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a0 - Variable in class etomica.potential.P4BondTorsion
a1 - Variable in class etomica.potential.P4BondTorsion
a2 - Variable in class etomica.potential.P4BondTorsion
a3 - Variable in class etomica.potential.P4BondTorsion
ab - Variable in class etomica.lattice.crystal.PrimitiveHexagonal
ab - Variable in class etomica.lattice.crystal.PrimitiveHexagonal2D
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
AboutBoxWindow.EtomicaGraphic() - Constructor for class etomica.graphics.AboutBoxWindow.EtomicaGraphic
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(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.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.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.).
AccumulatorAverage.StatType(String, int) - Constructor for class etomica.data.AccumulatorAverage.StatType
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(IRandom) - Constructor for class etomica.data.AccumulatorAverageCollapsingLog
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(int) - Constructor for class etomica.data.AccumulatorAverageCovariance
AccumulatorAverageCovariance.StatType - Class in etomica.data
AccumulatorAverageCovariance.StatType(String, int) - Constructor for class etomica.data.AccumulatorAverageCovariance.StatType
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.
AccumulatorHistory.DataSourceCount() - Constructor for class etomica.data.AccumulatorHistory.DataSourceCount
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
AccumulatorRatioAverage.StatType - Class in etomica.data
AccumulatorRatioAverage.StatType(String, int) - Constructor for class etomica.data.AccumulatorRatioAverage.StatType
action - Variable in class etomica.action.activity.ControllerEvent
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
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.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.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.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.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.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(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(IEvent) - Method in interface etomica.util.IListener
actions - Variable in class etomica.action.activity.ActivityGroupParallel
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
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(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
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
addAuthor(String) - Method in class etomica.graphics.DefaultToolbar
addBox(IBox) - Method in interface etomica.api.ISimulation: Adds a Box to the simulation.
addBox(IBox) - Method in class etomica.simulation.Simulation
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.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.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) - 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.
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.
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(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
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(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(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
addPropertyChangeListener(PropertyChangeListener) - Method in class etomica.graphics.Display
addRadioGroupActionListener(ActionListener) - Method in class etomica.graphics.DeviceThermoSlider: Add the specified listener to the list of listeners that will get invoked when the isothermal or adiabatic radio button is pushed.
addRangedPotential(IPotentialAtomic, IAtomType) - Method in class etomica.nbr.PotentialMasterNbr
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
addTemperatureSliderListener(ChangeListener) - Method in class etomica.graphics.DeviceThermoSlider: Add the specified listener to the list of listeners that will get invoked when the temperature slider value changes.
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.
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.HistoryCollapsing: adds data 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.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.integrator.IntegratorHardField: 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.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 - 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
agentIterator - Variable in class etomica.potential.PotentialCalculationForceSum
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.NeighborCellManager
agentManager - Variable in class etomica.nbr.CriterionPositionWall
agentManager - Variable in class etomica.nbr.CriterionSimple
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
agentSource - Variable in class etomica.atom.AtomLeafAgentManager
agentSource - Variable in class etomica.atom.MoleculeAgentManager
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.
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
AL10 - Static variable in class etomica.math.Gamma
align - Variable in class etomica.graphics.DisplayBox
align - Variable in class etomica.graphics.DisplayPolytope
ALL - Static variable in class etomica.units.Prefix
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.PotentialMasterList
allMoleculeList - Variable in class etomica.box.Box
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.PotentialMasterNbr
allPotentials - Variable in class etomica.potential.PotentialMasterMonatomic
alpha - Variable in class etomica.potential.EwaldSummation
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_NODRIFT - 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.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
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
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)
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 expires after returning a single atom pair, which is specified by a call to the setPair method.
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(AtomIteratorBasis, AtomIteratorBasis) - 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.
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
appendLine(IVector, IVector) - Method in interface etomica.graphics2.Renderable.Polyline
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
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.
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.
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
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.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.
assignColumnTo(int, double[]) - Method in class etomica.data.types.DataDoubleArray: 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.
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.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(double[]) - Method in class etomica.spaceNd.VectorND
AssociatedPolynomial - Class in etomica.util
AssociatedPolynomial() - Constructor for class etomica.util.AssociatedPolynomial
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.graphics2.SceneManager.SphereShapeWrapper
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.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: Global index of first atom of interest.
atom2 - Variable in class etomica.data.DataSourceAtomDistance
ATOM2_INDEX - Static variable in class etomica.util.Debug: Global 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
atomAgentManager - Variable in class etomica.graphics.BondListener
atomAgentManager - Variable in class etomica.potential.EwaldSummation
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
atomColor(IAtom) - Method in interface etomica.graphics2.ColorScheme
atomColor(IAtom) - Method in class etomica.graphics2.ColorSchemeByType: Initialize atom color to the color of its type
atomColor(IAtom) - Method in class etomica.graphics2.ColorSchemeColliders: Applies the special colors to the colliding pair while coloring all other atoms with baseColor.
atomColor(IAtom) - Method in class etomica.graphics2.ColorSchemeNull: Return without changing atom's color.
atomColor(IAtom) - Method in class etomica.graphics2.ColorSchemeSimple
atomColor(IAtom) - Method in class etomica.graphics2.ColorSchemeTemperature
AtomFilter - Interface in etomica.atom: Interface for a class that screens atoms according to some criterion.
atomFilter - Variable in class etomica.graphics.DisplayBox
atomFilter - Variable in class etomica.graphics2.SceneManager
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
atomicNumber - Variable in class etomica.chem.elements.ElementChemical
atomicPotentials - Variable in class etomica.potential.PotentialMasterLrc
AtomIterator - Interface in etomica.atom.iterator: Interface for classes that loop over a set of atoms.
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.
AtomIteratorBasisFilteredType - Class in etomica.atom.iterator
AtomIteratorBasisFilteredType(IAtomType) - Constructor for class etomica.atom.iterator.AtomIteratorBasisFilteredType
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
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 - 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, IBox) - Constructor for class etomica.atom.AtomLeafAgentManager
AtomLeafAgentManager.AgentIterator - Class in etomica.atom: Iterator that loops over the agents, skipping null elements
AtomLeafAgentManager.AgentIterator(AtomLeafAgentManager) - Constructor for class etomica.atom.AtomLeafAgentManager.AgentIterator
AtomLeafAgentManager.AgentSource - 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.MoleculeArrayList
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
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.EwaldSummation
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
AtomPositionGeometricCenterPBC - Class in etomica.atom: Calculates the geometric center over a set of atoms.
AtomPositionGeometricCenterPBC(ISpace, IBoundary) - Constructor for class etomica.atom.AtomPositionGeometricCenterPBC
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
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
atomsPerGroup - Variable in class etomica.species.SpeciesSpheres
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
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.AgentIterator(AtomTypeAgentManager) - Constructor for class etomica.atom.AtomTypeAgentManager.AgentIterator
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
AtomTypeOrientedSphere - Class in etomica.atom: Atom type for a sphere that has some feature depending upon an orientation coordinate.
AtomTypeOrientedSphere(IElement, double, ISpace) - Constructor for class etomica.atom.AtomTypeOrientedSphere
atomTypeRemovedNotify(IAtomType) - Method in class etomica.simulation.Simulation
AtomTypeSphere - Class in etomica.atom: Atom type for a simple monatomic atom that has a length scale associated with its size.
AtomTypeSphere(Simulation) - Constructor for class etomica.atom.AtomTypeSphere
AtomTypeSphere(IElement) - Constructor for class etomica.atom.AtomTypeSphere
AtomTypeSphere(IElement, double) - Constructor for class etomica.atom.AtomTypeSphere
AtomTypeWell - Class in etomica.atom
AtomTypeWell(IElement, double, double) - Constructor for class etomica.atom.AtomTypeWell
ATTO - Static variable in class etomica.units.Prefix: Prefix indicating 10^-18.
autoRowLabels - Variable in class etomica.graphics.DisplayTable
average - Variable in class etomica.data.AccumulatorAverage
AVERAGE - Static variable in class etomica.data.AccumulatorAverage.StatType
averageBox - Variable in class etomica.graphics.DisplayTextBoxesCAE
averages - Variable in class etomica.data.AccumulatorAverageCollapsingLog
avgDataInfo - 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, 6.0221415e23 molecules/mole.
axesTensor - Variable in class etomica.integrator.IntegratorRigidMatrixIterative

B

b - Variable in class etomica.graphics2.Color
b - Variable in class etomica.util.numerical.LinearFit.FitResult: The intercept of the y vs.
B2(double) - Static method in class etomica.statmech.LennardJones: Returns the 2nd virial coefficient.
BACK - Static variable in class etomica.util.Constants.Direction
BACKUP - Static variable in class etomica.util.FastFourierTransform
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.
baseColor - Variable in class etomica.graphics2.ColorSchemeSimple
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
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
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 4-atom basis fot an fcc crystal.
BasisOrthorhombicHexagonal() - Constructor for class etomica.lattice.crystal.BasisOrthorhombicHexagonal: Makes a fcc 4-atom basis.
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.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 class etomica.atom.iterator.TripletInnerSequential
beta - Variable in class etomica.potential.P4TorsionDreiding
bisectionMethodMinimizationBracket - Variable in class etomica.util.numerical.LineMinimization
BisectionMethodMinimumBracket - Class in etomica.util.numerical
BisectionMethodMinimumBracket() - Constructor for class etomica.util.numerical.BisectionMethodMinimumBracket
BLACK - Static variable in class etomica.graphics2.Color
BLOCK_CORRELATION - Static variable in class etomica.data.AccumulatorAverage.StatType
BLOCK_COVARIANCE - Static variable in class etomica.data.AccumulatorAverageCovariance.StatType
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
blockSize - Variable in class etomica.data.AccumulatorAverage
blockSums - Variable in class etomica.data.AccumulatorAverageCollapsing
blockSums - Variable in class etomica.data.AccumulatorAverageCollapsingLog
BLUE - Static variable in class etomica.graphics2.Color
BOLTZMANN_K - Static variable in class etomica.util.Constants: Boltzmann's constant, in (sim units)/kelvin.
bondedAtoms - Variable in class etomica.integrator.IntegratorVelocityVerletShake.BondConstraints
bondingPotential - Variable in class etomica.chem.models.ModelChain
bondIteratorsHash - Variable in class etomica.graphics.BondListener
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.models.water.P2Water3P
boundary - Variable in class etomica.models.water.P2Water4P
boundary - Variable in class etomica.models.water.TestEwaldTIP4PWater
boundary - Variable in class etomica.nbr.CriterionSimple
boundary - Variable in class etomica.potential.P1HardBoundary
boundary - Variable in class etomica.potential.P2MoleculeSoftTruncatedSwitched
boundary - Variable in class etomica.potential.P2ReactionFieldDipole
boundary - Variable in class etomica.potential.P2SoftSphericalTruncatedSwitched
boundary - Variable in class etomica.potential.P2SoftTruncated
boundary - Variable in class etomica.potential.P3BondAngle
boundary - Variable in class etomica.potential.P3BondAngleDreiding
boundary - Variable in class etomica.potential.P4BondTorsion
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 - 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.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.
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
boundaryVertices - Variable in class etomica.graphics2.SceneManager
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.atom.AtomLeafAgentManager
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.MeterKineticEnergyRigid
box - Variable in class etomica.data.meter.MeterPressureTensor
box - Variable in class etomica.data.meter.MeterProfileByAtoms
box - Variable in class etomica.data.meter.MeterRDF
box - Variable in class etomica.data.meter.MeterStructureFactor
box - Variable in class etomica.data.meter.MeterTemperature
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.graphics2.SceneManager
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.NeighborCellManager
box - Variable in class etomica.nbr.list.NeighborListManager
box - Variable in class etomica.potential.EwaldSummation
box - Variable in class etomica.potential.P2ReactionFieldDipole.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
BoxAgentManager - 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) - Constructor for class etomica.box.BoxAgentManager
BoxAgentManager(BoxAgentManager.BoxAgentSource, ISimulation) - Constructor for class etomica.box.BoxAgentManager
boxAgentManager - Variable in class etomica.nbr.CriterionSimple
boxAgentManager - Variable in class etomica.nbr.PotentialMasterNbr
BoxAgentManager.AgentIterator - Class in etomica.box: Iterator that loops over the agents, skipping null elements
BoxAgentManager.AgentIterator(BoxAgentManager) - Constructor for class etomica.box.BoxAgentManager.AgentIterator
BoxAgentManager.BoxAgentSource - Interface in etomica.box: Interface for an object that makes an agent to be placed in each atom upon construction.
boxAgentSource - Variable in class etomica.nbr.PotentialMasterNbr
BoxAgentSourceAtomManager - Class in etomica.box
BoxAgentSourceAtomManager(AtomLeafAgentManager.AgentSource) - 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
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.
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.
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
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
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.
BrentMethodwDerivative - Class in etomica.util.numerical
BrentMethodwDerivative() - Constructor for class etomica.util.numerical.BrentMethodwDerivative
brentMethodwDerivative - Variable in class etomica.util.numerical.LineMinimization
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.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.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.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.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

C

C - Static variable in class etomica.math.Gamma
c0 - Variable in class etomica.graphics.DisplayTable
calcBoth(double, double) - Method in class etomica.math.Gamma
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
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
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.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
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
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
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
Cell.CellFactory() - Constructor for class etomica.nbr.cell.Cell.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.
CellLattice.NeighborIterator(int, double) - Constructor for class etomica.lattice.CellLattice.NeighborIterator
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
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
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.potential.EwaldSummation.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
ChargeAgentSourceTIP4PWater - Class in etomica.models.water
ChargeAgentSourceTIP4PWater() - Constructor for class etomica.models.water.ChargeAgentSourceTIP4PWater
chargeH - Variable in class etomica.models.water.P2Water3P
chargeH - Variable in class etomica.models.water.P2Water4P
chargeHH - Variable in class etomica.models.water.P2Water3P
chargeHH - Variable in class etomica.models.water.P2Water4P
chargeM - Variable in class etomica.models.water.P2Water4P
chargeMH - Variable in class etomica.models.water.P2Water4P
chargeMM - Variable in class etomica.models.water.P2Water4P
chargeO - Variable in class etomica.models.water.P2Water3P
chargeOH - Variable in class etomica.models.water.P2Water3P
chargeOO - Variable in class etomica.models.water.P2Water3P
check() - Method in class etomica.util.TreeList: checks the tree for consistency of connections and ordering by sortKey.
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.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
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.AccumulatorAverage.StatType
choices() - Static method in class etomica.data.AccumulatorAverageCovariance.StatType
choices() - Static method in class etomica.data.AccumulatorRatioAverage.StatType
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.Direction
choicse() - Static method in class etomica.util.Constants.CompassDirection
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.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.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).
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.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
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
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
colliderColor - Variable in class etomica.graphics2.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
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.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.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.P2SquareWell: 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 - Class in etomica.graphics2
Color(float, float, float) - Constructor for class etomica.graphics2.Color
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
colorindex - Variable in class etomica.graphics2.ColorSchemeByType
colormap - Variable in class etomica.graphics2.ColorSchemeByType
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 - Interface in etomica.graphics2: Defines an interface to retrieve the Atom color from an Atom object
colorScheme - Variable in class etomica.graphics2.SceneManager
ColorScheme.Simple - Class in etomica.graphics: Colors all atoms with baseColor.
ColorScheme.Simple() - Constructor for class etomica.graphics.ColorScheme.Simple
ColorScheme.Simple(Color) - Constructor for class etomica.graphics.ColorScheme.Simple
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
ColorSchemeByType - Class in etomica.graphics2: Colors the atom according to the color given by its type field.
ColorSchemeByType() - Constructor for class etomica.graphics2.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
ColorSchemeColliders - Class in etomica.graphics2: This colorScheme acts to color differently the two atoms that are scheduled to collide next.
ColorSchemeColliders(IntegratorHard) - Constructor for class etomica.graphics2.ColorSchemeColliders
ColorSchemeCoordination - Class in etomica.graphics
ColorSchemeCoordination(ISimulation, PotentialMasterList, IBox) - Constructor for class etomica.graphics.ColorSchemeCoordination
ColorSchemeNeighbor - Class in etomica.graphics
ColorSchemeNeighbor(ISimulation, PotentialMasterList, IBox, int) - Constructor for class etomica.graphics.ColorSchemeNeighbor
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
ColorSchemeNull - Class in etomica.graphics2: Does nothing at any time to set atom's color, leaving color to be set to default value.
ColorSchemeNull() - Constructor for class etomica.graphics2.ColorSchemeNull
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
ColorSchemeSimple - Class in etomica.graphics2: Simplest color scheme - colors all atoms with baseColor.
ColorSchemeSimple(Color) - Constructor for class etomica.graphics2.ColorSchemeSimple
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
ColorSchemeTemperature - Class in etomica.graphics2: Colors atoms according to their kinetic energy.
ColorSchemeTemperature(int) - Constructor for class etomica.graphics2.ColorSchemeTemperature: Constructs with default low of 200K and high of 400K.
ColorSchemeTemperature(int, double, double) - Constructor for class etomica.graphics2.ColorSchemeTemperature
colorsProvided - Variable in class etomica.graphics2.ColorSchemeColliders: Indicate whether colors were provided - one of SetColors() functions must be called
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
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.
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
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(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
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
computeShiftOrigin(IAtom, IBoundary) - Method in class etomica.graphics.DisplayBoxCanvas1D
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
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.
ConfigurationLattice.MyLattice(SpaceLattice, IVector, IVector) - Constructor for class etomica.config.ConfigurationLattice.MyLattice
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
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.
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
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
ConformationWaterTIP4P - Class in etomica.models.water: Conformation for 4-point water molecule.
ConformationWaterTIP4P(ISpace) - Constructor for class etomica.models.water.ConformationWaterTIP4P
conjugateGradient(double[], double, FunctionMultiDimensionalDifferentiable) - Method in class etomica.util.numerical.ConjugateGradientMultiDimensional
ConjugateGradientMultiDimensional - Class in etomica.util.numerical
ConjugateGradientMultiDimensional() - Constructor for class etomica.util.numerical.ConjugateGradientMultiDimensional
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 - 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(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.ActionStatus(String) - Constructor for class etomica.action.activity.Controller.ActionStatus
Controller.UrgentWaitObject - Class in etomica.action.activity
Controller.UrgentWaitObject() - Constructor for class etomica.action.activity.Controller.UrgentWaitObject
Controller.WaitObject - Class in etomica.action.activity
Controller.WaitObject() - Constructor for class etomica.action.activity.Controller.WaitObject
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
ControllerEvent.Type(String, int) - Constructor for class etomica.action.activity.ControllerEvent.Type
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
CoordinateConverter - Class in etomica.math.geometry.coordinate
CoordinateConverter() - Constructor for class etomica.math.geometry.coordinate.CoordinateConverter
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.
coreDiameter - Variable in class etomica.potential.P2SquareWell
coreDiameterSquared - Variable in class etomica.potential.P2SquareWell
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
cosGamma - Static variable in class etomica.lattice.crystal.PrimitiveHexagonal
cosGamma - Static variable in class etomica.lattice.crystal.PrimitiveHexagonal2D
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.AccumulatorAverageCollapsingLog
count - Variable in class etomica.integrator.mcmove.MCMoveRotateMolecule3D
Count - Class in etomica.units: Unit class for the number, or quantity, of something.
count1 - Variable in class etomica.integrator.mcmove.MCMoveRotateMolecule3D
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.
covariance - Variable in class etomica.data.AccumulatorAverageCovariance
COVARIANCE - Static variable in class etomica.data.AccumulatorAverageCovariance.StatType
covSum - Variable in class etomica.data.AccumulatorAverageCovariance
createAndShowGUI() - Method in class etomica.units.UnitGraphics
createDecimalSliderStandardLabels(double) - Method in class etomica.graphics.DecimalSlider
createOffScreen(int, int) - Method in class etomica.graphics.DisplayCanvas
createPoly() - Method in interface etomica.graphics2.Renderable
createSphere() - Method in interface etomica.graphics2.Renderable
criterion - Variable in class etomica.potential.EwaldSummation
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.
CriterionAll - Class in etomica.nbr: Specifies that all atoms pairs are to be considered neighbors.
CriterionAll() - Constructor for class etomica.nbr.CriterionAll
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
CriterionPositionWall.DoubleWrapper() - Constructor for class etomica.nbr.CriterionPositionWall.DoubleWrapper
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
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
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.
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.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.lattice.RectangularLatticeNbrIterator
cursor - Variable in class etomica.util.HistoryCollapsing
cutoff - Variable in class etomica.potential.P2ReactionFieldDipole
cutoff2 - Variable in class etomica.potential.P2ReactionFieldDipole

D

D() - Method in class etomica.config.ConfigurationLattice.MyLattice
D - Variable in class etomica.integrator.IntegratorGear4NPH
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() - 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
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.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.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.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.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.
Dalton - Class in etomica.units
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.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.MeterRDF
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
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.
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.DataInfoDouble(String, Dimension) - Constructor for class etomica.data.types.DataDouble.DataInfoDouble
DataDouble.DataInfoDoubleFactory - Class in etomica.data.types
DataDouble.DataInfoDoubleFactory(DataDouble.DataInfoDouble) - Constructor for class etomica.data.types.DataDouble.DataInfoDoubleFactory
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.DataInfoDoubleArray(String, Dimension, int[]) - Constructor for class etomica.data.types.DataDoubleArray.DataInfoDoubleArray
DataDoubleArray.DataInfoDoubleArrayFactory - Class in etomica.data.types
DataDoubleArray.DataInfoDoubleArrayFactory(DataDoubleArray.DataInfoDoubleArray) - Constructor for class etomica.data.types.DataDoubleArray.DataInfoDoubleArrayFactory
DataDump - Class in etomica.data: DataPump acts both as a DataSink and a DataSource.
DataDump() - Constructor for class etomica.data.DataDump
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.DataInfoFunction(String, Dimension, DataSourceIndependent) - Constructor for class etomica.data.types.DataFunction.DataInfoFunction
DataFunction.DataInfoFunctionFactory - Class in etomica.data.types
DataFunction.DataInfoFunctionFactory(DataFunction.DataInfoFunction) - Constructor for class etomica.data.types.DataFunction.DataInfoFunctionFactory
dataGroup - Variable in class etomica.data.AccumulatorAverage
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.DataInfoGroup(String, Dimension, IEtomicaDataInfo[]) - Constructor for class etomica.data.types.DataGroup.DataInfoGroup
DataGroup.DataInfoGroupFactory - Class in etomica.data.types
DataGroup.DataInfoGroupFactory(DataGroup.DataInfoGroup) - Constructor for class etomica.data.types.DataGroup.DataInfoGroupFactory
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.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.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
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
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.
dataInfoGroup - Variable in class etomica.data.DataGroupSplitter
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
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.
DataSet.DataSetSink(DataSet.DataCasterJudge, DataSet) - Constructor for class etomica.data.DataSet.DataSetSink
DataSetListener - Interface in etomica.data: Interface for a class that performs some action in response to a change in a DataSet instance.
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.
dataSinkList - Variable in class etomica.data.DataFork
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
DataSinkTable.DataCasterJudgeTable() - Constructor for class etomica.data.DataSinkTable.DataCasterJudgeTable
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.
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
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
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.
DataSourceUniform.LimitType(String) - Constructor for class etomica.data.DataSourceUniform.LimitType
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
DataStreamAction - Class in etomica.data
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