- D - Variable in class geneticAlgorithm.recombination.DifferentialRecombination
-
D contains the standard deviations.
- dampSigma - Variable in class geneticAlgorithm.recombination.DifferentialRecombination
-
Damping for sigma.
- DARKBLUE - Static variable in class graphicInterfaces.growth.KmcCanvas
-
- data - Variable in class kineticMonteCarlo.lattice.perimeterStatistics.Statistics
-
- data - Variable in class utils.list.Node
-
- deck - Variable in class utils.edu.cornell.lassp.houle.rngPack.RandomShuffle
-
- decksize - Variable in class utils.edu.cornell.lassp.houle.rngPack.RandomShuffle
-
- deduct(double) - Static method in class utils.akting.operations.OperationFactory
-
- deduct(RichArray) - Method in class utils.akting.RichArray
-
- deduct(RichMatrix) - Method in class utils.akting.RichMatrix
-
- DeductOperation - Class in utils.akting.operations
-
- DeductOperation(double) - Constructor for class utils.akting.operations.DeductOperation
-
- deductValue - Variable in class utils.akting.operations.DeductOperation
-
- DEFSEED - Static variable in class utils.edu.cornell.lassp.houle.rngPack.Ranmar
-
Default seed.
- DEFSEED1 - Static variable in class utils.edu.cornell.lassp.houle.rngPack.Ranecu
-
default iseed1 = 12345
- DEFSEED2 - Static variable in class utils.edu.cornell.lassp.houle.rngPack.Ranecu
-
default iseed2 = 67890
- deleteAtom(AbstractAtom) - Method in class utils.list.AbstractList
-
- deleteAtom(AbstractAtom) - Method in class utils.list.BinnedList
-
Not tested.
- deleteAtom(AbstractAtom) - Method in class utils.list.LinearList
-
- deltaTime - Variable in class utils.list.AbstractList
-
- deltaTimeBetweenTwoAttachments - Variable in class basic.io.Restart
-
- deltaTimePerAtom - Variable in class basic.io.Restart
-
- deposit(AbstractGrowthAtom, boolean) - Method in class kineticMonteCarlo.lattice.AbstractGrowthLattice
-
- deposit(AbstractGrowthAtom, boolean) - Method in class kineticMonteCarlo.lattice.AgLattice
-
- deposit(AbstractGrowthAtom, boolean) - Method in class kineticMonteCarlo.lattice.AgUcLatticeSimple
-
- deposit(AbstractGrowthAtom, boolean) - Method in class kineticMonteCarlo.lattice.BasicGrowthLattice
-
- deposit(AbstractGrowthAtom, boolean) - Method in class kineticMonteCarlo.lattice.CatalysisLattice
-
- deposit(AbstractGrowthAtom, boolean) - Method in class kineticMonteCarlo.lattice.Concerted6LatticeSimple
-
- deposit(AbstractGrowthAtom, boolean) - Method in class kineticMonteCarlo.lattice.GrapheneLattice
-
- deposit(AbstractGrowthAtom, boolean) - Method in class kineticMonteCarlo.lattice.GrapheneLatticeSimple
-
- depositAtom(CatalysisAtom) - Method in class kineticMonteCarlo.kmcCore.catalysis.CatalysisKmc
-
- depositAtom(AbstractGrowthAtom) - Method in class kineticMonteCarlo.kmcCore.growth.AbstractGrowthKmc
-
- depositAtom(ConcertedAtom) - Method in class kineticMonteCarlo.kmcCore.growth.ConcertedKmc
-
- depositionFlux - Variable in class basic.Parser
-
- depositionPosition - Variable in class kineticMonteCarlo.atom.AbstractGrowthAtomAttributes
-
The position were atom is deposited.
- depositionRatePerSite - Variable in class geneticAlgorithm.AbstractGeneticAlgorithm
-
- depositionRatePerSite - Variable in class kineticMonteCarlo.kmcCore.growth.AbstractGrowthKmc
-
- depositionTime - Variable in class kineticMonteCarlo.atom.AbstractGrowthAtomAttributes
-
Stores when the atom has been deposited.
- depositNewAtom() - Method in class kineticMonteCarlo.kmcCore.catalysis.CatalysisKmc
-
- depositNewAtom() - Method in class kineticMonteCarlo.kmcCore.growth.AbstractGrowthKmc
-
- depositNewAtom() - Method in class kineticMonteCarlo.kmcCore.growth.ConcertedKmc
-
- depositNewAtom(int) - Method in class kineticMonteCarlo.kmcCore.growth.ConcertedKmc
-
Deposit new atom in with the given label.
- depositSeed() - Method in class kineticMonteCarlo.kmcCore.catalysis.CatalysisKmc
-
- depositSeed() - Method in class kineticMonteCarlo.kmcCore.etching.BasicKmc
-
- depositSeed() - Method in class kineticMonteCarlo.kmcCore.etching.SiKmc
-
- depositSeed() - Method in class kineticMonteCarlo.kmcCore.growth.AbstractGrowthKmc
-
- depositSeed() - Method in class kineticMonteCarlo.kmcCore.growth.ConcertedKmc
-
- depositSeed() - Method in interface kineticMonteCarlo.kmcCore.IKmc
-
- DEPTH - Static variable in class kineticMonteCarlo.unitCell.SiUnitCell
-
- depth(Node<T>) - Method in class utils.list.atoms.AvlTree
-
- depth - Variable in class utils.list.Node
-
- desiredHopDistancesMap - Variable in class kineticMonteCarlo.kmcCore.growth.devitaAccelerator.HopsPerStep
-
- desorpAtom() - Method in class kineticMonteCarlo.kmcCore.catalysis.CatalysisKmc
-
- DESORPTION - Static variable in class kineticMonteCarlo.process.CatalysisProcess
-
- desorptionEnergiesCo - Variable in class ratesLibrary.CatalysisRates
-
- desorptionEnergiesCoCusCoCus - Variable in class ratesLibrary.CatalysisRates
-
- desorptionEnergiesO2 - Variable in class ratesLibrary.CatalysisRates
-
- desorptionRateCoCusCoCus - Variable in class kineticMonteCarlo.kmcCore.catalysis.CatalysisFarkasKmc
-
- desorptionRateCOPerSite - Variable in class kineticMonteCarlo.kmcCore.catalysis.CatalysisKmc
-
- desorptionRateOPerSite - Variable in class kineticMonteCarlo.kmcCore.catalysis.CatalysisKmc
-
- destroyWorker() - Method in class kineticMonteCarlo.kmcCore.worker.KmcWorker
-
- devita - Variable in class basic.Parser
-
- DevitaAccelerator - Class in kineticMonteCarlo.kmcCore.growth.devitaAccelerator
-
- DevitaAccelerator(IDevitaLattice, HopsPerStep) - Constructor for class kineticMonteCarlo.kmcCore.growth.devitaAccelerator.DevitaAccelerator
-
- devitaConfig - Variable in class kineticMonteCarlo.kmcCore.growth.devitaAccelerator.DevitaAccelerator
-
- DevitaHopsConfig - Class in kineticMonteCarlo.kmcCore.growth.devitaAccelerator
-
- DevitaHopsConfig() - Constructor for class kineticMonteCarlo.kmcCore.growth.devitaAccelerator.DevitaHopsConfig
-
- diag(RichArray) - Static method in class utils.akting.RichMatrix
-
- diag() - Method in class utils.akting.RichMatrix
-
- diag(String) - Method in class utils.edu.cornell.lassp.houle.rngPack.Ranlux
-
- diagOn - Variable in class utils.edu.cornell.lassp.houle.rngPack.Ranlux
-
- die(String) - Static method in class utils.edu.cornell.lassp.houle.rngPack.RandomApp
-
- difference - Variable in class geneticAlgorithm.evaluationFunctions.AbstractPsdEvaluator
-
- DifferentialRecombination - Class in geneticAlgorithm.recombination
-
- DifferentialRecombination(int, int) - Constructor for class geneticAlgorithm.recombination.DifferentialRecombination
-
- diffPanel2d - Variable in class graphicInterfaces.MainInterface
-
- diffuseAtom() - Method in class kineticMonteCarlo.kmcCore.catalysis.CatalysisKmc
-
Moves an atom.
- diffuseAtom(AbstractGrowthAtom, AbstractGrowthAtom) - Method in class kineticMonteCarlo.kmcCore.growth.AbstractGrowthKmc
-
Moves an atom from origin to destination.
- diffuseAtom() - Method in class kineticMonteCarlo.kmcCore.growth.ConcertedKmc
-
Moves an atom.
- diffuseIsland() - Method in class kineticMonteCarlo.kmcCore.growth.ConcertedKmc
-
Moves an island.
- diffuseMultiAtom() - Method in class kineticMonteCarlo.kmcCore.growth.ConcertedKmc
-
- DIFFUSION - Static variable in class kineticMonteCarlo.process.CatalysisProcess
-
- diffusionEnergies - Variable in class ratesLibrary.CatalysisRates
-
- diffusionEnergiesCoCusCoCus - Variable in class ratesLibrary.CatalysisRates
-
- diffusionIndex - Variable in class utils.list.AbstractList
-
- diffusionMl - Variable in class ratesLibrary.AbstractBasicGrowthRates
-
- diffusionMl - Variable in class ratesLibrary.AgRatesFromPrbCox
-
Diffusion Mono Layer (F).
- diffusionMl - Variable in class ratesLibrary.AgSimpleRates
-
- diffusionMl - Variable in class ratesLibrary.concerted.AbstractConcertedRates
-
- diffusionMl - Variable in class ratesLibrary.GrapheneGaillardOneNeighbourRates
-
- diffusionMl - Variable in class ratesLibrary.GrapheneGaillardRates
-
- diffusionMl - Variable in class ratesLibrary.GrapheneGaillardSimpleRates
-
- diffusionMl - Variable in class ratesLibrary.GrapheneSchoenhalzRates
-
- diffusionMl - Variable in class ratesLibrary.GrapheneSyntheticRates
-
- diffusionRateCO - Variable in class kineticMonteCarlo.kmcCore.catalysis.CatalysisKmc
-
- diffusionRateCoCusCoCus - Variable in class kineticMonteCarlo.kmcCore.catalysis.CatalysisFarkasKmc
-
- diffusionRateMultiAtom - Variable in class kineticMonteCarlo.kmcCore.growth.ConcertedKmc
-
- diffusionRateO - Variable in class kineticMonteCarlo.kmcCore.catalysis.CatalysisKmc
-
- diffusionRatePerAtom - Variable in class kineticMonteCarlo.kmcCore.growth.ConcertedKmc
-
- diffusionRatePerIslandSize - Variable in class kineticMonteCarlo.kmcCore.growth.ConcertedKmc
-
- dimensions - Variable in class geneticAlgorithm.AbstractGeneticAlgorithm
-
Number of different genes.
- dimensions - Variable in class geneticAlgorithm.recombination.DifferentialRecombination
-
Number of objective variables/problem dimension.
- dimensions - Variable in class utils.psdAnalysis.PsdSignature2D
-
- direction - Variable in class kineticMonteCarlo.lattice.MultiAtom
-
MultiAtom has a certain direction that goes from atom 0 to atom 1.
- dispose() - Method in class geneticAlgorithm.evaluationFunctions.AbstractEvaluator
-
- dispose() - Method in class geneticAlgorithm.evaluationFunctions.AgBasicPsdEvaluator
-
- dispose() - Method in class geneticAlgorithm.evaluationFunctions.AgHierarchyEvaluator
-
- dispose() - Method in class geneticAlgorithm.evaluationFunctions.BasicGrowthPsdEvaluator
-
- dispose() - Method in class geneticAlgorithm.evaluationFunctions.MultithreadedPsdEvaluator
-
- dispose() - Method in class geneticAlgorithm.evaluationFunctions.SiBasicPsdEvaluator
-
- dispose() - Method in class graphicInterfaces.gaConvergence.GaProgressFrame
-
- dispose() - Method in class graphicInterfaces.gaConvergence.GaProgressFrame.ProgressUpdater
-
- dispose() - Method in class graphicInterfaces.growth.KmcCanvas
-
- distance(double, double, double, double) - Static method in class java.awt.geom.Point2D
-
Returns the distance between two points.
- distance(double, double) - Method in class java.awt.geom.Point2D
-
Returns the distance from this Point2D to
a specified point.
- distance(Point2D) - Method in class java.awt.geom.Point2D
-
Returns the distance from this Point2D to a
specified Point2D.
- distance(double, double, double) - Method in class javafx.geometry.Point3D
-
Computes the distance between this point and point (x1, y1, z1).
- distance(Point3D) - Method in class javafx.geometry.Point3D
-
Computes the distance between this point and the specified point.
- distancePerStep - Variable in class kineticMonteCarlo.atom.GrapheneAtom
-
- distanceSq(double, double, double, double) - Static method in class java.awt.geom.Point2D
-
Returns the square of the distance between two points.
- distanceSq(double, double) - Method in class java.awt.geom.Point2D
-
Returns the square of the distance from this
Point2D to a specified point.
- distanceSq(Point2D) - Method in class java.awt.geom.Point2D
-
Returns the square of the distance from this
Point2D to a specified Point2D.
- distributions - Static variable in class utils.edu.cornell.lassp.houle.rngPack.RandomApp
-
- divide(double) - Static method in class utils.akting.operations.OperationFactory
-
- DivideOperation - Class in utils.akting.operations
-
- DivideOperation(double) - Constructor for class utils.akting.operations.DivideOperation
-
- doActivationEnergyStudy - Variable in class kineticMonteCarlo.kmcCore.growth.ActivationEnergy
-
- doAdsorption - Variable in class kineticMonteCarlo.kmcCore.catalysis.CatalysisKmc
-
- doCatalysisAdsorption() - Method in class basic.Parser
-
Adsorb atoms during catalysis simulation.
- doCatalysisDesorption() - Method in class basic.Parser
-
Desorb atoms during catalysis simulation.
- doCatalysisDiffusion() - Method in class basic.Parser
-
Diffuse atom during catalysis simulation.
- doCatalysisO2Dissociation() - Method in class basic.Parser
-
Dissociates O2 atoms during catalysis simulation
Input "parameters" variable: catalysisO2Dissociation.
- doCatalysisReaction() - Method in class basic.Parser
-
Allow to react atoms during catalysis simulation.
- doDesorption - Variable in class kineticMonteCarlo.kmcCore.catalysis.CatalysisKmc
-
- doDiffusion - Variable in class kineticMonteCarlo.kmcCore.catalysis.CatalysisKmc
-
- doIslandDiffusion - Variable in class basic.Parser
-
- doIslandDiffusion() - Method in class basic.Parser
-
In concerted calculation mode, allow to island to move.
- doIslandDiffusion - Variable in class kineticMonteCarlo.kmcCore.growth.ConcertedKmc
-
- doMultiAtomDiffusion - Variable in class basic.Parser
-
- doMultiAtomDiffusion() - Method in class basic.Parser
-
In concerted calculation mode, allow to atoms on the edge to move.
- doMultiAtomDiffusion - Variable in class kineticMonteCarlo.kmcCore.growth.ConcertedKmc
-
- doO2Dissociation - Variable in class kineticMonteCarlo.kmcCore.catalysis.CatalysisKmc
-
- doOnePsd(float[][]) - Static method in class utils.psdAnalysis.PsdSignature2D
-
Does the PSD of the given surface.
- doPrintAllIterations() - Method in class basic.Parser
-
Print all iterations during catalysis simulation.
- doPrintAllIterations - Variable in class kineticMonteCarlo.kmcCore.catalysis.CatalysisKmc
-
- doProcess(MouseEvent) - Method in class graphicInterfaces.etching.mouseBehaviors.MouseTranslate
-
- doPsd() - Method in class basic.Parser
-
Selects to do a PSD analysis of the simulated system.
- doReaction - Variable in class kineticMonteCarlo.kmcCore.catalysis.CatalysisKmc
-
- doSimulation() - Method in class basic.AbstractSimulation
-
- dotProduct(double, double, double) - Method in class javafx.geometry.Point3D
-
Computes dot (scalar) product of the vector represented by this instance
and the specified vector.
- dotProduct(Point3D) - Method in class javafx.geometry.Point3D
-
Computes dot (scalar) product of the vector represented by this instance
and the specified vector.
- Double() - Constructor for class java.awt.geom.Point2D.Double
-
Constructs and initializes a Point2D with
coordinates (0, 0).
- Double(double, double) - Constructor for class java.awt.geom.Point2D.Double
-
Constructs and initializes a Point2D with the
specified coordinates.
- drawKmc(AbstractKmc) - Method in class graphicInterfaces.basic.BasicFrame
-
- drawKmc(AbstractKmc) - Method in class graphicInterfaces.etching.SiFrame
-
- drawKmc(AbstractKmc) - Method in interface graphicInterfaces.KmcGraphics
-