Updates line-drawing status depending on whether images are
on and the current draw boundary type.
updateEditor() PropertyText
updateF() DataSourceFunction
updateF() ClusterWheatleyPartitionScreening
updateF(BoxCluster) ClusterChainHS
updateF(BoxCluster) ClusterChainSoft
updateF(BoxCluster) ClusterSinglyConnected
updateF(BoxCluster) ClusterSum
updateF(BoxCluster) ClusterSumEF
updateF(BoxCluster) ClusterSumHS
updateF(BoxCluster) ClusterSumMultibody
updateF(BoxCluster) ClusterSumMultibodyShell
updateF(BoxCluster) ClusterSumPolarizableWertheimProduct
updateF(BoxCluster) ClusterSumPolarizableWertheimProduct4Pt
updateF(BoxCluster) ClusterSumPolarizableWertheimProduct4PtFinal
updateF(BoxCluster) ClusterSumShell
updateF(BoxCluster) ClusterWheatleyExtendSW
updateF(BoxCluster) ClusterWheatleyHS.AllSigs
updateF(BoxCluster) ClusterWheatleyHS
updateF(BoxCluster) ClusterWheatleyPartitionScreening
updateF(BoxCluster) ClusterWheatleyPT
updateF(BoxCluster) ClusterWheatleySoft
updateF(BoxCluster) ClusterWheatleySoftBD
updateF(BoxCluster) ClusterWheatleySoftDerivatives
updateF(BoxCluster) ClusterWheatleySoftDerivativesBD
updateF(BoxCluster) ClusterWheatleySoftDerivativesMix
updateF(BoxCluster) ClusterWheatleySoftDerivativesMixBD
updateF(BoxCluster) ClusterWheatleySoftMix
updateF(BoxCluster) ClusterWheatleySoftMixBD
updateF(CoordinatePairLeafSet, AtomPairSet) ClusterTreeEF
updateF(CoordinatePairSet, AtomPairSet) ClusterTree
updateFlowLines() RheologyGraphic
updateIntegrator() DeviceThermoSelector
set the integrator's temperature to the selected value
updateLine(int) DisplayBoxCanvasG3DSys
updateLists() NeighborListManagerMolecular
updateMrLast() IntegratorVerlet
updateNbrsIfNeeded() NeighborListManagerMolecular
Checks whether any atom needs neighbor list updating, and if
one is found, performs neighbor list updates of all atom
neighbor lists.
updateNbrsIfNeeded() NeighborListManager
Checks whether any atom needs neighbor list updating, and if
one is found, performs neighbor list updates of all atom
neighbor lists.
updateNeighborList() RectangularLatticeNbrIterator
updateNeighborList() RectangularLatticeNbrIteratorAdjacent
updateNeighborList() RectangularLatticeNbrIteratorSquare
Method called on reset if any calls were previously made
to setLattice, setSite, setRange, or setDirection.
updateNewMoleculePair(int[]) FindPairMoleculeIndex
updateNewMoleculePair(int[]) FindPairMoleculeIndexBetaN2
updatePiston() IntegratorHardPiston
recalculate collision times for all atoms with the wall/piston
updatePlane(int) DisplayBoxCanvasG3DSys
updateProperty(String, PropertyUpdate) PropertiesResource
updateQuaternion() Quaternion
First checks if all the components are numbers.
updateRCut() Sam
updateSize(Primitive, int[]) BoundaryDeformableLattice
updateVertices() Cube
updateVertices() Cuboid
updateVertices() LineSegment
updateVertices() Parallelepiped
Calculated vertices based on current values of edge vectors.
updateVertices() Parallelogram
Calculated vertices based on current values of edge vectors.
updateVertices() Point
Does nothing; the point is the vertex.
updateVertices() PolygonGeneral
updateVertices() PolyhedronGeneral
Calculates vertices from their internal representation, which
for a general polyhedron does nothing because the vertices are
the internal representation.
updateVertices() Polytope
This method should be defined by the subclass to calculate the vertices
in accordance with the internal representation of the polytope.
updateVertices() Rectangle
updateVertices() Square
updateVertices() TruncatedOctahedron
The following defines the vertices that the truncated octahedron will
have, based on Vector3D.
upList IntegratorHard
upList AtomNeighborLists
upList MoleculeNeighborLists
upListNow AtomIteratorArrayList
upListNow MoleculeIteratorArrayList
upListNow MpiIntraspecies1A
UpolAtkins PNCO2GCPM
UpolAtkins PNWaterGCPMReactionField
UPPER_MASK RandomMersenneTwister
uReactCO ReactionManagerCO
uReactCORev ReactionManagerCO
uReal() EwaldSummation
uReal() EwaldSumMolecules
usage() AkimaSplineSmootherMain
USAGE Main
Describes the command line options for the rasterizer
uSCFData P2QChemInterpolated
USE_PALETTE Colix
usearcball Token
useC10 P2HeSimplified
useE PYGenerator.IteratorEF
uSelf() EwaldSummation
uSelf() EwaldSumMolecules
useminimizationthread Token
useMomentum MeterCavityMapped
useMomentum MeterRDFMapped
useNeighborLists HSMDCavity.CavityParam
useNeighborLists HSMDWidom.HSMDParam
useNeighborLists HSMD3D.HSMD3DParam
Flag indicating whether neighbor list is to be used, default = true
usenumberlocalization Token
usePermutations ClusterBonds
usePhongExponent Shader
USER EnumVdw
usercolorscheme Token
useReverseEdges GraphImpl
userStylesheet SVGConverter
User stylesheet
useSurfaceOnly P2Cohesion
useSZ VirialCO2H2OSC.VirialCO2SCParam
useUB TestIGAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
useUB TestLJAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
Ushcats etomica.veos
Ushcats(BetaSource, int) Ushcats
uShift SimLJVacancy
uShift P2LJDipole
UShift(P2SoftSphericalTruncated) PotentialCalculationMappedVirialV.UShift
USine(P2SoftSphericalTruncated, double[][], double) PotentialCalculationMappedVirialV.USine
uSplitter DataSourceMuRoot
uStaticFcc(double) LennardJones
Potential energy per atom of a static fcc lattice with a LJ particle at
each site.
uSums PotentialCalculationSumCutoff
uTriplet PotentialCommonAtomic
uValues MCMoveClusterPolyhedraChain
uValues MCMoveClusterPolyhedraTree
uWeights VirialLJDU.VirialLJParam
uWeights VirialLJPT.VirialLJParam
V
v DropletAtomicGraphic.DataSourceVaporDensity
v NeighborCellManagerMolecular
v NeighborCellManager
v HSNPT.ActionSummer
v HSNPT.ColorSchemeDisplacement
v P2SpheroPolyhedron
v P3HydrogenManzhos.P3HydrogenManzhosMolecular
v IntSet
v(double, double) PotentialCalculationMappedVirialV.UShift
v(double, double) PotentialCalculationMappedVirialV.USine
v(double, double) PotentialCalculationMappedVirialV.VFunc
V IntegratorDimerRT
v0 LjMd3D.DataProcessorReweight
v0 MeterWidomInsertionCorrection
v1 ConformationChainZigZag
v1 ConformationChainZigZag2
v1 P4BondTorsion
v1 P4BondTorsionAlkaneXCCH
v2 ConformationChainZigZag
v2 ConformationChainZigZag2
v2 LjMd3Dv2y.LjMd3DParams
v2 HSNPT.ColorSchemeDisplacement
v2 P4BondTorsion
v2 P4BondTorsionAlkaneXCCH
v2 OrientationFull3D
v3 OrientationFull3D
vac2Sum DataSourceVAC
vacSum DataSourceVAC
valence Token
validate SVGConverter
Validation flag
validateBondList(IAtom, IAtomList, boolean) AssociationHelperBranched
Returns false if invalid bonding is recognized
validateBondList(IAtom, IAtomList, boolean) AssociationHelperDouble
validateBondList(IMolecule, IMoleculeList, boolean) AssociationHelperMolecule
Returns false if invalid bonding is recognized
validateConverterConfig(SVGConverter) Main
Template methods which subclasses may implement to do whatever is
needed.
value NumericFeature
value StringFeature
value DisplayTextBox
Object for displaying the value as a text field
value GlassGraphic.SFacButtonAction
value ClusterChainHS
value ClusterChainSoft
value ClusterCoupledFlipped
value ClusterCoupledFlippedMultivalue
value ClusterCoupledFlippedPartial
value ClusterSinglyConnected
value ClusterSum
value ClusterSumPolarizableWertheimProduct
value ClusterSumPolarizableWertheimProduct4Pt
value ClusterSumPolarizableWertheimProduct4PtFinal
value ClusterWheatleyHS
value ClusterWheatleyPartitionScreening
value ClusterWheatleyPT
value ClusterWheatleySoft
value ClusterWheatleySoftBD
value ClusterWheatleySoftDerivatives
value ClusterWheatleySoftDerivativesBD
value Token
value() Prefix
value() BigValue
Returns the value held by the instance (in true form, not as log, and with sign applied).
value() IBigValue
Returns the value held by the instance (in true form, not as log, and with sign applied).
value() MyBigDecimal
Returns the value held by the instance (in true form, not as log, and with sign applied).
value() IntSet.PropertyBin
value(double[][]) ClusterCollapsedTreeNode
value(double[][]) ClusterDiagramTree
value(double[][]) ClusterTreeNode
value(double[][][]) ClusterBonds
Returns the value of the cluster for the given set of atom pairs at the
given value of beta = 1/kT.
value(double[][][], double[][]) ClusterBondsNonAdditive
value(double, int) B3LJ
value(int, int[]) VirialHSBinMultiThreaded.DooDad
value(Graph) NumFieldNodes
value(Graph) NumRootNodes
value(BoxCluster) ClusterAbstract
Value of this cluster for the given pairset at the specified reciprocal
temperature.
value(BoxCluster) ClusterChainHS
value(BoxCluster) ClusterChainSoft
value(BoxCluster) ClusterConstant
value(BoxCluster) ClusterCoupledFlipped
value(BoxCluster) ClusterCoupledFlippedMultivalue
value(BoxCluster) ClusterCoupledFlippedPartial
value(BoxCluster) ClusterDifference
value(BoxCluster) ClusterExchange
value(BoxCluster) ClusterMultiToSingle
value(BoxCluster) ClusterMultivalueUmbrella
value(BoxCluster) ClusterSinglyConnected
value(BoxCluster) ClusterSum
value(BoxCluster) ClusterSumExternalField
value(BoxCluster) ClusterSumHS
value(BoxCluster) ClusterSumIC
value(BoxCluster) ClusterSumMultibody
value(BoxCluster) ClusterSumNonAdditiveTrimerEnergy
value(BoxCluster) ClusterSumPolarizable
value(BoxCluster) ClusterSumPolarizableWertheimProduct
value(BoxCluster) ClusterSumPolarizableWertheimProduct4Pt
value(BoxCluster) ClusterSumPolarizableWertheimProduct4PtFinal
value(BoxCluster) ClusterSumStickyEF
value(BoxCluster) ClusterTree
value(BoxCluster) ClusterWeightAbs
value(BoxCluster) ClusterWeightSumWall
value(BoxCluster) ClusterWeightUmbrella
value(BoxCluster) ClusterWheatleyExtendSW
value(BoxCluster) ClusterWheatleyHS
value(BoxCluster) ClusterWheatleyMultibodyDerivatives.ClusterRetrievePrimes
value(BoxCluster) ClusterWheatleyMultibodyDerivativesBD.ClusterRetrievePrimes
value(BoxCluster) ClusterWheatleyPartitionScreening
value(BoxCluster) ClusterWheatleyPT.ClusterRetrieveOrders
value(BoxCluster) ClusterWheatleyPT.ClusterRetrievePrimesBD
value(BoxCluster) ClusterWheatleyPT
value(BoxCluster) ClusterWheatleySoft
value(BoxCluster) ClusterWheatleySoftBD
value(BoxCluster) ClusterWheatleySoftDerivatives.ClusterRetrievePrimes
value(BoxCluster) ClusterWheatleySoftDerivatives.ClusterRetrievePrimesBD
value(BoxCluster) ClusterWheatleySoftDerivatives
value(BoxCluster) ClusterWheatleySoftDerivativesBD.ClusterRetrievePrimes
value(BoxCluster) ClusterWheatleySoftDerivativesBD
value(BoxCluster) VirialH2OGCPMD.Clusterfoo
value(List, boolean) CalcFFT
value12(int) ClusterSumIC
valueArray(BoxCluster) ClusterWheatleyExtendSW
valueBD ClusterCoupledFlippedMultivalue
valueBD ClusterWheatleySoftDerivatives
ValueCache etomica.liquidLJ
ValueCache(DataSourceScalar, Integrator) LjMd3D.ValueCache
ValueCache(DataSourceScalar, Integrator) ValueCache
valueChanged(ListSelectionEvent) Wigner3jGUI
Interpreter parser loop.
valueClusters SimulationVirialOverlap2
valueEditor() DimensionedDoubleEditor
valueForSig(long) ClusterWheatleyHS.AllSigs
ValueImpl etomica.graph.engine.impl
ValueImpl(String) ValueImpl
valueIsBD() ClusterCoupledFlippedMultivalue
valueIsBD() ClusterWheatleySoftDerivatives
Returns true if the value most recently returned by value() was computed with BD.
valueOf(int) BigIntegerPoly
Horner scheme to find the function value at the argument x
valueOf(String) P2HardSphereCavity.CollisionType
Returns the enum constant of this type with the specified name.
valueOf(String) DataSourceUniform.LimitType
Returns the enum constant of this type with the specified name.
valueOf(String) DeviceBox.LabelType
Returns the enum constant of this type with the specified name.
valueOf(String) DisplayTextBox.LabelType
Returns the enum constant of this type with the specified name.
valueOf(String) IntegratorMD.ThermostatType
Returns the enum constant of this type with the specified name.
valueOf(String) P2CO2Hellmann.Parameters
Returns the enum constant of this type with the specified name.
valueOf(String) PNCO2GCPM.Component
Returns the enum constant of this type with the specified name.
valueOf(String) PNGCPM.Component
Returns the enum constant of this type with the specified name.
valueOf(String) P2WaterSzalewicz.Component
Returns the enum constant of this type with the specified name.
valueOf(String) PNWaterGCPM.Component
Returns the enum constant of this type with the specified name.
valueOf(String) ConfigurationStorage.StorageType
Returns the enum constant of this type with the specified name.
valueOf(String) CorrelationSelf2.CorrelationType
Returns the enum constant of this type with the specified name.
valueOf(String) MeterCorrelation.CorrelationType
Returns the enum constant of this type with the specified name.
valueOf(String) MeterCorrelationSelf.CorrelationType
Returns the enum constant of this type with the specified name.
valueOf(String) SimGlass.PotentialChoice
Returns the enum constant of this type with the specified name.
valueOf(String) ParserLAMMPS.Truncation
Returns the enum constant of this type with the specified name.
valueOf(String) IteratorDirective.Direction
Returns the enum constant of this type with the specified name.
valueOf(String) StatusAction.Status
Returns the enum constant of this type with the specified name.
valueOf(String) Prefix
Returns the enum constant of this type with the specified name.
valueOf(String) Constants.CompassDirection
Returns the enum constant of this type with the specified name.
valueOf(String) EnumPotentialParamDescription
Returns the enum constant of this type with the specified name.
valueOf(String) EnumSiteName
Returns the enum constant of this type with the specified name.
valueOf(String) VirialHePI.FlexApproach
Returns the enum constant of this type with the specified name.
valueOf(String) VirialHePI.PotentialChoice
Returns the enum constant of this type with the specified name.
valueOf(String) VirialHePISysErr.FlexApproach
Returns the enum constant of this type with the specified name.
valueOf(String) VirialHSOrC.PotentialChoice
Returns the enum constant of this type with the specified name.
valueOf(String) VirialLJOrC.PotentialChoice
Returns the enum constant of this type with the specified name.
valueOf(String) EnumPalette
Returns the enum constant of this type with the specified name.
valueOf(String) EnumStereoMode
Returns the enum constant of this type with the specified name.
valueOf(String) EnumVdw
Returns the enum constant of this type with the specified name.
valueOf(BigInteger) BigIntegerPoly
Evaluate at some integer argument.
valueOf(Vector<BigInteger>, BigInteger) BigIntegerMath
Evaluate the value of an integer polynomial at some integer argument.
valueProps Wrapper
values P2WaterPotentialsJankowski
values() P2HardSphereCavity.CollisionType
Returns an array containing the constants of this enum type, in
the order they are declared.
values() DataSourceUniform.LimitType
Returns an array containing the constants of this enum type, in
the order they are declared.
values() DeviceBox.LabelType
Returns an array containing the constants of this enum type, in
the order they are declared.
values() DisplayTextBox.LabelType
Returns an array containing the constants of this enum type, in
the order they are declared.
values() IntegratorMD.ThermostatType
Returns an array containing the constants of this enum type, in
the order they are declared.
values() P2CO2Hellmann.Parameters
Returns an array containing the constants of this enum type, in
the order they are declared.
values() PNCO2GCPM.Component
Returns an array containing the constants of this enum type, in
the order they are declared.
values() PNGCPM.Component
Returns an array containing the constants of this enum type, in
the order they are declared.
values() P2WaterSzalewicz.Component
Returns an array containing the constants of this enum type, in
the order they are declared.
values() PNWaterGCPM.Component
Returns an array containing the constants of this enum type, in
the order they are declared.
values() ConfigurationStorage.StorageType
Returns an array containing the constants of this enum type, in
the order they are declared.
values() CorrelationSelf2.CorrelationType
Returns an array containing the constants of this enum type, in
the order they are declared.
values() MeterCorrelation.CorrelationType
Returns an array containing the constants of this enum type, in
the order they are declared.
values() MeterCorrelationSelf.CorrelationType
Returns an array containing the constants of this enum type, in
the order they are declared.
values() SimGlass.PotentialChoice
Returns an array containing the constants of this enum type, in
the order they are declared.
values() ParserLAMMPS.Truncation
Returns an array containing the constants of this enum type, in
the order they are declared.
values() IteratorDirective.Direction
Returns an array containing the constants of this enum type, in
the order they are declared.
values() StatusAction.Status
Returns an array containing the constants of this enum type, in
the order they are declared.
values() Prefix
Returns an array containing the constants of this enum type, in
the order they are declared.
values() IndexMap
values() Constants.CompassDirection
Returns an array containing the constants of this enum type, in
the order they are declared.
values() EnumPotentialParamDescription
Returns an array containing the constants of this enum type, in
the order they are declared.
values() EnumSiteName
Returns an array containing the constants of this enum type, in
the order they are declared.
values() VirialHePI.FlexApproach
Returns an array containing the constants of this enum type, in
the order they are declared.
values() VirialHePI.PotentialChoice
Returns an array containing the constants of this enum type, in
the order they are declared.
values() VirialHePISysErr.FlexApproach
Returns an array containing the constants of this enum type, in
the order they are declared.
values() VirialHSOrC.PotentialChoice
Returns an array containing the constants of this enum type, in
the order they are declared.
values() VirialLJOrC.PotentialChoice
Returns an array containing the constants of this enum type, in
the order they are declared.
values() EnumPalette
Returns an array containing the constants of this enum type, in
the order they are declared.
values() EnumStereoMode
Returns an array containing the constants of this enum type, in
the order they are declared.
values() EnumVdw
Returns an array containing the constants of this enum type, in
the order they are declared.
valueUsingPermutations(double[][][]) ClusterBonds
Returns value obtained by averaging over all unique permutations of the
point indices.
vanderwaals Token
VanderWaals etomica.veos
VanderWaals(double) VanderWaals
VanderWaals(double, int) VanderWaals
vanderwaalsMars Elements
Default table of van der Waals Radii.
vaporColor ColorSchemeLiquidVapor
vaporFccCoexDensities(double) LennardJones
Returns the densities of coexisting (saturated) vapor and fcc phases
(sublimation densities).
vaporFccCoexPressure(double) LennardJones
Returns the saturation pressure for vapor-fcc coexistence.
VARIABLE EnumPalette
VariableImpl etomica.graph.engine.impl
VariableImpl(String) VariableImpl
vBias MCMoveVolume
vBias LjMd3D.DataProcessorReweight
vBias MeterWidomInsertionCorrection
vCO MCMoveTorsionAceticAcid
vCO MCMoveClusterTorsionAceticAcid
vCount ClusterWheatleyPartitionScreening
vCut PotentialCalculationMappedRdf
vCut PotentialCalculationMappedEnergy
vCut PotentialCalculationMappedVirial
vCut PotentialCalculationMappedVirialV
vCut2 PotentialCalculationMappedVirialV.UShift
vCut2 PotentialCalculationMappedVirialV.USine
vDataSource MeterPressureByVolumeChange
vDotGradV MeterMappedAveragingSum.MoleculeAgent
vDotGradV PotentialCalculationVSum
vDotGradV() MeterMappedAveragingSum.MoleculeAgent
VdwPROBE Elements
vE MeterMappedAveragingSum.MoleculeAgent
vE MoleculeAgent
vE PotentialCalculationVSum
vE() MeterMappedAveragingSum.MoleculeAgent
vec Quaternion
vec P3HydrogenManzhos
vector DataSourceAtomDistance
vector ConformationCO2
vector ConformationNitrogen
vector ConformationNitrogenShellModel
vector Conformation7SiteRigidSF6
vector ConformationAnthracene3site
vector ConformationAnthraceneTraPPE
vector ConformationNaphthaleneTraPPE
vector ConformationPh3site
vector ConformationPhenanthreneTraPPE
vector Token
Vector etomica.space
Interface containing vector operations, accessor, and mutator methods.
vector1 MCMoveClusterMoleculeLayerMove
Vector1D etomica.space1d
Implementation of the Vector class for a 1-dimensional space.
Vector1D() Vector1D
Vector1D(double) Vector1D
Vector1D(double[]) Vector1D
Vector1D(Vector1D) Vector1D
vector2 MCMoveClusterMoleculeLayerMove
Vector2D etomica.space2d
Implementation of the Vector class for a 2-dimensional space.
Vector2D() Vector2D
Vector2D(double[]) Vector2D
Vector2D(double, double) Vector2D
Vector2D(Vector2D) Vector2D
Vector3D etomica.space3d
Implementation of the Vector class for a 3-dimensional space.
Vector3D() Vector3D
Vector3D(double[]) Vector3D
Vector3D(double, double, double) Vector3D
Vector3D(Vector3D) Vector3D
Vector3f org.jmol.util
A 3-element vector that is represented by single precision floating point
x,y,z coordinates.
Vector3f() Vector3f
VectorND etomica.spaceNd
Implementation of the Vector class for a 3-dimensional space.
VectorND(double[]) VectorND
VectorND(int) VectorND
VectorProperty etomica.meta.properties
Created by kofke on 7/24/17.
VectorProperty(Object, PropertyDescriptor) VectorProperty
vectorR P2Nitrogen
vectors ConformationChain2D
vectors Quadric
vectors() Primitive
Returns the primitive vectors.
vectorscale Token
VectorSerializer etomica.meta.serializers
VectorSerializer() VectorSerializer
VectorSource(Space) IntegratorMD.VectorSource
vectorsymmetry Token
VectorSystem(double[]) BenchBox.VectorSystem
vEE MeterMappedAveragingSum.MoleculeAgent
vEE MoleculeAgent
vEE PotentialCalculationVSum
vEE() MeterMappedAveragingSum.MoleculeAgent
vEEx MoleculeAgent
vEEx PotentialCalculationMoleculeAgentSum
vEEx PotentialCalculationPair
vEEx() MoleculeAgent
vEEy MoleculeAgent
vEEy PotentialCalculationMoleculeAgentSum
vEEy PotentialCalculationPair
vEEy() MoleculeAgent
vEHS ShapeParser.ShapeData
velocity AtomLeafDynamic
velocity MoleculeOrientedDynamic
Velocity etomica.units.dimensions
Dimension for all units of velocity, Length/Time
VELOCITY_SCALING IntegratorMD.ThermostatType
velocityButton PistonCylinderGraphic
VelocityWriter etomica.polydisperseHS
VelocityWriter(Integrator, Box, String, int) VelocityWriter
VEOS3SW etomica.modules.adsorption
VEOS3SW() VEOS3SW
verbose NewtonMinimization
verbose LJVacancyMin.SimOverlapParam
verbose P3CPSNonAdditiveHe
verbose P3CPSNonAdditiveHeLessSimplified
verbose P3CPSNonAdditiveHeOrig
verbose P3CPSNonAdditiveHeSimplified
verbose BnPCJSDHe.BnPCJSDHeParams
verbose BnPYCHe.BnPYHeParams
version JmolConstants
vertexColixes MeshSurface
vertexCount MeshSurface
vertexCount0 MeshSurface
vertexSets MeshSurface
vertexSource MeshSurface
vertexValues MeshSurface
vertices AtomTypeSpheroPolyhedron
vertices Polytope
These vertices are used in all external representations of the polygon.
vertices ShapeParser.ShapeData
vertices MeshSurface
vEx MoleculeAgent
vEx PotentialCalculationMoleculeAgentSum
vEx PotentialCalculationPair
vEx() MoleculeAgent
vEy MoleculeAgent
vEy PotentialCalculationMoleculeAgentSum
vEy PotentialCalculationPair
vEy() MoleculeAgent
vf PotentialCalculationMappedVirialV
vf AshtonWildingOsmoticVirial.simParams
vf GCRestrictedGibbsHS.simParams
vf GCWidomInsertHS.simParams
VF_ALGORITHM SearchState
VF2_ALGORITHM SearchState
VF2SearchState etomica.graph.isomorphism
VF2SearchState(VF2SearchState) VF2SearchState
VF2SearchState(Graph, Graph) VF2SearchState
VFSearchState etomica.graph.isomorphism
VFSearchState(VFSearchState) VFSearchState
VFSearchState(Graph, Graph) VFSearchState
vH2H2(double, double, double, double) P2HydrogenPatkowski
vH2H2(double, double, double, double) P2HydrogenPatkowskiAtomic
vH2H2(double, double, double, double, double, double) P2HydrogenHinde
vH2H2(double, double, double, double, double, double) P2HydrogenHindeAtomic
vH2H2H2(Vector[]) P3HydrogenManzhos
vhs VirialHSBinMultiThreaded.SimulationWorker
vhs VirialSQWBinMultiThreaded.SimulationWorker
vib IntegratorDimerMin
vib IntegratorDimerRT
vib0 SoftSphereSolidEOS
vib0 SoftSphereSolidEOSCalculator
vibration Token
vibrationperiod Token
vibrationscale Token
vibx Token
vibxyz Token
viby Token
vibz Token
ViewAlertMsgBox etomica.virial.GUI.views
ViewAlertMsgBox(String) ViewAlertMsgBox
ViewAlertMsgBoxSpeciesRemoval etomica.virial.GUI.views
ViewAlertMsgBoxSpeciesRemoval(String) ViewAlertMsgBoxSpeciesRemoval
ViewAlkaneLengthSelection etomica.virial.GUI.views
ViewAlkaneLengthSelection(String) ViewAlkaneLengthSelection
ViewConsoleOutputBox etomica.virial.GUI.views
ViewConsoleOutputBox() ViewConsoleOutputBox
viewer LatticeEditor
Viewer etomica.graph.engine
ViewSimEnvironmentSelection etomica.virial.GUI.views
ViewSimEnvironmentSelection(ModelSimulationEnvironment) ViewSimEnvironmentSelection
ViewSpeciesSelection etomica.virial.GUI.models
ViewSpeciesSelection etomica.virial.GUI.views
ViewSpeciesSelection(ModelSpeciesSelection, ModelSelectedSpecies) ViewSpeciesSelection
ViewSpeciesSelection(ModelSpeciesSelection, ModelSelectedSpecies) ViewSpeciesSelection
virial MeterPU
virial(IAtomList) P1WCAWall
virial(IAtomList) P1LepsHarmonic
virial(IAtomList) P2EAM
virial(IAtomList) PotentialCuLREP
virial(IAtomList) PotentialEAM_LS
virial(IAtomList) PotentialEAM
virial(IAtomList) PotentialEFS
virial(IAtomList) P1ImageHarmonic
virial(IAtomList) P1Wall
virial(IAtomList) Potential2SoftSphericalLSMulti
Virial of the pair as given by the du(double) method
virial(IAtomList) Potential2SoftSphericalLSMultiLat
Virial of the pair as given by the du(double) method
virial(IAtomList) P2CO2H2OWheatley
virial(IAtomList) P2CO2Hellmann
virial(IAtomList) P2WaterSzalewicz
virial(IAtomList) P1WCAPorousWall
virial(IAtomList) P1WCAWall
virial(IAtomList) P1Smash
virial(IAtomList) P2Cohesion
virial(IAtomList) P1Tension
virial(IAtomList) P1Tether
virial(IAtomList) P1Sinusoidal
virial(IAtomList) P1WCAWall
virial(IAtomList) EwaldSummation.P2EwaldReal
virial(IAtomList) EwaldSummation
virial(IAtomList) P1Harmonic
virial(IAtomList) P1HarmonicSite
virial(IAtomList) P1SoftBoundary
virial(IAtomList) P2HardAssociationConeDoubleSites
virial(IAtomList) P2HardAssociationConeFourSites
virial(IAtomList) P2HardAssociationConeOneSite
virial(IAtomList) P2Ideal
Returns zero.
virial(IAtomList) P2LJQ
virial(IAtomList) P2NitrogenHellmann
virial(IAtomList) P2SoftSphericalTruncated.P0Lrc
virial(IAtomList) P2SoftSphericalTruncatedSwitched
virial(IAtomList) P2SoftTruncated
Returns the 2nd derivative (r^2 d^2u/dr^2) of the wrapped potential if the separation
is less than the cutoff value
virial(IAtomList) P3BondAngle
virial(IAtomList) P3BondAngleDreiding
virial(IAtomList) P3CPSNonAdditiveHe
virial(IAtomList) P3CPSNonAdditiveHeLessSimplified
virial(IAtomList) P3CPSNonAdditiveHeOrig
virial(IAtomList) P3CPSNonAdditiveHeSimplified
virial(IAtomList) P4BondTorsion
virial(IAtomList) P4BondTorsionAlkaneXCCH
virial(IAtomList) P4BondTorsionOPLS
virial(IAtomList) P4TorsionDreiding
virial(IAtomList) Potential2SoftSpherical
Virial of the pair as given by the du(double) method
virial(IAtomList) Potential2SoftSphericalLS
Virial of the pair as given by the du(double) method
virial(IAtomList) PotentialSoft
virial(IAtomList) P2Spin
no virial is use here
virial(IMoleculeList) P2Nitrogen
virial(IMoleculeList) P2NitrogenAB
virial(IMoleculeList) P2NitrogenShellModel
virial(IMoleculeList) P2Water3PSoft
virial(IMoleculeList) P2Water4PSoft
virial(IMoleculeList) P22CLJmuQ
virial(IMoleculeList) P2HSDipole
virial(IMoleculeList) P2LJDipole
virial(IMoleculeList) P2MoleculeSoftTruncatedSwitched
virial(IMoleculeList) P2ReactionFieldDipole
virial(IMoleculeList) P2ReactionFieldDipoleTruncated.P0ReactionField
virial(IMoleculeList) P2ReactionFieldDipoleTruncated
virial(IMoleculeList) PotentialGroupSoft
virial(IMoleculeList) PotentialMolecularSoft
virial(IMoleculeList) P2LJDipole
Virial2CLJmuQ etomica.virial.simulations
LJ simulation using Mayer sampling to evaluate cluster integrals
Virial2CLJmuQ() Virial2CLJmuQ
Virial2CLJmuQ.Virial2CLJQParam etomica.virial.simulations
Inner class for parameters
Virial2CLJQ etomica.virial.simulations
LJ simulation using Mayer sampling to evaluate cluster integrals
Virial2CLJQ() Virial2CLJQ
Virial2CLJQ.Virial2CLJQParam etomica.virial.simulations
Inner class for parameters
Virial2CLJQParam() Virial2CLJmuQ.Virial2CLJQParam
Virial2CLJQParam() Virial2CLJQ.Virial2CLJQParam
Virial7SiteRigidSF6 etomica.virial.simulations
Virial coefficients calculation of SF6
7 sites LJ + rigid without Coulombic interaction
Reference: Samios, Molecular force field investigation for sulfur hexafluoride: A computer simulation study
Mayer sampling to evaluate cluster integrals
Virial7SiteRigidSF6() Virial7SiteRigidSF6
Virial7SiteRigidSF6.VirialSF6Param etomica.virial.simulations
Inner class for parameters
VirialAceticAcid etomica.virial.simulations
Mayer-sampling MC simulation for acetic acid using IMPROVED OPLS united-atom model
VirialAceticAcid() VirialAceticAcid
VirialAceticAcid.VirialParam etomica.virial.simulations
Inner class for parameters
VirialAceticAcidFlex etomica.virial.simulations
Mayer-sampling MC simulation for acetic acid using IMPROVED TraPPE-UA model
Flexible correction is included
VirialAceticAcidFlex() VirialAceticAcidFlex
VirialAceticAcidFlex.VirialParam etomica.virial.simulations
Inner class for parameters
VirialAlkane etomica.virial.simulations
Mayer sampling simulation for alkanes using the TraPPE force field.
VirialAlkane() VirialAlkane
VirialAlkane.VirialSiepmannSpheresParam etomica.virial.simulations
Inner class for parameters
VirialAlkaneEHTest etomica.virial.simulations
Mayer sampling simulation for alkanes using the TraPPE-Explicit Hydrogen force field.
VirialAlkaneEHTest() VirialAlkaneEHTest
VirialAlkaneEHTest.VirialParam etomica.virial.simulations
Inner class for parameters
VirialAlkaneFlex etomica.virial.simulations
Mayer sampling simulation for alkanes using the TraPPE force field.
VirialAlkaneFlex() VirialAlkaneFlex
VirialAlkaneFlex.VirialSiepmannSpheresParam etomica.virial.simulations
Inner class for parameters
VirialAlkaneFull etomica.virial.simulations
Mayer sampling simulation for alkanes using the TraPPE-United Atoms force field.
VirialAlkaneFull() VirialAlkaneFull
VirialAlkaneFull.VirialSiepmannSpheresParam etomica.virial.simulations
Inner class for parameters
VirialAlkaneMix etomica.virial.simulations
Mayer sampling simulation for alkanes using the dispersion interaction.
VirialAlkaneMix() VirialAlkaneMix
VirialAlkaneMix_Kong etomica.virial.simulations
VirialAlkaneMix_Kong() VirialAlkaneMix_Kong
VirialAlkaneMix_Kong.VirialAlkaneMixParam etomica.virial.simulations
Inner class for parameters
VirialAlkaneMix.VirialAlkaneMixParam etomica.virial.simulations
Inner class for parameters
VirialAlkaneMix2 etomica.virial.simulations
VirialAlkaneMix2() VirialAlkaneMix2
VirialAlkaneMix2_Kong etomica.virial.simulations
VirialAlkaneMix2_Kong() VirialAlkaneMix2_Kong
VirialAlkaneMix2_Kong.VirialAlkaneMixParam etomica.virial.simulations
Inner class for parameters
VirialAlkaneMix2.VirialAlkaneMixParam etomica.virial.simulations
Inner class for parameters
VirialAlkaneMixParam() VirialAlkaneMix_Kong.VirialAlkaneMixParam
VirialAlkaneMixParam() VirialAlkaneMix.VirialAlkaneMixParam
VirialAlkaneMixParam() VirialAlkaneMix2_Kong.VirialAlkaneMixParam
VirialAlkaneMixParam() VirialAlkaneMix2.VirialAlkaneMixParam
VirialAlkaneSKS etomica.virial.simulations
Mayer sampling simulation for alkanes using the SKS force field.
VirialAlkaneSKS() VirialAlkaneSKS
VirialAlkaneSKS.VirialSiepmannSpheresParam etomica.virial.simulations
Inner class for parameters
VirialAnthracene464 etomica.virial.simulations
Anthracene model , pure
support for CO2/An mixture calculation
3 site model from Iwai, this is 464 model
Mayer sampling to evaluate cluster integrals
VirialAnthracene464() VirialAnthracene464
VirialAnthracene464.VirialAnthracene545Param etomica.virial.simulations
6
Inner class for parameters
VirialAnthracene545 etomica.virial.simulations
Anthracene model , pure
support for CO2/An mixture calculation
3 site model from Iwai this is 545 model
Mayer sampling to evaluate cluster integrals
VirialAnthracene545() VirialAnthracene545
VirialAnthracene545.VirialAnthracene545Param etomica.virial.simulations
6
Inner class for parameters
VirialAnthracene545Param() VirialAnthracene464.VirialAnthracene545Param
VirialAnthracene545Param() VirialAnthracene545.VirialAnthracene545Param
VirialAnthraceneTraPPE etomica.virial.simulations
calculate the virial coefficients of Anthracene at given temperature
united atom TraPPE model, LJ no electrostatic, reference: TraPPE , Siepmann
* Mayer sampling to evaluate cluster integrals
VirialAnthraceneTraPPE() VirialAnthraceneTraPPE
VirialAnthraceneTraPPE.VirialAnthraceneTraPPEParam etomica.virial.simulations
6
Inner class for parameters
VirialAnthraceneTraPPEParam() VirialAnthraceneTraPPE.VirialAnthraceneTraPPEParam
VirialAssociatingFluid etomica.virial.simulations
VirialAssociatingFluid() VirialAssociatingFluid
VirialAssociatingFluid.VirialAssociatingFluidParam etomica.virial.simulations
VirialAssociatingFluid4points etomica.virial.simulations
VirialAssociatingFluid4points() VirialAssociatingFluid4points
VirialAssociatingFluid4points.VirialAssociatingFluidParam etomica.virial.simulations
VirialAssociatingFluidParam() WertheimGCPM3PtEBondDecomp.VirialAssociatingFluidParam
VirialAssociatingFluidParam() WertheimGCPM3PtThreeSite.VirialAssociatingFluidParam
VirialAssociatingFluidParam() WertheimGCPM4PtEBondDecompFinal.VirialAssociatingFluidParam
VirialAssociatingFluidParam() WertheimGCPM4PtThreeSite.VirialAssociatingFluidParam
VirialAssociatingFluidParam() WertheimGCPM4PtThreeSiteEDecompDirectSampling.VirialAssociatingFluidParam
VirialAssociatingFluidParam() TestIGAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
VirialAssociatingFluidParam() TestLJAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
VirialAssociatingFluidParam() TestLJAssociationMC3D_NPT.VirialAssociatingFluidParam
VirialAssociatingFluidParam() TestLJAssociationMC3D_NVTOld.VirialAssociatingFluidParam
VirialAssociatingFluidParam() DoubleAssociationSitesFluid2Pt.VirialAssociatingFluidParam
VirialAssociatingFluidParam() DoubleAssociationSitesFluid3Pt.VirialAssociatingFluidParam
VirialAssociatingFluidParam() DoubleAssociationSitesFluid4Pt.VirialAssociatingFluidParam
VirialAssociatingFluidParam() FourAssociationSitesFluid2Pt.VirialAssociatingFluidParam
VirialAssociatingFluidParam() SingleAssociationSiteFluid.VirialAssociatingFluidParam
VirialAssociatingFluidParam() SingleAssociationSiteFluid2.VirialAssociatingFluidParam
VirialAssociatingFluidParam() SingleAssociationSiteFluid2Pt.VirialAssociatingFluidParam
VirialAssociatingFluidParam() SingleAssociationSiteFluid3Pt.VirialAssociatingFluidParam
VirialAssociatingFluidParam() SingleAssociationSiteFluid4Points.VirialAssociatingFluidParam
VirialAssociatingFluidParam() SingleAssociationSiteFluid4Pt.VirialAssociatingFluidParam
VirialAssociatingFluidParam() SingleAssociationSiteFluidGraph.VirialAssociatingFluidParam
VirialAssociatingFluidParam() TestLJAssociationMC3D_NPT.VirialAssociatingFluidParam
VirialAssociatingFluidParam() VirialAssociatingFluid.VirialAssociatingFluidParam
VirialAssociatingFluidParam() VirialAssociatingFluid4points.VirialAssociatingFluidParam
VirialB2WaterTIP4P_DHS_difference etomica.virial.simulations
for water TIP4P
B2, dielectric constant
exp (-beta u(water) ) - exp(-beta u(DHS) )
VirialB2WaterTIP4P_DHS_difference() VirialB2WaterTIP4P_DHS_difference
VirialB2WaterTIP4P_DHS_difference.MuDeltaEBond etomica.virial.simulations
VirialB2WaterTIP4P_DHS_difference.P2WaterDHS etomica.virial.simulations
VirialB2WaterTIP4P_DHS_difference.VirialParam etomica.virial.simulations
Inner class for parameters
VirialB3C1HSDipole etomica.virial.simulations
B3,C1, dielectric constant
hard sphere with dipole in the center
three f bonds with mu_i * mu_j
June 2014
VirialB3C1HSDipole() VirialB3C1HSDipole
VirialB3C1HSDipole.VirialParam etomica.virial.simulations
Inner class for parameters
VirialB3C1TIP4Pwater etomica.virial.simulations
B3, C1, dielectric virial coefficient, TIP4P water
three f bonds with mu_i * mu_j
Dec 2014
VirialB3C1TIP4Pwater() VirialB3C1TIP4Pwater
VirialB3C1TIP4Pwater.MuFBond etomica.virial.simulations
VirialB3C1TIP4Pwater.VirialParam etomica.virial.simulations
Inner class for parameters
VirialB3C2HSDipole etomica.virial.simulations
B3,C2, dielectric constant
part two, test
hard sphere with dipole in the center
June 2014
VirialB3C2HSDipole() VirialB3C2HSDipole
VirialB3C2HSDipole.VirialParam etomica.virial.simulations
Inner class for parameters
VirialB3C2TIP4Pwater etomica.virial.simulations
B3,C2, dielectric virial coefficient, TIP4P water
two f bonds, one bond of mu_i * mu_j
Dec 2014
VirialB3C2TIP4Pwater() VirialB3C2TIP4Pwater
VirialB3C2TIP4Pwater.fPlusBetaEU etomica.virial.simulations
VirialB3C2TIP4Pwater.MuProduct etomica.virial.simulations
VirialB3C2TIP4Pwater.VirialParam etomica.virial.simulations
Inner class for parameters
VirialCH4AlkaneEHMix etomica.virial.simulations
Mayer sampling simulation for CH4(rigid, TraPPE-EH)-alkanes(TraPPE-EH) mixture
cross virial coefficients
Using VirialDiagramMix2 to generate diagrams
rigid diagrams and flex diagrams are calculated respectively(Bij = Bij[flexID=-1] + Bij[flexID=1])
VirialCH4AlkaneEHMix() VirialCH4AlkaneEHMix
VirialCH4AlkaneEHMix.VirialMixParam etomica.virial.simulations
Inner class for parameters
virialCluster(int, MayerFunction, boolean, MayerFunction, boolean) Standard
virialCluster(int, MayerFunction, MayerFunction, byte) ClusterAssociation
virialClusterMixture(int, MayerFunction[][], MayerFunction[][], int[]) Standard
virialClusterPolarizable(int, MayerFunction, boolean, boolean) Standard
virialClusterXS(int, MayerFunction, boolean, MayerFunction, boolean, int) Standard
VirialCO2 etomica.virial.simulations
LJ simulation using Mayer sampling to evaluate cluster integrals
VirialCO2() VirialCO2
VirialCO2.VirialCO2Param etomica.virial.simulations
Inner class for parameters
VirialCO2AlkaneEHMix etomica.virial.simulations
Mayer sampling simulation for CO2(rigid, TraPPE)-alkanes(TraPPE-EH) mixture
cross virial coefficients
Using VirialDiagramMix2 to generate diagrams
rigid diagrams and flex diagrams are calculated separately (Bij = Bij[flexID=-1] + Bij[flexID=1])
VirialCO2AlkaneEHMix() VirialCO2AlkaneEHMix
VirialCO2AlkaneEHMix.VirialMixParam etomica.virial.simulations
VirialCO2AlkaneUAMix etomica.virial.simulations
Mayer sampling simulation for CO2(rigid, TraPPE)-alkanes(TraPPE-UA) mixture cross virial coefficients
eovererr can be used
Using VirialDiagramMix2 to generate diagrams
see "VirialCO2AlkaneUARigid" B11 code(use rigid mix diagram)
rigid diagrams and flex diagrams are calculated respectively(Bij = Bij[flexID=-1] + Bij[flexID=0])
VirialCO2AlkaneUAMix() VirialCO2AlkaneUAMix
VirialCO2AlkaneUAMix.VirialMixParam etomica.virial.simulations
Inner class for parameters
VirialCO2anthracene464 etomica.virial.simulations
virial coefficients calculation
mixture of CO2 and anthracene
the code is modified from VirialCO2anthrancene545
Mayer sampling to evaluate cluster integrals
CO2 is modeled as single site, anthracene is model as three site model (464)
this is from Iwai et al, Monte carlo simulation of solubilities of Na, PH and An supercritical, Fluid Phase Equilibria 1998
VirialCO2anthracene464() VirialCO2anthracene464
VirialCO2anthracene464.VirialCO2anthracene545Param etomica.virial.simulations
Inner class for parameters
VirialCO2anthracene545 etomica.virial.simulations
virial coefficients calculation
mixture of CO2 and anthracene
the code is modified from virialco2SKSmix
Mayer sampling to evaluate cluster integrals
CO2 is modeled as single site, anthracene is model as three site model
this is from Iwai et al, Monte carlo simulation of solubilities of Na, PH and An supercritical, Fluid Phase Equilibria 1998
they modeled using 464 model or 545 model, this is 545 model
VirialCO2anthracene545() VirialCO2anthracene545
VirialCO2anthracene545.VirialCO2anthracene545Param etomica.virial.simulations
Inner class for parameters
VirialCO2anthracene545Param() VirialCO2anthracene464.VirialCO2anthracene545Param
VirialCO2anthracene545Param() VirialCO2anthracene545.VirialCO2anthracene545Param
VirialCO2AnthraceneTraPPE etomica.virial.simulations
TraPPE
mixture of CO2 and Anthracene
the code is modified from CO2/naphthalene TraPPE
LJ simulation using Mayer sampling to evaluate cluster integrals
VirialCO2AnthraceneTraPPE() VirialCO2AnthraceneTraPPE
VirialCO2AnthraceneTraPPE.VirialCO2AnthraceneTraPPEParam etomica.virial.simulations
Inner class for parameters
VirialCO2AnthraceneTraPPEParam() VirialCO2AnthraceneTraPPE.VirialCO2AnthraceneTraPPEParam
VirialCO2CH4Mix etomica.virial.simulations
Mayer sampling simulation for CO2(rigid, TraPPE)-CH4(rigid, TraPPE-EH) mixture
cross virial coefficients
Using VirialDiagramMix2 to generate diagrams
rigid diagrams only since both of the components are rigid
VirialCO2CH4Mix() VirialCO2CH4Mix
VirialCO2CH4Mix.VirialMixParam etomica.virial.simulations
Inner class for parameters
VirialCO2CH4UAMix etomica.virial.simulations
Mayer sampling simulation for CO2(rigid, TraPPE)-CH4(rigid, TraPPE-UA, single LJ site) mixture
cross virial coefficients
Using VirialDiagramMix2 to generate diagrams
both of the components are rigid
VirialCO2CH4UAMix() VirialCO2CH4UAMix
VirialCO2CH4UAMix.VirialMixParam etomica.virial.simulations
Inner class for parameters
VirialCO2CH4UAMixWheatley etomica.virial.simulations
Mayer sampling simulation for CO2(rigid, TraPPE)-CH4(rigid, TraPPE-UA, single LJ site) mixture
cross virial coefficients
Using VirialDiagramMix2 to generate diagrams
both of the components are rigid
Implement Wheatley method
VirialCO2CH4UAMixWheatley() VirialCO2CH4UAMixWheatley
VirialCO2CH4UAMixWheatley.VirialMixParam etomica.virial.simulations
Inner class for parameters
VirialCO2H2OGCPM etomica.virial.simulations
Computes CO2-H2O mixture virial coefficients using ab-initio potentials
for both components.
VirialCO2H2OGCPM() VirialCO2H2OGCPM
VirialCO2H2OGCPM.VirialParam etomica.virial.simulations
Inner class for parameters
VirialCO2H2OGCPMX etomica.virial.simulations
Computes CO2-H2O mixture virial coefficients using ab-initio potentials
for both components.
VirialCO2H2OGCPMX() VirialCO2H2OGCPMX
VirialCO2H2OGCPMX.VirialParam etomica.virial.simulations
Inner class for parameters
VirialCO2H2OSC etomica.virial.simulations
Computes CO2-H2O mixture virial coefficients using ab-initio potentials
for both components.
VirialCO2H2OSC() VirialCO2H2OSC
VirialCO2H2OSC.VirialCO2SCParam etomica.virial.simulations
Inner class for parameters
VirialCO2LJQ etomica.virial.simulations
single site LJ +QQ CO2 model , pure
Mayer sampling to evaluate cluster integrals with overlap sampling
From Albo model
VirialCO2LJQ() VirialCO2LJQ
VirialCO2LJQ.VirialCO2LJQParam etomica.virial.simulations
Inner class for parameters
VirialCO2LJQParam() VirialCO2LJQ.VirialCO2LJQParam
VirialCO2N2Mix etomica.virial.simulations
Mayer sampling simulation for CO2(rigid, TraPPE)-N2(rigid, TraPPE) mixture
cross virial coefficients
Using VirialDiagramMix2 to generate diagrams
rigid diagrams only since both of the components are rigid
VirialCO2N2Mix() VirialCO2N2Mix
VirialCO2N2Mix.VirialMixParam etomica.virial.simulations
Inner class for parameters
VirialCO2NaphthaleneLJQ etomica.virial.simulations
single site for CO2 and single site for naphthalene
mixture of CO2 and Naphthalene
the code is modified from virialco2SKSmix and virialCO2NaphthaleneTraPPE
LJ simulation using Mayer sampling to evaluate cluster integrals
parameters are from albo et al
VirialCO2NaphthaleneLJQ() VirialCO2NaphthaleneLJQ
VirialCO2NaphthaleneLJQ.VirialCO2NaphthaleneLJQParam etomica.virial.simulations
Inner class for parameters
VirialCO2NaphthaleneLJQParam() VirialCO2NaphthaleneLJQ.VirialCO2NaphthaleneLJQParam
VirialCO2NaphthaleneTraPPE etomica.virial.simulations
TraPPE
mixture of CO2 and Naphthalene
the code is modified from virialco2SKSmix
LJ simulation using Mayer sampling to evaluate cluster integrals
VirialCO2NaphthaleneTraPPE() VirialCO2NaphthaleneTraPPE
VirialCO2NaphthaleneTraPPE.VirialCO2TraPPEParam etomica.virial.simulations
Inner class for parameters
VirialCO2Param() VirialCO2.VirialCO2Param
VirialCO2Param() VirialCO2SKSMix.VirialCO2Param
VirialCO2PI etomica.virial.simulations
Mayer sampling simulation for path-integral virial coefficients of CO2.
VirialCO2PI() VirialCO2PI
VirialCO2PI.VirialH2PIParam etomica.virial.simulations
Inner class for parameters
VirialCO2SCParam() VirialCO2H2OSC.VirialCO2SCParam
VirialCO2SKSMix etomica.virial.simulations
LJ simulation using Mayer sampling to evaluate cluster integrals
VirialCO2SKSMix() VirialCO2SKSMix
VirialCO2SKSMix.VirialCO2Param etomica.virial.simulations
Inner class for parameters
VirialCO2TraPPE etomica.virial.simulations
TraPPE CO2 model , pure
LJ + electrostatic
Mayer sampling to evaluate cluster integrals
VirialCO2TraPPE() VirialCO2TraPPE
VirialCO2TraPPE.VirialCO2TraPPEParam etomica.virial.simulations
Inner class for parameters
VirialCO2TraPPEParam() VirialCO2NaphthaleneTraPPE.VirialCO2TraPPEParam
VirialCO2TraPPEParam() VirialCO2TraPPE.VirialCO2TraPPEParam
VirialCPSHeliumNonAdditive etomica.virial.simulations
VirialCPSHeliumNonAdditive() VirialCPSHeliumNonAdditive
VirialCPSHeliumNonAdditive.VirialParam etomica.virial.simulations
Inner class for parameters
VirialCPSHeliumNonAdditiveClassical etomica.virial.simulations
VirialCPSHeliumNonAdditiveClassical(Space) VirialCPSHeliumNonAdditiveClassical
VirialCPSHeliumNonAdditiveClassical_Correction etomica.virial.simulations
VirialCPSHeliumNonAdditiveClassical_Correction(Space) VirialCPSHeliumNonAdditiveClassical_Correction
VirialCPSHeliumNonAdditiveClassical_Correction.VirialParam etomica.virial.simulations
Inner class for parameters
VirialCPSHeliumNonAdditiveClassical.VirialParam etomica.virial.simulations
Inner class for parameters
virialData DataProcessorInterfacialTensionProfile
VirialDiagrams etomica.virial.cluster
VirialDiagrams(int, boolean, boolean) VirialDiagrams
VirialDiagrams(int, boolean, boolean, boolean) VirialDiagrams
VirialDiagrams.ArticulatedAt0 etomica.virial.cluster
VirialDiagrams.ComparatorNumFieldNodesExchange etomica.virial.cluster
VirialDiagramsMix etomica.virial.cluster
VirialDiagramsMix(int, boolean[], boolean[]) VirialDiagramsMix
VirialDiagramsMix(int, boolean[], boolean[], boolean) VirialDiagramsMix
VirialDiagramsMix2 etomica.virial.cluster
VirialDiagramsMix2(int, boolean[]) VirialDiagramsMix2
VirialDiagramsMix2(int, boolean[], boolean) VirialDiagramsMix2
VirialDiagramsMix2.MaxIsomorphCriteriaMixture etomica.virial.cluster
VirialDiagramsPT etomica.virial.cluster
VirialDiagramsPT(int, boolean, boolean) VirialDiagramsPT
VirialDiagramsPT(int, boolean, boolean, boolean) VirialDiagramsPT
VirialDiagramsPT.ArticulatedAt0 etomica.virial.cluster
VirialDiagramsPT.ComparatorNumFieldNodesExchange etomica.virial.cluster
VirialDiagramsPT.DiscardCriteria etomica.virial.cluster
VirialEmulNonAdditive etomica.virial.simulations
VirialEmulNonAdditive() VirialEmulNonAdditive
VirialEmulNonAdditive.VirialParam etomica.virial.simulations
Inner class for parameters
VirialExternalFieldConfinedOverlap etomica.virial.simulations
External Field simulation using Overlap2 sampling to evaluate cluster integrals
VirialExternalFieldConfinedOverlap() VirialExternalFieldConfinedOverlap
VirialExternalFieldConfinedOverlap.VirialExternalFieldParam etomica.virial.simulations
Inner class for parameters
VirialExternalFieldConfinedOverlapRho etomica.virial.simulations
External Field simulation using Overlap2 sampling to evaluate cluster integrals
VirialExternalFieldConfinedOverlapRho() VirialExternalFieldConfinedOverlapRho
VirialExternalFieldConfinedOverlapRho.VirialExternalFieldParam etomica.virial.simulations
Inner class for parameters
VirialExternalFieldConfinedOverlapSW etomica.virial.simulations
External Field simulation using Overlap2 sampling to evaluate cluster integrals
VirialExternalFieldConfinedOverlapSW() VirialExternalFieldConfinedOverlapSW
VirialExternalFieldConfinedOverlapSW.VirialExternalFieldParam etomica.virial.simulations
Inner class for parameters
VirialExternalFieldOverlapRho etomica.virial.simulations
External Field simulation using Overlap2 sampling to evaluate cluster integrals
VirialExternalFieldOverlapRho() VirialExternalFieldOverlapRho
VirialExternalFieldOverlapRho.VirialExternalFieldParam etomica.virial.simulations
Inner class for parameters
VirialExternalFieldParam() VirialExternalFieldConfinedOverlap.VirialExternalFieldParam
VirialExternalFieldParam() VirialExternalFieldConfinedOverlapRho.VirialExternalFieldParam
VirialExternalFieldParam() VirialExternalFieldConfinedOverlapSW.VirialExternalFieldParam
VirialExternalFieldParam() VirialExternalFieldOverlapRho.VirialExternalFieldParam
VirialGCPM etomica.virial.simulations
VirialGCPM() VirialGCPM
VirialGCPM.VirialGCPMParam etomica.virial.simulations
Inner class for parameters
VirialGCPMGraphic etomica.virial.simulations
VirialGCPMGraphic() VirialGCPMGraphic
VirialGCPMParam() VirialGCPM.VirialGCPMParam
VirialH2O etomica.virial.simulations
VirialH2O() VirialH2O
VirialH2O.VirialH2OParam etomica.virial.simulations
Inner class for parameters
VirialH2OGCPMD etomica.virial.simulations
Computes virial coefficients and its temperature derivatives for GCPM Water
VirialH2OGCPMD() VirialH2OGCPMD
VirialH2OGCPMD.Clusterfoo etomica.virial.simulations
VirialH2OGCPMD.VirialParam etomica.virial.simulations
Inner class for parameters
VirialH2OParam() VirialH2O.VirialH2OParam
VirialH2PI etomica.virial.simulations
Mayer sampling simulation
VirialH2PI() VirialH2PI
VirialH2PI.VirialH2PIParam etomica.virial.simulations
Inner class for parameters
VirialH2PIBoltzmann etomica.virial.simulations
VirialH2PIBoltzmann() VirialH2PIBoltzmann
VirialH2PIBoltzmann.VirialHePIParam etomica.virial.simulations
Inner class for parameters
VirialH2PIParam() VirialCO2PI.VirialH2PIParam
VirialH2PIParam() VirialH2PI.VirialH2PIParam
VirialH2PISimple etomica.virial.simulations
VirialH2PISimple() VirialH2PISimple
VirialH2PISimple.VirialH2PISimpleParam etomica.virial.simulations
Inner class for parameters
VirialH2PISimpleParam() VirialH2PISimple.VirialH2PISimpleParam
VirialH2PIXC etomica.virial.simulations
VirialH2PIXC() VirialH2PIXC
VirialH2PIXC.VirialHePIParam etomica.virial.simulations
Inner class for parameters
VirialH2PYCorrection etomica.virial.simulations
Computes corrections to Percus-Yevick approximations of B4 and B5 for a hydrogen pair potential.
VirialH2PYCorrection() VirialH2PYCorrection
VirialH2PYCorrection.VirialH2PYCParam etomica.virial.simulations
Inner class for parameters
VirialH2PYCParam() VirialH2PYCorrection.VirialH2PYCParam
VirialHardAssociationCone etomica.virial.simulations
Virial coefficients with single attraction site AssociationCone Potential using Mayer Sampling
VirialHardAssociationCone() VirialHardAssociationCone
VirialHardAssociationCone.VirialLJParam etomica.virial.simulations
VirialHardAssociationConeDoubleSites etomica.virial.simulations
Virial coefficients with double attraction site AssociationCone Potential using Mayer Sampling
VirialHardAssociationConeDoubleSites() VirialHardAssociationConeDoubleSites
VirialHardAssociationConeDoubleSites.VirialLJParam etomica.virial.simulations
VirialHeD etomica.virial.simulations
Computes additive virial coefficients using the pair potential1 for He of Przybytek et al.
VirialHeD() VirialHeD
VirialHeD.VirialParam etomica.virial.simulations
Inner class for parameters
VirialHeNonAdditive etomica.virial.simulations
VirialHeNonAdditive() VirialHeNonAdditive
VirialHeNonAdditive.VirialParam etomica.virial.simulations
Inner class for parameters
VirialHeNonAdditiveD etomica.virial.simulations
Adapted by Andrew from VirialHeNonAdditive
Computes only the nonadditive component of either the third, fourth, or fifth virial coefficient for the
ab initio non-additive trimer potential1 for He developed by Cencek, Patkowski, and Szalewicz (JCP 131 064105 2009).
VirialHeNonAdditiveD() VirialHeNonAdditiveD
VirialHeNonAdditiveD.VirialParam etomica.virial.simulations
Inner class for parameters
VirialHeNonAdditiveWheatley etomica.virial.simulations
Adapted by Andrew from VirialHeNonAdditive
Computes only the nonadditive component of either the third, fourth, or fifth virial coefficient for the
ab initio non-additive trimer potential for He developed by Cencek, Patkowski, and Szalewicz (JCP 131 064105 2009).
VirialHeNonAdditiveWheatley() VirialHeNonAdditiveWheatley
VirialHeNonAdditiveWheatley.VirialParam etomica.virial.simulations
Inner class for parameters
VirialHePCKLJS etomica.virial.simulations
Computes additive virial coefficients using the pair potential for He of Przybytek et al.
VirialHePCKLJS() VirialHePCKLJS
VirialHePCKLJS.VirialParam etomica.virial.simulations
Inner class for parameters
VirialHePCKLJSCHNCCorrection etomica.virial.simulations
Computes corrections to hypernetted-chain approximations of B4 and B5 for a helium pair potential.
VirialHePCKLJSCHNCCorrection() VirialHePCKLJSCHNCCorrection
VirialHePCKLJSCHNCCorrection.VirialLJParam etomica.virial.simulations
Inner class for parameters
VirialHePCKLJSPYCorrection etomica.virial.simulations
Computes corrections to Percus-Yevick approximations of B4 and B5 for a helium pair potential.
VirialHePCKLJSPYCorrection() VirialHePCKLJSPYCorrection
VirialHePCKLJSPYCorrection.VirialLJParam etomica.virial.simulations
Inner class for parameters
VirialHePCKLJSTempDeriv etomica.virial.simulations
Computes first or second temperatures (see firstDerivative variable) of additive virial coefficients using the
ab initio pair potential for helium from Przybytek et al.
VirialHePCKLJSTempDeriv() VirialHePCKLJSTempDeriv
VirialHePCKLJSTempDeriv.VirialParam etomica.virial.simulations
Inner class for parameters
VirialHePI etomica.virial.simulations
Mayer sampling simulation
VirialHePI() VirialHePI
VirialHePI_PotentialCorrection etomica.virial.simulations
Mayer sampling simulation
VirialHePI_PotentialCorrection() VirialHePI_PotentialCorrection
VirialHePI_PotentialCorrection.VirialHePIParam etomica.virial.simulations
Inner class for parameters
VirialHePI.FlexApproach etomica.virial.simulations
VirialHePI.PotentialChoice etomica.virial.simulations
VirialHePI.VirialHePIParam etomica.virial.simulations
Inner class for parameters
VirialHePIGraphic etomica.virial.simulations
Mayer sampling simulation
VirialHePIGraphic() VirialHePIGraphic
VirialHePIParam() VirialH2PIBoltzmann.VirialHePIParam
VirialHePIParam() VirialH2PIXC.VirialHePIParam
VirialHePIParam() VirialHePI_PotentialCorrection.VirialHePIParam
VirialHePIParam() VirialHePI.VirialHePIParam
VirialHePIParam() VirialHePISysErr.VirialHePIParam
VirialHePIParam() VirialHePIXC.VirialHePIParam
VirialHePIParam() VirialHePIXCEven.VirialHePIParam
VirialHePIParam() VirialHePIXCOdd.VirialHePIParam
VirialHePISysErr etomica.virial.simulations
Mayer sampling simulation
VirialHePISysErr() VirialHePISysErr
VirialHePISysErr.FlexApproach etomica.virial.simulations
VirialHePISysErr.VirialHePIParam etomica.virial.simulations
Inner class for parameters
VirialHePIXC etomica.virial.simulations
Mayer sampling simulation for alkanes using the TraPPE force field.
VirialHePIXC() VirialHePIXC
VirialHePIXC.VirialHePIParam etomica.virial.simulations
Inner class for parameters
VirialHePIXCEven etomica.virial.simulations
MSMC calculation for the "even" exchange component of helium-4 virial coefficients.
VirialHePIXCEven() VirialHePIXCEven
VirialHePIXCEven.VirialHePIParam etomica.virial.simulations
Inner class for parameters
VirialHePIXCOdd etomica.virial.simulations
MSMC calculation for pieces of the "odd" exchange component of helium-4 virial coefficients.
VirialHePIXCOdd() VirialHePIXCOdd
VirialHePIXCOdd.VirialHePIParam etomica.virial.simulations
Inner class for parameters
VirialHePYCorrection etomica.virial.simulations
Computes corrections to Percus-Yevick approximations of B4 and B5 for a helium pair potential.
VirialHePYCorrection() VirialHePYCorrection
VirialHePYCorrection.VirialHePYCParam etomica.virial.simulations
Inner class for parameters
VirialHePYCParam() VirialHePYCorrection.VirialHePYCParam
VirialHePYCParam() VirialHeSC.VirialHePYCParam
VirialHeSC etomica.virial.simulations
Computes virial coefficients for a helium pair potential.
VirialHeSC() VirialHeSC
VirialHeSC.VirialHePYCParam etomica.virial.simulations
Inner class for parameters
VirialHS etomica.virial.simulations
Calculation for virial coefficients of hard spheres
VirialHS() VirialHS
VirialHS.VirialHSParam etomica.virial.simulations
Inner class for parameters
VirialHSBinMultiThreaded etomica.virial.simulations
Calculation for virial coefficients of hard spheres
VirialHSBinMultiThreaded() VirialHSBinMultiThreaded
VirialHSBinMultiThreaded.DooDad etomica.virial.simulations
VirialHSBinMultiThreaded.SimulationWorker etomica.virial.simulations
VirialHSBinMultiThreaded.VirialHSBinParam etomica.virial.simulations
Inner class for parameters
VirialHSBinParam() VirialHSBinMultiThreaded.VirialHSBinParam
VirialHSBinParam() VirialSQWBinMultiThreaded.VirialHSBinParam
VirialHSMixture etomica.virial.simulations
Calculation for virial coefficients of hard sphere mixture
VirialHSMixture() VirialHSMixture
VirialHSMixture.VirialHSParam etomica.virial.simulations
Inner class for parameters
VirialHSMixtureOverlap etomica.virial.simulations
Calculation for virial coefficients of hard sphere mixture
VirialHSMixtureOverlap() VirialHSMixtureOverlap
VirialHSMixtureOverlap.VirialHSParam etomica.virial.simulations
Inner class for parameters
VirialHSOrC etomica.virial.simulations
Overlap sampling simulation to compute c(r) for HS
VirialHSOrC() VirialHSOrC
VirialHSOrC.PotentialChoice etomica.virial.simulations
VirialHSOrC.VirialLJrParam etomica.virial.simulations
Inner class for parameters
VirialHSParam() VirialPolymerOverlapMC.VirialHSParam
VirialHSParam() VirialPolymerOverlapWithMD.VirialHSParam
VirialHSParam() VirialPolymerOverlapWithMDB3.VirialHSParam
VirialHSParam() VirialHS.VirialHSParam
VirialHSParam() VirialHSMixture.VirialHSParam
VirialHSParam() VirialHSMixtureOverlap.VirialHSParam
VirialHSParam() VirialPolyhedra.VirialHSParam
VirialHSParam() VirialPolyhedra2.VirialHSParam
VirialHSParam() VirialSQWBinMultiRecalcW.VirialHSParam
VirialHSParam() VirialSQWRecalcSmallMem.VirialHSParam
VirialLJ etomica.virial.simulations
LJ simulation using Mayer sampling to evaluate cluster integrals
VirialLJ() VirialLJ
VirialLJ.VirialLJParam etomica.virial.simulations
Inner class for parameters
VirialLJBridge etomica.virial.simulations
MSMC computations (via overlap sampling) of the bridge diagram(s) within the
f-bond-only formulation.
VirialLJBridge() VirialLJBridge
VirialLJBridge.VirialLJParam etomica.virial.simulations
Inner class for parameters
VirialLJCHNCCorrection etomica.virial.simulations
LJ simulation using Mayer sampling to evaluate corrections to the HNC(c) approximations to B4 and B5
VirialLJCHNCCorrection() VirialLJCHNCCorrection
VirialLJCHNCCorrection.VirialLJParam etomica.virial.simulations
Inner class for parameters
VirialLJD etomica.virial.simulations
LJ simulation using Mayer sampling to evaluate cluster integrals
VirialLJD() VirialLJD
VirialLJD.VirialLJParam etomica.virial.simulations
Inner class for parameters
VirialLJDU etomica.virial.simulations
LJ simulation using Mayer sampling to evaluate cluster integrals.
VirialLJDU() VirialLJDU
VirialLJDU.VirialLJParam etomica.virial.simulations
Inner class for parameters
VirialLJMultiOverlap etomica.virial.simulations
LJ simulation using Mayer sampling to evaluate cluster integrals
VirialLJMultiOverlap() VirialLJMultiOverlap
VirialLJMultiOverlap.VirialMixParam etomica.virial.simulations
Inner class for parameters
VirialLJOrC etomica.virial.simulations
LJ simulation using Mayer sampling to evaluate cluster integrals
VirialLJOrC() VirialLJOrC
VirialLJOrC.PotentialChoice etomica.virial.simulations
VirialLJOrC.VirialLJrParam etomica.virial.simulations
Inner class for parameters
VirialLJOrICPYC etomica.virial.simulations
LJ simulation using Mayer sampling to evaluate cluster integrals
VirialLJOrICPYC() VirialLJOrICPYC
VirialLJOrICPYC.VirialLJrParam etomica.virial.simulations
Inner class for parameters
VirialLJParam() DirectSamplingTargetQCArReferenceAzizAr.VirialLJParam
VirialLJParam() LJTSRefLJ.VirialLJParam
VirialLJParam() VirialHardAssociationCone.VirialLJParam
VirialLJParam() VirialHardAssociationConeDoubleSites.VirialLJParam
VirialLJParam() VirialHePCKLJSCHNCCorrection.VirialLJParam
VirialLJParam() VirialHePCKLJSPYCorrection.VirialLJParam
VirialLJParam() VirialLJ.VirialLJParam
VirialLJParam() VirialLJBridge.VirialLJParam
VirialLJParam() VirialLJCHNCCorrection.VirialLJParam
VirialLJParam() VirialLJD.VirialLJParam
VirialLJParam() VirialLJDU.VirialLJParam
VirialLJParam() VirialLJPT.VirialLJParam
VirialLJParam() VirialLJPYCorrection.VirialLJParam
VirialLJParam() VirialLJSeries.VirialLJParam
VirialLJPT etomica.virial.simulations
LJ simulation using Mayer sampling to evaluate cluster integrals
VirialLJPT() VirialLJPT
VirialLJPT.VirialLJParam etomica.virial.simulations
Inner class for parameters
VirialLJPYCorrection etomica.virial.simulations
LJ simulation using Mayer sampling to evaluate corrections to the PY(c) approximations to B4 and B5
VirialLJPYCorrection() VirialLJPYCorrection
VirialLJPYCorrection.VirialLJParam etomica.virial.simulations
Inner class for parameters
VirialLJQB2 etomica.modules.vle
LJ simulation using Mayer sampling to evaluate cluster integrals
VirialLJQB2() VirialLJQB2
VirialLJrParam() VirialHSOrC.VirialLJrParam
VirialLJrParam() VirialLJOrC.VirialLJrParam
VirialLJrParam() VirialLJOrICPYC.VirialLJrParam
VirialLJSeries etomica.virial.simulations
LJ simulation using Mayer sampling to integrals that show up in series
expansion.
VirialLJSeries() VirialLJSeries
VirialLJSeries.VirialLJParam etomica.virial.simulations
Inner class for parameters
VirialMethaneEH etomica.virial.simulations
TraPPE-EH methane, CH4
Mayer sampling to evaluate cluster integrals
VirialMethaneEH() VirialMethaneEH
VirialMethaneEH.VirialMethaneParam etomica.virial.simulations
Inner class for parameters
VirialMethaneParam() VirialMethaneEH.VirialMethaneParam
VirialMixParam() VirialCH4AlkaneEHMix.VirialMixParam
VirialMixParam() VirialCO2AlkaneEHMix.VirialMixParam
VirialMixParam() VirialCO2AlkaneUAMix.VirialMixParam
VirialMixParam() VirialCO2CH4Mix.VirialMixParam
VirialMixParam() VirialCO2CH4UAMix.VirialMixParam
VirialMixParam() VirialCO2CH4UAMixWheatley.VirialMixParam
VirialMixParam() VirialCO2N2Mix.VirialMixParam
VirialMixParam() VirialLJMultiOverlap.VirialMixParam
VirialMixParam() VirialN2AlkaneEHMix.VirialMixParam
VirialMixParam() VirialN2AlkaneUAMix.VirialMixParam
VirialMixParam() VirialN2AlkaneUARigid.VirialMixParam
VirialMixParam() VirialN2CH4Mix.VirialMixParam
VirialMixParam() VirialN2CH4UAMix.VirialMixParam
VirialMixParam() VirialSF6LJAlkaneUAMix.VirialMixParam
VirialN2 etomica.virial.simulations
VirialN2() VirialN2
VirialN2.VirialN2Param etomica.virial.simulations
Inner class for parameters
VirialN2AlkaneEHMix etomica.virial.simulations
Mayer sampling simulation for N2(rigid, TraPPE)-alkanes(TraPPE-EH) mixture
cross virial coefficients
Using VirialDiagramMix2 to generate diagrams
rigid diagrams and flex diagrams are calculated respectively(Bij = Bij[flexID=-1] + Bij[flexID=1])
VirialN2AlkaneEHMix() VirialN2AlkaneEHMix
VirialN2AlkaneEHMix.VirialMixParam etomica.virial.simulations
Inner class for parameters
VirialN2AlkaneUAMix etomica.virial.simulations
Mayer sampling simulation for N2(rigid, TraPPE)-alkanes(TraPPE-UA) mixture
Martin and Siepmann, JPC(B) 102, 2569-2577 (1998)
eovererr can be used
cross virial coefficients
Using VirialDiagramMix2 to generate diagrams
see "VirialN2AlkaneUARigid" B11 code(use rigid mix diagram)
rigid diagrams and flex diagrams are calculated respectively(Bij = Bij[flexID=-1] + Bij[flexID=1])
VirialN2AlkaneUAMix() VirialN2AlkaneUAMix
VirialN2AlkaneUAMix.VirialMixParam etomica.virial.simulations
Inner class for parameters
VirialN2AlkaneUARigid etomica.virial.simulations
cross virial coefficients of mixture of N2 and alkanes(TraPPE-UA)
no flexible diagrams, just rigid diagrams
just for B11, see "VirialN2AlkaneMix" for flexible corrections
N2:use CO2EMP, C<==> "A", O<==>"N"
VirialN2AlkaneUARigid() VirialN2AlkaneUARigid
VirialN2AlkaneUARigid.VirialMixParam etomica.virial.simulations
Inner class for parameters
VirialN2CH4Mix etomica.virial.simulations
Mayer sampling simulation for N2(rigid, TraPPE)-CH4(TraPPE-EH) mixture
cross virial coefficients
Using VirialDiagramMix2 to generate diagrams
rigid diagrams
VirialN2CH4Mix() VirialN2CH4Mix
VirialN2CH4Mix.VirialMixParam etomica.virial.simulations
Inner class for parameters
VirialN2CH4UAMix etomica.virial.simulations
Mayer sampling simulation for N2(rigid, TraPPE)-CH4(rigid, TraPPE-UA) mixture
cross virial coefficients
Using VirialDiagramMix2 to generate diagrams
rigid diagrams only since both of the components are rigid
VirialN2CH4UAMix() VirialN2CH4UAMix
VirialN2CH4UAMix.VirialMixParam etomica.virial.simulations
Inner class for parameters
VirialN2Param() VirialN2.VirialN2Param
VirialN2Param() VirialN2PI.VirialN2Param
VirialN2Param() VirialN2TraPPE.VirialN2Param
VirialN2PI etomica.virial.simulations
VirialN2PI() VirialN2PI
VirialN2PI.VirialN2Param etomica.virial.simulations
Inner class for parameters
VirialN2TraPPE etomica.virial.simulations
TraPPE N2 model
Potoff and Siepmann.
VirialN2TraPPE() VirialN2TraPPE
VirialN2TraPPE.VirialN2Param etomica.virial.simulations
Inner class for parameters
VirialNaphthaleneTraPPE etomica.virial.simulations
TraPPE Naphthalene model , pure
LJ no electrostatic
Mayer sampling to evaluate cluster integrals
reference: TraPPE 4, Siepmann
VirialNaphthaleneTraPPE() VirialNaphthaleneTraPPE
VirialNaphthaleneTraPPE.VirialNaphthaleneTraPPEParam etomica.virial.simulations
6
Inner class for parameters
VirialNaphthaleneTraPPEParam() VirialNaphthaleneTraPPE.VirialNaphthaleneTraPPEParam
virialNonAdditiveTrimerEnergy(int, MayerFunction, Potential, boolean, boolean) Standard
VirialO2 etomica.virial.simulations
VirialO2() VirialO2
VirialO2.VirialO2Param etomica.virial.simulations
Inner class for parameters
VirialO2Param() VirialO2.VirialO2Param
VirialO2Param() VirialO2PI.VirialO2Param
VirialO2PI etomica.virial.simulations
VirialO2PI() VirialO2PI
VirialO2PI.VirialO2Param etomica.virial.simulations
Inner class for parameters
VirialOptimizer etomica.math.numerical
Class to determine B9 value that best fit the simulation results after
Pade Approximation [K/L]
VirialOptimizer(String, String) VirialOptimizer
VirialOptimizer.VirialParam etomica.math.numerical
VirialParam() PadeApproximation.VirialParam
VirialParam() VirialOptimizer.VirialParam
VirialParam() BnFlexibleContributionTraPPEUAMethanol.VirialParam
VirialParam() ReeHooverMC.VirialParam
VirialParam() VirialAceticAcid.VirialParam
VirialParam() VirialAceticAcidFlex.VirialParam
VirialParam() VirialAlkaneEHTest.VirialParam
VirialParam() VirialB2WaterTIP4P_DHS_difference.VirialParam
VirialParam() VirialB3C1HSDipole.VirialParam
VirialParam() VirialB3C1TIP4Pwater.VirialParam
VirialParam() VirialB3C2HSDipole.VirialParam
VirialParam() VirialB3C2TIP4Pwater.VirialParam
VirialParam() VirialCO2H2OGCPM.VirialParam
VirialParam() VirialCO2H2OGCPMX.VirialParam
VirialParam() VirialCPSHeliumNonAdditive.VirialParam
VirialParam() VirialCPSHeliumNonAdditiveClassical_Correction.VirialParam
VirialParam() VirialCPSHeliumNonAdditiveClassical.VirialParam
VirialParam() VirialEmulNonAdditive.VirialParam
VirialParam() VirialH2OGCPMD.VirialParam
VirialParam() VirialHeD.VirialParam
VirialParam() VirialHeNonAdditive.VirialParam
VirialParam() VirialHeNonAdditiveD.VirialParam
VirialParam() VirialHeNonAdditiveWheatley.VirialParam
VirialParam() VirialHePCKLJS.VirialParam
VirialParam() VirialHePCKLJSTempDeriv.VirialParam
VirialParam() VirialRowleyAlcohol.VirialParam
VirialParam() VirialTraPPE.VirialParam
VirialParam() VirialTraPPEAlcohol.VirialParam
VirialPh3site464Param() VirialPh464.VirialPh3site464Param
VirialPh3site545Param() VirialPh545.VirialPh3site545Param
VirialPh464 etomica.virial.simulations
Phenanthrene model , pure
support for CO2/phenanthrene mixture calculation
3 site model from Iwai this is 464 model
Mayer sampling to evaluate cluster integrals
VirialPh464() VirialPh464
VirialPh464.VirialPh3site464Param etomica.virial.simulations
6
Inner class for parameters
VirialPh545 etomica.virial.simulations
Phenanthrene model , pure
support for CO2/phenanthrene mixture calculation
3 site model from Iwai this is 545 model
Mayer sampling to evaluate cluster integrals
VirialPh545() VirialPh545
VirialPh545.VirialPh3site545Param etomica.virial.simulations
6
Inner class for parameters
VirialPhenanthreneTraPPE etomica.virial.simulations
TraPPE phenanthrene model , pure
LJ no electrostatic
Mayer sampling to evaluate cluster integrals
reference: TraPPE 4, Siepmann
VirialPhenanthreneTraPPE() VirialPhenanthreneTraPPE
VirialPhenanthreneTraPPE.VirialPhenanthreneTraPPEParam etomica.virial.simulations
Inner class for parameters
VirialPhenanthreneTraPPEParam() VirialPhenanthreneTraPPE.VirialPhenanthreneTraPPEParam
VirialPolyhedra etomica.virial.simulations
Calculation for virial coefficients of hard spheres
VirialPolyhedra() VirialPolyhedra
VirialPolyhedra.DataProcessorR2 etomica.virial.simulations
VirialPolyhedra.VirialHSParam etomica.virial.simulations
Inner class for parameters
VirialPolyhedra2 etomica.virial.simulations
Calculation for virial coefficients of hard spheres
VirialPolyhedra2() VirialPolyhedra2
VirialPolyhedra2.DataProcessorR2 etomica.virial.simulations
VirialPolyhedra2.VirialHSParam etomica.virial.simulations
Inner class for parameters
VirialPolymerOverlapMC etomica.starpolymer
star-polymer Virial calculations
VirialPolymerOverlapMC() VirialPolymerOverlapMC
VirialPolymerOverlapMC.VirialHSParam etomica.starpolymer
Inner class for parameters
VirialPolymerOverlapWithMD etomica.starpolymer
Calculation for virial coefficients of hard spheres
Edited for calculating protein 1HRB
VirialPolymerOverlapWithMD() VirialPolymerOverlapWithMD
VirialPolymerOverlapWithMD.VirialHSParam etomica.starpolymer
Inner class for parameters
VirialPolymerOverlapWithMDB3 etomica.starpolymer
Calculation for virial coefficients of hard spheres
Edited for calculating protein 1HRB
VirialPolymerOverlapWithMDB3() VirialPolymerOverlapWithMDB3
VirialPolymerOverlapWithMDB3.VirialHSParam etomica.starpolymer
Inner class for parameters
virialProfile DataSourceTensorVirialHardProfile
virialProfileWork DataSourceTensorVirialHardProfile
VirialRowleyAlcohol etomica.virial.simulations
Mayer-sampling MC simulation for methanol or ethanol using the potentials published in:
R.L.
VirialRowleyAlcohol() VirialRowleyAlcohol
VirialRowleyAlcohol.VirialParam etomica.virial.simulations
Inner class for parameters
virialSeriesCluster(int, MayerFunction[], int[]) Standard
VirialSF6LJAlkaneUAMix etomica.virial.simulations
Mayer sampling simulation for SF6(rigid, LJ sphere)-alkanes(TraPPE-UA) mixture cross virial coefficients
eovererr can be used
Using VirialDiagramMix2 to generate diagrams
rigid diagrams and flex diagrams are calculated respectively(Bij = Bij[flexID=-1] + Bij[flexID=0])
VirialSF6LJAlkaneUAMix() VirialSF6LJAlkaneUAMix
VirialSF6LJAlkaneUAMix.VirialMixParam etomica.virial.simulations
Inner class for parameters
VirialSF6Param() Virial7SiteRigidSF6.VirialSF6Param
VirialSiepmannSpheresParam() VirialAlkane.VirialSiepmannSpheresParam
VirialSiepmannSpheresParam() VirialAlkaneFlex.VirialSiepmannSpheresParam
VirialSiepmannSpheresParam() VirialAlkaneFull.VirialSiepmannSpheresParam
VirialSiepmannSpheresParam() VirialAlkaneSKS.VirialSiepmannSpheresParam
VirialSiepmannSpheresParam() VirialSwsPT.VirialSiepmannSpheresParam
VirialSQWBinMultiRecalcW etomica.virial.simulations
Calculation for virial coefficients of hard spheres
VirialSQWBinMultiRecalcW() VirialSQWBinMultiRecalcW
VirialSQWBinMultiRecalcW.VirialHSParam etomica.virial.simulations
Inner class for parameters
VirialSQWBinMultiThreaded etomica.virial.simulations
Calculation for virial coefficients of hard spheres
VirialSQWBinMultiThreaded() VirialSQWBinMultiThreaded
VirialSQWBinMultiThreaded.SimulationWorker etomica.virial.simulations
VirialSQWBinMultiThreaded.VirialHSBinParam etomica.virial.simulations
Inner class for parameters
VirialSQWRecalcSmallMem etomica.virial.simulations
Calculation for virial coefficients of hard spheres
VirialSQWRecalcSmallMem() VirialSQWRecalcSmallMem
VirialSQWRecalcSmallMem.VirialHSParam etomica.virial.simulations
Inner class for parameters
virialSum MeterPressureHard
virialSum Potential2SoftSphericalLSMultiLat.ReturnValue
virialSum PotentialCalculationSolidSuper
virialSum PotentialCalculationSolidSuperCut
virialSumCO DataSourceWallPressureCatalysis
virialSumCO2 DataSourceWallPressureCatalysis
virialSumIG DataSourceWallPressureMu
virialSumO2 DataSourceWallPressureCatalysis
virialSumSQW DataSourceWallPressureMu
VirialSW etomica.virial.simulations
SW simulation using Mayer sampling to evaluate cluster integrals
VirialSW() VirialSW
VirialSW.VirialSWParam etomica.virial.simulations
Inner class for parameters
VirialSWParam() VirialSW.VirialSWParam
VirialSwsPT etomica.virial.simulations
VirialSwsPT() VirialSwsPT
VirialSwsPT.VirialSiepmannSpheresParam etomica.virial.simulations
Inner class for parameters
VirialSWWE etomica.virial.simulations
VirialSWWE() VirialSWWE
VirialSWWE.VirialSWWEParam etomica.virial.simulations
Inner class for parameters
VirialSWWEParam() VirialSWWE.VirialSWWEParam
VirialTraPPE etomica.virial.simulations
Compute pure, binary, ternary and quaternary mixture virial coefficients using overlap sampling simulations
for some molecules using the TraPPE force fields.
VirialTraPPE() VirialTraPPE
VirialTraPPE.TraPPEParams etomica.virial.simulations
Inner class for TraPPE Parameters
VirialTraPPE.VirialParam etomica.virial.simulations
Inner class for parameters
VirialTraPPEAlcohol etomica.virial.simulations
Mayer-sampling MC simulation for methanol or ethanol using the TraPPE model: http://www.chem.umn.edu/groups/siepmann/trappe/intro.php
Set species, model (with or without point charges), virial-coefficent type (B2, B3, etc.),
and temperature in VirialParam() method at bottom of file.
VirialTraPPEAlcohol() VirialTraPPEAlcohol
VirialTraPPEAlcohol.VirialParam etomica.virial.simulations
Inner class for parameters
VirialWaterOverlap etomica.virial.simulations
Generic simulation using Mayer sampling to evaluate cluster integrals
VirialWaterOverlap() VirialWaterOverlap
viscosity() CGS
viscosity() LJ
viscosity() MKS
viscosity() UnitSystem.Sim
viscosity() UnitSystem
Viscosity etomica.units.dimensions
Dimension for all units of viscosity, Mass/(Length-Time)
visit(byte) AbstractTraversal
visit(byte, byte) BCVisitor
visit(byte, byte) CVisitor
visit(byte, byte) TraversalVisitor
visit(Edge) EdgeVisitor
visit(Node) NodeVisitor
visited Biconnected
visitEdges(EdgeVisitor) Graph
visitEdges(EdgeVisitor) GraphImpl
visitNodes(NodeVisitor) Graph
visitNodes(NodeVisitor) GraphImpl
visualrange Token
VLE etomica.heVLE
VLE etomica.modules.vle
VLE(VLESim, VLE.VLEParams) VLE
VLE(VLESim, Space) VLE
VLE.Applet etomica.modules.vle
VLE.VLEParams etomica.heVLE
VLEParams() VLE.VLEParams
VLESim etomica.heVLE
VLESim etomica.modules.vle
VLESim() VLESim
VLESim(VLESim.GEMCParams) VLESim
VLESim.GEMCParams etomica.heVLE
vmax Plot
vmin Plot
vN2Angles(double, double, double, double) P2NitrogenHellmann
vNew MCMoveVolume
vNew MCMoveVolumeSolidNPTMolecular
Vnlll P2HydrogenPatkowski
Vnlll P2HydrogenPatkowskiAtomic
vOH MCMoveTorsionAceticAcid
vOH MCMoveClusterTorsionAceticAcid
vol PotentialCalculationMappedRdf
vol PotentialCalculationMappedEnergy
vol PotentialCalculationMappedVirial
vol PotentialCalculationMappedVirialV
vOld P1Wall
vOld MCMoveVolumeSolidNPTMolecular
Volt etomica.units
The Volt unit of electric potential.
volume AccumulatorPTensor
volume DataSourceAvgPressure2
volume DataSourceMuRoot
volume DataSourceMuRoot1
volume DataSourceMuRootPMatch
volume DataSourcePMu
volume MeterSolidProps
volume MeterSolidPropsLJ
volume PotentialCalculationEFSSP
volume PotentialCalculationLJSP
volume EwaldSummation
volume EwaldSumMolecules
volume ShapeParser.ShapeData
volume Token
volume() BoundaryPistonCylinder
volume() Boundary
volume() BoundaryDeformablePeriodic
volume() BoundaryRectangular
Returns the "volume" of the rectangular region defined by this Boundary.
volume() CGS
volume() LJ
volume() MKS
volume() UnitSystem.Sim
volume() UnitSystem
Volume etomica.units.dimensions
Dimension for all volume units.
VolumeBias(double, int) LjMd3D.VolumeBias
volumeChanges LJMCGraphic
volumeChanges StatisticsMCGraphic
volumeRender(boolean) Graphics3D
volumeRender4(int, int, int, int) Graphics3D
vp(double, double) PotentialCalculationMappedVirialV.UShift
vp(double, double) PotentialCalculationMappedVirialV.USine
vp(double, double) PotentialCalculationMappedVirialV.VFunc
vScale MCMoveVolume
vScale MCMoveVolumeSolidNPTMolecular
vShift PotentialCalculationMappedRdf
vShift PotentialCalculationMappedEnergy
vShift PotentialCalculationMappedVirial
vShift PotentialCalculationMappedVirialV.UShift
vShift PotentialCalculationMappedVirialV.USine
vShift PotentialCalculationMappedVirialV
vSource MappedVirialLJVGr.LJMDParams
vSum MeterMappedAveragingSum
vSum MeterMappedAveragingVSum
vSum MeterMappedAveragingVSum3Pair
vSum MeterMappedAveragingVSumPair
vSumMinusIdeal MeterMappedAveragingVSum
vSumMinusIdeal MeterMappedAveragingVSum3Pair
vSumMinusIdeal MeterMappedAveragingVSumPair
vSumPair MeterMappedAveragingVSum
vSumPair MeterMappedAveragingVSum3Pair
vSumPair MeterMappedAveragingVSumPair
vSumPairMinusIdeal MeterMappedAveragingVSum
vSumPairMinusIdeal MeterMappedAveragingVSum3Pair
vSumPairMinusIdeal MeterMappedAveragingVSumPair
vSums PotentialCalculationSumCutoff
vTot IntegratorImageHarmonicMD
vTot IntegratorMDHarmonicMC
W
w EFSTungsten
w P1ImageHarmonic
w SimFe.LjMC3DParams
w SimIdealGas.LjMC3DParams
w SimLattice.LjMC3DParams
w SimLJ.LjMC3DParams
w P1Tension
w P2SpheroPolyhedron
w P3HydrogenManzhos
w VirialHSBinMultiThreaded.SimulationWorker
w VirialHSBinMultiThreaded.VirialHSBinParam
w VirialSQWBinMultiThreaded.SimulationWorker
w VirialSQWBinMultiThreaded.VirialHSBinParam
w Tuple4f
The w coordinate.
W IntegratorPolymer
W0 P2SpheroPolyhedron
W1 P2SpheroPolyhedron
W2 P2SpheroPolyhedron
w3j P2HydrogenPatkowski
w3j P2HydrogenPatkowskiAtomic
waitformoveto Token
walk(Graph, List<Byte>, byte, byte, byte) FFTDecomposition
walk(Graph, List<Byte>, byte, byte, byte) IsFFT
walkDimer() IntegratorDimerMin
Moves the half-dimer stepLength*N towards the energy minimum.
wallButton SamGraphic
wallDim P1WCAWall
wallDim P1WCAWall
wallDim P1WCAWall
walldistance VirialExternalFieldConfinedOverlap.VirialExternalFieldParam
walldistance VirialExternalFieldConfinedOverlapRho.VirialExternalFieldParam
walldistance VirialExternalFieldConfinedOverlapSW.VirialExternalFieldParam
wallForce PotentialCalculationForceSumWallForce
wallForce PotentialCalculationTorqueSumWallForce
wallForceSum PotentialCalculationForceSumWall
WallPlane etomica.modules.sam
Wrap a P1WCAWall and make it look like a Plane.
WallPlane(Space, P1WCAWall) WallPlane
wallPosition P1WCAWall
wallPotential DataSourceWallPressure
wallPotential PistonCylinder
wallPotential PotentialCalculationForceSumWall
wallPotential Sam
wallPotential WallPlane
WallRangeModifier(P1Wall, CriterionPositionWall) ColloidGraphic.WallRangeModifier
wallSpecies MeterWallPosition
warn(String) DefaultLogger
warn(String) Logger
Writes a log at WARN level.
warn(String) LoggerInterface
Writes a log at WARN level.
warnEx(String, Throwable) DefaultLogger
warnEx(String, Throwable) Logger
Writes a log at WARN level with detail on exception.
warnEx(String, Throwable) LoggerInterface
Writes a log at WARN level with detail on exception.
warningPrinted PotentialCalculationPressureTensor
WaterBox etomica.rotation
WaterBox() WaterBox
WaterBox.Applet etomica.rotation
WaterDroplet etomica.rotation
WaterDroplet() WaterDroplet
WaterDroplet.Applet etomica.rotation
WaterDropletMatrix etomica.rotation
WaterDropletMatrix() WaterDropletMatrix
WaterDropletMatrix.Applet etomica.rotation
WaterDropletRattle etomica.rotation
WaterDropletRattle() WaterDropletRattle
WaterDropletRattle.Applet etomica.rotation
WaterDropletShake etomica.rotation
WaterDropletShake() WaterDropletShake
WaterDropletShake.Applet etomica.rotation
WaterTrimer etomica.rotation
WaterTrimer() WaterTrimer
WaterTrimer.Applet etomica.rotation
WaterTrimerRattle etomica.rotation
WaterTrimerRattle() WaterTrimerRattle
WaterTrimerRattle.Applet etomica.rotation
WaterTrimerShake etomica.rotation
WaterTrimerShake() WaterTrimerShake
WaterTrimerShake.Applet etomica.rotation
Watt etomica.units
The Watt unit of power, equal to 1 J/s or 1 kg-m^2/s^3.
Wavenumber etomica.units.dimensions
Dimension for all units of spatial frequency, 1/Length.
waveVec MeterStructureFactor
waveVector MeterHarmonicCoordinate
waveVectorAction NormalModeAnalysisDisplay1DGraphic
waveVectorCoefficients CalcJacobian
waveVectorCoefficients MeterHarmonicEnergy
waveVectorCoefficients MeterHarmonicSingleEnergy
waveVectorFactory NormalModeAnalysisDisplay1D
waveVectorFactory NormalModeAnalysisDisplay2D
waveVectorFactory NormalModeAnalysisDisplay3D
waveVectorFactory NormalModes2D
waveVectorFactory NormalModes3D
waveVectorFactory WriteS
WaveVectorFactory etomica.normalmode
Interface for a class the returns the appropriate wave vectors for a box
and primitive
WaveVectorFactory1D etomica.normalmode
Wave vector factory that returns wave vectors for a 1D system.
WaveVectorFactory1D() WaveVectorFactory1D
WaveVectorFactory2D etomica.normalmode
Wave vector factory that returns wave vectors appropriate for a box with
a single-atom basis.
WaveVectorFactory2D(Primitive, Space) WaveVectorFactory2D
WaveVectorFactoryFcc etomica.normalmode
WaveVectorFactory implementation that returns wave vectors appropriate for
a cubic FCC lattice.
WaveVectorFactoryFcc(PrimitiveFcc, int) WaveVectorFactoryFcc
WaveVectorFactoryFromFile etomica.normalmode
Obtains wave vectors and coefficients from a file.
WaveVectorFactoryFromFile(String, int) WaveVectorFactoryFromFile
WaveVectorFactorySimple etomica.normalmode
Wave vector factory that returns wave vectors appropriate for a box with
a single-atom basis.
WaveVectorFactorySimple(Primitive, Space) WaveVectorFactorySimple
WaveVectorFactorySuperBox etomica.normalmode
WaveVectorFactorySuperBox(Primitive, Space) WaveVectorFactorySuperBox
waveVectorMethod ClathrateHarmonicFE.SimParams
waveVectorMethod NormalModesMolecular
waveVectorNum IntegratorHarmonic
waveVectorPostAction NormalModeAnalysisDisplay3DGraphic
waveVectors P1Sinusoidal
waveVectors CalcJacobian
waveVectors MeterHarmonicEnergy
waveVectors MeterHarmonicSingleEnergy
waveVectors NormalModesVariable
waveVectors WaveVectorFactory1D
waveVectors WaveVectorFactory2D
waveVectors WaveVectorFactoryFcc
waveVectors WaveVectorFactorySimple
wavevectorx NormalModeAnalysisDisplay3DGraphic
wavevectory NormalModeAnalysisDisplay3DGraphic
wavevectorz NormalModeAnalysisDisplay3DGraphic
WCA SimGlass.PotentialChoice
WCA VirialHSOrC.PotentialChoice
WCA VirialLJOrC.PotentialChoice
weight IntegratorTMMC
weight MeterVirialBDBin
weight MeterVirialBDBinMultiThreaded.MyData
weight MeterVirialBinMultiThreaded.MyData
weight MeterVirialEBinMultiThreaded.MyData
weight VirialH2OGCPMD.Clusterfoo
weightCluster ClusterWeightAbs
weightNew MCMoveClusterRingPartialRegrow
weightNew MCMoveClusterRingRegrow
weightNew MCMoveClusterRingRegrowExchange
weightNew MCMoveClusterRingScale
weightOld MCMoveClusterRingPartialRegrow
weightOld MCMoveClusterRingRegrow
weightOld MCMoveClusterRingRegrowExchange
weightOld MCMoveClusterRingScale
weightSum HistogramReweightedData
well2 MayerWell
wellConstant TestIGAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
wellConstant TestLJAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
wellConstant TestLJAssociationMC3D_NPT.VirialAssociatingFluidParam
wellConstant TestLJAssociationMC3D_NVTOld.VirialAssociatingFluidParam
wellConstant DoubleAssociationSitesFluid2Pt.VirialAssociatingFluidParam
wellConstant DoubleAssociationSitesFluid3Pt.VirialAssociatingFluidParam
wellConstant DoubleAssociationSitesFluid4Pt.VirialAssociatingFluidParam
wellConstant FourAssociationSitesFluid2Pt.VirialAssociatingFluidParam
wellConstant SingleAssociationSiteFluid2Pt.VirialAssociatingFluidParam
wellConstant SingleAssociationSiteFluid3Pt.VirialAssociatingFluidParam
wellConstant SingleAssociationSiteFluid4Pt.VirialAssociatingFluidParam
wellConstant SingleAssociationSiteFluidGraph.VirialAssociatingFluidParam
wellConstant TestLJAssociationMC3D_NPT.VirialAssociatingFluidParam
wellConstant VirialHardAssociationCone.VirialLJParam
wellConstant VirialHardAssociationConeDoubleSites.VirialLJParam
wellDiameter P2SquareWellBonding
wellDiameter P2SquareWellBondingCO
wellDiameter P2SquareWellSurface
wellDiameter P2SquareWellOneSide
wellDiameter P2DoubleWell
wellDiameter P2SquareWell
wellDiameter P2SquareWellRobust
wellDiameterSquared P2SquareWellBonding
wellDiameterSquared P2SquareWellBondingCO
wellDiameterSquared P2SquareWellSurface
wellDiameterSquared P2SquareWellOneSide
wellDiameterSquared P2DoubleWell
wellDiameterSquared P2PenetrableSquareWell
wellDiameterSquared P2SquareWell
wellDiameterSquared P2SquareWellRobust
wellManager P2SquareWellRobust
Wertheim2SiteAceticAcid etomica.association.AceticAcid
Wertheim coefficients calculation for acetic acid using IMPROVED OPLS united-atom model.
Wertheim2SiteAceticAcid() Wertheim2SiteAceticAcid
Wertheim2SiteAceticAcid.WertheimParam etomica.association.AceticAcid
Inner class for parameters
WertheimAssociatingFluidParam() WertheimGCPM4PtEBondDecomp.WertheimAssociatingFluidParam
WertheimDiagrams2SiteRho etomica.virial.cluster
Wertheim diagram generator for 2 site model
WertheimDiagrams2SiteRho(int, boolean, boolean, boolean, boolean) WertheimDiagrams2SiteRho
WertheimDiagrams2SiteRho(int, boolean, boolean, int, boolean) WertheimDiagrams2SiteRho
WertheimDiagrams3SiteRho etomica.virial.cluster
Wertheim diagram generator for GCPM water (3 site model)
WertheimDiagrams3SiteRho(int, boolean, boolean, boolean) WertheimDiagrams3SiteRho
WertheimDiagrams3SiteRho(int, boolean, boolean, boolean, boolean) WertheimDiagrams3SiteRho
WertheimGCPM3PtEBondDecomp etomica.association.GCPMWater
repulsive potential: energy of pair is greater than -3000cal/mol
attractive potential: energy of pair is less than -3000cal/mol
Wertheim's single attraction-site model of GCPM
Three Site model
e-bond in 3 body term is decomposed into eR and F
WertheimGCPM3PtEBondDecomp() WertheimGCPM3PtEBondDecomp
WertheimGCPM3PtEBondDecomp.VirialAssociatingFluidParam etomica.association.GCPMWater
WertheimGCPM3PtThreeSite etomica.association.GCPMWater
repulsive potential: energy of pair is greater than -association energy(cal/mol)
attractive potential: energy of pair is less than -association energy(cal/mol)
Wertheim's three attraction-site model of GCPM
Three point diagram
Three Site model
WertheimGCPM3PtThreeSite() WertheimGCPM3PtThreeSite
WertheimGCPM3PtThreeSite.VirialAssociatingFluidParam etomica.association.GCPMWater
WertheimGCPM4PtEBondDecomp etomica.association.GCPMWater
repulsive potential: energy of pair is greater than -2500cal/mol
attractive potential: energy of pair is less than -2500cal/mol
Wertheim's single attraction-site model of GCPM
Three Site model
e-bond in 4 body term is decomposed into eR and F
final revision Aug 2011
WertheimGCPM4PtEBondDecomp() WertheimGCPM4PtEBondDecomp
WertheimGCPM4PtEBondDecomp.WertheimAssociatingFluidParam etomica.association.GCPMWater
WertheimGCPM4PtEBondDecompFinal etomica.association.GCPMWater
repulsive potential: energy of pair is greater than -3000cal/mol
attractive potential: energy of pair is less than -3000cal/mol
Wertheim's single attraction-site model of GCPM
Three Site model
e-bond in 4 body term is decomposed into eR and F
Flipping is applied in 28E calculation
final revision Aug 2011
WertheimGCPM4PtEBondDecompFinal() WertheimGCPM4PtEBondDecompFinal
WertheimGCPM4PtEBondDecompFinal.VirialAssociatingFluidParam etomica.association.GCPMWater
WertheimGCPM4PtThreeSite etomica.association.GCPMWater
repulsive potential: energy of pair is greater than -association E(cal/mol)
attractive potential: energy of pair is less than -association E(cal/mol)
Wertheim's three attraction-site model of GCPM
4th order diagram
last revision Aug 2011
WertheimGCPM4PtThreeSite() WertheimGCPM4PtThreeSite
WertheimGCPM4PtThreeSite.VirialAssociatingFluidParam etomica.association.GCPMWater
WertheimGCPM4PtThreeSiteEDecompDirectSampling etomica.association.GCPMWater
repulsive potential: energy of pair is greater than -association E(cal/mol)
attractive potential: energy of pair is less than -association E(cal/mol)
Wertheim's three attraction-site model of GCPM
Direct Sampling
Non-additive 4th order diagram
WertheimGCPM4PtThreeSiteEDecompDirectSampling() WertheimGCPM4PtThreeSiteEDecompDirectSampling
WertheimGCPM4PtThreeSiteEDecompDirectSampling.VirialAssociatingFluidParam etomica.association.GCPMWater
WertheimParam() Wertheim2SiteAceticAcid.WertheimParam
WEST Constants.CompassDirection
which MultiharmonicGraphicMC.DataSourceAlphaFE
whichGraph SingleAssociationSiteFluidGraph.VirialAssociatingFluidParam
WHITE Colix
widom2Plot InsertionGraphic
widomCavityMax HSMDWidom.HSMDParam
widomHistPlot InsertionGraphic
width SVGConverter
Output image width.
width GData
wigner3j(String, String, String, String) Wigner3j
Wigner 3jn symbol.
Wigner3j etomica.veos.bigdecimal
Exact representations of Wigner 3jm and 3nj values of half-integer arguments.
Wigner3j() Wigner3j
Wigner3jGUI etomica.veos.bigdecimal
An interactive interface to the Wigner3j class.
Wigner3jGUI() Wigner3jGUI
wigner3jm(int, int, int, int, int, int) Wigner3j
The Wigner 3jm symbol (j1,j2,j3,m1,m2,m3).
wigner3jm(Rational, Rational, Rational, Rational, Rational, Rational) Wigner3j
The Wigner 3jm symbol (j1,j2,j3,m1,m2,m3).
wignerSeitzCell() Primitive
Returns the Wigner-Seitz cell specified by this primitive.
wignerSeitzCell() PrimitiveBcc
wignerSeitzCell() PrimitiveCubic
Returns a new Square (if primitive is 2D) or Cube (if 3D) with edges
given by the size of the primitive vectors.
wignerSeitzCell() PrimitiveFcc
wignerSeitzCell() PrimitiveGeneral
wignerSeitzCell() PrimitiveHexagonal
wignerSeitzCell() PrimitiveHexagonal2D
wignerSeitzCell() PrimitiveMonoclinic
wignerSeitzCell() PrimitiveOrthorhombic
wignerSeitzCell() PrimitiveOrthorhombicHexagonal
wignerSeitzCell() PrimitiveTetragonal
wignerSeitzCell() PrimitiveTriclinic
wignerSeitzCell() PrimitiveTrigonal
willDiscardNextData() HistoryCollapsingDiscard
willDiscardNextData() HistoryComplete
willDiscardNextData() HistoryScrolling
WINDOW_CLOSER SimulationGraphic
windowcentered Token
windowClosed(WindowEvent) ViewConsoleOutputBox
windowClosing(WindowEvent) ViewConsoleOutputBox
windowHeight GData
windowWidth GData
wireframe Token
WIREFRAME Bond
wireframerotation Token
withAtomFactory(SpeciesGeneral.AtomFactory) SpeciesBuilder
withConformation(IConformation) SpeciesBuilder
withDirection(int, int) SpeciesBuilder
within Token
withReplacement AccumulatorAverageBootstrap
withReplacement AccumulatorAverageCollapsingLog
wNew MCMoveClusterBondLength
wNew MCMoveClusterRotateArm
wNew MCMoveClusterAngleBend
wNew MCMoveClusterAngleBendAceticAcid
wNew MCMoveClusterRingPartialRegrow
wNew MCMoveClusterRingRegrow
wNew MCMoveClusterRingRegrowExchange
wNew MCMoveClusterRotateCH3
wNew MCMoveClusterTorsionAceticAcid
wNew MCMoveClusterTorsionAlkaneEH
wNew MCMoveClusterTorsionMulti
wNew MCMoveClusterWiggleAceticAcid
wNew MCMoveClusterWiggleAlkaneEH
wNew MCMoveClusterWiggleMulti
wOld MCMoveClusterBondLength
wOld MCMoveClusterRotateArm
wOld MCMoveClusterAngleBend
wOld MCMoveClusterAngleBendAceticAcid
wOld MCMoveClusterRingPartialRegrow
wOld MCMoveClusterRingRegrow
wOld MCMoveClusterRingRegrowExchange
wOld MCMoveClusterRotateCH3
wOld MCMoveClusterTorsionAceticAcid
wOld MCMoveClusterTorsionAlkaneEH
wOld MCMoveClusterTorsionMulti
wOld MCMoveClusterWiggleAceticAcid
wOld MCMoveClusterWiggleAlkaneEH
wOld MCMoveClusterWiggleMulti
work AccumulatorAverageBlockless
work AccumulatorAverageBlocklessSlim
work AccumulatorAverageFixed
work AccumulatorAverageFixedOutputFile
work DataSourceTensorVirialHard
work MeterDipoleSumSquaredMappedAverage
work PNCO2GCPM
work PNGCPM
work P2Nitrogen
work P2NitrogenAB
work P2NitrogenAnisotropic
work P2NitrogenShellModel
work P2Water3P
work P2Water4P
work PNWaterGCPM
work PNWaterGCPMReactionField
work AtomTestLiquid
work P1Tether
work MeterDDP
work MeterDP
work P2CO2EMP
work RotationTensor3D
work MeterMappedAveraging
work MeterMappedAveraging3Pair
work MeterMappedAveragingFreeEnergy
work MeterMappedAveragingPair
work MeterMappedAveragingPairExcess
work MeterMappedAveragingSum
work MeterMappedAveragingVSum3Pair
work MeterMappedAveragingVSumPair
work MeterPairSum
work1 BiasVolume2SiteAceticAcid
work1 BiasVolumeAceticAcid
work1 MCMoveWiggleAceticAcid
work1 CoordinateDefinitionMolecule
work1 CoordinateDefinitionMoleculeVolumeFluctuation
work1 MCMoveClusterRotateArm
work1 MCMoveRotateArm
work1 MCMoveWiggle
work1 MCMoveClusterAngleBend
work1 MCMoveClusterAngleBendAceticAcid
work1 MCMoveClusterTorsionAlkaneEH
work1 MCMoveClusterTorsionMulti
work1 MCMoveClusterWiggleAceticAcid
work1 MCMoveClusterWiggleAlkaneEH
work1 MCMoveClusterWiggleMulti
work2 BiasVolume2SiteAceticAcid
work2 BiasVolumeAceticAcid
work2 AccumulatorAverageFixed
work2 MCMoveWiggleAceticAcid
work2 MCMoveClusterRotateArm
work2 MCMoveRotateArm
work2 MCMoveWiggle
work2 MCMoveClusterAngleBend
work2 MCMoveClusterAngleBendAceticAcid
work2 MCMoveClusterTorsionAlkaneEH
work2 MCMoveClusterTorsionMulti
work2 MCMoveClusterWiggleAceticAcid
work2 MCMoveClusterWiggleAlkaneEH
work2 MCMoveClusterWiggleMulti
work3 MCMoveWiggleAceticAcid
work3 MCMoveClusterRotateArm
work3 MCMoveRotateArm
work3 MCMoveWiggle
work3 MCMoveClusterAngleBend
work3 MCMoveClusterAngleBendAceticAcid
work3 MCMoveClusterTorsionAlkaneEH
work3 MCMoveClusterTorsionMulti
work3 MCMoveClusterWiggleAceticAcid
work3 MCMoveClusterWiggleAlkaneEH
work3 MCMoveClusterWiggleMulti
workArray HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
workArray HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
workAveCosTheta MCMoveRotateMolecule3DN2AveCosThetaConstraint
workdTorq P2Nitrogen
workTensor IntegratorRigidIterative
workTensor IntegratorRigidMatrixIterative
workTensor IntegratorVelocityVerlet
workTensor IntegratorVerlet
workTensor OrientationCalcWater3P
workTensor OrientationCalcWater4P
workTensor IntegratorDroplet
workTensor PotentialCalculationPressureTensor
workTensor IntegratorVelocityVerletQuaternion
workTensor2 IntegratorDroplet
workTorqVec P2Nitrogen
workVec CalcAnalytical2ndDerivativeNitrogen
workVec CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
workVec P2Nitrogen
workVector IntegratorDimerMin
workVector IntegratorDimerRT
workVector MCMoveRotateMolecule3DConstraint
workVector CoordinateDefinitionLeaf
workVector MeterAtomicDisplacement
workVector MeterMappedAveragingVSum
workVector3 IntegratorDimerRT
wrapped Wrapper
wrappedClass Wrapper
wrappedCluster ClusterCoupledFlipped
wrappedCluster ClusterCoupledFlippedMultivalue
wrappedClusterBD ClusterCoupledFlippedMultivalue
wrappedDataSource MeterPressureByVolumeChange.DataSourceExp
wrappedId Wrapper
wrappedPotential P2XOrder
wrappedPotential P2HardWrapper
wrappedPotential P2MoleculeMonatomic
wrappedPotential P2SoftTruncated
wrappedPotentialMaster SimOverlapLJModule.APIPotentialTarget
wrapper ParseArgs
wrapper ReadParameters
wrapper WriteParameters
Wrapper T > - Class in etomica.meta.wrappers
Surrogate for an instance of an object that is part of a simulation, providing greater control over which
fields are made accessible in the simulation model.
Wrapper(T, SimulationModel, boolean) Wrapper
WrapperIndex etomica.meta
Provides a map between a class and the constructor of its appropriate wrapper type.
WrapperIndex() WrapperIndex
WrapperSerializer etomica.server.serializers
WrapperSerializer() WrapperSerializer
wRatio MCMoveClusterRingScale
write(Parser.CommandVariableValue) Interpreter
write(Exception) Console
write(Exception) ConsoleUI
write(String) Console
write(String) ConsoleUI
writeAtom(FileWriter, IAtom) WriteConfiguration
writeAtom(FileWriter, IAtom) WriteConfigurationOriented
writeAtom(FileWriter, IAtom) WriteConfigurationInterfacial
writeBlockData() AccumulatorAverageFixed
writeBoxRestart(FileWriter, int) SimulationVirialOverlap2
writeCombinedDataToFile(IDataSource[], String) GlassProd
writeConfiguration(String) IntegratorKMC
writeConfiguration(String) IntegratorKMCCluster
writeConfiguration(String) SimDirectBetaN2RPAngleToNoAngle
writeConfiguration(String) SimDirectBetaN2RPInitPert
writeConfiguration(String) SimDirectDisorderedAlphaN2RPInitPert
writeConfiguration(String) SimOverlapAlphaN2TP
writeConfiguration(String) SimOverlapBetaN2RPScaling
writeConfiguration(String) SimOverlapBetaN2TP
writeConfiguration(String) SimOverlapDisorderedAlphaN2RPScaling
writeConfiguration(String) SimOverlapDisorderedAlphaN2TP
writeConfiguration(String) SimFluidSoftSphere
WriteConfiguration etomica.action
Dumps a box's configuration to a file.
WriteConfiguration(Space) WriteConfiguration
WriteConfigurationBinary etomica.action
Dumps a box's configuration to a file.
WriteConfigurationBinary(Space) WriteConfigurationBinary
WriteConfigurationDLPOLY etomica.action
Dumps a box's configuration to a file.
WriteConfigurationDLPOLY() WriteConfigurationDLPOLY
WriteConfigurationInterfacial etomica.interfacial
Dumps a box's configuration to a file.
WriteConfigurationInterfacial(Space) WriteConfigurationInterfacial
WriteConfigurationOriented etomica.action
WriteConfiguration subclass capable of handling oriented atoms.
WriteConfigurationOriented(Space) WriteConfigurationOriented
WriteConfigurationP2DLPOLY etomica.action
Dumps a box's configuration to a file.
WriteConfigurationP2DLPOLY() WriteConfigurationP2DLPOLY
writeD(AkimaSplineSmoother, String, int) AkimaSplineSmootherMain
writeData(String) MeterVirialBDBin
writeData(String) MeterVirialBDBinMultiThreaded
writeData(String) MeterVirialBinMultiThreaded
writeData(String) MeterVirialEBinMultiThreaded
writeData(String, Map<IntSet, MeterVirialBDBinMultiThreaded.MyData>, long) MeterVirialBDBinMultiThreaded
writeData(String, Map<IntSet, MeterVirialBinMultiThreaded.MyData>, long) MeterVirialBinMultiThreaded
writeData(String, Map<IntSet, MeterVirialEBinMultiThreaded.MyData>, long, int) MeterVirialEBinMultiThreaded
writeDataToFile(IDataSource, IData, String) GlassProd
writeDataToFile(IDataSource, String) GlassProd
writeDataToFile(String) CalcVibrationalModes
writedb(Parser.CommandValue) Interpreter
writeDiagrams() ClusterDiagramTree
writeFile(MeterStructureFactor, double, int) ConfigFromFileLAMMPS
writeGraph(String) DataClusterer
writeIntervalPos PolydisperseHS.HSPolyParam
writeIntervalVel PolydisperseHS.HSPolyParam
writeLn() Console
writeLn() ConsoleUI
writeMethod ModifierGeneral
writeParameters() WriteParameters
Reads each line from inputFileName and attempts to match it with a field
from parameterWrapper and sets the field to the value from the file.
WriteParameters etomica.util
This class writes input parameters from a parameter wrapper Object to a file.
WriteParameters() WriteParameters
WriteParameters(String) WriteParameters
WriteParameters(String, ParameterBase) WriteParameters
writePosition WriteConfiguration
writePosition WriteConfigurationBinary
writer IntegratorDimerMin
writeRasmolScript(DiameterHashByType) PDBWriter
Writes a script for rasmol that initializes the radii of each atom type.
writeRasmolScript(DiameterHashByType) XYZWriter
Writes a script for rasmol that initializes the radii of each atom type.
writeRefPref VirialCPSHeliumNonAdditive.VirialParam
writeRefPref VirialCPSHeliumNonAdditiveClassical_Correction.VirialParam
writeRefPref VirialCPSHeliumNonAdditiveClassical.VirialParam
writeRefPref VirialHardAssociationCone.VirialLJParam
writeRefPref VirialHardAssociationConeDoubleSites.VirialLJParam
writeRefPref VirialHePCKLJS.VirialParam
writeRefPref VirialHePCKLJSCHNCCorrection.VirialLJParam
writeRefPref VirialHePCKLJSPYCorrection.VirialLJParam
writeRefPref VirialHePCKLJSTempDeriv.VirialParam
writeRefPref VirialHSMixtureOverlap.VirialHSParam
writeRefPref VirialLJ.VirialLJParam
writeRefPref VirialLJCHNCCorrection.VirialLJParam
writeRefPref VirialLJD.VirialLJParam
writeRefPref VirialLJDU.VirialLJParam
writeRefPref VirialLJPT.VirialLJParam
writeRefPref VirialLJPYCorrection.VirialLJParam
writeRefPref VirialLJSeries.VirialLJParam
writeRefPref VirialSW.VirialSWParam
WriteS etomica.normalmode
Class that writes out S from the MeterNormalMode, calculates
eigenvectors/values (writes them out) and calculates the harmonic free
energy from them.
WriteS(Space) WriteS
writeSetToFile(Set<Graph>, String) WertheimDiagrams3SiteRho
writeStateToFile(OutputStreamWriter) IntegratorOverlap
writeUdistribution(String) MeterNormalizedCoordBeta
writeUdistribution(String) MeterOrientationDistribution
writeUdistribution(String) MeterRotationDistributionGroup
writeWeights(String) MeterVirialBDBin
writeWeights(String) MeterVirialBDBinMultiThreaded
writeWeights(String) MeterVirialBinMultiThreaded
writeWeights(String) MeterVirialEBinMultiThreaded
writeWeights(String, Map<IntSet, MeterVirialBDBinMultiThreaded.MyData>) MeterVirialBDBinMultiThreaded
writeWeights(String, Map<IntSet, MeterVirialBinMultiThreaded.MyData>) MeterVirialBinMultiThreaded
writeWeights(String, Map<IntSet, MeterVirialEBinMultiThreaded.MyData>) MeterVirialEBinMultiThreaded
WS SimGlass.PotentialChoice
wvMap StructureFactorComponentCorrelation
wvTable NormalModeAnalysisDisplay3DGraphic
X
x DataDouble
The wrapped data value held by this object.
x DataTensor
The wrapped tensor data.
x DataVector
The wrapped vector data.
x ErfcBenchmark
x AkimaSpline
x AkimaSplineSmoother
x AkimaSplineSmootherApp
x AkimaSplineSmootherDyApp
x DataClusterWriter
x DataProcessorBounds
x CriterionPositionWall.DoubleWrapper
x Vector3D
x TensorND
x VectorND
x Grabber.CornerData
x Token
x AxisAngle4f
The x coordinate.
x Tuple3f
The x coordinate.
x Tuple3i
The x coordinate.
x Tuple4f
The x coordinate.
X EnumSiteName
X_DIM DevicePlotPoints
x0 PotentialCalculationMappedRdf
x0 PotentialCalculationMappedEnergy
x0 PotentialCalculationMappedVirial
x0 PotentialCalculationMappedVirialV
x0 SimEinStep1.SimOverlapParam
x0 SimEinStep1HCP.SimOverlapParam
x0 SimEinStep2.SimOverlapParam
x0 SimEinStep2HCP.SimOverlapParam
x2Sum DataSourceBlockAvgCor
x2Sum DataSourceCorrelation
x2Sum DataSourceMSDcorP
xCell ModifierYCells2D
xd AkimaSplineSmootherApp
xd AkimaSplineSmootherDyApp
xData DataSourceRmsVelocity
xData MeterStructureFactor
xData MeterMeanForce
xData MeterChainLength
xData AccumulatorPTensor
xData DataSourceHisogram
xData DataSourceHistogramMSD
xData DataSourcePMSDHistory
xData DataSourceTensorVirialHardProfile
xData MultiharmonicGraphicMC.DataSourceFunctionRaw
xData StatisticsMCGraphic.DataProcessorUndo
xData DataSourceFE
xData DataSourceFEHistogram
xData DataSourceImposedFEFit
xData DataSourceImposedFEHistogram
xData DataSourcePMu
xData DataSourcePN
xData MeterTiltHistogram
xDataInfo DataSourceRmsVelocity
xDataInfo MeterStructureFactor
xDataInfo MeterMeanForce
xDataInfo MeterChainLength
xDataInfo AccumulatorPTensor
xDataInfo DataSourceHisogram
xDataInfo DataSourceHistogramMSD
xDataInfo DataSourcePMSDHistory
xDataInfo DataSourceTensorVirialHardProfile
xDataInfo MultiharmonicGraphicMC.DataSourceFunctionRaw
xDataInfo StatisticsMCGraphic.DataProcessorUndo
xDataInfo DataSourceFE
xDataInfo DataSourceFEHistogram
xDataInfo DataSourceImposedFEFit
xDataInfo DataSourceImposedFEHistogram
xDataInfo DataSourcePMu
xDataInfo DataSourcePN
xDataInfo MeterTiltHistogram
xDataSource MeterCavityMapped
xDataSource MeterRDFMapped
xDataSource AccumulatorHistogram
xDataSource HistogramDataSource
xDataSource MeterDihedralAngle
xDataSource MeterProfileByAtoms
xDataSource MeterProfileByVolume
xDataSource MeterRDF
xDataSource MeterRDFPC
xDataSource PotentialCalculationRDF
xDataSource DataFunction.DataInfoFunction
xDataSource DataFunction.DataInfoFunctionFactory
xDataSource MeterMappedRdf
xDataSource PotentialCalculationMappedRdf
xDataSource DataSourceDensityFunction
xDataSource MeterCorrelation
xDataSource MeterGs
xDataSource MeterTiltRotationHistogram
xDataSource MeterWorkHarmonicTargetandReweighting
xDataSource MeterWorkTargetHarmonicandReweighting
xDataSource MeterBondLength
xDataSources AccumulatorHistory
xDropAxis DropletAtomic
XE(Vector) Vector
Sets this vector equal to the cross product of this vector with the
given vector (only works for 3D vectors).
XE(Vector) Vector1D
XE(Vector) Vector2D
XE(Vector) Vector3D
XE(Vector) VectorND
xGT GData
xInfo DataProcessorBounds
xIntercept() Plane
Returns the intercept of the plane with the x-axis.
xLabel DisplayPlot
xLast GData
xLat Potential2SoftSphericalLSMultiLatSlanty
xlateDown() G3DSys
Translate model 10% of pixel width down (+y)
xlateLeft() G3DSys
Translate model 10% of pixel width to the left (-x)
xlateRight() G3DSys
Translate model 10% of pixel width to the right (+x)
xlateUp() G3DSys
Translate model 10% of pixel width up (-y)
xlateXY(int, int) G3DSys
Trnaslate model x,y pixels
xLight Shader
xlog2Interval DataSourceHisogram
xlog2Interval DataSourceMSDcorP
xlog2Interval DataSourcePMSDHistory
xlp P1HydrogenMielke
xLT GData
xLxyz Potential2SoftSphericalLSMultiLatSlanty
xMax HistogramNotSoSimple
xMax HistogramReweightedData
xMax HistogramSimple
xMax MeterRDF
xMax MeterRDFPC
xMax PotentialCalculationRDF
xMax MCMoveAtomInRegion
xMax MeterMappedRdf
xMax PotentialCalculationMappedRdf
xMax MeterExcessAdsorbed
xMax MeterProfileByVolumeAdsorption
xMax MeterCorrelation
xMax MeterGs
xMax MeterBondLength
xmax_ Plot
xMaxp P3HydrogenManzhos
xMaxt P3HydrogenManzhos
xMin HistogramNotSoSimple
xMin HistogramReweightedData
xMin HistogramSimple
xMin MCMoveAtomInRegion
xMin MeterExcessAdsorbed
xMin MeterProfileByVolumeAdsorption
xmin_ Plot
xMinp P3HydrogenManzhos
xMint P3HydrogenManzhos
xmsdSum DataSourceMSDcorP
xor(Bitmap) Bitmap
Updates this bitmap with the result of the bitwise AND with the other bitmap: bitmap
= (bitmap ^ other).
xor(Bitmap) AbstractBitmap
xor(Bitmap) BitmapOfLong
TIME = O(1) for a compatible instance.
xor(Bitmap) BitmapOfLongVector
xor(BitSet) BitSet
Performs a logical XOR of this bit set with the bit set argument.
xPixel(double) Plot
Computes the x pixel value of a point in the world window.
xPixels Plot
xPos P2HydrogenPatkowski
xPos P2HydrogenPatkowskiAtomic
xPos P3HydrogenManzhos
xSlider InterfacialSWGraphic
xsteps StarPolymerMD.PolymerParam
xSum DataSourceBlockAvgCor
xSum DataSourceMSDcorP
xTag DataSourceRmsVelocity
xTag MeterStructureFactor
xTag MeterMeanForce
xTag MeterChainLength
xTag AccumulatorPTensor
xTag DataSourceHisogram
xTag DataSourceHistogramMSD
xTag DataSourcePMSDHistory
xTag DataSourceTensorVirialHardProfile
xTag MultiharmonicGraphicMC.DataSourceFunctionRaw
xTag StatisticsMCGraphic.DataProcessorUndo
xTag DataSourceFE
xTag DataSourceFEHistogram
xTag DataSourceImposedFEFit
xTag DataSourceImposedFEHistogram
xTag DataSourcePMu
xTag DataSourcePN
xTag MeterTiltHistogram
xValues HistogramDiscrete
xValues HistogramNotSoSimple
xValues HistogramReweightedData
xValues HistogramSimple
xValues HistoryCollapsing
xValues HistoryScrolling
xValues() Histogram
Returns the x values from the histogram as an array of doubles
xValues() HistogramDiscrete
xValues() HistogramNotSoSimple
xValues() HistogramReweightedData
xValues() HistogramSimple
xVecBox CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
xVecBox CalcNumerical2ndDerivativeNitrogen
xVecBox HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
xVecBox HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
xVecBox HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
xVecBox HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
xVecBox HarmonicBetaNitrogenModelPairMoleculeSequentialLS
xVecBox HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
xVecBox HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
xVecBox MinimizationBetaNitrogenModelLS
xveci PNCO2GCPM.P3GCPMAxilrodTeller
xveci PNGCPM.P3GCPMAxilrodTeller
xvecj PNCO2GCPM.P3GCPMAxilrodTeller
xvecj PNGCPM.P3GCPMAxilrodTeller
xveck PNCO2GCPM.P3GCPMAxilrodTeller
xveck PNGCPM.P3GCPMAxilrodTeller
xWork IntegratorRigidIterative
xWork IntegratorRigidMatrixIterative
xWork OrientationCalcWater3P
xWork OrientationCalcWater4P
xWork IntegratorVelocityVerletQuaternion
xx PNCO2GCPM.P3GCPMAxilrodTeller
xx PNGCPM.P3GCPMAxilrodTeller
xx Tensor3D
xy Tensor3D
XY_ZTOP JmolConstants
xySum DataSourceCorrelation
xyz AtomSignalMotion
xyz DataClusterWriter
xyz Token
XYZWriter etomica.action
Action that dumps a box's configuration to an XYZ file.
XYZWriter(Box) XYZWriter
xz Tensor3D
xz1 P1LepsHarmonic
xz2 P1LepsHarmonic
xzOrientationTensor CoordinateDefinitionNitrogen
xzOrientationTensor CoordinateDefinitionNitrogenSuperBox
xzOrientationTensor LatticeSumCrystalMolecular
Y
y MeterProfileByAtoms
y MCMoveOverlapListener
y LjMd3Dv2y.LjMd3DParams
y AkimaSpline
y AkimaSplineSmoother
y AkimaSplineSmootherApp
y AkimaSplineSmootherDyApp
y P3HydrogenManzhos
y Vector3D
y Grabber.CornerData
y Token
y AxisAngle4f
The y coordinate.
y Tuple3f
The y coordinate.
y Tuple3i
The y coordinate.
y Tuple4f
The y coordinate.
Y PadeApproximation
Y_DIM DevicePlotPoints
y0 AkimaSplineSmoother
y0 AkimaSplineSmootherApp
y0 AkimaSplineSmootherDyApp
y2Sum DataSourceCorrelation
yCell ModifierXCells2D
YELLOW Colix
YesRemoveSpeciesButtonListener() ControllerAlertMsgBoxSpeciesRemoval.YesRemoveSpeciesButtonListener
yGT GData
yield(IAction) Controller.ControllerHandle
yIntercept() Plane
Returns the intercept of the plane with the y-axis.
yLast GData
yLat Potential2SoftSphericalLSMultiLatSlanty
yLight Shader
yLT GData
yLxyz Potential2SoftSphericalLSMultiLatSlanty
ymax_ Plot
ymin_ Plot
YOCTO Prefix
yOffset ConfigurationCatalysis
yOffset ConfigurationSAM
yOrientationTensor CoordinateDefinitionNitrogen
yOrientationTensor CoordinateDefinitionNitrogenSuperBox
yOrientationTensor LatticeSumCrystalMolecular
YOTTA Prefix
yPixel(double) Plot
Computes the y pixel value of a point in the world window.
yPixels Plot
ySmooth AkimaSplineSmootherApp
ySmooth AkimaSplineSmootherDyApp
yTrue AkimaSplineSmootherDyApp
yVecBox CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
yVecBox CalcNumerical2ndDerivativeNitrogen
yVecBox HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
yVecBox HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
yVecBox HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
yVecBox HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
yVecBox HarmonicBetaNitrogenModelPairMoleculeSequentialLS
yVecBox HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
yVecBox HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
yVecBox MinimizationBetaNitrogenModelLS
yveci PNCO2GCPM.P3GCPMAxilrodTeller
yveci PNGCPM.P3GCPMAxilrodTeller
yvecj PNCO2GCPM.P3GCPMAxilrodTeller
yvecj PNGCPM.P3GCPMAxilrodTeller
yveck PNCO2GCPM.P3GCPMAxilrodTeller
yveck PNGCPM.P3GCPMAxilrodTeller
yWork IntegratorRigidMatrixIterative
yWork OrientationCalcWater3P
yWork OrientationCalcWater4P
yx Tensor3D
yy PNCO2GCPM.P3GCPMAxilrodTeller
yy PNGCPM.P3GCPMAxilrodTeller
yy Tensor3D
yz Tensor3D
yz1 P1LepsHarmonic
yz2 P1LepsHarmonic
Z
z Vector3D
z Token
z AxisAngle4f
The z coordinate.
z Tuple3f
The z coordinate.
z Tuple3i
The z coordinate.
z Tuple4f
The z coordinate.
Z PadeApproximation
Z P3CPSNonAdditiveHeSimplified
Z3 P3CPSNonAdditiveHe
Z3 P3CPSNonAdditiveHeLessSimplified
Z3 P3CPSNonAdditiveHeOrig
Z3_111 P3CPSNonAdditiveHe
Z3_111 P3CPSNonAdditiveHeLessSimplified
Z3_112 P3CPSNonAdditiveHe
Z3_113 P3CPSNonAdditiveHe
Z3_122 P3CPSNonAdditiveHe
Z3_222 P3CPSNonAdditiveHe
Z4211 P3CPSNonAdditiveHe
Z4211 P3CPSNonAdditiveHeLessSimplified
Z4211 P3CPSNonAdditiveHeOrig
Z4211_1112 P3CPSNonAdditiveHe
Z4211_1121 P3CPSNonAdditiveHe
Z4211_2111 P3CPSNonAdditiveHe
Z4220 P3CPSNonAdditiveHe
Z4220 P3CPSNonAdditiveHeLessSimplified
Z4220 P3CPSNonAdditiveHeOrig
Z4220_1111 P3CPSNonAdditiveHe
Z4220_1211 P3CPSNonAdditiveHe
Z4220_2111 P3CPSNonAdditiveHe
zbuf Graphics3D
zbufT Graphics3D
zdepth Token
zDepth GData
Zeolite etomica.zeolite
Zeolite() Zeolite
zeoliteSimGraphic etomica.zeolite
zeoliteSimGraphic(ZeoliteSimulation, Space) zeoliteSimGraphic
zeoliteSimGraphic(ZeoliteSimulation, Space, String) zeoliteSimGraphic
ZeoliteSimStart etomica.zeolite
ZeoliteSimStart(IntegratorMD, boolean, int) ZeoliteSimStart
ZeoliteSimStart(ZeoliteSimulation, zeoliteSimGraphic) ZeoliteSimStart
ZeoliteSimulation etomica.zeolite
Three-dimensional hard-sphere molecular dynamics simulation, using
neighbor listing.
ZeoliteSimulation() ZeoliteSimulation
ZEPTO Prefix
ZERO BitmapFactory
ZERO Rational
ZERO BigSurd
The value of zero.
ZERO BigSurdVec
The value of zero.
ZERO Ifactor
ZERO Rational
The constant 0.
ZERO BigValue
zerobasedxyzrasmol Token
zeroData() MeterCavityMapped
zeroData() MeterRDFMapped
zeroData() MeterRDF
zeroData() DataSourcePercolation
zeroData() DataSourceQ4
zeroData() MeterCorrelation
zeroData() MeterGs
Zero's out the RDF sum tracked by this meter.
zeroF P1ImageHarmonic
zeros DataDoubleBDArray
zeroSum() PotentialCalculationEnergySumEAM
Sets the energy sum to zero, typically to begin a new energy-sum calculation.
zeroSum() DataSourceEnergies.PotentialCalculationEnergies
zeroSum() DataSourceEnergies.PotentialCalculationEnergiesEAM
zeroSum() PotentialCalculationEnergySumCutoff
Sets the energy sum to zero, typically to begin a new energy-sum calculation.
zeroSum() PotentialCalculationSolidSuper
zeroSum() PotentialCalculationSolidSuperCut
zeroSum() PotentialCalculationEnergySum
Sets the energy sum to zero, typically to begin a new energy-sum calculation.
zeroSum() PotentialCalculationEnergySumBigDecimal
Sets the energy sum to zero, typically to begin a new energy-sum calculation.
zeroSum() PotentialCalculationFSum
zeroSum() PotentialCalculationHyperVirialSum
Sets the virial sum to zero, typically to begin a new virial-sum calculation.
zeroSum() PotentialCalculationMolecularVirialSum
Sets the virial sum to zero, typically to begin a new virial-sum calculation.
zeroSum() PotentialCalculationPhiSum
zeroSum() PotentialCalculationPhiSumHeisenberg
zeroSum() PotentialCalculationPressureTensor
zeroSum() PotentialCalculationVirialSum
Sets the virial sum to zero, typically to begin a new virial-sum calculation.
zeroSum() MoleculeAgent
zeroSum() PotentialCalculationFreeEnergy
zeroSum() PotentialCalculationFSum
zeroSum() PotentialCalculationHeisenberg
zeroSum() PotentialCalculationMoleculeAgentSum
zeroSum() PotentialCalculationMoleculeAgentSumMinusIdeal
zeroSum() PotentialCalculationMoleculeAgentSumMinusIdealPair
zeroSum() PotentialCalculationMoleculeAgentSumPair
zeroSum() PotentialCalculationPair
zeroSum() PotentialCalculationSumquare
zeroSums() PotentialCalculationSumCutoff
Sets the energy sum to zero, typically to begin a new energy-sum calculation.
zeroSums() PotentialCalculationSumCutoffLS
Sets the energy sum to zero, typically to begin a new energy-sum calculation.
zeta(int, MathContext) BigDecimalMath
Riemann zeta function.
zeta_AD P2HePCJS
zeta_BO P2HePCJS
zeta_QED P2HePCJS
zeta_REL P2HePCJS
zeta1(int) BigDecimalMath
Riemann zeta function.
ZETTA Prefix
ZFcc(double, double) LennardJones
Compressibility factor, P/rho/kT for the fcc solid.
zFluid(double) HardSphereFluid
Computes Z using the following equation
Z = exp([Ni * rho^(i-1)] + rho^11 [Mi x^i]) where x = a^rho
zFraction IntegratorDCVGCMD
zGT GData
zIntercept() Plane
Returns the intercept of the plane with the z-axis.
zk P2NitrogenAnisotropic
zl P2NitrogenAnisotropic
zLat Potential2SoftSphericalLSMultiLatSlanty
zLight Shader
zLT GData
zLxyz Potential2SoftSphericalLSMultiLatSlanty
zMargin Graphics3D
zMax ConfigurationLammps
zoomDown(int) G3DSys
Decrease the zoom level by i percent
zoomenabled Token
zoomlarge Token
zoomUp(int) G3DSys
Increase the zoom level by i percent
zshade Token
zShadeB GData
zShadeG GData
zshadepower Token
zShadePower GData
zShadeR GData
zShift MeterWallPosition
zslab Token
zSlab GData
zSolid(double) HardSphere
Returns the compressibility factor for solid (FCC) hard spheres at the
given density.
zSolid(double) HardSphereSolid
Returns the compressibility factor for solid (FCC) hard spheres at the
given density.
zSolidCorrection(double) HardSphereSolid
Returns the correction to high density expression for the
compressibility factor for solid (FCC) hard spheres at the given
density.
zVecBox CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
zVecBox CalcNumerical2ndDerivativeNitrogen
zVecBox HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
zVecBox HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
zVecBox HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
zVecBox HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
zVecBox HarmonicBetaNitrogenModelPairMoleculeSequentialLS
zVecBox HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
zVecBox HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
zVecBox MinimizationBetaNitrogenModelLS
zWork OrientationCalcWater3P
zWork OrientationCalcWater4P
zx Tensor3D
zy Tensor3D
zz PNCO2GCPM.P3GCPMAxilrodTeller
zz PNGCPM.P3GCPMAxilrodTeller
zz Tensor3D
_
_3dEnabled DisplayPolytope
_a Ellipse
_c Axes
_c Ball
_c Box
_c Ellipse
_c Line
_c Triangle
_d Ball
_d Bond
_d Ellipse
_gsys Figure
_id Figure
_p Ball
_p Ellipse
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