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A

A(double) - Method in class etomica.modules.adsorption.EOSSWPatel
 
a - Variable in class etomica.modules.rheology.IntegratorPolymer
 
A1(double) - Method in class etomica.modules.adsorption.EOSSWPatel
 
AAbonded - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibrium
 
ABbonded - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
 
ABbonded - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibrium
 
ac - Variable in class etomica.modules.multiharmonic.DataProcessorBounds
 
ac - Variable in class etomica.modules.multiharmonic.DataProcessorVar
 
acc - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceBias
 
accept(IAtom) - Method in class etomica.modules.chainequilibrium.AtomFilterChainLength
 
accept(IMolecule) - Method in class etomica.modules.chainequilibrium.AtomFilterChainLength
 
accept(IAtomList) - Method in class etomica.modules.colloid.ColloidSim.CriterionNone
 
accept(IAtom) - Method in class etomica.modules.droplet.AtomFilterLiquid
 
accept(IMolecule) - Method in class etomica.modules.droplet.AtomFilterLiquid
 
accept(IAtom) - Method in class etomica.modules.droplet.AtomFilterLiquidAtomic
 
accept(IMolecule) - Method in class etomica.modules.droplet.AtomFilterLiquidAtomic
 
accept(IAtomList) - Method in class etomica.modules.pistoncylinder.ApiFilteredCylinder.AtomFilterInCylinder
 
accept(IAtomList) - Method in class etomica.modules.render.RenderMD.CriterionCar
 
accept(IAtomList) - Method in class etomica.modules.sam.CriterionTether3
 
acceptNotify() - Method in class etomica.modules.adsorption.MyMCMove
 
acceptNotify() - Method in class etomica.modules.dcvgcmd.MyMCMove
 
acceptNotify() - Method in class etomica.modules.entropylottery.MCMoveAtomAdjacent
Method called by IntegratorMC in the event that the most recent trial is accepted.
acceptNotify() - Method in class etomica.modules.multiharmonic.MCMoveMultiHarmonic
 
accRefUa2 - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceUa2
 
accTargetUa2 - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceUa2
 
accumulator - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicMC
 
accumulator1 - Variable in class etomica.modules.dcvgcmd.DCVGCMD
 
accumulator2 - Variable in class etomica.modules.dcvgcmd.DCVGCMD
 
AccumulatorOverlapAverageUa2 - Class in etomica.modules.multiharmonic.overlap
Accumulator for taking ratio between two sums (and pretend it's an "average") Data added to this accumulator must be a 2-element DataDoubleArray
AccumulatorOverlapAverageUa2(int, boolean) - Constructor for class etomica.modules.multiharmonic.overlap.AccumulatorOverlapAverageUa2
 
ActionMoveWall(DeviceSlider, Sam, IAction) - Constructor for class etomica.modules.sam.SamGraphic.ActionMoveWall
 
actionPerformed(ActionEvent) - Method in class etomica.modules.clustergenerator.MyApplet.Starter
 
actionPerformed(ActionEvent) - Method in class etomica.modules.clustergenerator.MyApplet.Stopper
 
actionPerformed() - Method in class etomica.modules.colloid.ColloidGraphic.GraftAction
 
actionPerformed() - Method in class etomica.modules.entropylottery.DataSourceProbabilityDensity
 
actionPerformed() - Method in class etomica.modules.pistoncylinder.ActionPistonUpdate
 
actionPerformed() - Method in class etomica.modules.sam.SamGraphic.ActionMoveWall
 
ActionPistonUpdate - Class in etomica.modules.pistoncylinder
Action that informs the integrator that some property of the piston has changed (pressure, mass, velocity)
ActionPistonUpdate(IntegratorHardPiston) - Constructor for class etomica.modules.pistoncylinder.ActionPistonUpdate
 
activityIntegrate - Variable in class etomica.modules.adsorption.Adsorption
 
activityIntegrate - Variable in class etomica.modules.catalysis.Catalysis
 
activityIntegrate - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
 
activityIntegrate - Variable in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
 
activityIntegrate - Variable in class etomica.modules.colloid.ColloidSim
 
activityIntegrate - Variable in class etomica.modules.dcvgcmd.DCVGCMD
 
activityIntegrate - Variable in class etomica.modules.droplet.Droplet
 
activityIntegrate - Variable in class etomica.modules.droplet.DropletAtomic
 
activityIntegrate - Variable in class etomica.modules.ensembles.LJMC
 
activityIntegrate - Variable in class etomica.modules.entropylottery.EntropyLottery
 
activityIntegrate - Variable in class etomica.modules.insertion.Insertion
 
activityIntegrate - Variable in class etomica.modules.interfacial.InterfacialSW
 
activityIntegrate - Variable in class etomica.modules.ljmd.Ljmd
 
activityIntegrate - Variable in class etomica.modules.mu.Mu
 
activityIntegrate - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicMC
 
activityIntegrate - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicMC
 
activityIntegrate - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicMC
 
activityIntegrate - Variable in class etomica.modules.osmosis.OsmosisSim
 
activityIntegrate - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibrium
 
activityIntegrate - Variable in class etomica.modules.render.RenderMD
 
activityIntegrate - Variable in class etomica.modules.rheology.SimulationRheology
 
activityIntegrate - Variable in class etomica.modules.rosmosis.ReverseOsmosis
 
activityIntegrate - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
 
activityIntegrate - Variable in class etomica.modules.sam.Sam
 
activityIntegrate - Variable in class etomica.modules.swmd.Swmd
 
activityIntegrate - Variable in class etomica.modules.vle.VLESim
 
addCluster(ClusterDiagram) - Method in class etomica.modules.clustergenerator.MyApplet.Starter
 
addComponent(Component, JPanel, int, int, int, int) - Method in class etomica.modules.clustergenerator.MyApplet
Componet c is added to JPanel panel following the rule of GridBagLayout manager
addRadioGroupActionListener(ActionListener) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
Add the specified listener to the list of listeners that will get invoked when the isothermal or adiabatic radio button is pushed.
addStateChangedListener(ChangeListener) - Method in class etomica.modules.osmosis.Osmosis.InitializeMolecules
 
addTemperatureSliderListener(ChangeListener) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
Add the specified listener to the list of listeners that will get invoked when the temperature slider value changes.
addTensor(int, Tensor) - Method in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
Adds the given contribution to the virial sum for bin iBin.
Adsorption - Class in etomica.modules.adsorption
Simulation for Adsorption module.
Adsorption(ISpace) - Constructor for class etomica.modules.adsorption.Adsorption
 
AdsorptionGraphic - Class in etomica.modules.adsorption
Catalysis graphical app.
AdsorptionGraphic(Adsorption, ISpace) - Constructor for class etomica.modules.adsorption.AdsorptionGraphic
 
AdsorptionGraphic.Applet - Class in etomica.modules.adsorption
 
advanceAcrossTimeStep(double) - Method in class etomica.modules.pistoncylinder.IntegratorHardPiston
 
affectedAtomIterator - Variable in class etomica.modules.entropylottery.MCMoveAtomAdjacent
 
affectedAtoms() - Method in class etomica.modules.entropylottery.MCMoveAtomAdjacent
 
affectedAtoms() - Method in class etomica.modules.multiharmonic.MCMoveMultiHarmonic
 
agentManager - Variable in class etomica.modules.catalysis.ColorSchemeRadical
 
agentManager - Variable in class etomica.modules.catalysis.ConfigurationCatalysis
 
agentManager - Variable in class etomica.modules.catalysis.InteractionTracker
 
agentManager - Variable in class etomica.modules.catalysis.P2SquareWellBonding
 
agentManager - Variable in class etomica.modules.catalysis.P2SquareWellBondingCO
 
agentManager - Variable in class etomica.modules.catalysis.P2SquareWellSurface
 
agentManager - Variable in class etomica.modules.chainequilibrium.AtomFilterChainLength
 
agentManager - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
 
agentManager - Variable in class etomica.modules.chainequilibrium.ColorSchemeRadical
 
agentManager - Variable in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
 
agentManager - Variable in class etomica.modules.chainequilibrium.MeterChainLength
 
agentManager - Variable in class etomica.modules.chainequilibrium.MeterConversion
 
agentManager - Variable in class etomica.modules.chainequilibrium.P2SquareWellBonded
 
agentManager - Variable in class etomica.modules.chainequilibrium.P2SquareWellRadical
 
agentManager - Variable in class etomica.modules.droplet.AtomFilterLiquidAtomic
 
agentManager - Variable in class etomica.modules.droplet.IntegratorDroplet
 
agentManager - Variable in class etomica.modules.reactionequilibrium.MeterDimerFraction
 
agentManager - Variable in class etomica.modules.reactionequilibrium.P2SquareWellBonded
 
agentManager - Variable in class etomica.modules.rosmosis.MeterFlux
 
agentManager - Variable in class etomica.modules.rosmosis.P1Tether
 
agents - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibrium
 
ai - Variable in class etomica.modules.pistoncylinder.PistonCylinder
 
akima - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSinkReweightedDeltaU
 
akima - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
 
akima - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceBias
 
allAtoms - Variable in class etomica.modules.droplet.IntegratorDroplet
 
allData - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
 
allData - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceBias
 
allDone() - Method in class etomica.modules.clustergenerator.MyApplet.Starter
 
allLnAlpha - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
 
allLnAlpha - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceBias
 
allPermutations - Variable in class etomica.modules.clustergenerator.MyApplet
 
allPermutationsCB - Variable in class etomica.modules.clustergenerator.MyApplet
 
alpha - Variable in class etomica.modules.adsorption.EOSSWPatel
 
alpha - Variable in class etomica.modules.multiharmonic.mbar.MeterMBAR
 
alpha - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
 
alpha - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceBias
 
alpha - Variable in class etomica.modules.multiharmonic.umbrella.MeterUmbrella
 
alphaCenter - Variable in class etomica.modules.multiharmonic.mbar.MeterMBAR
 
alphaCenter - Variable in class etomica.modules.multiharmonic.overlap.AccumulatorOverlapAverageUa2
 
alphaChoice - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC
 
alphaData - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceAlphaChi
 
alphaData - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaAlpha
 
alphaData - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaChi
 
alphaData - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaAlpha
 
alphaData - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaChi
 
alphaFac - Variable in class etomica.modules.multiharmonic.umbrella.MeterUmbrella
 
alphaInfo - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceAlphaChi
 
alphaInfo - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaAlpha
 
alphaInfo - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaChi
 
alphaInfo - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaAlpha
 
alphaInfo - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaChi
 
alphaSource - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSinkReweightedDeltaU
 
alphaSource - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
 
alphaSource - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceBias
 
alphaSpan - Variable in class etomica.modules.multiharmonic.mbar.MeterMBAR
 
alphaSpan - Variable in class etomica.modules.multiharmonic.overlap.AccumulatorOverlapAverageUa2
 
alphaTag - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceAlphaChi
 
alphaTag - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaAlpha
 
alphaTag - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaChi
 
alphaTag - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaAlpha
 
alphaTag - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaChi
 
anglePanel - Variable in class etomica.modules.crystalviewer.LatticeEditor
 
aNumber - Variable in class etomica.modules.materialfracture.MeterElongation
 
aNumber - Variable in class etomica.modules.materialfracture.MeterStrain
 
ApiFilteredCylinder - Class in etomica.modules.pistoncylinder
Our own ApiFiltered that's box-dependent
ApiFilteredCylinder(ApiFilteredCylinder.AtomFilterInCylinder) - Constructor for class etomica.modules.pistoncylinder.ApiFilteredCylinder
 
ApiFilteredCylinder.AtomFilterInCylinder - Class in etomica.modules.pistoncylinder
Filter to expclude any pair with an atom within some distance from a wall.
Applet() - Constructor for class etomica.modules.adsorption.AdsorptionGraphic.Applet
 
Applet() - Constructor for class etomica.modules.catalysis.CatalysisGraphic.Applet
 
Applet() - Constructor for class etomica.modules.chainequilibrium.ChainEquilibriumGraphic.Applet
 
Applet() - Constructor for class etomica.modules.chainequilibrium.FreeRadicalPolymerizationGraphic.Applet
 
Applet() - Constructor for class etomica.modules.colloid.ColloidGraphic.Applet
 
Applet() - Constructor for class etomica.modules.crystalviewer.CrystalViewer.Applet
 
Applet() - Constructor for class etomica.modules.dcvgcmd.DCVGCMDGraphic.Applet
 
Applet() - Constructor for class etomica.modules.droplet.DropletAtomicGraphic.Applet
 
Applet() - Constructor for class etomica.modules.droplet.DropletGraphic.Applet
 
Applet() - Constructor for class etomica.modules.ensembles.LJMCGraphic.Applet
 
Applet() - Constructor for class etomica.modules.entropylottery.EntropyLotteryGraphic.Applet
 
Applet() - Constructor for class etomica.modules.insertion.InsertionGraphic.Applet
 
Applet() - Constructor for class etomica.modules.interfacial.InterfacialSWGraphic.Applet
 
Applet() - Constructor for class etomica.modules.joulethomson.JouleThomson.Applet
 
Applet() - Constructor for class etomica.modules.ljmd.LjmdGraphic.Applet
 
Applet() - Constructor for class etomica.modules.materialfracture.MaterialFractureGraphic.Applet
 
Applet() - Constructor for class etomica.modules.mu.MuGraphic.Applet
 
Applet() - Constructor for class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.Applet
 
Applet() - Constructor for class etomica.modules.multiharmonic.MultiharmonicGraphic.Applet
 
Applet() - Constructor for class etomica.modules.multiharmonic.MultiharmonicGraphicMC.Applet
 
Applet() - Constructor for class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.Applet
 
Applet() - Constructor for class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.Applet
 
Applet() - Constructor for class etomica.modules.osmosis.Osmosis.Applet
 
Applet() - Constructor for class etomica.modules.pistoncylinder.PistonCylinderGraphic.Applet
 
Applet() - Constructor for class etomica.modules.reactionequilibrium.ReactionEquilibriumGraphic.Applet
 
Applet() - Constructor for class etomica.modules.rheology.RheologyGraphic.Applet
 
Applet() - Constructor for class etomica.modules.rosmosis.ReverseOsmosisGraphic.Applet
 
Applet() - Constructor for class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.Applet
 
Applet() - Constructor for class etomica.modules.sam.SamGraphic.Applet
 
Applet() - Constructor for class etomica.modules.swmd.SwmdGraphic.Applet
 
Applet() - Constructor for class etomica.modules.vle.B2Fit.Applet
 
Applet() - Constructor for class etomica.modules.vle.VLE.Applet
 
areBonded(IAtom, IAtom) - Method in class etomica.modules.chainequilibrium.P2SquareWellBonded
This function tells you if two atoms are bonded This could probably be public, although a public version would need to first re-retrieve agents
areBonded(IAtom, IAtom) - Method in class etomica.modules.chainequilibrium.P2SquareWellRadical
This function tells you if two atoms are bonded
atom - Variable in class etomica.modules.entropylottery.MCMoveAtomAdjacent
 
atomColor - Variable in class etomica.modules.crystalviewer.ClipPlaneEditor
 
atomCount - Variable in class etomica.modules.entropylottery.MeterEntropy
 
AtomFilterChainLength - Class in etomica.modules.chainequilibrium
 
AtomFilterChainLength(AtomLeafAgentManager<IAtom[]>) - Constructor for class etomica.modules.chainequilibrium.AtomFilterChainLength
 
AtomFilterChainLength.LengthAgent - Class in etomica.modules.chainequilibrium
 
AtomFilterInCylinder(IBoundary, P1HardMovingBoundary, double) - Constructor for class etomica.modules.pistoncylinder.ApiFilteredCylinder.AtomFilterInCylinder
 
AtomFilterLiquid - Class in etomica.modules.droplet
 
AtomFilterLiquid(ISpace, IDataSource) - Constructor for class etomica.modules.droplet.AtomFilterLiquid
 
AtomFilterLiquidAtomic - Class in etomica.modules.droplet
 
AtomFilterLiquidAtomic(PotentialMasterList, IBox) - Constructor for class etomica.modules.droplet.AtomFilterLiquidAtomic
 
atomIterator - Variable in class etomica.modules.entropylottery.DataSourceProbabilityDensity
 
atomNumber - Variable in class etomica.modules.materialfracture.StrainColorScheme
 
atomNumberMod - Variable in class etomica.modules.materialfracture.StrainColorScheme
 
atomSetSinglet - Variable in class etomica.modules.pistoncylinder.IntegratorHardPiston
 
atomSource - Variable in class etomica.modules.entropylottery.MCMoveAtomAdjacent
 
AtomTag() - Constructor for class etomica.modules.chainequilibrium.MeterChainLength.AtomTag
 
AVG - Static variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
 
AVG - Static variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceBias
 
axis - Variable in class etomica.modules.droplet.AtomFilterLiquid
 
axis - Variable in class etomica.modules.droplet.ConfigurationDroplet
 

B

b - Variable in class etomica.modules.rheology.IntegratorPolymer
 
B2 - Variable in class etomica.modules.adsorption.VEOS3SW
 
B2(double, double) - Static method in class etomica.modules.vle.LJQB2
Returns B2 for the LJ+quadrupole model.
B2Fit - Class in etomica.modules.vle
 
B2Fit() - Constructor for class etomica.modules.vle.B2Fit
 
B2Fit.Applet - Class in etomica.modules.vle
 
B2Fit.FunctionB2LJQ - Class in etomica.modules.vle
Function using LJQB2 to evaluate B2 as a function of Q, epsilon, sigma and T.
B2Fit.FunctionMayerB2LJQ - Class in etomica.modules.vle
Function using Mayer sampling to evaluate B2 as a function of Q, epsilon, sigma and T.
B2Hash - Variable in class etomica.modules.vle.B2Fit.FunctionMayerB2LJQ
 
B3 - Variable in class etomica.modules.adsorption.VEOS3SW
 
b45 - Variable in class etomica.modules.sam.P1Sinusoidal
 
basisMolecules - Variable in class etomica.modules.sam.ConfigurationSAM
 
BasisOrthorhombicHexagonal3D(ISpace) - Constructor for class etomica.modules.catalysis.ConfigurationCatalysis.BasisOrthorhombicHexagonal3D
Makes a fcc 4-atom basis.
basisSurface - Variable in class etomica.modules.sam.ConfigurationSAM
 
BBbonded - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibrium
 
BCC - Variable in class etomica.modules.junit.crystalviewer.LatticePlaneTestUtility
 
BIAS - Static variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
 
BIAS - Static variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceBias
 
binSize - Variable in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
 
blankPanel - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
 
BLCPrimitiveHexagonalLatticePlaneTest - Class in etomica.modules.junit.crystalviewer
 
BLCPrimitiveHexagonalLatticePlaneTest(String) - Constructor for class etomica.modules.junit.crystalviewer.BLCPrimitiveHexagonalLatticePlaneTest
 
BLCPrimitiveHexagonalLatticePlaneTest.DoubleTwoDArray - Class in etomica.modules.junit.crystalviewer
 
BLCPrimitiveMonoclinicLatticePlaneTest - Class in etomica.modules.junit.crystalviewer
 
BLCPrimitiveMonoclinicLatticePlaneTest(String) - Constructor for class etomica.modules.junit.crystalviewer.BLCPrimitiveMonoclinicLatticePlaneTest
 
BLCPrimitiveMonoclinicLatticePlaneTest.DoubleTwoDArray - Class in etomica.modules.junit.crystalviewer
 
BLCPrimitiveOrthorhombicLatticePlaneTest - Class in etomica.modules.junit.crystalviewer
 
BLCPrimitiveOrthorhombicLatticePlaneTest(String) - Constructor for class etomica.modules.junit.crystalviewer.BLCPrimitiveOrthorhombicLatticePlaneTest
 
BLCPrimitiveOrthorhombicLatticePlaneTest.DoubleTwoDArray - Class in etomica.modules.junit.crystalviewer
 
BLCPrimitiveTetragonalLatticePlaneTest - Class in etomica.modules.junit.crystalviewer
 
BLCPrimitiveTetragonalLatticePlaneTest(String) - Constructor for class etomica.modules.junit.crystalviewer.BLCPrimitiveTetragonalLatticePlaneTest
 
BLCPrimitiveTetragonalLatticePlaneTest.DoubleTwoDArray - Class in etomica.modules.junit.crystalviewer
 
BLCPrimitiveTriclinicLatticePlaneTest - Class in etomica.modules.junit.crystalviewer
 
BLCPrimitiveTriclinicLatticePlaneTest(String) - Constructor for class etomica.modules.junit.crystalviewer.BLCPrimitiveTriclinicLatticePlaneTest
 
BLCPrimitiveTriclinicLatticePlaneTest.DoubleTwoDArray - Class in etomica.modules.junit.crystalviewer
 
blockCounter - Variable in class etomica.modules.multiharmonic.overlap.AccumulatorOverlapAverageUa2
 
bond(IAtom, IAtom) - Method in class etomica.modules.chainequilibrium.P2SquareWellBonded
this function will bond atoms a & b together
bond(IAtom, IAtom) - Method in class etomica.modules.chainequilibrium.P2SquareWellRadical
this function will bond atoms a & b together
bondCount - Variable in class etomica.modules.chainequilibrium.P2SquareWellBonded.RingResult
 
bondedAtom1 - Variable in class etomica.modules.catalysis.InteractionTracker.CatalysisAgent
 
bondedAtom2 - Variable in class etomica.modules.catalysis.InteractionTracker.CatalysisAgent
 
bondedSet - Variable in class etomica.modules.render.RenderMD.CriterionCar
 
bondFac - Variable in class etomica.modules.colloid.P2HardSphereMC
 
bondFac - Variable in class etomica.modules.colloid.P2SquareWellMonomer
 
BondInfo(int, int, double) - Constructor for class etomica.modules.render.ParseObj.BondInfo
 
bondingAgentManager - Variable in class etomica.modules.chainequilibrium.ColorSchemeStepWise
 
BondInteractionTypeToggler() - Constructor for class etomica.modules.clustergenerator.MyApplet.BondInteractionTypeToggler
 
bondL_CC - Variable in class etomica.modules.sam.Sam
 
bondList - Variable in class etomica.modules.render.ParseObj
 
bondManager - Variable in class etomica.modules.colloid.P2HardSphereMC
 
bondManager - Variable in class etomica.modules.colloid.P2SquareWellMonomer
 
bondManager - Variable in class etomica.modules.sam.CriterionTether3
 
bondMap - Variable in class etomica.modules.render.RenderMD.P2PenetrableCar
 
bondTheta - Variable in class etomica.modules.sam.Sam
 
bondTypeToggler - Variable in class etomica.modules.clustergenerator.MyApplet
 
BondTypeToggler() - Constructor for class etomica.modules.clustergenerator.MyApplet.BondTypeToggler
 
bothSides - Variable in class etomica.modules.adsorption.MyMCMove
 
boundaries - Variable in class etomica.modules.rosmosis.MeterFlux
 
boundary - Variable in class etomica.modules.adsorption.P1Wall
 
boundary - Variable in class etomica.modules.colloid.P1Wall
 
boundary - Variable in class etomica.modules.interfacial.MeterOrientation
 
boundaryCoefficients - Variable in class etomica.modules.rosmosis.MeterFlux
 
boundaryHardA - Variable in class etomica.modules.osmosis.OsmosisSim
 
boundaryHardB - Variable in class etomica.modules.osmosis.OsmosisSim
 
BoundaryPistonCylinder - Class in etomica.modules.pistoncylinder
Boundary class for PistonCylinder that accounts for the piston and collision radius when calculating the (available) volume
BoundaryPistonCylinder(ISpace) - Constructor for class etomica.modules.pistoncylinder.BoundaryPistonCylinder
 
boundarySemiB - Variable in class etomica.modules.osmosis.OsmosisSim
 
box - Variable in class etomica.modules.adsorption.Adsorption
 
box - Variable in class etomica.modules.adsorption.MeterExcessAdsorbed
 
box - Variable in class etomica.modules.catalysis.Catalysis
 
box - Variable in class etomica.modules.catalysis.MeterDensityCO
 
box - Variable in class etomica.modules.catalysis.MeterDensityCO2
 
box - Variable in class etomica.modules.catalysis.MeterDensityO2
 
box - Variable in class etomica.modules.chainequilibrium.AtomFilterChainLength
 
box - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
 
box - Variable in class etomica.modules.chainequilibrium.ColorSchemeRadical
 
box - Variable in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
 
box - Variable in class etomica.modules.chainequilibrium.MeterChainLength
 
box - Variable in class etomica.modules.chainequilibrium.MeterConversion
 
box - Variable in class etomica.modules.chainequilibrium.P2SquareWellBonded
 
box - Variable in class etomica.modules.colloid.ColloidSim
 
box - Variable in class etomica.modules.colloid.MeterEnd2End
 
box - Variable in class etomica.modules.crystalviewer.CrystalViewer
 
box - Variable in class etomica.modules.crystalviewer.LatticeEditor
 
box - Variable in class etomica.modules.dcvgcmd.DCVGCMD
 
box - Variable in class etomica.modules.droplet.Droplet
 
box - Variable in class etomica.modules.droplet.DropletAtomic
 
box - Variable in class etomica.modules.droplet.DropletGraphic.ModifierBoxSize
 
box - Variable in class etomica.modules.droplet.MeterDeformation
 
box - Variable in class etomica.modules.ensembles.LJMC
 
box - Variable in class etomica.modules.entropylottery.DataSourceProbabilityDensity
 
box - Variable in class etomica.modules.entropylottery.EntropyLottery
 
box - Variable in class etomica.modules.entropylottery.MeterEntropy
 
box - Variable in class etomica.modules.insertion.Insertion
 
box - Variable in class etomica.modules.interfacial.DataProcessorInterfacialTensionProfile
 
box - Variable in class etomica.modules.interfacial.InterfacialSW
 
box - Variable in class etomica.modules.interfacial.InterfacialSWGraphic.ModifierBoxSize
 
box - Variable in class etomica.modules.ljmd.Ljmd
 
box - Variable in class etomica.modules.materialfracture.MaterialFracture
 
box - Variable in class etomica.modules.materialfracture.MeterElongation
 
box - Variable in class etomica.modules.materialfracture.MeterLoad
 
box - Variable in class etomica.modules.materialfracture.MeterStrain
 
box - Variable in class etomica.modules.materialfracture.MeterStress
 
box - Variable in class etomica.modules.materialfracture.P1Tension
 
box - Variable in class etomica.modules.materialfracture.StrainColorScheme
 
box - Variable in class etomica.modules.mu.MeterDensitySides
 
box - Variable in class etomica.modules.mu.Mu
 
box - Variable in class etomica.modules.mu.MuGraphic.DataSinkExcludeOverlap
 
box - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicMC
 
box - Variable in class etomica.modules.osmosis.OsmosisSim
 
box - Variable in class etomica.modules.pistoncylinder.PistonCylinder
 
box - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibrium
 
box - Variable in class etomica.modules.render.RenderMD
The Box holding the atoms.
box - Variable in class etomica.modules.rheology.MeterEndToEnd
 
box - Variable in class etomica.modules.rheology.MeterNormalStress
 
box - Variable in class etomica.modules.rheology.MeterViscosity
 
box - Variable in class etomica.modules.rheology.SimulationRheology
 
box - Variable in class etomica.modules.rosmosis.MeterFlux
 
box - Variable in class etomica.modules.rosmosis.MeterOsmoticPressure
 
box - Variable in class etomica.modules.rosmosis.ReverseOsmosis
 
box - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic.DataSinkExcludeOverlap
 
box - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
 
box - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.DataSinkExcludeOverlap
 
box - Variable in class etomica.modules.sam.CriterionTether3
 
box - Variable in class etomica.modules.sam.MeterTilt
 
box - Variable in class etomica.modules.sam.MeterWallPressure
 
box - Variable in class etomica.modules.sam.Sam
 
box - Variable in class etomica.modules.swmd.Swmd
 
box - Variable in class etomica.modules.vle.MeterPressure2
 
boxA - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicMC
 
boxA - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicMC
 
boxB - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicMC
 
boxB - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicMC
 
boxDim - Variable in class etomica.modules.entropylottery.ModifierDimensions
 
boxH - Variable in class etomica.modules.crystalviewer.ClipPlaneEditor
 
boxK - Variable in class etomica.modules.crystalviewer.ClipPlaneEditor
 
boxL - Variable in class etomica.modules.crystalviewer.ClipPlaneEditor
 
boxLiquid - Variable in class etomica.modules.vle.VLESim
 
boxPanel - Variable in class etomica.modules.crystalviewer.LatticeEditor
 
boxVapor - Variable in class etomica.modules.vle.VLESim
 
broken - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceFE
 
bump(IAtomList, double) - Method in class etomica.modules.adsorption.P1Wall
 
bump(IAtomList, double) - Method in class etomica.modules.catalysis.P2SquareWellBonding
Implements collision dynamics between two square-well atoms.
bump(IAtomList, double) - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
Implements collision dynamics between two square-well atoms.
bump(IAtomList, double) - Method in class etomica.modules.catalysis.P2SquareWellSurface
Implements collision dynamics between two square-well atoms.
bump(IAtomList, double) - Method in class etomica.modules.chainequilibrium.P2SquareWellBonded
 
bump(IAtomList, double) - Method in class etomica.modules.chainequilibrium.P2SquareWellRadical
 
bump(IAtomList, double) - Method in class etomica.modules.colloid.P1Wall
 
bump(IAtomList, double) - Method in class etomica.modules.mu.P1MagicWall
 
bump(IAtomList, double) - Method in class etomica.modules.mu.P2SquareWellOneSide
Implements collision dynamics between two square-well atoms.
bump(IAtomList, double) - Method in class etomica.modules.osmosis.P1HardWall
 
bump(IAtomList, double) - Method in class etomica.modules.reactionequilibrium.P2SquareWellBonded
 
bump(IAtomList, double) - Method in class etomica.modules.render.RenderMD.P2PenetrableCar
 

C

c1 - Variable in class etomica.modules.adsorption.EOSSWPatel
 
c2 - Variable in class etomica.modules.adsorption.EOSSWPatel
 
c3 - Variable in class etomica.modules.adsorption.EOSSWPatel
 
calcB2(double, double) - Static method in class etomica.modules.vle.VirialLJQB2
 
calcConversion(IMoleculeList) - Method in class etomica.modules.chainequilibrium.MeterConversion
 
calcGageLength() - Method in class etomica.modules.materialfracture.MeterElongation
 
calcGageLength() - Method in class etomica.modules.materialfracture.MeterStrain
 
callCount - Variable in class etomica.modules.multiharmonic.mbar.MeterMBAR
 
Catalysis - Class in etomica.modules.catalysis
Simulation for Catalysis module.
Catalysis(ISpace, int) - Constructor for class etomica.modules.catalysis.Catalysis
 
CatalysisAgent() - Constructor for class etomica.modules.catalysis.InteractionTracker.CatalysisAgent
 
CatalysisGraphic - Class in etomica.modules.catalysis
Catalysis graphical app.
CatalysisGraphic(Catalysis, ISpace, boolean) - Constructor for class etomica.modules.catalysis.CatalysisGraphic
 
CatalysisGraphic.Applet - Class in etomica.modules.catalysis
 
cellSizeX - Variable in class etomica.modules.catalysis.ConfigurationCatalysis
 
cellSizeX - Variable in class etomica.modules.sam.ConfigurationSAM
 
cellSizeZ - Variable in class etomica.modules.catalysis.ConfigurationCatalysis
 
cellSizeZ - Variable in class etomica.modules.sam.ConfigurationSAM
 
center - Variable in class etomica.modules.crystalviewer.CrystalViewer
 
center - Variable in class etomica.modules.droplet.ConfigurationDroplet
 
center - Variable in class etomica.modules.droplet.MeterDeformation
 
center - Variable in class etomica.modules.rheology.IntegratorPolymer
 
centerAtomColor - Variable in class etomica.modules.materialfracture.StrainColorScheme
 
ChainEquilibriumGraphic - Class in etomica.modules.chainequilibrium
Module for chain reaction (polymerization) using ChainEquilibriumSim as the simulation class.
ChainEquilibriumGraphic(ChainEquilibriumSim, ISpace) - Constructor for class etomica.modules.chainequilibrium.ChainEquilibriumGraphic
 
ChainEquilibriumGraphic.Applet - Class in etomica.modules.chainequilibrium
 
ChainEquilibriumSim - Class in etomica.modules.chainequilibrium
 
ChainEquilibriumSim(ISpace) - Constructor for class etomica.modules.chainequilibrium.ChainEquilibriumSim
 
chainLength - Variable in class etomica.modules.chainequilibrium.AtomFilterChainLength.LengthAgent
 
chainLength - Variable in class etomica.modules.colloid.ColloidSim
 
chainLength - Variable in class etomica.modules.colloid.ConfigurationColloid
 
chainLength - Variable in class etomica.modules.colloid.MeterEnd2End
 
chainLength - Variable in class etomica.modules.colloid.NeighborListManagerColloid
 
chainLength - Variable in class etomica.modules.sam.Sam
 
chainLengthManager - Variable in class etomica.modules.chainequilibrium.AtomFilterChainLength
 
chainLengthManager - Variable in class etomica.modules.chainequilibrium.ColorSchemeRadical
 
chainNumber - Variable in class etomica.modules.chainequilibrium.ColorSchemeRadical.LengthAgent
 
chainPhi - Variable in class etomica.modules.sam.Sam
 
chainPsi - Variable in class etomica.modules.sam.Sam
 
chainTheta - Variable in class etomica.modules.sam.Sam
 
changeBox() - Method in class etomica.modules.crystalviewer.LatticeEditor
 
checkBox - Variable in class etomica.modules.clustergenerator.MyApplet
 
checkBox1 - Variable in class etomica.modules.clustergenerator.MyApplet
 
checkBox2 - Variable in class etomica.modules.clustergenerator.MyApplet
 
checkRing(IAtom, IAtom, int) - Method in class etomica.modules.chainequilibrium.P2SquareWellBonded
this function will bond atoms a & b together
chiData - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceAlphaChi
 
chiData - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaAlpha
 
chiData - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaChi
 
chiData - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaAlpha
 
chiData - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaChi
 
chiInfo - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceAlphaChi
 
chiInfo - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaAlpha
 
chiInfo - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaChi
 
chiInfo - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaAlpha
 
chiInfo - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaChi
 
chiTag - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceAlphaChi
 
chiTag - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaAlpha
 
chiTag - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaChi
 
chiTag - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaAlpha
 
chiTag - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaChi
 
circle(double, double, double, double) - Method in class etomica.modules.clustergenerator.Plot
 
clear() - Method in class etomica.modules.clustergenerator.Plot
Clears the plot.
ClipPlaneEditor - Class in etomica.modules.crystalviewer
Class that produces a panel with controls that presence, orientation and position of a plane that clips atoms from the display.
ClipPlaneEditor(ISimulation, LatticePlane, DisplayBox) - Constructor for class etomica.modules.crystalviewer.ClipPlaneEditor
 
clipPlaneEditor - Variable in class etomica.modules.crystalviewer.CrystalViewer
 
cluster - Variable in class etomica.modules.clustergenerator.MyApplet
 
ClusterPanel - Class in etomica.modules.clustergenerator
 
ClusterPanel(ClusterDiagram, boolean, boolean, boolean, boolean, boolean) - Constructor for class etomica.modules.clustergenerator.ClusterPanel
 
collisionAction(IntegratorHard.Agent) - Method in class etomica.modules.catalysis.DataSourceWallPressureCatalysis
Implementation of CollisionListener interface Adds collision virial (from potential) to accumulator
collisionAction(IntegratorHard.Agent) - Method in class etomica.modules.catalysis.InteractionTracker
 
collisionAction(IntegratorHard.Agent) - Method in class etomica.modules.insertion.InsertionGraphic.MeterWidom
 
collisionAction(IntegratorHard.Agent) - Method in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
Sums contribution to virial for each collision.
collisionAction(IntegratorHard.Agent) - Method in class etomica.modules.mu.DataSourceWallPressureMu
Implementation of CollisionListener interface Adds collision virial (from potential) to accumulator
collisionAction(IntegratorHard.Agent) - Method in class etomica.modules.osmosis.MeterOsmoticPressure
 
collisionAction(IntegratorHard.Agent) - Method in class etomica.modules.pistoncylinder.DataSourceWallPressure
Implementation of CollisionListener interface Adds collision virial (from potential) to accumulator
collisionTime(IAtomList, double) - Method in class etomica.modules.adsorption.P1Wall
 
collisionTime(IAtomList, double) - Method in class etomica.modules.catalysis.P2SquareWellBonding
Computes next time of collision of two square-well atoms, assuming free-flight kinematics.
collisionTime(IAtomList, double) - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
Computes next time of collision of two square-well atoms, assuming free-flight kinematics.
collisionTime(IAtomList, double) - Method in class etomica.modules.catalysis.P2SquareWellSurface
Computes next time of collision of two square-well atoms, assuming free-flight kinematics.
collisionTime(IAtomList, double) - Method in class etomica.modules.chainequilibrium.P2SquareWellBonded
Computes next time of collision of the two atoms, assuming free-flight kinematics.
collisionTime(IAtomList, double) - Method in class etomica.modules.chainequilibrium.P2SquareWellRadical
Computes next time of collision of the two atoms, assuming free-flight kinematics.
collisionTime(IAtomList, double) - Method in class etomica.modules.colloid.P1Wall
 
collisionTime(IAtomList, double) - Method in class etomica.modules.colloid.P2HardSphereMC
Computes next time of collision of two square-well atoms, assuming free-flight kinematics.
collisionTime(IAtomList, double) - Method in class etomica.modules.colloid.P2SquareWellMonomer
Computes next time of collision of two square-well atoms, assuming free-flight kinematics.
collisionTime(IAtomList, double) - Method in class etomica.modules.mu.P1MagicWall
 
collisionTime(IAtomList, double) - Method in class etomica.modules.mu.P2SquareWellOneSide
Computes next time of collision of two square-well atoms, assuming free-flight kinematics.
collisionTime(IAtomList, double) - Method in class etomica.modules.osmosis.P1HardWall
 
collisionTime(IAtomList, double) - Method in class etomica.modules.reactionequilibrium.P2SquareWellBonded
Computes next time of collision of the two atoms, assuming free-flight kinematics.
collisionTime(IAtomList, double) - Method in class etomica.modules.render.RenderMD.P2PenetrableCar
 
colloidDensityProfileMeter - Variable in class etomica.modules.colloid.ColloidGraphic
 
ColloidGraphic - Class in etomica.modules.colloid
Colloid module app.
ColloidGraphic(ColloidSim, Space) - Constructor for class etomica.modules.colloid.ColloidGraphic
 
ColloidGraphic.Applet - Class in etomica.modules.colloid
 
ColloidGraphic.GraftAction - Class in etomica.modules.colloid
 
ColloidGraphic.WallRangeModifier - Class in etomica.modules.colloid
 
colloidMonomerBondManager - Variable in class etomica.modules.colloid.ColloidSim
 
colloidMonomerBondManager - Variable in class etomica.modules.colloid.ConfigurationColloid
 
ColloidSim - Class in etomica.modules.colloid
Colloid simulation.
ColloidSim(Space) - Constructor for class etomica.modules.colloid.ColloidSim
 
ColloidSim.CriterionNone - Class in etomica.modules.colloid
 
colorAllAtoms() - Method in class etomica.modules.chainequilibrium.ColorSchemeRadical
 
colorAllAtoms() - Method in class etomica.modules.droplet.ColorSchemeDropletSurface
 
colorAllAtoms() - Method in class etomica.modules.droplet.ColorSchemeLiquidVapor
 
colorMaps - Variable in class etomica.modules.chainequilibrium.ColorSchemeStepWise
 
colorScheme - Variable in class etomica.modules.crystalviewer.ClipPlaneEditor
 
ColorSchemeDropletSurface - Class in etomica.modules.droplet
 
ColorSchemeDropletSurface(AtomFilterCollective) - Constructor for class etomica.modules.droplet.ColorSchemeDropletSurface
 
ColorSchemeLiquidVapor - Class in etomica.modules.droplet
 
ColorSchemeLiquidVapor(AtomFilterCollective) - Constructor for class etomica.modules.droplet.ColorSchemeLiquidVapor
 
ColorSchemePlane - Class in etomica.modules.crystalviewer
Colors atoms according to whether or not they are in a plane, as determined by the inPlane method of a Plane instance.
ColorSchemePlane(LatticePlane) - Constructor for class etomica.modules.crystalviewer.ColorSchemePlane
 
ColorSchemePlane(LatticePlane, Color, Color) - Constructor for class etomica.modules.crystalviewer.ColorSchemePlane
 
ColorSchemeRadical - Class in etomica.modules.catalysis
 
ColorSchemeRadical(ISimulation, AtomLeafAgentManager) - Constructor for class etomica.modules.catalysis.ColorSchemeRadical
 
ColorSchemeRadical - Class in etomica.modules.chainequilibrium
 
ColorSchemeRadical(ISimulation, AtomLeafAgentManager<IAtom[]>) - Constructor for class etomica.modules.chainequilibrium.ColorSchemeRadical
 
ColorSchemeRadical.LengthAgent - Class in etomica.modules.chainequilibrium
 
ColorSchemeStepWise - Class in etomica.modules.chainequilibrium
Color scheme for stepwise growth, based on the AtomType (alcohol vs.
ColorSchemeStepWise(ISimulation, AtomLeafAgentManager) - Constructor for class etomica.modules.chainequilibrium.ColorSchemeStepWise
 
combinationProbability - Variable in class etomica.modules.chainequilibrium.P2SquareWellRadical
 
ComponentEventMyPanel() - Constructor for class etomica.modules.clustergenerator.MyApplet.ComponentEventMyPanel
 
componentHidden(ComponentEvent) - Method in class etomica.modules.clustergenerator.MyApplet.ComponentEventMyPanel
 
componentMoved(ComponentEvent) - Method in class etomica.modules.clustergenerator.MyApplet.ComponentEventMyPanel
 
componentResized(ComponentEvent) - Method in class etomica.modules.clustergenerator.MyApplet.ComponentEventMyPanel
 
componentShown(ComponentEvent) - Method in class etomica.modules.clustergenerator.MyApplet.ComponentEventMyPanel
 
config - Variable in class etomica.modules.catalysis.Catalysis
 
config - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
 
config - Variable in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
 
config - Variable in class etomica.modules.dcvgcmd.DCVGCMD
 
config - Variable in class etomica.modules.droplet.Droplet
 
config - Variable in class etomica.modules.materialfracture.MaterialFracture
 
config - Variable in class etomica.modules.pistoncylinder.PistonCylinder
 
config - Variable in class etomica.modules.sam.Sam
 
configButton - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
 
configMembrane - Variable in class etomica.modules.rosmosis.ReverseOsmosis
 
configMembrane - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
 
configuration - Variable in class etomica.modules.colloid.ColloidSim
 
configuration - Variable in class etomica.modules.mu.Mu
 
ConfigurationCatalysis - Class in etomica.modules.catalysis
Configuration for catalysis module.
ConfigurationCatalysis(ISimulation, ISpace, ISpecies, ISpecies, ISpecies, AtomLeafAgentManager) - Constructor for class etomica.modules.catalysis.ConfigurationCatalysis
 
ConfigurationCatalysis.BasisOrthorhombicHexagonal3D - Class in etomica.modules.catalysis
 
ConfigurationColloid - Class in etomica.modules.colloid
 
ConfigurationColloid(ISpace, ISpecies, ISpecies, IRandom) - Constructor for class etomica.modules.colloid.ConfigurationColloid
 
ConfigurationDroplet - Class in etomica.modules.droplet
 
ConfigurationDroplet(IRandom, ISpace) - Constructor for class etomica.modules.droplet.ConfigurationDroplet
 
ConfigurationLatticeFreeRadical - Class in etomica.modules.chainequilibrium
Configuration that puts atoms randomly on a lattice and groups pairs of initiator atoms together as though they are a single molecule.
ConfigurationLatticeFreeRadical(SpaceLattice, ISpace, IRandom) - Constructor for class etomica.modules.chainequilibrium.ConfigurationLatticeFreeRadical
 
ConfigurationLatticeRandom - Class in etomica.modules.chainequilibrium
Configuration that puts atoms randomly on a lattice.
ConfigurationLatticeRandom(SpaceLattice, ISpace, IRandom) - Constructor for class etomica.modules.chainequilibrium.ConfigurationLatticeRandom
 
ConfigurationLatticeTube - Class in etomica.modules.dcvgcmd
Creates a configuration using a CubicLattice to specify positions.
ConfigurationLatticeTube(BravaisLatticeCrystal, double, ISpace) - Constructor for class etomica.modules.dcvgcmd.ConfigurationLatticeTube
 
ConfigurationLatticeTube(BravaisLatticeCrystal, double, IndexIteratorSizable, ISpace) - Constructor for class etomica.modules.dcvgcmd.ConfigurationLatticeTube
Constructor for ConfigurationLatticeTube.
ConfigurationMembrane - Class in etomica.modules.rosmosis
 
ConfigurationMembrane(ISimulation, ISpace) - Constructor for class etomica.modules.rosmosis.ConfigurationMembrane
 
ConfigurationMembraneWater - Class in etomica.modules.rosmosis
 
ConfigurationMembraneWater(ISimulation, Space) - Constructor for class etomica.modules.rosmosis.ConfigurationMembraneWater
 
ConfigurationSAM - Class in etomica.modules.sam
 
ConfigurationSAM(ISimulation, ISpace, ISpecies, ISpecies, PotentialMasterList) - Constructor for class etomica.modules.sam.ConfigurationSAM
 
ConfigurationZero - Class in etomica.modules.entropylottery
Configuration that simply puts all the Atoms at 0, or -0.5 if the box size is even (which makes the entropy lottery binning happy).
ConfigurationZero(ISpace) - Constructor for class etomica.modules.entropylottery.ConfigurationZero
 
conformation - Variable in class etomica.modules.catalysis.ConfigurationCatalysis
 
conformation - Variable in class etomica.modules.rheology.SimulationRheology
 
conformation - Variable in class etomica.modules.sam.ConfigurationSAM
 
ConformationPolymer - Class in etomica.modules.rheology
Places polymer in a blob near the origin.
ConformationPolymer(ISpace, IRandom) - Constructor for class etomica.modules.rheology.ConformationPolymer
 
ConformationTube - Class in etomica.modules.dcvgcmd
 
ConformationTube(ISpace, int) - Constructor for class etomica.modules.dcvgcmd.ConformationTube
 
ConnectedToggler() - Constructor for class etomica.modules.clustergenerator.MyApplet.ConnectedToggler
 
constMu - Variable in class etomica.modules.ensembles.LJMCGraphic
 
contains(double[]) - Method in class etomica.modules.junit.crystalviewer.BLCPrimitiveHexagonalLatticePlaneTest.DoubleTwoDArray
 
contains(double[]) - Method in class etomica.modules.junit.crystalviewer.BLCPrimitiveMonoclinicLatticePlaneTest.DoubleTwoDArray
 
contains(double[]) - Method in class etomica.modules.junit.crystalviewer.BLCPrimitiveOrthorhombicLatticePlaneTest.DoubleTwoDArray
 
contains(double[]) - Method in class etomica.modules.junit.crystalviewer.BLCPrimitiveTetragonalLatticePlaneTest.DoubleTwoDArray
 
contains(double[]) - Method in class etomica.modules.junit.crystalviewer.BLCPrimitiveTriclinicLatticePlaneTest.DoubleTwoDArray
 
contains(double[]) - Method in class etomica.modules.junit.crystalviewer.LatticeCubicSimpleLatticePlaneTest.DoubleTwoDArray
 
controller1 - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
 
controller1 - Variable in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
 
controller1 - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibrium
 
coreDiameter - Variable in class etomica.modules.catalysis.P2SquareWellBonding
 
coreDiameter - Variable in class etomica.modules.catalysis.P2SquareWellBondingCO
 
coreDiameter - Variable in class etomica.modules.catalysis.P2SquareWellSurface
 
coreDiameter - Variable in class etomica.modules.mu.P2SquareWellOneSide
 
coreDiameterSquared - Variable in class etomica.modules.catalysis.P2SquareWellBonding
 
coreDiameterSquared - Variable in class etomica.modules.catalysis.P2SquareWellBondingCO
 
coreDiameterSquared - Variable in class etomica.modules.catalysis.P2SquareWellSurface
 
coreDiameterSquared - Variable in class etomica.modules.mu.P2SquareWellOneSide
 
corrugationButton - Variable in class etomica.modules.sam.SamGraphic
 
count - Variable in class etomica.modules.multiharmonic.overlap.AccumulatorOverlapAverageUa2
 
createLatticeAndBox(int, int[], int[]) - Method in class etomica.modules.junit.crystalviewer.LatticePlaneTestUtility
 
criterion - Variable in class etomica.modules.colloid.ColloidGraphic.WallRangeModifier
 
criterion - Variable in class etomica.modules.render.RenderMD
 
criterion3 - Variable in class etomica.modules.sam.Sam
 
CriterionCar(ParseObj, IBox) - Constructor for class etomica.modules.render.RenderMD.CriterionCar
 
CriterionNone() - Constructor for class etomica.modules.colloid.ColloidSim.CriterionNone
 
CriterionTether3 - Class in etomica.modules.sam
Returns first leaf atom of each polymer molecule and the atom its bonded to.
CriterionTether3(ISimulation, ISpecies, IAtomType) - Constructor for class etomica.modules.sam.CriterionTether3
 
criterionWallMonomer - Variable in class etomica.modules.colloid.ColloidSim
 
crossPotentials - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierAtomDiameter
 
CrystalViewer - Class in etomica.modules.crystalviewer
 
CrystalViewer() - Constructor for class etomica.modules.crystalviewer.CrystalViewer
 
CrystalViewer.Applet - Class in etomica.modules.crystalviewer
 
CUBIC_DIAMOND - Variable in class etomica.modules.junit.crystalviewer.LatticePlaneTestUtility
 
currentCores - Variable in class etomica.modules.insertion.InsertionGraphic.MeterWidom
 
currentLattice - Variable in class etomica.modules.crystalviewer.LatticeEditor
 
currentWells - Variable in class etomica.modules.insertion.InsertionGraphic.MeterWidom
 
cursor - Variable in class etomica.modules.sam.CriterionTether3
 
cutoff - Variable in class etomica.modules.dcvgcmd.P1WCAWall
 
cutoff - Variable in class etomica.modules.droplet.AtomFilterLiquid
 
cutoff - Variable in class etomica.modules.sam.P1WCAWall
 
cutoff2 - Variable in class etomica.modules.sam.P1WCAWall
 
cutoffSq - Variable in class etomica.modules.droplet.AtomFilterLiquid
 
cycles - Variable in class etomica.modules.osmosis.Osmosis
 

D

d - Variable in class etomica.modules.rheology.MeterNormalStress
 
d2u(double) - Method in class etomica.modules.droplet.P2Cohesion
 
data - Variable in class etomica.modules.adsorption.DataSourceDensityFunction
 
data - Variable in class etomica.modules.catalysis.DataSourceWallPressureCatalysis
 
data - Variable in class etomica.modules.chainequilibrium.MeterChainLength
 
data - Variable in class etomica.modules.chainequilibrium.MolecularWeightAvg
 
data - Variable in class etomica.modules.chainequilibrium.MolecularWeightAvg2
 
data - Variable in class etomica.modules.droplet.DropletGraphic.DataProcessorTensorSplitter
 
data - Variable in class etomica.modules.droplet.MeterDeformation
 
data - Variable in class etomica.modules.entropylottery.DataSourceProbabilityDensity
 
data - Variable in class etomica.modules.entropylottery.EntropyProcessor
 
data - Variable in class etomica.modules.interfacial.DataProcessorInterfacialTensionProfile
 
data - Variable in class etomica.modules.interfacial.InterfacialSWGraphic.DataProcessorTensorSplitter
 
data - Variable in class etomica.modules.interfacial.MeterOrientation
 
data - Variable in class etomica.modules.ljmd.LjmdGraphic.DataProcessorTensorTrace
 
data - Variable in class etomica.modules.mu.DataSourceWallPressureMu
 
data - Variable in class etomica.modules.mu.MuGraphic.DataProcessorMu
 
data - Variable in class etomica.modules.multiharmonic.DataProcessorBias
 
data - Variable in class etomica.modules.multiharmonic.DataProcessorBounds
 
data - Variable in class etomica.modules.multiharmonic.DataProcessorDyDLnx
 
data - Variable in class etomica.modules.multiharmonic.mbar.MeterMBAR
 
data - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataProcessAHT
 
data - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
 
data - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceFunctionRaw
 
data - Variable in class etomica.modules.rosmosis.MeterFlux
 
data - Variable in class etomica.modules.rosmosis.MeterOsmoticPressure
 
data - Variable in class etomica.modules.sam.MeterTilt
 
data - Variable in class etomica.modules.sam.SamGraphic.DataPipeStressStrain
 
dataInfo - Variable in class etomica.modules.adsorption.DataSourceDensityFunction
 
dataInfo - Variable in class etomica.modules.catalysis.DataSourceWallPressureCatalysis
 
dataInfo - Variable in class etomica.modules.chainequilibrium.MeterChainLength
 
dataInfo - Variable in class etomica.modules.chainequilibrium.MolecularWeightAvg
 
dataInfo - Variable in class etomica.modules.chainequilibrium.MolecularWeightAvg2
 
dataInfo - Variable in class etomica.modules.droplet.MeterDeformation
 
dataInfo - Variable in class etomica.modules.entropylottery.DataSourceProbabilityDensity
 
dataInfo - Variable in class etomica.modules.interfacial.MeterOrientation
 
dataInfo - Variable in class etomica.modules.mu.DataSourceWallPressureMu
 
dataInfo - Variable in class etomica.modules.mu.MuGraphic.DataProcessorMu
 
dataInfo - Variable in class etomica.modules.multiharmonic.DataProcessorBias
 
dataInfo - Variable in class etomica.modules.multiharmonic.DataProcessorBounds
 
dataInfo - Variable in class etomica.modules.multiharmonic.DataProcessorDyDLnx
 
dataInfo - Variable in class etomica.modules.multiharmonic.mbar.MeterMBAR
 
dataInfo - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
 
dataInfo - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceFunctionRaw
 
dataInfo - Variable in class etomica.modules.multiharmonic.umbrella.MeterUmbrella
 
dataInfo - Variable in class etomica.modules.rosmosis.MeterFlux
 
dataInfo - Variable in class etomica.modules.rosmosis.MeterOsmoticPressure
 
dataInfo - Variable in class etomica.modules.sam.MeterTilt
 
dataInfo - Variable in class etomica.modules.sam.SamGraphic.DataPipeStressStrain
 
dataInterval - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
 
DataOverlapCaching - Class in etomica.modules.multiharmonic.overlap
DataOverlap subclass that caches return values.
DataOverlapCaching(DataOverlap.DataSourceOverlapAvg, DataOverlap.DataSourceOverlapAvg, AlphaSource, IntegratorOverlap) - Constructor for class etomica.modules.multiharmonic.overlap.DataOverlapCaching
 
DataPipeStressStrain(Sam) - Constructor for class etomica.modules.sam.SamGraphic.DataPipeStressStrain
 
DataProcessAHT(MultiharmonicGraphicMC.DataSourceUa, HistoryCollapsingDiscard) - Constructor for class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataProcessAHT
 
DataProcessorBias - Class in etomica.modules.multiharmonic
Data Processor which calculates the bias in the incoming data based on the true value of the free energy calculated from the
DataProcessorBias(DataSourceScalar) - Constructor for class etomica.modules.multiharmonic.DataProcessorBias
 
DataProcessorBounds - Class in etomica.modules.multiharmonic
Calculates upper or lower bound of the incoming data based on the standard deviation obtained from the accumulator.
DataProcessorBounds() - Constructor for class etomica.modules.multiharmonic.DataProcessorBounds
 
DataProcessorDyDLnx - Class in etomica.modules.multiharmonic
Calculates dy/dlnx vs.
DataProcessorDyDLnx() - Constructor for class etomica.modules.multiharmonic.DataProcessorDyDLnx
 
DataProcessorInterfacialTensionProfile - Class in etomica.modules.interfacial
 
DataProcessorInterfacialTensionProfile(ISpace) - Constructor for class etomica.modules.interfacial.DataProcessorInterfacialTensionProfile
 
DataProcessorMu(AccumulatorHistory, IntegratorBox) - Constructor for class etomica.modules.mu.MuGraphic.DataProcessorMu
 
DataProcessorTensorSplitter() - Constructor for class etomica.modules.droplet.DropletGraphic.DataProcessorTensorSplitter
 
DataProcessorTensorSplitter() - Constructor for class etomica.modules.interfacial.InterfacialSWGraphic.DataProcessorTensorSplitter
 
DataProcessorTensorTrace() - Constructor for class etomica.modules.ljmd.LjmdGraphic.DataProcessorTensorTrace
 
DataProcessorVar - Class in etomica.modules.multiharmonic
Data Processor whose sole purpose in life is to discard the incoming data and push on the standard deviation from the accumulator.
DataProcessorVar() - Constructor for class etomica.modules.multiharmonic.DataProcessorVar
 
dataPumpA - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicMC
 
DataSinkExcludeOverlap(IBox) - Constructor for class etomica.modules.mu.MuGraphic.DataSinkExcludeOverlap
 
DataSinkExcludeOverlap(IBox) - Constructor for class etomica.modules.rosmosis.ReverseOsmosisGraphic.DataSinkExcludeOverlap
 
DataSinkExcludeOverlap(Box) - Constructor for class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.DataSinkExcludeOverlap
 
DataSinkExcludeOverlap() - Constructor for class etomica.modules.swmd.SwmdGraphic.DataSinkExcludeOverlap
 
DataSinkReweightedDeltaU(AlphaSource) - Constructor for class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSinkReweightedDeltaU
 
dataSourceA - Variable in class etomica.modules.multiharmonic.umbrella.MeterUmbrella
 
DataSourceAlphaAlpha(DataOverlap) - Constructor for class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaAlpha
 
DataSourceAlphaAlpha(DataSourceVirialOverlap) - Constructor for class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaAlpha
 
DataSourceAlphaChi(MeterMBAR, MeterMBAR, boolean) - Constructor for class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceAlphaChi
 
DataSourceAlphaChi(DataOverlap, double) - Constructor for class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaChi
 
DataSourceAlphaChi(DataSourceVirialOverlap, double) - Constructor for class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaChi
 
DataSourceAlphaFE(AlphaSource, int) - Constructor for class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
 
dataSourceB - Variable in class etomica.modules.multiharmonic.umbrella.MeterUmbrella
 
DataSourceBias(AlphaSource) - Constructor for class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceBias
 
DataSourceChiSlope(DataOverlap) - Constructor for class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceChiSlope
 
DataSourceDensityFunction - Class in etomica.modules.adsorption
 
DataSourceDensityFunction(EOSSW, double, double) - Constructor for class etomica.modules.adsorption.DataSourceDensityFunction
 
DataSourceDensityFunction(EOSSW, double, double, boolean) - Constructor for class etomica.modules.adsorption.DataSourceDensityFunction
 
DataSourceFE(String, MeterMBAR, MeterMBAR, int) - Constructor for class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceFE
 
DataSourceFunctionRaw(double[], double[]) - Constructor for class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceFunctionRaw
 
DataSourceProbabilityDensity - Class in etomica.modules.entropylottery
 
DataSourceProbabilityDensity() - Constructor for class etomica.modules.entropylottery.DataSourceProbabilityDensity
 
dataSourceRefBias - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC
 
dataSourceRefFE - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC
 
dataSourceRefStdev - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC
 
dataSourceTargetBias - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC
 
dataSourceTargetFE - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC
 
dataSourceTargetStdev - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC
 
DataSourceTensorVirialHardProfile - Class in etomica.modules.interfacial
A DataSource that collects the average virial tensor as a function of position for one dimension.
DataSourceTensorVirialHardProfile(ISpace) - Constructor for class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
 
DataSourceTensorVirialHardProfile.DataSourceVirialProfile - Class in etomica.modules.interfacial
 
DataSourceUa(DataOverlap) - Constructor for class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceUa
 
DataSourceUa2(IntegratorOverlap, DataOverlap, AccumulatorAverage, AccumulatorAverage) - Constructor for class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceUa2
 
DataSourceVaporDensity(String, Dimension) - Constructor for class etomica.modules.droplet.DropletAtomicGraphic.DataSourceVaporDensity
 
DataSourceVirialProfile(DataSourceTensorVirialHardProfile) - Constructor for class etomica.modules.interfacial.DataSourceTensorVirialHardProfile.DataSourceVirialProfile
 
DataSourceWallPressure - Class in etomica.modules.pistoncylinder
data source front for virial sum from P1HardMovingBoundary returns pressure exerted on the wall by atoms
DataSourceWallPressure(ISpace, P1HardMovingBoundary) - Constructor for class etomica.modules.pistoncylinder.DataSourceWallPressure
 
DataSourceWallPressureCatalysis - Class in etomica.modules.catalysis
 
DataSourceWallPressureCatalysis(ISpace, ISpecies, ISpecies, AtomLeafAgentManager) - Constructor for class etomica.modules.catalysis.DataSourceWallPressureCatalysis
 
DataSourceWallPressureMu - Class in etomica.modules.mu
 
DataSourceWallPressureMu(ISpace) - Constructor for class etomica.modules.mu.DataSourceWallPressureMu
 
dataVar - Variable in class etomica.modules.multiharmonic.DataProcessorVar
 
DCVGCMD - Class in etomica.modules.dcvgcmd
Dual-control-volume grand-canonical molecular dynamics simulation.
DCVGCMD() - Constructor for class etomica.modules.dcvgcmd.DCVGCMD
 
DCVGCMDGraphic - Class in etomica.modules.dcvgcmd
 
DCVGCMDGraphic(DCVGCMD, ISpace) - Constructor for class etomica.modules.dcvgcmd.DCVGCMDGraphic
 
DCVGCMDGraphic.Applet - Class in etomica.modules.dcvgcmd
 
dda - Variable in class etomica.modules.multiharmonic.umbrella.MeterUmbrella
 
def - Variable in class etomica.modules.droplet.EllipseDisplayAction
 
DEFAULT_SIZE - Static variable in class etomica.modules.crystalviewer.LatticeEditor
 
deformation - Variable in class etomica.modules.droplet.ConfigurationDroplet
 
delete(int) - Method in class etomica.modules.render.ParseObj
Removes the vertex referenced by the given index from the list of vertices, removes its bonds from the list of bonds, shifts all vertex indexes down to fill its slot, and returns a list of indexes (after shifting) of vertices that were bonded to the given vertex.
density - Variable in class etomica.modules.droplet.DropletAtomic
 
density - Variable in class etomica.modules.render.RenderMD.RenderMDParam
 
density - Variable in class etomica.modules.vle.MCMoveMoleculeExchangeVLE
 
density - Variable in class etomica.modules.vle.MCMoveVolumeExchangeVLE
 
density - Variable in class etomica.modules.vle.VLESim
 
density1 - Variable in class etomica.modules.dcvgcmd.DCVGCMD
 
density2 - Variable in class etomica.modules.dcvgcmd.DCVGCMD
 
densityAccum - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibriumGraphic
 
densityBox - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
 
densityDisplay - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibriumGraphic
 
densityDisplayTextBox - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
 
densityMeter - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
 
densityProfileMeter - Variable in class etomica.modules.colloid.ColloidGraphic
 
densityProfileMeter - Variable in class etomica.modules.interfacial.InterfacialSWGraphic
 
densityProfileMeterA - Variable in class etomica.modules.adsorption.AdsorptionGraphic
 
densityProfileMeterB - Variable in class etomica.modules.adsorption.AdsorptionGraphic
 
DeviceThermoSliderGEMC - Class in etomica.modules.vle
Custom temperature slider for GEMC simulations.
DeviceThermoSliderGEMC(IController) - Constructor for class etomica.modules.vle.DeviceThermoSliderGEMC
 
diameterHash - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierAtomDiameter
 
diameterHash - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierAtomDiameter
 
dim - Variable in class etomica.modules.adsorption.MeterExcessAdsorbed
 
dim - Variable in class etomica.modules.adsorption.MyMCMove
 
dim - Variable in class etomica.modules.droplet.DropletGraphic.ModifierBoxSize
 
dim - Variable in class etomica.modules.interfacial.InterfacialSWGraphic.ModifierBoxSize
 
dim - Variable in class etomica.modules.rosmosis.MeterFlux
 
dimerPump - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibriumGraphic
 
display - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
 
display - Variable in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
 
display - Variable in class etomica.modules.crystalviewer.ClipPlaneEditor
 
display - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibrium
 
displayBox - Variable in class etomica.modules.crystalviewer.CrystalViewer
 
displayBox - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
 
DisplayBoxCanvas1DBins - Class in etomica.modules.entropylottery
Class used to define canvas onto which configuration is drawn
DisplayBoxCanvas1DBins(DisplayBox, Controller) - Constructor for class etomica.modules.entropylottery.DisplayBoxCanvas1DBins
 
displayCycles - Variable in class etomica.modules.osmosis.Osmosis
 
displayCycles - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
 
displayed - Variable in class etomica.modules.droplet.EllipseDisplayAction
 
displayEllipse(double) - Method in class etomica.modules.droplet.EllipseDisplayAction
 
displayPanel - Variable in class etomica.modules.clustergenerator.MyApplet
 
disproportionate(IAtom, IAtom) - Method in class etomica.modules.chainequilibrium.P2SquareWellRadical
this function will makes a and b unreactive by setting both to be bonded to themselves (a-a, b-b).
distanceTo(IVector) - Method in class etomica.modules.pistoncylinder.PistonPlane
 
distanceTo(IVector) - Method in class etomica.modules.sam.WallPlane
 
doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.modules.materialfracture.PotentialCalculationForceStress
Adds forces due to given potential acting on the atoms produced by the iterator.
doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.modules.rosmosis.PotentialCalculationForceSumWallForce
Adds forces and torques due to given potential acting on the atoms produced by the iterator.
doCalculation(IMoleculeList, IPotentialMolecular) - Method in class etomica.modules.rosmosis.PotentialCalculationTorqueSumWallForce
Adds forces and torques due to given potential acting on the atoms produced by the iterator.
doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.modules.rosmosis.PotentialCalculationTorqueSumWallForce
 
doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.modules.sam.PotentialCalculationForceSumWall
 
doConfigButton - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
 
doDensityInput - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
 
doDouble - Variable in class etomica.modules.rheology.MeterNormalStress
 
doFastButton - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
 
doFit(double[], double[]) - Method in class etomica.modules.interfacial.FitTanh
 
doNMoleculeSlider - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
 
doPaint(Graphics) - Method in class etomica.modules.entropylottery.DisplayBoxCanvas1DBins
doPaint is the method that handles the drawing of the box to the screen.
doRDF - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
 
doResetFilter - Variable in class etomica.modules.droplet.ColorSchemeLiquidVapor
 
doStepInternal() - Method in class etomica.modules.adsorption.IntegratorHybrid
 
doStepInternal() - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD
 
doStepInternal() - Method in class etomica.modules.droplet.IntegratorDroplet
 
doStepInternal() - Method in class etomica.modules.joulethomson.IntegratorJT
 
doStepInternal() - Method in class etomica.modules.pistoncylinder.IntegratorHardPiston
 
doStepInternal() - Method in class etomica.modules.rheology.IntegratorPolymer
 
doStepInternal() - Method in class etomica.modules.sam.IntegratorVelocityVerletSAM
 
doThermostatInternal() - Method in class etomica.modules.rheology.IntegratorPolymer
 
doTrial() - Method in class etomica.modules.adsorption.MyMCMove
Chooses and performs with equal probability an elementary molecule insertion or deletion.
doTrial() - Method in class etomica.modules.dcvgcmd.MyMCMove
Chooses and performs with equal probability an elementary molecule insertion or deletion.
doTrial() - Method in class etomica.modules.entropylottery.MCMoveAtomAdjacent
Method to perform trial move.
doTrial() - Method in class etomica.modules.multiharmonic.MCMoveMultiHarmonic
 
doTrial() - Method in class etomica.modules.vle.MCMoveMoleculeExchangeVLE
 
doTrial() - Method in class etomica.modules.vle.MCMoveVolumeExchangeVLE
 
DoubleTwoDArray(double[][]) - Constructor for class etomica.modules.junit.crystalviewer.BLCPrimitiveHexagonalLatticePlaneTest.DoubleTwoDArray
 
DoubleTwoDArray(double[][]) - Constructor for class etomica.modules.junit.crystalviewer.BLCPrimitiveMonoclinicLatticePlaneTest.DoubleTwoDArray
 
DoubleTwoDArray(double[][]) - Constructor for class etomica.modules.junit.crystalviewer.BLCPrimitiveOrthorhombicLatticePlaneTest.DoubleTwoDArray
 
DoubleTwoDArray(double[][]) - Constructor for class etomica.modules.junit.crystalviewer.BLCPrimitiveTetragonalLatticePlaneTest.DoubleTwoDArray
 
DoubleTwoDArray(double[][]) - Constructor for class etomica.modules.junit.crystalviewer.BLCPrimitiveTriclinicLatticePlaneTest.DoubleTwoDArray
 
DoubleTwoDArray(double[][]) - Constructor for class etomica.modules.junit.crystalviewer.LatticeCubicSimpleLatticePlaneTest.DoubleTwoDArray
 
doUpdate() - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
 
dPdRho(double) - Method in class etomica.modules.adsorption.EOSSWPatel
 
dPdRho(double) - Method in class etomica.modules.adsorption.VEOS3SW
 
dPlot - Variable in class etomica.modules.vle.B2Fit
 
dPlot - Variable in class etomica.modules.vle.B2Fit.FunctionB2LJQ
 
dPlot - Variable in class etomica.modules.vle.B2Fit.FunctionMayerB2LJQ
 
dr - Variable in class etomica.modules.colloid.MeterEnd2End
 
dr - Variable in class etomica.modules.droplet.IntegratorDroplet
 
dr - Variable in class etomica.modules.droplet.MeterDeformation
 
dr - Variable in class etomica.modules.insertion.InsertionGraphic.MeterWidom
 
dr - Variable in class etomica.modules.interfacial.MeterOrientation
 
dr - Variable in class etomica.modules.mu.P1MagicWall
 
dr - Variable in class etomica.modules.rheology.IntegratorPolymer
 
dr - Variable in class etomica.modules.rheology.MeterEndToEnd
 
dr - Variable in class etomica.modules.rheology.MeterNormalStress
 
dr - Variable in class etomica.modules.rheology.MeterViscosity
 
dr - Variable in class etomica.modules.sam.MeterTilt
 
draw(Graphics, int[], double) - Method in class etomica.modules.osmosis.Osmosis.MyWall
 
drawBonds - Variable in class etomica.modules.render.RenderMD.RenderMDParam
 
drOO - Variable in class etomica.modules.catalysis.P2SquareWellBondingCO
 
Droplet - Class in etomica.modules.droplet
Mesoscale simulation for Droplet module.
Droplet(Space) - Constructor for class etomica.modules.droplet.Droplet
 
DropletAtomic - Class in etomica.modules.droplet
Atomic simulation for Droplet module.
DropletAtomic(Space) - Constructor for class etomica.modules.droplet.DropletAtomic
 
DropletAtomicGraphic - Class in etomica.modules.droplet
Graphic UI for Droplet module.
DropletAtomicGraphic(DropletAtomic, Space) - Constructor for class etomica.modules.droplet.DropletAtomicGraphic
 
DropletAtomicGraphic.Applet - Class in etomica.modules.droplet
 
DropletAtomicGraphic.DataSourceVaporDensity - Class in etomica.modules.droplet
 
DropletGraphic - Class in etomica.modules.droplet
Graphic UI for Droplet module.
DropletGraphic(Droplet, Space) - Constructor for class etomica.modules.droplet.DropletGraphic
 
DropletGraphic.Applet - Class in etomica.modules.droplet
 
DropletGraphic.DataProcessorTensorSplitter - Class in etomica.modules.droplet
Inner class to find the total pressure of the system from the pressure tensor.
DropletGraphic.ModifierBoxSize - Class in etomica.modules.droplet
 
dropRadius - Variable in class etomica.modules.droplet.DropletAtomic
 
drPrev - Variable in class etomica.modules.rheology.IntegratorPolymer
 
drSum - Variable in class etomica.modules.sam.MeterTilt
 
drTot - Variable in class etomica.modules.colloid.MeterEnd2End
 
ds - Variable in class etomica.modules.rheology.IntegratorPolymer
 
dsvo - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaAlpha
 
dsvo - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaChi
 
dsvo - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceChiSlope
 
dsvo - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceUa
 
dsvo - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceUa2
 
dsvo - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaAlpha
 
dsvo - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaChi
 
du(double) - Method in class etomica.modules.droplet.P2Cohesion
 
dUnit - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
 
dUnit - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
 
dUnit - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic
 
dUnit - Variable in class etomica.modules.swmd.SwmdGraphic
 
dv - Variable in class etomica.modules.catalysis.P2SquareWellBonding
 
dv - Variable in class etomica.modules.catalysis.P2SquareWellBondingCO
 
dv - Variable in class etomica.modules.catalysis.P2SquareWellSurface
 
dv - Variable in class etomica.modules.droplet.P2Cohesion
 
dv - Variable in class etomica.modules.insertion.InsertionGraphic.MeterWidom
 
dv - Variable in class etomica.modules.mu.P1MagicWall
 
dv - Variable in class etomica.modules.mu.P2SquareWellOneSide
 
dvOO - Variable in class etomica.modules.catalysis.P2SquareWellBondingCO
 

E

eDrawBondsCB - Variable in class etomica.modules.clustergenerator.MyApplet
 
ei - Variable in class etomica.modules.multiharmonic.mbar.MeterMBAR
 
ellipse - Variable in class etomica.modules.droplet.DropletGraphic
 
ellipse - Variable in class etomica.modules.droplet.EllipseDisplayAction
 
EllipseDisplayAction - Class in etomica.modules.droplet
 
EllipseDisplayAction(SimulationGraphic, float) - Constructor for class etomica.modules.droplet.EllipseDisplayAction
 
enabled - Variable in class etomica.modules.sam.SamGraphic.ActionMoveWall
 
energy(IAtomList) - Method in class etomica.modules.adsorption.P1Wall
 
energy(IAtomList) - Method in class etomica.modules.colloid.P1Wall
 
energy(IAtomList) - Method in class etomica.modules.colloid.P2HardSphereMC
 
energy(IAtomList) - Method in class etomica.modules.colloid.P2SquareWellMonomer
 
energy(IAtomList) - Method in class etomica.modules.dcvgcmd.P1WCAPorousWall
 
energy(IAtomList) - Method in class etomica.modules.dcvgcmd.P1WCAWall
 
energy(IAtomList) - Method in class etomica.modules.droplet.P1Smash
 
energy(IAtomList) - Method in class etomica.modules.droplet.P2Cohesion
 
energy(IAtomList) - Method in class etomica.modules.materialfracture.P1Tension
 
energy(IAtomList) - Method in class etomica.modules.mu.P1MagicWall
 
energy(IAtomList) - Method in class etomica.modules.mu.P2SquareWellOneSide
 
energy(IAtomList) - Method in class etomica.modules.osmosis.P1HardWall
 
energy(IAtomList) - Method in class etomica.modules.rosmosis.P1Tether
 
energy(IAtomList) - Method in class etomica.modules.sam.P1Sinusoidal
 
energy(IAtomList) - Method in class etomica.modules.sam.P1WCAWall
 
energyChange() - Method in class etomica.modules.adsorption.P1Wall
 
energyChange() - Method in class etomica.modules.catalysis.P2SquareWellBonding
 
energyChange() - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
 
energyChange() - Method in class etomica.modules.catalysis.P2SquareWellSurface
 
energyChange() - Method in class etomica.modules.colloid.P1Wall
 
energyChange() - Method in class etomica.modules.entropylottery.MCMoveAtomAdjacent
 
energyChange() - Method in class etomica.modules.mu.P1MagicWall
 
energyChange() - Method in class etomica.modules.mu.P2SquareWellOneSide
 
energyChange() - Method in class etomica.modules.multiharmonic.MCMoveMultiHarmonic
 
energyChange() - Method in class etomica.modules.osmosis.P1HardWall
 
EnsembleToggler() - Constructor for class etomica.modules.joulethomson.IntegratorJT.EnsembleToggler
 
EntropyLottery - Class in etomica.modules.entropylottery
 
EntropyLottery(Space) - Constructor for class etomica.modules.entropylottery.EntropyLottery
 
EntropyLotteryGraphic - Class in etomica.modules.entropylottery
 
EntropyLotteryGraphic(EntropyLottery, Space) - Constructor for class etomica.modules.entropylottery.EntropyLotteryGraphic
 
EntropyLotteryGraphic.Applet - Class in etomica.modules.entropylottery
 
EntropyProcessor - Class in etomica.modules.entropylottery
Calculates the entropy of an incoming probability density using Stirling's approximation.
EntropyProcessor() - Constructor for class etomica.modules.entropylottery.EntropyProcessor
 
eos - Variable in class etomica.modules.adsorption.DataSourceDensityFunction
 
eos - Variable in class etomica.modules.adsorption.MeterExcessAdsorbed
 
eos - Variable in class etomica.modules.adsorption.ModifierPMu
 
EOSSW - Class in etomica.modules.adsorption
 
EOSSW() - Constructor for class etomica.modules.adsorption.EOSSW
 
EOSSWPatel - Class in etomica.modules.adsorption
EOS for square-well fluids as described by "Generalized equation of state for square-well potentials of variable range" B.
EOSSWPatel() - Constructor for class etomica.modules.adsorption.EOSSWPatel
 
epsBox - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
 
epsBox - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
 
epsBox - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic
 
epsBox - Variable in class etomica.modules.swmd.SwmdGraphic
 
epsilon - Variable in class etomica.modules.adsorption.EOSSW
 
epsilon - Variable in class etomica.modules.adsorption.P1Wall
 
epsilon - Variable in class etomica.modules.catalysis.P2SquareWellBonding
 
epsilon - Variable in class etomica.modules.catalysis.P2SquareWellBondingCO
 
epsilon - Variable in class etomica.modules.catalysis.P2SquareWellSurface
 
epsilon - Variable in class etomica.modules.colloid.P1Wall
 
epsilon - Variable in class etomica.modules.dcvgcmd.P1WCAWall
 
epsilon - Variable in class etomica.modules.droplet.P2Cohesion
 
epsilon - Variable in class etomica.modules.mu.P2SquareWellOneSide
 
epsilon - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
 
epsilon - Variable in class etomica.modules.render.RenderMD.RenderMDParam
 
epsilon - Variable in class etomica.modules.rosmosis.P1Tether
 
epsilon - Variable in class etomica.modules.sam.P1WCAWall
 
epsilon - Variable in class etomica.modules.swmd.SwmdGraphic
 
epsilon - Variable in class etomica.modules.vle.VLESim
 
epsilonBarrier - Variable in class etomica.modules.catalysis.P2SquareWellBonding
 
epsilonBarrier - Variable in class etomica.modules.catalysis.P2SquareWellBondingCO
 
epsilonBonding - Variable in class etomica.modules.catalysis.P2SquareWellBonding
 
epsilonBonding - Variable in class etomica.modules.catalysis.P2SquareWellBondingCO
 
epsilonCore - Variable in class etomica.modules.render.RenderMD.RenderMDParam
 
epsilonMembrane - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
 
epsilonSolute - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
 
epsilonSolvent - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
 
epsilonSq - Variable in class etomica.modules.droplet.P2Cohesion
 
epsWallWall - Variable in class etomica.modules.colloid.ColloidSim
 
errFac - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaChi
 
errFac - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaChi
 
etomica.modules.adsorption - package etomica.modules.adsorption
 
etomica.modules.catalysis - package etomica.modules.catalysis
 
etomica.modules.chainequilibrium - package etomica.modules.chainequilibrium
 
etomica.modules.clustergenerator - package etomica.modules.clustergenerator
 
etomica.modules.colloid - package etomica.modules.colloid
 
etomica.modules.crystalviewer - package etomica.modules.crystalviewer
 
etomica.modules.dcvgcmd - package etomica.modules.dcvgcmd
 
etomica.modules.droplet - package etomica.modules.droplet
 
etomica.modules.ensembles - package etomica.modules.ensembles
 
etomica.modules.entropylottery - package etomica.modules.entropylottery
 
etomica.modules.insertion - package etomica.modules.insertion
 
etomica.modules.interfacial - package etomica.modules.interfacial
 
etomica.modules.joulethomson - package etomica.modules.joulethomson
 
etomica.modules.junit.crystalviewer - package etomica.modules.junit.crystalviewer
 
etomica.modules.ljmd - package etomica.modules.ljmd
 
etomica.modules.materialfracture - package etomica.modules.materialfracture
 
etomica.modules.mu - package etomica.modules.mu
 
etomica.modules.multiharmonic - package etomica.modules.multiharmonic
 
etomica.modules.multiharmonic.mbar - package etomica.modules.multiharmonic.mbar
 
etomica.modules.multiharmonic.overlap - package etomica.modules.multiharmonic.overlap
 
etomica.modules.multiharmonic.umbrella - package etomica.modules.multiharmonic.umbrella
 
etomica.modules.osmosis - package etomica.modules.osmosis
 
etomica.modules.pistoncylinder - package etomica.modules.pistoncylinder
 
etomica.modules.reactionequilibrium - package etomica.modules.reactionequilibrium
 
etomica.modules.render - package etomica.modules.render
 
etomica.modules.rheology - package etomica.modules.rheology
 
etomica.modules.rosmosis - package etomica.modules.rosmosis
 
etomica.modules.sam - package etomica.modules.sam
 
etomica.modules.swmd - package etomica.modules.swmd
 
etomica.modules.vle - package etomica.modules.vle
 
eUnit - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
 
eUnit - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
 
eUnit - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic
 
eUnit - Variable in class etomica.modules.swmd.SwmdGraphic
 
excludeArticulationPairCB - Variable in class etomica.modules.clustergenerator.MyApplet
 
excludeArticulationPointCB - Variable in class etomica.modules.clustergenerator.MyApplet
 
excludeNodalPointCB - Variable in class etomica.modules.clustergenerator.MyApplet
 

F

f - Variable in class etomica.modules.droplet.MeterDeformation
 
f(double) - Method in class etomica.modules.vle.B2Fit.FunctionB2LJQ
 
f(double) - Method in class etomica.modules.vle.B2Fit.FunctionMayerB2LJQ
 
fac - Variable in class etomica.modules.droplet.P2Cohesion
 
FCC - Variable in class etomica.modules.junit.crystalviewer.LatticePlaneTestUtility
 
fDrawBondsCB - Variable in class etomica.modules.clustergenerator.MyApplet
 
file - Variable in class etomica.modules.render.RenderMD.RenderMDParam
 
filter - Variable in class etomica.modules.droplet.MeterDeformation
 
filter - Variable in class etomica.modules.pistoncylinder.ApiFilteredCylinder
 
findTetherBonds() - Method in class etomica.modules.sam.Sam
 
fitData - Variable in class etomica.modules.interfacial.FitTanh
 
fitDataInfo - Variable in class etomica.modules.interfacial.FitTanh
 
FitTanh - Class in etomica.modules.interfacial
 
FitTanh() - Constructor for class etomica.modules.interfacial.FitTanh
 
fixPistonButton - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
 
floodCircle(double, double, double, double) - Method in class etomica.modules.clustergenerator.Plot
 
floodInside(double, double, double, double) - Method in class etomica.modules.clustergenerator.Plot
 
flowLines - Variable in class etomica.modules.rheology.RheologyGraphic
 
fluxAccumulator - Variable in class etomica.modules.dcvgcmd.DCVGCMD
 
fluxMeters - Variable in class etomica.modules.dcvgcmd.DCVGCMD
 
foo() - Method in class etomica.modules.clustergenerator.MyApplet.Starter
 
foo() - Method in class etomica.modules.droplet.IntegratorDroplet
 
force - Variable in class etomica.modules.droplet.IntegratorDroplet.MyAgent
 
force() - Method in class etomica.modules.droplet.IntegratorDroplet.MyAgent
 
force - Variable in class etomica.modules.materialfracture.P1Tension
 
forceSum - Variable in class etomica.modules.droplet.IntegratorDroplet
 
forceSum - Variable in class etomica.modules.rosmosis.ReverseOsmosis
 
forceSum - Variable in class etomica.modules.sam.Sam
 
foundRing - Variable in class etomica.modules.chainequilibrium.P2SquareWellBonded.RingResult
 
fQ - Variable in class etomica.modules.rheology.IntegratorPolymer
 
FreeRadicalPolymerizationGraphic - Class in etomica.modules.chainequilibrium
Module for chain reaction (polymerization) using ChainEquilibriumSim as the simulation class.
FreeRadicalPolymerizationGraphic(FreeRadicalPolymerizationSim, ISpace) - Constructor for class etomica.modules.chainequilibrium.FreeRadicalPolymerizationGraphic
 
FreeRadicalPolymerizationGraphic.Applet - Class in etomica.modules.chainequilibrium
 
FreeRadicalPolymerizationSim - Class in etomica.modules.chainequilibrium
 
FreeRadicalPolymerizationSim() - Constructor for class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
 
FreeRadicalPolymerizationSim(ISpace) - Constructor for class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
 
full(IAtom) - Method in class etomica.modules.chainequilibrium.P2SquareWellBonded
This function will tell the user, if passed an atom weither or not that atom can bond
fullBondColorMap - Variable in class etomica.modules.catalysis.ColorSchemeRadical
 
fullColorMap - Variable in class etomica.modules.chainequilibrium.ColorSchemeRadical
 
FunctionB2LJQ() - Constructor for class etomica.modules.vle.B2Fit.FunctionB2LJQ
 
FunctionMayerB2LJQ() - Constructor for class etomica.modules.vle.B2Fit.FunctionMayerB2LJQ
 

G

g - Variable in class etomica.modules.droplet.P1Smash
 
gbConst - Variable in class etomica.modules.clustergenerator.MyApplet
 
gbLayout - Variable in class etomica.modules.clustergenerator.MyApplet
 
generateGraphicsCB - Variable in class etomica.modules.clustergenerator.MyApplet
 
generator - Variable in class etomica.modules.clustergenerator.MyApplet
 
getA() - Method in class etomica.modules.adsorption.MyMCMove
 
getA() - Method in class etomica.modules.dcvgcmd.MyMCMove
 
getA() - Method in class etomica.modules.entropylottery.MCMoveAtomAdjacent
 
getA() - Method in class etomica.modules.multiharmonic.MCMoveMultiHarmonic
 
getA() - Method in class etomica.modules.pistoncylinder.PistonPlane
 
getA() - Method in class etomica.modules.rheology.IntegratorPolymer
 
getA() - Method in class etomica.modules.sam.WallPlane
 
getAgentManager() - Method in class etomica.modules.catalysis.InteractionTracker
 
getAgentManager() - Method in class etomica.modules.chainequilibrium.ChainEquilibriumSim
 
getAgentManager() - Method in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
 
getAgentManager() - Method in class etomica.modules.reactionequilibrium.ReactionEquilibrium
 
getAlpha(int) - Method in class etomica.modules.multiharmonic.mbar.MeterMBAR
 
getAlpha() - Method in class etomica.modules.multiharmonic.umbrella.MeterUmbrella
 
getAlphaCenter() - Method in class etomica.modules.multiharmonic.mbar.MeterMBAR
 
getAlphaCenter() - Method in class etomica.modules.multiharmonic.overlap.AccumulatorOverlapAverageUa2
 
getAlphaFac() - Method in class etomica.modules.multiharmonic.umbrella.MeterUmbrella
 
getAlphaSpan() - Method in class etomica.modules.multiharmonic.mbar.MeterMBAR
 
getAlphaSpan() - Method in class etomica.modules.multiharmonic.overlap.AccumulatorOverlapAverageUa2
 
getAtomColor(IAtom) - Method in class etomica.modules.catalysis.ColorSchemeRadical
 
getAtomColor(IAtom) - Method in class etomica.modules.chainequilibrium.ColorSchemeRadical
 
getAtomColor(IAtom) - Method in class etomica.modules.chainequilibrium.ColorSchemeStepWise
 
getAtomColor(IAtom) - Method in class etomica.modules.crystalviewer.ColorSchemePlane
 
getAtomColor(IAtom) - Method in class etomica.modules.droplet.ColorSchemeDropletSurface
 
getAtomColor(IAtom) - Method in class etomica.modules.droplet.ColorSchemeLiquidVapor
 
getAtomColor(IAtom) - Method in class etomica.modules.materialfracture.StrainColorScheme
 
getAtomSource() - Method in class etomica.modules.entropylottery.MCMoveAtomAdjacent
 
getAverageAndError(int, double, boolean) - Method in class etomica.modules.multiharmonic.overlap.DataOverlapCaching
 
getB() - Method in class etomica.modules.entropylottery.MCMoveAtomAdjacent
Returns the log of the limiting-distribution probabilities of states, ln(Pj/Pi), for the states encountered before (i) and after (j) the most recent call to doTrial.
getB() - Method in class etomica.modules.multiharmonic.MCMoveMultiHarmonic
 
getB() - Method in class etomica.modules.pistoncylinder.PistonPlane
 
getB() - Method in class etomica.modules.rheology.IntegratorPolymer
 
getB() - Method in class etomica.modules.sam.P1Sinusoidal
 
getB() - Method in class etomica.modules.sam.WallPlane
 
getBarrier() - Method in class etomica.modules.catalysis.P2SquareWellBonding
 
getBarrier() - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
 
getBarrier() - Method in class etomica.modules.reactionequilibrium.P2SquareWellBonded
 
getBarrierDimension() - Method in class etomica.modules.reactionequilibrium.P2SquareWellBonded
 
getBasisMolecules() - Method in class etomica.modules.sam.ConfigurationSAM
 
getBasisSurface() - Method in class etomica.modules.sam.ConfigurationSAM
 
getBennetBias(int) - Method in class etomica.modules.multiharmonic.overlap.AccumulatorOverlapAverageUa2
Returns iParam'th factor used in the Bennet sum.
getBinSize() - Method in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
 
getBondFac() - Method in class etomica.modules.colloid.P2HardSphereMC
 
getBondFac() - Method in class etomica.modules.colloid.P2SquareWellMonomer
 
getBoolean() - Method in class etomica.modules.joulethomson.IntegratorJT.EnsembleToggler
 
getBoundaries() - Method in class etomica.modules.rosmosis.MeterFlux
 
getBox() - Method in class etomica.modules.chainequilibrium.AtomFilterChainLength
 
getBox() - Method in class etomica.modules.chainequilibrium.ColorSchemeRadical
 
getBox() - Method in class etomica.modules.chainequilibrium.MeterChainLength
 
getBox() - Method in class etomica.modules.dcvgcmd.MeterFlux
 
getBox() - Method in class etomica.modules.droplet.MeterDeformation
 
getBox() - Method in class etomica.modules.entropylottery.MeterEntropy
 
getBox() - Method in class etomica.modules.interfacial.DataProcessorInterfacialTensionProfile
 
getBox() - Method in class etomica.modules.junit.crystalviewer.LatticePlaneTestUtility
 
getBox() - Method in class etomica.modules.materialfracture.MeterElongation
 
getBox() - Method in class etomica.modules.materialfracture.MeterStrain
 
getBox() - Method in class etomica.modules.materialfracture.MeterStress
 
getBox() - Method in class etomica.modules.materialfracture.StrainColorScheme
 
getBox() - Method in class etomica.modules.multiharmonic.MeterFreeEnergy
 
getBox() - Method in class etomica.modules.reactionequilibrium.MeterDimerFraction
 
getBox() - Method in class etomica.modules.rosmosis.MeterFlux
 
getBox() - Method in class etomica.modules.vle.MeterPressure2
 
getBoxIndex() - Method in class etomica.modules.multiharmonic.mbar.MeterMBAR
 
getC() - Method in class etomica.modules.pistoncylinder.PistonPlane
 
getC() - Method in class etomica.modules.sam.WallPlane
 
getCallCount() - Method in class etomica.modules.multiharmonic.mbar.MeterMBAR
 
getCellSizeX() - Method in class etomica.modules.catalysis.ConfigurationCatalysis
 
getCellSizeX() - Method in class etomica.modules.sam.ConfigurationSAM
 
getCellSizeZ() - Method in class etomica.modules.catalysis.ConfigurationCatalysis
 
getCellSizeZ() - Method in class etomica.modules.sam.ConfigurationSAM
 
getCH2Type() - Method in class etomica.modules.sam.SpeciesAlkaneThiol
 
getCH3Type() - Method in class etomica.modules.sam.SpeciesAlkaneThiol
 
getChainLength() - Method in class etomica.modules.colloid.ColloidSim
 
getChainLength() - Method in class etomica.modules.colloid.ConfigurationColloid
 
getChainLength() - Method in class etomica.modules.rheology.SimulationRheology
 
getChainPhi(int) - Method in class etomica.modules.sam.Sam
 
getChainPsi() - Method in class etomica.modules.sam.Sam
 
getChainTheta() - Method in class etomica.modules.sam.Sam
 
getCluster() - Method in class etomica.modules.clustergenerator.ClusterPanel
 
getCollisionRadius() - Method in class etomica.modules.osmosis.MeterOsmoticPressure
Returns the collision radius used to calculate the accessible "area".
getCollisionRadius() - Method in class etomica.modules.osmosis.P1HardWall
Distance from the center of the sphere to the boundary at collision.
getCollisionRadiusDimension() - Method in class etomica.modules.osmosis.P1HardWall
Indicates collision radius has dimensions of Length.
getColloidSigma() - Method in class etomica.modules.colloid.ColloidSim
 
getColorIn() - Method in class etomica.modules.crystalviewer.ColorSchemePlane
 
getColorOut() - Method in class etomica.modules.crystalviewer.ColorSchemePlane
 
getCombinationProbability() - Method in class etomica.modules.chainequilibrium.P2SquareWellRadical
Returns the probability that two radicals will bond instead of becoming unreactive.
getConformation(int) - Method in class etomica.modules.sam.ConfigurationSAM
 
getCoreDiameter() - Method in class etomica.modules.catalysis.P2SquareWellBonding
Accessor method for core diameter.
getCoreDiameter() - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
Accessor method for core diameter.
getCoreDiameter() - Method in class etomica.modules.catalysis.P2SquareWellSurface
Accessor method for core diameter.
getCoreDiameter() - Method in class etomica.modules.mu.P2SquareWellOneSide
Accessor method for core diameter.
getCoreDiameterDimension() - Method in class etomica.modules.catalysis.P2SquareWellBonding
 
getCoreDiameterDimension() - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
 
getCoreDiameterDimension() - Method in class etomica.modules.catalysis.P2SquareWellSurface
 
getCoreDiameterDimension() - Method in class etomica.modules.mu.P2SquareWellOneSide
 
getCurrentLattice() - Method in class etomica.modules.crystalviewer.LatticeEditor
Returns the currently selected crystal.
getCurrentTime() - Method in class etomica.modules.adsorption.IntegratorHybrid
 
getCurrentTime() - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD
 
getCutoff() - Method in class etomica.modules.droplet.AtomFilterLiquid
 
getD() - Method in class etomica.modules.pistoncylinder.PistonPlane
 
getD() - Method in class etomica.modules.sam.WallPlane
 
getData() - Method in class etomica.modules.adsorption.DataSourceDensityFunction
 
getData() - Method in class etomica.modules.catalysis.DataSourceWallPressureCatalysis
 
getData() - Method in class etomica.modules.chainequilibrium.MeterChainLength
 
getData() - Method in class etomica.modules.droplet.MeterDeformation
 
getData() - Method in class etomica.modules.entropylottery.DataSourceProbabilityDensity
 
getData() - Method in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile.DataSourceVirialProfile
 
getData(IMolecule) - Method in class etomica.modules.interfacial.MeterOrientation
 
getData() - Method in class etomica.modules.mu.DataSourceWallPressureMu
 
getData() - Method in class etomica.modules.multiharmonic.mbar.MeterMBAR
 
getData() - Method in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceAlphaChi
 
getData() - Method in class etomica.modules.multiharmonic.overlap.AccumulatorOverlapAverageUa2
Implements DataSource interface, but you probably want to getData for a specific Bennet parameter.
getData() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaAlpha
 
getData() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaChi
 
getData() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
 
getData() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceFunctionRaw
 
getData() - Method in class etomica.modules.multiharmonic.umbrella.MeterUmbrella
 
getData() - Method in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaAlpha
 
getData() - Method in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaChi
 
getData() - Method in class etomica.modules.pistoncylinder.MeterRDFCylinder
 
getData() - Method in class etomica.modules.reactionequilibrium.MeterDimerFraction
 
getData() - Method in class etomica.modules.rosmosis.MeterFlux
 
getData() - Method in class etomica.modules.rosmosis.MeterOsmoticPressure
 
getData() - Method in class etomica.modules.sam.MeterTilt
 
getDataAsScalar() - Method in class etomica.modules.adsorption.MeterExcessAdsorbed
 
getDataAsScalar() - Method in class etomica.modules.catalysis.MeterDensityCO
 
getDataAsScalar() - Method in class etomica.modules.catalysis.MeterDensityCO2
 
getDataAsScalar() - Method in class etomica.modules.catalysis.MeterDensityO2
 
getDataAsScalar() - Method in class etomica.modules.chainequilibrium.MeterConversion
 
getDataAsScalar() - Method in class etomica.modules.colloid.MeterEnd2End
 
getDataAsScalar() - Method in class etomica.modules.dcvgcmd.MeterFlux
 
getDataAsScalar() - Method in class etomica.modules.droplet.DropletAtomicGraphic.DataSourceVaporDensity
 
getDataAsScalar() - Method in class etomica.modules.entropylottery.MeterEntropy
 
getDataAsScalar() - Method in class etomica.modules.insertion.InsertionGraphic.MeterWidom
 
getDataAsScalar() - Method in class etomica.modules.materialfracture.MeterElongation
 
getDataAsScalar() - Method in class etomica.modules.materialfracture.MeterLoad
 
getDataAsScalar() - Method in class etomica.modules.materialfracture.MeterStrain
 
getDataAsScalar() - Method in class etomica.modules.materialfracture.MeterStress
 
getDataAsScalar() - Method in class etomica.modules.mu.MeterDensitySides
 
getDataAsScalar() - Method in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceFE
 
getDataAsScalar() - Method in class etomica.modules.multiharmonic.MeterFreeEnergy
 
getDataAsScalar() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceBias
 
getDataAsScalar() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceChiSlope
 
getDataAsScalar() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceUa
 
getDataAsScalar() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceUa2
 
getDataAsScalar() - Method in class etomica.modules.osmosis.MeterOsmoticPressure
 
getDataAsScalar() - Method in class etomica.modules.pistoncylinder.DataSourceWallPressure
 
getDataAsScalar() - Method in class etomica.modules.rheology.MeterEndToEnd
 
getDataAsScalar() - Method in class etomica.modules.rheology.MeterNormalStress
 
getDataAsScalar() - Method in class etomica.modules.rheology.MeterViscosity
 
getDataAsScalar() - Method in class etomica.modules.sam.MeterWallPressure
 
getDataAsScalar() - Method in class etomica.modules.vle.MeterPressure2
Computes total pressure in box by summing virial over all pairs, and adding ideal-gas contribution.
getDataCaster(IEtomicaDataInfo) - Method in class etomica.modules.chainequilibrium.MolecularWeightAvg
 
getDataCaster(IEtomicaDataInfo) - Method in class etomica.modules.chainequilibrium.MolecularWeightAvg2
 
getDataCaster(IEtomicaDataInfo) - Method in class etomica.modules.droplet.DropletGraphic.DataProcessorTensorSplitter
 
getDataCaster(IEtomicaDataInfo) - Method in class etomica.modules.entropylottery.EntropyProcessor
 
getDataCaster(IEtomicaDataInfo) - Method in class etomica.modules.interfacial.DataProcessorInterfacialTensionProfile
 
getDataCaster(IEtomicaDataInfo) - Method in class etomica.modules.interfacial.FitTanh
 
getDataCaster(IEtomicaDataInfo) - Method in class etomica.modules.interfacial.InterfacialSWGraphic.DataProcessorTensorSplitter
 
getDataCaster(IEtomicaDataInfo) - Method in class etomica.modules.ljmd.LjmdGraphic.DataProcessorTensorTrace
 
getDataCaster(IEtomicaDataInfo) - Method in class etomica.modules.mu.MuGraphic.DataProcessorMu
 
getDataCaster(IEtomicaDataInfo) - Method in class etomica.modules.mu.MuGraphic.DataSinkExcludeOverlap
 
getDataCaster(IEtomicaDataInfo) - Method in class etomica.modules.multiharmonic.DataProcessorBias
 
getDataCaster(IEtomicaDataInfo) - Method in class etomica.modules.multiharmonic.DataProcessorBounds
 
getDataCaster(IEtomicaDataInfo) - Method in class etomica.modules.multiharmonic.DataProcessorDyDLnx
 
getDataCaster(IEtomicaDataInfo) - Method in class etomica.modules.multiharmonic.DataProcessorVar
 
getDataCaster(IEtomicaDataInfo) - Method in class etomica.modules.multiharmonic.overlap.AccumulatorOverlapAverageUa2
 
getDataCaster(IEtomicaDataInfo) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataProcessAHT
 
getDataCaster(IEtomicaDataInfo) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSinkReweightedDeltaU
 
getDataCaster(IEtomicaDataInfo) - Method in class etomica.modules.rosmosis.ReverseOsmosisGraphic.DataSinkExcludeOverlap
 
getDataCaster(IEtomicaDataInfo) - Method in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.DataSinkExcludeOverlap
 
getDataCaster(IEtomicaDataInfo) - Method in class etomica.modules.sam.SamGraphic.DataPipeStressStrain
 
getDataCaster(IEtomicaDataInfo) - Method in class etomica.modules.swmd.SwmdGraphic.DataSinkExcludeOverlap
 
getDataInfo() - Method in class etomica.modules.adsorption.DataSourceDensityFunction
 
getDataInfo() - Method in class etomica.modules.catalysis.DataSourceWallPressureCatalysis
 
getDataInfo() - Method in class etomica.modules.chainequilibrium.MeterChainLength
 
getDataInfo() - Method in class etomica.modules.droplet.MeterDeformation
 
getDataInfo() - Method in class etomica.modules.entropylottery.DataSourceProbabilityDensity
 
getDataInfo() - Method in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile.DataSourceVirialProfile
 
getDataInfo() - Method in class etomica.modules.mu.DataSourceWallPressureMu
 
getDataInfo() - Method in class etomica.modules.multiharmonic.mbar.MeterMBAR
 
getDataInfo() - Method in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceAlphaChi
 
getDataInfo() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaAlpha
 
getDataInfo() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaChi
 
getDataInfo() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
 
getDataInfo() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceFunctionRaw
 
getDataInfo() - Method in class etomica.modules.multiharmonic.umbrella.MeterUmbrella
 
getDataInfo() - Method in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaAlpha
 
getDataInfo() - Method in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaChi
 
getDataInfo() - Method in class etomica.modules.reactionequilibrium.MeterDimerFraction
 
getDataInfo() - Method in class etomica.modules.rosmosis.MeterFlux
 
getDataInfo() - Method in class etomica.modules.rosmosis.MeterOsmoticPressure
 
getDataInfo() - Method in class etomica.modules.sam.MeterTilt
 
getDeformation() - Method in class etomica.modules.droplet.ConfigurationDroplet
 
getDeltaN() - Method in class etomica.modules.dcvgcmd.MyMCMove
 
getDeltaU(IAtomKinetic, double, boolean, boolean) - Method in class etomica.modules.mu.P1MagicWall
 
getDeltaU(double) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSinkReweightedDeltaU
 
getDim() - Method in class etomica.modules.rosmosis.MeterFlux
 
getDimension() - Method in class etomica.modules.adsorption.ModifierPMu
 
getDimension(double, double) - Method in class etomica.modules.clustergenerator.Plot
Computes the separation in pixels of two points in the world window.
getDimension() - Method in class etomica.modules.colloid.ColloidGraphic.WallRangeModifier
 
getDimension() - Method in class etomica.modules.crystalviewer.LatticeEditor.NModifier
 
getDimension() - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD.Mu1Modulator
 
getDimension() - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD.Mu2Modulator
 
getDimension() - Method in class etomica.modules.droplet.DropletGraphic.ModifierBoxSize
 
getDimension() - Method in class etomica.modules.entropylottery.ModifierDimensions
 
getDimension() - Method in class etomica.modules.interfacial.InterfacialSWGraphic.ModifierBoxSize
 
getDimension() - Method in class etomica.modules.mu.MuGraphic.ModifierAtomDiameter
 
getDimension() - Method in class etomica.modules.mu.MuGraphic.ModifierEpsilon
 
getDimension() - Method in class etomica.modules.mu.MuGraphic.ModifierLambda
 
getDimension() - Method in class etomica.modules.pistoncylinder.ModifierPistonPressure
 
getDimension() - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic.ModifierAtomDiameter
 
getDimension() - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic.ModifierPistonDensity
 
getDimension() - Method in class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierAtomDiameter
 
getDimension() - Method in class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierEpsilon
 
getDimension() - Method in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierAtomDiameter
 
getDimension() - Method in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierEpsilon
 
getDimension() - Method in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierSoluteCharge
 
getDimension() - Method in class etomica.modules.sam.SamGraphic.ModifierWallPosition
 
getDimension() - Method in class etomica.modules.swmd.SwmdGraphic.ModifierAtomDiameter
 
getDv() - Method in class etomica.modules.droplet.P2Cohesion
 
getEpsilon() - Method in class etomica.modules.adsorption.P1Wall
 
getEpsilon() - Method in class etomica.modules.catalysis.P2SquareWellBonding
Accessor method for depth of well
getEpsilon() - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
Accessor method for depth of well
getEpsilon() - Method in class etomica.modules.catalysis.P2SquareWellSurface
Accessor method for depth of well
getEpsilon() - Method in class etomica.modules.colloid.P1Wall
 
getEpsilon() - Method in class etomica.modules.dcvgcmd.P1WCAPorousWall
 
getEpsilon() - Method in class etomica.modules.dcvgcmd.P1WCAWall
 
getEpsilon() - Method in class etomica.modules.droplet.P2Cohesion
 
getEpsilon() - Method in class etomica.modules.mu.P2SquareWellOneSide
Accessor method for depth of well
getEpsilon() - Method in class etomica.modules.render.RenderMD.P2PenetrableCar
 
getEpsilon() - Method in class etomica.modules.rosmosis.P1Tether
 
getEpsilon() - Method in class etomica.modules.sam.P1WCAWall
 
getEpsilon() - Method in class etomica.modules.vle.VLESim
 
getEpsilonBonding() - Method in class etomica.modules.catalysis.P2SquareWellBonding
 
getEpsilonBonding() - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
 
getEpsilonDimension() - Method in class etomica.modules.catalysis.P2SquareWellBonding
 
getEpsilonDimension() - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
 
getEpsilonDimension() - Method in class etomica.modules.catalysis.P2SquareWellSurface
 
getEpsilonDimension() - Method in class etomica.modules.mu.P2SquareWellOneSide
 
getFilter() - Method in class etomica.modules.droplet.MeterDeformation
 
getG() - Method in class etomica.modules.droplet.P1Smash
 
getIgnoredAtomType() - Method in class etomica.modules.chainequilibrium.MeterChainLength
 
getIndependentArrayDimension() - Method in class etomica.modules.chainequilibrium.MeterChainLength
 
getIndependentArrayDimension() - Method in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
 
getIndependentArrayDimension() - Method in class etomica.modules.multiharmonic.DataProcessorDyDLnx
 
getIndependentArrayDimension() - Method in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceAlphaChi
 
getIndependentArrayDimension() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaAlpha
 
getIndependentArrayDimension() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaChi
 
getIndependentArrayDimension() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
 
getIndependentArrayDimension() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceFunctionRaw
 
getIndependentArrayDimension() - Method in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaAlpha
 
getIndependentArrayDimension() - Method in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaChi
 
getIndependentData(int) - Method in class etomica.modules.chainequilibrium.MeterChainLength
 
getIndependentData(int) - Method in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
 
getIndependentData(int) - Method in class etomica.modules.multiharmonic.DataProcessorDyDLnx
 
getIndependentData(int) - Method in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceAlphaChi
 
getIndependentData(int) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaAlpha
 
getIndependentData(int) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaChi
 
getIndependentData(int) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
 
getIndependentData(int) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceFunctionRaw
 
getIndependentData(int) - Method in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaAlpha
 
getIndependentData(int) - Method in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaChi
 
getIndependentDataInfo(int) - Method in class etomica.modules.chainequilibrium.MeterChainLength
 
getIndependentDataInfo(int) - Method in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
 
getIndependentDataInfo(int) - Method in class etomica.modules.multiharmonic.DataProcessorDyDLnx
 
getIndependentDataInfo(int) - Method in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceAlphaChi
 
getIndependentDataInfo(int) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaAlpha
 
getIndependentDataInfo(int) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaChi
 
getIndependentDataInfo(int) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
 
getIndependentDataInfo(int) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceFunctionRaw
 
getIndependentDataInfo(int) - Method in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaAlpha
 
getIndependentDataInfo(int) - Method in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaChi
 
getIndependentTag() - Method in class etomica.modules.chainequilibrium.MeterChainLength
 
getIndependentTag() - Method in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
 
getIndependentTag() - Method in class etomica.modules.multiharmonic.DataProcessorDyDLnx
 
getIndependentTag() - Method in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceAlphaChi
 
getIndependentTag() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaAlpha
 
getIndependentTag() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaChi
 
getIndependentTag() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
 
getIndependentTag() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceFunctionRaw
 
getIndependentTag() - Method in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaAlpha
 
getIndependentTag() - Method in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaChi
 
getIntegrator() - Method in class etomica.modules.catalysis.DataSourceWallPressureCatalysis
 
getIntegrator() - Method in class etomica.modules.mu.DataSourceWallPressureMu
 
getInteriorColor() - Method in class etomica.modules.droplet.ColorSchemeDropletSurface
 
getIsothermalButtonsVisibility() - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
 
getLabel() - Method in class etomica.modules.adsorption.ModifierPMu
 
getLabel() - Method in class etomica.modules.colloid.ColloidGraphic.WallRangeModifier
 
getLabel() - Method in class etomica.modules.crystalviewer.LatticeEditor.NModifier
 
getLabel() - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD.Mu1Modulator
 
getLabel() - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD.Mu2Modulator
 
getLabel() - Method in class etomica.modules.droplet.DropletGraphic.ModifierBoxSize
 
getLabel() - Method in class etomica.modules.entropylottery.ModifierDimensions
 
getLabel() - Method in class etomica.modules.interfacial.InterfacialSWGraphic.ModifierBoxSize
 
getLabel() - Method in class etomica.modules.mu.MuGraphic.ModifierAtomDiameter
 
getLabel() - Method in class etomica.modules.mu.MuGraphic.ModifierEpsilon
 
getLabel() - Method in class etomica.modules.mu.MuGraphic.ModifierLambda
 
getLabel() - Method in class etomica.modules.pistoncylinder.ActionPistonUpdate
 
getLabel() - Method in class etomica.modules.pistoncylinder.ModifierPistonPressure
 
getLabel() - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic.ModifierAtomDiameter
 
getLabel() - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic.ModifierPistonDensity
 
getLabel() - Method in class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierAtomDiameter
 
getLabel() - Method in class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierEpsilon
 
getLabel() - Method in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierAtomDiameter
 
getLabel() - Method in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierEpsilon
 
getLabel() - Method in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierSoluteCharge
 
getLabel() - Method in class etomica.modules.sam.SamGraphic.ModifierWallPosition
 
getLabel() - Method in class etomica.modules.swmd.SwmdGraphic.ModifierAtomDiameter
 
getLambda() - Method in class etomica.modules.catalysis.P2SquareWellBonding
Accessor method for well-diameter multiplier.
getLambda() - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
Accessor method for well-diameter multiplier.
getLambda() - Method in class etomica.modules.catalysis.P2SquareWellSurface
Accessor method for well-diameter multiplier.
getLambda() - Method in class etomica.modules.mu.P2SquareWellOneSide
Accessor method for well-diameter multiplier.
getLambdaDimension() - Method in class etomica.modules.catalysis.P2SquareWellBonding
 
getLambdaDimension() - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
 
getLambdaDimension() - Method in class etomica.modules.catalysis.P2SquareWellSurface
 
getLambdaDimension() - Method in class etomica.modules.mu.P2SquareWellOneSide
 
getLastBestParam() - Method in class etomica.modules.interfacial.FitTanh
 
getLattice() - Method in class etomica.modules.junit.crystalviewer.LatticePlaneTestUtility
 
getLatticePlane() - Method in class etomica.modules.junit.crystalviewer.LatticePlaneTestUtility
 
getLatticePlaneSpacePosition() - Method in class etomica.modules.junit.crystalviewer.LatticePlaneTestUtility
 
getLiquidColor() - Method in class etomica.modules.droplet.ColorSchemeLiquidVapor
 
getLiquidFilter() - Method in class etomica.modules.droplet.P2Cohesion
 
getLoad() - Method in class etomica.modules.materialfracture.PotentialCalculationForceStress
 
getMaxNbrsVapor() - Method in class etomica.modules.droplet.AtomFilterLiquidAtomic
 
getMembraneDim() - Method in class etomica.modules.rosmosis.ConfigurationMembrane
 
getMembraneDim() - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
The dimension of the membrane (0=x, 1=y, 2=z).
getMembraneThickness() - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
Returns the thickness (angstroms) of each layer of the membrane (see getNumMembraneLayers)
getMembraneThicknessPerLayer() - Method in class etomica.modules.rosmosis.ConfigurationMembrane
 
getMembraneWidth() - Method in class etomica.modules.rosmosis.ConfigurationMembrane
 
getMembraneWidth() - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
Returns the width of the membrane.
getMinRadicalSites() - Method in class etomica.modules.catalysis.P2SquareWellSurface
 
getModifier() - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
 
getMoleculeAgentClass() - Method in class etomica.modules.rosmosis.MeterFlux
 
getMoleculeAgentClass() - Method in class etomica.modules.sam.CriterionTether3
 
getMoleculeDataInfo() - Method in class etomica.modules.interfacial.MeterOrientation
 
getMoleculeOffset() - Method in class etomica.modules.catalysis.ConfigurationCatalysis
 
getMoleculeOffset() - Method in class etomica.modules.sam.ConfigurationSAM
 
getMoment() - Method in class etomica.modules.vle.VLESim
 
getName() - Method in class etomica.modules.reactionequilibrium.MeterDimerFraction
 
getNBennetPoints() - Method in class etomica.modules.multiharmonic.overlap.AccumulatorOverlapAverageUa2
 
getNCellsX() - Method in class etomica.modules.catalysis.ConfigurationCatalysis
 
getNCellsX() - Method in class etomica.modules.sam.ConfigurationSAM
 
getNCellsZ() - Method in class etomica.modules.catalysis.ConfigurationCatalysis
 
getNCellsZ() - Method in class etomica.modules.sam.ConfigurationSAM
 
getNCrossLinkersAcid() - Method in class etomica.modules.chainequilibrium.ChainEquilibriumSim
 
getNDiAcid() - Method in class etomica.modules.chainequilibrium.ChainEquilibriumSim
 
getNDiol() - Method in class etomica.modules.chainequilibrium.ChainEquilibriumSim
 
getNGraft() - Method in class etomica.modules.colloid.ConfigurationColloid
 
getNMonoAcid() - Method in class etomica.modules.chainequilibrium.ChainEquilibriumSim
 
getNMonoOl() - Method in class etomica.modules.chainequilibrium.ChainEquilibriumSim
 
getnReactCO() - Method in class etomica.modules.catalysis.ReactionManagerCO
 
getNumAlpha() - Method in class etomica.modules.multiharmonic.mbar.MeterMBAR
 
getNumber() - Method in class etomica.modules.materialfracture.StrainColorScheme
 
getNumCO() - Method in class etomica.modules.catalysis.ConfigurationCatalysis
 
getNumMembraneLayers() - Method in class etomica.modules.rosmosis.ConfigurationMembrane
 
getNumMembraneLayers() - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
Returns the number of membrane layers.
getNumO2() - Method in class etomica.modules.catalysis.ConfigurationCatalysis
 
getNumSurfaceSites() - Method in class etomica.modules.catalysis.P2SquareWellBonding
 
getNumSurfaceSites() - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
 
getNumXCells() - Method in class etomica.modules.sam.Sam
 
getNumZCells() - Method in class etomica.modules.sam.Sam
 
getOffset() - Method in class etomica.modules.sam.P1Sinusoidal
 
getOverlapAverageAndError() - Method in class etomica.modules.multiharmonic.overlap.DataOverlapCaching
 
getPanel() - Method in class etomica.modules.crystalviewer.ClipPlaneEditor
 
getPanel() - Method in class etomica.modules.crystalviewer.LatticeEditor
 
getParameters() - Static method in class etomica.modules.render.RenderMD
 
getPoreCenters() - Method in class etomica.modules.dcvgcmd.P1WCAPorousWall
 
getPoreRadius() - Method in class etomica.modules.dcvgcmd.P1WCAPorousWall
 
getPotentialMaster() - Method in class etomica.modules.vle.MeterPressure2
Returns the integrator associated with this instance.
getPressureTensor() - Method in class etomica.modules.droplet.IntegratorDroplet
Returns the pressure tensor based on the forces calculated during the last time step.
getProfileDataInfo() - Method in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
 
getProfileDim() - Method in class etomica.modules.interfacial.DataProcessorInterfacialTensionProfile
 
getRange() - Method in class etomica.modules.adsorption.P1Wall
 
getRange() - Method in class etomica.modules.catalysis.P2SquareWellBonding
 
getRange() - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
 
getRange() - Method in class etomica.modules.catalysis.P2SquareWellSurface
 
getRange() - Method in class etomica.modules.colloid.P1Wall
 
getRange() - Method in class etomica.modules.dcvgcmd.P1WCAPorousWall
 
getRange() - Method in class etomica.modules.dcvgcmd.P1WCAWall
 
getRange() - Method in class etomica.modules.droplet.P1Smash
 
getRange() - Method in class etomica.modules.droplet.P2Cohesion
 
getRange() - Method in class etomica.modules.materialfracture.P1Tension
 
getRange() - Method in class etomica.modules.mu.P2SquareWellOneSide
 
getRange() - Method in class etomica.modules.sam.P1Sinusoidal
 
getRange() - Method in class etomica.modules.sam.P1WCAWall
 
getShearRate() - Method in class etomica.modules.rheology.IntegratorPolymer
 
getShearRateNumber() - Method in class etomica.modules.rheology.IntegratorPolymer
 
getSigma() - Method in class etomica.modules.adsorption.P1Wall
 
getSigma() - Method in class etomica.modules.colloid.P1Wall
 
getSigma() - Method in class etomica.modules.dcvgcmd.P1WCAPorousWall
Returns the radius.
getSigma() - Method in class etomica.modules.dcvgcmd.P1WCAWall
Returns the radius.
getSigma() - Method in class etomica.modules.sam.P1WCAWall
Returns the radius.
getSigma() - Method in class etomica.modules.vle.VLESim
 
getSigmaColloid() - Method in class etomica.modules.colloid.ConfigurationColloid
 
getSigmaMonomer() - Method in class etomica.modules.colloid.ConfigurationColloid
 
getSimulation() - Method in class etomica.modules.junit.crystalviewer.LatticePlaneTestUtility
 
getSoluteMoleFraction() - Method in class etomica.modules.rosmosis.ConfigurationMembrane
 
getSoluteMoleFraction() - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
Returns the mole fraction of solutes within the solute chamber.
getSolutionChamberDensity() - Method in class etomica.modules.rosmosis.ConfigurationMembrane
 
getSolutionChamberDensity() - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
Returns the number density of the solution chamber
getSolventChamberDensity() - Method in class etomica.modules.rosmosis.ConfigurationMembrane
 
getSolventChamberDensity() - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
Returns the number density of the solvent chamber
getSolventThermoFrac() - Method in class etomica.modules.chainequilibrium.P2SquareWellBonded
Returns the fraction of well energy that is gained or lost by an atom pair when they hop in or leave their well.
getSpecies() - Method in class etomica.modules.junit.crystalviewer.LatticePlaneTestUtility
 
getSpecies() - Method in class etomica.modules.rosmosis.MeterFlux
 
getSpeciesAgentClass() - Method in class etomica.modules.chainequilibrium.ColorSchemeStepWise
 
getSpeciesMembrane() - Method in class etomica.modules.rosmosis.ConfigurationMembrane
 
getSpeciesMembrane() - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
 
getSpeciesSolute() - Method in class etomica.modules.rosmosis.ConfigurationMembrane
 
getSpeciesSolute1() - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
 
getSpeciesSolute2() - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
 
getSpeciesSolvent() - Method in class etomica.modules.rosmosis.ConfigurationMembrane
 
getSpeciesSolvent() - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
 
getSpringConstant() - Method in class etomica.modules.materialfracture.P1Tension
 
getSpringConstantDimension() - Method in class etomica.modules.materialfracture.P1Tension
Not implemented correctly.
getSqErr(double[], double[]) - Method in class etomica.modules.interfacial.FitTanh
 
getSulfurType() - Method in class etomica.modules.sam.SpeciesAlkaneThiol
 
getSurfaceColor() - Method in class etomica.modules.droplet.ColorSchemeDropletSurface
 
getSurfaceYOffset() - Method in class etomica.modules.catalysis.ConfigurationCatalysis
 
getSurfaceYOffset() - Method in class etomica.modules.sam.ConfigurationSAM
 
getTag() - Method in class etomica.modules.adsorption.DataSourceDensityFunction
 
getTag() - Method in class etomica.modules.catalysis.DataSourceWallPressureCatalysis
 
getTag() - Method in class etomica.modules.chainequilibrium.MeterChainLength
 
getTag() - Method in class etomica.modules.droplet.MeterDeformation
 
getTag() - Method in class etomica.modules.entropylottery.DataSourceProbabilityDensity
 
getTag() - Method in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile.DataSourceVirialProfile
 
getTag() - Method in class etomica.modules.interfacial.MeterOrientation
 
getTag() - Method in class etomica.modules.mu.DataSourceWallPressureMu
 
getTag() - Method in class etomica.modules.multiharmonic.mbar.MeterMBAR
 
getTag() - Method in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceAlphaChi
 
getTag() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaAlpha
 
getTag() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaChi
 
getTag() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
 
getTag() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceFunctionRaw
 
getTag() - Method in class etomica.modules.multiharmonic.umbrella.MeterUmbrella
 
getTag() - Method in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaAlpha
 
getTag() - Method in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaChi
 
getTag() - Method in class etomica.modules.reactionequilibrium.MeterDimerFraction
 
getTag() - Method in class etomica.modules.rosmosis.MeterFlux
 
getTag() - Method in class etomica.modules.rosmosis.MeterOsmoticPressure
 
getTag() - Method in class etomica.modules.sam.MeterTilt
 
getTemperature() - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
 
getTolerance() - Method in class etomica.modules.interfacial.FitTanh
 
getUa2(int) - Method in class etomica.modules.multiharmonic.overlap.AccumulatorOverlapAverageUa2
Returns average value of expression used to determine optimal Bennet parameter (value[1]/(value[1]+expX[iParam]).
getuReactCO() - Method in class etomica.modules.catalysis.ReactionManagerCO
 
getuReactCORev() - Method in class etomica.modules.catalysis.ReactionManagerCO
 
getUseSurfaceOnly() - Method in class etomica.modules.droplet.P2Cohesion
 
getValue() - Method in class etomica.modules.adsorption.ModifierPMu
 
getValue() - Method in class etomica.modules.colloid.ColloidGraphic.WallRangeModifier
 
getValue() - Method in class etomica.modules.crystalviewer.LatticeEditor.NModifier
 
getValue() - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD.Mu1Modulator
 
getValue() - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD.Mu2Modulator
 
getValue() - Method in class etomica.modules.droplet.DropletGraphic.ModifierBoxSize
 
getValue() - Method in class etomica.modules.entropylottery.ModifierDimensions
 
getValue() - Method in class etomica.modules.interfacial.InterfacialSWGraphic.ModifierBoxSize
 
getValue() - Method in class etomica.modules.mu.MuGraphic.ModifierAtomDiameter
 
getValue() - Method in class etomica.modules.mu.MuGraphic.ModifierEpsilon
 
getValue() - Method in class etomica.modules.mu.MuGraphic.ModifierLambda
 
getValue() - Method in class etomica.modules.pistoncylinder.ModifierPistonPressure
 
getValue() - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic.ModifierAtomDiameter
 
getValue() - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic.ModifierPistonDensity
 
getValue() - Method in class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierAtomDiameter
 
getValue() - Method in class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierEpsilon
 
getValue() - Method in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierAtomDiameter
 
getValue() - Method in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierEpsilon
 
getValue() - Method in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierSoluteCharge
 
getValue() - Method in class etomica.modules.sam.SamGraphic.ModifierWallPosition
 
getValue() - Method in class etomica.modules.swmd.SwmdGraphic.ModifierAtomDiameter
 
getVaporColor() - Method in class etomica.modules.droplet.ColorSchemeLiquidVapor
 
getVirialProfile() - Method in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
Current value of the meter, obtained by dividing sum of collision virial contributions by time elapsed since last call.
getWallDim() - Method in class etomica.modules.dcvgcmd.P1WCAWall
 
getWallDim() - Method in class etomica.modules.sam.P1WCAWall
 
getWallForce() - Method in interface etomica.modules.rosmosis.IPotentialCalculationWallForce
 
getWallForce() - Method in class etomica.modules.rosmosis.PotentialCalculationForceSumWallForce
 
getWallForce() - Method in class etomica.modules.rosmosis.PotentialCalculationTorqueSumWallForce
 
getWallForce() - Method in class etomica.modules.sam.PotentialCalculationForceSumWall
 
getWallPosition() - Method in class etomica.modules.sam.P1WCAWall
 
getWallPotential() - Method in class etomica.modules.sam.PotentialCalculationForceSumWall
 
getYScale() - Method in class etomica.modules.entropylottery.DisplayBoxCanvas1DBins
 
getZ() - Method in class etomica.modules.dcvgcmd.P1WCAPorousWall
 
getZFraction() - Method in class etomica.modules.adsorption.MyMCMove
 
getZFraction() - Method in class etomica.modules.dcvgcmd.MyMCMove
Returns the zFraction.
goButton - Variable in class etomica.modules.clustergenerator.MyApplet
 
goFastButton - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
 
gradient(IAtomList) - Method in class etomica.modules.dcvgcmd.P1WCAPorousWall
 
gradient(IAtomList, Tensor) - Method in class etomica.modules.dcvgcmd.P1WCAPorousWall
 
gradient - Variable in class etomica.modules.dcvgcmd.P1WCAWall
 
gradient(IAtomList) - Method in class etomica.modules.dcvgcmd.P1WCAWall
 
gradient(IAtomList, Tensor) - Method in class etomica.modules.dcvgcmd.P1WCAWall
 
gradient - Variable in class etomica.modules.droplet.P1Smash
 
gradient(IAtomList, Tensor) - Method in class etomica.modules.droplet.P1Smash
 
gradient(IAtomList) - Method in class etomica.modules.droplet.P1Smash
 
gradient(IAtomList, Tensor) - Method in class etomica.modules.droplet.P2Cohesion
 
gradient(IAtomList) - Method in class etomica.modules.droplet.P2Cohesion
 
gradient(IAtomList, Tensor) - Method in class etomica.modules.materialfracture.P1Tension
 
gradient(IAtomList) - Method in class etomica.modules.materialfracture.P1Tension
 
gradient - Variable in class etomica.modules.rosmosis.P1Tether
 
gradient(IAtomList) - Method in class etomica.modules.rosmosis.P1Tether
 
gradient(IAtomList, Tensor) - Method in class etomica.modules.rosmosis.P1Tether
 
gradient - Variable in class etomica.modules.sam.P1Sinusoidal
 
gradient(IAtomList) - Method in class etomica.modules.sam.P1Sinusoidal
 
gradient(IAtomList, Tensor) - Method in class etomica.modules.sam.P1Sinusoidal
 
gradient - Variable in class etomica.modules.sam.P1WCAWall
 
gradient(IAtomList) - Method in class etomica.modules.sam.P1WCAWall
 
gradient(IAtomList, Tensor) - Method in class etomica.modules.sam.P1WCAWall
 
GraftAction(int) - Constructor for class etomica.modules.colloid.ColloidGraphic.GraftAction
 
graftVectors - Variable in class etomica.modules.colloid.ConfigurationColloid
 
graphic - Variable in class etomica.modules.droplet.EllipseDisplayAction
 
graphic() - Method in class etomica.modules.osmosis.Osmosis.InitializeMolecules
 
graphic(Object) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
 
graphicOut - Variable in class etomica.modules.clustergenerator.MyApplet
 
graphicOut2 - Variable in class etomica.modules.clustergenerator.MyApplet
 
graphicsToggler - Variable in class etomica.modules.clustergenerator.MyApplet
 
GraphicsToggler() - Constructor for class etomica.modules.clustergenerator.MyApplet.GraphicsToggler
 
greys - Variable in class etomica.modules.chainequilibrium.ColorSchemeRadical
 

H

halfL - Variable in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
 
harmonicStrength - Variable in class etomica.modules.sam.Sam
 
HCP - Variable in class etomica.modules.junit.crystalviewer.LatticePlaneTestUtility
 
headType - Variable in class etomica.modules.interfacial.InterfacialSW
 
hex - Variable in class etomica.modules.materialfracture.MeterElongation
 
hex - Variable in class etomica.modules.materialfracture.MeterStrain
 
hex - Variable in class etomica.modules.materialfracture.StrainColorScheme
 
HEXAGONAL - Variable in class etomica.modules.junit.crystalviewer.LatticePlaneTestUtility
 
highlightColor - Variable in class etomica.modules.crystalviewer.ClipPlaneEditor
 
hist - Variable in class etomica.modules.insertion.InsertionGraphic.MeterWidom
 
historyLength - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
 
hyperVirial(IAtomList) - Method in class etomica.modules.droplet.P2Cohesion
 

I

i(double, int) - Method in class etomica.modules.droplet.IntegratorDroplet
 
IDEAL_GAS - Static variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
 
identity - Variable in class etomica.modules.droplet.IntegratorDroplet
 
ig - Variable in class etomica.modules.mu.MeterDensitySides
 
ignoredAtomType - Variable in class etomica.modules.chainequilibrium.MeterChainLength
 
ignoreOverlap - Variable in class etomica.modules.mu.P2SquareWellOneSide
 
index - Variable in class etomica.modules.multiharmonic.mbar.MeterMBAR
 
init() - Method in class etomica.modules.adsorption.AdsorptionGraphic.Applet
 
init() - Method in class etomica.modules.catalysis.CatalysisGraphic.Applet
 
init() - Method in class etomica.modules.chainequilibrium.ChainEquilibriumGraphic.Applet
 
init() - Method in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationGraphic.Applet
 
init() - Method in class etomica.modules.clustergenerator.MyApplet
 
init() - Method in class etomica.modules.colloid.ColloidGraphic.Applet
 
init() - Method in class etomica.modules.crystalviewer.CrystalViewer.Applet
 
init() - Method in class etomica.modules.dcvgcmd.DCVGCMDGraphic.Applet
 
init() - Method in class etomica.modules.droplet.DropletAtomicGraphic.Applet
 
init() - Method in class etomica.modules.droplet.DropletGraphic.Applet
 
init() - Method in class etomica.modules.ensembles.LJMCGraphic.Applet
 
init() - Method in class etomica.modules.entropylottery.EntropyLotteryGraphic.Applet
 
init() - Method in class etomica.modules.insertion.InsertionGraphic.Applet
 
init() - Method in class etomica.modules.interfacial.InterfacialSWGraphic.Applet
 
init() - Method in class etomica.modules.joulethomson.JouleThomson.Applet
 
init() - Method in class etomica.modules.ljmd.LjmdGraphic.Applet
 
init() - Method in class etomica.modules.materialfracture.MaterialFractureGraphic.Applet
 
init() - Method in class etomica.modules.mu.MuGraphic.Applet
 
init() - Method in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.Applet
 
init() - Method in class etomica.modules.multiharmonic.MultiharmonicGraphic.Applet
 
init() - Method in class etomica.modules.multiharmonic.MultiharmonicGraphicMC.Applet
 
init() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.Applet
 
init() - Method in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.Applet
 
init() - Method in class etomica.modules.osmosis.Osmosis.Applet
 
init() - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic.Applet
 
init() - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic
Initialize all the bits based on previously set doConfigButton and doRDF.
init() - Method in class etomica.modules.reactionequilibrium.ReactionEquilibriumGraphic.Applet
 
init() - Method in class etomica.modules.rheology.RheologyGraphic.Applet
 
init() - Method in class etomica.modules.rosmosis.ReverseOsmosisGraphic.Applet
 
init() - Method in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.Applet
 
init() - Method in class etomica.modules.sam.SamGraphic.Applet
 
init() - Method in class etomica.modules.swmd.SwmdGraphic.Applet
 
init() - Method in class etomica.modules.vle.B2Fit.Applet
 
init() - Method in class etomica.modules.vle.VLE.Applet
 
initCar - Variable in class etomica.modules.render.RenderMD.RenderMDParam
 
initializeCoordinates(IBox) - Method in class etomica.modules.catalysis.ConfigurationCatalysis
 
initializeCoordinates(IBox) - Method in class etomica.modules.chainequilibrium.ConfigurationLatticeFreeRadical
Places the molecules in the given box on the positions of the lattice.
initializeCoordinates(IBox) - Method in class etomica.modules.chainequilibrium.ConfigurationLatticeRandom
 
initializeCoordinates(IBox) - Method in class etomica.modules.colloid.ConfigurationColloid
 
initializeCoordinates(IBox) - Method in class etomica.modules.dcvgcmd.ConfigurationLatticeTube
 
initializeCoordinates(IBox) - Method in class etomica.modules.droplet.ConfigurationDroplet
 
initializeCoordinates(IBox) - Method in class etomica.modules.entropylottery.ConfigurationZero
 
initializeCoordinates(IBox) - Method in class etomica.modules.rosmosis.ConfigurationMembrane
 
initializeCoordinates(IBox) - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
 
initializeCoordinates(IBox) - Method in class etomica.modules.sam.ConfigurationSAM
 
InitializeMolecules(ConfigurationLatticeWithPlane, SimulationRestart) - Constructor for class etomica.modules.osmosis.Osmosis.InitializeMolecules
 
initializePositions(IAtomList) - Method in class etomica.modules.dcvgcmd.ConformationTube
 
initializePositions(IAtomList) - Method in class etomica.modules.rheology.ConformationPolymer
 
initializing - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibrium
 
initializing - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibriumGraphic
 
initialSolute - Static variable in class etomica.modules.osmosis.OsmosisSim
 
initialSolvent - Static variable in class etomica.modules.osmosis.OsmosisSim
 
Insertion - Class in etomica.modules.insertion
 
Insertion(Space) - Constructor for class etomica.modules.insertion.Insertion
 
InsertionGraphic - Class in etomica.modules.insertion
 
InsertionGraphic(Insertion, Space) - Constructor for class etomica.modules.insertion.InsertionGraphic
 
InsertionGraphic.Applet - Class in etomica.modules.insertion
 
InsertionGraphic.MeterWidom - Class in etomica.modules.insertion
 
integrator - Variable in class etomica.modules.adsorption.ModifierPMu
 
integrator - Variable in class etomica.modules.adsorption.P1Wall
 
integrator - Variable in class etomica.modules.catalysis.Catalysis
 
integrator - Variable in class etomica.modules.colloid.ColloidSim
 
integrator - Variable in class etomica.modules.droplet.Droplet
 
integrator - Variable in class etomica.modules.droplet.DropletAtomic
 
integrator - Variable in class etomica.modules.ensembles.LJMC
 
integrator - Variable in class etomica.modules.entropylottery.EntropyLottery
 
integrator - Variable in class etomica.modules.insertion.Insertion
 
integrator - Variable in class etomica.modules.interfacial.InterfacialSW
 
integrator - Variable in class etomica.modules.ljmd.Ljmd
 
integrator - Variable in class etomica.modules.materialfracture.MaterialFracture
 
integrator - Variable in class etomica.modules.mu.Mu
 
integrator - Variable in class etomica.modules.mu.MuGraphic.DataProcessorMu
 
integrator - Variable in class etomica.modules.mu.MuGraphic.ModifierEpsilon
 
integrator - Variable in class etomica.modules.mu.MuGraphic.ModifierLambda
 
integrator - Variable in class etomica.modules.multiharmonic.overlap.DataOverlapCaching
 
integrator - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicMC
 
integrator - Variable in class etomica.modules.osmosis.OsmosisSim
 
integrator - Variable in class etomica.modules.pistoncylinder.PistonCylinder
 
integrator - Variable in class etomica.modules.render.RenderMD
The Integrator performing the dynamics.
integrator - Variable in class etomica.modules.rheology.MeterNormalStress
 
integrator - Variable in class etomica.modules.rheology.MeterViscosity
 
integrator - Variable in class etomica.modules.rheology.SimulationRheology
 
integrator - Variable in class etomica.modules.rosmosis.MeterFlux
 
integrator - Variable in class etomica.modules.rosmosis.ReverseOsmosis
 
integrator - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
 
integrator - Variable in class etomica.modules.sam.Sam
 
integrator - Variable in class etomica.modules.swmd.Swmd
 
integrator1 - Variable in class etomica.modules.vle.DeviceThermoSliderGEMC
 
integrator2 - Variable in class etomica.modules.vle.DeviceThermoSliderGEMC
 
integratorA - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicMC
 
integratorA - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicMC
 
integratorB - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicMC
 
integratorB - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicMC
 
integratorDCV - Variable in class etomica.modules.dcvgcmd.DCVGCMD
 
IntegratorDCVGCMD - Class in etomica.modules.dcvgcmd
 
IntegratorDCVGCMD(IPotentialMaster, double, ISpace, ISpecies, ISpecies) - Constructor for class etomica.modules.dcvgcmd.IntegratorDCVGCMD
 
IntegratorDCVGCMD.Mu1Modulator - Class in etomica.modules.dcvgcmd
 
IntegratorDCVGCMD.Mu2Modulator - Class in etomica.modules.dcvgcmd
 
IntegratorDroplet - Class in etomica.modules.droplet
Mesoscale integrator for Droplet module.
IntegratorDroplet(ISimulation, IPotentialMaster, ISpace) - Constructor for class etomica.modules.droplet.IntegratorDroplet
 
IntegratorDroplet(IPotentialMaster, IRandom, double, double, ISpace) - Constructor for class etomica.modules.droplet.IntegratorDroplet
 
IntegratorDroplet.MyAgent - Class in etomica.modules.droplet
 
integratorGEMC - Variable in class etomica.modules.vle.VLESim
 
integratorHard - Variable in class etomica.modules.catalysis.DataSourceWallPressureCatalysis
 
integratorHard - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
 
integratorHard - Variable in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
 
integratorHard - Variable in class etomica.modules.mu.DataSourceWallPressureMu
 
integratorHard1 - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibrium
 
IntegratorHardPiston - Class in etomica.modules.pistoncylinder
Integrator for DMD with a piston (P1HardMovingBoundary)
IntegratorHardPiston(ISimulation, IPotentialMaster, P1HardMovingBoundary, ISpace) - Constructor for class etomica.modules.pistoncylinder.IntegratorHardPiston
 
integratorHybrid - Variable in class etomica.modules.adsorption.Adsorption
 
IntegratorHybrid - Class in etomica.modules.adsorption
 
IntegratorHybrid(PotentialMasterHybrid, IntegratorMD, IntegratorMC, double) - Constructor for class etomica.modules.adsorption.IntegratorHybrid
 
integratorInitialized(IIntegratorEvent) - Method in class etomica.modules.catalysis.ReactionManagerCO
 
integratorInitialized(IIntegratorEvent) - Method in class etomica.modules.multiharmonic.mbar.MeterMBAR
 
IntegratorJT - Class in etomica.modules.joulethomson
 
IntegratorJT(IRandom, IntegratorBox, IntegratorBox) - Constructor for class etomica.modules.joulethomson.IntegratorJT
 
IntegratorJT.EnsembleToggler - Class in etomica.modules.joulethomson
 
integratorLiquid - Variable in class etomica.modules.vle.VLESim
 
integratorMC - Variable in class etomica.modules.adsorption.Adsorption
 
integratorMC - Variable in class etomica.modules.adsorption.IntegratorHybrid
 
integratorMD - Variable in class etomica.modules.adsorption.Adsorption
 
integratorMD - Variable in class etomica.modules.adsorption.IntegratorHybrid
 
integratorOS - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicMC
 
integratorOS - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceUa2
 
integratorOS - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicMC
 
IntegratorPolymer - Class in etomica.modules.rheology
Integrator for Brownian dynamics of a polymer in a flow field.
IntegratorPolymer(IPotentialMaster, IRandom, double, double, ISpace) - Constructor for class etomica.modules.rheology.IntegratorPolymer
 
integratorStepFinished(IIntegratorEvent) - Method in class etomica.modules.catalysis.ReactionManagerCO
 
integratorStepFinished(IIntegratorEvent) - Method in class etomica.modules.multiharmonic.mbar.MeterMBAR
 
integratorStepStarted(IIntegratorEvent) - Method in class etomica.modules.catalysis.ReactionManagerCO
 
integratorStepStarted(IIntegratorEvent) - Method in class etomica.modules.multiharmonic.mbar.MeterMBAR
 
integratorVapor - Variable in class etomica.modules.vle.VLESim
 
IntegratorVelocityVerletSAM - Class in etomica.modules.sam
Special integrator subclass that has the ability to prevent sulfur atoms from moving in the Y direction.
IntegratorVelocityVerletSAM(IPotentialMaster, IRandom, double, double, ISpace) - Constructor for class etomica.modules.sam.IntegratorVelocityVerletSAM
 
interactionAgentManager - Variable in class etomica.modules.catalysis.DataSourceWallPressureCatalysis
 
interactionAgentManager - Variable in class etomica.modules.catalysis.MeterDensityCO
 
interactionAgentManager - Variable in class etomica.modules.catalysis.MeterDensityCO2
 
interactionAgentManager - Variable in class etomica.modules.catalysis.MeterDensityO2
 
interactionTracker - Variable in class etomica.modules.catalysis.Catalysis
 
InteractionTracker - Class in etomica.modules.catalysis
 
InteractionTracker(IBox, ISpecies) - Constructor for class etomica.modules.catalysis.InteractionTracker
 
InteractionTracker.CatalysisAgent - Class in etomica.modules.catalysis
 
InterfacialSW - Class in etomica.modules.interfacial
Simulation for interfacial tension module.
InterfacialSW(Space) - Constructor for class etomica.modules.interfacial.InterfacialSW
 
InterfacialSWGraphic - Class in etomica.modules.interfacial
Graphic UI for interfacial tension module.
InterfacialSWGraphic(InterfacialSW, Space) - Constructor for class etomica.modules.interfacial.InterfacialSWGraphic
 
InterfacialSWGraphic.Applet - Class in etomica.modules.interfacial
 
InterfacialSWGraphic.DataProcessorTensorSplitter - Class in etomica.modules.interfacial
Inner class to find the total pressure of the system from the pressure tensor.
InterfacialSWGraphic.ModifierBoxSize - Class in etomica.modules.interfacial
 
interiorColor - Variable in class etomica.modules.droplet.ColorSchemeDropletSurface
 
IPotentialCalculationWallForce - Interface in etomica.modules.rosmosis
 
isAdiabatic() - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
 
isBroken - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceAlphaChi
 
isEmpty(IAtom) - Method in class etomica.modules.chainequilibrium.P2SquareWellRadical
 
isExpanded - Variable in class etomica.modules.interfacial.InterfacialSWGraphic
 
isIncludeLrc() - Method in class etomica.modules.vle.MeterPressure2
Indicates whether calculated energy should include long-range correction for potential truncation (true) or not (false).
isIsothermal() - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
 
isLiquid - Variable in class etomica.modules.adsorption.DataSourceDensityFunction
 
isRadical - Variable in class etomica.modules.catalysis.InteractionTracker.CatalysisAgent
 
isRadical(IAtom) - Method in class etomica.modules.chainequilibrium.P2SquareWellRadical
This function return true if the given atom is a radical (meaning that it has only one unreacted site).
isUpperBound - Variable in class etomica.modules.multiharmonic.DataProcessorBounds
 
itemStateChanged(ItemEvent) - Method in class etomica.modules.clustergenerator.MyApplet.BondInteractionTypeToggler
 
itemStateChanged(ItemEvent) - Method in class etomica.modules.clustergenerator.MyApplet.BondTypeToggler
 
itemStateChanged(ItemEvent) - Method in class etomica.modules.clustergenerator.MyApplet.ConnectedToggler
 
itemStateChanged(ItemEvent) - Method in class etomica.modules.clustergenerator.MyApplet.GraphicsToggler
 
itemStateChanged(ItemEvent) - Method in class etomica.modules.clustergenerator.MyApplet.NumbersToggler
 
itemStateChanged(ItemEvent) - Method in class etomica.modules.clustergenerator.MyApplet.PointsToggler
 
itemStateChanged(ItemEvent) - Method in class etomica.modules.clustergenerator.MyApplet.ReeHooverToggler
 
itemStateChanged(ItemEvent) - Method in class etomica.modules.joulethomson.JouleThomson.SpeciesChooser
 
iterator - Variable in class etomica.modules.multiharmonic.MCMoveMultiHarmonic
 

J

JouleThomson - Class in etomica.modules.joulethomson
Joule Thomson Experiment Ed Maginn [University of Notre Dame], David Kofke [University at Buffalo] Permits study of a system undergoing isothermal or isenthalpic expansion and compression.
JouleThomson(JouleThomsonSim, Space) - Constructor for class etomica.modules.joulethomson.JouleThomson
 
JouleThomson.Applet - Class in etomica.modules.joulethomson
 
JouleThomson.SpeciesChooser - Class in etomica.modules.joulethomson
 
JouleThomsonSim - Class in etomica.modules.joulethomson
 
JouleThomsonSim() - Constructor for class etomica.modules.joulethomson.JouleThomsonSim
 
JouleThomsonSim(Space) - Constructor for class etomica.modules.joulethomson.JouleThomsonSim
 

L

L - Variable in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
 
lambda - Variable in class etomica.modules.adsorption.EOSSW
 
lambda - Variable in class etomica.modules.catalysis.P2SquareWellBonding
 
lambda - Variable in class etomica.modules.catalysis.P2SquareWellBondingCO
 
lambda - Variable in class etomica.modules.catalysis.P2SquareWellSurface
 
lambda - Variable in class etomica.modules.insertion.InsertionGraphic
 
lambda - Variable in class etomica.modules.mu.P2SquareWellOneSide
 
lambda - Variable in class etomica.modules.pistoncylinder.PistonCylinder
 
lambda - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
 
lambda - Variable in class etomica.modules.render.RenderMD.RenderMDParam
 
lambda - Variable in class etomica.modules.swmd.SwmdGraphic
 
lamBox - Variable in class etomica.modules.insertion.InsertionGraphic
 
lamBox - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
 
lamBox - Variable in class etomica.modules.swmd.SwmdGraphic
 
lastCollisionVirial() - Method in class etomica.modules.adsorption.P1Wall
 
lastCollisionVirial - Variable in class etomica.modules.catalysis.P2SquareWellBonding
 
lastCollisionVirial() - Method in class etomica.modules.catalysis.P2SquareWellBonding
 
lastCollisionVirial - Variable in class etomica.modules.catalysis.P2SquareWellBondingCO
 
lastCollisionVirial() - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
 
lastCollisionVirial - Variable in class etomica.modules.catalysis.P2SquareWellSurface
 
lastCollisionVirial() - Method in class etomica.modules.catalysis.P2SquareWellSurface
 
lastCollisionVirial() - Method in class etomica.modules.colloid.P1Wall
 
lastCollisionVirial() - Method in class etomica.modules.mu.P1MagicWall
not yet implemented
lastCollisionVirial - Variable in class etomica.modules.mu.P2SquareWellOneSide
 
lastCollisionVirial() - Method in class etomica.modules.mu.P2SquareWellOneSide
 
lastCollisionVirial() - Method in class etomica.modules.osmosis.P1HardWall
not yet implemented
lastCollisionVirialr2 - Variable in class etomica.modules.catalysis.P2SquareWellBonding
 
lastCollisionVirialr2 - Variable in class etomica.modules.catalysis.P2SquareWellBondingCO
 
lastCollisionVirialr2 - Variable in class etomica.modules.catalysis.P2SquareWellSurface
 
lastCollisionVirialr2 - Variable in class etomica.modules.mu.P2SquareWellOneSide
 
lastCollisionVirialTensor() - Method in class etomica.modules.adsorption.P1Wall
 
lastCollisionVirialTensor - Variable in class etomica.modules.catalysis.P2SquareWellBonding
 
lastCollisionVirialTensor() - Method in class etomica.modules.catalysis.P2SquareWellBonding
 
lastCollisionVirialTensor - Variable in class etomica.modules.catalysis.P2SquareWellBondingCO
 
lastCollisionVirialTensor() - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
 
lastCollisionVirialTensor - Variable in class etomica.modules.catalysis.P2SquareWellSurface
 
lastCollisionVirialTensor() - Method in class etomica.modules.catalysis.P2SquareWellSurface
 
lastCollisionVirialTensor() - Method in class etomica.modules.colloid.P1Wall
 
lastCollisionVirialTensor() - Method in class etomica.modules.mu.P1MagicWall
not yet implemented.
lastCollisionVirialTensor - Variable in class etomica.modules.mu.P2SquareWellOneSide
 
lastCollisionVirialTensor() - Method in class etomica.modules.mu.P2SquareWellOneSide
 
lastCollisionVirialTensor() - Method in class etomica.modules.osmosis.P1HardWall
not yet implemented.
lastDeltaU - Variable in class etomica.modules.mu.P1MagicWall
 
lastEnergyChange - Variable in class etomica.modules.adsorption.P1Wall
 
lastEnergyChange - Variable in class etomica.modules.catalysis.P2SquareWellBonding
 
lastEnergyChange - Variable in class etomica.modules.catalysis.P2SquareWellBondingCO
 
lastEnergyChange - Variable in class etomica.modules.catalysis.P2SquareWellSurface
 
lastEnergyChange - Variable in class etomica.modules.colloid.P1Wall
 
lastEnergyChange - Variable in class etomica.modules.mu.P2SquareWellOneSide
 
lastProfileTime - Variable in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
 
lastResult - Variable in class etomica.modules.multiharmonic.overlap.DataOverlapCaching
 
lastStepCount - Variable in class etomica.modules.multiharmonic.overlap.DataOverlapCaching
 
lastStepPop - Variable in class etomica.modules.multiharmonic.overlap.DataOverlapCaching
 
lastTime - Variable in class etomica.modules.catalysis.DataSourceWallPressureCatalysis
 
lastTime - Variable in class etomica.modules.insertion.InsertionGraphic.MeterWidom
 
lastTime - Variable in class etomica.modules.mu.DataSourceWallPressureMu
 
lastTime2 - Variable in class etomica.modules.insertion.InsertionGraphic.MeterWidom
 
lastVirial - Variable in class etomica.modules.adsorption.P1Wall
 
lastVirial - Variable in class etomica.modules.colloid.P1Wall
 
lastVirialTensor - Variable in class etomica.modules.adsorption.P1Wall
 
lastVirialTensor - Variable in class etomica.modules.colloid.P1Wall
 
lastWallVirial() - Method in class etomica.modules.adsorption.P1Wall
 
lastWallVirial() - Method in class etomica.modules.colloid.P1Wall
 
LatticeCubicSimpleLatticePlaneTest - Class in etomica.modules.junit.crystalviewer
 
LatticeCubicSimpleLatticePlaneTest(String) - Constructor for class etomica.modules.junit.crystalviewer.LatticeCubicSimpleLatticePlaneTest
 
LatticeCubicSimpleLatticePlaneTest.DoubleTwoDArray - Class in etomica.modules.junit.crystalviewer
 
latticeEditor - Variable in class etomica.modules.crystalviewer.CrystalViewer
 
LatticeEditor - Class in etomica.modules.crystalviewer
Class that produces a panel with controls that permit editing of the structure of a lattice.
LatticeEditor(CrystalViewer, BravaisLattice[], String[], ISpace) - Constructor for class etomica.modules.crystalviewer.LatticeEditor
 
LatticeEditor.NModifier - Class in etomica.modules.crystalviewer
 
latticeNameHash - Variable in class etomica.modules.crystalviewer.LatticeEditor
 
latticePlane - Variable in class etomica.modules.crystalviewer.ClipPlaneEditor
 
latticePlane() - Method in class etomica.modules.crystalviewer.ClipPlaneEditor
 
latticePlane - Variable in class etomica.modules.crystalviewer.CrystalViewer
 
LatticePlaneTestUtility - Class in etomica.modules.junit.crystalviewer
 
LatticePlaneTestUtility() - Constructor for class etomica.modules.junit.crystalviewer.LatticePlaneTestUtility
 
leafType - Variable in class etomica.modules.interfacial.InterfacialSW
 
LengthAgent() - Constructor for class etomica.modules.chainequilibrium.AtomFilterChainLength.LengthAgent
 
LengthAgent() - Constructor for class etomica.modules.chainequilibrium.ColorSchemeRadical.LengthAgent
 
Li - Variable in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
 
linker - Variable in class etomica.modules.chainequilibrium.P2SquareWellBonded.RingResult
 
liquidColor - Variable in class etomica.modules.droplet.ColorSchemeLiquidVapor
 
liquidFilter - Variable in class etomica.modules.droplet.ColorSchemeDropletSurface
 
liquidFilter - Variable in class etomica.modules.droplet.ColorSchemeLiquidVapor
 
liquidFilter - Variable in class etomica.modules.droplet.Droplet
 
liquidFilter - Variable in class etomica.modules.droplet.P2Cohesion
 
LJMC - Class in etomica.modules.ensembles
 
LJMC(Space) - Constructor for class etomica.modules.ensembles.LJMC
 
LJMCGraphic - Class in etomica.modules.ensembles
 
LJMCGraphic(LJMC, Space) - Constructor for class etomica.modules.ensembles.LJMCGraphic
 
LJMCGraphic.Applet - Class in etomica.modules.ensembles
 
Ljmd - Class in etomica.modules.ljmd
 
Ljmd(Space) - Constructor for class etomica.modules.ljmd.Ljmd
 
LjmdGraphic - Class in etomica.modules.ljmd
 
LjmdGraphic(Ljmd, Space) - Constructor for class etomica.modules.ljmd.LjmdGraphic
 
LjmdGraphic.Applet - Class in etomica.modules.ljmd
 
LjmdGraphic.DataProcessorTensorTrace - Class in etomica.modules.ljmd
Inner class to find the total pressure of the system from the pressure tensor.
LJQB2 - Class in etomica.modules.vle
Class that provides method to compute the 2nd virial coefficient for the Lennard-Jones + point-quadrupole model potential.
LJQB2() - Constructor for class etomica.modules.vle.LJQB2
 
lnAlpha - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSinkReweightedDeltaU
 
lnN - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
 
load - Variable in class etomica.modules.materialfracture.PotentialCalculationForceStress
 
lowest(IAtom) - Method in class etomica.modules.chainequilibrium.P2SquareWellBonded
This will tell you what the lowest open space is in atom a
lowest(IAtom) - Method in class etomica.modules.chainequilibrium.P2SquareWellRadical
This will tell you what the lowest open space is in atom a

M

main(String[]) - Static method in class etomica.modules.adsorption.Adsorption
 
main(String[]) - Static method in class etomica.modules.adsorption.AdsorptionGraphic
 
main(String[]) - Static method in class etomica.modules.catalysis.Catalysis
 
main(String[]) - Static method in class etomica.modules.catalysis.CatalysisGraphic
 
main(String[]) - Static method in class etomica.modules.chainequilibrium.ChainEquilibriumGraphic
 
main(String[]) - Static method in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationGraphic
 
main(String[]) - Static method in class etomica.modules.colloid.ColloidGraphic
 
main(String[]) - Static method in class etomica.modules.colloid.ColloidSim
 
main(String[]) - Static method in class etomica.modules.crystalviewer.CrystalViewer
 
main(String[]) - Static method in class etomica.modules.dcvgcmd.DCVGCMDGraphic
 
main(String[]) - Static method in class etomica.modules.droplet.Droplet
 
main(String[]) - Static method in class etomica.modules.droplet.DropletAtomic
 
main(String[]) - Static method in class etomica.modules.droplet.DropletAtomicGraphic
 
main(String[]) - Static method in class etomica.modules.droplet.DropletGraphic
 
main(String[]) - Static method in class etomica.modules.ensembles.LJMC
 
main(String[]) - Static method in class etomica.modules.ensembles.LJMCGraphic
 
main(String[]) - Static method in class etomica.modules.entropylottery.EntropyLottery
 
main(String[]) - Static method in class etomica.modules.entropylottery.EntropyLotteryGraphic
 
main(String[]) - Static method in class etomica.modules.insertion.Insertion
 
main(String[]) - Static method in class etomica.modules.insertion.InsertionGraphic
 
main(String[]) - Static method in class etomica.modules.interfacial.FitTanh
 
main(String[]) - Static method in class etomica.modules.interfacial.InterfacialSW
 
main(String[]) - Static method in class etomica.modules.interfacial.InterfacialSWGraphic
 
main(String[]) - Static method in class etomica.modules.joulethomson.JouleThomson
 
main(String[]) - Static method in class etomica.modules.joulethomson.JouleThomsonSim
 
main(String[]) - Static method in class etomica.modules.ljmd.Ljmd
 
main(String[]) - Static method in class etomica.modules.ljmd.LjmdGraphic
 
main(String[]) - Static method in class etomica.modules.materialfracture.MaterialFractureGraphic
/* main method
main(String[]) - Static method in class etomica.modules.mu.Mu
 
main(String[]) - Static method in class etomica.modules.mu.MuGraphic
 
main(String[]) - Static method in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC
 
main(String[]) - Static method in class etomica.modules.multiharmonic.MultiharmonicGraphic
 
main(String[]) - Static method in class etomica.modules.multiharmonic.MultiharmonicGraphicMC
 
main(String[]) - Static method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC
 
main(String[]) - Static method in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC
 
main(String[]) - Static method in class etomica.modules.osmosis.Osmosis
 
main(String[]) - Static method in class etomica.modules.osmosis.OsmosisSim
 
main(String[]) - Static method in class etomica.modules.pistoncylinder.PistonCylinderGraphic
 
main(String[]) - Static method in class etomica.modules.reactionequilibrium.ReactionEquilibriumGraphic
 
main(String[]) - Static method in class etomica.modules.render.ParseObj
 
main(String[]) - Static method in class etomica.modules.render.RenderMDGraphic
 
main(String[]) - Static method in class etomica.modules.rheology.RheologyGraphic
 
main(String[]) - Static method in class etomica.modules.rheology.SimulationRheology
 
main(String[]) - Static method in class etomica.modules.rosmosis.ReverseOsmosis
 
main(String[]) - Static method in class etomica.modules.rosmosis.ReverseOsmosisGraphic
 
main(String[]) - Static method in class etomica.modules.rosmosis.ReverseOsmosisWater
 
main(String[]) - Static method in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic
 
main(String[]) - Static method in class etomica.modules.sam.Sam
 
main(String[]) - Static method in class etomica.modules.sam.SamGraphic
 
main(String[]) - Static method in class etomica.modules.swmd.Swmd
 
main(String[]) - Static method in class etomica.modules.swmd.SwmdGraphic
 
main(String[]) - Static method in class etomica.modules.vle.B2Fit
 
main(String[]) - Static method in class etomica.modules.vle.DeviceThermoSliderGEMC
 
main(String[]) - Static method in class etomica.modules.vle.LJQB2
 
main(String[]) - Static method in class etomica.modules.vle.VLE
 
main(String[]) - Static method in class etomica.modules.vle.VLESim
 
makeAgent(IAtom, IBox) - Method in class etomica.modules.catalysis.InteractionTracker
 
makeAgent(IAtom, IBox) - Method in class etomica.modules.chainequilibrium.AtomFilterChainLength
 
makeAgent(IAtom, IBox) - Method in class etomica.modules.chainequilibrium.ChainEquilibriumSim
Implementation of AtomAgentManager.AgentSource interface.
makeAgent(IAtom, IBox) - Method in class etomica.modules.chainequilibrium.ColorSchemeRadical
 
makeAgent(IAtomType) - Method in class etomica.modules.chainequilibrium.ColorSchemeStepWise
 
makeAgent(IAtom, IBox) - Method in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
Implementation of AtomAgentManager.AgentSource interface.
makeAgent(IAtom, IBox) - Method in class etomica.modules.chainequilibrium.MeterChainLength
 
makeAgent(IBox) - Method in class etomica.modules.colloid.NeighborListManagerColloid.NeighborListAgentSourceColloid
 
makeAgent(IAtom, IBox) - Method in class etomica.modules.droplet.AtomFilterLiquidAtomic
 
makeAgent(IAtom, IBox) - Method in class etomica.modules.droplet.IntegratorDroplet
 
makeAgent(IAtom, IBox) - Method in class etomica.modules.reactionequilibrium.ReactionEquilibrium
Implementation of Atom.AgentSource interface.
makeAgent(IMolecule) - Method in class etomica.modules.rosmosis.MeterFlux
 
makeAgent(IAtom, IBox) - Method in class etomica.modules.rosmosis.P1Tether
 
makeAgent(IMolecule) - Method in class etomica.modules.sam.CriterionTether3
 
makeDropShape() - Method in class etomica.modules.droplet.DropletAtomic
 
makeDWPlot - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC
 
makeGraphicsPanel() - Method in class etomica.modules.clustergenerator.MyApplet
 
managerPanel - Variable in class etomica.modules.clustergenerator.MyApplet
 
mass - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
 
mass - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibriumGraphic.MassEditor
 
mass - Variable in class etomica.modules.swmd.SwmdGraphic
 
massBox - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
 
massBox - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
 
massBox - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic
 
massBox - Variable in class etomica.modules.swmd.SwmdGraphic
 
MassEditor(SpeciesSpheresMono, String) - Constructor for class etomica.modules.reactionequilibrium.ReactionEquilibriumGraphic.MassEditor
 
massMembrane - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
 
massSolute - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
 
massSolvent - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
 
MaterialFracture - Class in etomica.modules.materialfracture
 
MaterialFracture() - Constructor for class etomica.modules.materialfracture.MaterialFracture
 
MaterialFractureGraphic - Class in etomica.modules.materialfracture
Graphical components for Material Fracture module
MaterialFractureGraphic(MaterialFracture) - Constructor for class etomica.modules.materialfracture.MaterialFractureGraphic
 
MaterialFractureGraphic.Applet - Class in etomica.modules.materialfracture
 
maxChainLength - Variable in class etomica.modules.chainequilibrium.AtomFilterChainLength
 
maxIterations - Variable in class etomica.modules.interfacial.FitTanh
 
maxNbrsVapor - Variable in class etomica.modules.droplet.AtomFilterLiquidAtomic
 
mcMoveAtom - Variable in class etomica.modules.ensembles.LJMC
 
MCMoveAtomAdjacent - Class in etomica.modules.entropylottery
Monte Carlo move that moves an atom by +/- 1 unit in a random dimension.
MCMoveAtomAdjacent(IRandom, ISpace) - Constructor for class etomica.modules.entropylottery.MCMoveAtomAdjacent
 
mcMoveID - Variable in class etomica.modules.ensembles.LJMC
 
mcMoveIDA - Variable in class etomica.modules.adsorption.Adsorption
 
mcMoveIDB - Variable in class etomica.modules.adsorption.Adsorption
 
MCMoveMoleculeExchangeVLE - Class in etomica.modules.vle
 
MCMoveMoleculeExchangeVLE(IPotentialMaster, IRandom, ISpace, IntegratorBox, IntegratorBox) - Constructor for class etomica.modules.vle.MCMoveMoleculeExchangeVLE
 
MCMoveMultiHarmonic - Class in etomica.modules.multiharmonic
MCMove which moves all atoms.
MCMoveMultiHarmonic(P1Harmonic, IRandom) - Constructor for class etomica.modules.multiharmonic.MCMoveMultiHarmonic
 
mcMoves() - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD
 
mcMoveVolume - Variable in class etomica.modules.ensembles.LJMC
 
MCMoveVolumeExchangeVLE - Class in etomica.modules.vle
 
MCMoveVolumeExchangeVLE(IPotentialMaster, IRandom, ISpace, IntegratorBox, IntegratorBox) - Constructor for class etomica.modules.vle.MCMoveVolumeExchangeVLE
 
membraneDim - Variable in class etomica.modules.rosmosis.ConfigurationMembrane
 
membraneDim - Variable in class etomica.modules.rosmosis.ConfigurationMembraneWater
 
membraneThicknessPerLayer - Variable in class etomica.modules.rosmosis.ConfigurationMembrane
 
membraneThicknessSlider - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
 
membraneThicknessSlider - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic
 
membraneTotalThickness - Variable in class etomica.modules.rosmosis.ConfigurationMembraneWater
 
membraneWidth - Variable in class etomica.modules.rosmosis.ConfigurationMembrane
 
membraneWidth - Variable in class etomica.modules.rosmosis.ConfigurationMembraneWater
 
membraneWidthSlider - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic
 
meter - Variable in class etomica.modules.droplet.AtomFilterLiquid
 
meter - Variable in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile.DataSourceVirialProfile
 
meterA - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceFE
 
meterB - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceFE
 
MeterChainLength - Class in etomica.modules.chainequilibrium
 
MeterChainLength(AtomLeafAgentManager<IAtom[]>) - Constructor for class etomica.modules.chainequilibrium.MeterChainLength
 
MeterChainLength.AtomTag - Class in etomica.modules.chainequilibrium
 
MeterConversion - Class in etomica.modules.chainequilibrium
Meter for the reaction conversion (fraction of reacted sites).
MeterConversion(IBox, AtomLeafAgentManager) - Constructor for class etomica.modules.chainequilibrium.MeterConversion
 
meterCountAtoms - Variable in class etomica.modules.adsorption.ModifierPMu
 
meterCycles - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
 
meterDeformation - Variable in class etomica.modules.droplet.Droplet
 
MeterDeformation - Class in etomica.modules.droplet
 
MeterDeformation(ISpace) - Constructor for class etomica.modules.droplet.MeterDeformation
 
meterDensity - Variable in class etomica.modules.vle.MCMoveMoleculeExchangeVLE
 
meterDensity - Variable in class etomica.modules.vle.MCMoveVolumeExchangeVLE
 
MeterDensityCO - Class in etomica.modules.catalysis
 
MeterDensityCO(IBox, ISpecies, AtomLeafAgentManager) - Constructor for class etomica.modules.catalysis.MeterDensityCO
 
MeterDensityCO2 - Class in etomica.modules.catalysis
 
MeterDensityCO2(IBox, ISpecies, AtomLeafAgentManager) - Constructor for class etomica.modules.catalysis.MeterDensityCO2
 
MeterDensityO2 - Class in etomica.modules.catalysis
 
MeterDensityO2(IBox, ISpecies, AtomLeafAgentManager) - Constructor for class etomica.modules.catalysis.MeterDensityO2
 
MeterDensitySides - Class in etomica.modules.mu
 
MeterDensitySides(IBox, ISpecies, boolean) - Constructor for class etomica.modules.mu.MeterDensitySides
 
MeterDimerFraction - Class in etomica.modules.reactionequilibrium
 
MeterDimerFraction(AtomLeafAgentManager) - Constructor for class etomica.modules.reactionequilibrium.MeterDimerFraction
 
meterDimerFraction - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibrium
 
meterE2E - Variable in class etomica.modules.colloid.ColloidGraphic
 
MeterElongation - Class in etomica.modules.materialfracture
 
MeterElongation() - Constructor for class etomica.modules.materialfracture.MeterElongation
 
MeterEnd2End - Class in etomica.modules.colloid
Measures the end-to-end squared distance for the colloid system, averaged across the grafted chains.
MeterEnd2End(ISpace) - Constructor for class etomica.modules.colloid.MeterEnd2End
 
MeterEndToEnd - Class in etomica.modules.rheology
Meter that measures that end to end distance of the molecules
MeterEndToEnd(ISpace) - Constructor for class etomica.modules.rheology.MeterEndToEnd
 
MeterEntropy - Class in etomica.modules.entropylottery
Calculates the entropy of the distribution of Atoms in a Box using Stirling's approximation.
MeterEntropy() - Constructor for class etomica.modules.entropylottery.MeterEntropy
 
MeterExcessAdsorbed - Class in etomica.modules.adsorption
 
MeterExcessAdsorbed(ISpecies, EOSSW) - Constructor for class etomica.modules.adsorption.MeterExcessAdsorbed
 
MeterFlux - Class in etomica.modules.dcvgcmd
 
MeterFlux(MyMCMove, IntegratorDCVGCMD) - Constructor for class etomica.modules.dcvgcmd.MeterFlux
 
MeterFlux - Class in etomica.modules.rosmosis
Meter to measure flux across a boundary or boundaries.
MeterFlux(ISimulation, ISpace) - Constructor for class etomica.modules.rosmosis.MeterFlux
 
meterFlux0 - Variable in class etomica.modules.dcvgcmd.DCVGCMD
 
meterFlux1 - Variable in class etomica.modules.dcvgcmd.DCVGCMD
 
meterFlux2 - Variable in class etomica.modules.dcvgcmd.DCVGCMD
 
meterFlux3 - Variable in class etomica.modules.dcvgcmd.DCVGCMD
 
MeterFreeEnergy - Class in etomica.modules.multiharmonic
Computes the free-enery difference through free-energy perturbation.
MeterFreeEnergy(P1Harmonic, P1Harmonic) - Constructor for class etomica.modules.multiharmonic.MeterFreeEnergy
 
MeterLoad - Class in etomica.modules.materialfracture
Meter that calculates the stress within the gage cell.
MeterLoad(PotentialCalculationForceStress) - Constructor for class etomica.modules.materialfracture.MeterLoad
 
MeterMBAR - Class in etomica.modules.multiharmonic.mbar
 
MeterMBAR(DataSourceScalar[], double) - Constructor for class etomica.modules.multiharmonic.mbar.MeterMBAR
 
MeterNormalStress - Class in etomica.modules.rheology
Meter to measure normal stress of a polymer in a shear field.
MeterNormalStress(ISpace) - Constructor for class etomica.modules.rheology.MeterNormalStress
 
MeterOrientation - Class in etomica.modules.interfacial
Meter for collecting the molecular orientation of the dimer.
MeterOrientation(ISpace) - Constructor for class etomica.modules.interfacial.MeterOrientation
 
MeterOsmoticPressure - Class in etomica.modules.osmosis
Osmotic pressure meter that calculates the difference in
MeterOsmoticPressure(ISpace, P1HardBoundary[]) - Constructor for class etomica.modules.osmosis.MeterOsmoticPressure
 
MeterOsmoticPressure - Class in etomica.modules.rosmosis
Meter to measure flux across a boundary or boundaries.
MeterOsmoticPressure(IPotentialCalculationWallForce, IBox) - Constructor for class etomica.modules.rosmosis.MeterOsmoticPressure
 
meterOverlapA - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceAlphaChi
 
meterOverlapA - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicMC
 
meterOverlapB - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceAlphaChi
 
meterOverlapB - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicMC
 
meterPE - Variable in class etomica.modules.insertion.InsertionGraphic.MeterWidom
 
meterPE - Variable in class etomica.modules.multiharmonic.mbar.MeterMBAR
 
MeterPressure2 - Class in etomica.modules.vle
Meter for evaluation of the soft-potential pressure in a box.
MeterPressure2(ISpace) - Constructor for class etomica.modules.vle.MeterPressure2
 
MeterProfileByVolumeAdsorption - Class in etomica.modules.adsorption
 
MeterProfileByVolumeAdsorption(ISpace) - Constructor for class etomica.modules.adsorption.MeterProfileByVolumeAdsorption
 
MeterRDFCylinder - Class in etomica.modules.pistoncylinder
MeterRDF sublcass that properly calculates the RDF for the Piston/Cylinder apparatus.
MeterRDFCylinder(ISpace) - Constructor for class etomica.modules.pistoncylinder.MeterRDFCylinder
 
MeterStrain - Class in etomica.modules.materialfracture
 
MeterStrain() - Constructor for class etomica.modules.materialfracture.MeterStrain
 
MeterStress - Class in etomica.modules.materialfracture
Meter that calculates the stress within the gage cell.
MeterStress(PotentialCalculationForceStress) - Constructor for class etomica.modules.materialfracture.MeterStress
 
MeterTilt - Class in etomica.modules.sam
Meter that measures the average tilt angle (not the angle of average tilt!)
MeterTilt(ISpace, ISpecies) - Constructor for class etomica.modules.sam.MeterTilt
 
MeterUmbrella - Class in etomica.modules.multiharmonic.umbrella
 
MeterUmbrella(IEtomicaDataSource, IEtomicaDataSource, double) - Constructor for class etomica.modules.multiharmonic.umbrella.MeterUmbrella
Meter to measure the "overlap" function for free energy calculations, used as input to an AccumulatorVirialOverlapSingleAverage.
meterUmbrella - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicMC
 
MeterViscosity - Class in etomica.modules.rheology
Meter to measure the viscosity of a polymer in a shear field.
MeterViscosity(ISpace) - Constructor for class etomica.modules.rheology.MeterViscosity
 
MeterWallPressure - Class in etomica.modules.sam
 
MeterWallPressure(PotentialCalculationForceSumWall) - Constructor for class etomica.modules.sam.MeterWallPressure
 
meterWidom - Variable in class etomica.modules.insertion.InsertionGraphic
 
MeterWidom() - Constructor for class etomica.modules.insertion.InsertionGraphic.MeterWidom
 
minOCOr2 - Variable in class etomica.modules.catalysis.P2SquareWellBonding
 
minOOr2 - Variable in class etomica.modules.catalysis.P2SquareWellBondingCO
 
minRadicalSites - Variable in class etomica.modules.catalysis.P2SquareWellSurface
 
mixPotentials - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierEpsilon
 
mixPotentials - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierEpsilon
 
mixPotentialsM - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierSoluteCharge
 
mixPotentialsP - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierSoluteCharge
 
ModifierAtomDiameter(MuGraphic, SpeciesSpheresMono, P2SquareWellOneSide, P2SquareWellOneSide, P2SquareWellOneSide) - Constructor for class etomica.modules.mu.MuGraphic.ModifierAtomDiameter
 
ModifierAtomDiameter() - Constructor for class etomica.modules.pistoncylinder.PistonCylinderGraphic.ModifierAtomDiameter
 
ModifierAtomDiameter(SpeciesSpheresMono, P2LennardJones, SpeciesSpheresMono[], P2LennardJones[], DiameterHashByType) - Constructor for class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierAtomDiameter
 
ModifierAtomDiameter(SpeciesSpheresMono, P2LennardJones, P2LennardJones[], P2LennardJones[], DiameterHashByType) - Constructor for class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierAtomDiameter
 
ModifierAtomDiameter() - Constructor for class etomica.modules.swmd.SwmdGraphic.ModifierAtomDiameter
 
ModifierBoxSize(ISpace, IBox, int, IAction) - Constructor for class etomica.modules.droplet.DropletGraphic.ModifierBoxSize
 
ModifierBoxSize(ISpace, IBox, int, IAction) - Constructor for class etomica.modules.interfacial.InterfacialSWGraphic.ModifierBoxSize
 
ModifierDimensions - Class in etomica.modules.entropylottery
 
ModifierDimensions(ISpace, IBox) - Constructor for class etomica.modules.entropylottery.ModifierDimensions
 
ModifierEpsilon(P2SquareWellOneSide, P2SquareWellOneSide, P2SquareWellOneSide, IntegratorBox) - Constructor for class etomica.modules.mu.MuGraphic.ModifierEpsilon
 
ModifierEpsilon(P2LennardJones, P2LennardJones[], P2LennardJones[]) - Constructor for class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierEpsilon
 
ModifierEpsilon(P2LennardJones, P2LennardJones[], P2LennardJones[]) - Constructor for class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierEpsilon
 
ModifierLambda(P2SquareWellOneSide, P2SquareWellOneSide, P2SquareWellOneSide, IntegratorBox) - Constructor for class etomica.modules.mu.MuGraphic.ModifierLambda
 
ModifierPistonDensity() - Constructor for class etomica.modules.pistoncylinder.PistonCylinderGraphic.ModifierPistonDensity
 
ModifierPistonPressure - Class in etomica.modules.pistoncylinder
Modifier for the piston pressure.
ModifierPistonPressure(ISpace, P1HardMovingBoundary, Dimension) - Constructor for class etomica.modules.pistoncylinder.ModifierPistonPressure
 
ModifierPMu - Class in etomica.modules.adsorption
 
ModifierPMu(P2SquareWell, IntegratorBox, EOSSW, MyMCMove, MeterExcessAdsorbed) - Constructor for class etomica.modules.adsorption.ModifierPMu
 
ModifierSoluteCharge(P2Electrostatic, P2Electrostatic, P2Electrostatic, P2Electrostatic[], P2Electrostatic[]) - Constructor for class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierSoluteCharge
 
ModifierWallPosition(Sam) - Constructor for class etomica.modules.sam.SamGraphic.ModifierWallPosition
 
MolecularWeightAvg - Class in etomica.modules.chainequilibrium
Takes output from MeterChainLength as input and outputs the number-average molecular weight.
MolecularWeightAvg() - Constructor for class etomica.modules.chainequilibrium.MolecularWeightAvg
 
MolecularWeightAvg2 - Class in etomica.modules.chainequilibrium
Takes output from MeterChainLength as input and outputs the weight-average molecular weight.
MolecularWeightAvg2() - Constructor for class etomica.modules.chainequilibrium.MolecularWeightAvg2
 
moleculeOffset - Variable in class etomica.modules.catalysis.ConfigurationCatalysis
 
moleculeOffset - Variable in class etomica.modules.sam.ConfigurationSAM
 
moleFractionLeft - Variable in class etomica.modules.osmosis.Osmosis
 
moleFractionRight - Variable in class etomica.modules.osmosis.Osmosis
 
moment - Variable in class etomica.modules.droplet.MeterDeformation
 
moment - Variable in class etomica.modules.vle.VLESim
 
MONOCLINIC - Variable in class etomica.modules.junit.crystalviewer.LatticePlaneTestUtility
 
monomerMonomerBondManager - Variable in class etomica.modules.colloid.ColloidSim
 
monomerMonomerBondManager - Variable in class etomica.modules.colloid.ConfigurationColloid
 
monomerMonomerBondManager - Variable in class etomica.modules.colloid.P1Wall
 
mouseClicked(MouseEvent) - Method in class etomica.modules.clustergenerator.MyApplet.MouseEventClusterPanel
 
mouseEntered(MouseEvent) - Method in class etomica.modules.clustergenerator.MyApplet.MouseEventClusterPanel
 
MouseEventClusterPanel() - Constructor for class etomica.modules.clustergenerator.MyApplet.MouseEventClusterPanel
 
mouseExited(MouseEvent) - Method in class etomica.modules.clustergenerator.MyApplet.MouseEventClusterPanel
 
mousePressed(MouseEvent) - Method in class etomica.modules.clustergenerator.MyApplet.MouseEventClusterPanel
 
mouseReleased(MouseEvent) - Method in class etomica.modules.clustergenerator.MyApplet.MouseEventClusterPanel
 
move - Variable in class etomica.modules.adsorption.ModifierPMu
 
moveA - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicMC
 
moveB - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicMC
 
moveWallAction - Variable in class etomica.modules.sam.SamGraphic
 
mu(double) - Method in class etomica.modules.adsorption.EOSSW
 
mu(double) - Method in class etomica.modules.adsorption.EOSSWPatel
 
mu(double) - Method in class etomica.modules.adsorption.VEOS3SW
 
Mu - Class in etomica.modules.mu
 
Mu(ISpace) - Constructor for class etomica.modules.mu.Mu
 
Mu1Modulator() - Constructor for class etomica.modules.dcvgcmd.IntegratorDCVGCMD.Mu1Modulator
 
Mu2Modulator() - Constructor for class etomica.modules.dcvgcmd.IntegratorDCVGCMD.Mu2Modulator
 
muForPressure(double) - Method in class etomica.modules.adsorption.EOSSW
 
muForPressure(double) - Method in class etomica.modules.adsorption.EOSSWPatel
 
muForPressure(double) - Method in class etomica.modules.adsorption.VEOS3SW
 
MuGraphic - Class in etomica.modules.mu
 
MuGraphic(Mu, ISpace) - Constructor for class etomica.modules.mu.MuGraphic
 
MuGraphic.Applet - Class in etomica.modules.mu
 
MuGraphic.DataProcessorMu - Class in etomica.modules.mu
 
MuGraphic.DataSinkExcludeOverlap - Class in etomica.modules.mu
 
MuGraphic.ModifierAtomDiameter - Class in etomica.modules.mu
 
MuGraphic.ModifierEpsilon - Class in etomica.modules.mu
 
MuGraphic.ModifierLambda - Class in etomica.modules.mu
 
muHistory - Variable in class etomica.modules.mu.MuGraphic.DataProcessorMu
 
Multiharmonic - Class in etomica.modules.multiharmonic
TODO To change the template for this generated type comment go to Window - Preferences - Java - Code Style - Code Templates
Multiharmonic() - Constructor for class etomica.modules.multiharmonic.Multiharmonic
 
MultiharmonicGraphic - Class in etomica.modules.multiharmonic
 
MultiharmonicGraphic(Multiharmonic, ISpace) - Constructor for class etomica.modules.multiharmonic.MultiharmonicGraphic
 
MultiharmonicGraphic.Applet - Class in etomica.modules.multiharmonic
 
MultiharmonicGraphicMC - Class in etomica.modules.multiharmonic.mbar
 
MultiharmonicGraphicMC(MultiharmonicMC, ISpace) - Constructor for class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC
 
MultiharmonicGraphicMC - Class in etomica.modules.multiharmonic
 
MultiharmonicGraphicMC(MultiharmonicMC, ISpace) - Constructor for class etomica.modules.multiharmonic.MultiharmonicGraphicMC
 
MultiharmonicGraphicMC - Class in etomica.modules.multiharmonic.overlap
 
MultiharmonicGraphicMC(MultiharmonicMC, ISpace) - Constructor for class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC
 
MultiharmonicGraphicMC - Class in etomica.modules.multiharmonic.umbrella
 
MultiharmonicGraphicMC(MultiharmonicMC, ISpace) - Constructor for class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC
 
MultiharmonicGraphicMC.Applet - Class in etomica.modules.multiharmonic.mbar
 
MultiharmonicGraphicMC.Applet - Class in etomica.modules.multiharmonic
 
MultiharmonicGraphicMC.Applet - Class in etomica.modules.multiharmonic.overlap
 
MultiharmonicGraphicMC.Applet - Class in etomica.modules.multiharmonic.umbrella
 
MultiharmonicGraphicMC.DataProcessAHT - Class in etomica.modules.multiharmonic.overlap
 
MultiharmonicGraphicMC.DataSinkReweightedDeltaU - Class in etomica.modules.multiharmonic.overlap
 
MultiharmonicGraphicMC.DataSourceAlphaAlpha - Class in etomica.modules.multiharmonic.overlap
 
MultiharmonicGraphicMC.DataSourceAlphaAlpha - Class in etomica.modules.multiharmonic.umbrella
 
MultiharmonicGraphicMC.DataSourceAlphaChi - Class in etomica.modules.multiharmonic.mbar
 
MultiharmonicGraphicMC.DataSourceAlphaChi - Class in etomica.modules.multiharmonic.overlap
 
MultiharmonicGraphicMC.DataSourceAlphaChi - Class in etomica.modules.multiharmonic.umbrella
 
MultiharmonicGraphicMC.DataSourceAlphaFE - Class in etomica.modules.multiharmonic.overlap
 
MultiharmonicGraphicMC.DataSourceBias - Class in etomica.modules.multiharmonic.overlap
 
MultiharmonicGraphicMC.DataSourceChiSlope - Class in etomica.modules.multiharmonic.overlap
 
MultiharmonicGraphicMC.DataSourceFE - Class in etomica.modules.multiharmonic.mbar
 
MultiharmonicGraphicMC.DataSourceFunctionRaw - Class in etomica.modules.multiharmonic.overlap
 
MultiharmonicGraphicMC.DataSourceUa - Class in etomica.modules.multiharmonic.overlap
 
MultiharmonicGraphicMC.DataSourceUa2 - Class in etomica.modules.multiharmonic.overlap
 
MultiharmonicMC - Class in etomica.modules.multiharmonic.mbar
MC version of multi-harmonic simulation.
MultiharmonicMC() - Constructor for class etomica.modules.multiharmonic.mbar.MultiharmonicMC
 
MultiharmonicMC - Class in etomica.modules.multiharmonic
MC version of multi-harmonic simulation.
MultiharmonicMC() - Constructor for class etomica.modules.multiharmonic.MultiharmonicMC
 
MultiharmonicMC - Class in etomica.modules.multiharmonic.overlap
MC version of multi-harmonic simulation.
MultiharmonicMC() - Constructor for class etomica.modules.multiharmonic.overlap.MultiharmonicMC
 
MultiharmonicMC - Class in etomica.modules.multiharmonic.umbrella
MC version of multi-harmonic simulation.
MultiharmonicMC() - Constructor for class etomica.modules.multiharmonic.umbrella.MultiharmonicMC
 
mUnit - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
 
mUnit - Variable in class etomica.modules.swmd.SwmdGraphic
 
muProfileMeter - Variable in class etomica.modules.interfacial.InterfacialSWGraphic
 
MyAgent(ISpace) - Constructor for class etomica.modules.droplet.IntegratorDroplet.MyAgent
 
MyApplet - Class in etomica.modules.clustergenerator
 
MyApplet() - Constructor for class etomica.modules.clustergenerator.MyApplet
 
MyApplet.BondInteractionTypeToggler - Class in etomica.modules.clustergenerator
Options for type of bond-interaction (e-bonds, f-bonds, etc)
MyApplet.BondTypeToggler - Class in etomica.modules.clustergenerator
Options for type of bond array
MyApplet.ComponentEventMyPanel - Class in etomica.modules.clustergenerator
This class is to be notified to graphicOut2 when the window of applet is resized
MyApplet.ConnectedToggler - Class in etomica.modules.clustergenerator
 
MyApplet.GraphicsToggler - Class in etomica.modules.clustergenerator
 
MyApplet.MouseEventClusterPanel - Class in etomica.modules.clustergenerator
This class is for showing bonds of selected cluster in GraphicPanel
MyApplet.NumbersToggler - Class in etomica.modules.clustergenerator
Options for showing index of particle or not
MyApplet.PointsToggler - Class in etomica.modules.clustergenerator
Option of showing particles or not
MyApplet.ReeHooverToggler - Class in etomica.modules.clustergenerator
Options for type of bond-interaction (e-bonds, f-bonds, etc)
MyApplet.Starter - Class in etomica.modules.clustergenerator
 
MyApplet.Stopper - Class in etomica.modules.clustergenerator
 
myData - Variable in class etomica.modules.mu.MuGraphic.DataSinkExcludeOverlap
 
myData - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic.DataSinkExcludeOverlap
 
myData - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.DataSinkExcludeOverlap
 
myData - Variable in class etomica.modules.swmd.SwmdGraphic.DataSinkExcludeOverlap
 
MyMCMove - Class in etomica.modules.adsorption
 
MyMCMove(IntegratorBox, IRandom, ISpace, double, double, int) - Constructor for class etomica.modules.adsorption.MyMCMove
Constructor for MyMCMove.
MyMCMove - Class in etomica.modules.dcvgcmd
 
MyMCMove(IntegratorBox, IRandom, ISpace, double) - Constructor for class etomica.modules.dcvgcmd.MyMCMove
Constructor for MyMCMove.
myPanel - Variable in class etomica.modules.clustergenerator.MyApplet
 
MySpeciesEditor(SpeciesSpheresMono, String) - Constructor for class etomica.modules.reactionequilibrium.ReactionEquilibriumGraphic.MySpeciesEditor
 
MyWall() - Constructor for class etomica.modules.osmosis.Osmosis.MyWall
 

N

nAlpha - Variable in class etomica.modules.multiharmonic.mbar.MeterMBAR
 
names - Static variable in class etomica.modules.joulethomson.JouleThomson.SpeciesChooser
 
nAtoms - Variable in class etomica.modules.render.ParseObj
 
nBins - Variable in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
 
nBody() - Method in class etomica.modules.adsorption.P1Wall
 
nBody - Variable in class etomica.modules.clustergenerator.MyApplet
 
nBody() - Method in class etomica.modules.colloid.P1Wall
 
nBody() - Method in class etomica.modules.droplet.P1Smash
 
nBody() - Method in class etomica.modules.materialfracture.P1Tension
 
nBody() - Method in class etomica.modules.sam.P1Sinusoidal
 
nBodyField - Variable in class etomica.modules.clustergenerator.MyApplet
 
nCellsX - Variable in class etomica.modules.catalysis.ConfigurationCatalysis
 
nCellsX - Variable in class etomica.modules.sam.ConfigurationSAM
 
nCellsZ - Variable in class etomica.modules.catalysis.ConfigurationCatalysis
 
nCellsZ - Variable in class etomica.modules.sam.ConfigurationSAM
 
nCO - Variable in class etomica.modules.catalysis.ConfigurationCatalysis
 
nCrossLinkersAcid - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
 
nData - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
 
nDataInfo - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
 
nDataSource - Variable in class etomica.modules.multiharmonic.DataProcessorDyDLnx
 
nDiAcid - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
 
nDiol - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
 
needUpdate(IAtom) - Method in class etomica.modules.colloid.ColloidSim.CriterionNone
 
needUpdate(IAtom) - Method in class etomica.modules.render.RenderMD.CriterionCar
 
needUpdate(IAtom) - Method in class etomica.modules.sam.CriterionTether3
 
neighborBonds(int) - Method in class etomica.modules.render.ParseObj
 
NeighborListAgentSourceColloid(double, ISpace) - Constructor for class etomica.modules.colloid.NeighborListManagerColloid.NeighborListAgentSourceColloid
 
NeighborListManagerColloid - Class in etomica.modules.colloid
 
NeighborListManagerColloid(PotentialMasterList, double, IBox, ISpace) - Constructor for class etomica.modules.colloid.NeighborListManagerColloid
 
NeighborListManagerColloid.NeighborListAgentSourceColloid - Class in etomica.modules.colloid
 
neighborManager - Variable in class etomica.modules.mu.P1MagicWall
 
neighbors(int) - Method in class etomica.modules.render.ParseObj
 
neighborSetup() - Method in class etomica.modules.colloid.NeighborListManagerColloid
 
newData - Variable in class etomica.modules.entropylottery.DataSourceProbabilityDensity
 
next() - Method in class etomica.modules.pistoncylinder.ApiFilteredCylinder
 
nGraft - Variable in class etomica.modules.colloid.ColloidGraphic.GraftAction
 
nGraft - Variable in class etomica.modules.colloid.ColloidSim
 
nGraft - Variable in class etomica.modules.colloid.ConfigurationColloid
 
NModifier() - Constructor for class etomica.modules.crystalviewer.LatticeEditor.NModifier
 
nMonoAcid - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
 
nMonoOl - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
 
nNominalAtoms - Variable in class etomica.modules.droplet.DropletAtomic
 
nO2 - Variable in class etomica.modules.catalysis.ConfigurationCatalysis
 
nominalDiameter - Variable in class etomica.modules.droplet.EllipseDisplayAction
 
nonintervalAction(IntegratorNonintervalEvent) - Method in class etomica.modules.entropylottery.DataSourceProbabilityDensity
 
nReactCO - Variable in class etomica.modules.catalysis.ReactionManagerCO
 
nReacted - Variable in class etomica.modules.chainequilibrium.MeterConversion
 
nRootField - Variable in class etomica.modules.clustergenerator.MyApplet
 
nSlider - Variable in class etomica.modules.droplet.DropletGraphic
 
nSlider - Variable in class etomica.modules.interfacial.InterfacialSWGraphic
 
nSlider - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
 
nSlider - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibriumGraphic.MySpeciesEditor
 
nSurfaceBonds - Variable in class etomica.modules.catalysis.InteractionTracker.CatalysisAgent
 
nSurfaceSites - Variable in class etomica.modules.catalysis.P2SquareWellBonding
 
nSurfaceSites - Variable in class etomica.modules.catalysis.P2SquareWellBondingCO
 
nSurfactantSlider - Variable in class etomica.modules.interfacial.InterfacialSWGraphic
 
nTag - Variable in class etomica.modules.multiharmonic.DataProcessorDyDLnx
 
nTag - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
 
numAtoms - Variable in class etomica.modules.swmd.SwmdGraphic.DataSinkExcludeOverlap
 
NumbersToggler() - Constructor for class etomica.modules.clustergenerator.MyApplet.NumbersToggler
 
numCellsSlider - Variable in class etomica.modules.sam.SamGraphic
 
numMembraneLayers - Variable in class etomica.modules.rosmosis.ConfigurationMembrane
 
numMembraneLayers - Variable in class etomica.modules.rosmosis.ConfigurationMembraneWater
 
numXCells - Variable in class etomica.modules.sam.Sam
 
numZCells - Variable in class etomica.modules.sam.Sam
 

O

offset - Variable in class etomica.modules.sam.P1Sinusoidal
 
oldEpsilon - Variable in class etomica.modules.vle.B2Fit.FunctionMayerB2LJQ
 
oldG - Variable in class etomica.modules.droplet.EllipseDisplayAction
 
oldQ - Variable in class etomica.modules.vle.B2Fit.FunctionMayerB2LJQ
 
oldSigma - Variable in class etomica.modules.vle.B2Fit.FunctionMayerB2LJQ
 
oldStep - Variable in class etomica.modules.rosmosis.MeterFlux
 
oldTime - Variable in class etomica.modules.rosmosis.MeterFlux
 
oldValue - Variable in class etomica.modules.adsorption.ModifierPMu
 
omdth - Variable in class etomica.modules.rheology.IntegratorPolymer
 
onlyDoublyConnectedCB - Variable in class etomica.modules.clustergenerator.MyApplet
 
onlySinglyConnectedCB - Variable in class etomica.modules.clustergenerator.MyApplet
 
orientationPlot - Variable in class etomica.modules.interfacial.InterfacialSWGraphic
 
orientationProfileMeter - Variable in class etomica.modules.interfacial.InterfacialSWGraphic
 
orientationProfilePump - Variable in class etomica.modules.interfacial.InterfacialSWGraphic
 
originalGageLength - Variable in class etomica.modules.materialfracture.MeterElongation
 
originalGageLength - Variable in class etomica.modules.materialfracture.MeterStrain
 
ORTHORHOMBIC - Variable in class etomica.modules.junit.crystalviewer.LatticePlaneTestUtility
 
osg - Variable in class etomica.modules.clustergenerator.Plot
 
Osmosis - Class in etomica.modules.osmosis
Osmosis module.
Osmosis(OsmosisSim, ISpace) - Constructor for class etomica.modules.osmosis.Osmosis
 
Osmosis.Applet - Class in etomica.modules.osmosis
 
Osmosis.InitializeMolecules - Class in etomica.modules.osmosis
 
Osmosis.MyWall - Class in etomica.modules.osmosis
 
osmosisPMeter - Variable in class etomica.modules.osmosis.Osmosis
 
OsmosisSim - Class in etomica.modules.osmosis
Osmosis simulation.
OsmosisSim(Space) - Constructor for class etomica.modules.osmosis.OsmosisSim
 
otherPotentials - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierAtomDiameter
 
otherPurePotentials - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierEpsilon
 
otherPurePotentials - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierAtomDiameter
 
otherPurePotentials - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierEpsilon
 
otherSpecies - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierAtomDiameter
 
outNData - Variable in class etomica.modules.multiharmonic.DataProcessorDyDLnx
 
outNDataInfo - Variable in class etomica.modules.multiharmonic.DataProcessorDyDLnx
 
output - Variable in class etomica.modules.clustergenerator.MyApplet
 
overlapAvgA - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC
 
overlapAvgB - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC
 

P

p1 - Variable in class etomica.modules.colloid.ColloidGraphic.WallRangeModifier
 
p1 - Variable in class etomica.modules.multiharmonic.MCMoveMultiHarmonic
 
p1BoundaryA - Variable in class etomica.modules.mu.Mu
 
p1BoundaryB - Variable in class etomica.modules.mu.Mu
 
P1HardWall - Class in etomica.modules.osmosis
 
P1HardWall(ISpace) - Constructor for class etomica.modules.osmosis.P1HardWall
 
P1HardWall(ISpace, double) - Constructor for class etomica.modules.osmosis.P1HardWall
 
p1Intra - Variable in class etomica.modules.sam.Sam
 
P1MagicWall - Class in etomica.modules.mu
 
P1MagicWall(ISpace, PotentialMasterList) - Constructor for class etomica.modules.mu.P1MagicWall
 
P1Sinusoidal - Class in etomica.modules.sam
 
P1Sinusoidal(ISpace) - Constructor for class etomica.modules.sam.P1Sinusoidal
 
p1Smash - Variable in class etomica.modules.droplet.Droplet
 
p1Smash - Variable in class etomica.modules.droplet.DropletAtomic
 
P1Smash - Class in etomica.modules.droplet
Gravity-like potential that pushes the molecules toward the center.
P1Smash(ISpace) - Constructor for class etomica.modules.droplet.P1Smash
 
p1SurfaceBond - Variable in class etomica.modules.sam.Sam
 
p1Tension - Variable in class etomica.modules.materialfracture.MaterialFracture
 
P1Tension - Class in etomica.modules.materialfracture
 
P1Tension(ISpace) - Constructor for class etomica.modules.materialfracture.P1Tension
 
P1Tether - Class in etomica.modules.rosmosis
Potential for a harmonic tether.
P1Tether(IBox, ISpecies, ISpace) - Constructor for class etomica.modules.rosmosis.P1Tether
 
P1Wall - Class in etomica.modules.adsorption
 
P1Wall(ISpace) - Constructor for class etomica.modules.adsorption.P1Wall
 
P1Wall - Class in etomica.modules.colloid
 
P1Wall(ISpace, AtomLeafAgentManager) - Constructor for class etomica.modules.colloid.P1Wall
 
p1WallA - Variable in class etomica.modules.adsorption.Adsorption
 
p1WallA - Variable in class etomica.modules.mu.Mu
 
p1WallB - Variable in class etomica.modules.adsorption.Adsorption
 
p1WallB - Variable in class etomica.modules.mu.Mu
 
p1WallColloid - Variable in class etomica.modules.colloid.ColloidSim
 
p1WallMonomer - Variable in class etomica.modules.colloid.ColloidSim
 
P1WCAPorousWall - Class in etomica.modules.dcvgcmd
This acts as a 1-body WCA potential wall perpendicular to the z direction with a hole.
P1WCAPorousWall(ISpace) - Constructor for class etomica.modules.dcvgcmd.P1WCAPorousWall
 
P1WCAPorousWall(ISpace, double, double) - Constructor for class etomica.modules.dcvgcmd.P1WCAPorousWall
 
P1WCAWall - Class in etomica.modules.dcvgcmd
1-D potential that has a WCA form in the Z direction.
P1WCAWall(ISpace, int) - Constructor for class etomica.modules.dcvgcmd.P1WCAWall
 
P1WCAWall(ISpace, int, double, double) - Constructor for class etomica.modules.dcvgcmd.P1WCAWall
 
P1WCAWall - Class in etomica.modules.sam
1-D potential that has a WCA form in the Z direction.
P1WCAWall(ISpace, int) - Constructor for class etomica.modules.sam.P1WCAWall
 
P1WCAWall(ISpace, int, double, double) - Constructor for class etomica.modules.sam.P1WCAWall
 
p2 - Variable in class etomica.modules.adsorption.ModifierPMu
 
p2 - Variable in class etomica.modules.droplet.Droplet
 
p2 - Variable in class etomica.modules.mu.MuGraphic.ModifierAtomDiameter
 
p2 - Variable in class etomica.modules.mu.MuGraphic.ModifierEpsilon
 
p2 - Variable in class etomica.modules.mu.MuGraphic.ModifierLambda
 
p2AA - Variable in class etomica.modules.adsorption.Adsorption
 
p2AA - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
 
p2AA - Variable in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
 
p2AB - Variable in class etomica.modules.adsorption.Adsorption
 
p2AB - Variable in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
 
p2BB - Variable in class etomica.modules.adsorption.Adsorption
 
p2BB - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
 
p2BB - Variable in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
 
p2Bond - Variable in class etomica.modules.interfacial.InterfacialSW
 
p2BondCC - Variable in class etomica.modules.sam.Sam
 
p2BondCS - Variable in class etomica.modules.sam.Sam
 
p2CH2 - Variable in class etomica.modules.sam.Sam
 
p2CH2CH3 - Variable in class etomica.modules.sam.Sam
 
p2CH2CH3t - Variable in class etomica.modules.sam.Sam
 
p2CH2Surface - Variable in class etomica.modules.sam.Sam
 
p2CH2t - Variable in class etomica.modules.sam.Sam
 
p2CH3 - Variable in class etomica.modules.sam.Sam
 
p2CH3t - Variable in class etomica.modules.sam.Sam
 
P2Cohesion - Class in etomica.modules.droplet
Cohesive potential for mesoscale droplet simulation
P2Cohesion(ISpace) - Constructor for class etomica.modules.droplet.P2Cohesion
 
P2HardSphereMC - Class in etomica.modules.colloid
 
P2HardSphereMC(ISpace, AtomLeafAgentManager<? extends IAtomList>) - Constructor for class etomica.modules.colloid.P2HardSphereMC
 
p2Head - Variable in class etomica.modules.interfacial.InterfacialSW
 
p2HeadHead - Variable in class etomica.modules.interfacial.InterfacialSW
 
p2HeadTail - Variable in class etomica.modules.interfacial.InterfacialSW
 
p2LJ - Variable in class etomica.modules.droplet.DropletAtomic
 
p2LJ - Variable in class etomica.modules.materialfracture.MaterialFracture
 
p2LJQ - Variable in class etomica.modules.vle.VLESim
 
p2LJt - Variable in class etomica.modules.droplet.DropletAtomic
 
p2mc - Variable in class etomica.modules.colloid.ColloidSim
 
p2mc - Variable in class etomica.modules.colloid.NeighborListManagerColloid
 
p2Mix - Variable in class etomica.modules.mu.MuGraphic.ModifierAtomDiameter
 
p2Mix - Variable in class etomica.modules.mu.MuGraphic.ModifierEpsilon
 
p2Mix - Variable in class etomica.modules.mu.MuGraphic.ModifierLambda
 
p2mm - Variable in class etomica.modules.colloid.ColloidSim
 
p2Other - Variable in class etomica.modules.mu.MuGraphic.ModifierAtomDiameter
 
p2Other - Variable in class etomica.modules.mu.MuGraphic.ModifierEpsilon
 
p2Other - Variable in class etomica.modules.mu.MuGraphic.ModifierLambda
 
P2PenetrableCar(ISpace, ParseObj, IBox) - Constructor for class etomica.modules.render.RenderMD.P2PenetrableCar
 
p2pseudo - Variable in class etomica.modules.colloid.ColloidSim
 
p2pseudo - Variable in class etomica.modules.colloid.NeighborListManagerColloid
 
p2S - Variable in class etomica.modules.sam.Sam
 
p2SCH2 - Variable in class etomica.modules.sam.Sam
 
p2SCH2t - Variable in class etomica.modules.sam.Sam
 
P2SquareWellBonded - Class in etomica.modules.chainequilibrium
Similar to square-well potential, but considers and alters bonding states with collisions.
P2SquareWellBonded(ISpace, AtomLeafAgentManager, double, double, double) - Constructor for class etomica.modules.chainequilibrium.P2SquareWellBonded
 
P2SquareWellBonded - Class in etomica.modules.reactionequilibrium
Similar to square-well potential, but considers and alters bonding states with collisions.
P2SquareWellBonded(ISpace, AtomLeafAgentManager, double, double, double, boolean) - Constructor for class etomica.modules.reactionequilibrium.P2SquareWellBonded
 
P2SquareWellBonded.RingResult - Class in etomica.modules.chainequilibrium
 
P2SquareWellBonding - Class in etomica.modules.catalysis
Basic square-well potential.
P2SquareWellBonding(ISpace, AtomLeafAgentManager, double, double, double, int, double, double, double) - Constructor for class etomica.modules.catalysis.P2SquareWellBonding
 
P2SquareWellBondingCO - Class in etomica.modules.catalysis
Basic square-well potential.
P2SquareWellBondingCO(ISpace, AtomLeafAgentManager, double, double, double, int, double, double, double) - Constructor for class etomica.modules.catalysis.P2SquareWellBondingCO
 
P2SquareWellMonomer - Class in etomica.modules.colloid
 
P2SquareWellMonomer(ISpace, AtomLeafAgentManager) - Constructor for class etomica.modules.colloid.P2SquareWellMonomer
 
P2SquareWellOneSide - Class in etomica.modules.mu
Basic square-well potential.
P2SquareWellOneSide(ISpace) - Constructor for class etomica.modules.mu.P2SquareWellOneSide
 
P2SquareWellOneSide(ISpace, double, double, double, boolean) - Constructor for class etomica.modules.mu.P2SquareWellOneSide
 
P2SquareWellRadical - Class in etomica.modules.chainequilibrium
Similar to square-well potential, but considers and alters bonding states with collisions based on free radical reactions.
P2SquareWellRadical(ISpace, AtomLeafAgentManager, double, double, double, IRandom) - Constructor for class etomica.modules.chainequilibrium.P2SquareWellRadical
 
P2SquareWellSurface - Class in etomica.modules.catalysis
Basic square-well potential.
P2SquareWellSurface(ISpace, AtomLeafAgentManager) - Constructor for class etomica.modules.catalysis.P2SquareWellSurface
 
P2SquareWellSurface(ISpace, AtomLeafAgentManager, double, double, double, int) - Constructor for class etomica.modules.catalysis.P2SquareWellSurface
 
p2St - Variable in class etomica.modules.sam.Sam
 
p2SulfurSurfaceLJ - Variable in class etomica.modules.sam.Sam
 
p2SurfaceBond - Variable in class etomica.modules.sam.Sam
 
p2Tail - Variable in class etomica.modules.interfacial.InterfacialSW
 
p2TailTail - Variable in class etomica.modules.interfacial.InterfacialSW
 
p2Truncated - Variable in class etomica.modules.vle.VLESim
 
p3Bond - Variable in class etomica.modules.sam.Sam
 
p4BondCCCC - Variable in class etomica.modules.sam.Sam
 
p4BondCCCS - Variable in class etomica.modules.sam.Sam
 
paint() - Method in class etomica.modules.clustergenerator.ClusterPanel
 
paint() - Method in class etomica.modules.clustergenerator.Plot
Classes which inherit from Plot must define this method.
paint(Graphics) - Method in class etomica.modules.clustergenerator.Plot
 
panel - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibrium
 
param - Variable in class etomica.modules.interfacial.FitTanh
 
parentColor - Variable in class etomica.modules.materialfracture.StrainColorScheme
 
ParseObj - Class in etomica.modules.render
 
ParseObj(String) - Constructor for class etomica.modules.render.ParseObj
 
ParseObj.BondInfo - Class in etomica.modules.render
 
parser - Variable in class etomica.modules.render.RenderMD
 
pc - Variable in class etomica.modules.materialfracture.MaterialFracture
 
pc - Variable in class etomica.modules.materialfracture.MeterLoad
 
pc - Variable in class etomica.modules.materialfracture.MeterStress
 
pc - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
 
pc - Variable in class etomica.modules.rosmosis.MeterOsmoticPressure
 
pc - Variable in class etomica.modules.sam.MeterWallPressure
 
phiSlider - Variable in class etomica.modules.sam.SamGraphic
 
PistonCylinder - Class in etomica.modules.pistoncylinder
Simple hard-sphere MD in piston-cylinder apparatus
PistonCylinder(int) - Constructor for class etomica.modules.pistoncylinder.PistonCylinder
 
PistonCylinderGraphic - Class in etomica.modules.pistoncylinder
 
PistonCylinderGraphic(PistonCylinder, ISpace) - Constructor for class etomica.modules.pistoncylinder.PistonCylinderGraphic
Creates a PistonCylinder graphic instance.
PistonCylinderGraphic.Applet - Class in etomica.modules.pistoncylinder
 
PistonCylinderGraphic.ModifierAtomDiameter - Class in etomica.modules.pistoncylinder
 
PistonCylinderGraphic.ModifierPistonDensity - Class in etomica.modules.pistoncylinder
 
PistonPlane - Class in etomica.modules.pistoncylinder
Wrap a P1HardMovingBoundary and make it look like a Plane.
PistonPlane(ISpace, P1HardMovingBoundary) - Constructor for class etomica.modules.pistoncylinder.PistonPlane
 
pistonPotential - Variable in class etomica.modules.pistoncylinder.MeterRDFCylinder
 
pistonPotential - Variable in class etomica.modules.pistoncylinder.PistonCylinder
 
pistonPotential - Variable in class etomica.modules.pistoncylinder.PistonPlane
 
pistonUpdateRequested() - Method in class etomica.modules.pistoncylinder.IntegratorHardPiston
 
Plot - Class in etomica.modules.clustergenerator
Used from comphys.graphic.plot A class which makes plotting a little more convenient than using Java's Graphics methods.
Plot() - Constructor for class etomica.modules.clustergenerator.Plot
Constructor sets default size of the plot
Plot(Color, int, int) - Constructor for class etomica.modules.clustergenerator.Plot
 
plotBox(double, double, double, double) - Method in class etomica.modules.clustergenerator.Plot
 
plotD - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
 
plotLine(double, double, double, double) - Method in class etomica.modules.clustergenerator.Plot
 
plotP - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
 
plotRDF - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
 
plotsPane - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
 
plotString(String, double, double) - Method in class etomica.modules.clustergenerator.Plot
 
plotStringCenter(String, double, double) - Method in class etomica.modules.clustergenerator.Plot
 
plotT - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
 
PointsToggler() - Constructor for class etomica.modules.clustergenerator.MyApplet.PointsToggler
 
polymerList - Variable in class etomica.modules.sam.CriterionTether3
 
polymerSpecies - Variable in class etomica.modules.sam.CriterionTether3
 
populateArrays(int, boolean) - Method in class etomica.modules.multiharmonic.overlap.DataOverlapCaching
 
poreCenter - Variable in class etomica.modules.dcvgcmd.DCVGCMD
 
positionDefinition - Variable in class etomica.modules.rosmosis.ConfigurationMembrane
 
positionDefinition - Variable in class etomica.modules.rosmosis.ConfigurationMembraneWater
 
positionDefinition - Variable in class etomica.modules.rosmosis.MeterFlux
 
positionDefinition - Variable in class etomica.modules.sam.Sam
 
potential - Variable in class etomica.modules.dcvgcmd.DCVGCMD
 
potential - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierAtomDiameter
 
potential - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierEpsilon
 
potential - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierAtomDiameter
 
potential - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierEpsilon
 
potential1 - Variable in class etomica.modules.dcvgcmd.DCVGCMD
 
potential11 - Variable in class etomica.modules.rosmosis.ReverseOsmosis
 
potential12 - Variable in class etomica.modules.rosmosis.ReverseOsmosis
 
potential22 - Variable in class etomica.modules.rosmosis.ReverseOsmosis
 
potentialA - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicMC
 
potentialA - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicMC
 
potentialA - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicMC
 
potentialAA - Variable in class etomica.modules.mu.Mu
 
potentialAA - Variable in class etomica.modules.osmosis.OsmosisSim
 
potentialAB - Variable in class etomica.modules.mu.Mu
 
potentialAB - Variable in class etomica.modules.osmosis.OsmosisSim
 
potentialB - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicMC
 
potentialB - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicMC
 
potentialB - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicMC
 
potentialBB - Variable in class etomica.modules.mu.Mu
 
potentialBB - Variable in class etomica.modules.osmosis.OsmosisSim
 
potentialBonded - Variable in class etomica.modules.render.RenderMD
 
PotentialCalculationForceStress - Class in etomica.modules.materialfracture
 
PotentialCalculationForceStress(ISpace) - Constructor for class etomica.modules.materialfracture.PotentialCalculationForceStress
 
PotentialCalculationForceSumWall - Class in etomica.modules.sam
 
PotentialCalculationForceSumWall(P1WCAWall) - Constructor for class etomica.modules.sam.PotentialCalculationForceSumWall
 
PotentialCalculationForceSumWallForce - Class in etomica.modules.rosmosis
Sums the force and torque on each iterated atom or molecule and adds it to the agent associated with the atom.
PotentialCalculationForceSumWallForce(IPotential) - Constructor for class etomica.modules.rosmosis.PotentialCalculationForceSumWallForce
 
PotentialCalculationTorqueSumWallForce - Class in etomica.modules.rosmosis
Sums the force and torque on each iterated atom or molecule and adds it to the agent associated with the atom.
PotentialCalculationTorqueSumWallForce(IPotential) - Constructor for class etomica.modules.rosmosis.PotentialCalculationTorqueSumWallForce
 
potentialCC - Variable in class etomica.modules.catalysis.Catalysis
 
potentialChooser - Variable in class etomica.modules.insertion.InsertionGraphic
 
potentialChooser - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
 
potentialChooser - Variable in class etomica.modules.swmd.SwmdGraphic
 
potentialChooserListener - Variable in class etomica.modules.insertion.InsertionGraphic
 
potentialChooserListener - Variable in class etomica.modules.mu.MuGraphic
 
potentialChooserListener - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
 
potentialChooserListener - Variable in class etomica.modules.swmd.SwmdGraphic
 
potentialCO - Variable in class etomica.modules.catalysis.Catalysis
 
potentialCS - Variable in class etomica.modules.catalysis.Catalysis
 
potentialCS - Variable in class etomica.modules.catalysis.P2SquareWellBondingCO
 
potentialGhost - Variable in class etomica.modules.insertion.Insertion
 
potentialHS - Variable in class etomica.modules.insertion.InsertionGraphic
 
potentialHS - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
 
potentialHS - Variable in class etomica.modules.swmd.SwmdGraphic
 
potentialIdeal - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
 
potentialIdeal - Variable in class etomica.modules.swmd.SwmdGraphic
 
potentialLJClCl - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
 
potentialLJNaCl - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
 
potentialLJNaNa - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
 
potentialLJOCl - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
 
potentialLJONa - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
 
potentialM1 - Variable in class etomica.modules.rosmosis.ReverseOsmosis
 
potentialM2 - Variable in class etomica.modules.rosmosis.ReverseOsmosis
 
potentialMaster - Variable in class etomica.modules.catalysis.ConfigurationCatalysis
 
potentialMaster - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
 
potentialMaster - Variable in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
 
potentialMaster - Variable in class etomica.modules.colloid.ColloidSim
 
potentialMaster - Variable in class etomica.modules.droplet.DropletAtomic
 
potentialMaster - Variable in class etomica.modules.mu.P1MagicWall
 
potentialMaster - Variable in class etomica.modules.render.RenderMD
 
potentialMaster - Variable in class etomica.modules.sam.ConfigurationSAM
 
potentialMaster - Variable in class etomica.modules.sam.Sam
 
potentialMaster - Variable in class etomica.modules.vle.MeterPressure2
 
potentialMasterA - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicMC
 
potentialMasterB - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicMC
 
potentialMCl - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
 
potentialMM - Variable in class etomica.modules.rosmosis.ReverseOsmosis
 
potentialMM - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
 
potentialMNa - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
 
potentialMO - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
 
potentialOO - Variable in class etomica.modules.catalysis.Catalysis
 
potentialOS - Variable in class etomica.modules.catalysis.Catalysis
 
potentialQClCl - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
 
potentialQHCl - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
 
potentialQHNa - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
 
potentialQNaCl - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
 
potentialQNaNa - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
 
potentialQOCl - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
 
potentialQONa - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
 
potentialSW - Variable in class etomica.modules.insertion.InsertionGraphic
 
potentialSW - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
 
potentialSW - Variable in class etomica.modules.swmd.SwmdGraphic
 
potentialTether - Variable in class etomica.modules.rosmosis.PotentialCalculationForceSumWallForce
 
potentialTether - Variable in class etomica.modules.rosmosis.PotentialCalculationTorqueSumWallForce
 
potentialTether - Variable in class etomica.modules.rosmosis.ReverseOsmosis
 
potentialTether - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
 
potentialwall - Variable in class etomica.modules.dcvgcmd.DCVGCMD
 
potentialwall1 - Variable in class etomica.modules.dcvgcmd.DCVGCMD
 
potentialwallPorousA - Variable in class etomica.modules.dcvgcmd.DCVGCMD
 
potentialwallPorousA1 - Variable in class etomica.modules.dcvgcmd.DCVGCMD
 
potentialwallPorousB - Variable in class etomica.modules.dcvgcmd.DCVGCMD
 
potentialwallPorousB1 - Variable in class etomica.modules.dcvgcmd.DCVGCMD
 
potentialWater - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
 
potentialWrapper - Variable in class etomica.modules.colloid.ColloidSim
 
potentialWrapper - Variable in class etomica.modules.insertion.Insertion
 
potentialWrapper - Variable in class etomica.modules.pistoncylinder.PistonCylinder
 
potentialWrapper - Variable in class etomica.modules.swmd.Swmd
 
pressure - Variable in class etomica.modules.adsorption.DataSourceDensityFunction
 
pressure(double) - Method in class etomica.modules.adsorption.EOSSW
 
pressure(double) - Method in class etomica.modules.adsorption.EOSSWPatel
 
pressure - Variable in class etomica.modules.adsorption.MeterExcessAdsorbed
 
pressure(double) - Method in class etomica.modules.adsorption.VEOS3SW
 
pressureDisplayTextBox - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
 
pressureMeter - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
 
pressureSlider - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
 
pressureSliderPanel - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
 
pressureTensor - Variable in class etomica.modules.droplet.IntegratorDroplet
 
processData(IData) - Method in class etomica.modules.chainequilibrium.MolecularWeightAvg
 
processData(IData) - Method in class etomica.modules.chainequilibrium.MolecularWeightAvg2
 
processData(IData) - Method in class etomica.modules.droplet.DropletGraphic.DataProcessorTensorSplitter
 
processData(IData) - Method in class etomica.modules.entropylottery.EntropyProcessor
 
processData(IData) - Method in class etomica.modules.interfacial.DataProcessorInterfacialTensionProfile
 
processData(IData) - Method in class etomica.modules.interfacial.FitTanh
 
processData(IData) - Method in class etomica.modules.interfacial.InterfacialSWGraphic.DataProcessorTensorSplitter
 
processData(IData) - Method in class etomica.modules.ljmd.LjmdGraphic.DataProcessorTensorTrace
 
processData(IData) - Method in class etomica.modules.mu.MuGraphic.DataProcessorMu
 
processData(IData) - Method in class etomica.modules.mu.MuGraphic.DataSinkExcludeOverlap
 
processData(IData) - Method in class etomica.modules.multiharmonic.DataProcessorBias
 
processData(IData) - Method in class etomica.modules.multiharmonic.DataProcessorBounds
 
processData(IData) - Method in class etomica.modules.multiharmonic.DataProcessorDyDLnx
 
processData(IData) - Method in class etomica.modules.multiharmonic.DataProcessorVar
 
processData(IData) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataProcessAHT
 
processData(IData) - Method in class etomica.modules.rosmosis.ReverseOsmosisGraphic.DataSinkExcludeOverlap
 
processData(IData) - Method in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.DataSinkExcludeOverlap
 
processData(IData) - Method in class etomica.modules.sam.SamGraphic.DataPipeStressStrain
 
processData(IData) - Method in class etomica.modules.swmd.SwmdGraphic.DataSinkExcludeOverlap
 
processDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.chainequilibrium.MolecularWeightAvg
 
processDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.chainequilibrium.MolecularWeightAvg2
 
processDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.droplet.DropletGraphic.DataProcessorTensorSplitter
 
processDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.entropylottery.EntropyProcessor
 
processDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.interfacial.DataProcessorInterfacialTensionProfile
 
processDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.interfacial.FitTanh
 
processDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.interfacial.InterfacialSWGraphic.DataProcessorTensorSplitter
 
processDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.ljmd.LjmdGraphic.DataProcessorTensorTrace
 
processDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.mu.MuGraphic.DataProcessorMu
 
processDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.mu.MuGraphic.DataSinkExcludeOverlap
 
processDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.multiharmonic.DataProcessorBias
 
processDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.multiharmonic.DataProcessorBounds
 
processDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.multiharmonic.DataProcessorDyDLnx
 
processDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.multiharmonic.DataProcessorVar
 
processDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataProcessAHT
 
processDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.rosmosis.ReverseOsmosisGraphic.DataSinkExcludeOverlap
 
processDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.DataSinkExcludeOverlap
 
processDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.sam.SamGraphic.DataPipeStressStrain
 
processDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.swmd.SwmdGraphic.DataSinkExcludeOverlap
 
profile1 - Variable in class etomica.modules.dcvgcmd.DCVGCMD
 
profile1pump - Variable in class etomica.modules.dcvgcmd.DCVGCMD
 
profile2 - Variable in class etomica.modules.dcvgcmd.DCVGCMD
 
profile2pump - Variable in class etomica.modules.dcvgcmd.DCVGCMD
 
profileData - Variable in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
 
profileDataInfo - Variable in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
 
profileDim - Variable in class etomica.modules.interfacial.DataProcessorInterfacialTensionProfile
 
profilePlot - Variable in class etomica.modules.interfacial.InterfacialSWGraphic
 
pSat() - Method in class etomica.modules.adsorption.EOSSW
 
pSoluteMM - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierSoluteCharge
 
pSolutePM - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierSoluteCharge
 
pSolutePP - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierSoluteCharge
 
pt - Variable in class etomica.modules.materialfracture.MaterialFracture
 
pThermalize - Variable in class etomica.modules.adsorption.P1Wall
 
pUnit - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
 
pUnit - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
 
pUnit - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic
 
pUnit - Variable in class etomica.modules.swmd.SwmdGraphic
 
putData(IData) - Method in class etomica.modules.multiharmonic.overlap.AccumulatorOverlapAverageUa2
Add the given values to the sums and block sums
putData(IData) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSinkReweightedDeltaU
 
putDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.multiharmonic.overlap.AccumulatorOverlapAverageUa2
 
putDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSinkReweightedDeltaU
 
pvBox - Variable in class etomica.modules.crystalviewer.LatticeEditor
 

R

r - Variable in class etomica.modules.rheology.ConformationPolymer
 
r - Variable in class etomica.modules.rheology.IntegratorPolymer
 
r - Variable in class etomica.modules.sam.P1Sinusoidal
 
r0 - Variable in class etomica.modules.droplet.IntegratorDroplet.MyAgent
 
radicalColorMap - Variable in class etomica.modules.catalysis.ColorSchemeRadical
 
radicalColorMap - Variable in class etomica.modules.chainequilibrium.ColorSchemeRadical
 
radioB - Variable in class etomica.modules.clustergenerator.MyApplet
 
radioB1 - Variable in class etomica.modules.clustergenerator.MyApplet
 
random - Variable in class etomica.modules.adsorption.P1Wall
 
random - Variable in class etomica.modules.chainequilibrium.ConfigurationLatticeFreeRadical
 
random - Variable in class etomica.modules.chainequilibrium.ConfigurationLatticeRandom
 
random - Variable in class etomica.modules.chainequilibrium.P2SquareWellRadical
 
random - Variable in class etomica.modules.colloid.ConfigurationColloid
 
random - Variable in class etomica.modules.droplet.ConfigurationDroplet
 
random - Variable in class etomica.modules.entropylottery.MCMoveAtomAdjacent
 
random - Variable in class etomica.modules.multiharmonic.MCMoveMultiHarmonic
 
random - Variable in class etomica.modules.rheology.ConformationPolymer
 
randomizer - Variable in class etomica.modules.adsorption.P1Wall
 
range - Variable in class etomica.modules.adsorption.MyMCMove
 
range - Variable in class etomica.modules.adsorption.P1Wall
 
range - Variable in class etomica.modules.colloid.P1Wall
 
ratio - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSinkReweightedDeltaU
 
rdfListener - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
 
rdfPump - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
 
ReactionEquilibrium - Class in etomica.modules.reactionequilibrium
 
ReactionEquilibrium() - Constructor for class etomica.modules.reactionequilibrium.ReactionEquilibrium
 
ReactionEquilibriumGraphic - Class in etomica.modules.reactionequilibrium
 
ReactionEquilibriumGraphic(ReactionEquilibrium, ISpace) - Constructor for class etomica.modules.reactionequilibrium.ReactionEquilibriumGraphic
 
ReactionEquilibriumGraphic.Applet - Class in etomica.modules.reactionequilibrium
 
ReactionEquilibriumGraphic.MassEditor - Class in etomica.modules.reactionequilibrium
 
ReactionEquilibriumGraphic.MySpeciesEditor - Class in etomica.modules.reactionequilibrium
 
reactionManagerCO - Variable in class etomica.modules.catalysis.Catalysis
 
ReactionManagerCO - Class in etomica.modules.catalysis
 
ReactionManagerCO(Catalysis) - Constructor for class etomica.modules.catalysis.ReactionManagerCO
 
ready - Variable in class etomica.modules.vle.B2Fit.FunctionMayerB2LJQ
 
reconfig - Variable in class etomica.modules.droplet.DropletGraphic.ModifierBoxSize
 
reconfig - Variable in class etomica.modules.interfacial.InterfacialSWGraphic.ModifierBoxSize
 
recursiveTag(IAtom, int) - Method in class etomica.modules.chainequilibrium.AtomFilterChainLength
 
recursiveTag(IAtom, int) - Method in class etomica.modules.chainequilibrium.ColorSchemeRadical
 
recursiveTag(IAtom) - Method in class etomica.modules.chainequilibrium.MeterChainLength
 
reeHooverCB - Variable in class etomica.modules.clustergenerator.MyApplet
 
ReeHooverToggler() - Constructor for class etomica.modules.clustergenerator.MyApplet.ReeHooverToggler
 
refreshSize() - Method in class etomica.modules.entropylottery.DisplayBoxCanvas1DBins
 
rejectNotify() - Method in class etomica.modules.adsorption.MyMCMove
 
rejectNotify() - Method in class etomica.modules.entropylottery.MCMoveAtomAdjacent
Method called by IntegratorMC in the event that the most recent trial move is rejected.
rejectNotify() - Method in class etomica.modules.multiharmonic.MCMoveMultiHarmonic
 
releaseAgent(InteractionTracker.CatalysisAgent, IAtom, IBox) - Method in class etomica.modules.catalysis.InteractionTracker
 
releaseAgent(AtomFilterChainLength.LengthAgent, IAtom, IBox) - Method in class etomica.modules.chainequilibrium.AtomFilterChainLength
 
releaseAgent(IAtom[], IAtom, IBox) - Method in class etomica.modules.chainequilibrium.ChainEquilibriumSim
 
releaseAgent(ColorSchemeRadical.LengthAgent, IAtom, IBox) - Method in class etomica.modules.chainequilibrium.ColorSchemeRadical
 
releaseAgent(Object, IAtomType) - Method in class etomica.modules.chainequilibrium.ColorSchemeStepWise
 
releaseAgent(IAtom[], IAtom, IBox) - Method in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
 
releaseAgent(MeterChainLength.AtomTag, IAtom, IBox) - Method in class etomica.modules.chainequilibrium.MeterChainLength
 
releaseAgent(Boolean, IAtom, IBox) - Method in class etomica.modules.droplet.AtomFilterLiquidAtomic
 
releaseAgent(IntegratorDroplet.MyAgent, IAtom, IBox) - Method in class etomica.modules.droplet.IntegratorDroplet
 
releaseAgent(IAtom, IAtom, IBox) - Method in class etomica.modules.reactionequilibrium.ReactionEquilibrium
 
releaseAgent(Object, IMolecule) - Method in class etomica.modules.rosmosis.MeterFlux
 
releaseAgent(IVectorMutable, IAtom, IBox) - Method in class etomica.modules.rosmosis.P1Tether
 
releaseAgent(Object, IMolecule) - Method in class etomica.modules.sam.CriterionTether3
 
RenderMD - Class in etomica.modules.render
Three-dimensional hard-sphere molecular dynamics simulation, using neighbor listing.
RenderMD(ISpace) - Constructor for class etomica.modules.render.RenderMD
Sole public constructor, makes a simulation using a 3D space.
RenderMD(ISpace, RenderMD.RenderMDParam) - Constructor for class etomica.modules.render.RenderMD
 
RenderMD.CriterionCar - Class in etomica.modules.render
 
RenderMD.P2PenetrableCar - Class in etomica.modules.render
 
RenderMD.RenderMDParam - Class in etomica.modules.render
Inner class for parameters understood by the HSMD3D constructor
RenderMDGraphic - Class in etomica.modules.render
 
RenderMDGraphic(RenderMD, Space) - Constructor for class etomica.modules.render.RenderMDGraphic
 
RenderMDParam() - Constructor for class etomica.modules.render.RenderMD.RenderMDParam
 
REPAINT_INTERVAL - Static variable in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC
 
REPAINT_INTERVAL - Static variable in class etomica.modules.multiharmonic.MultiharmonicGraphicMC
 
REPAINT_INTERVAL - Static variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC
 
REPAINT_INTERVAL - Static variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC
 
REPULSION_ATTRACTION - Static variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
 
REPULSION_ONLY - Static variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
 
reset() - Method in class etomica.modules.adsorption.EOSSW
 
reset() - Method in class etomica.modules.adsorption.EOSSWPatel
 
reset() - Method in class etomica.modules.adsorption.IntegratorHybrid
 
reset() - Method in class etomica.modules.adsorption.MeterProfileByVolumeAdsorption
 
reset() - Method in class etomica.modules.adsorption.ModifierPMu
 
reset() - Method in class etomica.modules.adsorption.VEOS3SW
 
reset() - Method in class etomica.modules.catalysis.InteractionTracker
 
reset() - Method in class etomica.modules.chainequilibrium.MeterChainLength
 
reset(IAtom) - Method in class etomica.modules.colloid.ColloidSim.CriterionNone
 
reset() - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD
 
reset() - Method in class etomica.modules.droplet.IntegratorDroplet
 
reset() - Method in class etomica.modules.entropylottery.DataSourceProbabilityDensity
 
reset() - Method in class etomica.modules.insertion.InsertionGraphic.MeterWidom
 
reset() - Method in class etomica.modules.joulethomson.IntegratorJT
 
reset() - Method in class etomica.modules.materialfracture.PotentialCalculationForceStress
 
reset() - Method in class etomica.modules.multiharmonic.mbar.MeterMBAR
 
reset() - Method in class etomica.modules.multiharmonic.overlap.AccumulatorOverlapAverageUa2
Resets all sums to zero
reset() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSinkReweightedDeltaU
 
reset() - Method in class etomica.modules.pistoncylinder.IntegratorHardPiston
 
reset() - Method in class etomica.modules.pistoncylinder.MeterRDFCylinder
 
reset(IAtom) - Method in class etomica.modules.render.RenderMD.CriterionCar
 
reset() - Method in class etomica.modules.rosmosis.PotentialCalculationForceSumWallForce
Re-zeros the force vectors.
reset() - Method in class etomica.modules.rosmosis.PotentialCalculationTorqueSumWallForce
Re-zeros the force vectors.
reset(IAtom) - Method in class etomica.modules.sam.CriterionTether3
 
reset() - Method in class etomica.modules.sam.PotentialCalculationForceSumWall
 
reset() - Method in class etomica.modules.vle.B2Fit.FunctionMayerB2LJQ
 
resetAction - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibriumGraphic
 
resetBonds() - Method in class etomica.modules.chainequilibrium.ChainEquilibriumSim
 
resetBonds() - Method in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
 
resetFilter() - Method in class etomica.modules.chainequilibrium.AtomFilterChainLength
 
resetFilter() - Method in class etomica.modules.droplet.AtomFilterLiquid
 
resetFilter() - Method in class etomica.modules.droplet.AtomFilterLiquidAtomic
 
resetPiston() - Method in class etomica.modules.pistoncylinder.IntegratorHardPiston
 
resetStepCount() - Method in class etomica.modules.adsorption.IntegratorHybrid
 
restartAction - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibrium
 
ReverseOsmosis - Class in etomica.modules.rosmosis
Reverse osmosis simulation, based on simulation code by Sohail Murad.
ReverseOsmosis(Space) - Constructor for class etomica.modules.rosmosis.ReverseOsmosis
 
ReverseOsmosisGraphic - Class in etomica.modules.rosmosis
Graphical and data collection bits for reverse osmosis simulation.
ReverseOsmosisGraphic(ReverseOsmosis, Space) - Constructor for class etomica.modules.rosmosis.ReverseOsmosisGraphic
 
ReverseOsmosisGraphic.Applet - Class in etomica.modules.rosmosis
 
ReverseOsmosisGraphic.DataSinkExcludeOverlap - Class in etomica.modules.rosmosis
 
ReverseOsmosisGraphic.ModifierAtomDiameter - Class in etomica.modules.rosmosis
 
ReverseOsmosisGraphic.ModifierEpsilon - Class in etomica.modules.rosmosis
 
ReverseOsmosisWater - Class in etomica.modules.rosmosis
Reverse osmosis simulation, based on simulation code by Sohail Murad.
ReverseOsmosisWater(Space) - Constructor for class etomica.modules.rosmosis.ReverseOsmosisWater
 
ReverseOsmosisWaterGraphic - Class in etomica.modules.rosmosis
Graphical and data collection bits for reverse osmosis simulation.
ReverseOsmosisWaterGraphic(ReverseOsmosisWater) - Constructor for class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic
 
ReverseOsmosisWaterGraphic.Applet - Class in etomica.modules.rosmosis
 
ReverseOsmosisWaterGraphic.DataSinkExcludeOverlap - Class in etomica.modules.rosmosis
 
ReverseOsmosisWaterGraphic.ModifierAtomDiameter - Class in etomica.modules.rosmosis
 
ReverseOsmosisWaterGraphic.ModifierEpsilon - Class in etomica.modules.rosmosis
 
ReverseOsmosisWaterGraphic.ModifierSoluteCharge - Class in etomica.modules.rosmosis
 
rg - Variable in class etomica.modules.droplet.MeterDeformation
 
RheologyGraphic - Class in etomica.modules.rheology
Module for "Macromolecular dynamics related to rheological properties through Brownian dynamics simulations", designed by Lewis Wedgewood.
RheologyGraphic(SimulationRheology) - Constructor for class etomica.modules.rheology.RheologyGraphic
 
RheologyGraphic.Applet - Class in etomica.modules.rheology
 
rhoc - Static variable in class etomica.modules.adsorption.EOSSW
 
rhoForPressure(double) - Method in class etomica.modules.adsorption.EOSSW
 
rhoForPressure(double) - Method in class etomica.modules.adsorption.EOSSWPatel
 
rhoForPressure(double) - Method in class etomica.modules.adsorption.VEOS3SW
 
ringResult - Variable in class etomica.modules.chainequilibrium.P2SquareWellBonded
 
RingResult() - Constructor for class etomica.modules.chainequilibrium.P2SquareWellBonded.RingResult
 
rp - Variable in class etomica.modules.droplet.IntegratorDroplet.MyAgent
 
running - Variable in class etomica.modules.clustergenerator.MyApplet
 

S

s - Variable in class etomica.modules.rheology.IntegratorPolymer
 
Sam - Class in etomica.modules.sam
Self-assembled monolayer module.
Sam() - Constructor for class etomica.modules.sam.Sam
 
SamGraphic - Class in etomica.modules.sam
 
SamGraphic(Sam) - Constructor for class etomica.modules.sam.SamGraphic
 
SamGraphic.ActionMoveWall - Class in etomica.modules.sam
 
SamGraphic.Applet - Class in etomica.modules.sam
 
SamGraphic.DataPipeStressStrain - Class in etomica.modules.sam
 
SamGraphic.ModifierWallPosition - Class in etomica.modules.sam
 
scaleSetSize(int, int) - Method in class etomica.modules.entropylottery.DisplayBoxCanvas1DBins
Sets the size of the display to a new value and scales the image so that the box fits in the canvas in the same proportion as before.
scaleSlider - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
 
seenArrays - Variable in class etomica.modules.multiharmonic.overlap.DataOverlapCaching
 
seenParams - Variable in class etomica.modules.multiharmonic.overlap.DataOverlapCaching
 
serial - Variable in class etomica.modules.droplet.EllipseDisplayAction
 
setA(double) - Method in class etomica.modules.rheology.IntegratorPolymer
 
setAccumulator(AccumulatorAverageCollapsingLog) - Method in class etomica.modules.multiharmonic.DataProcessorBounds
 
setAccumulator(AccumulatorAverageCollapsingLog) - Method in class etomica.modules.multiharmonic.DataProcessorVar
 
setAccumulators(AccumulatorAverageCollapsingLog[]) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceBias
 
setAdiabatic() - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
Set the Adiabatic button to its selected state.
setAgentManager(AtomLeafAgentManager) - Method in class etomica.modules.rosmosis.PotentialCalculationTorqueSumWallForce
 
setAlpha(double[], double[]) - Method in class etomica.modules.multiharmonic.mbar.MeterMBAR
sets the range of parameter values used for Bennets method.
setAlpha(double) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
 
setAlpha(double) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceBias
 
setAlpha(double) - Method in class etomica.modules.multiharmonic.umbrella.MeterUmbrella
 
setAlphaFac(double) - Method in class etomica.modules.multiharmonic.umbrella.MeterUmbrella
 
setAtomNumber(int) - Method in class etomica.modules.materialfracture.MeterElongation
 
setAtomNumber(int) - Method in class etomica.modules.materialfracture.MeterStrain
 
setAtomSource(AtomSource) - Method in class etomica.modules.entropylottery.MCMoveAtomAdjacent
 
setB(double) - Method in class etomica.modules.rheology.IntegratorPolymer
 
setB(double) - Method in class etomica.modules.sam.P1Sinusoidal
 
setBarrier(double) - Method in class etomica.modules.catalysis.P2SquareWellBonding
 
setBarrier(double) - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
 
setBarrier(double) - Method in class etomica.modules.reactionequilibrium.P2SquareWellBonded
 
setBasisMolecules(Basis) - Method in class etomica.modules.sam.ConfigurationSAM
 
setBasisSurface(Basis) - Method in class etomica.modules.sam.ConfigurationSAM
 
setBennetParam(double, double) - Method in class etomica.modules.multiharmonic.overlap.AccumulatorOverlapAverageUa2
sets the range of parameter values used for Bennets method.
setBinSize(double) - Method in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
 
setBondedSurfaceAtoms(IMolecule, IAtomList) - Method in class etomica.modules.sam.CriterionTether3
 
setBondFac(double) - Method in class etomica.modules.colloid.P2HardSphereMC
 
setBondFac(double) - Method in class etomica.modules.colloid.P2SquareWellMonomer
 
setBoolean(boolean) - Method in class etomica.modules.joulethomson.IntegratorJT.EnsembleToggler
 
setBoundaries(int, double[], int[]) - Method in class etomica.modules.rosmosis.MeterFlux
 
setBounds(int, int, int, int) - Method in class etomica.modules.entropylottery.DisplayBoxCanvas1DBins
 
setBox(IBox) - Method in class etomica.modules.adsorption.IntegratorHybrid
 
setBox(IBox) - Method in class etomica.modules.adsorption.MeterExcessAdsorbed
 
setBox(IBox) - Method in class etomica.modules.adsorption.MyMCMove
 
setBox(IBox) - Method in class etomica.modules.adsorption.P1Wall
 
setBox(IBox) - Method in class etomica.modules.chainequilibrium.AtomFilterChainLength
 
setBox(IBox) - Method in class etomica.modules.chainequilibrium.ColorSchemeRadical
 
setBox(IBox) - Method in class etomica.modules.chainequilibrium.MeterChainLength
 
setBox(IBox) - Method in class etomica.modules.chainequilibrium.P2SquareWellBonded
 
setBox(IBox) - Method in class etomica.modules.colloid.ColloidSim.CriterionNone
 
setBox(IBox) - Method in class etomica.modules.colloid.MeterEnd2End
 
setBox(IBox) - Method in class etomica.modules.colloid.P1Wall
 
setBox(IBox) - Method in class etomica.modules.dcvgcmd.MeterFlux
 
setBox(IBox) - Method in class etomica.modules.dcvgcmd.MyMCMove
 
setBox(IBox) - Method in class etomica.modules.droplet.IntegratorDroplet
 
setBox(IBox) - Method in class etomica.modules.droplet.MeterDeformation
 
setBox(IBox) - Method in class etomica.modules.droplet.P1Smash
 
setBox(IBox) - Method in class etomica.modules.entropylottery.DataSourceProbabilityDensity
 
setBox(IBox) - Method in class etomica.modules.entropylottery.MCMoveAtomAdjacent
 
setBox(IBox) - Method in class etomica.modules.entropylottery.MeterEntropy
 
setBox(IBox) - Method in class etomica.modules.interfacial.DataProcessorInterfacialTensionProfile
 
setBox(IBox) - Method in class etomica.modules.interfacial.MeterOrientation
 
setBox(IBox) - Method in class etomica.modules.materialfracture.MeterElongation
 
setBox(IBox) - Method in class etomica.modules.materialfracture.MeterStrain
 
setBox(IBox) - Method in class etomica.modules.materialfracture.MeterStress
 
setBox(IBox) - Method in class etomica.modules.materialfracture.P1Tension
 
setBox(IBox) - Method in class etomica.modules.materialfracture.StrainColorScheme
 
setBox(IBox) - Method in class etomica.modules.mu.P1MagicWall
 
setBox(IBox) - Method in class etomica.modules.multiharmonic.MCMoveMultiHarmonic
 
setBox(IBox) - Method in class etomica.modules.multiharmonic.MeterFreeEnergy
 
setBox(IBox) - Method in class etomica.modules.reactionequilibrium.MeterDimerFraction
 
setBox(IBox) - Method in class etomica.modules.render.RenderMD.CriterionCar
 
setBox(IBox) - Method in class etomica.modules.rheology.MeterEndToEnd
 
setBox(IBox) - Method in class etomica.modules.rheology.MeterNormalStress
 
setBox(IBox) - Method in class etomica.modules.rheology.MeterViscosity
 
setBox(IBox) - Method in class etomica.modules.rosmosis.MeterFlux
 
setBox(IBox) - Method in class etomica.modules.sam.CriterionTether3
 
setBox(IBox) - Method in class etomica.modules.sam.MeterTilt
 
setBox(IBox) - Method in class etomica.modules.sam.MeterWallPressure
 
setBox(IBox) - Method in class etomica.modules.sam.P1Sinusoidal
 
setBox(IBox) - Method in class etomica.modules.vle.MeterPressure2
 
setBoxIndex(int) - Method in class etomica.modules.multiharmonic.mbar.MeterMBAR
 
setCellSize(double, double) - Method in class etomica.modules.sam.P1Sinusoidal
 
setCellSizeX(double) - Method in class etomica.modules.catalysis.ConfigurationCatalysis
 
setCellSizeX(double) - Method in class etomica.modules.sam.ConfigurationSAM
 
setCellSizeZ(double) - Method in class etomica.modules.catalysis.ConfigurationCatalysis
 
setCellSizeZ(double) - Method in class etomica.modules.sam.ConfigurationSAM
 
setChainLength(int) - Method in class etomica.modules.colloid.ColloidSim
 
setChainLength(int) - Method in class etomica.modules.colloid.ConfigurationColloid
 
setChainLength(int) - Method in class etomica.modules.colloid.MeterEnd2End
 
setChainLength(int) - Method in class etomica.modules.colloid.NeighborListManagerColloid
 
setChainLength(int) - Method in class etomica.modules.rheology.SimulationRheology
 
setChainLength(int) - Method in class etomica.modules.sam.Sam
 
setChainPhi(int, double) - Method in class etomica.modules.sam.Sam
 
setChainPsi(double) - Method in class etomica.modules.sam.Sam
 
setChainTheta(double) - Method in class etomica.modules.sam.Sam
 
setCollisionRadius(double) - Method in class etomica.modules.osmosis.MeterOsmoticPressure
Sets the collision radius used to calculate accessible "area" assuming that the relevant hard "boundaries" form right-angles with other hard boundaries.
setCollisionRadius(double) - Method in class etomica.modules.osmosis.P1HardWall
Distance from the center of the sphere to the boundary at collision.
setColloidMonomerBondManager(AtomLeafAgentManager) - Method in class etomica.modules.colloid.ConfigurationColloid
 
setColloidSigma(double) - Method in class etomica.modules.colloid.ColloidSim
 
setColor(IAtomType, int, Color) - Method in class etomica.modules.chainequilibrium.ColorSchemeStepWise
Sets atoms of the given type and number of bonds to be the given color.
setColor(String) - Method in class etomica.modules.clustergenerator.Plot
 
setColorIn(Color) - Method in class etomica.modules.crystalviewer.ColorSchemePlane
Color for atoms that are in the plane.
setColorOut(Color) - Method in class etomica.modules.crystalviewer.ColorSchemePlane
Color for atoms that are out of the plane.
setCombinationProbability(double) - Method in class etomica.modules.chainequilibrium.P2SquareWellRadical
Sets the probability that two radicals will bond instead of becoming unreactive.
setConformation(int, ConformationChainZigZag) - Method in class etomica.modules.sam.ConfigurationSAM
 
setController(IController) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
Set the temperature slider controller.
setCoreDiameter(double) - Method in class etomica.modules.catalysis.P2SquareWellBonding
Accessor method for core diameter.
setCoreDiameter(double) - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
Accessor method for core diameter.
setCoreDiameter(double) - Method in class etomica.modules.catalysis.P2SquareWellSurface
Accessor method for core diameter.
setCoreDiameter(double) - Method in class etomica.modules.mu.P2SquareWellOneSide
Accessor method for core diameter.
setCSPotential(P2SquareWellSurface) - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
 
setCutoff(double) - Method in class etomica.modules.droplet.AtomFilterLiquid
 
setDeformation(double) - Method in class etomica.modules.droplet.ConfigurationDroplet
 
setDimensions(int) - Method in class etomica.modules.junit.crystalviewer.LatticePlaneTestUtility
 
setDims(int[]) - Method in class etomica.modules.rheology.MeterNormalStress
 
setDoConfigButton(boolean) - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic
Enable the config (and velocity) buttons.
setDoDensityInput(boolean) - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic
Enable the RDF plot.
setDoDouble(boolean) - Method in class etomica.modules.rheology.MeterNormalStress
 
setDoFastButton(boolean) - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic
 
setDoNMoleculeSlider(boolean) - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic
Enable the # of molecules slider.
setDoRDF(boolean) - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic
Enable the RDF plot.
setDoResetFilter(boolean) - Method in class etomica.modules.droplet.ColorSchemeLiquidVapor
 
setDrawNumbersOfBlack(boolean) - Method in class etomica.modules.clustergenerator.MyApplet.Starter
 
setDrawNumbersOfWhite(boolean) - Method in class etomica.modules.clustergenerator.MyApplet.Starter
 
setDrawPoints(boolean) - Method in class etomica.modules.clustergenerator.MyApplet.Starter
 
setDv(double) - Method in class etomica.modules.droplet.P2Cohesion
 
setEditValues(boolean) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
Set whether the temperature text box should be editable.
setEpsilon(double) - Method in class etomica.modules.adsorption.EOSSW
 
setEpsilon(double) - Method in class etomica.modules.adsorption.P1Wall
 
setEpsilon(double) - Method in class etomica.modules.catalysis.P2SquareWellBonding
Accessor method for depth of well
setEpsilon(double) - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
Accessor method for depth of well
setEpsilon(double) - Method in class etomica.modules.catalysis.P2SquareWellSurface
Accessor method for depth of well
setEpsilon(double) - Method in class etomica.modules.colloid.P1Wall
 
setEpsilon(double) - Method in class etomica.modules.dcvgcmd.P1WCAPorousWall
 
setEpsilon(double) - Method in class etomica.modules.dcvgcmd.P1WCAWall
 
setEpsilon(double) - Method in class etomica.modules.droplet.P2Cohesion
 
setEpsilon(double) - Method in class etomica.modules.junit.crystalviewer.BLCPrimitiveHexagonalLatticePlaneTest.DoubleTwoDArray
 
setEpsilon(double) - Method in class etomica.modules.junit.crystalviewer.BLCPrimitiveMonoclinicLatticePlaneTest.DoubleTwoDArray
 
setEpsilon(double) - Method in class etomica.modules.junit.crystalviewer.BLCPrimitiveOrthorhombicLatticePlaneTest.DoubleTwoDArray
 
setEpsilon(double) - Method in class etomica.modules.junit.crystalviewer.BLCPrimitiveTetragonalLatticePlaneTest.DoubleTwoDArray
 
setEpsilon(double) - Method in class etomica.modules.junit.crystalviewer.BLCPrimitiveTriclinicLatticePlaneTest.DoubleTwoDArray
 
setEpsilon(double) - Method in class etomica.modules.junit.crystalviewer.LatticeCubicSimpleLatticePlaneTest.DoubleTwoDArray
 
setEpsilon(double) - Method in class etomica.modules.mu.P2SquareWellOneSide
Accessor method for depth of well
setEpsilon(double) - Method in class etomica.modules.render.RenderMD.P2PenetrableCar
 
setEpsilon(double) - Method in class etomica.modules.rosmosis.P1Tether
 
setEpsilon(double) - Method in class etomica.modules.sam.P1WCAWall
 
setEpsilon(double) - Method in class etomica.modules.vle.VLESim
 
setEpsilonBonding(double) - Method in class etomica.modules.catalysis.P2SquareWellBonding
 
setEpsilonBonding(double) - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
 
setExtraData(IEtomicaDataSource) - Method in class etomica.modules.entropylottery.DisplayBoxCanvas1DBins
Sets a data source used to draw an extra set of "atoms".
setFilter(AtomFilter) - Method in class etomica.modules.droplet.MeterDeformation
 
setFreeRadicalColor(IAtomType, Color) - Method in class etomica.modules.chainequilibrium.ColorSchemeRadical
 
setFullBondColor(IAtomType, Color) - Method in class etomica.modules.catalysis.ColorSchemeRadical
 
setFullColor(IAtomType, Color) - Method in class etomica.modules.chainequilibrium.ColorSchemeRadical
 
setG(double) - Method in class etomica.modules.droplet.P1Smash
 
setHexagonal(boolean) - Method in class etomica.modules.materialfracture.MeterElongation
 
setHexagonal(boolean) - Method in class etomica.modules.materialfracture.MeterStrain
 
setHexagonal(boolean) - Method in class etomica.modules.materialfracture.StrainColorScheme
 
setIgnoredAtomType(IAtomType) - Method in class etomica.modules.chainequilibrium.MeterChainLength
 
setIncludeLrc(boolean) - Method in class etomica.modules.vle.MeterPressure2
Sets flag indicating whether calculated energy should include long-range correction for potential truncation (true) or not (false).
setIntegrator(IntegratorHard) - Method in class etomica.modules.catalysis.DataSourceWallPressureCatalysis
Registers meter as a collisionListener to the integrator, and sets up a DataSourceTimer to keep track of elapsed time of integrator.
setIntegrator(IntegratorHard) - Method in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
 
setIntegrator(IntegratorHard) - Method in class etomica.modules.mu.DataSourceWallPressureMu
Registers meter as a collisionListener to the integrator, and sets up a DataSourceTimer to keep track of elapsed time of integrator.
setIntegrator(IntegratorPolymer) - Method in class etomica.modules.rheology.MeterNormalStress
 
setIntegrator(IntegratorPolymer) - Method in class etomica.modules.rheology.MeterViscosity
 
setIntegrator(IntegratorBox) - Method in class etomica.modules.rosmosis.MeterFlux
 
setIntegrators(IntegratorMC, IntegratorMD, IRandom) - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD
 
setIntegrators(IntegratorBox, IntegratorBox) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
Sets the integrator for the device.
setInteriorColor(Color) - Method in class etomica.modules.droplet.ColorSchemeDropletSurface
 
setIsothermal(boolean) - Method in class etomica.modules.adsorption.IntegratorHybrid
 
setIsothermal(boolean) - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD
 
setIsothermal() - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
Set the Isothermal button to its selected state.
setIsothermalButtonsVisibility(boolean) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
 
setIsUpperBound(boolean) - Method in class etomica.modules.multiharmonic.DataProcessorBounds
 
setLambda(double) - Method in class etomica.modules.adsorption.EOSSW
 
setLambda(double) - Method in class etomica.modules.catalysis.P2SquareWellBonding
Accessor method for well-diameter multiplier.
setLambda(double) - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
Accessor method for well-diameter multiplier.
setLambda(double) - Method in class etomica.modules.catalysis.P2SquareWellSurface
Accessor method for well-diameter multiplier.
setLambda(double) - Method in class etomica.modules.mu.P2SquareWellOneSide
Accessor method for well-diameter multiplier.
setLatticePlanePosition(double) - Method in class etomica.modules.junit.crystalviewer.LatticePlaneTestUtility
 
setLiquidColor(Color) - Method in class etomica.modules.droplet.ColorSchemeLiquidVapor
 
setLiquidFilter(AtomFilter) - Method in class etomica.modules.droplet.P2Cohesion
 
setMaximum(double) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
Set the maximum value for the temperature.
setMaxIterations(int) - Method in class etomica.modules.interfacial.FitTanh
 
setMaxNbrsVapor(int) - Method in class etomica.modules.droplet.AtomFilterLiquidAtomic
 
setMCMoveInsertDelete(MyMCMove, MyMCMove) - Method in class etomica.modules.adsorption.IntegratorHybrid
 
setMDStepRepetitions(int) - Method in class etomica.modules.adsorption.IntegratorHybrid
 
setMDStepRepetitions(int) - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD
 
setMembraneDim(int) - Method in class etomica.modules.rosmosis.ConfigurationMembrane
 
setMembraneDim(int) - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
 
setMembraneThickness(double) - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
 
setMembraneThicknessPerLayer(double) - Method in class etomica.modules.rosmosis.ConfigurationMembrane
 
setMembraneWidth(int) - Method in class etomica.modules.rosmosis.ConfigurationMembrane
 
setMembraneWidth(int) - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
 
setMinimum(double) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
Set the minimum value for the temperature.
setMinRadicalSites(int) - Method in class etomica.modules.catalysis.P2SquareWellSurface
 
setModifier(Modifier) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
Set the temperature modifier object.
setMoleculeAgentManager(MoleculeAgentManager) - Method in class etomica.modules.rosmosis.PotentialCalculationTorqueSumWallForce
 
setMoleculeOffset(IVectorMutable) - Method in class etomica.modules.catalysis.ConfigurationCatalysis
 
setMoleculeOffset(IVectorMutable) - Method in class etomica.modules.sam.ConfigurationSAM
 
setMoment(double) - Method in class etomica.modules.vle.VLESim
 
setMonomerMonomerBondManager(AtomLeafAgentManager) - Method in class etomica.modules.colloid.ConfigurationColloid
 
setMu(double, double) - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD
 
setName(String) - Method in class etomica.modules.reactionequilibrium.MeterDimerFraction
 
setNCellsX(int) - Method in class etomica.modules.catalysis.ConfigurationCatalysis
 
setNCellsX(int) - Method in class etomica.modules.sam.ConfigurationSAM
 
setNCellsZ(int) - Method in class etomica.modules.catalysis.ConfigurationCatalysis
 
setNCellsZ(int) - Method in class etomica.modules.sam.ConfigurationSAM
 
setNCrossLinkersAcid(int) - Method in class etomica.modules.chainequilibrium.ChainEquilibriumSim
 
setNDiAcid(int) - Method in class etomica.modules.chainequilibrium.ChainEquilibriumSim
 
setNDiol(int) - Method in class etomica.modules.chainequilibrium.ChainEquilibriumSim
 
setNGraft(int) - Method in class etomica.modules.colloid.ConfigurationColloid
 
setNMonoAcid(int) - Method in class etomica.modules.chainequilibrium.ChainEquilibriumSim
 
setNMonoOl(int) - Method in class etomica.modules.chainequilibrium.ChainEquilibriumSim
 
setnReactCO(int) - Method in class etomica.modules.catalysis.ReactionManagerCO
 
setNumAlpha(int) - Method in class etomica.modules.multiharmonic.mbar.MeterMBAR
 
setNumAlpha(int) - Method in class etomica.modules.multiharmonic.overlap.AccumulatorOverlapAverageUa2
 
setNumber(double) - Method in class etomica.modules.materialfracture.StrainColorScheme
 
setNumCO(int) - Method in class etomica.modules.catalysis.ConfigurationCatalysis
 
setNumGraft(int) - Method in class etomica.modules.colloid.ColloidSim
 
setNumMembraneLayers(int) - Method in class etomica.modules.rosmosis.ConfigurationMembrane
 
setNumMembraneLayers(int) - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
 
setNumO2(int) - Method in class etomica.modules.catalysis.ConfigurationCatalysis
 
setNumSurfaceSites(int) - Method in class etomica.modules.catalysis.P2SquareWellBonding
 
setNumSurfaceSites(int) - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
 
setNumXCells(int) - Method in class etomica.modules.sam.Sam
 
setNumZCells(int) - Method in class etomica.modules.sam.Sam
 
setOffset(IVectorMutable) - Method in class etomica.modules.sam.P1Sinusoidal
 
setOverlapSplitter(DataSplitter) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
 
setPistonPotential(P1HardMovingBoundary) - Method in class etomica.modules.pistoncylinder.BoundaryPistonCylinder
 
setPoreCenters(IVectorMutable[]) - Method in class etomica.modules.dcvgcmd.P1WCAPorousWall
 
setPoreRadius(double) - Method in class etomica.modules.dcvgcmd.P1WCAPorousWall
 
setPotential(String) - Method in class etomica.modules.insertion.InsertionGraphic
 
setPotential(P1HardMovingBoundary) - Method in class etomica.modules.pistoncylinder.MeterRDFCylinder
 
setPotential(String) - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic
 
setPotential(String) - Method in class etomica.modules.swmd.SwmdGraphic
 
setPotentialMaster(IPotentialMaster) - Method in class etomica.modules.vle.MeterPressure2
Sets the integrator associated with this instance.
setPotentialMC(IPotentialAtomic) - Method in class etomica.modules.colloid.NeighborListManagerColloid
 
setPotentialPseudo(IPotentialAtomic) - Method in class etomica.modules.colloid.NeighborListManagerColloid
 
setPrecision(int) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
Set the precision of the scrollbar.
setPressure(double) - Method in class etomica.modules.adsorption.DataSourceDensityFunction
 
setPressure(double) - Method in class etomica.modules.adsorption.MeterExcessAdsorbed
 
setProfileDim(int) - Method in class etomica.modules.interfacial.DataProcessorInterfacialTensionProfile
 
setRadicalColor(IAtomType, Color) - Method in class etomica.modules.catalysis.ColorSchemeRadical
 
setRange(int, double, double) - Method in class etomica.modules.adsorption.MeterExcessAdsorbed
 
setRange(double, double) - Method in class etomica.modules.adsorption.MeterProfileByVolumeAdsorption
 
setRange(double) - Method in class etomica.modules.adsorption.P1Wall
 
setRange(double) - Method in class etomica.modules.colloid.P1Wall
 
setRepaintInterval(int) - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic
 
setShearRateNumber(double) - Method in class etomica.modules.rheology.IntegratorPolymer
 
setShowValues(boolean) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
Set whether the temperature text box should be displayed.
setSigma(double) - Method in class etomica.modules.adsorption.EOSSW
 
setSigma(double) - Method in class etomica.modules.adsorption.P1Wall
 
setSigma(double) - Method in class etomica.modules.colloid.P1Wall
 
setSigma(double) - Method in class etomica.modules.dcvgcmd.P1WCAPorousWall
Sets the radius.
setSigma(double) - Method in class etomica.modules.dcvgcmd.P1WCAWall
Sets the radius.
setSigma(double) - Method in class etomica.modules.sam.P1WCAWall
Sets the radius.
setSigma(double) - Method in class etomica.modules.vle.VLESim
 
setSigmaColloid(double) - Method in class etomica.modules.colloid.ConfigurationColloid
 
setSigmaMonomer(double) - Method in class etomica.modules.colloid.ConfigurationColloid
 
setSize(int, int) - Method in class etomica.modules.clustergenerator.Plot
Sets width and height of plot in pixels.
setSliderMajorValues(int) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
Set the number of "major" values that should be shown on the temperature slider.
setSliderPostAction(IAction) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
Set the post slider value changed action.
setSoluteMoleFraction(double) - Method in class etomica.modules.rosmosis.ConfigurationMembrane
 
setSoluteMoleFraction(double) - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
 
setSolutionChamberDensity(double) - Method in class etomica.modules.rosmosis.ConfigurationMembrane
 
setSolutionChamberDensity(double) - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
 
setSolventChamberDensity(double) - Method in class etomica.modules.rosmosis.ConfigurationMembrane
 
setSolventChamberDensity(double) - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
 
setSolventThermoFrac(double) - Method in class etomica.modules.chainequilibrium.P2SquareWellBonded
Sets the fraction of well energy that is gained by an atom pair when they hop in their well.
setSpecies(ISpecies) - Method in class etomica.modules.adsorption.MyMCMove
 
setSpecies(ISpecies, ISpecies) - Method in class etomica.modules.chainequilibrium.ConfigurationLatticeFreeRadical