A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

S

sampledSurface - Variable in class basic.AbstractSimulation

sampledSurface - Variable in class geneticAlgorithm.evaluationFunctions.AgBasicPsdEvaluator

sampledSurface - Variable in class geneticAlgorithm.evaluationFunctions.BasicGrowthPsdEvaluator

sampledSurface - Variable in class geneticAlgorithm.evaluationFunctions.SiBasicPsdEvaluator

samples.agAgGrowth - package samples.agAgGrowth

samples.basic - package samples.basic

samples.convergences.agAgGrowth - package samples.convergences.agAgGrowth

samples.convergences.siEtching - package samples.convergences.siEtching

samples.grapheneCvdGrowth - package samples.grapheneCvdGrowth

samples.silicon - package samples.silicon

samples.worker - package samples.worker

scale - Variable in class graphicInterfaces.etching.mouseBehaviors.MouseTranslate

scale - Variable in class graphicInterfaces.etching.mouseBehaviors.MouseZoom

scale - Variable in class graphicInterfaces.growth.KmcCanvas

scale(float[][], int) - Static method in class utils.MathUtils

Given an original surface it reduces by the given factor.

scale(float[][], double) - Static method in class utils.MathUtils

See MathUtils.scale(float[][], int)

scaleGene(double, int) - Method in class geneticAlgorithm.Individual

scaleIndividualRates(Population) - Method in class geneticAlgorithm.AbstractGeneticAlgorithm

Deprecated.

scaleLabel - Variable in class graphicInterfaces.MainInterface

scrollPane - Variable in class graphicInterfaces.MainInterface

search(T) - Method in class utils.list.atoms.AtomsArrayList

Return an atom with the same atom Id that was given from the list.

search(T) - Method in class utils.list.atoms.AtomsAvlTree

Not yet implemented.

search(T) - Method in class utils.list.atoms.AvlTree

search(T) - Method in interface utils.list.atoms.IAtomsCollection

searchEnergies - Variable in class geneticAlgorithm.evaluationFunctions.AgBasicPsdEvaluator

searchEnergies - Variable in class geneticAlgorithm.evaluationFunctions.BasicGrowthPsdEvaluator

searchEnergy - Variable in class geneticAlgorithm.restrictions.AgReduced6Restriction

searchEnergy - Variable in class geneticAlgorithm.restrictions.BasicGrowthRestriction

searchPerimeterOffsetReentrance() - Method in class kineticMonteCarlo.kmcCore.growth.RoundPerimeter

seeds - Variable in class utils.edu.cornell.lassp.houle.rngPack.Ranlux

Select(Population, int) - Method in interface geneticAlgorithm.selection.ISelection

Select(Population, int) - Method in class geneticAlgorithm.selection.RandomSelection

Select(Population, int) - Method in class geneticAlgorithm.selection.RankingSelection

selection - Variable in class geneticAlgorithm.AbstractGeneticAlgorithm

selectivePressure - Variable in class geneticAlgorithm.selection.RankingSelection

selective pressure, choose in interval [1, 2]

semaphore - Variable in class utils.psdAnalysis.PsdSignature2D

serialVersionUID - Static variable in class java.awt.geom.Point2D.Double

serialVersionUID - Static variable in class java.awt.geom.Point2D.Float

set(Object) - Method in class utils.list.BinnedListIterator

set111() - Method in class graphicInterfaces.etching.mouseBehaviors.MouseRotate

set111() - Method in class graphicInterfaces.etching.mouseBehaviors.MouseTranslate

set111() - Method in class graphicInterfaces.etching.mouseBehaviors.MouseZoom

set_projection(int) - Method in class graphicInterfaces.etching.mouseBehaviors.MouseTranslate

setAccelerator(DevitaAccelerator) - Method in class kineticMonteCarlo.kmcCore.growth.AbstractGrowthKmc

setActive(boolean) - Method in class kineticMonteCarlo.process.AbstractProcess

setAngle(double) - Method in class kineticMonteCarlo.atom.AbstractGrowthAtom

setAngles() - Method in class kineticMonteCarlo.lattice.AbstractGrowthLattice

setArea(int) - Method in class kineticMonteCarlo.kmcCore.growth.AbstractGrowthKmc

setArraysNeigh() - Method in class kineticMonteCarlo.unitCell.SiUnitCell

setAsBulk() - Method in class kineticMonteCarlo.atom.BasicAtom

setAsBulk() - Method in class kineticMonteCarlo.atom.SiAtom

setAtomPerimeter() - Method in class kineticMonteCarlo.kmcCore.growth.AbstractGrowthKmc

Internal method to select the perimeter size and type.

setAtoms(AbstractGrowthAtom[][]) - Method in class kineticMonteCarlo.lattice.AbstractGrowthLattice

setAtomsTypesCounter(int) - Method in class kineticMonteCarlo.lattice.AbstractGrowthLattice

setAttributes(AbstractGrowthAtomAttributes) - Method in class kineticMonteCarlo.atom.AbstractGrowthAtom

setAttributes(AbstractGrowthAtomAttributes) - Method in class kineticMonteCarlo.atom.CatalysisAtom

setAuto(boolean) - Method in class graphicInterfaces.surfaceViewer2D.Panel2D

setBaseLocation(int, int) - Method in class graphicInterfaces.growth.KmcCanvas

setBinsLevels(int) - Method in class basic.Parser

setBondsProbability(double[]) - Method in class kineticMonteCarlo.atom.AbstractGrowthAtom

setBondsProbability(double, int) - Method in class kineticMonteCarlo.atom.AbstractGrowthAtom

Set the given probability in the given neighbour position.

setCalculationMode(String) - Method in class basic.Parser

setCartesianPosition(Point3D) - Method in class kineticMonteCarlo.atom.AbstractGrowthAtom

setCartesianSuperCell(Point3D) - Method in class kineticMonteCarlo.atom.AbstractGrowthAtom

setCartSizeX(int) - Method in class basic.Parser

setCartSizeY(int) - Method in class basic.Parser

setCartSizeZ(int) - Method in class basic.Parser

setCentreOfMass(Point2D) - Method in class kineticMonteCarlo.lattice.Island

setColor(double, Graphics) - Method in class graphicInterfaces.surfaceViewer2D.Panel2D

setColorMap(int) - Method in class graphicInterfaces.surfaceViewer2D.Frame2D

setColormap(int) - Method in class graphicInterfaces.surfaceViewer2D.Panel2D

setColorMap(int) - Method in class graphicInterfaces.surfaceViewer2D.SurfaceViewerPanel2D

setColorMap(int) - Method in interface graphicInterfacesCommon.surfaceViewer2D.IFrame2D

setConcertedEnergies(double[]) - Method in class ratesLibrary.concerted.AbstractConcertedRates

setContext(Object) - Method in class main.Configurator

setContext(Object) - Method in interface main.IConfigurator

setContext(Object) - Method in class main.PcConfigurator

It does not need any context.

setCorrectionFactor(double) - Method in class ratesLibrary.CatalysisRates

Scales prefactor.

setCrm(double) - Method in class geneticAlgorithm.Population

setCurrentOccupiedArea(int) - Method in class kineticMonteCarlo.kmcCore.growth.AbstractGrowthKmc

This has to be called only once from AgKmc or GrapheneKmc.

setCurrentPerimeter(List<AbstractGrowthAtom>) - Method in class kineticMonteCarlo.kmcCore.growth.RoundPerimeter

setCurrentPopulation(Population) - Method in class geneticAlgorithm.evaluationFunctions.AbstractPsdEvaluator

setCurrentSimulation(int) - Method in class geneticAlgorithm.evaluationFunctions.AbstractPsdEvaluator

setData(int[][]) - Method in class kineticMonteCarlo.lattice.perimeterStatistics.Statistics

To properly initialise in the not abstract constructor

setData(T) - Method in class utils.list.Node

setDepositionFlux(double) - Method in class ratesLibrary.AbstractBasicGrowthRates

Diffusion Mono Layer (F).

setDepositionFlux(double) - Method in class ratesLibrary.AgRatesFromPrbCox

Diffusion Mono Layer (F).

setDepositionFlux(double) - Method in class ratesLibrary.AgSimpleRates

Diffusion Mono Layer (F).

setDepositionFlux(double) - Method in class ratesLibrary.basic.RatesCase

setDepositionFlux(double) - Method in class ratesLibrary.CatalysisRates

setDepositionFlux(double) - Method in class ratesLibrary.concerted.AbstractConcertedRates

Diffusion Mono Layer (F).

setDepositionFlux(double) - Method in class ratesLibrary.GrapheneGaillardOneNeighbourRates

Diffusion Mono Layer (F).

setDepositionFlux(double) - Method in class ratesLibrary.GrapheneGaillardRates

Diffusion Mono Layer (F).

setDepositionFlux(double) - Method in class ratesLibrary.GrapheneGaillardSimpleRates

Diffusion Mono Layer (F).

setDepositionFlux(double) - Method in class ratesLibrary.GrapheneSchoenhalzRates

Diffusion Mono Layer (F).

setDepositionFlux(double) - Method in class ratesLibrary.GrapheneSyntheticRates

Diffusion Mono Layer (F).

setDepositionFlux(double) - Method in interface ratesLibrary.IRates

setDepositionFlux(double) - Method in class ratesLibrary.SiRatesFromPreGosalvez

setDepositionPosition(Point3D) - Method in class kineticMonteCarlo.atom.AbstractGrowthAtom

setDepositionPosition(Point3D) - Method in class kineticMonteCarlo.atom.AbstractGrowthAtomAttributes

setDepositionProbability(double) - Method in class utils.list.AbstractList

setDepositionRate(double, double) - Method in class kineticMonteCarlo.kmcCore.AbstractKmc

setDepositionRate(double, double) - Method in class kineticMonteCarlo.kmcCore.growth.AbstractGrowthKmc

setDepositionRate(double, double) - Method in interface kineticMonteCarlo.kmcCore.IKmc

setDepositionTime(double) - Method in class kineticMonteCarlo.atom.AbstractGrowthAtom

Stores when the atom has been deposited.

setDepositionTime(double) - Method in class kineticMonteCarlo.atom.AbstractGrowthAtomAttributes

Stores when the atom has been deposited.

setDepth(int) - Method in class utils.list.Node

setDesorptionEnergiesCo(double[]) - Method in class ratesLibrary.CatalysisRates

setDesorptionEnergiesCoCusCoCus(double[]) - Method in class ratesLibrary.CatalysisRates

setDesorptionEnergiesO2(double[][]) - Method in class ratesLibrary.CatalysisRates

setDiag(boolean) - Method in class utils.edu.cornell.lassp.houle.rngPack.Ranlux

Turns diagnostic messages on and off.

setDifference(float[][]) - Method in class graphicInterfaces.MainInterface

setDiffusionEnergies(double[][][]) - Method in class ratesLibrary.CatalysisRates

setDiffusionEnergiesCoCusCoCus(double[]) - Method in class ratesLibrary.CatalysisRates

setDiffusionProbability(double) - Method in class utils.list.AbstractList

setDirection(int) - Method in class kineticMonteCarlo.lattice.MultiAtom

Set the direction of the MultiAtom, from atom at position 0 to atom 1.

setDistancePerStep(int, int) - Method in class kineticMonteCarlo.kmcCore.growth.devitaAccelerator.HopsPerStep

setEnergies(double[][]) - Method in class ratesLibrary.AbstractBasicGrowthRates

setEnergies(double[][]) - Method in class ratesLibrary.concerted.AbstractConcertedRates

setError(int, double) - Method in class geneticAlgorithm.Individual

setError(double) - Method in class graphicInterfaces.MainInterface

setError(double) - Method in class graphicInterfaces.surfaceViewer2D.SurfaceViewerPanel2D

setEvolutionaryAlgorithm(String) - Method in class basic.Parser

setExpectedSimulationTime(double) - Method in class geneticAlgorithm.AbstractGeneticAlgorithm

setExpectedSimulationTime(double) - Method in class geneticAlgorithm.evaluationFunctions.AbstractPsdEvaluator

setExperimentalMesh(float[][]) - Method in class graphicInterfaces.MainInterface

setExperimentalPsd(float[][]) - Method in class geneticAlgorithm.AbstractGeneticAlgorithm

setExtraLevels(int) - Method in class basic.Parser

setFactor(double) - Method in class graphicInterfaces.etching.mouseBehaviors.MouseRocking

setFactor(double, double) - Method in class graphicInterfaces.etching.mouseBehaviors.MouseRocking

setFactor(double) - Method in class graphicInterfaces.etching.mouseBehaviors.MouseRotate

setFactor(double, double) - Method in class graphicInterfaces.etching.mouseBehaviors.MouseRotate

Set the x-axis amd y-axis movement multipler with xFactor and yFactor respectively.

setFactor(double) - Method in class graphicInterfaces.etching.mouseBehaviors.MouseZoom

Set the y-axis movement multipler with factor.

setGene(int, double) - Method in class geneticAlgorithm.Individual

setGraphics(IgaProgressFrame) - Method in class geneticAlgorithm.AbstractGeneticAlgorithm

setGraphics(IgaProgressFrame) - Method in interface geneticAlgorithm.IGeneticAlgorithm

setHexaSizeI(int) - Method in class kineticMonteCarlo.lattice.AbstractLattice

setHexaSizeJ(int) - Method in class kineticMonteCarlo.lattice.AbstractLattice

setHexaSizeK(int) - Method in class kineticMonteCarlo.lattice.AbstractLattice

setHierarchy(double[]) - Method in class geneticAlgorithm.AbstractGeneticAlgorithm

setHierarchy(double[]) - Method in class geneticAlgorithm.evaluationFunctions.AbstractPsdEvaluator

setHierarchy(double[]) - Method in class geneticAlgorithm.evaluationFunctions.AgBasicPsdEvaluator

Sets the expected rates hierarchies, based on the objective rates (genes)

setHierarchy(double[]) - Method in class geneticAlgorithm.evaluationFunctions.AgThreadedPsdEvaluator

setHierarchy(double[]) - Method in class geneticAlgorithm.evaluationFunctions.BasicGrowthPsdEvaluator

Sets the expected rates hierarchies, based on the objective rates (genes).

setHierarchy(double[]) - Method in class geneticAlgorithm.evaluationFunctions.SiBasicPsdEvaluator

setHierarchy(double[]) - Method in class geneticAlgorithm.evaluationFunctions.SiThreadedPsdEvaluator

setHops(int) - Method in class kineticMonteCarlo.atom.AbstractGrowthAtom

setHops(int) - Method in class kineticMonteCarlo.atom.AbstractGrowthAtomAttributes

setId(short) - Method in class kineticMonteCarlo.atom.SiAtom

setIndividual(Individual) - Method in class geneticAlgorithm.evaluationFunctions.BasicGrowthPsdEvaluator.Runner

setIndividual(Individual, int) - Method in class geneticAlgorithm.Population

Sets an individual to position pos

setInnerPerimeter() - Method in class kineticMonteCarlo.atom.AbstractGrowthAtom

setInsideCircle(int, boolean) - Method in class kineticMonteCarlo.lattice.AbstractGrowthLattice

Defines which atoms are inside from the current position (centre) and given radius.

setInsideSquare(int) - Method in class kineticMonteCarlo.lattice.AbstractGrowthLattice

Defines which atoms are inside from the current position.

setIslandNumber(int) - Method in class kineticMonteCarlo.atom.AbstractGrowthAtom

setIslandNumber(int) - Method in class kineticMonteCarlo.atom.AbstractGrowthAtomAttributes

setIslandNumber(int) - Method in class kineticMonteCarlo.lattice.Island

setIterationNumber(int) - Method in class geneticAlgorithm.Population

setIterations(int) - Method in class kineticMonteCarlo.kmcCore.AbstractKmc

setKmc(AbstractKmc) - Method in class basic.AbstractSimulation

setKMC(BasicKmc) - Method in class graphicInterfaces.basic.BasicPanel

setLattice(AbstractLattice) - Method in class kineticMonteCarlo.kmcCore.AbstractKmc

setLattice(AbstractGrowthLattice) - Method in class kineticMonteCarlo.kmcCore.growth.AbstractGrowthKmc

setLeft(Node<T>) - Method in class utils.list.Node

setLevel(int) - Method in class utils.list.AbstractList

setLevel(int) - Method in class utils.list.Node

setList(Boolean) - Method in class kineticMonteCarlo.atom.AbstractAtom

setList(Boolean) - Method in interface kineticMonteCarlo.atom.IAtom

setListType(String) - Method in class basic.Parser

Sets the internal list type to be used.

setLocation(double, double) - Method in class java.awt.geom.Point2D.Double

Sets the location of this Point2D to the specified double coordinates.

setLocation(double, double) - Method in class java.awt.geom.Point2D.Float

Sets the location of this Point2D to the specified double coordinates.

setLocation(float, float) - Method in class java.awt.geom.Point2D.Float

Sets the location of this Point2D to the specified float coordinates.

setLocation(double, double) - Method in class java.awt.geom.Point2D

Sets the location of this Point2D to the specified double coordinates.

setLocation(Point2D) - Method in class java.awt.geom.Point2D

Sets the location of this Point2D to the same coordinates as the specified Point2D object.

setLogScale(boolean) - Method in class graphicInterfaces.surfaceViewer2D.Frame2D

setLogScale(boolean) - Method in class graphicInterfaces.surfaceViewer2D.Panel2D

setLogScale(boolean) - Method in class graphicInterfaces.surfaceViewer2D.SurfaceViewerPanel2D

setLogScale(boolean) - Method in interface graphicInterfacesCommon.surfaceViewer2D.IFrame2D

setM4f(Matrix4f) - Method in class graphicInterfaces.etching.mouseBehaviors.MouseRotate

setM4f(Matrix4f) - Method in class graphicInterfaces.etching.mouseBehaviors.MouseTranslate

setM4f(Matrix4f) - Method in class graphicInterfaces.etching.mouseBehaviors.MouseZoom

setMainInterface(MainInterface) - Method in class geneticAlgorithm.AbstractGeneticAlgorithm

Sets the main interface, starts a thread which will be responsible to update it and assigns the main interface to the evaluator (to be able to also update it with the current surface and PSD).

setMax(double) - Method in class graphicInterfaces.surfaceViewer2D.Frame2D

setMax(double) - Method in class graphicInterfaces.surfaceViewer2D.Panel2D

setMax(double) - Method in class graphicInterfaces.surfaceViewer2D.SurfaceViewerPanel2D

setMax(double) - Method in interface graphicInterfacesCommon.surfaceViewer2D.IFrame2D

setMaxAccumulatedSteps(int) - Method in class kineticMonteCarlo.kmcCore.growth.devitaAccelerator.DevitaHopsConfig

setMaxDistanceHops(int) - Method in class kineticMonteCarlo.kmcCore.growth.devitaAccelerator.DevitaHopsConfig

setMaxPerimeter(float, float) - Method in class kineticMonteCarlo.kmcCore.growth.RoundPerimeter

setMesh(float[][]) - Method in class graphicInterfaces.surfaceViewer2D.Frame2D

setMesh(float[][]) - Method in class graphicInterfaces.surfaceViewer2D.SurfaceViewerPanel2D

setMesh(float[][]) - Method in interface graphicInterfacesCommon.surfaceViewer2D.IFrame2D

setMillerX(int) - Method in class basic.Parser

setMillerY(int) - Method in class basic.Parser

setMillerZ(int) - Method in class basic.Parser

setMin(double) - Method in class graphicInterfaces.surfaceViewer2D.Frame2D

setMin(double) - Method in class graphicInterfaces.surfaceViewer2D.Panel2D

setMin(double) - Method in class graphicInterfaces.surfaceViewer2D.SurfaceViewerPanel2D

setMin(double) - Method in interface graphicInterfacesCommon.surfaceViewer2D.IFrame2D

setMinAccumulatedSteps(int) - Method in class kineticMonteCarlo.kmcCore.growth.devitaAccelerator.DevitaHopsConfig

setMinDistanceHops(int) - Method in class kineticMonteCarlo.kmcCore.growth.devitaAccelerator.DevitaHopsConfig

setMinRadius() - Method in class kineticMonteCarlo.kmcCore.growth.RoundPerimeter

setMultiAtomEnergies(double[]) - Method in class ratesLibrary.concerted.AbstractConcertedRates

setMultiAtomNumber(int) - Method in class kineticMonteCarlo.atom.AbstractGrowthAtom

setMultiplier(int) - Method in class kineticMonteCarlo.atom.AbstractGrowthAtom

setN1(int) - Method in class kineticMonteCarlo.atom.GrapheneAtom

setNeighbour(AbstractAtom, int) - Method in class kineticMonteCarlo.atom.AbstractAtom

setNeighbour(AbstractGrowthAtom, int) - Method in class kineticMonteCarlo.atom.AbstractGrowthAtom

setNeighbour(AbstractGrowthAtom, int) - Method in class kineticMonteCarlo.atom.AgAtom

setNeighbour(AbstractAtom, int) - Method in class kineticMonteCarlo.atom.BasicAtom

setNeighbour(AbstractGrowthAtom, int) - Method in class kineticMonteCarlo.atom.BasicGrowthAtom

setNeighbour(AbstractGrowthAtom, int) - Method in class kineticMonteCarlo.atom.CatalysisAtom

setNeighbour(AbstractGrowthAtom, int) - Method in class kineticMonteCarlo.atom.GrapheneAtom

setNeighbour(AbstractAtom, int) - Method in interface kineticMonteCarlo.atom.IAtom

setNeighbour(AbstractAtom, int) - Method in class kineticMonteCarlo.atom.SiAtom

setNeighbours(GrapheneAtom[]) - Method in class kineticMonteCarlo.atom.GrapheneAtom

setNeighbours(GrapheneAtom[]) - Method in class kineticMonteCarlo.atom.GrapheneAtomSchoenhalz

setNext(Node<T>) - Method in class utils.list.Node

setNImmobile(int) - Method in class kineticMonteCarlo.atom.AgAtom

setNMobile(int) - Method in class kineticMonteCarlo.atom.AgAtom

setNumberOfAtoms(int) - Method in class kineticMonteCarlo.lattice.Island

setNumberOfNeighbours(int) - Method in class kineticMonteCarlo.atom.AbstractAtom

setNumberOfNeighbours(int) - Method in interface kineticMonteCarlo.atom.IAtom

setNumberOfSimulations(int) - Method in class basic.Parser

setOccupied(boolean) - Method in class kineticMonteCarlo.atom.AbstractAtom

setOffspringGenes(RichMatrix) - Method in class geneticAlgorithm.Population

setOnList(byte, boolean) - Method in class kineticMonteCarlo.atom.AbstractGrowthAtom

setOnList(byte, boolean) - Method in class kineticMonteCarlo.lattice.Island

setOnList(byte, boolean) - Method in interface kineticMonteCarlo.process.IElement

setOuterPerimeter() - Method in class kineticMonteCarlo.atom.AbstractGrowthAtom

setOutside(boolean) - Method in class kineticMonteCarlo.atom.AbstractGrowthAtom

setOverlayText(String) - Method in class graphicInterfaces.etching.Canvas3DOverlay

setParent(IProbabilityHolder) - Method in class utils.list.AbstractList

setPaused(boolean) - Method in class graphicInterfaces.growth.KmcCanvas

setPaused(boolean) - Method in class kineticMonteCarlo.lattice.AbstractLattice

setPerimeter(RoundPerimeter) - Method in class kineticMonteCarlo.kmcCore.growth.AbstractGrowthKmc

setPopulation(int) - Method in class basic.Parser

setPosX(double) - Method in class kineticMonteCarlo.unitCell.CatalysisUc

setPosX(double) - Method in class kineticMonteCarlo.unitCell.Simple3dUc

setPosX(double) - Method in class kineticMonteCarlo.unitCell.SimpleUc

setPosY(double) - Method in class kineticMonteCarlo.unitCell.CatalysisUc

setPosY(double) - Method in class kineticMonteCarlo.unitCell.Simple3dUc

setPosY(double) - Method in class kineticMonteCarlo.unitCell.SimpleUc

setPosZ(double) - Method in class kineticMonteCarlo.unitCell.Simple3dUc

setPressure(byte, double) - Method in class ratesLibrary.CatalysisRates

setPressureCO(double) - Method in class ratesLibrary.CatalysisRates

Sets pressure for CO given in atmospheres and saved in Pa.

setPressureO2(double) - Method in class ratesLibrary.CatalysisRates

Sets pressure for O2 given in atmospheres and saved in Pa.

setPrintId(boolean) - Method in class graphicInterfaces.growth.KmcCanvas

setPrintIslandNumber(boolean) - Method in class graphicInterfaces.growth.KmcCanvas

setPrintMultiAtom(boolean) - Method in class graphicInterfaces.growth.KmcCanvas

setProbabilities(double[]) - Method in class kineticMonteCarlo.atom.AbstractAtom

setProbabilities(double[]) - Method in interface kineticMonteCarlo.atom.IAtom

setProbabilities(double[]) - Method in class kineticMonteCarlo.lattice.AbstractLattice

setProbabilities(double[]) - Method in class kineticMonteCarlo.lattice.BasicLattice

setProbabilities(double[]) - Method in class kineticMonteCarlo.lattice.SiLattice

setProcceses(AbstractProcess[]) - Method in class kineticMonteCarlo.atom.AbstractGrowthAtom

setProgress(float[]) - Method in class graphicInterfaces.gaConvergence.GaProgressPanel

setProgress(float[]) - Method in class graphicInterfaces.MainInterface

setPsd(float[][]) - Method in class geneticAlgorithm.evaluationFunctions.AbstractPsdEvaluator

Set the reference PSD matrix for future comparisons and starts its norms.

setPsd(float[][]) - Method in class graphicInterfaces.surfaceViewer2D.Panel2D

setPsdSizeX(int) - Method in class geneticAlgorithm.evaluationFunctions.AbstractPsdEvaluator

setPsdSizeY(int) - Method in class geneticAlgorithm.evaluationFunctions.AbstractPsdEvaluator

setRate(byte, double) - Method in class kineticMonteCarlo.atom.AbstractGrowthAtom

setRate(byte, double) - Method in class kineticMonteCarlo.lattice.Island

setRate(double) - Method in class kineticMonteCarlo.process.AbstractProcess

setRate(byte, double) - Method in interface kineticMonteCarlo.process.IElement

setRates(IRates) - Method in class basic.AbstractSimulation

setRates(CatalysisRates) - Method in class kineticMonteCarlo.kmcCore.catalysis.CatalysisFarkasKmc

setRates(CatalysisRates) - Method in class kineticMonteCarlo.kmcCore.catalysis.CatalysisKmc

setRates(double[][]) - Method in class kineticMonteCarlo.kmcCore.growth.ActivationEnergy

setRates(AbstractConcertedRates) - Method in class kineticMonteCarlo.kmcCore.growth.ConcertedKmc

setRates(double[], double[]) - Method in class ratesLibrary.basic.RatesCase

setRates(double[]) - Method in class utils.list.AbstractList

setReactionEnergiesCoO(double[][]) - Method in class ratesLibrary.CatalysisRates

setReactionEnergiesCoOcoCusCoCus(double[]) - Method in class ratesLibrary.CatalysisRates

setRemoved() - Method in class kineticMonteCarlo.atom.AbstractAtom

setRemoved() - Method in interface kineticMonteCarlo.atom.IAtom

setRepeats(int) - Method in class geneticAlgorithm.evaluationFunctions.AbstractPsdEvaluator

setRestart(Restart) - Method in class utils.psdAnalysis.PsdSignature2D

setRight(Node<T>) - Method in class utils.list.Node

setRotacion(double[]) - Method in class kineticMonteCarlo.unitCell.SiUnitCell

setScale(float, float) - Method in class graphicInterfaces.etching.mouseBehaviors.MouseZoom

setScale(int) - Method in class graphicInterfaces.growth.KmcCanvas

setSeed(long) - Method in class utils.edu.cornell.lassp.houle.rngPack.RanMT

setSeed(int[]) - Method in class utils.edu.cornell.lassp.houle.rngPack.RanMT

An alternative, more complete, method of seeding the pseudo random number generator.

setShift(boolean) - Method in class graphicInterfaces.surfaceViewer2D.Frame2D

setShift(boolean) - Method in class graphicInterfaces.surfaceViewer2D.Panel2D

setShift(boolean) - Method in class graphicInterfaces.surfaceViewer2D.SurfaceViewerPanel2D

setShift(boolean) - Method in interface graphicInterfacesCommon.surfaceViewer2D.IFrame2D

setShowGraphics(boolean) - Method in class geneticAlgorithm.evaluationFunctions.AbstractEvaluator

setShowGraphics(boolean) - Method in class geneticAlgorithm.evaluationFunctions.AgThreadedPsdEvaluator

setShowGraphics(boolean) - Method in class geneticAlgorithm.evaluationFunctions.SiThreadedPsdEvaluator

setSimulationMesh(float[][]) - Method in class graphicInterfaces.MainInterface

setSimulationTime(double) - Method in class geneticAlgorithm.Individual

setStatusBar(String) - Method in class graphicInterfaces.MainInterface

setSumRate(byte, double) - Method in class kineticMonteCarlo.atom.AbstractGrowthAtom

setSumRate(byte, double) - Method in class kineticMonteCarlo.lattice.Island

setSumRate(double) - Method in class kineticMonteCarlo.process.AbstractProcess

setSumRate(byte, double) - Method in interface kineticMonteCarlo.process.IElement

setSurface(float[][]) - Method in class graphicInterfaces.MainInterface

setTemperature(float) - Method in class basic.Parser

setTerraceToTerraceProbability(double) - Method in class kineticMonteCarlo.kmcCore.growth.AbstractGrowthKmc

setTextInfo(String) - Method in class graphicInterfaces.surfaceViewer2D.Panel2D

setTotalAtoms(int) - Method in class utils.list.AbstractList

setType(byte) - Method in class kineticMonteCarlo.atom.AbstractGrowthAtom

setType(byte) - Method in class kineticMonteCarlo.atom.CatalysisAtomAttributes

setUnitCellSize(int) - Method in class kineticMonteCarlo.lattice.AbstractLattice

setupCallback(MouseBehaviorCallback) - Method in class graphicInterfaces.etching.mouseBehaviors.MouseRocking

setupCallback(MouseBehaviorCallback) - Method in class graphicInterfaces.etching.mouseBehaviors.MouseRotate

The transformChanged method in the callback class will be called every time the transform is updated

setupCallback(MouseBehaviorCallback) - Method in class graphicInterfaces.etching.mouseBehaviors.MouseZoom

The transformChanged method in the callback class will be called every time the transform is updated

setVisible(boolean) - Method in interface graphicInterfacesCommon.growth.IGrowthKmcFrame

setVisible(boolean) - Method in interface graphicInterfacesCommon.surfaceViewer2D.IFrame2D

setVisited(boolean) - Method in class kineticMonteCarlo.atom.AbstractGrowthAtom

When counting islands, we have to keep track of the visited atoms.

setWheight(float) - Method in class geneticAlgorithm.evaluationFunctions.AbstractEvaluator

setWheight(float) - Method in interface geneticAlgorithm.evaluationFunctions.IEvaluation

setX() - Method in class graphicInterfaces.etching.mouseBehaviors.MouseRotate

setX() - Method in class graphicInterfaces.etching.mouseBehaviors.MouseTranslate

setX() - Method in class graphicInterfaces.etching.mouseBehaviors.MouseZoom

setY() - Method in class graphicInterfaces.etching.mouseBehaviors.MouseRotate

setY() - Method in class graphicInterfaces.etching.mouseBehaviors.MouseTranslate

setY() - Method in class graphicInterfaces.etching.mouseBehaviors.MouseZoom

setZ() - Method in class graphicInterfaces.etching.mouseBehaviors.MouseRotate

setZ() - Method in class graphicInterfaces.etching.mouseBehaviors.MouseTranslate

setZ() - Method in class graphicInterfaces.etching.mouseBehaviors.MouseZoom

shift - Variable in class graphicInterfaces.surfaceViewer2D.Panel2D

shift - Variable in class kineticMonteCarlo.lattice.AgUcLattice

List to store free area that current atom has.

shiftCheckBox - Variable in class graphicInterfaces.surfaceViewer2D.SurfaceViewerPanel2D

showGraphics - Variable in class geneticAlgorithm.evaluationFunctions.AbstractEvaluator

showGraphics() - Method in class geneticAlgorithm.evaluationFunctions.AbstractEvaluator

showPSDControls(boolean) - Method in class graphicInterfaces.surfaceViewer2D.Frame2D

showPSDControls(boolean) - Method in interface graphicInterfacesCommon.surfaceViewer2D.IFrame2D

SiAtom - Class in kineticMonteCarlo.atom

SiAtom(double, double, double) - Constructor for class kineticMonteCarlo.atom.SiAtom

SiBasicPsdEvaluator - Class in geneticAlgorithm.evaluationFunctions

SiBasicPsdEvaluator(Parser, int) - Constructor for class geneticAlgorithm.evaluationFunctions.SiBasicPsdEvaluator

SICK - Static variable in class kineticMonteCarlo.atom.AbstractAtom

SiEtchingKmcConvergence - Class in samples.convergences.siEtching

SiEtchingKmcConvergence() - Constructor for class samples.convergences.siEtching.SiEtchingKmcConvergence

SiFrame - Class in graphicInterfaces.etching

SiFrame() - Constructor for class graphicInterfaces.etching.SiFrame

sigma - Variable in class geneticAlgorithm.recombination.DifferentialRecombination

Step size in CMA-ES.

sigma - Variable in class ratesLibrary.CatalysisRates

Symmetry number.

SiInitialisator - Class in geneticAlgorithm.populationInitialisation

SiInitialisator() - Constructor for class geneticAlgorithm.populationInitialisation.SiInitialisator

SiKmc - Class in kineticMonteCarlo.kmcCore.etching

SiKmc(Parser) - Constructor for class kineticMonteCarlo.kmcCore.etching.SiKmc

sil - Variable in class graphicInterfaces.etching.SiFrame

SiLattice - Class in kineticMonteCarlo.lattice

SiLattice(int, int, int, int, int, int) - Constructor for class kineticMonteCarlo.lattice.SiLattice

SiliconMultithreadedPsdCalculation - Class in samples.silicon

SiliconMultithreadedPsdCalculation() - Constructor for class samples.silicon.SiliconMultithreadedPsdCalculation

SiliconPsdDifferencesBetweenTemperatures - Class in samples.silicon

SiliconPsdDifferencesBetweenTemperatures() - Constructor for class samples.silicon.SiliconPsdDifferencesBetweenTemperatures

simple - Variable in class kineticMonteCarlo.lattice.BasicGrowthLattice

Simple3dUc - Class in kineticMonteCarlo.unitCell

Really simple unit cell, which will contain only one atom.

Simple3dUc(int, int, AbstractAtom) - Constructor for class kineticMonteCarlo.unitCell.Simple3dUc

Simple3dUc(int, int, int, AbstractAtom) - Constructor for class kineticMonteCarlo.unitCell.Simple3dUc

SimpleAgAgGrowthKmcSimulation - Class in samples.agAgGrowth

SimpleAgAgGrowthKmcSimulation() - Constructor for class samples.agAgGrowth.SimpleAgAgGrowthKmcSimulation

SimpleAgAgGrowthKmcSimulation.paintLoop - Class in samples.agAgGrowth

Private class responsible to repaint every 100 ms the KMC frame.

SimpleBasicKmcSimulation - Class in samples.basic

SimpleBasicKmcSimulation() - Constructor for class samples.basic.SimpleBasicKmcSimulation

SimpleGrapheneKmcSimulation - Class in samples.grapheneCvdGrowth

SimpleGrapheneKmcSimulation() - Constructor for class samples.grapheneCvdGrowth.SimpleGrapheneKmcSimulation

SimpleGrapheneKmcSimulation.paintLoop - Class in samples.grapheneCvdGrowth

Private class responsible to repaint every 100 ms the KMC frame.

SimpleKmcSimulationWithWorker - Class in samples.worker

SimpleKmcSimulationWithWorker() - Constructor for class samples.worker.SimpleKmcSimulationWithWorker

SimpleSiliconKmcFftAnalisys - Class in samples.silicon

SimpleSiliconKmcFftAnalisys() - Constructor for class samples.silicon.SimpleSiliconKmcFftAnalisys

SimpleSiliconKmcSimulation - Class in samples.silicon

SimpleSiliconKmcSimulation() - Constructor for class samples.silicon.SimpleSiliconKmcSimulation

SimpleUc - Class in kineticMonteCarlo.unitCell

Really simple unit cell, which will contain only one atom.

SimpleUc(int, int, AbstractGrowthAtom) - Constructor for class kineticMonteCarlo.unitCell.SimpleUc

simulate() - Method in class kineticMonteCarlo.kmcCore.AbstractKmc

Does the actual simulation.

simulate(double) - Method in class kineticMonteCarlo.kmcCore.AbstractKmc

Does the actual simulation.

simulate(int) - Method in class kineticMonteCarlo.kmcCore.AbstractKmc

Does the actual simulation.

simulate() - Method in class kineticMonteCarlo.kmcCore.catalysis.CatalysisKmc

simulate() - Method in class kineticMonteCarlo.kmcCore.growth.AbstractGrowthKmc

simulate() - Method in class kineticMonteCarlo.kmcCore.growth.ConcertedKmc

simulate() - Method in interface kineticMonteCarlo.kmcCore.IKmc

simulate(double) - Method in interface kineticMonteCarlo.kmcCore.IKmc

simulate(int) - Method in interface kineticMonteCarlo.kmcCore.IKmc

simulate(IFinishListener, int) - Method in class kineticMonteCarlo.kmcCore.worker.KmcWorker

simulate(double, IFinishListener, int) - Method in class kineticMonteCarlo.kmcCore.worker.KmcWorker

simulate(int, IFinishListener, int) - Method in class kineticMonteCarlo.kmcCore.worker.KmcWorker

simulate(IIntervalListener, IFinishListener, int, int) - Method in class kineticMonteCarlo.kmcCore.worker.KmcWorker

simulatedSteps - Variable in class kineticMonteCarlo.kmcCore.catalysis.CatalysisKmc

simulatedSteps - Variable in class kineticMonteCarlo.kmcCore.growth.AbstractGrowthKmc

simulatedSteps - Variable in class kineticMonteCarlo.kmcCore.growth.ConcertedKmc

simulation - Variable in class geneticAlgorithm.AbstractGeneticAlgorithm

simulationCount - Variable in class geneticAlgorithm.evaluationFunctions.AgBasicPsdEvaluator

simulationCount - Variable in class geneticAlgorithm.evaluationFunctions.BasicGrowthPsdEvaluator

simulationNumber - Variable in class kineticMonteCarlo.kmcCore.growth.ConcertedKmc

simulationPanel2d - Variable in class graphicInterfaces.MainInterface

simulations - Variable in class basic.AbstractSimulation

simulationTime - Variable in class geneticAlgorithm.Individual

simulationTime - Static variable in class main.Morphokinetics

simulationTime - Variable in class utils.akting.RichArray

simulationType - Variable in class kineticMonteCarlo.kmcCore.worker.KmcWorker

sin() - Static method in class utils.akting.operations.OperationFactory

SINGLE - Static variable in class kineticMonteCarlo.process.ConcertedProcess

SinOperation - Class in utils.akting.operations

SinOperation() - Constructor for class utils.akting.operations.SinOperation

SiPointArray - Class in graphicInterfaces.etching

SiPointArray(float[]) - Constructor for class graphicInterfaces.etching.SiPointArray

SiRatesFromPreGosalvez - Class in ratesLibrary

Etch rates data obtained from Gosalvez Et al - Physical Review E 68 (2003) 031604.

SiRatesFromPreGosalvez() - Constructor for class ratesLibrary.SiRatesFromPreGosalvez

SiRestriction - Class in geneticAlgorithm.restrictions

SiRestriction() - Constructor for class geneticAlgorithm.restrictions.SiRestriction

SiSimulation - Class in basic

SiSimulation(Parser) - Constructor for class basic.SiSimulation

sites - Variable in class kineticMonteCarlo.kmcCore.catalysis.CatalysisKmc

sites - Variable in class kineticMonteCarlo.kmcCore.growth.ConcertedKmc

SiThreadedPsdEvaluator - Class in geneticAlgorithm.evaluationFunctions

SiThreadedPsdEvaluator(Parser, int, int) - Constructor for class geneticAlgorithm.evaluationFunctions.SiThreadedPsdEvaluator

SiUnitCell - Class in kineticMonteCarlo.unitCell

SiUnitCell() - Constructor for class kineticMonteCarlo.unitCell.SiUnitCell

size() - Method in class geneticAlgorithm.Population

size() - Method in class kineticMonteCarlo.lattice.AbstractGrowthLattice

size() - Method in class kineticMonteCarlo.lattice.AbstractLattice

size() - Method in class kineticMonteCarlo.lattice.AgUcLattice

size() - Method in class kineticMonteCarlo.unitCell.AgUc

Number of elements per unit cell.

size - Variable in class kineticMonteCarlo.unitCell.CatalysisUc

size() - Method in class kineticMonteCarlo.unitCell.CatalysisUc

Number of elements.

size() - Method in interface kineticMonteCarlo.unitCell.IUc

Number of elements.

size - Variable in class kineticMonteCarlo.unitCell.Simple3dUc

size() - Method in class kineticMonteCarlo.unitCell.Simple3dUc

Number of elements.

size - Variable in class kineticMonteCarlo.unitCell.SimpleUc

size() - Method in class kineticMonteCarlo.unitCell.SimpleUc

Number of elements.

size() - Method in class kineticMonteCarlo.unitCell.SiUnitCell

size() - Method in class utils.list.atoms.AtomsArrayList

size() - Method in class utils.list.atoms.AtomsAvlTree

size() - Method in interface utils.list.atoms.IAtomsCollection

SIZE_X - Static variable in class kineticMonteCarlo.unitCell.AgUc

SIZE_X - Static variable in interface kineticMonteCarlo.unitCell.IUc

SIZE_Y - Static variable in class kineticMonteCarlo.unitCell.AgUc

SIZE_Y - Static variable in interface kineticMonteCarlo.unitCell.IUc

SIZE_Z - Static variable in interface kineticMonteCarlo.unitCell.IUc

sizeI - Variable in class kineticMonteCarlo.lattice.AgUcLattice

How many unit cells are in X axis.

sizeJ - Variable in class kineticMonteCarlo.lattice.AgUcLattice

How many unit cells are in Y axis.

sizes - Variable in class utils.psdAnalysis.PsdSignature2D

slope - Variable in class utils.LinearRegression

slope() - Method in class utils.LinearRegression

Returns the slope β of the best of the best-fit line y = α + β x.

slopeStdErr() - Method in class utils.LinearRegression

Returns the standard error of the estimate for the slope.

sortedIndexes() - Method in class utils.akting.RichArray

SPACE_CELL - Static variable in class kineticMonteCarlo.unitCell.SiUnitCell

spinnerScale - Variable in class graphicInterfaces.growth.GrowthKmcFrame

spinnerScaleStateChanged(ChangeEvent) - Method in class graphicInterfaces.growth.GrowthKmcFrame

sqrt() - Static method in class utils.akting.operations.OperationFactory

SqrtOperation - Class in utils.akting.operations

SqrtOperation() - Constructor for class utils.akting.operations.SqrtOperation

SQUARE - Static variable in class kineticMonteCarlo.kmcCore.growth.RoundPerimeter

stack - Variable in class kineticMonteCarlo.atom.ArrayStack

stackdeck() - Method in class utils.edu.cornell.lassp.houle.rngPack.RandomShuffle

start - Variable in class kineticMonteCarlo.kmcCore.catalysis.CatalysisKmc

startMouseX - Variable in class graphicInterfaces.growth.GrowthKmcFrame

startMouseX - Variable in class graphicInterfaces.MainInterface

startMouseY - Variable in class graphicInterfaces.growth.GrowthKmcFrame

startMouseY - Variable in class graphicInterfaces.MainInterface

startTime - Variable in class basic.AbstractSimulation

staticRandom - Variable in class basic.AbstractSimulation

StaticRandom - Class in utils

StaticRandom() - Constructor for class utils.StaticRandom

StaticRandom(boolean) - Constructor for class utils.StaticRandom

stationary - Variable in class kineticMonteCarlo.kmcCore.catalysis.CatalysisKmc

stationaryStep - Variable in class kineticMonteCarlo.kmcCore.catalysis.CatalysisKmc

Statistics - Class in kineticMonteCarlo.lattice.perimeterStatistics

Statistics(String) - Constructor for class kineticMonteCarlo.lattice.perimeterStatistics.Statistics

statusbar - Variable in class graphicInterfaces.growth.GrowthKmcFrame

statusbar - Variable in class graphicInterfaces.MainInterface

statusFlagValue - Variable in enum basic.EvaluatorType.evaluatorFlag

statusFlagValue - Variable in enum basic.io.OutputType.formatFlag

std() - Method in class utils.akting.RichArray

Calculates the standard deviation of an array

std() - Method in class utils.akting.RichMatrix

Calculates the standard deviation of a matrix

stepFunction(double) - Method in class geneticAlgorithm.evaluationFunctions.AgBasicPsdEvaluator

stepFunction(double) - Method in class geneticAlgorithm.evaluationFunctions.BasicGrowthPsdEvaluator

steps - Variable in class kineticMonteCarlo.kmcCore.catalysis.CatalysisKmc

stopError - Variable in class basic.Parser

stopError - Variable in class geneticAlgorithm.AbstractGeneticAlgorithm

The stop error.

storeSimulationTimes(Population) - Method in class geneticAlgorithm.evaluationFunctions.MultithreadedPsdEvaluator

strategy - Variable in class graphicInterfaces.growth.KmcCanvas

Buffer Strategy.

subArray(int, int) - Method in class utils.akting.RichArray

subtract(double, double, double) - Method in class javafx.geometry.Point3D

Returns a point with the specified coordinates subtracted from the coordinates of this point.

subtract(Point3D) - Method in class javafx.geometry.Point3D

Returns a point with the coordinates of the specified point subtracted from the coordinates of this point.

subtractOccupied() - Method in class kineticMonteCarlo.lattice.AbstractGrowthLattice

Subtracts an occupied location from the counter.

sum() - Method in class utils.akting.RichArray

sum(RichArray) - Method in class utils.akting.RichArray

sum(RichMatrix) - Method in class utils.akting.RichMatrix

sumDistance - Variable in class kineticMonteCarlo.lattice.Island

sumProbabilities - Variable in class kineticMonteCarlo.kmcCore.growth.AbstractGrowthKmc

sumRate - Variable in class kineticMonteCarlo.process.AbstractProcess

Attribute for AVL tree.

surface - Variable in class kineticMonteCarlo.kmcCore.growth.ActivationEnergy

surface - Variable in class utils.list.LinearList

surfacePanel2d - Variable in class graphicInterfaces.MainInterface

surfaceSizes - Variable in class basic.AbstractSimulation

surfaceSizeX - Variable in class utils.psdAnalysis.PsdSignature2D

surfaceSizeY - Variable in class utils.psdAnalysis.PsdSignature2D

surfaceType - Variable in class basic.Parser

See Parser.getSurfaceType().

SurfaceViewerPanel2D - Class in graphicInterfaces.surfaceViewer2D

SurfaceViewerPanel2D(String) - Constructor for class graphicInterfaces.surfaceViewer2D.SurfaceViewerPanel2D

svar0 - Variable in class utils.LinearRegression

svar1 - Variable in class utils.LinearRegression

swapAtomsInMultiAtom(AbstractGrowthAtom, AbstractGrowthAtom) - Method in class kineticMonteCarlo.lattice.AbstractGrowthLattice

swapAttributes(AbstractGrowthAtom) - Method in class kineticMonteCarlo.atom.AbstractGrowthAtom

swapAttributes(AbstractGrowthAtom) - Method in class kineticMonteCarlo.atom.CatalysisAtom

swapIsland(Island, Island) - Method in class kineticMonteCarlo.lattice.AbstractGrowthLattice

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