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A

A - Variable in class etomica.models.co2.P2CO2Hellmann
 
a - Variable in class etomica.models.water.P2Water4PSoft
 
A - Variable in class etomica.models.water.PNWaterGCPM
 
A - Variable in class etomica.potential.P2HePCKLJS
 
a - Static variable in class etomica.potential.P2HePCKLJS
 
a - Variable in class etomica.potential.P2HSDipole
 
a - Variable in class etomica.potential.P2LJDipole
 
A - Variable in class etomica.potential.P2NitrogenHellmann
 
a - Variable in class etomica.potential.P2ReactionFieldDipole
 
A - Variable in class etomica.potential.P3CPSNonAdditiveHe
 
A - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
 
A - Variable in class etomica.potential.P3CPSNonAdditiveHeOrig
 
A - Variable in class etomica.potential.P3CPSNonAdditiveHeSimplified
 
A - Variable in class etomica.potential.P3HydrogenManzhos
 
a - Variable in class etomica.potential.PotentialCalculationPhiSum
 
a - Static variable in class etomica.statmech.HardSphereFluid
 
a - Variable in class etomica.util.numerical.NonLinearCurveDiffFitting
 
a - Variable in class etomica.util.numerical.NonLinearCurveFitting
 
a - Variable in class etomica.util.numerical.PadeApproximation
 
A0 - Variable in class etomica.potential.P2HeSimplified
 
a0 - Static variable in class etomica.potential.P2WaterPotentialsJankowski
 
a0 - Variable in class etomica.potential.P4BondTorsion
 
a0 - Variable in class etomica.potential.P4BondTorsionAlkaneXCCH
 
a0 - Variable in class etomica.potential.Potential2SoftSphericalLS
 
A0 - Static variable in class etomica.statmech.HardSphereSolid
 
A1 - Variable in class etomica.potential.P2HeSimplified
 
a1 - Variable in class etomica.potential.P2QChemInterpolated
 
a1 - Variable in class etomica.potential.P2QChemInterpolated.DampingParams
 
a1 - Variable in class etomica.potential.P3AdditiveQChem.DampingParams
 
a1 - Variable in class etomica.potential.P3QChem.DampingParams
 
a1 - Variable in class etomica.potential.P4BondTorsion
 
a1 - Variable in class etomica.potential.P4BondTorsionAlkaneXCCH
 
A2 - Variable in class etomica.potential.P2HeSimplified
 
a2 - Variable in class etomica.potential.P2QChemInterpolated
 
a2 - Variable in class etomica.potential.P2QChemInterpolated.DampingParams
 
a2 - Variable in class etomica.potential.P3AdditiveQChem.DampingParams
 
a2 - Variable in class etomica.potential.P3QChem.DampingParams
 
a2 - Variable in class etomica.potential.P4BondTorsion
 
a2 - Variable in class etomica.potential.P4BondTorsionAlkaneXCCH
 
A3 - Variable in class etomica.potential.P2HeSimplified
 
a3 - Variable in class etomica.potential.P4BondTorsion
 
a3 - Variable in class etomica.potential.P4BondTorsionAlkaneXCCH
 
AA - Static variable in class etomica.models.co2.P2CO2Hellmann
 
AA - Static variable in class etomica.potential.P2NitrogenHellmann
 
aam - Variable in class etomica.graphics.DisplayBoxCanvasG3DSys
 
aamOriented - Variable in class etomica.graphics.DisplayBoxCanvasG3DSys
 
ab - Variable in class etomica.lattice.crystal.PrimitiveHexagonal
 
ab - Variable in class etomica.lattice.crystal.PrimitiveHexagonal2D
 
AB - Static variable in class etomica.models.co2.P2CO2Hellmann
 
AB - Static variable in class etomica.potential.P2NitrogenHellmann
 
abicipeso4(double, double, double, double) - Static method in class etomica.potential.P2O2Bartolomei
 
AbnormalCompletionException - Exception in 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() - Constructor for exception etomica.exception.AbnormalCompletionException
Constructor for AbnormalCompletionException
AbnormalCompletionException(String) - Constructor for exception etomica.exception.AbnormalCompletionException
Constructor for MethodNotImplementedException.
AboutBoxWindow - Class in etomica.graphics
 
AboutBoxWindow(Component, String) - Constructor for class etomica.graphics.AboutBoxWindow
 
AboutBoxWindow(Component) - Constructor for class etomica.graphics.AboutBoxWindow
 
AboutBoxWindow(Component, String, String[], String[]) - Constructor for class etomica.graphics.AboutBoxWindow
 
AboutBoxWindow.EtomicaGraphic - Class in etomica.graphics
 
Abs() - Constructor for class etomica.util.Function.Abs
 
AbstractLattice - 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.
accept(IAtom) - Method in interface etomica.atom.AtomFilter
Returns true if atom is passes test of filter.
accept(IMolecule) - Method in interface etomica.atom.AtomFilter
 
accept(IAtom) - Method in class etomica.atom.AtomFilterInShape
Returns true if the atom's position is inside the shape.
accept(IMolecule) - Method in class etomica.atom.AtomFilterInShape
 
accept(IAtom) - Method in class etomica.atom.AtomFilterStatic
 
accept(IMolecule) - Method in class etomica.atom.AtomFilterStatic
 
accept(IAtom) - Method in class etomica.lattice.LatticePlane
 
accept(IMolecule) - Method in class etomica.lattice.LatticePlane
 
accept(IAtomList) - Method in class etomica.nbr.CriterionAdapter
Implementation of this method should introduce new criterion and return true if pair meets this criterion and that of the wrapped NeighborCriterion.
accept(IAtomList) - Method in class etomica.nbr.CriterionAll
Always returns true, indicating that all atoms pairs are neighbors.
accept(IAtomList) - Method in class etomica.nbr.CriterionBondedSimple
 
accept(IAtomList) - Method in class etomica.nbr.CriterionInterMolecular
 
accept(IAtomList) - Method in class etomica.nbr.CriterionMolecular
Returns false if pair is/isn't in same molecule (depending on setting of intraMolecular); if matches this criterion, return value will be that given by any subCriterion.
accept(IAtomList) - Method in class etomica.nbr.CriterionMolecularNonAdjacent
 
accept(IAtomList) - Method in class etomica.nbr.CriterionNone
Always returns false, indicating that no atoms pairs are neighbors.
accept(IAtomList) - Method in class etomica.nbr.CriterionPositionWall
 
accept(IAtomList) - Method in class etomica.nbr.CriterionSimple
 
accept(IAtomList) - Method in class etomica.nbr.CriterionType
Returns true if the AtomType of the atom matches the AtomType given at construction and if the wrapped criterion accept also returns true.
accept(IAtomList) - Method in class etomica.nbr.CriterionTypePair
Returns true if the AtomTypes for the pair of atoms match the AtomTypes given at construction (without regard to the order of the pair), and if the wrapped criterion also accepts the pair.
accept(IAtomList) - Method in class etomica.nbr.CriterionTypesCombination
Returns true if the AtomTypes for the pair of atoms match the AtomTypes given at construction (without regard to the order of the AtomSet), and if the wrapped criterion also accepts the AtomSet.
accept(IAtomList) - Method in class etomica.nbr.CriterionTypesMulti
Returns true if the AtomTypes for the pair of atoms match the AtomTypes given at construction (without regard to the order of the AtomSet), and if the wrapped criterion also accepts the AtomSet.
accept(IMoleculeList) - Method in class etomica.nbr.molecule.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) - Method in class etomica.nbr.molecule.CriterionAllMolecular
Always returns true, indicating that all atoms pairs are neighbors.
accept(IMoleculeList) - Method in class etomica.nbr.molecule.CriterionSimpleMolecular
 
accept(IMoleculeList) - Method in class etomica.nbr.molecule.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) - Method in class etomica.nbr.molecule.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) - Method in interface etomica.nbr.molecule.NeighborCriterionMolecular
 
accept(IAtomList) - Method in interface etomica.nbr.NeighborCriterion
 
ACCEPT_ALL - Static variable in class etomica.atom.AtomFilterStatic
Static instance of a filter that accepts all atoms.
ACCEPT_NONE - Static variable in class etomica.atom.AtomFilterStatic
Static instance of a filter that rejects all atoms.
acceptanceProbability() - Method in class etomica.integrator.mcmove.MCMoveTracker
Returns the average probability of accepting the move associated with this tracker.
acceptanceRatio() - Method in class etomica.integrator.mcmove.MCMoveTracker
Returns the fraction of accepted trials of the move associated with this tracker.
acceptanceTarget - Variable in class etomica.integrator.mcmove.MCMoveStepTracker
 
acceptNotify() - Method in class etomica.integrator.mcmove.MCMove
Method called by IntegratorMC in the event that the most recent trial is accepted.
acceptNotify() - Method in class etomica.integrator.mcmove.MCMoveAtom
Method called by IntegratorMC in the event that the most recent trial is accepted.
acceptNotify() - Method in class etomica.integrator.mcmove.MCMoveBoxSize
 
acceptNotify() - Method in class etomica.integrator.mcmove.MCMoveDimer
Method called by IntegratorMC in the event that the most recent trial is accepted.
acceptNotify() - Method in class etomica.integrator.mcmove.MCMoveDimerRotate
Method called by IntegratorMC in the event that the most recent trial is accepted.
acceptNotify() - Method in class etomica.integrator.mcmove.MCMoveInsertDelete
 
acceptNotify() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteBiased
 
acceptNotify() - Method in class etomica.integrator.mcmove.MCMoveMolecule
Method called by IntegratorMC in the event that the most recent trial is accepted.
acceptNotify() - Method in class etomica.integrator.mcmove.MCMoveMoleculeExchange
 
acceptNotify() - Method in class etomica.integrator.mcmove.MCMoveSemigrand
 
acceptNotify() - Method in class etomica.integrator.mcmove.MCMoveSwapConfiguration
Swaps positions of molecules in two boxes.
acceptNotify() - Method in class etomica.integrator.mcmove.MCMoveVolume
 
acceptNotify() - Method in class etomica.integrator.mcmove.MCMoveVolumeExchange
 
accumulator - Variable in class etomica.junit.data.AccumulatorAverageTestBase
 
accumulatorAction - Variable in class etomica.action.SimulationRestart
 
AccumulatorAverage - Class in etomica.data
Accumulator that keeps statistics for averaging and error analysis.
AccumulatorAverage() - Constructor for class etomica.data.AccumulatorAverage
Default constructor sets block size to Default value, and sets the interval for pushing the output data (pushInterval) to 100.
AccumulatorAverage(long) - Constructor for class etomica.data.AccumulatorAverage
 
accumulatorAverage - Variable in class etomica.graphics.DisplayTextBoxesCAE
 
AccumulatorAverage.StatType - Class in 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.).
AccumulatorAverageBlockless - Class in etomica.data
AccumulatorAverage that does not use blocks (best used when each sample is independent).
AccumulatorAverageBlockless() - Constructor for class etomica.data.AccumulatorAverageBlockless
Default constructor sets block size to Default value, and sets the interval for pushing the output data (pushInterval) to 100.
AccumulatorAverageBlockless.AllData - Class in etomica.data
 
AccumulatorAverageBlockless.StatType - Class in 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 - Class in etomica.data
AccumulatorAverage that does not use blocks (best used when each sample is independent).
AccumulatorAverageBlocklessSlim() - Constructor for class etomica.data.AccumulatorAverageBlocklessSlim
 
AccumulatorAverageBlocklessSlim.StatType - Class in 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.).
AccumulatorAverageCollapsing - Class in etomica.data
AccumulatorAverage that adjusts the block size during the simulation.
AccumulatorAverageCollapsing() - Constructor for class etomica.data.AccumulatorAverageCollapsing
Default constructor sets block size to Default value, and sets the interval for pushing the output data (pushInterval) to 100.
AccumulatorAverageCollapsing(int) - Constructor for class etomica.data.AccumulatorAverageCollapsing
 
AccumulatorAverageCollapsing(int, int) - Constructor for class etomica.data.AccumulatorAverageCollapsing
 
AccumulatorAverageCollapsingLog - Class in 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() - Constructor for class etomica.data.AccumulatorAverageCollapsingLog
 
AccumulatorAverageCollapsingLog(int) - Constructor for class etomica.data.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) - Constructor for class etomica.data.AccumulatorAverageCollapsingLog
 
AccumulatorAverageCollapsingLog(IRandom, int) - Constructor for class etomica.data.AccumulatorAverageCollapsingLog
 
AccumulatorAverageCollapsingLogAB - Class in etomica.data
 
AccumulatorAverageCollapsingLogAB() - Constructor for class etomica.data.AccumulatorAverageCollapsingLogAB
 
AccumulatorAverageCollapsingLogAB(IRandom) - Constructor for class etomica.data.AccumulatorAverageCollapsingLogAB
 
AccumulatorAverageCollapsingTest - Class in etomica.junit.data
 
AccumulatorAverageCollapsingTest() - Constructor for class etomica.junit.data.AccumulatorAverageCollapsingTest
 
AccumulatorAverageCovariance - Class in 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() - Constructor for class etomica.data.AccumulatorAverageCovariance
 
AccumulatorAverageCovariance(boolean) - Constructor for class etomica.data.AccumulatorAverageCovariance
 
AccumulatorAverageCovariance(long) - Constructor for class etomica.data.AccumulatorAverageCovariance
 
AccumulatorAverageCovariance(long, boolean) - Constructor for class etomica.data.AccumulatorAverageCovariance
 
AccumulatorAverageFixed - Class in etomica.data
AccumulatorAverage that maintains a fixed block size.
AccumulatorAverageFixed() - Constructor for class etomica.data.AccumulatorAverageFixed
Default constructor sets block size to Default value, and sets the interval for pushing the output data (pushInterval) to 100.
AccumulatorAverageFixed(long) - Constructor for class etomica.data.AccumulatorAverageFixed
 
AccumulatorAverageFixedOutputFile - Class in etomica.data
AccumulatorAverage that maintains a fixed block size.
AccumulatorAverageFixedOutputFile() - Constructor for class etomica.data.AccumulatorAverageFixedOutputFile
Default constructor sets block size to Default value, and sets the interval for pushing the output data (pushInterval) to 100.
AccumulatorAverageFixedOutputFile(int) - Constructor for class etomica.data.AccumulatorAverageFixedOutputFile
 
AccumulatorAverageFixedTest - Class in etomica.junit.data
 
AccumulatorAverageFixedTest() - Constructor for class etomica.junit.data.AccumulatorAverageFixedTest
 
AccumulatorAverageTestBase - Class in etomica.junit.data
 
AccumulatorAverageTestBase(AccumulatorAverage) - Constructor for class etomica.junit.data.AccumulatorAverageTestBase
 
AccumulatorCounter - Class in etomica.data
Data processor that simply counts the number of times its addData method is invoked.
AccumulatorCounter() - Constructor for class etomica.data.AccumulatorCounter
 
AccumulatorHistogram - Class in etomica.data
Accumulator that keeps histogram of data.
AccumulatorHistogram() - Constructor for class etomica.data.AccumulatorHistogram
Creates instance using HistogramSimple factory and specifying histograms having 100 bins.
AccumulatorHistogram(Histogram) - Constructor for class etomica.data.AccumulatorHistogram
Creates instance using given histogram factory with default nBins of 100.
AccumulatorHistogram(Histogram, int) - Constructor for class etomica.data.AccumulatorHistogram
Creates instance using the given histogram factory making histograms having the given number of bins.
AccumulatorHistory - Class in etomica.data
Accumulator that keeps history of data.
AccumulatorHistory() - Constructor for class etomica.data.AccumulatorHistory
Creates instance using HistorySimple factory and specifying historys having 100 bins.
AccumulatorHistory(History) - Constructor for class etomica.data.AccumulatorHistory
 
accumulatorHistory - Variable in class etomica.graphics.ActionHistoryWindow
 
AccumulatorHistory.DataSourceCount - Class in etomica.data
Simple DataSource to use as a default time DataSource.
AccumulatorRatioAverage - Class in etomica.data
Accumulator for calculating ratio between two sums
AccumulatorRatioAverage() - Constructor for class etomica.data.AccumulatorRatioAverage
 
AccumulatorRatioAverage(long) - Constructor for class etomica.data.AccumulatorRatioAverage
 
AccumulatorRatioAverageCovariance - Class in etomica.data
Accumulator for calculating ratio between sums.
AccumulatorRatioAverageCovariance() - Constructor for class etomica.data.AccumulatorRatioAverageCovariance
 
AccumulatorRatioAverageCovariance(long) - Constructor for class etomica.data.AccumulatorRatioAverageCovariance
 
AccumulatorRatioAverageCovarianceFull - Class in etomica.data
Accumulator for calculating ratio between sums.
AccumulatorRatioAverageCovarianceFull() - Constructor for class etomica.data.AccumulatorRatioAverageCovarianceFull
 
AccumulatorRatioAverageCovarianceFull(long) - Constructor for class etomica.data.AccumulatorRatioAverageCovarianceFull
 
action - Variable in class etomica.action.activity.ControllerEvent
 
action - Variable in class etomica.util.Grabber.CornerSetListener
 
ActionConfigWindow - Class in etomica.graphics
Action that opens a new window and dumps the coordinates into the window.
ActionConfigWindow(IBox) - Constructor for class etomica.graphics.ActionConfigWindow
 
ActionCornerSetter(Grabber, int) - Constructor for class etomica.util.Grabber.ActionCornerSetter
 
actionExceptionMap - Variable in class etomica.action.activity.Controller
 
ActionGraphic - Class in etomica.graphics
Wrapper of an etomica Action that permits it to be used as a java.awt action listener.
ActionGraphic(IAction) - Constructor for class etomica.graphics.ActionGraphic
 
ActionGroup - Interface in etomica.action
 
ActionGroupSeries - Class in etomica.action
A set of Action instances grouped and performed in series as if a single action.
ActionGroupSeries() - Constructor for class etomica.action.ActionGroupSeries
Constructs an action group that holds no actions.
ActionGroupSeries(IAction[]) - Constructor for class etomica.action.ActionGroupSeries
Defines group via the given array of actions.
actionHash - Variable in class etomica.graphics.DeviceSelector
 
ActionHistoryWindow - Class in etomica.graphics
Action that opens a new window and dumps the coordinates into the window.
ActionHistoryWindow(AccumulatorHistory) - Constructor for class etomica.graphics.ActionHistoryWindow
 
ActionIntegrate - Class in etomica.action
Action that repeatedly invokes an Integrator's doStep method.
ActionIntegrate(IIntegrator) - Constructor for class etomica.action.ActionIntegrate
Constructs activity to generate configurations with the given integrator.
ActionIntegrate(IIntegrator, boolean) - Constructor for class etomica.action.ActionIntegrate
 
actionPerformed() - Method in class etomica.action.ActionGroupSeries
Invokes the actionPerformed method of all actions in the method, in the order given by the array at construction.
actionPerformed() - Method in class etomica.action.ActionIntegrate
Main loop for conduct of integration.
actionPerformed() - Method in class etomica.action.ActionToggle
Toggles the state of the target object (true to false, false to true).
actionPerformed() - Method in class etomica.action.Activity
Sets integrator to begin isActive on its own thread.
actionPerformed(IAtom) - Method in interface etomica.action.AtomAction
 
actionPerformed(IAtom) - Method in class etomica.action.AtomActionRandomizeVelocity
Assigns velocity to atom with components selected from a Maxwell-Boltzmann distribution with temperature most recently set for the action.
actionPerformed(IAtom) - Method in class etomica.action.AtomActionRotateBy
 
actionPerformed(IAtom) - Method in class etomica.action.AtomActionTranslateBy
 
actionPerformed() - Method in class etomica.action.BoxDeleteMolecules
Performs the action of deleting accept == false molecules, considering all molecules in the box last given to setBox.
actionPerformed() - Method in class etomica.action.BoxImposePbc
 
actionPerformed() - Method in class etomica.action.BoxInflate
Performs boundary dimension change
actionPerformed() - Method in class etomica.action.BoxInflateAnisotropic
Performs anisotropic inflation.
actionPerformed() - Method in class etomica.action.BoxInflateDeformable
Performs isotropic inflation.
actionPerformed() - Method in class etomica.action.BoxQuench
 
actionPerformed() - Method in class etomica.action.BoxRandomizeMomenta
 
actionPerformed() - Method in class etomica.action.BoxScaleMomenta
 
actionPerformed() - Method in class etomica.action.CalcVibrationalModes
 
actionPerformed() - Method in class etomica.action.ControllerToggle
 
actionPerformed() - Method in interface etomica.action.IAction
Completes the action defined by the class implementing this interface.
actionPerformed() - Method in class etomica.action.IntegratorReset
 
actionPerformed(IMolecule) - Method in interface etomica.action.MoleculeAction
 
actionPerformed(IMolecule) - Method in class etomica.action.MoleculeActionTranslateTo
 
actionPerformed(IMolecule) - Method in class etomica.action.MoleculeChildAtomAction
 
actionPerformed() - Method in class etomica.action.PDBWriter
 
actionPerformed() - Method in class etomica.action.SimulationDataAction
 
actionPerformed() - Method in class etomica.action.SimulationRestart
Resets boxs, integrators, and accumulators.
actionPerformed() - Method in class etomica.action.WriteConfiguration
Writes the leaf Atom coordinates to the file confName.pos_new.
actionPerformed() - Method in class etomica.action.WriteConfigurationBinary
Writes the leaf Atom coordinates to the file confName.pos_new.
actionPerformed() - Method in class etomica.action.WriteConfigurationDLPOLY
Writes the leaf Atom coordinates to the file confName.pos_new.
actionPerformed() - Method in class etomica.action.WriteConfigurationP2DLPOLY
Writes the leaf Atom coordinates to the file CONFIG.
actionPerformed() - Method in class etomica.action.XYZWriter
 
actionPerformed(IEvent) - Method in class etomica.data.DataLogger
Close file when integrator is done.
actionPerformed() - Method in class etomica.data.DataPump
Transmits the data from the source to the sink.
actionPerformed() - Method in class etomica.data.DataPumpListenerPow
 
actionPerformed() - Method in class etomica.data.DataPumpListenerSmart
 
actionPerformed() - Method in class etomica.data.DataStreamAction
 
actionPerformed(Object) - Method in class etomica.data.DataStreamAction
 
actionPerformed() - Method in class etomica.data.meter.MeterDihedralAngle
Measures the dihedral angle's for the current configuration of the given box.
actionPerformed() - Method in class etomica.data.meter.MeterRDF
Takes the RDF for the current configuration of the given box.
actionPerformed() - Method in class etomica.data.meter.MeterRDFPC
Takes the RDF for the current configuration of the given box.
actionPerformed() - Method in class etomica.data.meter.MeterStructureFactor
 
actionPerformed() - Method in class etomica.graphics.ActionConfigWindow
 
actionPerformed(ActionEvent) - Method in class etomica.graphics.ActionGraphic
 
actionPerformed() - Method in class etomica.graphics.ActionGraphic
 
actionPerformed() - Method in class etomica.graphics.ActionHistoryWindow
 
actionPerformed() - Method in class etomica.graphics.ActionVelocityWindow
 
actionPerformed() - Method in class etomica.graphics.Device.ActionSet
 
actionPerformed(ActionEvent) - Method in class etomica.graphics.DisplayPlot.DataWriter
 
actionPerformed(ActionEvent) - Method in class etomica.graphics.DisplayPlot.RawDataWindowOpener
 
actionPerformed() - Method in class etomica.graphics.DisplayPolytope
 
actionPerformed(IEvent) - Method in class etomica.integrator.IntegratorPT.BoxTracker
Method called when two boxes are successfully exchanged.
actionPerformed() - Method in class etomica.integrator.IntegratorRigidMatrixIterative.BoxImposePbcMolecule
 
actionPerformed() - Method in class etomica.integrator.mcmove.MCMoveIDBiasAction
 
actionPerformed(IEvent) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
 
actionPerformed(IEvent) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
 
actionPerformed(IEvent) - Method in class etomica.integrator.mcmove.MCMoveOverlapListener
 
actionPerformed(IMoleculeList) - Method in class etomica.junit.atom.iterator.MpiInterspecies1ATest.SpeciesTestAction
 
actionPerformed(IMoleculeList) - Method in interface etomica.junit.atom.MoleculesetAction
 
actionPerformed() - Method in class etomica.modifier.ModifyAction
Executes the setValue method of the wrapped modifier, using the value given in the most recent call to this.setValue.
actionPerformed(ActionEvent) - Method in class etomica.util.Grabber.ActionCornerSetter
 
actionPerformed(IEvent) - Method in interface etomica.util.IListener
 
actionPerformed() - Method in class etomica.util.numerical.AkimaSplineSmootherApp.PlotAction
 
actionPerformed() - Method in class etomica.util.numerical.AkimaSplineSmootherDyApp.PlotAction
 
actions - Variable in class etomica.action.activity.ActivityGroupParallel
 
ActionSet() - Constructor for class etomica.graphics.Device.ActionSet
 
ActionStatus(String) - Constructor for class etomica.action.activity.Controller.ActionStatus
 
actionStatusMap - Variable in class etomica.action.activity.Controller
 
ActionToggle - Class in etomica.action
Action that toggles a boolean value.
ActionToggle(ModifierBoolean) - Constructor for class etomica.action.ActionToggle
 
ActionToggle(ModifierBoolean, String, String) - Constructor for class etomica.action.ActionToggle
 
ActionVelocityWindow - Class in etomica.graphics
Action that opens a new window and dumps the velocities into the window.
ActionVelocityWindow(IBox) - Constructor for class etomica.graphics.ActionVelocityWindow
 
active - Variable in class etomica.data.DataAccumulator
Flag specifying whether the manager responds to integrator events
activeCornerSetter - Variable in class etomica.util.Grabber
 
Activity - Class in etomica.action
An Action that supports the capability of pausing/unpausing and terminating on request.
Activity() - Constructor for class etomica.action.Activity
Create class with a simple default label.
Activity(Activity) - Constructor for class etomica.action.Activity
Copy constructor.
ActivityGroup - Interface in etomica.action.activity
 
ActivityGroupParallel - Class in etomica.action.activity
Organizer of simulation actions to be executed in parallel, each on its own thread.
ActivityGroupParallel() - Constructor for class etomica.action.activity.ActivityGroupParallel
 
ActivityGroupParallel(IAction[]) - Constructor for class etomica.action.activity.ActivityGroupParallel
 
ActivityGroupSeries - Class in etomica.action.activity
Organizer of simulation actions to be executed in series.
ActivityGroupSeries() - Constructor for class etomica.action.activity.ActivityGroupSeries
 
ActivityIntegrate - Class in etomica.action.activity
Activity that repeatedly invokes an Integrator's doStep method.
ActivityIntegrate(IIntegrator) - Constructor for class etomica.action.activity.ActivityIntegrate
Constructs activity to generate configurations with the given integrator (which is final).
ActivityIntegrate(IIntegrator, int, boolean) - Constructor for class etomica.action.activity.ActivityIntegrate
 
activityIntegrate - Variable in class etomica.simulation.prototypes.HSMD2D_noNbr
 
add(IAtom) - Method in class etomica.atom.AtomArrayList
 
add(IMolecule) - Method in class etomica.atom.MoleculeArrayList
 
add(Feature) - Method in class etomica.compatibility.FeatureSet
 
add(String, String) - Method in class etomica.compatibility.FeatureSet
 
add(String, double) - Method in class etomica.compatibility.FeatureSet
 
add(Requirement) - Method in class etomica.compatibility.RequirementSet
 
add(Display) - Method in class etomica.graphics.SimulationGraphic
 
add(Device) - Method in class etomica.graphics.SimulationGraphic
Adds displays graphic to the simulation display pane
add(P2HardBondedList.MyBond) - Method in class etomica.potential.P2HardBondedList.BondArrayList
 
add(IFunction) - Method in class etomica.util.FunctionChain
Adds the given function to the chain of functions.
add(Object) - Method in class etomica.util.ObjectArrayList
Appends the specified element to the end of this list.
add(int, Object) - Method in class etomica.util.ObjectArrayList
Inserts the specified element at the specified position in this list.
add(TreeLinker) - Method in class etomica.util.TreeList
 
addAction(IAction) - Method in interface etomica.action.ActionGroup
Adds the given newAction to this group.
addAction(IAction) - Method in class etomica.action.ActionGroupSeries
Adds the given action to the group.
addAction(IAction) - Method in class etomica.action.activity.ActivityGroupParallel
 
addAction(IAction) - Method in class etomica.action.activity.ActivityGroupSeries
Adds the given action to the list of actions.
addAction(IAction) - Method in class etomica.action.activity.Controller
 
addAgent(IAtom) - Method in class etomica.atom.AtomLeafAgentManager
Adds an agent for the given leaf atom to the agents array.
addAgent(IAtom, int) - Method in class etomica.atom.AtomLeafAgentManager
Adds an agent for the given leaf atom to the agents array at the given index.
addAgent(IAtomType) - Method in class etomica.atom.AtomTypeAgentManager
 
addAgent(IMolecule) - Method in class etomica.atom.MoleculeAgentManager
 
addAgent(ISpecies) - Method in class etomica.atom.SpeciesAgentManager
 
addAgent(IBox) - Method in class etomica.box.BoxAgentManager
 
addAll(IAtomList) - Method in class etomica.atom.AtomArrayList
 
addAll(IMoleculeList) - Method in class etomica.atom.MoleculeArrayList
 
addAsTab(Component, String, boolean) - Method in class etomica.graphics.SimulationGraphic
 
addAtom(IAtom) - Method in class etomica.nbr.cell.Cell
 
addAtomNotify(IAtom) - Method in class etomica.nbr.list.NeighborListManager
Constructs neighbor lists for the given atom
addAtomNotify(IAtom) - Method in class etomica.nbr.list.NeighborListManagerSlanty
Constructs neighbor lists for the given atom
addAuthor(String) - Method in class etomica.graphics.DefaultToolbar
 
addBDOne(BigDecimal) - Static method in class etomica.data.types.DataDoubleBDArray
 
addBDZero(BigDecimal) - Static method in class etomica.data.types.DataDoubleBDArray
 
addBox(IBox) - Method in interface etomica.api.ISimulation
Adds a Box to the simulation.
addBox(IBox) - Method in class etomica.simulation.Simulation
 
addButton(String, IAction) - Method in class etomica.graphics.DeviceButtonGroup
Adds a radio button with the given label, which (when selected) performs the given action.
addChildAtom(IAtom) - Method in class etomica.atom.Molecule
Adds the given Atom as a child of this Atom.
addChildType(IAtomType) - Method in class etomica.species.Species
 
addChildType(IAtomType) - Method in class etomica.species.SpeciesSpheresHetero
Adds the given factory as a child of this factory.
addCollisionListener(IntegratorHard.CollisionListener) - Method in class etomica.integrator.IntegratorHard
Registers an object that implements the CollisionListener interface.
addContributor(String) - Method in class etomica.graphics.DefaultToolbar
 
addCriterion(IteratorDirective.PotentialCriterion) - Method in class etomica.atom.iterator.IteratorDirective
Adds criterion to set of criteria for potentials.
addData(IData) - Method in class etomica.data.AccumulatorAverageBlockless
Add the given values to the sums and block sums.
addData(IData) - Method in class etomica.data.AccumulatorAverageBlocklessSlim
Add the given values to the sums and block sums.
addData(IData) - Method in class etomica.data.AccumulatorAverageCollapsing
Add the given values to the sums and block sums.
addData(IData) - Method in class etomica.data.AccumulatorAverageCollapsingLog
Add the given values to the sums and block sums.
addData(IData) - Method in class etomica.data.AccumulatorAverageCollapsingLogAB
Add the given values to the sums and block sums.
addData(IData) - Method in class etomica.data.AccumulatorAverageCovariance
 
addData(IData) - Method in class etomica.data.AccumulatorAverageFixed
Add the given values to the sums and block sums.
addData(IData) - Method in class etomica.data.AccumulatorAverageFixedOutputFile
Add the given values to the sums and block sums.
addData(IData) - Method in class etomica.data.AccumulatorCounter
Increments the counter.
addData(IData) - Method in class etomica.data.AccumulatorHistogram
Adds each value in the given Data to its own histogram.
addData(IData) - Method in class etomica.data.AccumulatorHistory
Adds each value in the given array to its own history.
addData(IData) - Method in class etomica.data.DataAccumulator
Defined by subclass to specify what this accumulator does when data is added to it.
addDataListener(DataSetListener) - Method in class etomica.data.DataSet
 
addDataSink(IDataSink, AccumulatorAverage.StatType[]) - Method in class etomica.data.AccumulatorAverage
Adds a new DataSink that will receive a specific subset of the statistics generated by this accumulator.
addDataSink(IDataSink, AccumulatorAverageBlockless.StatType[]) - Method in class etomica.data.AccumulatorAverageBlockless
Adds a new DataSink that will receive a specific subset of the statistics generated by this accumulator.
addDataSink(IDataSink) - Method in class etomica.data.DataFork
 
addDataSink(IDataSink) - Method in interface etomica.data.DataPipeForked
Adds the given DataSink to those receiving the Data entering this DataFork, keeping all previously entered DataSinks.
addDataSink(IDataSink) - Method in class etomica.data.DataProcessorForked
Adds the given DataSink to those receiving the Data entering this DataFork, keeping all previously entered DataSinks.
addDataSource(IEtomicaDataSource) - Method in class etomica.data.DataSourceGroup
Adds the given DataSource to those held by the group.
addDataSource(IEtomicaDataSource) - Method in class etomica.data.DataTableAverages
Adds the given data source to those feeding the table.
addDownNbr(IAtom, int) - Method in class etomica.nbr.list.AtomNeighborLists
Adds the given atom as a "down" neighbor interacting via the potential with the given index.
addDownNbr(IMolecule, int) - Method in class etomica.nbr.list.molecule.MoleculeNeighborLists
Adds the given atom as a "down" neighbor interacting via the potential with the given index.
addDrawable(Drawable) - Method in class etomica.graphics.DisplayBox
 
addDrawable(Object) - Method in class etomica.graphics.DisplayBox
 
addIntegrator(IIntegrator) - Method in class etomica.integrator.IntegratorGEMC
 
addIntegrator(IIntegrator) - Method in class etomica.integrator.IntegratorManagerMC
 
addIntegrator(IntegratorBox) - Method in class etomica.integrator.IntegratorPT
Adds the given integrator to those managed by this integrator, and includes integrator's box to the set among which configurations are swapped.
addLine(LineSegment) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
 
addListener(IBoundaryListener) - Method in interface etomica.api.IBoundaryEventManager
Adds the given listener to this event manager.
addListener(IBoxListener) - Method in interface etomica.api.IBoxEventManager
Adds the given listener to this event manager.
addListener(IIntegratorListener) - Method in interface etomica.api.IIntegratorEventManager
Adds the given listener to this event manager.
addListener(ISimulationListener) - Method in interface etomica.api.ISimulationEventManager
 
addListener(IBoxListener) - Method in class etomica.box.BoxEventManager
 
addListener(DeviceTernarySelector.Listener) - Method in class etomica.graphics.DeviceTernarySelector
 
addListener(IIntegratorListener) - Method in class etomica.integrator.IntegratorEventManager
 
addListener(IIntegratorListener) - Method in class etomica.listener.IntegratorListenerGroupSeries
Adds the given action to the group.
addListener(IListener) - Method in interface etomica.listener.ListenerGroup
Adds the given newAction to this group.
addListener(INeighborListListenerMolecular) - Method in class etomica.nbr.list.molecule.NeighborListEventManagerMolecular
 
addListener(INeighborListListener) - Method in class etomica.nbr.list.NeighborListEventManager
 
addListener(ISimulationListener) - Method in class etomica.simulation.SimulationEventManager
 
addListener(IBoundaryListener) - Method in class etomica.space.BoundaryEventManager
 
addListener(IListener) - Method in class etomica.util.EventManager
 
addListener(IListener, boolean) - Method in class etomica.util.EventManager
 
addListener(IListener) - Method in interface etomica.util.IEventManager
Adds the given listener to this event manager.
addMCMove(MCMove) - Method in class etomica.integrator.mcmove.MCMoveManager
Adds the given MCMove to the set of moves performed by the integrator and recalculates move frequencies.
addModel(Model) - Method in interface etomica.api.IPotentialMaster
Add the given Model's intramolecular potentials to this PotentialMaster
addModel(Model) - Method in class etomica.graphics.BondListener
Infroms the BondListener that is should track bonds associated with all molecules of the given Model.
addModel(Model) - Method in class etomica.potential.PotentialMaster
 
addMolecule(IMolecule) - Method in interface etomica.api.IBox
Adds the given molecule to the this box.
addMolecule(IMolecule) - Method in class etomica.box.Box
 
addMolecule(IMolecule) - Method in class etomica.nbr.cell.molecule.CellMolecular
 
addMoleculeNotify(IMolecule) - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular
Constructs neighbor lists for the given atom
addMoleculeNotify(IMolecule) - Method in class etomica.nbr.list.molecule.NeighborListManagerSlantyMolecular
Constructs neighbor lists for the given molecule
addNewMolecule(ISpecies) - Method in class etomica.box.Box
 
addObject(Object[], Object) - Static method in class etomica.util.Arrays
Returns an array formed from adding the newObject to the elements in the given array.
addOption(String, IAction) - Method in class etomica.graphics.DeviceSelector
 
addParser(ParameterParser) - Method in class etomica.util.ParameterBase
 
addPlane(Plane) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
 
addPotential(IPotentialMolecular, ISpecies[]) - Method in interface etomica.api.IPotentialMaster
Indicates to the PotentialMaster that the given potential should apply to the specified species.
addPotential(IPotentialAtomic, IAtomType[]) - Method in interface etomica.api.IPotentialMaster
Indicates to the PotentialMaster that the given potential should apply to the specified atom types.
addPotential(IPotentialMolecular, ISpecies[]) - Method in class etomica.nbr.molecule.PotentialMasterNbrMolecular
 
addPotential(IPotentialAtomic, AtomsetIteratorBasisDependent, IAtomType[]) - Method in class etomica.nbr.PotentialGroupNbr
 
addPotential(IPotentialMolecular, ISpecies[]) - Method in class etomica.nbr.PotentialMasterHybrid
 
addPotential(IPotentialMolecular, ISpecies[]) - Method in class etomica.nbr.PotentialMasterNbr
 
addPotential(IPotential) - Method in class etomica.potential.PotentialArray
Identifies the given potential to this type instance and returns the index assigned to it.
addPotential(IPotential, IAtomType) - Method in class etomica.potential.PotentialArrayByType
Identifies the given potential to this type instance and returns the index assigned to it.
addPotential(IPotentialMolecular) - Method in class etomica.potential.PotentialArrayMolecular
Identifies the given potential to this type instance and returns the index assigned to it.
addPotential(IPotentialAtomic, IAtomType[]) - Method in class etomica.potential.PotentialGroup
Adds the given potential and sets it up to apply to the atoms in the basis having the given types.
addPotential(IPotentialAtomic, AtomsetIteratorBasisDependent) - Method in class etomica.potential.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, IAtomType[]) - Method in class etomica.potential.PotentialGroup
 
addPotential(IPotentialMolecular, ISpecies[]) - Method in class etomica.potential.PotentialMaster
 
addPotential(IPotentialAtomic, IAtomType[]) - Method in class etomica.potential.PotentialMaster
 
addPotential(IPotentialMolecular, MoleculesetIteratorPDT, ISpecies[]) - Method in class etomica.potential.PotentialMaster
 
addPotential(IPotentialMolecular) - Method in class etomica.potential.PotentialMasterLrc
 
addPotential(IPotentialAtomic) - Method in class etomica.potential.PotentialMasterLrc
 
addPotential(IPotentialMolecular, ISpecies[]) - Method in class etomica.potential.PotentialMasterMonatomic
 
addPotential(IPotentialAtomic, IAtomType[]) - Method in class etomica.potential.PotentialMasterMonatomic
 
addPotentialNbrList(IPotentialAtomic, IAtomType[], NeighborCriterion) - Method in class etomica.nbr.list.PotentialMasterList
Add the given potential to be used for the given atom types and the given criterion.
addPropertyChangeListener(PropertyChangeListener) - Method in class etomica.graphics.Display
 
addPropertyChangeListener(PropertyChangeListener) - Method in class etomica.util.Grabber.ActionCornerSetter
 
addRangedPotential(IPotentialMolecular, ISpecies) - Method in class etomica.nbr.molecule.PotentialMasterNbrMolecular
 
addRangedPotential(IPotentialAtomic, IAtomType) - Method in class etomica.nbr.PotentialMasterNbr
 
addRangedPotentialForSpecies(IPotentialMolecular, ISpecies[]) - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular
Adds the potential as a ranged potential that applies to the given AtomTypes.
addRangedPotentialForSpecies(IPotentialMolecular, ISpecies[]) - Method in class etomica.nbr.molecule.PotentialMasterNbrMolecular
 
addRangedPotentialForTypes(IPotentialAtomic, IAtomType[]) - Method in class etomica.nbr.list.PotentialMasterList
Adds the potential as a ranged potential that applies to the given AtomTypes.
addRangedPotentialForTypes(IPotentialAtomic, IAtomType[]) - Method in class etomica.nbr.PotentialMasterHybrid
 
addRangedPotentialForTypes(IPotentialAtomic, IAtomType[]) - Method in class etomica.nbr.PotentialMasterNbr
 
addRangedPotentialForTypes(IPotentialAtomic, IAtomType[]) - Method in class etomica.nbr.site.PotentialMasterSite
 
addSpecies(ISpecies) - Method in interface etomica.api.ISimulation
Adds species to the list of all ISpecies in the simulation, and adds notifies all IBoxes of the new ISpecies.
addSpecies(ISpecies) - Method in class etomica.config.ConfigurationLatticeWithPlane
 
addSpecies(ISpecies) - Method in class etomica.simulation.Simulation
 
addSpeciesNotify(ISpecies) - Method in interface etomica.api.IBox
Notifies the IBox that the given species has been added to the simulation.
addSpeciesNotify(ISpecies) - Method in class etomica.box.Box
 
addTag(DataTag) - Method in class etomica.data.DataInfo
Adds the tag
addTag(DataTag) - Method in interface etomica.data.IEtomicaDataInfo
Adds the tag to this IDataInfo object.
addTag(DataTag) - Method in class etomica.data.types.DataGroup.DataInfoGroup
 
addTags(DataTag[]) - Method in class etomica.data.DataInfo
Convenience method to add all of the given tags.
addTags(DataTag[]) - Method in interface etomica.data.IEtomicaDataInfo
Convenience method to add all of the given tags.
addTags(DataTag[]) - Method in class etomica.data.types.DataGroup.DataInfoGroup
 
addUpNbr(IAtom, int) - Method in class etomica.nbr.list.AtomNeighborLists
Adds the given atom as a "down" neighbor interacting via the potential with the given index.
addUpNbr(IMolecule, int) - Method in class etomica.nbr.list.molecule.MoleculeNeighborLists
Adds the given atom as a "down" neighbor interacting via the potential with the given index.
addValue(double) - Method in interface etomica.util.Histogram
Adds the given value to the Histogram
addValue(double) - Method in class etomica.util.HistogramCollapsing
 
addValue(double) - Method in class etomica.util.HistogramDiscrete
 
addValue(double) - Method in class etomica.util.HistogramExpanding
 
addValue(double, double) - Method in class etomica.util.HistogramNotSoSimple
 
addValue(double) - Method in class etomica.util.HistogramNotSoSimple
 
addValue(double, double) - Method in class etomica.util.HistogramReweightedData
 
addValue(double) - Method in class etomica.util.HistogramReweightedData
 
addValue(double) - Method in class etomica.util.HistogramSimple
 
addValue(double, double) - Method in interface etomica.util.History
Adds the given x, y pair to the History.
addValue(double, double) - Method in class etomica.util.HistoryCollapsingAverage
adds data to the history.
addValue(double, double) - Method in class etomica.util.HistoryCollapsingDiscard
adds data to the history.
addValue(double, double) - Method in class etomica.util.HistoryComplete
 
addValue(double, double) - Method in class etomica.util.HistoryScrolling
 
addValueChangedListener(DeviceBoxValueChangedListener) - Method in class etomica.graphics.DeviceBox
Add an object to be notified when the DeviceBox value to changes
adjustInterval - Variable in class etomica.integrator.mcmove.MCMoveStepTracker
 
adjustStep - Variable in class etomica.integrator.mcmove.MCMoveStepTracker
 
adjustStepSize() - Method in class etomica.integrator.mcmove.MCMoveStepTracker
 
advanceAcrossTimeStep(double) - Method in class etomica.integrator.IntegratorHard
Advances all atom coordinates by tStep, without any intervening collisions.
advanceAcrossTimeStep(double) - Method in class etomica.potential.P1HardMovingBoundary
 
affectedAtomIterator - Variable in class etomica.integrator.mcmove.MCMoveAtom
 
affectedAtomIterator - Variable in class etomica.integrator.mcmove.MCMoveBoxSize
 
affectedAtomIterator - Variable in class etomica.integrator.mcmove.MCMoveDimer
 
affectedAtomIterator - Variable in class etomica.integrator.mcmove.MCMoveDimerRotate
 
affectedAtomIterator - Variable in class etomica.integrator.mcmove.MCMoveInsertDelete
 
affectedAtomIterator - Variable in class etomica.integrator.mcmove.MCMoveMolecule
 
affectedAtomIterator - Variable in class etomica.integrator.mcmove.MCMoveVolume
 
affectedAtoms(IBox) - Method in class etomica.integrator.mcmove.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() - Method in class etomica.integrator.mcmove.MCMoveAtom
 
affectedAtoms(IBox) - Method in class etomica.integrator.mcmove.MCMoveBox
 
affectedAtoms() - Method in class etomica.integrator.mcmove.MCMoveBox
 
affectedAtoms() - Method in class etomica.integrator.mcmove.MCMoveBoxSize
 
affectedAtoms - Variable in class etomica.integrator.mcmove.MCMoveDimer
 
affectedAtoms() - Method in class etomica.integrator.mcmove.MCMoveDimer
 
affectedAtoms - Variable in class etomica.integrator.mcmove.MCMoveDimerRotate
 
affectedAtoms() - Method in class etomica.integrator.mcmove.MCMoveDimerRotate
 
affectedAtoms() - Method in class etomica.integrator.mcmove.MCMoveInsertDelete
Returns an iterator giving molecule that is being added or deleted in the current or most recent trial.
affectedAtoms() - Method in class etomica.integrator.mcmove.MCMoveMolecule
 
affectedAtoms(IBox) - Method in class etomica.integrator.mcmove.MCMoveMoleculeExchange
 
affectedAtoms() - Method in class etomica.integrator.mcmove.MCMoveSemigrand
 
affectedAtoms(IBox) - Method in class etomica.integrator.mcmove.MCMoveSwapConfiguration
 
affectedAtoms() - Method in class etomica.integrator.mcmove.MCMoveVolume
 
affectedAtoms(IBox) - Method in class etomica.integrator.mcmove.MCMoveVolumeExchange
 
affectedMoleculeIterator - Variable in class etomica.integrator.mcmove.MCMoveMolecule
 
affectedMolecules(IBox) - Method in interface etomica.integrator.mcmove.MCMoveMolecular
 
affectedMolecules(IBox) - Method in class etomica.integrator.mcmove.MCMoveMolecule
 
Agent(ISpace) - Constructor for class etomica.integrator.IntegratorConNVT.Agent
 
Agent(ISpace) - Constructor for class etomica.integrator.IntegratorGear4.Agent
 
Agent(IAtom, IntegratorHard) - Constructor for class etomica.integrator.IntegratorHard.Agent
 
Agent(ISpace) - Constructor for class etomica.integrator.IntegratorVerlet.Agent
 
agentClass - Variable in class etomica.atom.AtomLeafAgentManager
 
AgentIterator(AtomLeafAgentManager<E>) - Constructor for class etomica.atom.AtomLeafAgentManager.AgentIterator
 
AgentIterator(AtomTypeAgentManager) - Constructor for class etomica.atom.AtomTypeAgentManager.AgentIterator
 
AgentIterator(MoleculeAgentManager) - Constructor for class etomica.atom.MoleculeAgentManager.AgentIterator
 
AgentIterator(SpeciesAgentManager) - Constructor for class etomica.atom.SpeciesAgentManager.AgentIterator
 
AgentIterator(BoxAgentManager<E>) - Constructor for class etomica.box.BoxAgentManager.AgentIterator
 
agentIterator - Variable in class etomica.potential.PotentialCalculationForceSum
 
agentManager - Variable in class etomica.atom.DiameterHashByType
 
agentManager - Variable in class etomica.graphics.ColorSchemeCollectiveAgent
 
agentManager - Variable in class etomica.integrator.IntegratorConNVT
 
agentManager - Variable in class etomica.integrator.IntegratorGear4
 
agentManager - Variable in class etomica.integrator.IntegratorHard
 
agentManager - Variable in class etomica.integrator.IntegratorVelocityVerlet
 
agentManager - Variable in class etomica.integrator.IntegratorVelocityVerletShake
 
agentManager - Variable in class etomica.integrator.IntegratorVerlet
 
agentManager - Variable in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
 
agentManager - Variable in class etomica.nbr.cell.NeighborCellManager
 
agentManager - Variable in class etomica.nbr.CriterionPositionWall
 
agentManager - Variable in class etomica.nbr.CriterionSimple
 
agentManager - Variable in class etomica.nbr.molecule.CriterionSimpleMolecular
 
agentManager1Body - Variable in class etomica.nbr.list.molecule.NeighborListManagerMolecular
 
agentManager1Body - Variable in class etomica.nbr.list.NeighborListManager
 
agentManager2Body - Variable in class etomica.nbr.list.molecule.NeighborListManagerMolecular
 
agentManager2Body - Variable in class etomica.nbr.list.NeighborListManager
 
agents - Variable in class etomica.atom.AtomLeafAgentManager
 
agents - Variable in class etomica.atom.AtomTypeAgentManager
 
agents - Variable in class etomica.atom.MoleculeAgentManager
 
agents - Variable in class etomica.atom.SpeciesAgentManager
 
agents - Variable in class etomica.box.BoxAgentManager
 
agents - Variable in class etomica.potential.P2SemiclassicalAtomic
 
agents - Variable in class etomica.potential.P2SemiclassicalMolecular
 
agentSource - Variable in class etomica.atom.AtomLeafAgentManager
 
agentSource - Variable in class etomica.atom.MoleculeAgentManager
 
agentSource - Variable in class etomica.box.BoxAgentManager
 
ai - Variable in class etomica.graphics.DeviceDelaySlider
 
Ai - Variable in class etomica.potential.PotentialCalculationPhiSum
 
aiInner - Variable in class etomica.atom.iterator.ApiInnerVariable
The iterators used to generate the sets of atoms.
aiInner - Variable in class etomica.atom.iterator.ApiIntergroup
 
aiInner - Variable in class etomica.atom.iterator.MpiInnerVariable
The iterators used to generate the sets of atoms.
aiInnerSize - Variable in class etomica.atom.iterator.ApiIntergroupExchange
 
aiOuter - Variable in class etomica.atom.iterator.ApiInnerVariable
 
aiOuter - Variable in class etomica.atom.iterator.ApiIntergroup
 
aiOuter - Variable in class etomica.atom.iterator.MpiInnerVariable
 
aiOuter - Variable in class etomica.atom.iterator.MpiIntraspecies1A
 
aiOuterSize - Variable in class etomica.atom.iterator.ApiIntergroupExchange
 
aj - Variable in class etomica.models.water.P2WaterSzalewicz
 
Aj - Variable in class etomica.potential.PotentialCalculationPhiSum
 
aj3 - Variable in class etomica.models.water.P2WaterSzalewicz
 
AkimaSpline - Class in etomica.util.numerical
DataProcessor that interpolates incoming data using an Akima spline interpolation scheme.
AkimaSpline() - Constructor for class etomica.util.numerical.AkimaSpline
 
AkimaSplineSmoother - Class in etomica.util.numerical
Optimization algorithm which attempts to smooth data without moving any point far from its original location.
AkimaSplineSmoother(IRandom) - Constructor for class etomica.util.numerical.AkimaSplineSmoother
 
AkimaSplineSmootherApp - Class in etomica.util.numerical
App to drive AkimaSplineSmoother
AkimaSplineSmootherApp(String) - Constructor for class etomica.util.numerical.AkimaSplineSmootherApp
 
AkimaSplineSmootherApp.Applet - Class in etomica.util.numerical
 
AkimaSplineSmootherApp.IntegratorSmoother - Class in etomica.util.numerical
 
AkimaSplineSmootherApp.PlotAction - Class in etomica.util.numerical
 
AkimaSplineSmootherDy - Class in etomica.util.numerical
Optimization algorithm which attempts to smooth data without moving any point far from its original location.
AkimaSplineSmootherDy(IRandom) - Constructor for class etomica.util.numerical.AkimaSplineSmootherDy
 
AkimaSplineSmootherDyApp - Class in etomica.util.numerical
App to drive AkimaSplineSmoother
AkimaSplineSmootherDyApp(String) - Constructor for class etomica.util.numerical.AkimaSplineSmootherDyApp
 
AkimaSplineSmootherDyApp.Applet - Class in etomica.util.numerical
 
AkimaSplineSmootherDyApp.IntegratorSmoother - Class in etomica.util.numerical
 
AkimaSplineSmootherDyApp.PlotAction - Class in etomica.util.numerical
 
AkimaSplineSmootherMain - Class in etomica.util.numerical
Main method to drive AkimaSplineSmoother
AkimaSplineSmootherMain() - Constructor for class etomica.util.numerical.AkimaSplineSmootherMain
 
AL10 - Static variable in class etomica.math.Gamma
 
al1l2l0(int, int, int, double, double, double) - Method in class etomica.potential.P2HydrogenPatkowski
 
al1l2l0(int, int, int, double, double, double) - Method in class etomica.potential.P2HydrogenPatkowskiAtomic
 
alamda - Variable in class etomica.util.numerical.NonLinearCurveDiffFitting
 
alamda - Variable in class etomica.util.numerical.NonLinearCurveFitting
 
alfst - Static variable in class etomica.potential.P2WaterPotentialsJankowski
 
align - Variable in class etomica.graphics.DisplayBox
 
align - Variable in class etomica.graphics.DisplayPolytope
 
align_on_z_axis(IVectorMutable[], IVectorMutable[]) - Static method in class etomica.potential.P2WaterPotentialsJankowski
 
alignedV1 - Static variable in class etomica.potential.P2WaterPotentialsJankowski
 
alignedV2 - Static variable in class etomica.potential.P2WaterPotentialsJankowski
 
ALL - Static variable in class etomica.units.Prefix
 
allAtoms - Variable in class etomica.data.meter.MeterRDFPC
 
allAtoms - Variable in class etomica.integrator.IntegratorVelocityVerlet
 
allAtoms - Variable in class etomica.integrator.IntegratorVelocityVerletShake
 
allAtoms(MoleculesetIterator, MoleculesetAction) - Static method in class etomica.junit.atom.iterator.MoleculeIteratorTestAbstract
 
allAtoms(IAtomList) - Static method in class etomica.util.Debug
determines if all of the atoms in the given array are set to be debugged (via ATOMx_NUM and setAtoms(box)).
allAtoms(IMoleculeList) - Static method in class etomica.util.Debug
determines if all of the atoms in the given array are set to be debugged (via ATOMx_NUM and setAtoms(box)).
allAtoms - Variable in class etomica.util.numerical.CalcGradientDifferentiable
 
allCriteria - Variable in class etomica.nbr.list.molecule.PotentialMasterListMolecular
 
allCriteria - Variable in class etomica.nbr.list.PotentialMasterList
 
AllData(long, IData, IData) - Constructor for class etomica.data.AccumulatorAverageBlockless.AllData
 
allMoleculeList - Variable in class etomica.box.Box
 
allOr - Variable in class etomica.models.water.P2WaterSzalewicz
 
allOr0 - Variable in class etomica.models.co2.P2CO2H2OWheatley
 
allOr0 - Variable in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
 
allOr0 - Variable in class etomica.potential.P2NitrogenHellmann.P2N2QFH
 
allOr1 - Variable in class etomica.models.co2.P2CO2H2OWheatley
 
allOr1 - Variable in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
 
allOr1 - Variable in class etomica.potential.P2NitrogenHellmann.P2N2QFH
 
ALLOWED - Static variable in class etomica.units.Prefix
Constant used when invoking constructor of SimpleUnit class to indicate that the unit permits the use of a prefix.
allPotentials - Variable in class etomica.nbr.molecule.PotentialMasterNbrMolecular
 
allPotentials - Variable in class etomica.nbr.PotentialMasterNbr
 
allPotentials - Variable in class etomica.potential.PotentialMasterMonatomic
 
alpha - Variable in class etomica.models.co2.P2CO2Hellmann
 
alpha - Variable in class etomica.potential.EwaldSummation
 
alpha - Variable in class etomica.potential.EwaldSumMolecules
 
alpha - Static variable in class etomica.potential.P1HydrogenMielke
 
alpha - Static variable in class etomica.potential.P2HePCKLJS
 
alpha - Variable in class etomica.potential.P2NitrogenHellmann
 
alpha - Variable in class etomica.potential.P3AxilrodTeller.MyAgent
 
alpha - Variable in class etomica.potential.P3CPSNonAdditiveHe
 
alpha - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
 
alpha - Variable in class etomica.potential.P3CPSNonAdditiveHeOrig
 
alpha - Variable in class etomica.potential.P3CPSNonAdditiveHeSimplified
 
alpha - Variable in class etomica.potential.P3Induction
 
alpha - Variable in class etomica.potential.P3Induction.MyAgent
 
alpha - Variable in class etomica.util.numerical.NonLinearCurveDiffFitting
 
alpha - Variable in class etomica.util.numerical.NonLinearCurveFitting
 
alpha2 - Variable in class etomica.potential.EwaldSummation
 
alpha3 - Variable in class etomica.potential.EwaldSummation
 
alphaA - Static variable in class etomica.models.co2.P2CO2Hellmann
 
alphaA - Static variable in class etomica.potential.P2NitrogenHellmann
 
alphaB - Static variable in class etomica.models.co2.P2CO2Hellmann
 
alphaB - Static variable in class etomica.potential.P2NitrogenHellmann
 
alphaIso - Static variable in class etomica.potential.P3NitrogenHellmannNonAdditive
 
alphaIsoSim - Static variable in class etomica.potential.P3NitrogenHellmannNonAdditive
 
alphaPar - Variable in class etomica.models.co2.PNCO2GCPM
 
alphaPar - Variable in class etomica.models.co2.PNGCPM.GCPMAgent
 
alphaPerp - Variable in class etomica.models.co2.PNCO2GCPM
 
alphaPerp - Variable in class etomica.models.co2.PNGCPM.GCPMAgent
 
alphaPol - Variable in class etomica.models.water.PNWaterGCPM
 
ALPREC - Static variable in class etomica.math.Gamma
 
Ampere - Class in etomica.units
The ampere unit of electrical current.
ANDERSEN - Static variable in class etomica.integrator.IntegratorMD.ThermostatType
 
ANDERSEN_SCALING - Static variable in class etomica.integrator.IntegratorMD.ThermostatType
 
ANDERSEN_SINGLE - Static variable in class etomica.integrator.IntegratorMD.ThermostatType
 
angle - Variable in class etomica.lattice.crystal.Primitive
 
angle - Variable in class etomica.potential.P3BondAngle
 
angle - Variable in class etomica.potential.P3CPSNonAdditiveHeOrig
 
angle - Variable in class etomica.space2d.Orientation2D
 
Angle - Class in etomica.units
Base for all angular units.
angle() - Method in class etomica.units.systems.CGS
 
angle() - Method in class etomica.units.systems.LJ
 
angle() - Method in class etomica.units.systems.MKS
 
angle() - Method in class etomica.units.systems.UnitSystem
 
angle() - Method in class etomica.units.systems.UnitSystem.Sim
 
angleHOH - Static variable in class etomica.models.water.ConformationWater3P
 
angleHOH - Static variable in class etomica.models.water.ConformationWaterTIP4P
 
angles - Static variable in class etomica.potential.P2WaterPotentialsJankowski
 
Angstrom - Class in etomica.units
 
angularMomentum - Variable in class etomica.atom.MoleculeOrientedDynamic
 
angularVelocity - Variable in class etomica.atom.AtomOrientedDynamic
 
angularVelocity - Variable in class etomica.data.meter.MeterKineticEnergyRigid
 
ANIntergroupCoupled - Class in etomica.atom.iterator
Iterator that returns coupled iterates of any size; the first set contains the first atom from each basis.
ANIntergroupCoupled(int) - Constructor for class etomica.atom.iterator.ANIntergroupCoupled
 
ANIntergroupExchange - Class in etomica.atom.iterator
 
ANIntergroupExchange(int) - Constructor for class etomica.atom.iterator.ANIntergroupExchange
 
anIntragroupExchange - Variable in class etomica.atom.iterator.ANIntergroupExchange
 
ANIntragroupExchange - Class in etomica.atom.iterator
 
ANIntragroupExchange(int, int) - Constructor for class etomica.atom.iterator.ANIntragroupExchange
 
anoise - Static variable in class etomica.potential.P2WaterPotentialsJankowski
 
anx - Static variable in class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
 
anyAtom(IAtomList) - Static method in class etomica.util.Debug
determines whether any of the atoms in the given array are set to be debugged (via ATOMx_NUM)
anyMolecule(IMoleculeList) - Static method in class etomica.util.Debug
determines whether any of the atoms in the given array are set to be debugged (via ATOMx_NUM)
api - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbrCell
 
Api1ACell - Class in etomica.nbr.cell
Generates pairs that are cell-based neighbors of a specific Atom.
Api1ACell(int, double, BoxAgentManager) - Constructor for class etomica.nbr.cell.Api1ACell
Constructor makes iterator that must have box specified and then be reset() before iteration.
Api1ASite - Class in etomica.nbr.site
Iteration is performed using site lists.
Api1ASite(int, BoxAgentManager) - Constructor for class etomica.nbr.site.Api1ASite
Constructor makes iterator that must have box specified and then be reset() before iteration.
ApiAACell - Class in etomica.nbr.cell
Returns iterates formed from all cell-based neighbor pairs.
ApiAACell(int, double, IBox) - Constructor for class etomica.nbr.cell.ApiAACell
Constructor makes iterator that must have box specified and then be reset() before iteration.
ApiBuilder - Class in etomica.atom.iterator
Provides static methods for construction of some useful pair iterators.
ApiBuilderTest - Class in etomica.junit.atom.iterator
Tests the iterators made by the various static methods in ApiBuilder.
ApiBuilderTest() - Constructor for class etomica.junit.atom.iterator.ApiBuilderTest
 
apiDown - Variable in class etomica.atom.iterator.MpiIntraspecies1A
 
ApiIndexList - Class in etomica.atom.iterator
Iterator that returns intramolecular pairs of atoms with specific indices.
ApiIndexList(int[][]) - Constructor for class etomica.atom.iterator.ApiIndexList
Constructs iterator without defining atoms in pair.
ApiInnerVariable - Class in 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) - Constructor for class etomica.atom.iterator.ApiInnerVariable
Construct a pair iterator using the given atom iterators.
ApiInnerVariable(AtomIterator, AtomIteratorAtomDependent, boolean) - Constructor for class etomica.atom.iterator.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 - Class in etomica.atom.iterator
Returns all pairs formed from two different untabbed lists of atoms.
ApiInterArrayList() - Constructor for class etomica.atom.iterator.ApiInterArrayList
Construct iterator with an empty lists.
ApiInterArrayList(IAtomList, IAtomList) - Constructor for class etomica.atom.iterator.ApiInterArrayList
Constructs iterator to return pairs from the given lists.
ApiIntergroup - Class in etomica.atom.iterator
Iterator that returns pairs formed using two different basis atoms, so that the iterates are taken from two different groups.
ApiIntergroup() - Constructor for class etomica.atom.iterator.ApiIntergroup
Default iterator is an ApiInnerFixed formed from two AtomIteratorBasis instances.
ApiIntergroup(AtomIteratorBasisDependent, AtomIteratorBasisDependent) - Constructor for class etomica.atom.iterator.ApiIntergroup
Constructs a pair iterator that returns iterates from the given pairIterator, which is expected to contain two basis-dependent iterators.
ApiIntergroupCoupled - Class in etomica.atom.iterator
Iterator that returns coupled iterates; the first pair contains the first atom from each basis.
ApiIntergroupCoupled() - Constructor for class etomica.atom.iterator.ApiIntergroupCoupled
 
ApiIntergroupCoupled(AtomIteratorBasis, AtomIteratorBasis) - Constructor for class etomica.atom.iterator.ApiIntergroupCoupled
 
ApiIntergroupExchange - Class in etomica.atom.iterator
 
ApiIntergroupExchange(int) - Constructor for class etomica.atom.iterator.ApiIntergroupExchange
 
ApiIntergroupIntraSpecies - Class in 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) - Constructor for class etomica.atom.iterator.ApiIntergroupIntraSpecies
Constructs a pair iterator that returns iterates from the given pairIterator, which is expected to contain two basis-dependent iterators.
ApiIntraArrayList - Class in etomica.atom.iterator
Returns all pairs formed from a single list of atoms.
ApiIntraArrayList() - Constructor for class etomica.atom.iterator.ApiIntraArrayList
Construct iterator with an empty list.
ApiIntraArrayList(IAtomList) - Constructor for class etomica.atom.iterator.ApiIntraArrayList
Constructs iterator to return pairs from the given list.
ApiIntragroup - Class in etomica.atom.iterator
Returns iterates from the childList of a single basis atom.
ApiIntragroup() - Constructor for class etomica.atom.iterator.ApiIntragroup
Constructor makes iterator that must have basis specified and then be reset() before iteration.
ApiIntragroup(AtomIteratorAtomDependent, AtomIteratorAtomDependent) - Constructor for class etomica.atom.iterator.ApiIntragroup
 
ApiIntragroup(AtomsetIteratorBasisDependent, AtomIteratorAtomDependent, AtomIteratorAtomDependent) - Constructor for class etomica.atom.iterator.ApiIntragroup
 
ApiLeafAtoms - Class in etomica.atom.iterator
Iterator that returns all pairs that can be formed from all leaf atoms of a given box.
ApiLeafAtoms() - Constructor for class etomica.atom.iterator.ApiLeafAtoms
Creates new pair iterator that requires reset() before beginning iteration.
ApiLeafAtomsTest - Class in etomica.junit.atom.iterator
Unit test for ApiLeafAtoms
ApiLeafAtomsTest() - Constructor for class etomica.junit.atom.iterator.ApiLeafAtomsTest
 
apiUp - Variable in class etomica.atom.iterator.MpiIntraspecies1A
 
Applet() - Constructor for class etomica.graphics.DisplayPolytope.Applet
 
Applet() - Constructor for class etomica.simulation.prototypes.LjMd3D.Applet
 
Applet() - Constructor for class etomica.util.numerical.AkimaSplineSmootherApp.Applet
 
Applet() - Constructor for class etomica.util.numerical.AkimaSplineSmootherDyApp.Applet
 
applyExponentPattern(String) - Method in class etomica.util.ScientificFormat
 
applyLocalizedPattern(String) - Method in class etomica.util.ScientificFormat
 
applyMantissaPattern(String) - Method in class etomica.util.ScientificFormat
 
applyPattern(String) - Method in class etomica.util.ScientificFormat
apply this pattern
applyTranslationRotation() - Method in class etomica.math.geometry.Polytope
Calculate transformed vertices from current values of vertices, position, and orientation.
appName - Variable in class etomica.graphics.SimulationGraphic
 
Area - Class in etomica.units
Base for all area units.
area() - Method in class etomica.units.systems.CGS
 
area() - Method in class etomica.units.systems.LJ
 
area() - Method in class etomica.units.systems.MKS
 
area() - Method in class etomica.units.systems.UnitSystem
 
area() - Method in class etomica.units.systems.UnitSystem.Sim
 
arep - Variable in class etomica.potential.P2HydrogenHinde
 
arep - Variable in class etomica.potential.P2HydrogenHindeAtomic
 
aResidualFcc(double, double) - Static method in class etomica.statmech.LennardJones
Molar Helmholtz free energy for the fcc solid, in excess of an ideal gas at the same temperature and density.
arg() - Method in class etomica.math.Complex
Argument of this Complex number, the angle in radians with the x-axis in polar coordinates.
Argon - Class in etomica.chem.elements
Class for the Argon element.
Argon(String) - Constructor for class etomica.chem.elements.Argon
 
Argon(String, double) - Constructor for class etomica.chem.elements.Argon
 
arrayCollect(String[], String[]) - Static method in class etomica.util.Strings
Takes the elements of two string arrays and collects them into a new array containing both sets of strings.
arrayIndex(int[]) - Method in class etomica.lattice.RectangularLattice
Returns the index in the 1-d array for the site corresponding to the given lattice index.
ArrayReader1D - Class in etomica.util.numerical
Reads in lots of 1D arrays from a file.
ArrayReader1D() - Constructor for class etomica.util.numerical.ArrayReader1D
 
Arrays - Class in etomica.util
Non-instantiable class with static utility methods for working with arrays.
arrayShape - Variable in class etomica.data.types.DataDoubleArray.DataInfoDoubleArray
 
arrayShape - Variable in class etomica.data.types.DataDoubleBDArray.DataInfoDoubleBDArray
 
Asolid(double) - Static method in class etomica.statmech.HardSphereFluid
Returns the difference between absolute free energies between the given densities for solid (FCC) hard spheres.
Asolid(double, int) - Static method in class etomica.statmech.HardSphereFluid
 
Asolid(double) - Static method in class etomica.statmech.HardSphereSolid
Returns the difference between absolute free energies between the given densities for solid (FCC) hard spheres.
Asolid(double, int) - Static method in class etomica.statmech.HardSphereSolid
 
assignCell(IMolecule) - Method in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
Assigns the cell for the given atom.
assignCell(IAtom) - Method in class etomica.nbr.cell.NeighborCellManager
Assigns the cell for the given atom.
assignCellAll() - Method in interface etomica.box.BoxCellManager
Assigns cells to all molecules in the box.
assignCellAll() - Method in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
Assigns cells to all interacting atoms in the box.
assignCellAll() - Method in class etomica.nbr.cell.NeighborCellManager
Assigns cells to all interacting atoms in the box.
assignCellAll() - Method in class etomica.nbr.site.NeighborSiteManager
Should not be called, because cell assignments are made as atoms are created.
assignColumnFrom(int, double[]) - Method in class etomica.data.types.DataDoubleArray
Assigns values in given array to the i-th "hypercolumn" of this data array.
assignColumnFrom(int, BigDecimal[]) - Method in class etomica.data.types.DataDoubleBDArray
Assigns values in given array to the i-th "hypercolumn" of this data array.
assignColumnTo(int, double[]) - Method in class etomica.data.types.DataDoubleArray
Assigns values in the i=th "hypercolumn" of this array to the given array.
assignColumnTo(int, BigDecimal[]) - Method in class etomica.data.types.DataDoubleBDArray
Assigns values in the i=th "hypercolumn" of this array to the given array.
assignSubsectionFrom(int[], double[]) - Method in class etomica.data.types.DataDoubleArray
Assigns values in the given array to the subsection of this array beginning at the specified index.
assignSubsectionFrom(int[], double[]) - Method in class etomica.data.types.DataDoubleBDArray
Assigns values in the given array to the subsection of this array beginning at the specified index.
assignTo(double[]) - Method in interface etomica.api.IVector
Assigns the components of this vector to the elements of the given array.
assignTo(double[]) - Method in interface etomica.data.IData
Fills the given array with the values held by this Data instance.
assignTo(double[]) - Method in class etomica.data.types.DataDouble
Returns a new one-element array formed from the current value of this instance.
assignTo(double[]) - Method in class etomica.data.types.DataDoubleArray
Returns the encapsulated array, implementing the Data interface.
assignTo(double[]) - Method in class etomica.data.types.DataDoubleBDArray
Returns the encapsulated array, implementing the Data interface.
assignTo(double[]) - Method in class etomica.data.types.DataGroup
 
assignTo(double[]) - Method in class etomica.data.types.DataTable
Returns a new array formed from the values held by the data instance.
assignTo(double[]) - Method in class etomica.data.types.DataTensor
Returns a new array formed by the elements of the wrapped tensor.
assignTo(double[]) - Method in class etomica.data.types.DataVector
Assigns the elements of the wrapped vector to the given array.
assignTo(IVectorMutable[]) - Method in interface etomica.space.Tensor
Assigns the tensor elements column-wise to the given vectors.
assignTo(double[]) - Method in interface etomica.space.Tensor
Fills the given array with the elements of this tensor.
assignTo(double[][]) - Method in interface etomica.space.Tensor
 
assignTo(IVectorMutable[]) - Method in class etomica.space1d.Tensor1D
 
assignTo(double[]) - Method in class etomica.space1d.Tensor1D
 
assignTo(double[][]) - Method in class etomica.space1d.Tensor1D
 
assignTo(double[]) - Method in class etomica.space1d.Vector1D
 
assignTo(IVectorMutable[]) - Method in class etomica.space2d.Tensor2D
 
assignTo(double[]) - Method in class etomica.space2d.Tensor2D
 
assignTo(double[][]) - Method in class etomica.space2d.Tensor2D
 
assignTo(double[]) - Method in class etomica.space2d.Vector2D
 
assignTo(IVectorMutable[]) - Method in class etomica.space3d.Tensor3D
 
assignTo(double[]) - Method in class etomica.space3d.Tensor3D
 
assignTo(double[][]) - Method in class etomica.space3d.Tensor3D
 
assignTo(double[]) - Method in class etomica.space3d.Vector3D
 
assignTo(IVectorMutable[]) - Method in class etomica.spaceNd.TensorND
 
assignTo(double[]) - Method in class etomica.spaceNd.TensorND
 
assignTo(double[][]) - Method in class etomica.spaceNd.TensorND
 
assignTo(double[]) - Method in class etomica.spaceNd.VectorND
 
AssociatedPolynomial - Class in etomica.util
 
AssociatedPolynomial() - Constructor for class etomica.util.AssociatedPolynomial
 
asymp(double, double, double, double) - Method in class etomica.potential.P2HydrogenPatkowski
 
asymp(double, double, double, double) - Method in class etomica.potential.P2HydrogenPatkowskiAtomic
 
Atom - Class in etomica.atom
Atom that represents a physical atom with a position.
Atom(ISpace, IAtomType) - Constructor for class etomica.atom.Atom
 
Atom(ISpace) - Constructor for class etomica.atom.Atom
Makes a simple atom for the given space.
atom - Variable in class etomica.atom.AtomSetSinglet
 
atom - Variable in class etomica.atom.MoleculeSetSinglet
 
atom - Variable in class etomica.box.BoxAtomEvent
 
atom - Variable in class etomica.integrator.IntegratorHard.Agent
 
atom() - Method in class etomica.integrator.IntegratorHard.Agent
 
atom - Variable in class etomica.integrator.mcmove.MCMoveAtom
 
atom - Variable in class etomica.integrator.mcmove.MCMoveDimer
 
atom - Variable in class etomica.integrator.mcmove.MCMoveDimerRotate
 
atom - Variable in class etomica.potential.PotentialReactive.BondChangeData
 
atom0 - Variable in class etomica.atom.AtomPair
 
atom0 - Variable in class etomica.atom.MoleculePair
 
atom1 - Variable in class etomica.atom.AtomPair
 
atom1 - Variable in class etomica.atom.iterator.ApiIntergroupExchange
 
atom1 - Variable in class etomica.atom.MoleculePair
 
atom1 - Variable in class etomica.data.DataSourceAtomDistance
 
atom1 - Variable in class etomica.integrator.mcmove.MCMoveDimer
 
atom1 - Variable in class etomica.integrator.mcmove.MCMoveDimerRotate
 
ATOM1_INDEX - Static variable in class etomica.util.Debug
Atom index of first atom of interest.
atom2 - Variable in class etomica.atom.iterator.ApiIntergroupExchange
 
atom2 - Variable in class etomica.data.DataSourceAtomDistance
 
ATOM2_INDEX - Static variable in class etomica.util.Debug
Atom index of second atom of interest.
atom_aC_A - Static variable in class etomica.action.IntegratorDimerApproach
 
atom_aC_B - Static variable in class etomica.action.IntegratorDimerApproach
 
atom_aH_A - Static variable in class etomica.action.IntegratorDimerApproach
 
atom_aH_B - Static variable in class etomica.action.IntegratorDimerApproach
 
atom_H1_A - Static variable in class etomica.action.IntegratorDimerApproach
 
atom_O_A - Static variable in class etomica.action.IntegratorDimerApproach
 
atom_O_B - Static variable in class etomica.action.IntegratorDimerApproach
 
ATOM_SIZE - Static variable in class etomica.util.Debug
The minimum allowable distance between Atoms.
AtomAction - Interface in etomica.action
Interface for a class that can perform an action on an atom.
AtomActionRandomizeVelocity - Class in 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) - Constructor for class etomica.action.AtomActionRandomizeVelocity
Constructs class to assign velocities according to the given temperature.
atomActionRandomizeVelocity - Variable in class etomica.action.BoxRandomizeMomenta
 
atomActionRandomizeVelocity - Variable in class etomica.integrator.IntegratorMD
 
AtomActionRotateBy - Class in 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(ISpace) - Constructor for class etomica.action.AtomActionRotateBy
 
atomActionRotateBy - Variable in class etomica.action.IntegratorDimerApproach
 
AtomActionTranslateBy - Class in etomica.action
Moves (translates) an atom by a specified vector amount.
AtomActionTranslateBy(ISpace) - Constructor for class etomica.action.AtomActionTranslateBy
 
atomActionTranslateBy - Variable in class etomica.action.IntegratorDimerApproach
 
atomActionTranslateTo - Variable in class etomica.config.ConfigurationLattice
 
atomActionTranslateTo - Variable in class etomica.config.ConfigurationLatticeSimple
 
atomAdded(IAtom) - Method in class etomica.box.BoxEventManager
 
AtomAgent(ISpace) - Constructor for class etomica.integrator.IntegratorRigidMatrixIterative.AtomAgent
 
atomAgentClass - Variable in class etomica.box.BoxAgentSourceAtomManager
 
atomAgentManager - Variable in class etomica.data.meter.MeterDipoleSumSquaredMappedAverage
 
atomAgentManager - Variable in class etomica.graphics.BondListener
 
atomAgentManager - Variable in class etomica.potential.EwaldSummation
 
atomAgentManager - Variable in class etomica.potential.EwaldSumMolecules
 
atomAgentManager - Variable in class etomica.potential.P1HarmonicSite
 
atomAgentSource - Variable in class etomica.box.BoxAgentSourceAtomManager
 
atomArray - Variable in class etomica.atom.iterator.TripletInnerSequential
 
AtomArrayList - Class in etomica.atom
 
AtomArrayList() - Constructor for class etomica.atom.AtomArrayList
 
AtomArrayList(int) - Constructor for class etomica.atom.AtomArrayList
 
AtomArrayListTest - Class in etomica.junit.atom
 
AtomArrayListTest() - Constructor for class etomica.junit.atom.AtomArrayListTest
 
AtomFilter - Interface in etomica.atom
Interface for a class that screens atoms according to some criterion.
atomFilter - Variable in class etomica.graphics.DisplayBox
 
AtomFilterCollective - Interface in etomica.atom
Filter that needs to be informed whenever something has changed and the filtered status of atoms should be redetermined.
AtomFilterInShape - Class in etomica.atom
Filter that accepts atom if it is inside a specified Shape instance.
AtomFilterInShape(Shape) - Constructor for class etomica.atom.AtomFilterInShape
Create filter in which position definition is given by atom's type.
AtomFilterStatic - Class in etomica.atom
 
atomGroupActionRotateBy - Variable in class etomica.action.IntegratorDimerApproach
 
atomGroupActionTranslateBy - Variable in class etomica.action.IntegratorDimerApproach
 
AtomGroupVelocityAverage - Class in etomica.atom
Calculates the mass average velocity over a set of atoms.
AtomGroupVelocityAverage(ISpace) - Constructor for class etomica.atom.AtomGroupVelocityAverage
 
AtomHydrogen - Class in etomica.atom
 
AtomHydrogen(ISpace, IAtomTypeOriented, double) - Constructor for class etomica.atom.AtomHydrogen
 
atomicNumber - Variable in class etomica.chem.elements.ElementChemical
 
atomicPotentials - Variable in class etomica.potential.PotentialMasterLrc
 
atomicTensor(IAtom, IAtom) - Method in interface etomica.models.water.P2Water4PSoft.AtomicTensorAtomicPair
 
atomicToMolecularD(IMolecule, IMolecule) - Method in class etomica.models.water.P2Water4PSoft
 
AtomIterator - Interface in etomica.atom.iterator
Interface for classes that loop over a set of atoms.
atomIterator - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
 
AtomIterator0() - Constructor for class etomica.potential.PotentialMaster.AtomIterator0
 
AtomIteratorAllLeafType - Class in etomica.atom.iterator
Iterator for all the molecules of a set of species in a box.
AtomIteratorAllLeafType(IAtomType[]) - Constructor for class etomica.atom.iterator.AtomIteratorAllLeafType
 
AtomIteratorArrayList - Class in etomica.atom.iterator
An atom iterator of the elements from an AtomArrayList (in proper sequence).
AtomIteratorArrayList(IteratorDirective.Direction) - Constructor for class etomica.atom.iterator.AtomIteratorArrayList
Constructs new iterator with an empty list.
AtomIteratorArrayList(IteratorDirective.Direction, int) - Constructor for class etomica.atom.iterator.AtomIteratorArrayList
Constructs new iterator set to iterate given list (upon reset).
AtomIteratorArrayList(IteratorDirective.Direction, int, AtomToIndex, AtomToAtomLeafList) - Constructor for class etomica.atom.iterator.AtomIteratorArrayList
 
AtomIteratorArrayListAdjacent - Class in etomica.atom.iterator
Returns one or both of the atoms adjacent to a specified atom in its parent's child list.
AtomIteratorArrayListAdjacent(IteratorDirective.Direction) - Constructor for class etomica.atom.iterator.AtomIteratorArrayListAdjacent
Constructor gives iterator not ready for iteration.
AtomIteratorArrayListAdjacent(IteratorDirective.Direction, AtomToIndex, AtomToAtomLeafList) - Constructor for class etomica.atom.iterator.AtomIteratorArrayListAdjacent
 
AtomIteratorArrayListAdjacentTest - Class in etomica.junit.atom.iterator
Unit test for AtomIteratorSequenceAdjacent
AtomIteratorArrayListAdjacentTest() - Constructor for class etomica.junit.atom.iterator.AtomIteratorArrayListAdjacentTest
 
AtomIteratorArrayListSimple - Class in etomica.atom.iterator
An atom iterator of the elements from an AtomArrayList (in proper sequence).
AtomIteratorArrayListSimple() - Constructor for class etomica.atom.iterator.AtomIteratorArrayListSimple
Constructs new iterator with an empty list.
AtomIteratorArrayListSimple(IAtomList) - Constructor for class etomica.atom.iterator.AtomIteratorArrayListSimple
Constructs new iterator set to iterate given list (upon reset).
AtomIteratorArrayListTest - Class in etomica.junit.atom.iterator
Unit test for AtomIteratorArrayList.
AtomIteratorArrayListTest() - Constructor for class etomica.junit.atom.iterator.AtomIteratorArrayListTest
 
AtomIteratorAtomDependent - Interface in etomica.atom.iterator
Interface for an atom iterator that can be altered by setting of an atom.
AtomIteratorBasis - Class in etomica.atom.iterator
Elementary basis-dependent iterator that gives atoms meeting specification of a basis and a target.
AtomIteratorBasis() - Constructor for class etomica.atom.iterator.AtomIteratorBasis
Constructor makes iterator in an unset condition; must set basis and call reset before beginning iteration.
AtomIteratorBasisAdjustableStart - Class in etomica.atom.iterator
Elementary basis-dependent iterator that gives atoms meeting specification of a basis and a target.
AtomIteratorBasisAdjustableStart() - Constructor for class etomica.atom.iterator.AtomIteratorBasisAdjustableStart
Constructor makes iterator in an unset condition; must set basis and call reset before beginning iteration.
AtomIteratorBasisDependent - Interface in etomica.atom.iterator
 
AtomIteratorBasisFilteredType - Class in etomica.atom.iterator
 
AtomIteratorBasisFilteredType(IAtomType) - Constructor for class etomica.atom.iterator.AtomIteratorBasisFilteredType
 
AtomIteratorBasisFilteredType2 - Class in etomica.atom.iterator
This iterator returns atoms that are one of two types.
AtomIteratorBasisFilteredType2(IAtomType, IAtomType) - Constructor for class etomica.atom.iterator.AtomIteratorBasisFilteredType2
 
AtomIteratorBasisTest - Class in etomica.junit.atom.iterator
Unit test for AtomIteratorSinglet class.
AtomIteratorBasisTest() - Constructor for class etomica.junit.atom.iterator.AtomIteratorBasisTest
 
AtomIteratorBoxDependent - Interface in etomica.atom.iterator
Interface indicating that an atom iterator can determine appropriate atoms for iteration given an arbitrary box.
AtomIteratorCell - Class in etomica.nbr.cell
Returns occupants of all cells as iterates.
AtomIteratorCell(int, BoxAgentManager) - Constructor for class etomica.nbr.cell.AtomIteratorCell
Constructor makes iterator that must have box specified and then be reset() before iteration.
AtomIteratorLeafAtoms - Class in etomica.atom.iterator
Iterator that will loop over all leaf atoms in a box.
AtomIteratorLeafAtoms() - Constructor for class etomica.atom.iterator.AtomIteratorLeafAtoms
Creates iterator with no box specified.
AtomIteratorLeafAtoms(IBox) - Constructor for class etomica.atom.iterator.AtomIteratorLeafAtoms
Creates iterator conditioned to give all leaf atoms of the specified box.
AtomIteratorLeafAtomsTest - Class in etomica.junit.atom.iterator
Unit test for AtomIteratorLeafAtoms
AtomIteratorLeafAtomsTest() - Constructor for class etomica.junit.atom.iterator.AtomIteratorLeafAtomsTest
 
AtomIteratorLeafFilteredType - Class in etomica.atom.iterator
 
AtomIteratorLeafFilteredType(IBox, IAtomType) - Constructor for class etomica.atom.iterator.AtomIteratorLeafFilteredType
 
AtomIteratorNbr(NeighborListManager) - Constructor for class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbr
 
AtomIteratorNbrCell(double, BoxAgentManager<? extends BoxCellManager>, IBox) - Constructor for class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbrCell
 
AtomIteratorNull - Class in etomica.atom.iterator
Static iterator that returns no atoms.
AtomIteratorSinglet - Class in 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() - Constructor for class etomica.atom.iterator.AtomIteratorSinglet
Constructs iterator without defining atom.
AtomIteratorSinglet(IAtom) - Constructor for class etomica.atom.iterator.AtomIteratorSinglet
Constructs iterator specifying that it return the given atom.
AtomIteratorSingletTest - Class in etomica.junit.atom.iterator
Unit test for AtomIteratorSinglet class.
AtomIteratorSingletTest() - Constructor for class etomica.junit.atom.iterator.AtomIteratorSingletTest
 
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>, IBox, Class) - Constructor for class etomica.atom.AtomLeafAgentManager
 
AtomLeafAgentManager.AgentIterator<E> - Class in etomica.atom
Iterator that loops over the agents, skipping null elements
AtomLeafAgentManager.AgentSource<E> - Interface in etomica.atom
Interface for an object that wants an agent associated with each Atom in a Box.
AtomLeafDynamic - Class in etomica.atom
 
AtomLeafDynamic(ISpace, IAtomType) - Constructor for class etomica.atom.AtomLeafDynamic
 
atomLeafIndexChanged(IAtom, int) - Method in class etomica.box.BoxEventManager
 
AtomLeafsetIterator - Interface in etomica.atom.iterator
Interface for classes that loop over a set of atoms.
atomList - Variable in class etomica.atom.AtomArrayList
 
atomList - Variable in class etomica.atom.iterator.ANIntragroupExchange
 
atomLists - Variable in class etomica.atom.iterator.ANIntergroupCoupled
 
AtomListWrapper - Class in etomica.atom
AtomSet formed by wrapping an AtomArrayList.
AtomListWrapper() - Constructor for class etomica.atom.AtomListWrapper
Wraps a new atom array of the given length.
AtomListWrapper(IAtomList) - Constructor for class etomica.atom.AtomListWrapper
Makes a new instance holding the atoms in the given atom set.
AtomListWrapper(AtomArrayList) - Constructor for class etomica.atom.AtomListWrapper
Wraps the given atom array.
AtomNeighborLists - Class in etomica.nbr.list
Class used to maintain neighbor lists.
AtomNeighborLists() - Constructor for class etomica.nbr.list.AtomNeighborLists
Constructs sequencer for the given atom.
AtomOriented - Class in etomica.atom
 
AtomOriented(ISpace, IAtomType) - Constructor for class etomica.atom.AtomOriented
 
AtomOriented(ISpace, IAtomType, boolean) - Constructor for class etomica.atom.AtomOriented
 
AtomOrientedDynamic - Class in etomica.atom
 
AtomOrientedDynamic(ISpace, IAtomType) - Constructor for class etomica.atom.AtomOrientedDynamic
 
AtomOrientedDynamic(ISpace, IAtomType, boolean) - Constructor for class etomica.atom.AtomOrientedDynamic
 
AtomOrientedQuaternion - Class in etomica.atom
 
AtomOrientedQuaternion(ISpace, IAtomType) - Constructor for class etomica.atom.AtomOrientedQuaternion
 
AtomPair - Class in etomica.atom
Data structure that contains two mutable atom instances.
AtomPair() - Constructor for class etomica.atom.AtomPair
 
AtomPair(IAtom, IAtom) - Constructor for class etomica.atom.AtomPair
 
atomPair - Variable in class etomica.nbr.list.PotentialMasterList
 
atomPair - Variable in class etomica.potential.PotentialMasterMonatomic
 
AtomPositionCOM - Class in etomica.atom
Calculates the center of mass (COM) over a set of atoms.
AtomPositionCOM(ISpace) - Constructor for class etomica.atom.AtomPositionCOM
 
atomPositionCOM - Variable in class etomica.integrator.IntegratorRigidIterative
 
atomPositionCOM - Variable in class etomica.integrator.IntegratorRigidMatrixIterative
 
atomPositionCOM - Variable in class etomica.models.water.OrientationCalcWater3P
 
atomPositionCOM - Variable in class etomica.models.water.OrientationCalcWater4P
 
AtomPositionFirstAtom - Class in etomica.atom
Returns the position of the first child leaf atom.
AtomPositionFirstAtom() - Constructor for class etomica.atom.AtomPositionFirstAtom
 
AtomPositionGeometricCenter - Class in etomica.atom
Calculates the geometric center over a set of atoms.
AtomPositionGeometricCenter(ISpace) - Constructor for class etomica.atom.AtomPositionGeometricCenter
 
AtomPositionGeometricCenterAlkaneEH - Class in etomica.atom
Calculates the geometric center over a set of atoms.
AtomPositionGeometricCenterAlkaneEH(ISpace, ISpecies) - Constructor for class etomica.atom.AtomPositionGeometricCenterAlkaneEH
 
AtomPositionGeometricCenterPBC - Class in etomica.atom
Calculates the geometric center over a set of atoms.
AtomPositionGeometricCenterPBC(ISpace, IBoundary) - Constructor for class etomica.atom.AtomPositionGeometricCenterPBC
 
AtomPotential1ListSource(PotentialMasterList) - Constructor for class etomica.nbr.list.NeighborListManager.AtomPotential1ListSource
 
AtomPotentialList - Class in 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() - Constructor for class etomica.nbr.list.AtomPotentialList
Constructs sequencer for the given atom.
atomRemoved(IAtom) - Method in class etomica.box.BoxEventManager
 
atoms - Variable in class etomica.atom.iterator.ANIntergroupCoupled
 
atoms - Variable in class etomica.atom.iterator.ANIntergroupExchange
 
atoms - Variable in class etomica.atom.iterator.ANIntragroupExchange
 
atoms - Variable in class etomica.potential.PotentialMolecularMonatomic
 
Atomset3IteratorIndexList - Class in etomica.atom.iterator
Atomset Iterator that iterates over set-of-three atoms
Atomset3IteratorIndexList(int[][]) - Constructor for class etomica.atom.iterator.Atomset3IteratorIndexList
Constructs iterator without defining set of atoms.
Atomset4IteratorIndexList - Class in etomica.atom.iterator
Atomset Iterator that iterates over set-of-four atoms
Atomset4IteratorIndexList(int[][]) - Constructor for class etomica.atom.iterator.Atomset4IteratorIndexList
Constructs iterator without defining set of atoms.
atomSetA - Variable in class etomica.action.IntegratorDimerApproach
 
AtomSetAllMolecules - Class in etomica.box
 
AtomSetAllMolecules() - Constructor for class etomica.box.AtomSetAllMolecules
 
AtomsetArray - Class in etomica.atom
AtomSet formed by wrapping an Atom array.
AtomsetArray(int) - Constructor for class etomica.atom.AtomsetArray
Wraps a new atom array of the given length.
AtomsetArray(IAtomList) - Constructor for class etomica.atom.AtomsetArray
Makes a new instance holding the atoms in the given atom set.
AtomsetArray(AtomsetArray) - Constructor for class etomica.atom.AtomsetArray
Copy constructor, wrapping a new array unique to this instance but holding the same atoms as the given atom set.
AtomsetArray(IAtom[]) - Constructor for class etomica.atom.AtomsetArray
Wraps the given atom array.
atomSetB - Variable in class etomica.action.IntegratorDimerApproach
 
AtomsetIterator - Interface in etomica.atom.iterator
Interface for classes that loop over a set of atoms.
AtomsetIteratorAllLeafAtoms - Class in etomica.atom.iterator
Iterator for all the molecules of a set of species in a box.
AtomsetIteratorAllLeafAtoms() - Constructor for class etomica.atom.iterator.AtomsetIteratorAllLeafAtoms
 
AtomsetIteratorBasisDependent - Interface in etomica.atom.iterator
Interface for an AtomIterator that can be conditioned with target and basis atoms.
AtomsetIteratorBoxDependent - Interface in etomica.atom.iterator
Interface indicating that an iterator can determine appropriate atoms for iteration given an arbitrary box.
AtomsetIteratorCellular - Interface in etomica.nbr.cell
Interface for atomset iterators that use cell-based neighbor lists for iteration.
AtomsetIteratorDirectable - Interface in etomica.atom.iterator
Interface for an iterator that can interpret specification of direction UP or DOWN.
AtomsetIteratorPDT - Interface in etomica.atom.iterator
This is an interface for iterators that are box dependent, directable, and targetable.
AtomsetIteratorTargetable - Interface in etomica.atom.iterator
Interface for an iterator that can be targeted at one or more atoms.
AtomSetSinglet - Class in etomica.atom
Data structure that contains a single mutable atom instance.
AtomSetSinglet() - Constructor for class etomica.atom.AtomSetSinglet
 
AtomSetSinglet(IAtom) - Constructor for class etomica.atom.AtomSetSinglet
 
atomSetSinglet - Variable in class etomica.atom.iterator.ApiIntergroup
 
atomSetSinglet - Variable in class etomica.atom.iterator.AtomIteratorArrayListAdjacent
 
atomSetSinglet - Variable in class etomica.atom.iterator.AtomIteratorArrayListSimple
 
atomSetSinglet - Variable in class etomica.atom.iterator.AtomIteratorSinglet
 
atomSetSinglet - Variable in class etomica.atom.iterator.MoleculeIteratorArrayListSimple
 
atomSetSinglet - Variable in class etomica.atom.iterator.MoleculeIteratorSinglet
 
atomSetSinglet - Variable in class etomica.graphics.BondListener
 
atomSetSinglet - Variable in class etomica.integrator.IntegratorHard.Agent
 
atomSetSinglet - Variable in class etomica.nbr.cell.AtomIteratorCell
 
atomSetSinglet - Variable in class etomica.nbr.list.NeighborListManager
 
atomSetSinglet - Variable in class etomica.nbr.list.PotentialMasterList
 
atomSetSinglet - Variable in class etomica.nbr.PotentialGroupNbr
 
atomSetSinglet - Variable in class etomica.nbr.site.PotentialMasterSite
 
atomSetSinglet - Variable in class etomica.potential.PotentialMasterMonatomic
 
AtomSite - Class in etomica.nbr.site
Site used to form array of cells for cell-based neighbor listing.
AtomSite(int) - Constructor for class etomica.nbr.site.AtomSite
 
AtomSource - Interface in etomica.atom
Interface for objects when return atoms (meeting some specification) from a box.
atomSource - Variable in class etomica.integrator.mcmove.MCMoveAtom
 
atomSource - Variable in class etomica.integrator.mcmove.MCMoveDimer
 
atomSource - Variable in class etomica.integrator.mcmove.MCMoveDimerRotate
 
AtomSourceRandomLeaf - Class in etomica.atom
AtomSource that returns a completely random leaf atom.
AtomSourceRandomLeaf() - Constructor for class etomica.atom.AtomSourceRandomLeaf
 
AtomSourceRandomSpecies - Class in etomica.atom
AtomSource that returns a completely random leaf atom.
AtomSourceRandomSpecies() - Constructor for class etomica.atom.AtomSourceRandomSpecies
 
AtomSourceRandomSpecies(IRandom, ISpecies) - Constructor for class etomica.atom.AtomSourceRandomSpecies
 
atomsPerGroup - Variable in class etomica.species.SpeciesSpheres
 
AtomTimeAction() - Constructor for class etomica.integrator.IntegratorAnalytic.AtomTimeAction
 
AtomToAtomLeafList - Interface in etomica.atom
Interface for class that determines an AtomArrayList given an atom.
atomToAtomSet - Variable in class etomica.atom.iterator.MpiIntraspecies1A
 
AtomToAtomSetFixed - Class in etomica.atom
 
AtomToAtomSetFixed() - Constructor for class etomica.atom.AtomToAtomSetFixed
 
AtomToIndex - Interface in etomica.atom
Interface for class that associates an integer with an atom.
AtomToIndexChild - Class in etomica.atom
Defines the index as the Atom's node's index.
AtomToIndexChild() - Constructor for class etomica.atom.AtomToIndexChild
 
AtomToParentChildList - Class in etomica.atom
 
AtomToParentChildList() - Constructor for class etomica.atom.AtomToParentChildList
 
atomToPosVec(IAtom) - Static method in class etomica.potential.P2WaterPotentialsJankowski
 
atomTranslator - Variable in class etomica.data.DataSourcePositionedBoltzmannFactor
 
atomTranslator - Variable in class etomica.integrator.mcmove.MCMoveInsertDelete
 
atomTypeAddedNotify(IAtomType) - Method in class etomica.simulation.Simulation
 
AtomTypeAgentManager - Class in etomica.atom
AtomTypeAgentManager acts on behalf of client classes (an AgentSource) to manage agents in every AtomType in a box.
AtomTypeAgentManager(AtomTypeAgentManager.AgentSource) - Constructor for class etomica.atom.AtomTypeAgentManager
 
AtomTypeAgentManager(AtomTypeAgentManager.AgentSource, ISimulation) - Constructor for class etomica.atom.AtomTypeAgentManager
 
AtomTypeAgentManager.AgentIterator - Class in etomica.atom
Iterator that loops over the agents, skipping null elements
AtomTypeAgentManager.AgentSource - Interface in etomica.atom
Interface for an object that wants an agent associated with each AtomType in a Simulation.
atomTypeIndexChanged(IAtomType, int) - Method in class etomica.simulation.SimulationEventManager
 
AtomTypeLeaf - Class in etomica.atom
Type for an atom that is a leaf in the species hierarchy.
AtomTypeLeaf(IElement) - Constructor for class etomica.atom.AtomTypeLeaf
 
atomTypeMaxIndexChanged(int) - Method in class etomica.simulation.SimulationEventManager
 
atomTypeOrientedManager - Variable in class etomica.graphics.DisplayBoxCanvasG3DSys
 
AtomTypeOrientedSphere - Class in etomica.atom
Atom type for a sphere that has some feature depending upon an orientation coordinate.
AtomTypeOrientedSphere(IElement, ISpace) - Constructor for class etomica.atom.AtomTypeOrientedSphere
 
atomTypeRemovedNotify(IAtomType) - Method in class etomica.simulation.Simulation
 
atomTypes - Variable in class etomica.potential.P2SquareWellRobust
 
atomTypes - Variable in class etomica.species.SpeciesSpheresCustom
 
AtomTypeSpheroPolyhedron - Class in etomica.atom
 
AtomTypeSpheroPolyhedron(IElement, ISpace, List<IVector>, double) - Constructor for class etomica.atom.AtomTypeSpheroPolyhedron
 
atry - Variable in class etomica.util.numerical.NonLinearCurveDiffFitting
 
atry - Variable in class etomica.util.numerical.NonLinearCurveFitting
 
ATTO - Static variable in class etomica.units.Prefix
Prefix indicating 10-18.
autoRowLabels - Variable in class etomica.graphics.DisplayTable
 
AVERAGE - Static variable in class etomica.data.AccumulatorAverage
 
average - Variable in class etomica.data.AccumulatorAverage
 
AVERAGE - Static variable in class etomica.data.AccumulatorAverageBlockless
 
average - Variable in class etomica.data.AccumulatorAverageBlockless
 
AVERAGE - Static variable in class etomica.data.AccumulatorAverageBlocklessSlim
 
averageBox - Variable in class etomica.graphics.DisplayTextBoxesCAE
 
averages - Variable in class etomica.data.AccumulatorAverageCollapsingLog
 
avgEnergy - Variable in class etomica.simulation.prototypes.LjMd3D
 
AVOGADRO - Static variable in class etomica.util.Constants
Avogadro's number, 6.02214129(27)e23 molecules/mole.
axesTensor - Variable in class etomica.integrator.IntegratorRigidMatrixIterative
 

B

b - Variable in class etomica.models.co2.P2CO2Hellmann
 
B - Variable in class etomica.potential.P2HePCKLJS
 
b - Static variable in class etomica.potential.P2HePCKLJS
 
b - Variable in class etomica.potential.P2NitrogenHellmann
 
b - Variable in class etomica.potential.P2WaterPotentialsJankowski
 
B - Variable in class etomica.potential.P3CPSNonAdditiveHeSimplified
 
b - Variable in class etomica.potential.P3CPSNonAdditiveHeSimplified
 
b - Variable in class etomica.potential.P3HydrogenManzhos
 
b - Variable in class etomica.util.numerical.PadeApproximation
 
B2(double) - Static method in class etomica.statmech.LennardJones
Returns the 2nd virial coefficient.
B9Optimizer - Class in etomica.util.numerical
Class to determine B9 value that best fit the simulation results
B9Optimizer(String, String) - Constructor for class etomica.util.numerical.B9Optimizer
 
B9Optimizer.VirialParam - Class in etomica.util.numerical
 
bA - Static variable in class etomica.models.co2.P2CO2Hellmann
 
bA - Static variable in class etomica.potential.P2NitrogenHellmann
 
BACK - Static variable in class etomica.util.Constants.Direction
 
backwardDataMap - Variable in class etomica.data.DataSet
 
Bar - Class in etomica.units
The bar unit of pressure, equal to 10^5 N/m^2.
Barye - Class in etomica.units
The barye unit of pressure, equal to 1 dyn/cm^2.
baseUnits() - Method in class etomica.units.systems.UnitSystem
 
basis - Variable in class etomica.lattice.BravaisLatticeCrystal
 
Basis - Class in etomica.lattice.crystal
General basis class that hold scaled coordinates of atoms within a unit cell.
Basis(IVector[]) - Constructor for class etomica.lattice.crystal.Basis
 
basis - Variable in class etomica.potential.EwaldSummation
 
basis - Variable in class etomica.potential.P2QChemInterpolated
 
basis - Variable in class etomica.potential.P2QChemInterpolated.DampingParams
 
basis - Variable in class etomica.potential.P3AdditiveQChem.DampingParams
 
basis - Variable in class etomica.potential.P3QChem.DampingParams
 
BasisBetaSnA5 - Class in etomica.lattice.crystal
Basis that helps construct a beta-tin crystal.
BasisBetaSnA5() - Constructor for class etomica.lattice.crystal.BasisBetaSnA5
 
BasisCubicBcc - Class in etomica.lattice.crystal
A 2-atom basis for a bcc crystal
BasisCubicBcc() - Constructor for class etomica.lattice.crystal.BasisCubicBcc
Makes a bcc 2-atom basis.
BasisCubicDiamond - Class in etomica.lattice.crystal
An 8-atom basis that for a diamond crystal.
BasisCubicDiamond() - Constructor for class etomica.lattice.crystal.BasisCubicDiamond
Makes a diamond-on-fcc 8-atom basis.
BasisCubicFcc - Class in etomica.lattice.crystal
A 4-atom basis fot an fcc crystal.
BasisCubicFcc() - Constructor for class etomica.lattice.crystal.BasisCubicFcc
Makes a fcc 4-atom basis.
BasisCubicFccDiamond - Class in etomica.lattice.crystal
A 2-atom basis that makes a diamond crystal using a BravaisLattice having a Cubic primitive with an fcc basis.
BasisCubicFccDiamond() - Constructor for class etomica.lattice.crystal.BasisCubicFccDiamond
Makes a diamond-on-fcc 2-atom basis using the given factory to make the atoms.
BasisHcp - Class in etomica.lattice.crystal
A 2-atom basis for an hcp crystal.
BasisHcp() - Constructor for class etomica.lattice.crystal.BasisHcp
 
BasisHcpBaseCentered - Class in etomica.lattice.crystal
A 2-atom basis for an hcp crystal (base-centered or side-centered)
BasisHcpBaseCentered() - Constructor for class etomica.lattice.crystal.BasisHcpBaseCentered
 
BasisMonatomic - Class in etomica.lattice.crystal
Single-atom basis with the coordinate at the origin.
BasisMonatomic(ISpace) - Constructor for class etomica.lattice.crystal.BasisMonatomic
Creates a single-atom basis with the coordinate at the origin.
BasisOrthorhombicHexagonal - Class in etomica.lattice.crystal
A 2D hexagonal 2-atom basis
BasisOrthorhombicHexagonal() - Constructor for class etomica.lattice.crystal.BasisOrthorhombicHexagonal
Makes a 2D hexagonal 2-atom basis
basisSize() - Method in class etomica.atom.iterator.ANIntergroupCoupled
Returns 2, indicating that the setBasis method expects an array of two atoms.
basisSize() - Method in class etomica.atom.iterator.ANIntergroupExchange
Returns 2, indicating that the setBasis method expects an array of two atoms.
basisSize() - Method in class etomica.atom.iterator.ANIntragroupExchange
Returns 2, indicating that the setBasis method expects an array of two atoms.
basisSize() - Method in class etomica.atom.iterator.ApiIndexList
 
basisSize() - Method in class etomica.atom.iterator.ApiIntergroup
Returns 2, indicating that the setBasis method expects an array of two atoms.
basisSize() - Method in class etomica.atom.iterator.ApiIntragroup
Returns 1, indicating the the array given to the setBasis method should have only one element.
basisSize() - Method in class etomica.atom.iterator.AtomIteratorBasis
Returns 1, indicating that only a single-atom basis is appropriate.
basisSize() - Method in class etomica.atom.iterator.AtomIteratorBasisAdjustableStart
Returns 1, indicating that only a single-atom basis is appropriate.
basisSize() - Method in class etomica.atom.iterator.Atomset3IteratorIndexList
 
basisSize() - Method in class etomica.atom.iterator.Atomset4IteratorIndexList
 
basisSize() - Method in class etomica.atom.iterator.AtomsetIteratorAllLeafAtoms
 
basisSize() - Method in interface etomica.atom.iterator.AtomsetIteratorBasisDependent
Indicates the size of the basis needed to set the iterator.
basisSize() - Method in interface etomica.atom.iterator.MoleculesetIteratorBasisDependent
Indicates the size of the basis needed to set the iterator.
basisSize() - Method in class etomica.atom.iterator.TripletInnerSequential
 
basisSize() - Method in class etomica.potential.PotentialMaster.AtomIterator0
 
bB - Static variable in class etomica.models.co2.P2CO2Hellmann
 
bB - Static variable in class etomica.potential.P2NitrogenHellmann
 
bdrij - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
 
bdrij - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSCTI
 
besselI(int, double) - Static method in class etomica.math.SpecialFunctions
Calculates the modified bessel function of the first kind (I) for a given order and the variable x.
beta - Static variable in class etomica.potential.P1HydrogenMielke
 
beta - Variable in class etomica.potential.P4TorsionDreiding
 
beta - Variable in class etomica.util.numerical.NonLinearCurveDiffFitting
 
beta - Variable in class etomica.util.numerical.NonLinearCurveFitting
 
beta3 - Variable in class etomica.potential.P3CPSNonAdditiveHe
 
beta3 - Variable in class etomica.potential.P3CPSNonAdditiveHeOrig
 
beta3_111 - Static variable in class etomica.potential.P3CPSNonAdditiveHe
 
beta3_111 - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
 
beta3_112 - Static variable in class etomica.potential.P3CPSNonAdditiveHe
 
beta3_113 - Static variable in class etomica.potential.P3CPSNonAdditiveHe
 
beta3_122 - Static variable in class etomica.potential.P3CPSNonAdditiveHe
 
beta3_222 - Static variable in class etomica.potential.P3CPSNonAdditiveHe
 
beta4211 - Variable in class etomica.potential.P3CPSNonAdditiveHe
 
beta4211 - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
 
beta4211 - Variable in class etomica.potential.P3CPSNonAdditiveHeOrig
 
beta4211_1112 - Static variable in class etomica.potential.P3CPSNonAdditiveHe
 
beta4211_1121 - Static variable in class etomica.potential.P3CPSNonAdditiveHe
 
beta4211_2111 - Static variable in class etomica.potential.P3CPSNonAdditiveHe
 
beta4220 - Variable in class etomica.potential.P3CPSNonAdditiveHe
 
beta4220 - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
 
beta4220 - Variable in class etomica.potential.P3CPSNonAdditiveHeOrig
 
beta4220_1111 - Static variable in class etomica.potential.P3CPSNonAdditiveHe
 
beta4220_1211 - Static variable in class etomica.potential.P3CPSNonAdditiveHe
 
beta4220_2111 - Static variable in class etomica.potential.P3CPSNonAdditiveHe
 
bGuess - Variable in class etomica.util.numerical.B9Optimizer
 
bGuess - Variable in class etomica.util.numerical.VirialOptimizer
 
biasOld - Variable in class etomica.integrator.mcmove.MCMoveVolume
 
bigAngle - Static variable in class etomica.potential.P3CPSNonAdditiveHe
 
bigAngle - Static variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
 
bigAngle - Static variable in class etomica.potential.P3CPSNonAdditiveHeOrig
 
bigAngle - Static variable in class etomica.potential.P3CPSNonAdditiveHeSimplified
 
binom - Static variable in class etomica.math.SpecialFunctions
 
binom - Static variable in class etomica.potential.P2O2Bartolomei
 
bisectorVec - Static variable in class etomica.potential.P2WaterPotentialsJankowski
 
BishopPipin(double, double, double, double) - Method in class etomica.potential.P2HydrogenPatkowski
 
BishopPipin(double, double, double, double) - Method in class etomica.potential.P2HydrogenPatkowskiAtomic
 
bl - Static variable in class etomica.potential.P2WaterPotentialsJankowski
 
blMax - Static variable in class etomica.potential.P2HydrogenHindePatkowskiAtomic
 
blN2 - Static variable in class etomica.potential.P2NitrogenHellmann
 
blN2 - Static variable in class etomica.potential.P3NitrogenHellmannNonAdditive
 
BLOCK_CORRELATION - Static variable in class etomica.data.AccumulatorAverage
 
BLOCK_COVARIANCE - Static variable in class etomica.data.AccumulatorAverageCovariance
 
blockCorrelation - Variable in class etomica.data.AccumulatorAverage
 
blockCountDown - Variable in class etomica.data.AccumulatorAverage
 
blockCounter - Variable in class etomica.data.AccumulatorAverageFixedOutputFile
 
blockCovariance - Variable in class etomica.data.AccumulatorAverageCovariance
 
blockCovSum - Variable in class etomica.data.AccumulatorAverageCovariance
 
blockDataSink - Variable in class etomica.data.AccumulatorAverageFixed
 
blockSize - Variable in class etomica.data.AccumulatorAverage
 
blockSums - Variable in class etomica.data.AccumulatorAverageCollapsing
 
blockSums - Variable in class etomica.data.AccumulatorAverageCollapsingLog
 
bmu - Variable in class etomica.integrator.mcmove.MCMoveIDBiasAction
 
bohrConv - Variable in class etomica.models.water.P2WaterSzalewicz
 
BohrRadius - Class in etomica.units
The Borh Radius unit of length, corresponding to the size of a Hydrogen atom's electron cloud.
BOLTZMANN_K - Static variable in class etomica.util.Constants
Boltzmann's constant, in (sim units)/kelvin.
BONDAC - Static variable in class etomica.models.water.P2HardAssociationGCPMReference
 
BONDAC - Static variable in class etomica.models.water.PNWaterGCPMThreeSite
 
BondArrayList() - Constructor for class etomica.potential.P2HardBondedList.BondArrayList
 
BONDBC - Static variable in class etomica.models.water.P2HardAssociationGCPMReference
 
BONDBC - Static variable in class etomica.models.water.PNWaterGCPMThreeSite
 
BONDCA - Static variable in class etomica.models.water.P2HardAssociationGCPMReference
 
BONDCA - Static variable in class etomica.models.water.PNWaterGCPMThreeSite
 
BONDCB - Static variable in class etomica.models.water.P2HardAssociationGCPMReference
 
BONDCB - Static variable in class etomica.models.water.PNWaterGCPMThreeSite
 
BondChangeData() - Constructor for class etomica.potential.PotentialReactive.BondChangeData
 
BondConstraints(int[][], double[]) - Constructor for class etomica.integrator.IntegratorVelocityVerletShake.BondConstraints
 
bondedAtoms - Variable in class etomica.integrator.IntegratorVelocityVerletShake.BondConstraints
 
bondedAtoms - Variable in class etomica.integrator.mcmove.MCMoveWiggleAceticAcid
 
bondingAngleRestriction - Variable in class etomica.models.water.PNWaterGCPMThreeSite
 
bondingPotential - Variable in class etomica.chem.models.ModelChain
 
bondIteratorsHash - Variable in class etomica.graphics.BondListener
 
bondL - Variable in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
 
bondLength - Variable in class etomica.atom.AtomHydrogen
 
bondLength - Variable in class etomica.config.ConformationLinear
 
bondLengthOH - Static variable in class etomica.models.water.ConformationWater3P
 
bondLengthOH - Static variable in class etomica.models.water.ConformationWaterTIP4P
 
bondLengths - Variable in class etomica.integrator.IntegratorVelocityVerletShake.BondConstraints
 
BondListener - Class in etomica.graphics
BondListener listens for Atoms being added to the Simulation, determines what covalent bonds (if any) apply to the new Atom and informs a BondManager of any new bonds.
BondListener(IBox, BondManager) - Constructor for class etomica.graphics.BondListener
Creates a new BondListener for the given Box, using the given BondManager to actually create or remove bonds.
bondManager - Variable in class etomica.graphics.BondListener
 
BondManager - Interface in etomica.graphics
The BondManager is responsible for creation and disposal of bonds between atom pairs.
BORDER - Static variable in class etomica.graphics.DeviceBox.LabelType
 
BORDER - Static variable in class etomica.graphics.DisplayTextBox.LabelType
 
BOT - Static variable in class etomica.math.Gamma
 
BOTEXP - Static variable in class etomica.math.Gamma
 
BOTTOM - Static variable in class etomica.graphics.DisplayBox
 
BOTTOM - Static variable in class etomica.graphics.DisplayPolytope
 
BOTTOM - Static variable in class etomica.util.Constants.Direction
 
boundary - Variable in class etomica.atom.AtomPositionGeometricCenterPBC
 
boundary - Variable in class etomica.data.meter.PotentialCalculationRDF
 
boundary - Variable in class etomica.graphics.ColorSchemeOverlap
 
boundary - Variable in class etomica.models.co2.PNCO2GCPM
 
boundary - Variable in class etomica.models.co2.PNGCPM
 
boundary - Variable in class etomica.models.water.P2Water3P
 
boundary - Variable in class etomica.models.water.P2Water4P
 
boundary - Variable in class etomica.models.water.P2WaterTIP4PHardCore
 
boundary - Variable in class etomica.models.water.PNWaterGCPM
 
boundary - Variable in class etomica.models.water.TestEwaldTIP4PWater
 
boundary - Variable in class etomica.nbr.CriterionSimple
 
boundary - Variable in class etomica.nbr.molecule.CriterionSimpleMolecular
 
boundary - Variable in class etomica.potential.P1HardBoundary
 
boundary - Variable in class etomica.potential.P1HydrogenMielke
 
boundary - Variable in class etomica.potential.P2CO2EMP
 
boundary - Variable in class etomica.potential.P2DiscreteFeynmanHibbs
 
boundary - Variable in class etomica.potential.P2EffectiveFeynmanHibbs
 
boundary - Variable in class etomica.potential.P2HydrogenHinde
 
boundary - Variable in class etomica.potential.P2HydrogenHindeAtomic
 
boundary - Variable in class etomica.potential.P2HydrogenHindePatkowski
 
boundary - Variable in class etomica.potential.P2HydrogenHindePatkowskiAtomic
 
boundary - Variable in class etomica.potential.P2HydrogenPatkowski
 
boundary - Variable in class etomica.potential.P2HydrogenPatkowskiAtomic
 
boundary - Variable in class etomica.potential.P2MoleculeSoftTruncatedSwitched
 
boundary - Variable in class etomica.potential.P2MoleculeTruncated
 
boundary - Variable in class etomica.potential.P2NitrogenHellmann
 
boundary - Variable in class etomica.potential.P2O2Bartolomei
 
boundary - Variable in class etomica.potential.P2QChem
 
boundary - Variable in class etomica.potential.P2ReactionFieldDipole
 
boundary - Variable in class etomica.potential.P2ReactionFieldDipoleTruncated
 
boundary - Variable in class etomica.potential.P2SoftSphericalTruncatedSwitched
 
boundary - Variable in class etomica.potential.P2SoftTruncated
 
boundary - Variable in class etomica.potential.P2SpheroPolyhedron
 
boundary - Variable in class etomica.potential.P2WaterPotentialsJankowski
 
boundary - Variable in class etomica.potential.P3AxilrodTeller
 
boundary - Variable in class etomica.potential.P3BondAngle
 
boundary - Variable in class etomica.potential.P3BondAngleDreiding
 
boundary - Variable in class etomica.potential.P3CPSNonAdditiveHe
 
boundary - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
 
boundary - Variable in class etomica.potential.P3CPSNonAdditiveHeOrig
 
boundary - Variable in class etomica.potential.P3CPSNonAdditiveHeSimplified
 
boundary - Variable in class etomica.potential.P3HydrogenATM
 
boundary - Variable in class etomica.potential.P3HydrogenManzhos
 
boundary - Variable in class etomica.potential.P3Induction
 
boundary - Variable in class etomica.potential.P3NitrogenHellmannNonAdditive
 
boundary - Variable in class etomica.potential.P4BondTorsion
 
boundary - Variable in class etomica.potential.P4BondTorsionAlkaneXCCH
 
boundary - Variable in class etomica.potential.P4TorsionDreiding
 
boundary - Variable in class etomica.potential.Potential1
 
boundary - Variable in class etomica.potential.Potential2HardSpherical
 
boundary - Variable in class etomica.potential.Potential2SoftSpherical
 
boundary - Variable in class etomica.potential.Potential2SoftSphericalLS
 
boundary - Variable in class etomica.potential.PotentialEmul
 
Boundary - Class in etomica.space
Parent class of boundary objects that describe the size and periodic nature of the box boundaries.
Boundary(ISpace, Polytope) - Constructor for class etomica.space.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.
boundary - Variable in class etomica.space.BoundaryEvent
 
BoundaryDeformableLattice - Class in etomica.space
Deformable boundary that takes the shape of a primitive with some number of cells in each dimension.
BoundaryDeformableLattice(Primitive, int[]) - Constructor for class etomica.space.BoundaryDeformableLattice
Creates boundary with the shape of the given primitive and the given number of cells for each dimension.
BoundaryDeformableLattice(Primitive, double[]) - Constructor for class etomica.space.BoundaryDeformableLattice
Creates boundary with the shape of the given primitive and the given number of cells for each dimension.
BoundaryDeformablePeriodic - Class in etomica.space
Boundary shaped as an arbitrary parallelepiped.
BoundaryDeformablePeriodic(ISpace) - Constructor for class etomica.space.BoundaryDeformablePeriodic
Make a cubic boundary with edges of length equal to the default boxSize and periodic in every direction.
BoundaryDeformablePeriodic(ISpace, double) - Constructor for class etomica.space.BoundaryDeformablePeriodic
Make a cubic boundary of specified edge length and periodicity.
BoundaryDeformablePeriodic(ISpace, IVector[]) - Constructor for class etomica.space.BoundaryDeformablePeriodic
Make a parallelepiped boundary of specified shape and periodicity.
BoundaryDeformablePeriodicTest - Class in etomica.junit.space
 
BoundaryDeformablePeriodicTest() - Constructor for class etomica.junit.space.BoundaryDeformablePeriodicTest
 
BoundaryEvent - Class in etomica.space
 
BoundaryEvent(IBoundary) - Constructor for class etomica.space.BoundaryEvent
 
BoundaryEventManager - Class in etomica.space
 
BoundaryEventManager() - Constructor for class etomica.space.BoundaryEventManager
 
boundaryInflate(IBoundaryEvent) - Method in interface etomica.api.IBoundaryListener
 
boundaryInflate(IBoundaryEvent) - Method in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
 
boundaryInflate(IBoundaryEvent) - Method in class etomica.nbr.cell.NeighborCellManager
 
boundaryPadding - Variable in class etomica.config.ConfigurationLattice
 
BoundaryRectangular - Class in etomica.space
Boundary that is in the shape of a rectangular parallelepiped.
BoundaryRectangular(ISpace) - Constructor for class etomica.space.BoundaryRectangular
Constructs cubic boundary of the given periodicity, using the space and default box-size given by the Simulation.
BoundaryRectangular(ISpace, double) - Constructor for class etomica.space.BoundaryRectangular
Constructs cubic boundary of the given periodicity with each edge of length boxSize
BoundaryRectangular(ISpace, double[]) - Constructor for class etomica.space.BoundaryRectangular
Constructs rectangular boundary of the given periodicity with edges given by the values in the array boxSize.
BoundaryRectangularNonperiodic - Class in etomica.space
Boundary that is not periodic in any direction.
BoundaryRectangularNonperiodic(ISpace) - Constructor for class etomica.space.BoundaryRectangularNonperiodic
Make a boundary with unit volume.
BoundaryRectangularPeriodic - Class in etomica.space
Rectangular boundary that is periodic in every dimension.
BoundaryRectangularPeriodic(ISpace) - Constructor for class etomica.space.BoundaryRectangularPeriodic
Constructs cubic boundary with the default box-size given by the Simulation.
BoundaryRectangularPeriodic(ISpace, double) - Constructor for class etomica.space.BoundaryRectangularPeriodic
Constructs cubic boundary for the given Space, with each edge of length boxSize.
BoundaryRectangularPeriodic(ISpace, double[]) - Constructor for class etomica.space.BoundaryRectangularPeriodic
Constructs rectangular boundary for the given Space, with each edge of length boxSize.
BoundaryRectangularPore - Class in etomica.space
Class for implementing pore periodic boundary conditions, in which one dimension is periodic.
BoundaryRectangularPore(ISpace) - Constructor for class etomica.space.BoundaryRectangularPore
Makes cubic volume with the x-dimension (index 0) not periodic.
BoundaryRectangularPore(ISpace, int) - Constructor for class etomica.space.BoundaryRectangularPore
Makes cubic volume with the indicated dimension not periodic.
BoundaryRectangularPore(ISpace, int, double) - Constructor for class etomica.space.BoundaryRectangularPore
Constructor for periodic boundary conditions with a slit in the given dimension.
BoundaryRectangularSlit - Class in etomica.space
Class for implementing slit periodic boundary conditions, in which one dimension is not periodic.
BoundaryRectangularSlit(ISpace) - Constructor for class etomica.space.BoundaryRectangularSlit
Makes cubic volume with the x-dimension (index 0) not periodic.
BoundaryRectangularSlit(int, ISpace) - Constructor for class etomica.space.BoundaryRectangularSlit
Makes cubic volume with the indicated dimension not periodic.
BoundaryRectangularSlit(int, double, ISpace) - Constructor for class etomica.space.BoundaryRectangularSlit
Constructor for periodic boundary conditions with a slit in the given dimension.
BoundaryTruncatedOctahedron - Class in etomica.space3d
This class enables creation of a periodic truncated-octahedron boundary.
BoundaryTruncatedOctahedron(ISpace) - Constructor for class etomica.space3d.BoundaryTruncatedOctahedron
 
BoundaryTruncatedOctahedron(ISpace, double) - Constructor for class etomica.space3d.BoundaryTruncatedOctahedron
 
box - Variable in class etomica.action.BoxActionAdapter
 
box - Variable in class etomica.action.BoxRandomizeMomenta
 
box - Variable in class etomica.action.BoxScaleMomenta
 
box - Variable in class etomica.action.WriteConfiguration
 
box - Variable in class etomica.atom.AtomLeafAgentManager
 
box - Variable in class etomica.atom.AtomSourceRandomSpecies
 
box - Variable in class etomica.atom.iterator.MoleculeIteratorAll
 
box - Variable in class etomica.atom.iterator.MpiIntraspecies1A
 
box - Variable in class etomica.atom.MoleculeAgentManager
 
box - Variable in class etomica.atom.MoleculeSourceRandomMolecule
 
Box - Class in etomica.box
A Box collects all atoms that interact with one another; atoms in different boxs do not interact.
Box(ISpace) - Constructor for class etomica.box.Box
Constructs box with default rectangular periodic boundary.
Box(IBoundary, ISpace) - Constructor for class etomica.box.Box
Constructs box with the given boundary
box - Variable in class etomica.box.BoxEvent
 
box - Variable in class etomica.box.RandomPositionSourceDeformable
 
box - Variable in class etomica.box.RandomPositionSourceRectangular
 
box - Variable in class etomica.data.DataProcessorInterfacialTension
 
box - Variable in class etomica.data.meter.MeterDihedralAngle
 
box - Variable in class etomica.data.meter.MeterHyperVirial
 
box - Variable in class etomica.data.meter.MeterKineticEnergyRigid
 
box - Variable in class etomica.data.meter.MeterPotentialEnergy
 
box - Variable in class etomica.data.meter.MeterPressure
 
box - Variable in class etomica.data.meter.MeterPressureTensor
 
box - Variable in class etomica.data.meter.MeterProfileByAtoms
 
box - Variable in class etomica.data.meter.MeterProfileByVolume
 
box - Variable in class etomica.data.meter.MeterRDF
 
box - Variable in class etomica.data.meter.MeterRDFPC
 
box - Variable in class etomica.data.meter.MeterStructureFactor
 
box - Variable in class etomica.data.meter.MeterTemperature
 
box - Variable in class etomica.data.meter.MeterWidomInsertion
 
box - Variable in exception etomica.exception.ConfigurationOverlapException
 
box - Variable in class etomica.graphics.BondListener
 
box - Variable in class etomica.graphics.DeviceNSelector
 
box - Variable in class etomica.integrator.IntegratorBox
 
box - Variable in class etomica.integrator.IntegratorRigidMatrixIterative.BoxImposePbcMolecule
 
box - Variable in class etomica.integrator.mcmove.MCMoveBox
 
box - Variable in class etomica.models.water.TestEwaldTIP4PWater
 
box - Variable in class etomica.modifier.ModifierNMolecule
 
box - Variable in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
 
box - Variable in class etomica.nbr.cell.NeighborCellManager
 
box - Variable in class etomica.nbr.list.molecule.NeighborListManagerMolecular
 
box - Variable in class etomica.nbr.list.NeighborListManager
 
box - Variable in class etomica.potential.EwaldSummation
 
box - Variable in class etomica.potential.EwaldSumMolecules
 
box - Variable in class etomica.potential.P2ReactionFieldDipole.P0ReactionField
 
box - Variable in class etomica.potential.P2ReactionFieldDipoleTruncated.P0ReactionField
 
box - Variable in class etomica.potential.Potential0Lrc
 
box - Variable in class etomica.potential.PotentialGroup
 
box - Variable in class etomica.simulation.prototypes.ChainHSMD3D
 
box - Variable in class etomica.simulation.prototypes.HsMc2d
 
box - Variable in class etomica.simulation.prototypes.HSMD2D
 
box - Variable in class etomica.simulation.prototypes.HSMD2D_noNbr
 
box - Variable in class etomica.simulation.prototypes.HSMD3D
The Box holding the atoms.
box - Variable in class etomica.simulation.prototypes.HSMD3DNoNbr
 
box - Variable in class etomica.simulation.prototypes.LjMd2D
 
box - Variable in class etomica.simulation.prototypes.LjMd3D
 
box - Variable in class etomica.simulation.prototypes.SoftSphere3d
 
box - Variable in class etomica.simulation.prototypes.SwMd2D
 
box - Variable in class etomica.simulation.prototypes.SWMD3D
 
box - Variable in class etomica.space.Boundary
 
box - Variable in class etomica.tests.TestHSMD3D
 
box - Variable in class etomica.tests.TestLJMC3D
 
box - Variable in class etomica.tests.TestSWChain
 
box - Variable in class etomica.util.numerical.CalcGradientDifferentiable
 
box1 - Variable in class etomica.integrator.mcmove.MCMoveMoleculeExchange
 
box1 - Variable in class etomica.simulation.prototypes.GEMCWithRotation
 
box2 - Variable in class etomica.integrator.mcmove.MCMoveMoleculeExchange
 
box2 - Variable in class etomica.simulation.prototypes.GEMCWithRotation
 
BOX_INDEX - Static variable in class etomica.util.Debug
index of box of interest.
BoxAction - Interface in etomica.action
Elementary action performed on a box.
BoxActionAdapter - Class in etomica.action
Convenience class used to define a BoxAction.
BoxActionAdapter() - Constructor for class etomica.action.BoxActionAdapter
 
boxAdded(IBox) - Method in class etomica.simulation.SimulationEventManager
 
boxAgentClass - Variable in class etomica.box.BoxAgentManager
 
BoxAgentManager<E> - Class in etomica.box
BoxAgentManager acts on behalf of client classes (a BoxAgentSource) to manage agents for each Box in a simulation.
BoxAgentManager(BoxAgentManager.BoxAgentSource<E>, Class) - Constructor for class etomica.box.BoxAgentManager
 
BoxAgentManager(BoxAgentManager.BoxAgentSource<E>, Class, ISimulation) - Constructor for class etomica.box.BoxAgentManager
 
boxAgentManager - Variable in class etomica.nbr.CriterionSimple
 
boxAgentManager - Variable in class etomica.nbr.molecule.CriterionSimpleMolecular
 
boxAgentManager - Variable in class etomica.nbr.molecule.PotentialMasterNbrMolecular
 
boxAgentManager - Variable in class etomica.nbr.PotentialMasterNbr
 
boxAgentManager - Variable in class etomica.potential.P1HarmonicSite
 
BoxAgentManager.AgentIterator<E> - Class in etomica.box
Iterator that loops over the agents, skipping null elements
BoxAgentManager.BoxAgentSource<E> - Interface in etomica.box
Interface for an object that makes an agent to be placed in each atom upon construction.
BoxAgentSiteSource(int, ISpace) - Constructor for class etomica.nbr.site.PotentialMasterSite.BoxAgentSiteSource
 
boxAgentSource - Variable in class etomica.nbr.molecule.PotentialMasterNbrMolecular
 
boxAgentSource - Variable in class etomica.nbr.PotentialMasterNbr
 
BoxAgentSourceAtomManager<E> - Class in etomica.box
 
BoxAgentSourceAtomManager(AtomLeafAgentManager.AgentSource<E>, Class) - Constructor for class etomica.box.BoxAgentSourceAtomManager
 
BoxAgentSourceCellManager - Class in etomica.nbr.cell
BoxAgentSource responsible for creating a NeighborCellManager.
BoxAgentSourceCellManager(ISimulation, IAtomPositionDefinition, ISpace) - Constructor for class etomica.nbr.cell.BoxAgentSourceCellManager
 
BoxAgentSourceCellManagerList - Class in etomica.nbr.list
BoxAgentSource responsible for creating a NeighborCellManager.
BoxAgentSourceCellManagerList(ISimulation, IAtomPositionDefinition, ISpace) - Constructor for class etomica.nbr.list.BoxAgentSourceCellManagerList
 
BoxAgentSourceCellManagerListMolecular - Class in etomica.nbr.list.molecule
BoxAgentSource responsible for creating a NeighborCellManagerMolecular.
BoxAgentSourceCellManagerListMolecular(ISimulation, IAtomPositionDefinition, ISpace) - Constructor for class etomica.nbr.list.molecule.BoxAgentSourceCellManagerListMolecular
 
BoxAgentSourceCellManagerMolecular - Class in etomica.nbr.cell.molecule
BoxAgentSource responsible for creating a NeighborCellManagerMolecular.
BoxAgentSourceCellManagerMolecular(ISimulation, IAtomPositionDefinition, ISpace) - Constructor for class etomica.nbr.cell.molecule.BoxAgentSourceCellManagerMolecular
 
BoxAgentSourceMoleculeManager - Class in etomica.box
 
BoxAgentSourceMoleculeManager(MoleculeAgentManager.MoleculeAgentSource, ISimulation) - Constructor for class etomica.box.BoxAgentSourceMoleculeManager
 
boxAtomAdded(IBoxAtomEvent) - Method in interface etomica.api.IBoxListener
 
boxAtomAdded(IBoxAtomEvent) - Method in class etomica.atom.MoleculeAgentManager
 
boxAtomAdded(IBoxAtomEvent) - Method in class etomica.box.BoxListenerAdapter
 
boxAtomAdded(IBoxAtomEvent) - Method in class etomica.integrator.IntegratorMD
 
BoxAtomEvent - Class in etomica.box
Event that conveys some happening with respect to an Atom in a Box.
BoxAtomEvent(IBox, IAtom) - Constructor for class etomica.box.BoxAtomEvent
 
BoxAtomIndexEvent - Class in etomica.box
Event that conveys that the maximum global index in a Box has changed.
BoxAtomIndexEvent(IBox, IAtom, int) - Constructor for class etomica.box.BoxAtomIndexEvent
 
boxAtomLeafIndexChanged(IBoxAtomIndexEvent) - Method in interface etomica.api.IBoxListener
 
boxAtomLeafIndexChanged(IBoxAtomIndexEvent) - Method in class etomica.atom.AtomLeafAgentManager
 
boxAtomLeafIndexChanged(IBoxAtomIndexEvent) - Method in class etomica.atom.MoleculeAgentManager
 
boxAtomLeafIndexChanged(IBoxAtomIndexEvent) - Method in class etomica.box.BoxListenerAdapter
 
boxAtomLeafIndexChanged(IBoxAtomIndexEvent) - Method in class etomica.integrator.IntegratorMD
 
boxAtomRemoved(IBoxAtomEvent) - Method in interface etomica.api.IBoxListener
 
boxAtomRemoved(IBoxAtomEvent) - Method in class etomica.atom.MoleculeAgentManager
 
boxAtomRemoved(IBoxAtomEvent) - Method in class etomica.box.BoxListenerAdapter
 
boxAtomRemoved(IBoxAtomEvent) - Method in class etomica.integrator.IntegratorMD
 
BoxCellManager - Interface in etomica.box
Interface for class that handles assignment of atoms to cells in a box.
BoxDeleteMolecules - Class in etomica.action
Deletes molecules from a box as determined by an AtomFilter.
BoxDeleteMolecules(AtomFilter) - Constructor for class etomica.action.BoxDeleteMolecules
 
BoxEvent - Class in etomica.box
Event that conveys some happening with respect to a box or the things it contains.
BoxEvent(IBox) - Constructor for class etomica.box.BoxEvent
 
BoxEventManager - Class in etomica.box
 
BoxEventManager(IBox) - Constructor for class etomica.box.BoxEventManager
 
boxGlobalAtomIndexChanged(IBoxIndexEvent) - Method in interface etomica.api.IBoxListener
 
boxGlobalAtomIndexChanged(IBoxIndexEvent) - Method in class etomica.atom.MoleculeAgentManager
 
boxGlobalAtomIndexChanged(IBoxIndexEvent) - Method in class etomica.box.BoxListenerAdapter
 
boxGlobalAtomIndexChanged(IBoxIndexEvent) - Method in class etomica.integrator.IntegratorMD
 
BoxGlobalAtomIndexEvent - Class in etomica.box
Event that conveys that the maximum global index in a Box has changed.
BoxGlobalAtomIndexEvent(IBox, int) - Constructor for class etomica.box.BoxGlobalAtomIndexEvent
 
boxGlobalAtomLeafIndexChanged(IBoxIndexEvent) - Method in interface etomica.api.IBoxListener
 
boxGlobalAtomLeafIndexChanged(IBoxIndexEvent) - Method in class etomica.atom.AtomLeafAgentManager
 
boxGlobalAtomLeafIndexChanged(IBoxIndexEvent) - Method in class etomica.atom.MoleculeAgentManager
 
boxGlobalAtomLeafIndexChanged(IBoxIndexEvent) - Method in class etomica.box.BoxListenerAdapter
 
boxGlobalAtomLeafIndexChanged(IBoxIndexEvent) - Method in class etomica.integrator.IntegratorMD
 
BoxImposePbc - Class in etomica.action
Action that imposes the central-image effect of a box having periodic boundaries.
BoxImposePbc(ISpace) - Constructor for class etomica.action.BoxImposePbc
Creates the action without specifying a box.
BoxImposePbc(IBox, ISpace) - Constructor for class etomica.action.BoxImposePbc
Creates the action ready to perform on the given box.
BoxImposePbcMolecule(Box, Space) - Constructor for class etomica.integrator.IntegratorRigidMatrixIterative.BoxImposePbcMolecule
 
BoxIndexEvent - Class in etomica.box
Event that conveys that the maximum leaf index in a Box has changed (or is about to change).
BoxIndexEvent(IBox, int) - Constructor for class etomica.box.BoxIndexEvent
 
BoxInflate - Class in 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(ISpace) - Constructor for class etomica.action.BoxInflate
Constructs action with a default scale of 1.0.
BoxInflate(IBox, ISpace) - Constructor for class etomica.action.BoxInflate
Constructs action ready to be performed on the given box.
BoxInflateAnisotropic - Class in etomica.action
Class that perform anisotropic angle fluctuation
BoxInflateAnisotropic(ISpace) - Constructor for class etomica.action.BoxInflateAnisotropic
 
BoxInflateAnisotropic(IBox, ISpace) - Constructor for class etomica.action.BoxInflateAnisotropic
 
BoxInflateDeformable - Class in 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(ISpace) - Constructor for class etomica.action.BoxInflateDeformable
 
BoxInflateDeformable(IBox, ISpace) - Constructor for class etomica.action.BoxInflateDeformable
 
BoxListenerAdapter - Class in etomica.box
 
BoxListenerAdapter() - Constructor for class etomica.box.BoxListenerAdapter
 
boxMoleculeAdded(IBoxMoleculeEvent) - Method in interface etomica.api.IBoxListener
 
boxMoleculeAdded(IBoxMoleculeEvent) - Method in class etomica.atom.AtomLeafAgentManager
 
boxMoleculeAdded(IBoxMoleculeEvent) - Method in class etomica.atom.MoleculeAgentManager
 
boxMoleculeAdded(IBoxMoleculeEvent) - Method in class etomica.box.BoxListenerAdapter
 
boxMoleculeAdded(IBoxMoleculeEvent) - Method in class etomica.integrator.IntegratorHard
 
boxMoleculeAdded(IBoxMoleculeEvent) - Method in class etomica.integrator.IntegratorMD
 
BoxMoleculeAddedEvent - Class in etomica.box
Event that conveys that an Atom has been added to a Box.
BoxMoleculeAddedEvent(IBox, IMolecule) - Constructor for class etomica.box.BoxMoleculeAddedEvent
 
BoxMoleculeCountEvent - Class in etomica.box
 
BoxMoleculeCountEvent(IBox, ISpecies, int) - Constructor for class etomica.box.BoxMoleculeCountEvent
 
BoxMoleculeEvent - Class in etomica.box
 
BoxMoleculeEvent(IBox, IMolecule) - Constructor for class etomica.box.BoxMoleculeEvent
 
boxMoleculeIndexChanged(IBoxMoleculeIndexEvent) - Method in interface etomica.api.IBoxListener
 
boxMoleculeIndexChanged(IBoxMoleculeIndexEvent) - Method in class etomica.atom.MoleculeAgentManager
 
boxMoleculeIndexChanged(IBoxMoleculeIndexEvent) - Method in class etomica.box.BoxListenerAdapter
 
boxMoleculeIndexChanged(IBoxMoleculeIndexEvent) - Method in class etomica.integrator.IntegratorMD
 
BoxMoleculeIndexEvent - Class in etomica.box
Event that conveys that an Atom's global index in a box has changed.
BoxMoleculeIndexEvent(IBox, IMolecule, int) - Constructor for class etomica.box.BoxMoleculeIndexEvent
 
boxMoleculeRemoved(IBoxMoleculeEvent) - Method in interface etomica.api.IBoxListener
 
boxMoleculeRemoved(IBoxMoleculeEvent) - Method in class etomica.atom.AtomLeafAgentManager
 
boxMoleculeRemoved(IBoxMoleculeEvent) - Method in class etomica.atom.MoleculeAgentManager
 
boxMoleculeRemoved(IBoxMoleculeEvent) - Method in class etomica.box.BoxListenerAdapter
 
boxMoleculeRemoved(IBoxMoleculeEvent) - Method in class etomica.integrator.IntegratorMD
 
BoxMoleculeRemovedEvent - Class in etomica.box
Event that conveys that an Atom has been removed from a Box.
BoxMoleculeRemovedEvent(IBox, IMolecule) - Constructor for class etomica.box.BoxMoleculeRemovedEvent
 
boxNeighborsUpdated(IBoxEvent) - Method in class etomica.box.BoxListenerAdapter
 
boxNumberMolecules(IBoxMoleculeCountEvent) - Method in interface etomica.api.IBoxListener
 
boxNumberMolecules(IBoxMoleculeCountEvent) - Method in class etomica.atom.MoleculeAgentManager
 
boxNumberMolecules(IBoxMoleculeCountEvent) - Method in class etomica.box.BoxListenerAdapter
 
boxNumberMolecules(IBoxMoleculeCountEvent) - Method in class etomica.integrator.IntegratorMD
 
BoxQuench - Class in etomica.action
Scales all velocities of a box so that its kinetic temperature is equal to a given value.
BoxQuench(int) - Constructor for class etomica.action.BoxQuench
 
BoxQuench(double, int) - Constructor for class etomica.action.BoxQuench
Constructs class without specifying box and using Default temperature.
BoxQuench(IBox, double) - Constructor for class etomica.action.BoxQuench
Constructs class ready to perform quench on given box to given temperature.
BoxRandomizeMomenta - Class in etomica.action
Randomizes the velocities of all the leaf atoms in an IBox based on the Maxwell-Boltzmann distribution.
BoxRandomizeMomenta(IBox, IRandom) - Constructor for class etomica.action.BoxRandomizeMomenta
 
boxRemoved(IBox) - Method in class etomica.simulation.SimulationEventManager
 
boxScale - Variable in class etomica.integrator.mcmove.MCMoveBoxSize
 
BoxScaleMomenta - Class in etomica.action
Scales the momenta of all the leaf atoms in an IBox such that the kinetic temperature matches some value.
BoxScaleMomenta(IBox, ISpace) - Constructor for class etomica.action.BoxScaleMomenta
 
boxSize - Variable in class etomica.potential.EwaldSummation
 
boxSize - Variable in class etomica.potential.EwaldSumMolecules
 
BoxTracker() - Constructor for class etomica.integrator.IntegratorPT.BoxTracker
 
boxWellManager - Variable in class etomica.potential.P2SquareWellRobust
 
BravaisLattice - Class in 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) - Constructor for class etomica.lattice.BravaisLattice
 
BravaisLatticeCrystal - Class in etomica.lattice
A lattice with sites given by the "atom" sites of a crystal.
BravaisLatticeCrystal(Primitive, Basis) - Constructor for class etomica.lattice.BravaisLatticeCrystal
Constructs a lattice having sites given by the "atom" sites of the given crystal.
broken3body - Static variable in class etomica.models.water.P2WaterSzalewicz
 
bruteForceNearestImage(IVector) - Method in class etomica.junit.space.BoundaryDeformablePeriodicTest
 
buf - Variable in class etomica.util.RandomNumberGeneratorUnix
 
bump(IAtomList, double) - Method in class etomica.potential.P1HardBoundary
 
bump(IAtomList, double) - Method in class etomica.potential.P1HardMovingBoundary
 
bump(IAtomList, double) - Method in class etomica.potential.P1HardPeriodic
Performs no action.
bump(IAtomList, double) - Method in class etomica.potential.P2DoubleWell
Implements collision dynamics between two square-well atoms.
bump(IAtomList, double) - Method in class etomica.potential.P2HardAssociation
Implements the collision dynamics.
bump(IAtomList, double) - Method in class etomica.potential.P2HardBond
Implements collision dynamics for pair attempting to separate beyond tether distance
bump(IAtomList, double) - Method in class etomica.potential.P2HardBondedList
 
bump(IAtomList, double) - Method in class etomica.potential.P2HardSphere
Implements collision dynamics and updates lastCollisionVirial
bump(IAtomList, double) - Method in class etomica.potential.P2HardWrapper
 
bump(IAtomList, double) - Method in class etomica.potential.P2Ideal
Does nothing.
bump(IAtomList, double) - Method in class etomica.potential.P2PenetrableBond
Implements collision dynamics between two square-well atoms.
bump(IAtomList, double) - Method in class etomica.potential.P2PenetrableSphere
Implements collision dynamics between two penetrable-sphere atoms.
bump(IAtomList, double) - Method in class etomica.potential.P2PenetrableSquareWell
Implements collision dynamics between two square-well atoms.
bump(IAtomList, double) - Method in class etomica.potential.P2RoughSphere
Implements collision dynamics and updates lastCollisionVirial Assumes atoms have same size and mass
bump(IAtomList, double) - Method in class etomica.potential.P2SquareWell
Implements collision dynamics between two square-well atoms.
bump(IAtomList, double) - Method in class etomica.potential.P2SquareWellRobust
Implements collision dynamics between two square-well atoms.
bump(IAtomList, double) - Method in class etomica.potential.P2Tether
Implements collision dynamics for pair attempting to separate beyond tether distance
bump(IAtomList, double) - Method in interface etomica.potential.PotentialHard
Implements the collision dynamics.
button - Variable in class etomica.graphics.DeviceButton
 
buttonActions - Variable in class etomica.graphics.DeviceButtonGroup
 
buttonCorner1 - Variable in class etomica.util.Grabber
 
buttonCorner2 - Variable in class etomica.util.Grabber
 
buttonGroup - Variable in class etomica.graphics.DeviceButtonGroup
 
buttonPanel - Variable in class etomica.graphics.DeviceButtonGroup
 
buttons - Variable in class etomica.graphics.DeviceButtonGroup
 
bveci - Variable in class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
 
bveci - Variable in class etomica.models.co2.PNGCPM.P3GCPMAxilrodTeller
 
bvecj - Variable in class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
 
bvecj - Variable in class etomica.models.co2.PNGCPM.P3GCPMAxilrodTeller
 
bveck - Variable in class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
 
bveck - Variable in class etomica.models.co2.PNGCPM.P3GCPMAxilrodTeller
 
bVirial - Variable in class etomica.util.numerical.B9Optimizer
 
bVirial - Variable in class etomica.util.numerical.VirialOptimizer
 
bVirialFromFile - Variable in class etomica.util.numerical.B9Optimizer
 
bVirialFromFile - Variable in class etomica.util.numerical.VirialOptimizer
 

C

C - Static variable in class etomica.math.Gamma
 
c - Static variable in class etomica.models.water.P2WaterSzalewicz
 
C - Variable in class etomica.potential.P2HePCKLJS
 
c - Static variable in class etomica.potential.P2WaterPotentialsJankowski
 
c - Static variable in class etomica.statmech.HardSphereSolid
 
c - Variable in class etomica.util.numerical.PadeApproximation
 
c - Variable in class etomica.util.numerical.PadeApproximation.VirialParam
 
c0 - Variable in class etomica.graphics.DisplayTable
 
c10 - Static variable in class etomica.potential.P1HydrogenMielke
 
C10Data - Variable in class etomica.potential.P2QChemInterpolated
 
c3 - Static variable in class etomica.models.water.P2WaterSzalewicz
 
c5 - Variable in class etomica.potential.P2HydrogenHinde
 
c5 - Variable in class etomica.potential.P2HydrogenHindeAtomic
 
C6 - Variable in class etomica.models.co2.P2CO2Hellmann
 
c6 - Static variable in class etomica.potential.P1HydrogenMielke
 
c6 - Variable in class etomica.potential.P2HydrogenHinde
 
c6 - Variable in class etomica.potential.P2HydrogenHindeAtomic
 
c6 - Variable in class etomica.potential.P2NitrogenHellmann
 
c6 - Static variable in class etomica.potential.P2O2Bartolomei
 
C6A - Static variable in class etomica.models.co2.P2CO2Hellmann
 
c6A - Static variable in class etomica.potential.P2NitrogenHellmann
 
C6B - Static variable in class etomica.models.co2.P2CO2Hellmann
 
c6B - Static variable in class etomica.potential.P2NitrogenHellmann
 
C6BO - Static variable in class etomica.potential.P2HePCKLJS
 
C6Data - Variable in class etomica.potential.P2QChemInterpolated
 
C8 - Variable in class etomica.models.co2.P2CO2Hellmann
 
c8 - Static variable in class etomica.potential.P1HydrogenMielke
 
c8 - Variable in class etomica.potential.P2HydrogenHinde
 
c8 - Variable in class etomica.potential.P2HydrogenHindeAtomic
 
c8 - Static variable in class etomica.potential.P2O2Bartolomei
 
C8A - Static variable in class etomica.models.co2.P2CO2Hellmann
 
C8B - Static variable in class etomica.models.co2.P2CO2Hellmann
 
C8Data - Variable in class etomica.potential.P2QChemInterpolated
 
C9iso - Static variable in class etomica.potential.P3NitrogenHellmannNonAdditive
 
C9isoSim - Static variable in class etomica.potential.P3NitrogenHellmannNonAdditive
 
calcBoth(double, double) - Method in class etomica.math.Gamma
 
calcdMudP(double, double) - Static method in class etomica.statmech.HardSphereSolid
 
calcdmudrho(double, double) - Static method in class etomica.statmech.HardSphereSolid
 
calcdPdrho(double, double) - Static method in class etomica.statmech.HardSphereSolid
 
calcErr(int, int) - Method in class etomica.util.numerical.AkimaSplineSmoother
 
calcErr(int, int) - Method in class etomica.util.numerical.AkimaSplineSmootherDy
 
calcFacs() - Method in class etomica.potential.P2DiscreteFeynmanHibbs
 
calcGamma(double, double) - Method in class etomica.math.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) - Method in class etomica.math.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 - Class in etomica.util.numerical
Uses finite difference methods to determine the second order differential of the potential (i.e.
CalcGradientDifferentiable(IBox, IPotentialMaster, IMoleculeList, ISpace) - Constructor for class etomica.util.numerical.CalcGradientDifferentiable
 
calcLegendrePolynomial(int, double) - Static method in class etomica.math.SpecialFunctions
Calculates Pn(x), Legendre polynomial of order n for the given input value.
calcOrientation(IMolecule, IOrientationFull3D) - Method in interface etomica.atom.OrientationCalc
Calculates the orientation of the given molecule and stores that in the given orientation.
calcOrientation(IMolecule, IOrientationFull3D) - Method in class etomica.atom.OrientationCalcAtom
 
calcOrientation(IMolecule, double[]) - Method in interface etomica.atom.OrientationCalcQuaternion
 
calcOrientation(IMolecule, double[]) - Method in class etomica.models.water.OrientationCalcWater3P
 
calcOrientation(IMolecule, IOrientationFull3D) - Method in class etomica.models.water.OrientationCalcWater3P
 
calcOrientation(IMolecule, double[]) - Method in class etomica.models.water.OrientationCalcWater4P
 
calcOrientation(IMolecule, IOrientationFull3D) - Method in class etomica.models.water.OrientationCalcWater4P
 
calcpPade(int, int, double) - Method in class etomica.util.numerical.VirialOptimizer
 
calcpVirial(double) - Method in class etomica.util.numerical.B9Optimizer
 
calcSupport(AtomTypeSpheroPolyhedron, IVectorMutable) - Method in class etomica.potential.P2SpheroPolyhedron
 
calculate(IBox, IteratorDirective, PotentialCalculation) - Method in interface etomica.api.IPotentialMaster
Performs the given PotentialCalculation on the atoms of the given Box.
calculate(IBox, IteratorDirective, PotentialCalculation) - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular
Overrides superclass method to enable direct neighbor-list iteration instead of iteration via species/potential hierarchy.
calculate(IMolecule, IteratorDirective.Direction, PotentialCalculation, NeighborListManagerMolecular) - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular
 
calculate(IBox, IteratorDirective, PotentialCalculation) - Method in class etomica.nbr.list.PotentialMasterList
Overrides superclass method to enable direct neighbor-list iteration instead of iteration via species/potential hierarchy.
calculate(IMolecule, IteratorDirective.Direction, PotentialCalculation, NeighborListManager) - Method in class etomica.nbr.list.PotentialMasterList
Performs given PotentialCalculation using potentials/neighbors associated with the given atom (if any).
calculate(IAtom, IteratorDirective.Direction, PotentialCalculation, NeighborListManager) - Method in class etomica.nbr.list.PotentialMasterList
 
calculate(IBox, IteratorDirective, PotentialCalculation) - Method in class etomica.nbr.PotentialMasterHybrid
Overrides superclass method to enable direct neighbor-list iteration instead of iteration via species/potential hierarchy.
calculate(IBox, IteratorDirective, PotentialCalculation) - Method in class etomica.nbr.site.PotentialMasterSite
Overrides superclass method to enable direct neighbor-list iteration instead of iteration via species/potential hierarchy.
calculate(IAtom, PotentialCalculation) - Method in class etomica.nbr.site.PotentialMasterSite
Performs given PotentialCalculation using potentials/neighbors associated with the given atom (if any).
calculate(MoleculesetIterator, IteratorDirective.Direction, IAtom, PotentialCalculation) - Method in class etomica.potential.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.
calculate(IBox, IteratorDirective, PotentialCalculation) - Method in class etomica.potential.PotentialMaster
 
calculate(IBox, IteratorDirective, PotentialCalculation) - Method in class etomica.potential.PotentialMasterLrc
Performs given PotentialCalculation on all LRC potentials added to this group.
calculate(IBox, IteratorDirective, PotentialCalculation) - Method in class etomica.potential.PotentialMasterMonatomic
 
calculate(IAtom, IAtomList, int, PotentialArrayByType, IteratorDirective.Direction, PotentialCalculation) - Method in class etomica.potential.PotentialMasterMonatomic
 
calculateEnergy(double) - Method in class etomica.potential.P22CLJQ
 
calculateForces() - Method in class etomica.integrator.IntegratorGear4
 
calculateForces() - Method in class etomica.integrator.IntegratorGear4NPH
 
calculateLatticeDimensions(int, IVector) - Method in class etomica.config.ConfigurationLattice
 
calculateLatticeDimensions(int, IVector) - Method in class etomica.config.ConfigurationLatticeSimple
 
calculateRangeIndependent(IMolecule, IteratorDirective.Direction, IAtom, PotentialCalculation) - Method in class etomica.nbr.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(FunctionGeneral) - Method in class etomica.lattice.LatticeSum
 
calculateSum(FunctionGeneral) - Method in class etomica.lattice.LatticeSumCrystal
 
CalcVibrationalModes - Class in etomica.action
Calculates the eigenvalues of an NxN matrix.
CalcVibrationalModes() - Constructor for class etomica.action.CalcVibrationalModes
 
callCount - Variable in class etomica.data.meter.MeterRDF
 
callCount - Variable in class etomica.data.meter.MeterRDFPC
 
Calorie - Class in etomica.units
The Joule unit of energy, equal to 1 N-m or 1 kg-m^2/s^2.
Candela - Class in 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.
canvas - Variable in class etomica.graphics.DisplayBox
 
canvas - Variable in class etomica.graphics.DisplayPolytope
 
capitalize(String) - Static method in class etomica.util.Strings
Capitalizes the first letter of the given string.
Carbon - Class in etomica.chem.elements
Class for the Carbon element.
Carbon(String) - Constructor for class etomica.chem.elements.Carbon
 
Carbon(String, double) - Constructor for class etomica.chem.elements.Carbon
 
cartA - Static variable in class etomica.potential.P2WaterPotentialsJankowski
 
cartB - Static variable in class etomica.potential.P2WaterPotentialsJankowski
 
CastGroupOfTablesToDataTable - Class in etomica.data.types
A DataProcessor that converts a homogeneous DataGroup into a multidimensional DataDoubleArray.
CastGroupOfTablesToDataTable() - Constructor for class etomica.data.types.CastGroupOfTablesToDataTable
Sole constructor.
CastGroupToDoubleArray - Class in etomica.data.types
A DataProcessor that converts a homogeneous DataGroup into a multidimensional DataDoubleArray.
CastGroupToDoubleArray() - Constructor for class etomica.data.types.CastGroupToDoubleArray
Sole constructor.
CastToDouble - Class in etomica.data.types
A DataProcessor that converts a Data instance into a DataDouble.
CastToDouble() - Constructor for class etomica.data.types.CastToDouble
Sole constructor.
CastToDoubleArray - Class in etomica.data.types
A DataProcessor that converts a Data instance into a DataDoubleArray.
CastToDoubleArray() - Constructor for class etomica.data.types.CastToDoubleArray
Sole constructor.
CastToGroup - Class in etomica.data.types
A DataProcessor that effectively wraps a Data instance into a DataGroup.
CastToGroup() - Constructor for class etomica.data.types.CastToGroup
Sole constructor.
CastToTable - Class in etomica.data.types
A DataProcessor that converts a Data instance into a DataTable.
CastToTable() - Constructor for class etomica.data.types.CastToTable
Sole constructor.
cavityDipole - Variable in class etomica.potential.P2ReactionFieldDipole
 
cavityDipole - Variable in class etomica.potential.P2ReactionFieldDipoleTruncated
 
cc - Static variable in class etomica.statmech.HardSphereSolid
 
cclec - Static variable in class etomica.potential.P2O2Bartolomei
 
ccpol2Angles - Static variable in class etomica.potential.P2WaterPotentialsJankowski
 
ccpol2BL - Static variable in class etomica.potential.P2WaterPotentialsJankowski
 
cdataIso - Static variable in class etomica.potential.P2HydrogenPatkowskiIso
 
cdum - Variable in class etomica.potential.P2HydrogenPatkowski
 
cdum - Variable in class etomica.potential.P2HydrogenPatkowskiAtomic
 
cdz - Static variable in class etomica.statmech.HardSphereSolid
 
Cell - Class in etomica.nbr.cell
Site used to form array of cells for cell-based neighbor listing.
Cell(int) - Constructor for class etomica.nbr.cell.Cell
 
Cell.CellFactory - Class in etomica.nbr.cell
 
CellFactory() - Constructor for class etomica.nbr.cell.Cell.CellFactory
 
CellFactory() - Constructor for class etomica.nbr.cell.molecule.CellMolecular.CellFactory
 
CellLattice - Class in etomica.lattice
A lattice of arbitrarily-sized rectangular cells, such that a point in space can be associated with one of the cells.
CellLattice(ISpace, IVector, SiteFactory) - Constructor for class etomica.lattice.CellLattice
 
CellLattice.NeighborIterator - Class in 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 - Class in etomica.nbr.cell.molecule
Site used to form array of cells for cell-based neighbor listing.
CellMolecular(int) - Constructor for class etomica.nbr.cell.molecule.CellMolecular
 
CellMolecular.CellFactory - Class in etomica.nbr.cell.molecule
 
cellRange - Variable in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
 
cellRange - Variable in class etomica.nbr.cell.NeighborCellManager
 
center - Variable in class etomica.atom.AtomPositionGeometricCenterPBC
 
CENTER - Static variable in class etomica.graphics.DisplayBox
 
CENTER - Static variable in class etomica.graphics.DisplayPolytope
 
centerMass - Variable in class etomica.models.water.P2Water4PSoft
 
CENTI - Static variable in class etomica.units.Prefix
Prefix indicating 10-2 = 0.01.
centralImage(IVector) - Method in interface etomica.api.IBoundary
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(IVector) - Method in class etomica.space.BoundaryDeformablePeriodic
 
centralImage(IVector) - Method in class etomica.space.BoundaryRectangularNonperiodic
Returns a vector with all elements zero.
centralImage(IVector) - Method in class etomica.space.BoundaryRectangularPeriodic
 
centralImage(IVector) - Method in class etomica.space.BoundaryRectangularPore
 
centralImage(IVector) - Method in class etomica.space.BoundaryRectangularSlit
 
centralImage(IVector) - Method in class etomica.space3d.BoundaryTruncatedOctahedron
 
centralOrigin - Variable in class etomica.graphics.DisplayBox
Coordinate origin for central image Explicit to 2D because drawing is done to 2D image
centralOrigin - Variable in class etomica.graphics.DisplayPolytope
Coordinate origin for central image Explicit to 2D because drawing is done to 2D image
cex - Static variable in class etomica.potential.P2HydrogenPatkowski
 
cex - Static variable in class etomica.potential.P2HydrogenPatkowskiAtomic
 
cexIso - Static variable in class etomica.potential.P2HydrogenPatkowskiIso
 
cgc(int, int, int, int, int, int, int) - Method in class etomica.potential.P2HydrogenPatkowski
 
cgc(int, int, int, int, int, int, int) - Method in class etomica.potential.P2HydrogenPatkowskiAtomic
 
CGS - Class in etomica.units.systems
Centimeter-Gram-Second system of units.
CGS() - Constructor for class etomica.units.systems.CGS
 
ChainHSMD3D - Class in etomica.simulation.prototypes
 
Charge - Class in etomica.chem.electrostatics
 
Charge() - Constructor for class etomica.chem.electrostatics.Charge
 
Charge(double) - Constructor for class etomica.chem.electrostatics.Charge
 
charge - Variable in class etomica.models.co2.PNGCPM.GCPMAgent
 
charge - Variable in class etomica.potential.EwaldSummation.MyCharge
 
charge - Variable in class etomica.potential.EwaldSumMolecules.MyCharge
 
Charge - Class in etomica.units
The dimension for electrical charge.
charge() - Method in class etomica.units.systems.CGS
 
charge() - Method in class etomica.units.systems.LJ
 
charge() - Method in class etomica.units.systems.MKS
 
charge() - Method in class etomica.units.systems.UnitSystem
 
charge() - Method in class etomica.units.systems.UnitSystem.Sim
 
charge2 - Variable in class etomica.models.co2.PNGCPM.GCPMAgent
 
ChargeAgentSourceTIP4PWater - Class in etomica.models.water
 
ChargeAgentSourceTIP4PWater() - Constructor for class etomica.models.water.ChargeAgentSourceTIP4PWater
 
chargeAll - Variable in class etomica.models.co2.PNCO2GCPM
 
chargeC - Variable in class etomica.models.co2.PNCO2GCPM
 
chargeCC - Variable in class etomica.potential.P2CO2EMP
 
chargeCO - Variable in class etomica.potential.P2CO2EMP
 
chargeH - Variable in class etomica.models.water.P2Water3P
 
chargeH - Variable in class etomica.models.water.P2Water4P
 
chargeH - Variable in class etomica.models.water.P2WaterTIP4PHardCore
 
chargeH - Variable in class etomica.models.water.PNWaterGCPM
 
chargeHH - Variable in class etomica.models.water.P2Water3P
 
chargeHH - Variable in class etomica.models.water.P2Water4P
 
chargeHH - Variable in class etomica.models.water.P2WaterTIP4PHardCore
 
chargeM - Variable in class etomica.models.water.P2Water4P
 
chargeM - Variable in class etomica.models.water.P2WaterTIP4PHardCore
 
chargeM - Variable in class etomica.models.water.PNWaterGCPM
 
chargeMH - Variable in class etomica.models.water.P2Water4P
 
chargeMH - Variable in class etomica.models.water.P2WaterTIP4PHardCore
 
chargeMM - Variable in class etomica.models.water.P2Water4P
 
chargeMM - Variable in class etomica.models.water.P2WaterTIP4PHardCore
 
chargeO - Variable in class etomica.models.co2.PNCO2GCPM
 
chargeO - Variable in class etomica.models.water.P2Water3P
 
chargeOH - Variable in class etomica.models.water.P2Water3P
 
chargeOO - Variable in class etomica.models.water.P2Water3P
 
chargeOO - Variable in class etomica.potential.P2CO2EMP
 
check() - Method in class etomica.util.TreeList
checks the tree for consistency of connections and ordering by sortKey.
checkCore - Static variable in class etomica.models.co2.P2CO2H2OWheatley
 
checkCoreCO - Static variable in class etomica.models.co2.P2CO2H2OWheatley
 
checkDimensions() - Method in class etomica.lattice.CellLattice.NeighborIterator
Checks whether lattice dimensions have changed, and updates integer neighbor range if they have.
checkDimensions() - Method in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
Checks the box's dimensions to make sure the number of cells is appropriate.
checkDimensions() - Method in class etomica.nbr.cell.NeighborCellManager
Checks the box's dimensions to make sure the number of cells is appropriate.
checkE - Static variable in class etomica.potential.P2ElectrostaticWithHardCore
 
checkOHBondLength() - Method in class etomica.action.IntegratorDimerApproach
 
checkString(String) - Static method in class etomica.units.UnitFilter
 
checkUnitSystemString(String) - Static method in class etomica.units.UnitFilter
 
childCount - Variable in class etomica.species.SpeciesSpheresHetero
 
childIndex - Variable in class etomica.atom.AtomTypeLeaf
 
childList - Variable in class etomica.atom.iterator.TripletInnerSequential
 
childList - Variable in class etomica.atom.Molecule
 
childTypes - Variable in class etomica.species.Species
 
chisq - Variable in class etomica.util.numerical.NonLinearCurveDiffFitting
 
chisq - Variable in class etomica.util.numerical.NonLinearCurveFitting
 
chiSum - Variable in class etomica.integrator.mcmove.MCMoveTracker
 
Chlorine - Class in etomica.chem.elements
Class for the Chlorine element.
Chlorine(String) - Constructor for class etomica.chem.elements.Chlorine
 
Chlorine(String, double) - Constructor for class etomica.chem.elements.Chlorine
 
choices() - Method in class etomica.action.activity.Controller.ActionStatus
 
choices() - Static method in class etomica.action.activity.ControllerEvent.Type
 
choices() - Static method in class etomica.atom.iterator.IteratorDirective.Direction
 
choices() - Static method in class etomica.data.AccumulatorRatioAverageCovariance
 
choices() - Static method in class etomica.data.AccumulatorRatioAverageCovarianceFull
 
choices() - Static method in class etomica.data.DataSourceUniform.LimitType
 
choices() - Static method in class etomica.graphics.DeviceBox.LabelType
 
choices() - Static method in class etomica.graphics.DisplayTextBox.LabelType
 
choices() - Static method in class etomica.integrator.IntegratorEvent.Type
 
choices() - Static method in class etomica.integrator.IntegratorMD.ThermostatType
 
choices() - Static method in class etomica.integrator.IntegratorNonintervalEvent.NonintervalEventType
 
choices() - Static method in class etomica.util.Constants.Alignment
 
choices() - Static method in class etomica.util.Constants.CompassDirection
 
choices() - Static method in class etomica.util.Constants.Direction
 
Chop() - Constructor for class etomica.util.Function.Chop
Constructs with default cutoff value of 2 Double.MIN_VALUE.
Chop(double) - Constructor for class etomica.util.Function.Chop
 
chrg3 - Static variable in class etomica.models.water.P2WaterSzalewicz
 
chs() - Method in class etomica.math.Complex
Negative of this complex number (chs stands for change sign).
Circle - Class in etomica.math.geometry
A circle in 2D.
Circle() - Constructor for class etomica.math.geometry.Circle
Creates circle with unit radius
Circle(double) - Constructor for class etomica.math.geometry.Circle
Creates circle of the given radius.
classlist() - Static method in class etomica.units.Lister
 
ClassRequirement - Class in etomica.compatibility
 
clear() - Method in class etomica.atom.AtomArrayList
 
clear() - Method in class etomica.atom.DiameterHashByElement
 
clear() - Method in class etomica.atom.iterator.IteratorDirective
Puts directive in default state of no atoms specified, up direction, no potential criteria applied, no LRC included.
clear() - Method in class etomica.atom.MoleculeArrayList
 
clear() - Method in class etomica.potential.P2HardBondedList.BondArrayList
 
clear() - Method in class etomica.util.ObjectArrayList
Removes all of the elements from this list.
clearLists(Lister[]) - Method in class etomica.junit.atom.iterator.IteratorTestAbstract
Clears the list of each lister in the array.
clearLists(ListerMolecule[]) - Method in class etomica.junit.atom.iterator.MoleculeIteratorTestAbstract
Clears the list of each ListerMolecule in the array.
clearNbrs() - Method in class etomica.nbr.list.AtomNeighborLists
Clears neighbor lists, removing all listed neighbor atoms.
clearNbrs() - Method in class etomica.nbr.list.AtomPotentialList
Clears neighbor lists, resetting all flags to false (not interacting).
clearNbrs() - Method in class etomica.nbr.list.molecule.MoleculeNeighborLists
Clears neighbor lists, removing all listed neighbor molecules.
clearNbrs() - Method in class etomica.nbr.list.molecule.MoleculePotentialList
Clears neighbor lists, resetting all flags to false (not interacting).
clearTags() - Method in class etomica.data.DataInfo
Removes all tags.
clearTags() - Method in interface etomica.data.IEtomicaDataInfo
Removes all tags.
clone() - Method in class etomica.atom.iterator.IteratorDirective.PotentialCriterion
 
clone() - Method in interface etomica.space.Tensor
 
clone() - Method in class etomica.space1d.Tensor1D
Support of implementation of Cloneable interface.
clone() - Method in class etomica.space2d.Tensor2D
Support of implementation of Cloneable interface.
clone() - Method in class etomica.space3d.Tensor3D
Support of implementation of Cloneable interface.
clone() - Method in class etomica.spaceNd.TensorND
 
clone() - Method in class etomica.util.ObjectArrayList
Returns a shallow copy of this ArrayList instance.
clone() - Method in class etomica.util.ScientificFormat
 
closeFile() - Method in class etomica.data.AccumulatorAverageFixedOutputFile
 
closeFile() - Method in class etomica.data.DataLogger
 
cm - Variable in class etomica.potential.P2SemiclassicalMolecular.MoleculeInfoBrute
 
cmtoau - Static variable in class etomica.potential.P2WaterPotentialsJankowski
 
cmzFix - Static variable in class etomica.models.water.P2WaterSzalewicz
 
cn - Variable in class etomica.potential.P3HydrogenManzhos
 
CO - Variable in class etomica.models.co2.P2CO2H2OWheatley
 
coef - Variable in class etomica.potential.P2HydrogenHinde
 
coef - Variable in class etomica.potential.P2HydrogenHindeAtomic
 
coefficient_fourier - Variable in class etomica.potential.EwaldSumMolecules
 
collapseBlocks() - Method in class etomica.data.AccumulatorAverageCollapsing
 
collapseData(double) - Method in class etomica.util.HistogramCollapsing
Collapses existing data and expands x range sufficiently so that the given x value is within the range of the histogram.
collapseData() - Method in class etomica.util.HistoryCollapsing
 
collapseData() - Method in class etomica.util.HistoryCollapsingAverage
 
collapseData() - Method in class etomica.util.HistoryCollapsingDiscard
 
colliderAgent - Variable in class etomica.integrator.IntegratorHard
 
colliderAgent() - Method in class etomica.integrator.IntegratorHard
 
colliderColor - Variable in class etomica.graphics.ColorSchemeColliders
Color applied to the downList atom of the colliding pair
collisionAction(IntegratorHard.Agent) - Method in class etomica.data.DataSourceTensorVirialHard
Sums contribution to virial for each collision.
collisionAction(IntegratorHard.Agent) - Method in class etomica.data.meter.MeterPressureHard
Implementation of CollisionListener interface Adds collision virial (from potential) to accumulator
collisionAction(IntegratorHard.Agent) - Method in class etomica.data.meter.MeterPressureHardTensor
 
collisionAction(IntegratorHard.Agent) - Method in interface etomica.integrator.IntegratorHard.CollisionListener
 
collisionCount - Variable in class etomica.integrator.IntegratorHard
 
collisionDiameter - Variable in class etomica.potential.P2HardSphere
Separation at which spheres first overlap
collisionHandlerDown - Variable in class etomica.integrator.IntegratorHard
 
collisionHandlerUp - Variable in class etomica.integrator.IntegratorHard
 
CollisionHandlerUp() - Constructor for class etomica.integrator.IntegratorHard.CollisionHandlerUp
 
collisionListenerHead - Variable in class etomica.integrator.IntegratorHard
 
collisionPartner - Variable in class etomica.integrator.IntegratorHard.Agent
 
collisionPartner() - Method in class etomica.integrator.IntegratorHard.Agent
 
collisionPotential - Variable in class etomica.integrator.IntegratorHard.Agent
 
collisionTime() - Method in class etomica.integrator.IntegratorHard.Agent
Accessor method for the time to next collision of this atom
collisionTime(IAtomList, double) - Method in class etomica.potential.P1HardBoundary
 
collisionTime(IAtomList, double) - Method in class etomica.potential.P1HardMovingBoundary
 
collisionTime(IAtomList, double) - Method in class etomica.potential.P1HardPeriodic
 
collisionTime(IAtomList, double) - Method in class etomica.potential.P2DoubleWell
Computes next time of collision of two square-well atoms, assuming free-flight kinematics.
collisionTime(IAtomList, double) - Method in class etomica.potential.P2HardAssociation
Computes the next time of collision of the given atomPair assuming free flight.
collisionTime(IAtomList, double) - Method in class etomica.potential.P2HardBond
Time at which two atoms will reach the end of their tether, assuming free-flight kinematics
collisionTime(IAtomList, double) - Method in class etomica.potential.P2HardBondedList
 
collisionTime(IAtomList, double) - Method in class etomica.potential.P2HardSphere
Time to collision of pair, assuming free-flight kinematics
collisionTime(IAtomList, double) - Method in class etomica.potential.P2HardWrapper
 
collisionTime(IAtomList, double) - Method in class etomica.potential.P2Ideal
Returns Double.POSITIVE_INFINITY.
collisionTime(IAtomList, double) - Method in class etomica.potential.P2PenetrableBond
 
collisionTime(IAtomList, double) - Method in class etomica.potential.P2PenetrableSphere
Computes next time of collision of two square-well atoms, assuming free-flight kinematics.
collisionTime(IAtomList, double) - Method in class etomica.potential.P2PenetrableSquareWell
Computes next time of collision of two square-well atoms, assuming free-flight kinematics.
collisionTime(IAtomList, double) - Method in class etomica.potential.P2SquareWell
Computes next time of collision of two square-well atoms, assuming free-flight kinematics.
collisionTime(IAtomList, double) - Method in class etomica.potential.P2SquareWellRobust
Computes next time of collision of two square-well atoms, assuming free-flight kinematics.
collisionTime(IAtomList, double) - Method in class etomica.potential.P2Tether
Time at which two atoms will reach the end of their tether, assuming free-flight kinematics
collisionTime(IAtomList, double) - Method in interface etomica.potential.PotentialHard
Computes the time of collision of the given atom(s) with the hard potential, assuming no intervening collisions.
collisionTimeStep - Variable in class etomica.integrator.IntegratorHard
 
collisionValue(IntegratorHard.Agent) - Method in class etomica.data.DataSourceTensorVirialHard
Contribution to the virial from the most recent collision of the given pair/potential.
collisionValue(IntegratorHard.Agent) - Method in interface etomica.data.meter.DataSourceCollisional
 
collisionValue(IntegratorHard.Agent) - Method in class etomica.data.meter.MeterPressureHard
Implementation of Meter.MeterCollisional interface.
color - Variable in class etomica.graphics.DisplayBoxCanvasG3DSys.OrientedSite
 
colorAllAtoms() - Method in interface etomica.graphics.ColorSchemeCollective
Determine color of all atoms.
colorAllAtoms() - Method in class etomica.graphics.ColorSchemeCollectiveAgent
 
colorAllAtoms() - Method in class etomica.graphics.ColorSchemeCoordination
 
colorAllAtoms() - Method in class etomica.graphics.ColorSchemeNeighbor
 
colorAllAtoms() - Method in class etomica.graphics.ColorSchemeNeighborCell
 
colorAllAtoms() - Method in class etomica.graphics.ColorSchemeOverlap
 
colors - Variable in class etomica.graphics.ColorSchemeOverlap
 
ColorScheme - Class in etomica.graphics
Class that defines the algorithm used to determine atoms colors when drawn to DisplayBox.
ColorScheme() - Constructor for class etomica.graphics.ColorScheme
 
ColorScheme(Color) - Constructor for class etomica.graphics.ColorScheme
 
colorScheme - Variable in class etomica.graphics.DisplayBox
 
ColorScheme.Simple - Class in etomica.graphics
Colors all atoms with baseColor.
ColorSchemeByType - Class in etomica.graphics
Colors the atom according to the color given by its type field.
ColorSchemeByType(ISimulation) - Constructor for class etomica.graphics.ColorSchemeByType
 
ColorSchemeCell - Class in etomica.graphics
 
ColorSchemeCell(PotentialMasterNbr, IRandom, IBox) - Constructor for class etomica.graphics.ColorSchemeCell
 
ColorSchemeCollective - Interface in etomica.graphics
 
ColorSchemeCollectiveAgent - Class in 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(IBox) - Constructor for class etomica.graphics.ColorSchemeCollectiveAgent
 
ColorSchemeColliders - Class in etomica.graphics
This colorScheme acts to color differently the two atoms that are scheduled to collide next.
ColorSchemeColliders(IntegratorHard) - Constructor for class etomica.graphics.ColorSchemeColliders
 
ColorSchemeCoordination - Class in etomica.graphics
 
ColorSchemeCoordination(ISimulation, PotentialMasterList, IBox) - Constructor for class etomica.graphics.ColorSchemeCoordination
 
ColorSchemeNeighbor - Class in etomica.graphics
Color atoms based on being neighbors of the reference atom
ColorSchemeNeighbor(ISimulation, PotentialMasterList, IBox) - Constructor for class etomica.graphics.ColorSchemeNeighbor
 
ColorSchemeNeighborCell - Class in etomica.graphics
Colors atoms based on being in a neighboring cell to a reference atom.
ColorSchemeNeighborCell(ISimulation, PotentialMasterNbr, IBox, int) - Constructor for class etomica.graphics.ColorSchemeNeighborCell
 
ColorSchemeNull - Class in etomica.graphics
Does nothing at any time to set atom's color, leaving color to be set to default value.
ColorSchemeNull() - Constructor for class etomica.graphics.ColorSchemeNull
 
ColorSchemeOverlap - Class in etomica.graphics
Color atoms based on how many overlaps they have with their neighbors
ColorSchemeOverlap(ISpace, PotentialMasterList, IBox) - Constructor for class etomica.graphics.ColorSchemeOverlap
 
ColorSchemeRandom - Class in etomica.graphics
 
ColorSchemeRandom(IBox, IRandom) - Constructor for class etomica.graphics.ColorSchemeRandom
 
ColorSchemeRandomByMolecule - Class in etomica.graphics
 
ColorSchemeRandomByMolecule(ISimulation, IBox, IRandom) - Constructor for class etomica.graphics.ColorSchemeRandomByMolecule
 
ColorSchemeTemperature - Class in etomica.graphics
Colors atoms according to their kinetic energy.
ColorSchemeTemperature() - Constructor for class etomica.graphics.ColorSchemeTemperature
Constructs with default low of 200K and high of 400K.
ColorSchemeTemperature(double, double) - Constructor for class etomica.graphics.ColorSchemeTemperature
 
cols - Variable in class etomica.graphics.DeviceButtonGroup
 
columnHeaders - Variable in class etomica.graphics.DisplayTable
 
columnInfoFactories - Variable in class etomica.data.types.DataTable.DataInfoTableFactory
 
com0 - Variable in class etomica.models.water.OrientationCalcWater3P
 
com0 - Variable in class etomica.models.water.OrientationCalcWater4P
 
com0 - Variable in class etomica.models.water.P2WaterSzalewicz
 
com0 - Variable in class etomica.potential.P2HydrogenHinde
 
com0 - Variable in class etomica.potential.P2HydrogenHindeAtomic
 
com0 - Variable in class etomica.potential.P2HydrogenHindePatkowski
 
com0 - Variable in class etomica.potential.P2HydrogenHindePatkowskiAtomic
 
com0 - Variable in class etomica.potential.P2HydrogenPatkowski
 
com0 - Variable in class etomica.potential.P2HydrogenPatkowskiAtomic
 
com1 - Variable in class etomica.models.water.P2Water4P
 
com1 - Variable in class etomica.potential.P2HydrogenHinde
 
com1 - Variable in class etomica.potential.P2HydrogenHindeAtomic
 
com1 - Variable in class etomica.potential.P2HydrogenHindePatkowski
 
com1 - Variable in class etomica.potential.P2HydrogenHindePatkowskiAtomic
 
com1 - Variable in class etomica.potential.P2HydrogenPatkowski
 
com1 - Variable in class etomica.potential.P2HydrogenPatkowskiAtomic
 
com2 - Variable in class etomica.models.water.P2Water4P
 
com3 - Variable in class etomica.models.water.P2WaterSzalewicz
 
CombinationIterator - Class in etomica.math.discrete
Iterator that returns different combinations of n integers taken k at a time.
CombinationIterator(int, int) - Constructor for class etomica.math.discrete.CombinationIterator
Constructor for CombinationIterator.
comHack - Static variable in class etomica.potential.P2WaterPotentialsJankowski
 
comHackDist - Static variable in class etomica.potential.P2WaterPotentialsJankowski
 
compareTo(IAtomType) - Method in class etomica.atom.AtomTypeLeaf
 
compareTo(Feature) - Method in class etomica.compatibility.Feature
 
compareTo(int, Feature) - Method in class etomica.compatibility.Feature
 
compareTo(Feature) - Method in class etomica.compatibility.NumericFeature
 
compareTo(int, Feature) - Method in class etomica.compatibility.NumericFeature
 
compareTo(Feature) - Method in class etomica.compatibility.StringFeature
 
compareTo(int, Feature) - Method in class etomica.compatibility.StringFeature
 
COMPLETED - Static variable in class etomica.action.activity.Controller.ActionStatus
 
completedActions - Variable in class etomica.action.activity.ActivityGroupSeries
 
Complex - Class in etomica.math
handle complex variables and relevant operations from Internet
Complex(double, double) - Constructor for class etomica.math.Complex
Constructs the complex number z = u + i*v
component - Variable in class etomica.graphics.DeviceSlider
Object with property being modulated
component - Variable in class etomica.graphics.DeviceSpinner
Object with property being modulated
component - Variable in class etomica.models.co2.PNCO2GCPM
 
component - Variable in class etomica.models.co2.PNGCPM
 
component - Variable in class etomica.models.water.P2WaterSzalewicz
 
component(int, int) - Method in interface etomica.space.Tensor
 
component(int, int) - Method in class etomica.space1d.Tensor1D
 
component(int, int) - Method in class etomica.space2d.Tensor2D
 
component(int, int) - Method in class etomica.space3d.Tensor3D
 
component(int, int) - Method in class etomica.spaceNd.TensorND
 
ComponentEventControllerButton() - Constructor for class etomica.graphics.DeviceTrioControllerButton.ComponentEventControllerButton
 
componentHidden(ComponentEvent) - Method in class etomica.graphics.DeviceTrioControllerButton.ComponentEventControllerButton
 
componentMoved(ComponentEvent) - Method in class etomica.graphics.DeviceTrioControllerButton.ComponentEventControllerButton
 
componentResized(ComponentEvent) - Method in class etomica.graphics.DeviceTrioControllerButton.ComponentEventControllerButton
 
componentShown(ComponentEvent) - Method in class etomica.graphics.DeviceTrioControllerButton.ComponentEventControllerButton
 
CompoundDimension - Class in etomica.units
 
CompoundDimension(Dimension[], double[]) - Constructor for class etomica.units.CompoundDimension
 
CompoundDimension(Dimension[], double[], String) - Constructor for class etomica.units.CompoundDimension
 
CompoundUnit - Class in etomica.units
 
CompoundUnit(Unit[], double[]) - Constructor for class etomica.units.CompoundUnit
 
CompoundUnit(Unit[], double[], String, String) - Constructor for class etomica.units.CompoundUnit
 
computeImageParameters() - Method in class etomica.graphics.DisplayBox
 
computeImageParameters() - Method in class etomica.graphics.DisplayPolytope
 
computeImageParameters2(int, int) - Method in class etomica.graphics.DisplayBox
 
computeImageParameters2(int, int) - Method in class etomica.graphics.DisplayPolytope
 
computeOrigin(int, int, int) - Method in class etomica.graphics.DisplayPolytope
 
computeRMSD(double[]) - Method in class etomica.util.numerical.NonLinearCurveDiffFitting
 
computeRMSD(double[]) - Method in class etomica.util.numerical.NonLinearCurveFitting
 
computeScaledSysParams(double, double, double, double) - Static method in class etomica.potential.EwaldSummation
 
computeShiftOrigin(IAtom, IBoundary) - Method in class etomica.graphics.DisplayBoxCanvas1D
 
comWi - Variable in class etomica.models.water.PNWaterGCPM
 
comWj - Variable in class etomica.models.water.PNWaterGCPM
 
configuration - Variable in class etomica.action.SimulationRestart
 
Configuration - Interface in etomica.config
General class for assignment of molecules to positions in a box.
ConfigurationFile - Class in etomica.config
reads configuration coordinates from a file and assigns them to the leaf atoms in a box
ConfigurationFile(String) - Constructor for class etomica.config.ConfigurationFile
 
ConfigurationFileBinary - Class in etomica.config
reads configuration coordinates from a binary file and assigns them to the leaf atoms in a box.
ConfigurationFileBinary(String) - Constructor for class etomica.config.ConfigurationFileBinary
 
ConfigurationFileTIP4P - Class in etomica.models.water
This reads from a configuration file containing only H, H and O.
ConfigurationFileTIP4P(String, ISpace, boolean) - Constructor for class etomica.models.water.ConfigurationFileTIP4P
 
ConfigurationLattice - Class in etomica.config
Constructs configuration that has the molecules placed on the sites of a lattice.
ConfigurationLattice(SpaceLattice, ISpace) - Constructor for class etomica.config.ConfigurationLattice
Constructs class using instance of IndexIteratorRectangular as the default index iterator.
ConfigurationLattice(SpaceLattice, IndexIteratorSizable, ISpace) - Constructor for class etomica.config.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.MyLattice - Class in etomica.config
Used to store the state of a lattice.
ConfigurationLatticeSimple - Class in etomica.config
Constructs configuration that has the molecules placed on the sites of a lattice.
ConfigurationLatticeSimple(SpaceLattice, ISpace) - Constructor for class etomica.config.ConfigurationLatticeSimple
Constructs class using instance of IndexIteratorRectangular as the default index iterator.
ConfigurationLatticeSimple(SpaceLattice, IndexIteratorSizable, ISpace) - Constructor for class etomica.config.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.
ConfigurationLatticeWithPlane - Class in etomica.config
Constructs configuration that has the molecules placed on the sites of a lattice.
ConfigurationLatticeWithPlane(SpaceLattice, Plane, ISpace) - Constructor for class etomica.config.ConfigurationLatticeWithPlane
Constructs class using instance of IndexIteratorRectangular as the default index iterator.
ConfigurationOrientedFile - Class in etomica.config
ConfigurationFile subclass capable of handling oriented atoms.
ConfigurationOrientedFile(String, ISpace) - Constructor for class etomica.config.ConfigurationOrientedFile
 
ConfigurationOverlapException - Exception in etomica.exception
Exception thrown when an overlap is detected in the configuration of a box, subject to the status of an ignoreOverlap flag.
ConfigurationOverlapException(IBox) - Constructor for exception etomica.exception.ConfigurationOverlapException
Constructor for ConfigurationOverlapException
ConfigurationReplicate - Class in etomica.config
 
ConfigurationReplicate() - Constructor for class etomica.config.ConfigurationReplicate
 
ConfigurationZincblende - Class in 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, ISpace) - Constructor for class etomica.config.ConfigurationZincblende
 
confluentHypergeometric1F1(double, double, double) - Static method in class etomica.math.SpecialFunctions
The confluent hypergeometric function, usually given the symbol 1F1.
confName - Variable in class etomica.action.WriteConfiguration
 
confName - Variable in class etomica.config.ConfigurationFile
 
confName - Variable in class etomica.config.ConfigurationFileBinary
 
conformation - Variable in class etomica.chem.models.ModelChain
 
conformation - Variable in class etomica.species.Species
 
ConformationChain - Class in etomica.config
General class for a collection of linearly linked atoms.
ConformationChain(ISpace) - Constructor for class etomica.config.ConformationChain
 
ConformationChain2D - Class in etomica.config
 
ConformationChain2D(ISpace, IVector[]) - Constructor for class etomica.config.ConformationChain2D
 
ConformationChain3D - Class in etomica.config
 
ConformationChain3D(ISpace, IVector[]) - Constructor for class etomica.config.ConformationChain3D
 
ConformationChainLinear - Class in etomica.config
Places atoms in a straight line.
ConformationChainLinear(ISpace) - Constructor for class etomica.config.ConformationChainLinear
 
ConformationChainLinear(ISpace, double) - Constructor for class etomica.config.ConformationChainLinear
 
ConformationChainLinear(ISpace, double, double[]) - Constructor for class etomica.config.ConformationChainLinear
 
ConformationChainZigZag - Class in etomica.config
Takes two vectors, and returns them in repeating order to form a zig-zag chain molecule.
ConformationChainZigZag(ISpace) - Constructor for class etomica.config.ConformationChainZigZag
 
ConformationChainZigZag(ISpace, IVector, IVector) - Constructor for class etomica.config.ConformationChainZigZag
 
ConformationChainZigZag2 - Class in etomica.config
 
ConformationChainZigZag2(ISpace) - Constructor for class etomica.config.ConformationChainZigZag2
 
ConformationChainZigZag2(ISpace, IVector, IVector) - Constructor for class etomica.config.ConformationChainZigZag2
 
ConformationGeneric - Class in etomica.config
 
ConformationGeneric(IVector[]) - Constructor for class etomica.config.ConformationGeneric
 
ConformationLinear - Class in etomica.config
Places atoms in a straight line.
ConformationLinear(ISpace) - Constructor for class etomica.config.ConformationLinear
 
ConformationLinear(ISpace, double) - Constructor for class etomica.config.ConformationLinear
 
ConformationLinear(ISpace, double, double[]) - Constructor for class etomica.config.ConformationLinear
 
ConformationWater - Class in etomica.config
 
ConformationWater(ISpace) - Constructor for class etomica.config.ConformationWater
 
ConformationWater3P - Class in etomica.models.water
Conformation for 3-point water molecule.
ConformationWater3P(ISpace) - Constructor for class etomica.models.water.ConformationWater3P
 
ConformationWaterGCPM - Class in etomica.models.water
 
ConformationWaterGCPM(ISpace) - Constructor for class etomica.models.water.ConformationWaterGCPM
 
ConformationWaterGCPMCOM - Class in etomica.models.water
Conformation for 4-point water molecule (plus 1 site at the COM).
ConformationWaterGCPMCOM(ISpace) - Constructor for class etomica.models.water.ConformationWaterGCPMCOM
 
ConformationWaterTIP4P - Class in etomica.models.water
Conformation for 4-point water molecule.
ConformationWaterTIP4P(ISpace) - Constructor for class etomica.models.water.ConformationWaterTIP4P
 
conjugate() - Method in class etomica.math.Complex
Complex conjugate of this Complex number (the conjugate of x+i*y is x-i*y).
conjugate() - Method in class etomica.math.Quaternion
Returns the complex conjugate of the Quaternion q.
Constant() - Constructor for class etomica.util.Function.Constant
 
Constant(double) - Constructor for class etomica.util.Function.Constant
 
Constants - Class in etomica.util
Collection of assorted physical constants.
Constants.Alignment - Class in etomica.util
Enumerated type for specifying HORIZONTAL/VERTICAL alignment.
Constants.CompassDirection - Class in etomica.util
Enumerated type for the compass directions NORTH, SOUTH, EAST, WEST.
Constants.Direction - Class in etomica.util
Enumerated type for the directions TOP, BOTTOM, LEFT, RIGHT, FRONT, BACK.
contains(IAtom) - Method in class etomica.atom.AtomArrayList
Returns true if the given atom is in the list, false otherwise
CONTAINS - Static variable in class etomica.compatibility.Feature
 
contains(IVector) - Method in class etomica.math.geometry.Cube
Returns true if the given vector lies inside (or on the surface of) this cell, false otherwise.
contains(IVector) - Method in class etomica.math.geometry.Cuboid
Returns true if the given vector lies inside (or on the surface of) this cell, false otherwise.
contains(IVector) - Method in class etomica.math.geometry.Hypersphere
Returns true if the given point lies on or in the sphere.
contains(IVector) - Method in class etomica.math.geometry.LineSegment
Returns true if the given vector lies between the ends of the segment, on the line joining them.
contains(IVector) - Method in class etomica.math.geometry.Parallelepiped
Returns true if the given vector lies inside (or on the surface of) this cell, false otherwise.
contains(IVector) - Method in class etomica.math.geometry.Parallelogram
Returns true if the given vector lies inside (or on the surface of) this cell, false otherwise.
contains(IVector) - Method in class etomica.math.geometry.Point
Returns true if this point is at exactly the same location as the point defined by the given vector.
contains(IVector) - Method in class etomica.math.geometry.PolygonGeneral
Returns true if the given point lies inside or on an edge of the polygon
contains(IVector) - Method in class etomica.math.geometry.PolyhedronGeneral
Returns true if the given point lies inside or on an edge of the polyhedron
contains(IVector) - Method in class etomica.math.geometry.Polytope
Returns true if the given vector lies inside the polytope, false otherwise.
contains(IVector) - Method in class etomica.math.geometry.Rectangle
Returns true if the given vector lies inside (or on the surface of) this cell, false otherwise.
contains(IVector) - Method in interface etomica.math.geometry.Shape
Returns true if the point described by the vector lies in or on the enclosed region.
contains(IVector) - Method in class etomica.math.geometry.Square
Returns true if the given vector lies inside (or on the surface of) this cell, false otherwise.
contains(IVector) - Method in class etomica.math.geometry.TruncatedOctahedron
 
contains(IAtom) - Method in class etomica.potential.P2HardBondedList.BondArrayList
 
contains(IPotentialAtomic) - Method in class etomica.potential.PotentialGroup
Indicates if a given potential is a sub-potential of this group.
contains(double) - Method in class etomica.util.DoubleRange
Indicates if a value falls within the range of this instance.
contains(int) - Method in class etomica.util.IntegerRange
Indicates if a value falls within the range of this instance.
contains(Object) - Method in class etomica.util.ObjectArrayList
Returns true if this list contains the specified element.
controlGraphic() - Method in class etomica.graphics.DevicePlotPoints
Returns the top level panel that the points table and (if parameters are vertically-oriented) function parameter slider components sit on.
Controller - Class in etomica.action.activity
Organizer and executor of actions performed by the simulation.
Controller() - Constructor for class etomica.action.activity.Controller
 
controller - Variable in class etomica.action.activity.ControllerEvent
 
controller - Variable in class etomica.action.ControllerActionAdapter
 
controller - Variable in class etomica.graphics.Device
 
controller - Variable in class etomica.graphics.DisplayBox
 
controller - Variable in class etomica.graphics.DisplayCanvas
 
controller - Variable in class etomica.graphics.SimulationGraphic
 
controller - Variable in class etomica.simulation.prototypes.HsMc2d
 
controller - Variable in class etomica.simulation.prototypes.LjMd2D
 
controller - Variable in class etomica.simulation.prototypes.LjMd3D
 
controller - Variable in class etomica.simulation.prototypes.SoftSphere3d
 
controller - Variable in class etomica.simulation.prototypes.SwMd2D
 
controller - Variable in class etomica.simulation.prototypes.SWMD3D
 
controller - Variable in class etomica.tests.TestLJMC3D
 
Controller.ActionStatus - Class in etomica.action.activity
Enumerated type describing the status of an action.
Controller.UrgentWaitObject - Class in etomica.action.activity
 
Controller.WaitObject - Class in etomica.action.activity
 
ControllerAction - Interface in etomica.action
Elementary action performed on a controller.
ControllerActionAdapter - Class in etomica.action
Convenience class used to define a ControllerAction.
ControllerActionAdapter() - Constructor for class etomica.action.ControllerActionAdapter
 
ControllerEvent - Class in etomica.action.activity
 
ControllerEvent(IController, ControllerEvent.Type) - Constructor for class etomica.action.activity.ControllerEvent
 
ControllerEvent(IController, ControllerEvent.Type, IAction) - Constructor for class etomica.action.activity.ControllerEvent
 
ControllerEvent.Type - Class in etomica.action.activity
 
ControllerEventManager - Class in etomica.action.activity
 
ControllerEventManager() - Constructor for class etomica.action.activity.ControllerEventManager
 
ControllerToggle - Class in etomica.action
Switches controller between paused and unpaused conditions, or starts it if not yet active.
ControllerToggle() - Constructor for class etomica.action.ControllerToggle
 
controlPanel - Variable in class etomica.graphics.SimulationPanel
 
coord - Variable in class etomica.graphics.DisplayBoxCanvasG3DSys.OrientedSite
 
coord2 - Variable in class etomica.graphics.DisplayBoxCanvasG3DSys.OrientedFullSite
 
coord3 - Variable in class etomica.graphics.DisplayBoxCanvasG3DSys.OrientedFullSite
 
CoordinateConverter - Class in etomica.math.geometry.coordinate
 
CoordinateConverter() - Constructor for class etomica.math.geometry.coordinate.CoordinateConverter
 
coords - Variable in class etomica.config.ConformationGeneric
 
Copper - Class in etomica.chem.elements
Class for the Copper element.
Copper(String) - Constructor for class etomica.chem.elements.Copper
 
Copper(String, double) - Constructor for class etomica.chem.elements.Copper
 
copy() - Method in class etomica.lattice.crystal.Primitive
Returns a new, identical instance of this primitive.
copy() - Method in class etomica.lattice.crystal.PrimitiveBcc
Returns a new PrimitiveCubic with the same size as this one.
copy() - Method in class etomica.lattice.crystal.PrimitiveCubic
Returns a new PrimitiveCubic with the same size as this one.
copy() - Method in class etomica.lattice.crystal.PrimitiveFcc
Returns a new PrimitiveCubic with the same size as this one.
copy() - Method in class etomica.lattice.crystal.PrimitiveGeneral
 
copy() - Method in class etomica.lattice.crystal.PrimitiveHexagonal
Returns a new PrimitiveHexagonal with the same size as this one.
copy() - Method in class etomica.lattice.crystal.PrimitiveHexagonal2D
Returns a new PrimitiveHexagonal with the same size as this one.
copy() - Method in class etomica.lattice.crystal.PrimitiveMonoclinic
Returns a new, identical instance of this primitive.
copy() - Method in class etomica.lattice.crystal.PrimitiveOrthorhombic
Returns a new, identical instance of this primitive.
copy() - Method in class etomica.lattice.crystal.PrimitiveOrthorhombicHexagonal
Returns a new, identical instance of this primitive.
copy() - Method in class etomica.lattice.crystal.PrimitiveTetragonal
Returns a new PrimitiveTetragonal with the same size as this one.
copy() - Method in class etomica.lattice.crystal.PrimitiveTriclinic
Returns a new, identical instance of this primitive.
copy() - Method in class etomica.lattice.crystal.PrimitiveTrigonal
Returns a new, identical instance of this primitive.
core - Static variable in class etomica.models.co2.P2CO2H2OWheatley
 
core - Static variable in class etomica.models.water.P2WaterSzalewicz
 
core - Variable in class etomica.models.water.PNWaterGCPM
 
coreCO - Static variable in class etomica.models.co2.P2CO2H2OWheatley
 
coreDiameter - Variable in class etomica.potential.P2DoubleWell
 
coreDiameter - Variable in class etomica.potential.P2PenetrableSphere
 
coreDiameter - Variable in class etomica.potential.P2SquareWell
 
coreDiameter - Variable in class etomica.potential.P2SquareWellRobust
 
coreDiameterSquared - Variable in class etomica.potential.P2DoubleWell
 
coreDiameterSquared - Variable in class etomica.potential.P2PenetrableSphere
 
coreDiameterSquared - Variable in class etomica.potential.P2PenetrableSquareWell
 
coreDiameterSquared - Variable in class etomica.potential.P2SquareWell
 
coreDiameterSquared - Variable in class etomica.potential.P2SquareWellRobust
 
coreFac - Variable in class etomica.models.co2.PNCO2GCPM
 
coreFac - Variable in class etomica.models.co2.PNGCPM
 
cornerData - Variable in class etomica.util.Grabber
 
CornerData() - Constructor for class etomica.util.Grabber.CornerData
 
CornerSetListener(Grabber, Grabber.ActionCornerSetter, int) - Constructor for class etomica.util.Grabber.CornerSetListener
 
corrector() - Method in class etomica.integrator.IntegratorGear4
 
corrector() - Method in class etomica.integrator.IntegratorGear4NPH
 
correlationSum - Variable in class etomica.data.AccumulatorAverageCollapsing
 
correlationSum - Variable in class etomica.data.AccumulatorAverageFixed
 
correlationSum - Variable in class etomica.data.AccumulatorAverageFixedOutputFile
 
cos() - Method in class etomica.math.Complex
Cosine of this Complex number (doesn't change this Complex number).
cos1m2ThetaDiff - Variable in class etomica.potential.P3CPSNonAdditiveHe
 
cos1m2ThetaDiff - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
 
cos2ThetaDiff - Variable in class etomica.potential.P3CPSNonAdditiveHe
 
cos2ThetaDiff - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
 
cosg - Variable in class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
 
cosg - Variable in class etomica.models.co2.PNGCPM.P3GCPMAxilrodTeller
 
cosGamma - Static variable in class etomica.lattice.crystal.PrimitiveHexagonal
 
cosGamma - Static variable in class etomica.lattice.crystal.PrimitiveHexagonal2D
 
cosh() - Method in class etomica.math.Complex
Hyperbolic cosine of this Complex number (doesn't change this Complex number).
coskrj - Variable in class etomica.potential.EwaldSummation
 
cosNTheta - Variable in class etomica.potential.P3CPSNonAdditiveHe
 
cosNTheta - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
 
cosThetaDiff - Variable in class etomica.potential.P3CPSNonAdditiveHe
 
cosThetaDiff - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
 
cosThetaSum - Variable in class etomica.potential.P3CPSNonAdditiveHe
 
cosThetaSum - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
 
Coulomb - Class in etomica.units
The coulomb unit of electrical charge.
count - Variable in class etomica.box.BoxMoleculeCountEvent
 
count - Variable in class etomica.data.AccumulatorAverage
 
count - Variable in class etomica.data.AccumulatorAverageBlockless.AllData
 
count - Variable in class etomica.data.AccumulatorAverageBlockless
 
count - Variable in class etomica.data.AccumulatorAverageBlocklessSlim
 
count - Variable in class etomica.data.AccumulatorAverageCollapsingLog
 
Count - Class in etomica.units
Unit class for the number, or quantity, of something.
count - Variable in class etomica.util.HistogramNotSoSimple
 
counter - Variable in class etomica.atom.iterator.ANIntergroupCoupled
 
counter - Variable in class etomica.atom.iterator.ANIntergroupExchange
 
counter - Variable in class etomica.atom.iterator.ANIntragroupExchange
 
countMolecules(String) - Static method in class etomica.potential.PotentialEmul
 
counts - Variable in class etomica.util.HistogramDiscrete
 
counts - Variable in class etomica.util.HistogramNotSoSimple
 
counts - Variable in class etomica.util.HistogramSimple
 
countTest(AtomLeafsetIterator, int) - Method in class etomica.junit.atom.iterator.IteratorTestAbstract
Tests that iterator gives a specific number of iterates.
countTest(MoleculesetIterator, int) - Method in class etomica.junit.atom.iterator.MoleculeIteratorTestAbstract
Tests that iterator gives a specific number of iterates.
covar - Variable in class etomica.util.numerical.NonLinearCurveDiffFitting
 
covar - Variable in class etomica.util.numerical.NonLinearCurveFitting
 
COVARIANCE - Static variable in class etomica.data.AccumulatorAverageCovariance
 
covariance - Variable in class etomica.data.AccumulatorAverageCovariance
 
covSum - Variable in class etomica.data.AccumulatorAverageCovariance
 
createAndShowGUI() - Method in class etomica.units.UnitGraphics
 
createDecimalSliderStandardLabels(double) - Method in class etomica.graphics.DecimalSlider
 
createDisplayBoxPaintAction(IBox) - Method in class etomica.graphics.SimulationGraphic
 
createOffScreen(int, int) - Method in class etomica.graphics.DisplayCanvas
 
crep - Variable in class etomica.potential.P2HydrogenHinde
 
crep - Variable in class etomica.potential.P2HydrogenHindeAtomic
 
criterion - Variable in class etomica.potential.PotentialGroup
 
CriterionAdapter - Class in etomica.nbr
Wraps another criterion while adding additional criteria to the acceptance decision.
CriterionAdapter(NeighborCriterion) - Constructor for class etomica.nbr.CriterionAdapter
Constructs criterion that wraps the given criterion.
CriterionAdapterMolecular - Class in etomica.nbr.molecule
Wraps another criterion while adding additional criteria to the acceptance decision.
CriterionAdapterMolecular(NeighborCriterionMolecular) - Constructor for class etomica.nbr.molecule.CriterionAdapterMolecular
Constructs criterion that wraps the given criterion.
CriterionAll - Class in etomica.nbr
Specifies that all atoms pairs are to be considered neighbors.
CriterionAll() - Constructor for class etomica.nbr.CriterionAll
 
CriterionAllMolecular - Class in etomica.nbr.molecule
Specifies that all atoms pairs are to be considered neighbors.
CriterionAllMolecular() - Constructor for class etomica.nbr.molecule.CriterionAllMolecular
 
CriterionBondedSimple - Class in etomica.nbr
 
CriterionBondedSimple(NeighborCriterion) - Constructor for class etomica.nbr.CriterionBondedSimple
 
CriterionInterMolecular - Class in etomica.nbr
Pair criterion that judges whether two atoms are or are not in the same molecule.
CriterionInterMolecular(NeighborCriterion) - Constructor for class etomica.nbr.CriterionInterMolecular
Constructs criterion in default state such that intramolecular pairs are rejected, and intermolecular pairs are accepted.
CriterionMolecular - Class in etomica.nbr
Pair criterion that judges whether two atoms are or are not in the same molecule.
CriterionMolecular(NeighborCriterion) - Constructor for class etomica.nbr.CriterionMolecular
Constructs criterion in default state such that intramolecular pairs are rejected, and intermolecular pairs are accepted.
CriterionMolecularNonAdjacent - Class in etomica.nbr
Pair criterion that judges whether two atoms are or are not in the same molecule, and whether or not they are separated by a minimum number of bonds.
CriterionMolecularNonAdjacent(NeighborCriterion) - Constructor for class etomica.nbr.CriterionMolecularNonAdjacent
 
CriterionNone - Class in etomica.nbr
 
CriterionNone() - Constructor for class etomica.nbr.CriterionNone
 
CriterionPositionWall - Class in etomica.nbr
Simple neighbor criterion based on distance moved by a leaf atom since the last update.
CriterionPositionWall(ISimulation) - Constructor for class etomica.nbr.CriterionPositionWall
 
CriterionPositionWall.DoubleWrapper - Class in etomica.nbr
 
CriterionSimple - Class in etomica.nbr
Simple neighbor criterion based on distance moved by a leaf atom since the last update.
CriterionSimple(ISimulation, ISpace, double, double) - Constructor for class etomica.nbr.CriterionSimple
 
CriterionSimpleMolecular - Class in 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(ISimulation, ISpace, double, double) - Constructor for class etomica.nbr.molecule.CriterionSimpleMolecular
 
CriterionSpecies - Class in etomica.nbr.molecule
Filters molecule to match a given species.
CriterionSpecies(NeighborCriterionMolecular, ISpecies) - Constructor for class etomica.nbr.molecule.CriterionSpecies
 
CriterionSpeciesPair - Class in etomica.nbr.molecule
Filters molecule pairs to match a given pair of Species.
CriterionSpeciesPair(NeighborCriterionMolecular, ISpecies, ISpecies) - Constructor for class etomica.nbr.molecule.CriterionSpeciesPair
 
CriterionType - Class in etomica.nbr
Filters atoms to match a given AtomType.
CriterionType(NeighborCriterion, IAtomType) - Constructor for class etomica.nbr.CriterionType
 
CriterionTypePair - Class in etomica.nbr
Filters atoms pairs to match a given pair of AtomTypes.
CriterionTypePair(NeighborCriterion, IAtomType, IAtomType) - Constructor for class etomica.nbr.CriterionTypePair
 
CriterionTypesCombination - Class in etomica.nbr
Filters AtomSets to match a given set of AtomTypes.
CriterionTypesCombination(NeighborCriterion, IAtomType[]) - Constructor for class etomica.nbr.CriterionTypesCombination
 
CriterionTypesMulti - Class in etomica.nbr
Filters AtomSets to match a given set of AtomTypes.
CriterionTypesMulti(NeighborCriterion, IAtomType[]) - Constructor for class etomica.nbr.CriterionTypesMulti
 
csp - Static variable in class etomica.potential.P2HydrogenPatkowski
 
csp - Static variable in class etomica.potential.P2HydrogenPatkowskiAtomic
 
cspIso - Static variable in class etomica.potential.P2HydrogenPatkowskiIso
 
cten - Variable in class etomica.potential.P2HydrogenHinde
 
cten - Variable in class etomica.potential.P2HydrogenHindeAtomic
 
cType - Variable in class etomica.models.water.SpeciesWater4PCOM
 
Cube - Class in etomica.math.geometry
A geometric cube.
Cube(ISpace) - Constructor for class etomica.math.geometry.Cube
Constructs a cube of unit size.
Cube(ISpace, double) - Constructor for class etomica.math.geometry.Cube
Constructs a cube with edge length having the given value.
cubeRoot(double) - Static method in class etomica.space3d.Vector3D
 
CubicCentimeter - Class in etomica.units
The cubic centimeter unit of volume, cm^3.
CubicLattice - Interface in etomica.lattice
Lattice or crystal with cubic symmetry, such that its spatial size can be characterized by a single value, the lattice constant.
CubicMeter - Class in etomica.units
The cubic meter unit of volume, m^3.
Cuboid - Class in 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(ISpace) - Constructor for class etomica.math.geometry.Cuboid
Constructs a cuboid with equal faces of unit size (a cube).
Cuboid(ISpace, double, double, double) - Constructor for class etomica.math.geometry.Cuboid
Constructs a cuboid with edges of lengths having the given values.
CURRENT - Static variable in class etomica.action.activity.Controller.ActionStatus
 
Current - Class in etomica.units
The dimension for electrical current.
current() - Method in class etomica.units.systems.CGS
 
current() - Method in class etomica.units.systems.LJ
 
current() - Method in class etomica.units.systems.MKS
 
current() - Method in class etomica.units.systems.UnitSystem
 
current() - Method in class etomica.units.systems.UnitSystem.Sim
 
currentAction - Variable in class etomica.action.activity.ActivityGroupSeries
 
currentBlockSum - Variable in class etomica.data.AccumulatorAverageCollapsing
 
currentBlockSum - Variable in class etomica.data.AccumulatorAverageFixed
 
currentBlockSum - Variable in class etomica.data.AccumulatorAverageFixedOutputFile
 
currentBox - Variable in class etomica.graphics.DisplayTextBoxesCAE
 
currentKineticEnergy - Variable in class etomica.integrator.IntegratorMD
 
currentPotentialEnergy - Variable in class etomica.integrator.IntegratorBox
 
currentTime - Variable in class etomica.integrator.IntegratorMD
 
cursor - Variable in class etomica.atom.iterator.ApiIndexList
 
cursor - Variable in class etomica.atom.iterator.AtomIteratorArrayListSimple
Index of element to be returned by subsequent call to next.
cursor - Variable in class etomica.atom.iterator.MoleculeIteratorArrayListSimple
Index of element to be returned by subsequent call to next.
cursor - Variable in class etomica.atom.iterator.TripletInnerSequential
 
cursor - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbr
 
cursor - Variable in class etomica.lattice.RectangularLatticeNbrIterator
 
cursor - Variable in class etomica.util.HistoryCollapsing
 
cutoff - Variable in class etomica.potential.P2ReactionFieldDipole
 
cutoff - Variable in class etomica.potential.P2ReactionFieldDipoleTruncated
 
cutoff2 - Variable in class etomica.potential.P2ReactionFieldDipole
 
cutoff2 - Variable in class etomica.potential.P2ReactionFieldDipoleTruncated
 
cutoffRatio - Variable in class etomica.potential.P2MoleculeTruncated
 
cutoffRatio - Variable in class etomica.potential.P2ReactionFieldDipoleTruncated
 
cVector - Variable in class etomica.action.BoxInflateAnisotropic
 
cVectorOld - Variable in class etomica.action.BoxInflateAnisotropic
 

D

D() - Method in class etomica.config.ConfigurationLattice.MyLattice
 
D - Variable in class etomica.integrator.IntegratorGear4NPH
 
D - Variable in class etomica.integrator.mcmove.MCMoveVolume
 
D() - Method in interface etomica.lattice.AbstractLattice
Dimension of the lattice.
D() - Method in class etomica.lattice.BravaisLattice
 
D() - Method in class etomica.lattice.BravaisLatticeCrystal
Returns the spatial dimension + 1.
D - Variable in class etomica.lattice.crystal.Primitive
 
D - Variable in class etomica.lattice.RectangularLattice
 
D() - Method in class etomica.lattice.RectangularLattice
 
D - Variable in class etomica.lattice.RectangularLatticeNbrIterator
 
D() - Method in class etomica.lattice.RectangularLatticeNbrIterator
 
D() - Method in class etomica.math.geometry.Hypersphere
 
D - Variable in class etomica.math.geometry.Polytope
 
D() - Method in class etomica.math.geometry.Polytope
The dimension of this polytope, which is not necessarily the dimension of the space it is embedded in.
D() - Method in interface etomica.math.geometry.Shape
Returns the spatial dimension of the shape.
d(int, double, double) - Method in class etomica.potential.P2HydrogenPatkowski
 
d(int, double, double) - Method in class etomica.potential.P2HydrogenPatkowskiAtomic
 
d(int, double, double) - Method in class etomica.potential.P2HydrogenPatkowskiIso
 
d(int, double, double) - Static method in class etomica.potential.P2WaterPotentialsJankowski
 
D - Static variable in class etomica.potential.P3HydrogenManzhos
 
d - Static variable in class etomica.potential.P3HydrogenManzhos
 
D() - Method in interface etomica.space.ISpace
The dimension of this space.
D() - Method in class etomica.space.Space
 
D() - Method in interface etomica.space.Tensor
 
D() - Method in class etomica.space1d.Space1D
 
D() - Method in class etomica.space1d.Tensor1D
 
D() - Method in class etomica.space2d.Space2D
 
D() - Method in class etomica.space2d.Tensor2D
 
D() - Method in class etomica.space3d.Space3D
 
D() - Method in class etomica.space3d.Tensor3D
 
D() - Method in class etomica.spaceNd.TensorND
 
d - Variable in class etomica.util.numerical.PadeApproximation.VirialParam
 
d0 - Variable in class etomica.potential.P3HydrogenManzhos
 
d2 - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
 
d2dfac - Variable in class etomica.util.numerical.AkimaSplineSmoother
 
d2fac - Variable in class etomica.util.numerical.AkimaSplineSmoother
 
d2tot - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
 
d2tot - Variable in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
 
d2tot - Variable in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
 
d2tot - Variable in class etomica.potential.P2NitrogenHellmann.P2N2QFH
 
d2u(double) - Method in class etomica.potential.P1HydrogenMielke
 
d2u(double) - Method in interface etomica.potential.P1IntraMolecular
 
d2u(double) - Method in class etomica.potential.P2Anharmonic
The second derivative of the pair energy, times the square of the separation: r^2 d^2u/dr^2.
d2u(double) - Method in class etomica.potential.P2ArgonAziz1993
The second derivative of the pair energy, times the square of the separation: r^2 d^2u/dr^2.
d2u(double) - Method in class etomica.potential.P2ArgonSlavicekEtAl2003
The second derivative of the pair energy, times the square of the separation: r^2 d^2u/dr^2.
d2u(double) - Method in class etomica.potential.P2ArgonTangAndToennies2003
The second derivative of the pair energy, times the square of the separation: r^2 d^2u/dr^2.
d2u(double) - Method in class etomica.potential.P2DiscreteFeynmanHibbs.P2HeEmpericalQuantum
 
d2u(double) - Method in class etomica.potential.P2Dreiding
The second derivative of the pair energy, times the square of the separation: r^2 d^2u/dr^2.
d2u(double) - Method in class etomica.potential.P2Electrostatic
 
d2u(double) - Method in class etomica.potential.P2ElectrostaticWithHardCore
 
d2u(double) - Method in class etomica.potential.P2Exp6
The second derivative of the pair energy, times the square of the separation: r^2 d^2u/dr^2.
d2u(double) - Method in class etomica.potential.P2Exp6Buckingham
The second derivative of the pair energy, times the square of the separation: r^2 d^2u/dr^2.
d2u(double) - Method in class etomica.potential.P2Fene
The second derivative of the pair energy, times the square of the separation: r^2 d^2u/dr^2.
d2u(double) - Method in class etomica.potential.P2Harmonic
The second derivative of the pair energy, times the square of the separation: r^2 d^2u/dr^2.
d2u(double) - Method in class etomica.potential.P2HePCKLJS
The second derivative of the pair energy, times the square of the separation: r^2 d^2u/dr^2.
d2u(double) - Method in class etomica.potential.P2HeSimplified
The second derivative of the pair energy, times the square of the separation: r^2 d^2u/dr^2.
d2u(double) - Method in class etomica.potential.P2HydrogenPatkowskiIso
 
d2u(double) - Method in class etomica.potential.P2LennardJones
The second derivative of the pair energy, times the square of the separation: r^2 d^2u/dr^2.
d2u(double) - Method in class etomica.potential.P2LennardJonesDreiding
The second derivative of the pair energy, times the square of the separation: r^2 d^2u/dr^2.
d2u(double) - Method in class etomica.potential.P2LJQQ
 
d2u(double) - Method in class etomica.potential.P2ModifiedMorse
The second derivative of the pair energy, times the square of the separation: r^2 d^2u/dr^2.
d2u(double) - Method in class etomica.potential.P2Morse
The second derivative of the pair energy, times the square of the separation: r^2 d^2u/dr^2.
d2u(double) - Method in class etomica.potential.P2QChemInterpolated
The second derivative of the pair energy, times the square of the separation: r^2 d^2u/dr^2.
d2u(double) - Method in class etomica.potential.P2SoftSphere
The second derivative of the pair energy, times the square of the separation: r^2 d^2u/dr^2.
d2u(double) - Method in class etomica.potential.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) - Method in class etomica.potential.P2WCA
The second derivative of the pair energy, times the square of the separation: r^2 d^2u/dr^2.
d2u(double) - Method in class etomica.potential.Potential2SoftSpherical
The second derivative of the pair energy, times the square of the separation: r^2 d^2u/dr^2.
d2uCorrection(double) - Method in class etomica.potential.P2SoftSphericalTruncated.P0Lrc
Uses result from integration-by-parts to evaluate integral of r2 d2u/dr2 using integral of u.
d3dfac - Variable in class etomica.util.numerical.AkimaSplineSmoother
 
d3fac - Variable in class etomica.util.numerical.AkimaSplineSmoother
 
da - Variable in class etomica.util.numerical.NonLinearCurveDiffFitting
 
da - Variable in class etomica.util.numerical.NonLinearCurveFitting
 
daDef - Variable in class etomica.integrator.mcmove.MCMoveOverlapListener
 
Dalton - Class in etomica.units
 
damp(int, double, double) - Method in class etomica.models.water.P2WaterSzalewicz
 
DampingParams() - Constructor for class etomica.potential.P2QChemInterpolated.DampingParams
 
DampingParams() - Constructor for class etomica.potential.P3AdditiveQChem.DampingParams
 
DampingParams() - Constructor for class etomica.potential.P3QChem.DampingParams
 
daSpan - Variable in class etomica.integrator.mcmove.MCMoveOverlapListener
 
data - Variable in class etomica.data.AccumulatorCounter
 
data - Variable in class etomica.data.DataDump
 
data - Variable in class etomica.data.DataProcessorChemicalPotential
 
data - Variable in class etomica.data.DataProcessorFunction
 
data - Variable in class etomica.data.DataProcessorInterfacialTension
 
data - Variable in class etomica.data.DataSourcePositionedBoltzmannFactor
 
data - Variable in class etomica.data.DataSourceScalar
 
data - Variable in class etomica.data.DataSourceTensorVirialHard
 
data - Variable in class etomica.data.meter.MeterDihedralAngle
 
data - Variable in class etomica.data.meter.MeterDipoleSumSquaredMappedAverage
 
data - Variable in class etomica.data.meter.MeterHyperVirial
 
data - Variable in class etomica.data.meter.MeterPressureByVolumeChange.DataSourceExp
 
data - Variable in class etomica.data.meter.MeterPressureTensor
 
data - Variable in class etomica.data.meter.MeterPressureTensorFromIntegrator
 
data - Variable in class etomica.data.meter.MeterProfileByAtoms
 
data - Variable in class etomica.data.meter.MeterProfileByVolume
 
data - Variable in class etomica.data.meter.MeterRDF
 
data - Variable in class etomica.data.meter.MeterRDFPC
 
data - Variable in class etomica.data.types.DataGroup
 
data - Variable in class etomica.junit.data.types.DataGroupTest
 
DataAccumulator - Class in etomica.data
DataProcessor that accumulates and transforms given data and intermittently transmits processed data to other DataSink(s).
DataAccumulator() - Constructor for class etomica.data.DataAccumulator
Constructs accumulator with no initial DataSink.
DataAccumulator(IDataSink) - Constructor for class etomica.data.DataAccumulator
Constructs DataAccumulator with the given DataSink.
DataArrayWriter - Class in etomica.data
A DataWriter that writes out data as a table with optional column headings
DataArrayWriter() - Constructor for class etomica.data.DataArrayWriter
 
DataCasterJudgeFunction() - Constructor for class etomica.graphics.DisplayPlot.DataCasterJudgeFunction
 
DataCasterJudgeTable() - Constructor for class etomica.data.DataSinkTable.DataCasterJudgeTable
 
dataChanged(DataSet.DataSetSink) - Method in class etomica.data.DataSet
Notifies the DataSet that new Data has arrived for the given psuedo DataSink.
dataChanged(DataSet) - Method in interface etomica.data.DataSetListener
Method called when one or more pieces of data have changed.
dataChanged(DataSet.DataSetSink) - Method in class etomica.data.DataSinkTable
 
dataChanged(DataSet) - Method in class etomica.graphics.DisplayPlot
Causes the display of the plot to be updated.
dataChanged(DataSet) - Method in class etomica.graphics.DisplayTable
Causes the display of the plot to be updated.
dataCountChanged(DataSet) - Method in interface etomica.data.DataSetListener
Method called when a Data object is added.
dataCountChanged(DataSet) - Method in class etomica.graphics.DisplayPlot
Updates the units array for the new column, using the default units.
dataCountChanged(DataSet) - Method in class etomica.graphics.DisplayTable
Updates the units array for any new or deleted columns, using the default units for new columns.
DataDistributer - Class in etomica.data
DataSink that takes a Data object and pushes it to a dataSink chosen by an indexer.
DataDistributer(DataDistributer.Indexer, DataSplitter.IDataSinkFactory) - Constructor for class etomica.data.DataDistributer
 
DataDistributer.Indexer - Interface in etomica.data
 
DataDouble - Class in etomica.data.types
Data object wrapping a single mutable value of type double.
DataDouble() - Constructor for class etomica.data.types.DataDouble
Constructs a new instance with given descriptors.
DataDouble.DataInfoDouble - Class in etomica.data.types
 
DataDouble.DataInfoDoubleFactory - Class in etomica.data.types
 
DataDoubleArray - Class in etomica.data.types
Data object that wraps a mutable array of doubles.
DataDoubleArray(int) - Constructor for class etomica.data.types.DataDoubleArray
Constructs a new one-dimensional array of the given length.
DataDoubleArray(int[]) - Constructor for class etomica.data.types.DataDoubleArray
Constructs a new multidimensional array of the given shape.
DataDoubleArray(int[], double[]) - Constructor for class etomica.data.types.DataDoubleArray
Wraps the given array, xData in a DataDoubleArray of the given shape.
DataDoubleArray.DataInfoDoubleArray - Class in etomica.data.types
 
DataDoubleArray.DataInfoDoubleArrayFactory - Class in etomica.data.types
 
DataDoubleBDArray - Class in etomica.data.types
Data object that wraps a array of BigDecimals.
DataDoubleBDArray(int, int) - Constructor for class etomica.data.types.DataDoubleBDArray
Constructs a new one-dimensional array of the given length.
DataDoubleBDArray(int[], int) - Constructor for class etomica.data.types.DataDoubleBDArray
Constructs a new multidimensional array of the given shape.
DataDoubleBDArray.DataInfoDoubleBDArray - Class in etomica.data.types
 
DataDoubleBDArray.DataInfoDoubleBDArrayFactory - Class in etomica.data.types
 
DataDump - Class in etomica.data
DataPump acts both as a DataSink and a DataSource.
DataDump() - Constructor for class etomica.data.DataDump
 
dataDy - Variable in class etomica.util.numerical.AkimaSplineSmootherApp
 
dataDy - Variable in class etomica.util.numerical.AkimaSplineSmootherDyApp
 
dataDy2 - Variable in class etomica.util.numerical.AkimaSplineSmootherApp
 
dataDy2 - Variable in class etomica.util.numerical.AkimaSplineSmootherDyApp
 
dataDy3 - Variable in class etomica.util.numerical.AkimaSplineSmootherDyApp
 
dataEy - Variable in class etomica.util.numerical.AkimaSplineSmootherApp
 
dataEy - Variable in class etomica.util.numerical.AkimaSplineSmootherDyApp
 
DataFork - Class in etomica.data
DataSink that takes a data stream and forwards it across multiple sinks.
DataFork() - Constructor for class etomica.data.DataFork
Constructs with no initial DataSinks.
DataFork(IDataSink[]) - Constructor for class etomica.data.DataFork
Constructs to forward data to the given sinks.
DataFunction - Class in etomica.data.types
Collects two or more DataDoubleArray instances, and organizes them into "dependent" and "independent" subgroups.
DataFunction(int[], double[]) - Constructor for class etomica.data.types.DataFunction
Forms a DataFunction using the given independent and dependent data instances.
DataFunction(int[]) - Constructor for class etomica.data.types.DataFunction
Forms a DataFunction with the given array shape.
DataFunction.DataInfoFunction - Class in etomica.data.types
 
DataFunction.DataInfoFunctionFactory - Class in etomica.data.types
 
dataGroup - Variable in class etomica.data.AccumulatorAverage
 
dataGroup - Variable in class etomica.data.AccumulatorAverageBlockless
 
DataGroup - Class in etomica.data.types
Gathers one or more Data instances into a single Data object.
DataGroup(IData[]) - Constructor for class etomica.data.types.DataGroup
Forms a data group from the given array of data objects.
DataGroup.DataInfoGroup - Class in etomica.data.types
 
DataGroup.DataInfoGroupFactory - Class in etomica.data.types
 
DataGroupFilter - Class in etomica.data
Extracts one or more of the Data instances wrapped in a DataGroup.
DataGroupFilter(int) - Constructor for class etomica.data.DataGroupFilter
Creates a filter that will take the DataGroup element indicated by the index, counting from 0.
DataGroupFilter(int[]) - Constructor for class etomica.data.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 - Class in etomica.data
DataSink that takes a DataGroup object and pushes each sub-Data object from the incoming DataGroup to a different stream.
DataGroupSplitter() - Constructor for class etomica.data.DataGroupSplitter
 
DataGroupTest - Class in etomica.junit.data.types
 
DataGroupTest() - Constructor for class etomica.junit.data.types.DataGroupTest
 
DataHistogram - Class in etomica.data
DataProcessor that creates a histogram from each piece of data that comes in.
DataHistogram(int, DoubleRange) - Constructor for class etomica.data.DataHistogram
Creates instance using HistogramSimple and specifying histograms having the given number of bins and the given range.
DataHistogram(Histogram) - Constructor for class etomica.data.DataHistogram
Creates instance using the given histogram.
dataInfo - Variable in class etomica.data.DataDistributer
 
dataInfo - Variable in class etomica.data.DataDump
 
dataInfo - Variable in class etomica.data.DataFork
 
DataInfo - Class in etomica.data
Object associated with a Data instance and which provides descriptive information about the data encapsulated in it.
DataInfo(String, Dimension) - Constructor for class etomica.data.DataInfo
Constructs new instance with descriptive label and dimension.
dataInfo - Variable in class etomica.data.DataProcessor
 
dataInfo - Variable in class etomica.data.DataSourcePositionedBoltzmannFactor
 
dataInfo - Variable in class etomica.data.DataSourceScalar
 
dataInfo - Variable in class etomica.data.DataSourceTensorVirialHard
 
dataInfo - Variable in class etomica.data.DataSplitter
 
dataInfo - Variable in class etomica.data.meter.MeterDipoleSumSquaredMappedAverage
 
dataInfo - Variable in class etomica.data.meter.MeterHyperVirial
 
dataInfo - Variable in class etomica.data.meter.MeterPressureByVolumeChange.DataSourceExp
 
dataInfo - Variable in class etomica.data.meter.MeterPressureTensor
 
dataInfo - Variable in class etomica.data.meter.MeterPressureTensorFromIntegrator
 
dataInfo - Variable in class etomica.data.meter.MeterProfileByAtoms
 
dataInfo - Variable in class etomica.data.meter.MeterProfileByVolume
 
dataInfoChanged(DataSet.DataSetSink) - Method in class etomica.data.DataSet
Notifies the DataSet that new DataInfo has arrived for the given psuedo DataSink.
dataInfoChanged(DataSet.DataSetSink) - Method in class etomica.data.DataSinkTable
 
DataInfoDouble(String, Dimension) - Constructor for class etomica.data.types.DataDouble.DataInfoDouble
 
DataInfoDoubleArray(String, Dimension, int[]) - Constructor for class etomica.data.types.DataDoubleArray.DataInfoDoubleArray
 
DataInfoDoubleArrayFactory(DataDoubleArray.DataInfoDoubleArray) - Constructor for class etomica.data.types.DataDoubleArray.DataInfoDoubleArrayFactory
 
DataInfoDoubleBDArray(String, Dimension, int[], int) - Constructor for class etomica.data.types.DataDoubleBDArray.DataInfoDoubleBDArray
 
DataInfoDoubleBDArrayFactory(DataDoubleBDArray.DataInfoDoubleBDArray) - Constructor for class etomica.data.types.DataDoubleBDArray.DataInfoDoubleBDArrayFactory
 
DataInfoDoubleFactory(DataDouble.DataInfoDouble) - Constructor for class etomica.data.types.DataDouble.DataInfoDoubleFactory
 
DataInfoFactory - Class in etomica.data
Interface for a mutable DataInfo factory.
DataInfoFactory(IEtomicaDataInfo) - Constructor for class etomica.data.DataInfoFactory
Creates a new instance using the info held by the template.
DataInfoFunction(String, Dimension, DataSourceIndependent) - Constructor for class etomica.data.types.DataFunction.DataInfoFunction
 
DataInfoFunctionFactory(DataFunction.DataInfoFunction) - Constructor for class etomica.data.types.DataFunction.DataInfoFunctionFactory
 
dataInfoGroup - Variable in class etomica.data.DataGroupSplitter
 
DataInfoGroup(String, Dimension, IEtomicaDataInfo[]) - Constructor for class etomica.data.types.DataGroup.DataInfoGroup
 
DataInfoGroupFactory(DataGroup.DataInfoGroup) - Constructor for class etomica.data.types.DataGroup.DataInfoGroupFactory
 
DataInfoTable(String, IEtomicaDataInfo[], int, String[]) - Constructor for class etomica.data.types.DataTable.DataInfoTable
 
DataInfoTableFactory(DataTable.DataInfoTable) - Constructor for class etomica.data.types.DataTable.DataInfoTableFactory
 
DataInfoTensor(String, Dimension, ISpace) - Constructor for class etomica.data.types.DataTensor.DataInfoTensor
 
DataInfoTensorFactory(DataTensor.DataInfoTensor) - Constructor for class etomica.data.types.DataTensor.DataInfoTensorFactory
 
DataInfoVector(String, Dimension, ISpace) - Constructor for class etomica.data.types.DataVector.DataInfoVector
 
DataInfoVectorFactory(DataVector.DataInfoVector) - Constructor for class etomica.data.types.DataVector.DataInfoVectorFactory
 
DataLogger - Class in etomica.data
DataSink that manages a FileWriter and also listens to non-interval integrator events and sends appropriate data to a DataWriter.
DataLogger() - Constructor for class etomica.data.DataLogger
 
DataLogger.DataWriter - Interface in etomica.data
Interface for a DataSink that actually writes data to a file
DataPipe - Interface in etomica.data
Interface for an object through which data can flow.
DataPipeForked - Interface in etomica.data
 
DataProcessor - Class in etomica.data
An object that receives Data, processes it, and pushes the result on to a DataSink.
DataProcessor() - Constructor for class etomica.data.DataProcessor
 
DataProcessorChemicalPotential - Class in 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() - Constructor for class etomica.data.DataProcessorChemicalPotential
 
DataProcessorForked - Class in etomica.data
A DataProcessor that can handle multiple sinks, passing the same Data to each.
DataProcessorForked() - Constructor for class etomica.data.DataProcessorForked
 
DataProcessorFunction - Class in etomica.data
Applies a simple scalar function to all elements of the Data that passes through.
DataProcessorFunction(IFunction) - Constructor for class etomica.data.DataProcessorFunction
 
DataProcessorInterfacialTension - Class in etomica.data
Data Processor that takes the virial components as input data and returns the interfacial tension.
DataProcessorInterfacialTension(ISpace) - Constructor for class etomica.data.DataProcessorInterfacialTension
 
DataPump - Class in etomica.data
A DataProcessor whose action is to actively take Data from a DataSource and send it to DataSinks.
DataPump(IEtomicaDataSource, IDataSink) - Constructor for class etomica.data.DataPump
Constructs DataPump with the given DataSource and DataSink.
dataPump - Variable in class etomica.graphics.DisplayTimer
 
DataPumpListener - Class in etomica.data
 
DataPumpListener(IEtomicaDataSource, IDataSink) - Constructor for class etomica.data.DataPumpListener
 
DataPumpListener(IEtomicaDataSource, IDataSink, int) - Constructor for class etomica.data.DataPumpListener
 
DataPumpListenerPow - Class in etomica.data
DataPump class that takes data at steps 2^i, i=0,1,2,3...
DataPumpListenerPow(IEtomicaDataSource, IDataSink) - Constructor for class etomica.data.DataPumpListenerPow
 
DataPumpListenerPow(IEtomicaDataSource, IDataSink, long, int, int) - Constructor for class etomica.data.DataPumpListenerPow
 
DataPumpListenerPowStrict - Class in etomica.data
DataPump class that takes data at steps pow^i, i=0,1,2,3...
DataPumpListenerPowStrict(IEtomicaDataSource, IDataSink) - Constructor for class etomica.data.DataPumpListenerPowStrict
 
DataPumpListenerPowStrict(IEtomicaDataSource, IDataSink, int) - Constructor for class etomica.data.DataPumpListenerPowStrict
 
DataPumpListenerSmart - Class in 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(IEtomicaDataSource, IDataSink, HistoryCollapsingDiscard) - Constructor for class etomica.data.DataPumpListenerSmart
 
DataPumpListenerSmart(IEtomicaDataSource, IDataSink, int, HistoryCollapsingDiscard) - Constructor for class etomica.data.DataPumpListenerSmart
 
dataPumps - Variable in class etomica.data.DataTableAverages
 
DataSet - Class in etomica.data
Receives and organizes data from multiple streams.
DataSet() - Constructor for class etomica.data.DataSet
 
DataSet(DataSet.DataCasterJudge) - Constructor for class etomica.data.DataSet
 
dataSet - Variable in class etomica.graphics.DisplayPlot
 
DataSet.DataCasterJudge - Interface in etomica.data
 
DataSet.DataSetSink - Class in etomica.data
A special DataSink used by the DataSet to receive Data and DataInfo from a single stream.
DataSetListener - Interface in etomica.data
Interface for a class that performs some action in response to a change in a DataSet instance.
DataSetSink(DataSet.DataCasterJudge, DataSet) - Constructor for class etomica.data.DataSet.DataSetSink
 
dataSink - Variable in class etomica.data.DataProcessor
 
DataSinkConsole - Class in etomica.data
Writes data to console or another print stream.
DataSinkConsole() - Constructor for class etomica.data.DataSinkConsole
Makes class using System.out as the default output stream.
DataSinkConsole(PrintStream) - Constructor for class etomica.data.DataSinkConsole
Constructor that permits specification of the output printstream.
dataSinkFactory - Variable in class etomica.data.DataDistributer
 
dataSinkFactory - Variable in class etomica.data.DataSplitter
 
dataSinkList - Variable in class etomica.data.DataFork
 
dataSinks - Variable in class etomica.data.DataDistributer
 
dataSinks - Variable in class etomica.data.DataGroupSplitter
 
dataSinks - Variable in class etomica.data.DataSplitter
 
DataSinkTable - Class in 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() - Constructor for class etomica.data.DataSinkTable
 
DataSinkTable.DataCasterJudgeTable - Class in etomica.data
 
dataSource - Variable in class etomica.data.DataPump
 
DataSourceAcceptanceProbability - Class in etomica.data
Data source giving the average acceptance probability of MCMove type moves.
DataSourceAcceptanceProbability() - Constructor for class etomica.data.DataSourceAcceptanceProbability
Constructs with no MCMove specified.
DataSourceAcceptanceProbability(MCMove) - Constructor for class etomica.data.DataSourceAcceptanceProbability
 
DataSourceAcceptanceRatio - Class in etomica.data
Data source giving the acceptance rate of MCMove type moves.
DataSourceAcceptanceRatio() - Constructor for class etomica.data.DataSourceAcceptanceRatio
Constructs with no MCMove specified.
DataSourceAcceptanceRatio(MCMove) - Constructor for class etomica.data.DataSourceAcceptanceRatio
 
DataSourceAtomDistance - Class in etomica.data
 
DataSourceAtomDistance(ISpace) - Constructor for class etomica.data.DataSourceAtomDistance
 
DataSourceAtomic - Interface in etomica.data
Interface for a DataSource that can return a value given an arbitrary atom.
DataSourceCollisional - Interface in etomica.data.meter
Interface for a meter that can return a value based on a hard-potential collision.
DataSourceCount() - Constructor for class etomica.data.AccumulatorHistory.DataSourceCount
 
DataSourceCountCollisions - Class in etomica.data
This is a data source to count the number of collisions processed by a hard-potential integrator.
DataSourceCountCollisions() - Constructor for class etomica.data.DataSourceCountCollisions
Sets up data source with no integrator specified.
DataSourceCountCollisions(IntegratorHard) - Constructor for class etomica.data.DataSourceCountCollisions
 
DataSourceCountSteps - Class in etomica.data
Data source that fronts the Integrator's step count as a piece of Data.
DataSourceCountSteps() - Constructor for class etomica.data.DataSourceCountSteps
Sets up data source to count integrator steps.
DataSourceCountSteps(IIntegrator) - Constructor for class etomica.data.DataSourceCountSteps
 
DataSourceCountTime - Class in etomica.data
Data source that keeps track of the elapsed simulation time of an MD integrator.
DataSourceCountTime() - Constructor for class etomica.data.DataSourceCountTime
Sets up data source with no integrator specified.
DataSourceCountTime(IntegratorMD) - Constructor for class etomica.data.DataSourceCountTime
 
DataSourceExp(DataSourceUniform) - Constructor for class etomica.data.meter.MeterPressureByVolumeChange.DataSourceExp
 
DataSourceFunction - Class in etomica.data
Datasource formed as a wrapper around a function.
DataSourceFunction() - Constructor for class etomica.data.DataSourceFunction
 
DataSourceFunction(IFunction) - Constructor for class etomica.data.DataSourceFunction
 
DataSourceFunction(String, Dimension, IFunction, int) - Constructor for class etomica.data.DataSourceFunction
 
DataSourceFunction(String, Dimension, IFunction, int, String, Dimension) - Constructor for class etomica.data.DataSourceFunction
 
DataSourceGroup - Class in etomica.data
Collects one or more data sources into a single DataSource.
DataSourceGroup() - Constructor for class etomica.data.DataSourceGroup
Forms a DataSourceGroup that contains no data sources, and which will give an empty DataGroup for getData.
DataSourceGroup(IEtomicaDataSource[]) - Constructor for class etomica.data.DataSourceGroup
Forms a DataGroup containing the given data sources.
DataSourceIndependent - Interface in etomica.data
Interface for an object that can provide X Data objects on request.
DataSourceIndependentSimple - Class in 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) - Constructor for class etomica.data.DataSourceIndependentSimple
 
DataSourceIndependentSimple(double[][], DataDoubleArray.DataInfoDoubleArray[]) - Constructor for class etomica.data.DataSourceIndependentSimple
 
dataSourceInfo - Variable in class etomica.data.DataPump
 
DataSourceMolecular - Interface in etomica.data
Interface for a DataSource that can return a value given an arbitrary atom.
DataSourcePoints - Class in etomica.data
 
DataSourcePoints(String, Dimension, Dimension) - Constructor for class etomica.data.DataSourcePoints
 
DataSourcePositioned - Interface in etomica.data
Interface for a DataSource that can return a value given an arbitrary position.
DataSourcePositionedBoltzmannFactor - Class in 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(ISpace) - Constructor for class etomica.data.DataSourcePositionedBoltzmannFactor
 
DataSourceRmsVelocity - Class in etomica.data
Meter for the root-mean-square velocity of a set of atoms.
DataSourceRmsVelocity() - Constructor for class etomica.data.DataSourceRmsVelocity
 
DataSourceRmsVelocity(Histogram) - Constructor for class etomica.data.DataSourceRmsVelocity
 
DataSourceScalar - Class in etomica.data
Particular data source for which the data is a simple scalar of type double.
DataSourceScalar(String, Dimension) - Constructor for class etomica.data.DataSourceScalar
 
DataSourceTensorVirialHard - Class in etomica.data
A MeterTensor that returns the virial component of the pressure tensor for a hard potential.
DataSourceTensorVirialHard(ISpace) - Constructor for class etomica.data.DataSourceTensorVirialHard
 
DataSourceTensorVirialHard(ISpace, IntegratorHard) - Constructor for class etomica.data.DataSourceTensorVirialHard
 
DataSourceUniform - Class in etomica.data
A DataSource object that provides a set of uniformly spaced values between two limits.
DataSourceUniform() - Constructor for class etomica.data.DataSourceUniform
Default constructor.
DataSourceUniform(String, Dimension) - Constructor for class etomica.data.DataSourceUniform
 
DataSourceUniform(String, Dimension, int, double, double) - Constructor for class etomica.data.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) - Constructor for class etomica.data.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 - Class in etomica.data
Typed constant that indicates the way limits of the range are interpreted.
DataSplitter - Class in etomica.data
DataSink that takes a Data object and pushes each numerical value from the incoming Data to a different stream.
DataSplitter() - Constructor for class etomica.data.DataSplitter
 
DataSplitter.IDataSinkFactory - Interface in etomica.data
 
DataStreamAction - Class in etomica.data
 
DataStreamAction() - Constructor for class etomica.data.DataStreamAction
 
DataStreamHeader - Class in etomica.simulation
 
DataTable - Class in etomica.data.types
Data object that holds double[] arrays as if they are columns in a table.
DataTable(int, int) - Constructor for class etomica.data.types.DataTable
Creates a new table with a specified number of columns all of a given length.
DataTable(DataDoubleArray[]) - Constructor for class etomica.data.types.DataTable
 
dataTable - Variable in class etomica.graphics.DisplayTable
 
DataTable.DataInfoTable - Class in etomica.data.types
 
DataTable.DataInfoTableFactory - Class in etomica.data.types
 
DataTableAverages - Class in etomica.data
Convenience class for a data table that collects the AccumulatorAverage statistics for a collection of DataSource instances.
DataTableAverages(IIntegrator) - Constructor for class etomica.data.DataTableAverages
Sets up table with default types that give the current value, the average, and the error bars.
DataTableAverages(IIntegrator, int, ArrayList<DataPump>) - Constructor for class etomica.data.DataTableAverages
 
DataTableAverages(IIntegrator, AccumulatorAverage.StatType[], int, IEtomicaDataSource[], ArrayList<DataPump>) - Constructor for class etomica.data.DataTableAverages
Sets up table with no sources.
DataTableListener - Interface in etomica.data
Interface for a class that performs some action in response to a change in a DataSinkTable instance.
DataTableWriter - Class in etomica.data
A DataWriter that writes out data as a table with optional column headings
DataTableWriter() - Constructor for class etomica.data.DataTableWriter
 
DataTag - Class in etomica.data
Class whose sole purpose is to implement Serializable so that data tags are serializable
DataTag() - Constructor for class etomica.data.DataTag
 
DataTagBag - Class in etomica.graphics
Simple class that associates a set of tags with an object (unit, label, etc)
DataTagBag(DataTag[], Object) - Constructor for class etomica.graphics.DataTagBag
 
DataTensor - Class in etomica.data.types
Data object wrapping a single mutable value of type (Space) Tensor.
DataTensor(ISpace) - Constructor for class etomica.data.types.DataTensor
Constructs a new instance with the given DataInfo, wrapping a new Tensor instance from the given space.
DataTensor.DataInfoTensor - Class in etomica.data.types
 
DataTensor.DataInfoTensorFactory - Class in etomica.data.types
 
dataTrueEy - Variable in class etomica.util.numerical.AkimaSplineSmootherDyApp
 
DataVector - Class in etomica.data.types
Data object wrapping a single mutable value of type (Space) Vector.
DataVector(ISpace) - Constructor for class etomica.data.types.DataVector
Constructs a new instance with the given DataInfo, wrapping a new Vector instance from the given space.
DataVector.DataInfoVector - Class in etomica.data.types
 
DataVector.DataInfoVectorFactory - Class in etomica.data.types
 
dataWalkerAction(Object) - Method in class etomica.action.ResetAccumulators
 
dataWalkerAction(Object) - Method in class etomica.action.ResetAccumulatorsAveraged
 
dataWalkerAction(Object) - Method in class etomica.data.DataStreamAction
 
DataWriter(int, DisplayPlot) - Constructor for class etomica.graphics.DisplayPlot.DataWriter
 
DBDEN - Static variable in class etomica.math.Gamma
 
DBNUM - Static variable in class etomica.math.Gamma
 
DC - Static variable in class etomica.math.Gamma
 
dd(int, double, double) - Method in class etomica.potential.P2HydrogenPatkowski
 
dd(int, double, double) - Method in class etomica.potential.P2HydrogenPatkowskiAtomic
 
dd - Variable in class etomica.util.numerical.AkimaSplineSmootherApp.PlotAction
 
dd - Variable in class etomica.util.numerical.AkimaSplineSmootherDyApp.PlotAction
 
ddamp(int, double, double) - Method in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
 
dDimension() - Method in class etomica.units.DimensionRatio
 
DE(IVector) - Method in interface etomica.api.IVectorMutable
Divide-equals (/=) operation.
DE(IData) - Method in interface etomica.data.IData
Divide-equals (/=) operation.
DE(double) - Method in interface etomica.data.IData
Divide-equals (*=) operation, dividing all values in data by given value.
DE(IData) - Method in class etomica.data.types.DataDouble
Divide-equals (/=) operation.
DE(double) - Method in class etomica.data.types.DataDouble
Divide-equals (/=) operation.
DE(IData) - Method in class etomica.data.types.DataDoubleArray
Divide-equals (/=) operation.
DE(double) - Method in class etomica.data.types.DataDoubleArray
Divide-equals (*=) operation.
DE(IData) - Method in class etomica.data.types.DataDoubleBDArray
Divide-equals (/=) operation.
DE(double) - Method in class etomica.data.types.DataDoubleBDArray
Times-equals (*=) operation.
DE(IData) - Method in class etomica.data.types.DataGroup
 
DE(double) - Method in class etomica.data.types.DataGroup
 
DE(IData) - Method in class etomica.data.types.DataTensor
Divide-equals (/=) operation.
DE(double) - Method in class etomica.data.types.DataTensor
Divide-equals (*=) operation.
DE(IData) - Method in class etomica.data.types.DataVector
Divide-equals (/=) operation.
DE(double) - Method in class etomica.data.types.DataVector
Divide-equals (*=) operation.
DE(Tensor) - Method in interface etomica.space.Tensor
 
DE(Tensor) - Method in class etomica.space1d.Tensor1D
 
DE(IVector) - Method in class etomica.space1d.Vector1D
 
DE(Tensor) - Method in class etomica.space2d.Tensor2D
 
DE(IVector) - Method in class etomica.space2d.Vector2D
 
DE(Tensor) - Method in class etomica.space3d.Tensor3D
 
DE(IVector) - Method in class etomica.space3d.Vector3D
 
DE(Tensor) - Method in class etomica.spaceNd.TensorND
 
DE(IVector) - Method in class etomica.spaceNd.VectorND
 
deactivate() - Method in class etomica.util.Grabber.ActionCornerSetter
 
debug - Variable in class etomica.models.co2.P2CO2Hellmann
 
debug - Static variable in class etomica.models.water.P2WaterSzalewicz
 
debug - Static variable in class etomica.potential.PotentialCalculationEnergySum
 
Debug - Class in 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() - Constructor for class etomica.util.Debug
 
DEBUG_NOW - Static variable in class etomica.util.Debug
true if debugging is currently enabled (when the integrator reaches step START)
debugging - Variable in class etomica.models.co2.P2CO2H2OWheatley
 
debugme - Static variable in class etomica.models.co2.PNCO2GCPM
 
debugme - Static variable in class etomica.models.co2.PNGCPM
 
debugMoleculePair - Static variable in class etomica.util.Debug
 
debugPair - Static variable in class etomica.util.Debug
 
Debye - Class in etomica.units
The debye unit of electrical dipole moment, equal to 10^-18 statC-cm, or 3.33564e-30 C-m.
decapitalize(String) - Static method in class etomica.util.Strings
Converts the first letter of the given string to lower case.
DECI - Static variable in class etomica.units.Prefix
Prefix indicating 10-1 = 0.1.
Decimal - Class in 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 - Class in etomica.graphics
Slider that permits variation of decimal (non-integer) values.
DecimalSlider() - Constructor for class etomica.graphics.DecimalSlider
 
decrementCollisionTime(double) - Method in class etomica.integrator.IntegratorHard.Agent
Decreases the recorded time to collision of this atom This action is performed when the atom is advanced without a collision
DEFAULT_ATOM_COLOR - Static variable in class etomica.graphics.ColorScheme
 
DEFAULT_INIT_SIZE - Static variable in class etomica.atom.AtomArrayList
 
DEFAULT_INIT_SIZE - Static variable in class etomica.atom.MoleculeArrayList
 
DEFAULT_MAX_TEMPERATURE - Static variable in class etomica.graphics.DeviceThermoSlider
 
DEFAULT_MIN_TEMPERATURE - Static variable in class etomica.graphics.DeviceThermoSlider
 
defaultAdjustInterval - Variable in class etomica.integrator.mcmove.MCMoveStepTracker
 
defaultAdjustStep - Variable in class etomica.integrator.mcmove.MCMoveStepTracker
 
defaultColor - Variable in class etomica.graphics.ColorScheme
 
defaultColorsUsed - Variable in class etomica.graphics.ColorSchemeByType
 
defaultFileName() - Method in class etomica.data.DataLogger
 
defaultIOUnit() - Method in class etomica.data.DataSourceAcceptanceProbability
 
defaultIOUnit() - Method in class etomica.data.DataSourceAcceptanceRatio
 
defaultMouseListener - Variable in class etomica.util.Grabber
 
DefaultMouseListener(Grabber) - Constructor for class etomica.util.Grabber.DefaultMouseListener
 
DefaultToolbar - Class in etomica.graphics
 
DefaultToolbar() - Constructor for class etomica.graphics.DefaultToolbar
 
DefaultToolbar(JPanel, String) - Constructor for class etomica.graphics.DefaultToolbar
 
defdfmt - Static variable in class etomica.util.ScientificFormat
 
defefmt - Static variable in class etomica.util.ScientificFormat
 
deform(Tensor) - Method in class etomica.space.BoundaryDeformablePeriodic
Applies the given deformation tensor to the boundary in its current shape.
Degree - Class in etomica.units
Standard degree angular unit, such that for example a right angle is 90 degrees.
DEKA - Static variable in class etomica.units.Prefix
Prefix indicating 10+1 = 10.
delayExponent - Variable in class etomica.graphics.DeviceDelaySlider
 
deleteCandidates - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
 
deleteCandidates - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
 
deleteCandidateSet - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
 
deleteCandidateTimes - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
 
deleteCandidateTimes - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
 
deleteRow(int) - Method in class etomica.graphics.DeviceTableModelGeneric
Delete an entire row from the table
delta - Variable in class etomica.action.IntegratorDimerApproach
 
deltaA(double, double, int) - Method in class etomica.statmech.HardSphere
Returns the difference between absolute free energies between the given densities for solid (FCC) hard spheres.
deltaEps - Variable in class etomica.potential.P2PenetrableSquareWell
 
deltaX - Variable in class etomica.action.BoxInflateAnisotropic
 
deltaX - Variable in class etomica.util.HistogramNotSoSimple
 
deltaX - Variable in class etomica.util.HistogramReweightedData
 
deltaX - Variable in class etomica.util.HistogramSimple
 
denominator - Variable in class etomica.util.Rational
 
denominator() - Method in class etomica.util.Rational
Returns the denominator.
dense - Variable in class etomica.potential.P2QChemInterpolated
 
density - Variable in class etomica.statmech.HardSphereSolid.EOSParams
 
densityForMu(double) - Static method in class etomica.statmech.HardSphereSolid
 
densityForPressure(double) - Static method in class etomica.statmech.HardSphereSolid
 
densityProfileSource - Variable in class etomica.data.DataProcessorChemicalPotential
 
dest - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
 
dest - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
 
determinant() - Method in interface etomica.space.Tensor
 
determinant() - Method in class etomica.space1d.Tensor1D
 
determinant() - Method in class etomica.space2d.Tensor2D
 
determinant() - Method in class etomica.space3d.Tensor3D
 
determinant() - Method in class etomica.spaceNd.TensorND
 
Device - Class in etomica.graphics
Base class for all Devices.
Device() - Constructor for class etomica.graphics.Device
 
Device(IController) - Constructor for class etomica.graphics.Device
 
Device.ActionSet - Class in etomica.graphics
 
DeviceBox - Class in etomica.graphics
A simple device the permits editing of a single value via a textbox with an associated label.
DeviceBox() - Constructor for class etomica.graphics.DeviceBox
 
DeviceBox.LabelType - Class in etomica.graphics
Typed constant used to indicate the type of label to be used with the display.
deviceBoxValueChanged(DeviceBoxValueChangedEvent) - Method in class etomica.graphics.DeviceBox
 
deviceBoxValueChanged(DeviceBoxValueChangedEvent) - Method in interface etomica.graphics.DeviceBoxValueChangedListener
 
DeviceBoxValueChangedEvent - Class in etomica.graphics
 
DeviceBoxValueChangedEvent(DeviceBox, int) - Constructor for class etomica.graphics.DeviceBoxValueChangedEvent
 
DeviceBoxValueChangedListener - Interface in etomica.graphics
Interface that should be implemented to receive a value changed event when a DeviceBox updateValue method is called.
DeviceButton - Class in etomica.graphics
Button that causes an action to be performed.
DeviceButton(IController) - Constructor for class etomica.graphics.DeviceButton
Constructs button that is not connected to any action.
DeviceButton(IController, IAction) - Constructor for class etomica.graphics.DeviceButton
Constructs a button connected to the given action.
DeviceButtonGroup - Class in etomica.graphics
Add etomica device for a group of radio buttons.
DeviceButtonGroup(IController, int) - Constructor for class etomica.graphics.DeviceButtonGroup
 
DeviceCheckBox - Class in etomica.graphics
Button that toggles a boolean value via a check box.
DeviceCheckBox(ModifierBoolean) - Constructor for class etomica.graphics.DeviceCheckBox
 
DeviceCheckBox(String, ModifierBoolean) - Constructor for class etomica.graphics.DeviceCheckBox
 
DeviceControllerButton - Class in etomica.graphics
Button that attaches to a controller to toggle its pause/resume state.
DeviceControllerButton(Controller) - Constructor for class etomica.graphics.DeviceControllerButton
 
DeviceDelaySlider - Class in etomica.graphics
 
DeviceDelaySlider(IController, ActivityIntegrate) - Constructor for class etomica.graphics.DeviceDelaySlider
 
deviceList() - Method in class etomica.graphics.SimulationGraphic
 
DeviceNSelector - Class in etomica.graphics
Slider that selects the number of atoms of a given species in a box.
DeviceNSelector() - Constructor for class etomica.graphics.DeviceNSelector
 
DeviceNSelector(IController) - Constructor for class etomica.graphics.DeviceNSelector
 
DevicePlotPoints - Class in etomica.graphics
 
DevicePlotPoints(IFunction[], String[], String[]) - Constructor for class etomica.graphics.DevicePlotPoints
 
DevicePlotPoints(String[], IFunction[], String[], boolean) - Constructor for class etomica.graphics.DevicePlotPoints
 
DeviceSelector - Class in etomica.graphics
Generic Device that has a combo box.
DeviceSelector(IController) - Constructor for class etomica.graphics.DeviceSelector
 
DeviceSlider - Class in etomica.graphics
Device the changes a property using a graphical slider, via a Modifier.
DeviceSlider(IController) - Constructor for class etomica.graphics.DeviceSlider
 
DeviceSlider(IController, Object, String) - Constructor for class etomica.graphics.DeviceSlider
Constructs a slider connected to the given property of the given object
DeviceSlider(IController, Modifier) - Constructor for class etomica.graphics.DeviceSlider
Constructs a slider connected to the get/set Value methods of the given Modifier
DeviceSpinner - Class in etomica.graphics
Device the changes a property using a graphical spinner, via a Modifier.
DeviceSpinner(IController) - Constructor for class etomica.graphics.DeviceSpinner
 
DeviceSpinner(IController, Object, String) - Constructor for class etomica.graphics.DeviceSpinner
Constructs a spinner connected to the given property of the given object
DeviceSpinner(IController, Modifier) - Constructor for class etomica.graphics.DeviceSpinner
Constructs a spinner connected to the get/set Value methods of the given Modifier
DeviceSpinner.SpinnerListener - Class in etomica.graphics
Spinner listener, which relays the spinner change events to the modifier
DeviceTable - Class in etomica.graphics
Presents a table of numeric properties that can be edited by typing in values.
DeviceTable(String[]) - Constructor for class etomica.graphics.DeviceTable
 
DeviceTable(TableModel) - Constructor for class etomica.graphics.DeviceTable
 
DeviceTableModelGeneric - Class in etomica.graphics
 
DeviceTableModelGeneric(Object[][], String[]) - Constructor for class etomica.graphics.DeviceTableModelGeneric
 
DeviceTernarySelector - Class in etomica.graphics
Selector for fractions in a ternary system.
DeviceTernarySelector() - Constructor for class etomica.graphics.DeviceTernarySelector
 
DeviceTernarySelector(String[]) - Constructor for class etomica.graphics.DeviceTernarySelector
Creates a new devices using the given labels for the diagram.
DeviceTernarySelector.Listener - Interface in etomica.graphics
 
DeviceTernarySelector.MyEventManager - Class in etomica.graphics
 
DeviceThermoSelector - Class in etomica.graphics
Permits selection of temperature from a discrete set of values.
DeviceThermoSelector(Simulation, IntegratorBox) - Constructor for class etomica.graphics.DeviceThermoSelector
Constructor that specifies Kelvin as temperature units.
DeviceThermoSelector(IController, Unit, boolean) - Constructor for class etomica.graphics.DeviceThermoSelector
 
DeviceThermoSlider - Class in etomica.graphics
 
DeviceThermoSlider(IController, IntegratorBox) - Constructor for class etomica.graphics.DeviceThermoSlider
 
DeviceToggleButton - Class in etomica.graphics
Button that toggles a boolean value.
DeviceToggleButton(IController) - Constructor for class etomica.graphics.DeviceToggleButton
 
DeviceToggleButton(IController, ModifierBoolean) - Constructor for class etomica.graphics.DeviceToggleButton
 
DeviceToggleButton(IController, ModifierBoolean, String, String) - Constructor for class etomica.graphics.DeviceToggleButton
 
DeviceToggleRadioButtons - Class in etomica.graphics
Button that toggles a boolean value using a pair of radio buttons.
DeviceToggleRadioButtons(ModifierBoolean) - Constructor for class etomica.graphics.DeviceToggleRadioButtons
Constructor with default labels of a blank title and "True" and "False" for the true/false labels.
DeviceToggleRadioButtons(ModifierBoolean, String, String, String) - Constructor for class etomica.graphics.DeviceToggleRadioButtons
 
DeviceTrioControllerButton - Class in 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(ISimulation, ISpace, Controller) - Constructor for class etomica.graphics.DeviceTrioControllerButton
Contructs device with buttons that affect the given simulation.
DeviceTrioControllerButton() - Constructor for class etomica.graphics.DeviceTrioControllerButton
No-argument contructor gives device that performs no action until setSimulation is used to specify the target simulation.
DeviceTrioControllerButton.ComponentEventControllerButton - Class in etomica.graphics
Inner class that catches action of simulation panel
df(int, double) - Method in class etomica.util.Function.Abs
 
df(int, double) - Method in class etomica.util.Function.Constant
 
df(int, double) - Method in class etomica.util.Function.Exp
 
df(int, double) - Method in class etomica.util.Function.Identity
 
df(int, double) - Method in class etomica.util.Function.Linear
 
df(int, double) - Method in class etomica.util.Function.Log
 
df(int, double) - Method in class etomica.util.Function.Reciprocal
 
df(int, double) - Method in class etomica.util.Function.Sqrt
 
df(int, double) - Method in class etomica.util.FunctionChain
Evaluates derivative via the chain rule.
df(int, double) - Method in interface etomica.util.FunctionDifferentiable
 
df(int[], double[]) - Method in interface etomica.util.FunctionMultiDimensionalDifferentiable
Returns the derivative indicated by the array d evaluated at the given point x.
df(int[], double[]) - Method in class etomica.util.numerical.CalcGradientDifferentiable
 
df(int[], double[]) - Method in class etomica.util.numerical.FiniteDifferenceDerivative
 
df(int, double[], double) - Method in class etomica.util.numerical.FittingFunctionNonLinear
 
df(int, double[], double) - Method in class etomica.util.numerical.FittingFunctionNonLinearB
 
df(int, double) - Method in class etomica.util.numerical.Function1d
 
df2(int[], double[]) - Method in class etomica.util.numerical.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) - Method in class etomica.statmech.MaxwellBoltzmann.Distribution
 
dfmt - Variable in class etomica.util.ScientificFormat
 
dHSCore - Static variable in class etomica.potential.P2NitrogenHellmann
 
diameter - Variable in class etomica.graphics.DisplayBoxCanvasG3DSys.OrientedSite
 
DiameterHash - Interface in etomica.atom
This provides an interface for a class that acts like a hashmap for atomic diameters.
diameterHash - Variable in class etomica.graphics.DisplayBox
 
DiameterHashByElement - Class in etomica.atom
This class hashes atomic diameters based on the element.
DiameterHashByElement() - Constructor for class etomica.atom.DiameterHashByElement
 
DiameterHashByElementType - Class in etomica.atom
This class hashes atomic diameters based on both element and atom type.
DiameterHashByElementType(ISimulation) - Constructor for class etomica.atom.DiameterHashByElementType
 
DiameterHashByType - Class in etomica.atom
This class hashes atomic diameters based on the atom type.
DiameterHashByType(ISimulation) - Constructor for class etomica.atom.DiameterHashByType
 
diameterManagerByElement - Variable in class etomica.atom.DiameterHashByElementType
 
diff - Variable in class etomica.util.numerical.B9Optimizer
 
diff - Variable in class etomica.util.numerical.VirialOptimizer
 
digits - Variable in class etomica.graphics.DisplayTable
 
dihedralAngle(Plane) - Method in class etomica.math.geometry.Plane
Dihedral angle between this plane and the given plane.
dim - Variable in class etomica.action.BoxQuench
 
dim - Variable in class etomica.lattice.IndexIteratorIncreasing
 
dim - Variable in class etomica.spaceNd.TensorND
 
dimension - Variable in class etomica.data.DataInfoFactory
 
DIMENSION - Static variable in class etomica.units.Angle
 
DIMENSION - Static variable in class etomica.units.Area
 
DIMENSION - Static variable in class etomica.units.Charge
Singleton instance of this class.
dimension() - Method in class etomica.units.CompoundUnit
 
DIMENSION - Static variable in class etomica.units.Current
Singleton instance of this class.
Dimension - Class in etomica.units
Parent of all Dimension classes, which describe the physical dimensions (e.g., mass, length, force) of a quantity.
Dimension(String, double, double, double) - Constructor for class etomica.units.Dimension
 
Dimension(String, double, double, double, double, double, double, double) - Constructor for class etomica.units.Dimension
 
Dimension(String, double[]) - Constructor for class etomica.units.Dimension
 
DIMENSION - Static variable in class etomica.units.Dipole
 
DIMENSION - Static variable in class etomica.units.ElectricPotential
Singleton instance of this class.
DIMENSION - Static variable in class etomica.units.Energy
Singleton instance of this class.
DIMENSION - Static variable in class etomica.units.Force
 
DIMENSION - Static variable in class etomica.units.Fraction
Singleton instance of this class.
DIMENSION - Static variable in class etomica.units.Length
Singleton instance of this class.
DIMENSION - Static variable in class etomica.units.LuminousIntensity
Singleton instance of this class.
DIMENSION - Static variable in class etomica.units.Mass
Singleton instance of this class.
DIMENSION - Static variable in class etomica.units.Null
Singleton instance of this class.
dimension() - Method in class etomica.units.PrefixedUnit
Returns the dimension of this baseUnit.
DIMENSION - Static variable in class etomica.units.Pressure
Singleton instance of this class.
dimension(int) - Static method in class etomica.units.Pressure
Returns the Dimension instance for the "pressure" appropriate to the given dimension.
DIMENSION - Static variable in class etomica.units.Pressure2D
 
DIMENSION - Static variable in class etomica.units.Quantity
Singleton instance of this class.
dimension() - Method in class etomica.units.SimpleUnit
Returns the dimension of this base unit.
dimension() - Method in class etomica.units.systems.LJ.LJUnit
 
DIMENSION - Static variable in class etomica.units.Temperature
Singleton instance of this class.
DIMENSION - Static variable in class etomica.units.Time
Singleton instance of this class.
DIMENSION - Static variable in class etomica.units.Undefined
Singleton instance of this class.
dimension() - Method in interface etomica.units.Unit
Returns the dimension of the unit.
DIMENSION - Static variable in class etomica.units.Viscosity
Singleton instance of this class.
DIMENSION - Static variable in class etomica.units.Volume
Singleton instance of this class.
dimension(int) - Static method in class etomica.units.Volume
Returns the Dimension instance for the "volume" appropriate to the given dimension.
Dimensioned - Interface in etomica.units
Interface for an object with an associated physical dimension.
DimensionedDoubleEditor - Class in etomica.graphics
Editor to set the value of a double-type property having units associated with it.
DimensionedDoubleEditor(Dimension) - Constructor for class etomica.graphics.DimensionedDoubleEditor
 
DimensionRatio - Class in etomica.units
Class to form a dimension from ratio of two dimensions.
DimensionRatio(Dimension, Dimension) - Constructor for class etomica.units.DimensionRatio
 
DimensionRatio(String, Dimension, Dimension) - Constructor for class etomica.units.DimensionRatio
 
dimensions() - Method in class etomica.graphics.DisplayPolytope
returns dimensions of polytope as the (max - min) value in each dimension for all the vertices.
dimensions - Variable in class etomica.space.BoundaryRectangular
 
dimensions - Variable in class etomica.space3d.BoundaryTruncatedOctahedron
 
dimensionsHalf - Variable in class etomica.space.BoundaryRectangularPeriodic
 
dimensionsHalf - Variable in class etomica.space.BoundaryRectangularPore
 
dimensionsHalf - Variable in class etomica.space.BoundaryRectangularSlit
 
dimensionsHalf - Variable in class etomica.space3d.BoundaryTruncatedOctahedron
 
dimensionString() - Static method in class etomica.units.Lister
 
dimerPotential - Variable in class etomica.integrator.mcmove.MCMoveDimer
 
dimerPotential - Variable in class etomica.integrator.mcmove.MCMoveDimerRotate
 
dimVector - Variable in class etomica.action.BoxInflate
 
dipind(int, int, int[], int[]) - Static method in class etomica.potential.P2WaterPotentialsJankowski
 
dipole - Variable in class etomica.models.aceticAcid.DipoleSourceAceticAcid
 
dipole - Variable in class etomica.models.water.DipoleSourceWater
 
Dipole - Class in etomica.units
Base unit for electrical dipole moment.
dipole() - Method in class etomica.units.systems.CGS
 
dipole() - Method in class etomica.units.systems.LJ
 
dipole() - Method in class etomica.units.systems.MKS
 
dipole() - Method in class etomica.units.systems.UnitSystem
 
dipole() - Method in class etomica.units.systems.UnitSystem.Sim
 
DipoleSource - Interface in etomica.atom
Interface for something that can calculate the dipole of a molecule.
dipoleSource - Variable in class etomica.data.meter.MeterDipoleSumSquaredMappedAverage
 
dipoleSource - Variable in class etomica.potential.P1ExternalField
 
dipoleSource - Variable in class etomica.potential.P2ReactionFieldDipole
 
dipoleSource - Variable in class etomica.potential.P2ReactionFieldDipoleTruncated
 
dipoleSource - Variable in class etomica.potential.PotentialCalculationPhiSum
 
DipoleSourceAceticAcid - Class in etomica.models.aceticAcid
dipole for acetic acid
DipoleSourceAceticAcid(ISpace) - Constructor for class etomica.models.aceticAcid.DipoleSourceAceticAcid
 
DipoleSourceWater - Class in etomica.models.water
Implementation of DipoleSource that can handle water molecules that are MoleculeOriented.
DipoleSourceWater(ISpace) - Constructor for class etomica.models.water.DipoleSourceWater
 
dipoleStrength - Variable in class etomica.models.water.DipoleSourceWater
 
dir0 - Variable in class etomica.potential.P2SpheroPolyhedron
 
dir1 - Variable in class etomica.potential.P2SpheroPolyhedron
 
dir2 - Variable in class etomica.potential.P2SpheroPolyhedron
 
direction() - Method in class etomica.atom.iterator.IteratorDirective
 
direction - Variable in class etomica.atom.iterator.MpiIntraspecies1A
 
direction - Variable in class etomica.config.ConfigurationOrientedFile
 
direction - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbr
 
direction - Variable in class etomica.space2d.Orientation2D
 
direction - Variable in class etomica.space3d.Orientation3D
 
direction - Variable in class etomica.space3d.OrientationFull3D
 
dirty - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
 
dirty - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
 
dirty - Variable in class etomica.util.numerical.AkimaSpline
 
DirtyObject - Interface in etomica.util
 
disp - Variable in class etomica.potential.P2QChemInterpolated
 
disp - Variable in class etomica.potential.P3AdditiveQChem.DampingParams
 
disp - Variable in class etomica.potential.P3QChem.DampingParams
 
displacementLimit2 - Variable in class etomica.nbr.CriterionSimple
 
displacementLimit2 - Variable in class etomica.nbr.molecule.CriterionSimpleMolecular
 
Display - Class in etomica.graphics
Superclass of all classes that display something from the simulation.
Display() - Constructor for class etomica.graphics.Display
 
display - Variable in class etomica.simulation.prototypes.LjMd2D
 
display - Variable in class etomica.simulation.prototypes.SwMd2D
 
display - Variable in class etomica.simulation.prototypes.SWMD3D
 
displayBoundary - Variable in class etomica.graphics.DisplayBox
 
DisplayBox - Class in etomica.graphics
Displays a picture of a box, with configurations of molecules, boundaries, and other objects as appropriate, assuming 2-dimensional system.
DisplayBox(ISimulation, IBox, ISpace, Controller) - Constructor for class etomica.graphics.DisplayBox
Warning: after instantiation, clients using G3DSys may need to toggle display.canvas.setVisible false and then true to fix the 'sometimes gray' bug.
displayBox - Variable in class etomica.graphics.DisplayCanvas
 
DisplayBoxCanvas1D - Class in etomica.graphics
 
DisplayBoxCanvas1D(ISpace, DisplayBox, Controller) - Constructor for class etomica.graphics.DisplayBoxCanvas1D
 
DisplayBoxCanvas2D - Class in etomica.graphics
 
DisplayBoxCanvas2D(DisplayBox, ISpace, Controller) - Constructor for class etomica.graphics.DisplayBoxCanvas2D
 
DisplayBoxCanvasG3DSys - Class in etomica.graphics
 
DisplayBoxCanvasG3DSys(ISimulation, DisplayBox, ISpace, Controller) - Constructor for class etomica.graphics.DisplayBoxCanvasG3DSys
 
DisplayBoxCanvasG3DSys.OrientedAgentSource - Class in etomica.graphics
 
DisplayBoxCanvasG3DSys.OrientedFullSite - Class in etomica.graphics
 
DisplayBoxCanvasG3DSys.OrientedSite - Class in etomica.graphics
 
DisplayBoxSpin2D - Class in etomica.graphics
 
DisplayBoxSpin2D(DisplayBox, NeighborSiteManager, ISpace, Controller) - Constructor for class etomica.graphics.DisplayBoxSpin2D
 
DisplayCanvas - Class in etomica.graphics
Superclass for classes that display information from simulation by painting to a canvas.
DisplayCanvas(Controller) - Constructor for class etomica.graphics.DisplayCanvas
Construct a DisplayCanvas using the given controller (which may be null).
displayList() - Method in class etomica.graphics.SimulationGraphic
 
DisplayPlot - Class in etomica.graphics
Class for creating a plot of simulation data.
DisplayPlot() - Constructor for class etomica.graphics.DisplayPlot
Creates a plot with a new, empty, DataSinkTable.
DisplayPlot(DataSet) - Constructor for class etomica.graphics.DisplayPlot
Creates a plot using data from the given table.
displayPlot - Variable in class etomica.graphics.EtomicaPlot
 
DisplayPlot.DataCasterJudgeFunction - Class in etomica.graphics
 
DisplayPlot.DataWriter - Class in etomica.graphics
Writes a file with the raw data from a plot.
DisplayPlot.PopupListener - Class in etomica.graphics
 
DisplayPlot.RawDataWindowOpener - Class in etomica.graphics
Opens a window with the raw data from a plot.
DisplayPolytope - Class in etomica.graphics
Displays a picture of a polytope.
DisplayPolytope(Polytope) - Constructor for class etomica.graphics.DisplayPolytope
 
DisplayPolytope.Applet - Class in etomica.graphics
 
DisplayPolytopeCanvas2D - Class in etomica.graphics
 
DisplayPolytopeCanvas2D(DisplayPolytope) - Constructor for class etomica.graphics.DisplayPolytopeCanvas2D
 
DisplayPolytopeCanvasG3DSys - Class in etomica.graphics
 
DisplayPolytopeCanvasG3DSys(DisplayPolytope) - Constructor for class etomica.graphics.DisplayPolytopeCanvasG3DSys
 
DisplayScrollingGraph - Class in etomica.graphics
 
DisplayScrollingGraph() - Constructor for class etomica.graphics.DisplayScrollingGraph
 
DisplayTable - Class in etomica.graphics
Presents data in a tabular form.
DisplayTable() - Constructor for class etomica.graphics.DisplayTable
 
DisplayTable(DataSinkTable) - Constructor for class etomica.graphics.DisplayTable
 
DisplayTextBox - Class in etomica.graphics
A simple display of a single value in a textbox with an associated label.
DisplayTextBox() - Constructor for class etomica.graphics.DisplayTextBox
 
DisplayTextBox.LabelType - Class in etomica.graphics
Typed constant used to indicate the type of label to be used with the display.
DisplayTextBoxesCAE - Class in etomica.graphics
Display that presents three boxes with the current value, average, and error, respectively, given by an AccumulatorAverage.
DisplayTextBoxesCAE() - Constructor for class etomica.graphics.DisplayTextBoxesCAE
 
DisplayTimer - Class in etomica.graphics
DisplayBox to present the elapsed time in a molecular dynamics simulation.
DisplayTimer(IntegratorMD) - Constructor for class etomica.graphics.DisplayTimer
 
dispose() - Method in class etomica.atom.AtomLeafAgentManager
Notifies the AtomAgentManager it should disconnect itself as a listener and release all of its agents.
dispose() - Method in class etomica.atom.AtomTypeAgentManager
Unregisters this class as a listener for AtomType-related events and releases its agents.
dispose() - Method in class etomica.atom.MoleculeAgentManager
Notifies the AtomAgentManager it should disconnect itself as a listener.
dispose() - Method in class etomica.atom.SpeciesAgentManager
Unregisters this class as a listener for AtomType-related events and releases its agents.
dispose() - Method in class etomica.box.BoxAgentManager
Notifies the BoxAgentManager that it should release all agents and stop listening for events from the simulation.
dispose() - Method in class etomica.graphics.DisplayCanvas
 
dispose() - Method in class etomica.graphics.DisplayTimer
Unhooks the DisplayTimer from the integrator
dispose() - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular
 
dispose() - Method in class etomica.nbr.list.NeighborListManager
 
dispose() - Method in class etomica.util.RandomNumberGeneratorUnix
Cleanup, close the file.
distanceTo(IVector) - Method in class etomica.math.geometry.Plane
Perpendicular distance from the plane to the given point.
distanceTo(IVector) - Method in class etomica.math.geometry.Polyhedron
Returns the perpendicular distance to the nearest face of the polyhedron.
distPol - Variable in class etomica.models.water.P2WaterSzalewicz
 
Distribution(ISpace, double, double) - Constructor for class etomica.statmech.MaxwellBoltzmann.Distribution
 
div(Complex) - Method in class etomica.math.Complex
Division of Complex numbers (doesn't change this Complex number).
divisor - Variable in class etomica.potential.Potential0Lrc
 
DLGA(double) - Static method in class etomica.math.Gamma
 
dmptab - Variable in class etomica.models.water.P2WaterSzalewicz
 
dn - Variable in class etomica.potential.P3HydrogenManzhos
 
doAction(IAction) - Method in class etomica.graphics.Device
Method called by subclasses to execute the action of the device.
doAction(IAction) - Method in class etomica.graphics.DeviceSlider
 
doActionNow(IAction) - Method in class etomica.action.activity.Controller
Pauses current activity, executes given action, then resumes current activity.
doActionNow(IAction) - Method in interface etomica.action.activity.IController
Pauses current activity, executes given action, then resumes current activity.
doApplyPBC - Variable in class etomica.action.WriteConfiguration
 
doApplyPBC - Variable in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
 
doApplyPBC - Variable in class etomica.nbr.cell.NeighborCellManager
 
doApplyPBC - Variable in class etomica.nbr.list.molecule.NeighborListManagerMolecular
 
doApplyPBC - Variable in class etomica.nbr.list.NeighborListManager
 
doAveraging - Variable in class etomica.util.HistogramNotSoSimple
 
doBlockSum() - Method in class etomica.data.AccumulatorAverageCollapsing
Performs the block sum after blockSize calls to addData.
doBlockSum() - Method in class etomica.data.AccumulatorAverageCovariance
 
doBlockSum() - Method in class etomica.data.AccumulatorAverageFixed
Performs the block sum after blockSize calls to addData.
doBlockSum() - Method in class etomica.data.AccumulatorAverageFixedOutputFile
Performs the block sum after blockSize calls to addData.
doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.data.meter.PotentialCalculationRDF
 
doCalculation(IAtomList, IPotential) - Method in class etomica.integrator.IntegratorGear4NPH.ForceSumNPH
 
doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.integrator.IntegratorHard.CollisionHandlerUp
 
doCalculation(IAtomList, IPotentialAtomic) - Method in interface etomica.potential.PotentialCalculation
Method giving the specific calculation performed by this class.
doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.potential.PotentialCalculationEnergySum
Adds to the energy sum the energy values obtained from application of the given potential to the atoms.
doCalculation(IMoleculeList, IPotentialMolecular) - Method in class etomica.potential.PotentialCalculationEnergySum
Adds to the energy sum the energy values obtained from application of the given potential to the molecules.
doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.potential.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) - Method in class etomica.potential.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) - Method in class etomica.potential.PotentialCalculationForcePressureSum
Adds forces due to given potential acting on the atoms produced by the iterator.
doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.potential.PotentialCalculationForceSum
Adds forces due to given potential acting on the atoms produced by the iterator.
doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.potential.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(IMoleculeList, IPotentialMolecular) - Method in interface etomica.potential.PotentialCalculationMolecular
Method giving the specific calculation performed by this class.
doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.potential.PotentialCalculationMolecularVirialSum
 
doCalculation(IMoleculeList, IPotentialMolecular) - Method in class etomica.potential.PotentialCalculationMolecularVirialSum
 
doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.potential.PotentialCalculationPhiSum
 
doCalculation(IMoleculeList, IPotentialMolecular) - Method in class etomica.potential.PotentialCalculationPhiSum
 
doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.potential.PotentialCalculationPressureTensor
Adds the pressure tensor contribution based on the forces acting on each pair of atoms produced by the iterator.
doCalculation(IMoleculeList, IPotentialMolecular) - Method in class etomica.potential.PotentialCalculationTorqueSum
Adds forces and torques due to given potential acting on the atoms produced by the iterator.
doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.potential.PotentialCalculationTorqueSum
Adds forces and torques due to given potential acting on the atoms produced by the iterator.
doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.potential.PotentialCalculationVirialSum
Adds to the virial sum the energy values obtained from application of the given potential to the atoms produced by the given iterator.
doClear - Variable in class etomica.graphics.DisplayPlot
 
doContinue() - Method in class etomica.action.Activity
 
dodebug - Static variable in class etomica.integrator.IntegratorMC
 
doDown - Variable in class etomica.lattice.RectangularLatticeNbrIterator
 
doEnforceBounds - Variable in class etomica.data.DataSourceUniform
 
doFit(double[], double[]) - Static method in class etomica.util.numerical.LinearFit
 
doFit(double[], double[], double[]) - Static method in class etomica.util.numerical.LinearFit
 
doFit(int, double[], double[]) - Static method in class etomica.util.numerical.PolynomialFit
Perform polynomial fit of the given order.
doFit(int, double[], double[], double[]) - Static method in class etomica.util.numerical.PolynomialFit
Perform polynomial fit of the given order with the given weights (w).
doGlobalMoves() - Method in class etomica.integrator.IntegratorManagerMC
Method to select and perform an elementary Monte Carlo move.
doGoDown - Variable in class etomica.atom.iterator.MpiIntraspecies1A
 
doGoDown - Variable in class etomica.atom.iterator.TripletInnerSequential
 
doGoUp - Variable in class etomica.atom.iterator.TripletInnerSequential
 
doIncludeACInError - Variable in class etomica.data.AccumulatorAverage
 
doInterpolateHole() - Method in class etomica.util.numerical.AkimaSplineSmoother
 
doInterpolateHole2() - Method in class etomica.util.numerical.AkimaSplineSmoother
 
doInterpolation(double[]) - Method in class etomica.util.numerical.AkimaSpline
 
doInterpolationDy(double[]) - Method in class etomica.util.numerical.AkimaSpline
 
doJustTilt - Variable in class etomica.util.numerical.AkimaSplineSmootherDyApp.PlotAction
 
doNBodyStuff(IMolecule, PotentialCalculation, int, IPotentialMolecular, NeighborListManagerMolecular) - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular
Invokes the PotentialCalculationMolecular for the given Molecule with its up and down neighbors as a single MoleculeSet.
doNBodyStuff(IAtom, PotentialCalculation, int, IPotentialAtomic, NeighborListManager) - Method in class etomica.nbr.list.PotentialMasterList
Invokes the PotentialCalculation for the given Atom with its up and down neighbors as a single AtomSet.
done - Variable in class etomica.atom.iterator.ANIntragroupExchange
 
doNonEquilibrium - Variable in class etomica.potential.PotentialCalculationPressureTensor
 
doPaint(Graphics) - Method in class etomica.graphics.DisplayBoxCanvas1D
doPaint is the method that handles the drawing of the box to the screen.
doPaint(Graphics) - Method in class etomica.graphics.DisplayBoxCanvas2D
Method that handles the drawing of the box to the screen.
doPaint(Graphics) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
 
doPaint(Graphics) - Method in class etomica.graphics.DisplayCanvas
 
doPaint(Graphics) - Method in class etomica.graphics.DisplayPolytopeCanvas2D
doPaint is the method that handles the drawing of the box to the screen.
doPaint(Graphics) - Method in class etomica.graphics.DisplayPolytopeCanvasG3DSys
 
doPaint(Graphics) - Method in class etomica.graphics.DisplayScrollingGraph
 
doParseArgs(ParameterBase, String[]) - Static method in class etomica.util.ParseArgs
 
doRandStep() - Method in class etomica.util.numerical.AkimaSplineSmoother
 
doRealSum - Variable in class etomica.potential.EwaldSummation
 
doRotation(int, IMolecule, double, double) - Method in class etomica.models.water.P2Water4PSoft
 
doSerialize - Variable in class etomica.util.EventManager.Linker
 
doShiftInitY() - Method in class etomica.util.numerical.AkimaSplineSmootherDy
 
doShowCurrent - Variable in class etomica.graphics.DisplayTextBoxesCAE
 
doStep() - Method in interface etomica.api.IIntegrator
Performs the elementary integration step, such as a molecular dynamics time step, or a Monte Carlo trial.
doStep() - Method in class etomica.integrator.Integrator
 
doStep() - Method in class etomica.util.numerical.AkimaSplineSmoother
 
doStep() - Method in class etomica.util.numerical.AkimaSplineSmootherDy
 
doStepInternal() - Method in class etomica.action.IntegratorDimerApproach
 
doStepInternal() - Method in class etomica.integrator.Integrator
Performs the elementary integration step, such as a molecular dynamics time step, or a Monte Carlo trial.
doStepInternal() - Method in class etomica.integrator.IntegratorAnalytic
 
doStepInternal() - Method in class etomica.integrator.IntegratorConNVT
 
doStepInternal() - Method in class etomica.integrator.IntegratorGear4
 
doStepInternal() - Method in class etomica.integrator.IntegratorGear4NPH
 
doStepInternal() - Method in class etomica.integrator.IntegratorHard
Steps all atoms across time interval timeStep, handling all intervening collisions.
doStepInternal() - Method in class etomica.integrator.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() - Method in class etomica.integrator.IntegratorMC
Method to select and perform an elementary Monte Carlo move.
doStepInternal() - Method in class etomica.integrator.IntegratorMD
 
doStepInternal() - Method in class etomica.integrator.IntegratorRigidIterative
 
doStepInternal() - Method in class etomica.integrator.IntegratorRigidMatrixIterative
 
doStepInternal() - Method in class etomica.integrator.IntegratorVelocityVerlet
 
doStepInternal() - Method in class etomica.integrator.IntegratorVelocityVerletRattle
 
doStepInternal() - Method in class etomica.integrator.IntegratorVelocityVerletShake
 
doStepInternal() - Method in class etomica.integrator.IntegratorVerlet
 
doStepInternal() - Method in class etomica.util.numerical.AkimaSplineSmootherApp.IntegratorSmoother
 
doStepInternal() - Method in class etomica.util.numerical.AkimaSplineSmootherDyApp.IntegratorSmoother
 
doStrictBlockData - Variable in class etomica.data.AccumulatorAverageFixed
 
doSum112(double[], double[], double[], double[], double) - Method in class etomica.potential.P3CPSNonAdditiveHe
 
doSum113(double[], double[], double[], double[], double) - Method in class etomica.potential.P3CPSNonAdditiveHe
 
doSum122(double[], double[], double[], double[], double, double) - Method in class etomica.potential.P3CPSNonAdditiveHe
 
doSum644(double[], double[], double[], double[], double, double, double, double) - Method in class etomica.potential.P3CPSNonAdditiveHe
 
doSum660(double[], double[], double) - Method in class etomica.potential.P3CPSNonAdditiveHe
 
doSum734(double[], double[], double[], double[], double, double, double, double) - Method in class etomica.potential.P3CPSNonAdditiveHe
 
doSum770(double[], double[], double[]) - Method in class etomica.potential.P3CPSNonAdditiveHe
 
doSum833(double[], double[], double[], double, double, double) - Method in class etomica.potential.P3CPSNonAdditiveHe
 
doSum860(double[], double[], double) - Method in class etomica.potential.P3CPSNonAdditiveHe
 
doSums(double[], double) - Method in class etomica.data.AccumulatorAverageCollapsingLog
Performs the block sum after
doSwap - Variable in class etomica.atom.iterator.ApiInnerVariable
 
doSwap - Variable in class etomica.atom.iterator.MpiInnerVariable
 
dot(IVector) - Method in interface etomica.api.IVector
Returns the dot product of this vector with the given one.
dot(IVector) - Method in class etomica.space1d.Vector1D
 
dot(IVector) - Method in class etomica.space2d.Vector2D
 
dot(IVector) - Method in class etomica.space3d.Vector3D
 
dot(IVector) - Method in class etomica.spaceNd.VectorND
 
doThermostat() - Method in class etomica.integrator.IntegratorMD
thermostat implementation.
doThermostatInternal() - Method in class etomica.integrator.IntegratorMD
Fires the thermostat if the appropriate interval has been reached.
doTransform(IAtom) - Method in class etomica.integrator.mcmove.MCMoveDimerRotate
 
doTransform() - Method in class etomica.integrator.mcmove.MCMoveRotateMolecule3D
 
doTransform(IMolecule, IVector, RotationTensor) - Static method in class etomica.models.water.OrientationCalcWater3P
 
doTransform(IMolecule, IVector, RotationTensor) - Static method in class etomica.models.water.OrientationCalcWater4P
 
doTransform(IMolecule) - Method in class etomica.models.water.P2Water4PSoft
 
doTrial() - Method in class etomica.integrator.mcmove.MCMove
Method to perform trial move.
doTrial() - Method in class etomica.integrator.mcmove.MCMoveAtom
Method to perform trial move.
doTrial() - Method in class etomica.integrator.mcmove.MCMoveAtomInRegion
 
doTrial() - Method in class etomica.integrator.mcmove.MCMoveBoxSize
 
doTrial() - Method in class etomica.integrator.mcmove.MCMoveDimer
Method to perform trial move.
doTrial() - Method in class etomica.integrator.mcmove.MCMoveDimerRotate
Method to perform trial move.
doTrial() - Method in class etomica.integrator.mcmove.MCMoveInsertDelete
Chooses and performs with equal probability an elementary molecule insertion or deletion.
doTrial() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
 
doTrial() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
 
doTrial() - Method in class etomica.integrator.mcmove.MCMoveMolecule
 
doTrial() - Method in class etomica.integrator.mcmove.MCMoveMoleculeExchange
 
doTrial() - Method in class etomica.integrator.mcmove.MCMoveRotate
 
doTrial() - Method in class etomica.integrator.mcmove.MCMoveRotateMolecule3D
 
doTrial() - Method in class etomica.integrator.mcmove.MCMoveSemigrand
 
doTrial() - Method in class etomica.integrator.mcmove.MCMoveSwapConfiguration
 
doTrial() - Method in class etomica.integrator.mcmove.MCMoveTorsionAceticAcid
 
doTrial() - Method in class etomica.integrator.mcmove.MCMoveVolume
 
doTrial() - Method in class etomica.integrator.mcmove.MCMoveVolumeExchange
 
doTrial() - Method in class etomica.integrator.mcmove.MCMoveWiggleAceticAcid
 
DoubleRange - Class in etomica.util
 
DoubleRange(double, double) - Constructor for class etomica.util.DoubleRange
Constructs the range defined by given values.
DoubleWrapper() - Constructor for class etomica.nbr.CriterionPositionWall.DoubleWrapper
 
doUp - Variable in class etomica.lattice.RectangularLatticeNbrIterator
 
doUpdate() - Method in class etomica.graphics.DeviceBox
Updates the display of the box with the current value given by the modifier.
doUpdate() - Method in class etomica.graphics.DeviceSlider
 
doUpdate() - Method in class etomica.graphics.DeviceSpinner
 
doUpdate() - Method in class etomica.graphics.DisplayPlot
Redraws the plot.
doUpdate() - Method in class etomica.graphics.DisplayPolytope
 
doUpdate() - Method in class etomica.graphics.DisplayScrollingGraph
 
doWait() - Method in class etomica.action.Activity
Method to put activity in a condition of being paused.
DOWN - Static variable in class etomica.atom.iterator.IteratorDirective.Direction
 
downList - Variable in class etomica.integrator.IntegratorHard
 
downList - Variable in class etomica.nbr.list.AtomNeighborLists
 
downList - Variable in class etomica.nbr.list.molecule.MoleculeNeighborLists
 
dpolx - Static variable in class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
 
dr - Variable in class etomica.atom.AtomPositionGeometricCenterPBC
 
dr - Variable in class etomica.data.meter.MeterDipoleSumSquaredMappedAverage
 
dr - Variable in class etomica.data.meter.PotentialCalculationRDF
 
dr - Variable in class etomica.graphics.ColorSchemeOverlap
 
dr - Variable in class etomica.integrator.IntegratorVelocityVerletShake
 
dr - Variable in class etomica.integrator.mcmove.MCMoveDimer
 
dr - Variable in class etomica.integrator.mcmove.MCMoveDimerRotate
 
dr - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
 
dr - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
 
dr - Variable in class etomica.models.water.P2Water4PSoft
 
dr - Variable in class etomica.nbr.CriterionPositionWall
 
dr - Variable in class etomica.nbr.CriterionSimple
 
dr - Variable in class etomica.nbr.molecule.CriterionSimpleMolecular
 
dr - Variable in class etomica.potential.P2DiscreteFeynmanHibbs
 
dr - Variable in class etomica.potential.P2EffectiveFeynmanHibbs
 
dr - Variable in class etomica.potential.P2HydrogenHinde
 
dr - Variable in class etomica.potential.P2HydrogenHindeAtomic
 
dr - Variable in class etomica.potential.P2HydrogenHindePatkowski
 
dr - Variable in class etomica.potential.P2HydrogenHindePatkowskiAtomic
 
dr - Variable in class etomica.potential.P2HydrogenPatkowski
 
dr - Variable in class etomica.potential.P2HydrogenPatkowskiAtomic
 
dr - Variable in class etomica.potential.P2MoleculeSoftTruncatedSwitched
 
dr - Variable in class etomica.potential.P2MoleculeTruncated
 
dr - Variable in class etomica.potential.P2O2Bartolomei.P2O2TI
 
dr - Variable in class etomica.potential.P2ReactionFieldDipole
 
dr - Variable in class etomica.potential.P2ReactionFieldDipoleTruncated
 
dr - Variable in class etomica.potential.P2SoftSphericalTruncatedSwitched
 
dr - Variable in class etomica.potential.P2SoftTruncated
 
dr - Variable in class etomica.potential.P2SpheroPolyhedron
 
dr - Variable in class etomica.potential.P3HydrogenATM
 
dR - Variable in class etomica.potential.P3HydrogenGarberoglioMolecular
 
dr - Variable in class etomica.potential.Potential2HardSpherical
 
dr - Variable in class etomica.potential.Potential2SoftSpherical
 
dr - Variable in class etomica.potential.Potential2SoftSphericalLS
 
dr - Variable in class etomica.potential.PotentialCalculationPhiSum
 
dr0 - Variable in class etomica.models.water.P2Water4PSoft
 
dr01 - Variable in class etomica.potential.P2Exp6
 
dr01 - Variable in class etomica.potential.P2Exp6Buckingham
 
dr01 - Variable in class etomica.potential.P2LennardJonesDreiding
 
dr1 - Variable in class etomica.integrator.IntegratorGear4.Agent
 
dr1 - Variable in class etomica.models.water.P2Water4PSoft
 
dr1 - Variable in class etomica.potential.P2ReactionFieldDipole
 
dr1 - Variable in class etomica.potential.P3AxilrodTeller
 
dr1 - Variable in class etomica.potential.P3Induction
 
dr12 - Variable in class etomica.potential.P3BondAngle
 
dr12 - Variable in class etomica.potential.P3BondAngleDreiding
 
dr12 - Variable in class etomica.potential.P4TorsionDreiding
 
dr2 - Variable in class etomica.integrator.IntegratorGear4.Agent
 
dr2 - Variable in class etomica.potential.P3AxilrodTeller
 
dr2 - Variable in class etomica.potential.P3Induction
 
dr21 - Variable in class etomica.potential.P4BondTorsion
 
dr21 - Variable in class etomica.potential.P4BondTorsionAlkaneXCCH
 
dr23 - Variable in class etomica.potential.P3BondAngle
 
dr23 - Variable in class etomica.potential.P3BondAngleDreiding
 
dr23 - Variable in class etomica.potential.P4BondTorsion
 
dr23 - Variable in class etomica.potential.P4BondTorsionAlkaneXCCH
 
dr23 - Variable in class etomica.potential.P4TorsionDreiding
 
dr3 - Variable in class etomica.integrator.IntegratorGear4.Agent
 
dr34 - Variable in class etomica.potential.P4BondTorsion
 
dr34 - Variable in class etomica.potential.P4BondTorsionAlkaneXCCH
 
dr34 - Variable in class etomica.potential.P4TorsionDreiding
 
dr4 - Variable in class etomica.integrator.IntegratorGear4.Agent
 
dra - Variable in class etomica.potential.P4TorsionDreiding
 
drAB - Variable in class etomica.potential.P3CPSNonAdditiveHe
 
drAB - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
 
drAB - Variable in class etomica.potential.P3CPSNonAdditiveHeOrig
 
drAB - Variable in class etomica.potential.P3CPSNonAdditiveHeSimplified
 
drAC - Variable in class etomica.potential.P3CPSNonAdditiveHe
 
drAC - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
 
drAC - Variable in class etomica.potential.P3CPSNonAdditiveHeOrig
 
drAC - Variable in class etomica.potential.P3CPSNonAdditiveHeSimplified
 
draw(Graphics, int[], double) - Method in interface etomica.graphics.Drawable
 
draw(Graphics, int[], double) - Method in class etomica.potential.P1HardBoundary
 
draw(Graphics, int[], double) - Method in class etomica.potential.P1HardMovingBoundary
 
DRAW_BOUNDARY_ALL - Static variable in class etomica.graphics.DisplayCanvas
 
DRAW_BOUNDARY_MAX - Static variable in class etomica.graphics.DisplayCanvas
 
DRAW_BOUNDARY_NONE - Static variable in class etomica.graphics.DisplayCanvas
 
DRAW_BOUNDARY_OUTLINE - Static variable in class etomica.graphics.DisplayCanvas
 
DRAW_BOUNDARY_SHELL - Static variable in class etomica.graphics.DisplayCanvas
 
Drawable - Interface in etomica.graphics
 
drawAtom(Graphics, int[], IAtom) - Method in class etomica.graphics.DisplayBoxCanvas2D
 
drawAtom(Graphics, int[], IAtom) - Method in class etomica.graphics.DisplayBoxSpin2D
 
drawLineList - Variable in class etomica.graphics.DisplayPlot
 
drawSize - Variable in class etomica.graphics.DisplayBox
Size of drawing region of central image, in pixels
drawSize - Variable in class etomica.graphics.DisplayPolytope
Size of drawing region of central image, in pixels
drb - Variable in class etomica.potential.P4TorsionDreiding
 
drBC - Variable in class etomica.potential.P3CPSNonAdditiveHe
 
drBC - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
 
drBC - Variable in class etomica.potential.P3CPSNonAdditiveHeOrig
 
drBC - Variable in class etomica.potential.P3CPSNonAdditiveHeSimplified
 
drbxa - Variable in class etomica.potential.P4TorsionDreiding</