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

I

i24 - Variable in class utils.edu.cornell.lassp.houle.rngPack.Ranlux

i97 - Variable in class utils.edu.cornell.lassp.houle.rngPack.Ranmar

IAtom - Interface in kineticMonteCarlo.atom

This interface defines the minimum methods that an atom class have to have.

IAtomsCollection<T extends java.lang.Comparable<T>> - Interface in utils.list.atoms

IBasicRates - Interface in ratesLibrary.basic

IConfigurator - Interface in main

Common interface for Android/PC configurators.

icons - Static variable in class utils.edu.cornell.lassp.houle.rngPack.Ranlux

id - Variable in class kineticMonteCarlo.atom.AbstractGrowthAtom

Unique identifier.

id - Variable in class kineticMonteCarlo.atom.SiAtom

idButton - Variable in class graphicInterfaces.growth.GrowthKmcFrame

idButtonPressed() - Method in class graphicInterfaces.growth.GrowthKmcFrame

idButtonState - Variable in class graphicInterfaces.growth.GrowthKmcFrame

identifyAddMultiAtom(AbstractGrowthAtom) - Method in class kineticMonteCarlo.lattice.AbstractGrowthLattice

Counts the number of islands from current atom.

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

Counts the number of islands that the simulation has.

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

Counts the number of islands from current atom.

identifyRemoveMultiAtomIsland(AbstractGrowthAtom) - Method in class kineticMonteCarlo.lattice.AbstractGrowthLattice

IDevitaLattice - Interface in kineticMonteCarlo.lattice

idMi - Variable in class graphicInterfaces.growth.GrowthKmcFrame

IElement - Interface in kineticMonteCarlo.process

IEvaluation - Interface in geneticAlgorithm.evaluationFunctions

IEvaluator - Interface in geneticAlgorithm.evaluationFunctions

IFinishListener - Interface in kineticMonteCarlo.kmcCore.worker

IFrame2D - Interface in graphicInterfacesCommon.surfaceViewer2D

IgaProgressFrame - Interface in graphicInterfaces.gaConvergence

IGeneticAlgorithm - Interface in geneticAlgorithm

igiga - Static variable in class utils.edu.cornell.lassp.houle.rngPack.Ranlux

IGrowthKmcFrame - Interface in graphicInterfacesCommon.growth

iHexa - Variable in class basic.io.CatalysisData

iHexa - Variable in class kineticMonteCarlo.atom.AbstractGrowthAtom

Hexagonal i coordinate.

iInit - Variable in class kineticMonteCarlo.unitCell.SiUnitCell

IInitialisator - Interface in geneticAlgorithm.populationInitialisation

IIntervalListener - Interface in kineticMonteCarlo.kmcCore.worker

IKmc - Interface in kineticMonteCarlo.kmcCore

imageName - Variable in class graphicInterfaces.growth.KmcCanvas

imageName - Variable in class graphicInterfaces.surfaceViewer2D.Frame2D

IMutation - Interface in geneticAlgorithm.mutation

in24 - Variable in class utils.edu.cornell.lassp.houle.rngPack.Ranlux

includePerimeterList - Variable in class kineticMonteCarlo.lattice.AbstractGrowthLattice

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

Adds an empty area, maintaining the island size.

increaseSize() - Method in class graphicInterfaces.growth.GrowthKmcFrame

ind - Variable in class geneticAlgorithm.evaluationFunctions.BasicGrowthPsdEvaluator.Runner

INDIANRED - Static variable in class graphicInterfaces.growth.KmcCanvas

Individual - Class in geneticAlgorithm

This class models an individual of a Genetic algorithm.

Individual(int, int) - Constructor for class geneticAlgorithm.Individual

Individual(double[], double[]) - Constructor for class geneticAlgorithm.Individual

Individual(double[]) - Constructor for class geneticAlgorithm.Individual

individual1 - Variable in class geneticAlgorithm.Couple

individual2 - Variable in class geneticAlgorithm.Couple

IndividualGroup - Class in geneticAlgorithm

IndividualGroup(int) - Constructor for class geneticAlgorithm.IndividualGroup

individuals - Variable in class geneticAlgorithm.Population

init() - Method in class kineticMonteCarlo.lattice.AgLattice

init() - Method in class kineticMonteCarlo.lattice.BasicGrowthLattice

init() - Method in class kineticMonteCarlo.lattice.CatalysisLattice

init() - Method in class utils.printByHandHelper

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

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

Iterates over all lattice sites and initialises adsorption probabilities.

initCatalysis(int) - Method in class basic.io.Restart

initComponents() - Method in class graphicInterfaces.basic.BasicFrame

This method is called from within the constructor to initialize the form.

initComponents() - Method in class graphicInterfaces.basic.BasicPanel

This method is called from within the constructor to initialize the form.

initComponents() - Method in class graphicInterfaces.etching.SiFrame

This method is called from within the constructor to initialize the form.

initComponents() - Method in class graphicInterfaces.gaConvergence.GaProgressFrame

This method is called from within the constructor to initialize the form.

initComponents() - Method in class graphicInterfaces.gaConvergence.GaProgressPanel

This method is called from within the constructor to initialise the form.

initComponents() - Method in class graphicInterfaces.growth.GrowthKmcFrame

This method is called from within the constructor to initialise the form.

initComponents() - Method in class graphicInterfaces.surfaceViewer2D.Frame2D

This method is called from within the constructor to initialize the form.

initComponents() - Method in class graphicInterfaces.surfaceViewer2D.Panel2D

This method is called from within the constructor to initialize the form.

initComponents() - Method in class graphicInterfaces.surfaceViewer2D.SurfaceViewerPanel2D

This method is called from within the constructor to initialise the form.

initConcerted(int) - Method in class basic.io.Restart

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

Start with fully covered surface.

initDouble() - Method in class kineticMonteCarlo.kmcCore.growth.ActivationEnergy

initDouble1(int) - Method in class kineticMonteCarlo.kmcCore.growth.ActivationEnergy

initDouble3() - Method in class kineticMonteCarlo.kmcCore.growth.ActivationEnergy

initDouble4() - Method in class kineticMonteCarlo.kmcCore.growth.ActivationEnergy

initGrowth() - Method in class graphicInterfaces.MainInterface

This method is called from within the constructor to initialise the form.

initialisation - Variable in class geneticAlgorithm.AbstractGeneticAlgorithm

initialise() - Method in class geneticAlgorithm.AbstractGeneticAlgorithm

initialise() - Method in interface geneticAlgorithm.IGeneticAlgorithm

initialise(Population) - Method in class geneticAlgorithm.recombination.DifferentialRecombination

Initialises the first population and assigns values to sigma and xMean.

initialise(Population) - Method in interface geneticAlgorithm.recombination.IRecombination

initialise(Population) - Method in class geneticAlgorithm.recombination.RealRecombination

Does nothing

initialise() - Method in class geneticAlgorithm.restrictions.AgReduced6Restriction

initialise() - Method in class geneticAlgorithm.restrictions.AgReducedRestriction

initialise() - Method in class geneticAlgorithm.restrictions.AgRestriction

initialise() - Method in class geneticAlgorithm.restrictions.BasicGrowthRestriction

initialise() - Method in class geneticAlgorithm.restrictions.RestrictionOperator

initialise() - Method in class geneticAlgorithm.restrictions.SiRestriction

initialise() - Method in class graphicInterfaces.growth.KmcCanvas

Call this before starting game loop, it initialises the bufferStrategy.

initialise(double[]) - Method in class kineticMonteCarlo.kmcCore.worker.KmcWorker

initialiseEnergies() - Method in class ratesLibrary.GrapheneGaillardOneNeighbourRates

initialiseEnergies() - Method in class ratesLibrary.GrapheneGaillardSimpleRates

initialiseEnergies() - Method in class ratesLibrary.GrapheneSyntheticRates

Using energies instead of direct rates.

initialiseKmc() - Method in class basic.AbstractSimulation

Initialises Kmc, the basic simulation class

initialiseKmc() - Method in class basic.AgSimulation

initialiseKmc() - Method in class basic.AgUcSimulation

initialiseKmc() - Method in class basic.BasicGrowthSimulation

initialiseKmc() - Method in class basic.CatalysisSimulation

initialiseKmc() - Method in class basic.ConcertedSimulation

initialiseKmc() - Method in class basic.GrapheneSimulation

initialiseKmc() - Method in class basic.SiSimulation

initialiseKmc() - Static method in class samples.agAgGrowth.AgAgPsdTest

initialiseKmc() - Static method in class samples.agAgGrowth.SimpleAgAgGrowthKmcSimulation

initialiseKmc() - Static method in class samples.grapheneCvdGrowth.SimpleGrapheneKmcSimulation

initialiseLimits(double, double, double) - Method in class kineticMonteCarlo.atom.SiAtom

Initialises limits in X, Y and Z.

initialiseNeighborHoodCache() - Static method in class kineticMonteCarlo.lattice.GrapheneLattice

initialiseRates(IRates, Parser) - Method in class basic.AbstractEtchingSimulation

initialiseRates(IRates, Parser) - Method in class basic.AbstractGrowthSimulation

initialiseRates(IRates, Parser) - Method in class basic.AbstractSimulation

initialiseRates(IRates, Parser) - Method in class basic.CatalysisSimulation

initialiseRates(IRates, Parser) - Method in class basic.ConcertedSimulation

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

Default rates to jump from one type to the other.

initialiseRates(double[][][]) - Method in class kineticMonteCarlo.atom.CatalysisAtom

Default rates to jump from one type to the other.

initialiseRates(double[]) - Method in class kineticMonteCarlo.kmcCore.AbstractKmc

Initialises the rates of the simulation.

initialiseRates(double[]) - Method in class kineticMonteCarlo.kmcCore.etching.BasicKmc

This model ignores the deposition rate.

initialiseRates(double[]) - Method in class kineticMonteCarlo.kmcCore.etching.SiKmc

This model ignores the deposition rate.

initialiseRates(double[]) - Method in class kineticMonteCarlo.kmcCore.growth.AbstractGrowthKmc

initialiseRates(double[]) - Method in interface kineticMonteCarlo.kmcCore.IKmc

initialiseRates(double[][]) - Method in class kineticMonteCarlo.lattice.AbstractGrowthLattice

Default rates to jump from one type to the other.

initialiseRates(double[][][]) - Method in class kineticMonteCarlo.lattice.CatalysisLattice

Default rates to jump from one type to the other.

initialiseRates() - Method in class ratesLibrary.GrapheneSyntheticRates

initialiseRates(AgRatesFromPrbCox, AgKmc) - Static method in class samples.agAgGrowth.AgAgPsdTest

initialiseRates(AgRatesFromPrbCox, AgKmc) - Static method in class samples.agAgGrowth.SimpleAgAgGrowthKmcSimulation

initialiseRates(GrapheneSyntheticRates, GrapheneKmc) - Static method in class samples.grapheneCvdGrowth.SimpleGrapheneKmcSimulation

initialize() - Method in class graphicInterfaces.etching.mouseBehaviors.MouseRocking

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

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

initInt() - Method in class kineticMonteCarlo.kmcCore.growth.ActivationEnergy

initLong() - Method in class kineticMonteCarlo.kmcCore.growth.ActivationEnergy

initRateEnergyMap(double) - Method in class ratesLibrary.GrapheneSchoenhalzRates

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

Iterates over all lattice sites and initialises adsorption probabilities.

initUI() - Method in class graphicInterfaces.MainInterface

innerPerimeter - Variable in class kineticMonteCarlo.atom.AbstractGrowthAtom

innerPerimeter - Variable in class kineticMonteCarlo.lattice.AbstractGrowthLattice

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

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

Current atom is added.

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

Do nothing

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

insert(Node<T>, T) - Method in class utils.list.atoms.AvlTree

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

intercept - Variable in class utils.LinearRegression

intercept() - Method in class utils.LinearRegression

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

interceptStdErr() - Method in class utils.LinearRegression

Returns the standard error of the estimate for the intercept.

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

interconnectAtoms() - Method in class kineticMonteCarlo.lattice.BasicLattice

interconnectAtoms(short[], byte[]) - Method in class kineticMonteCarlo.lattice.SiLattice

Atoms inter-connection.

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

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

invsqrtC - Variable in class geneticAlgorithm.recombination.DifferentialRecombination

C^-1/2

invsqrtCovariance(RichMatrix, RichArray) - Static method in class utils.akting.RichMatrix

IProbabilityHolder - Interface in utils.list

IProgressable - Interface in geneticAlgorithm

IRates - Interface in ratesLibrary

IRecombination - Interface in geneticAlgorithm.recombination

IReinsertion - Interface in geneticAlgorithm.reinsertion

Performs the reinsertion of one population into another.

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

isActive() - Method in class kineticMonteCarlo.process.AbstractProcess

Current process can be executed.

isAuto() - Method in class graphicInterfaces.surfaceViewer2D.Panel2D

isCatalysis - Variable in class basic.io.Restart

isConcerted - Variable in class basic.io.Restart

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

isDiffusionFixed() - Method in class basic.Parser

Decides if diffusion must be fixed.

isDimer() - Method in class kineticMonteCarlo.atom.ConcertedAtom

isDtooLarge() - Method in class geneticAlgorithm.AbstractGeneticAlgorithm

isDtooLarge() - Method in class geneticAlgorithm.recombination.DifferentialRecombination

Condition exceeds 1e14

isDtooLarge() - Method in interface geneticAlgorithm.recombination.IRecombination

isDtooLarge() - Method in class geneticAlgorithm.recombination.RealRecombination

Does nothing

iseed1 - Variable in class utils.edu.cornell.lassp.houle.rngPack.Ranecu

iseed2 - Variable in class utils.edu.cornell.lassp.houle.rngPack.Ranecu

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

ISelection - Interface in geneticAlgorithm.selection

isEligible() - Method in class kineticMonteCarlo.atom.AgAtom

isEligible() - Method in class kineticMonteCarlo.atom.AgAtomSimple

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

isEligible() - Method in class kineticMonteCarlo.atom.BasicGrowthAtom

isEligible() - Method in class kineticMonteCarlo.atom.CatalysisAtom

isEligible() - Method in class kineticMonteCarlo.atom.GrapheneAtom

KINK and BULK atom types are considered immobile atoms.

isEligible() - Method in class kineticMonteCarlo.atom.GrapheneAtomGaillard

Only BULK atom types are considered immobile atoms.

isEligible() - Method in class kineticMonteCarlo.atom.GrapheneAtomGaillard1Neighbour

Only BULK atom types are considered immobile atoms.

isEligible() - Method in class kineticMonteCarlo.atom.GrapheneAtomGaillardSimple

Only BULK atom types are considered immobile atoms.

isEligible() - Method in class kineticMonteCarlo.atom.GrapheneAtomSchoenhalz

Only BULK atom types are considered immobile atoms.

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

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

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

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

isEmpty() - Method in class utils.list.atoms.AvlTree

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

isEnergySearch() - Method in class basic.Parser

isEvaluatorParallel() - Method in class basic.Parser

isExpDistribution() - Method in class basic.Parser

Chooses between exponential distribution of the random genes (true) or linear distribution (false)

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

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

Checks if the current atom has occupied neighbours.

isIsolated() - Method in class kineticMonteCarlo.atom.CatalysisAtom

Tells when current atom is completely surrounded.

iSize - Variable in class kineticMonteCarlo.unitCell.SiUnitCell

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

ISLAND - Static variable in class kineticMonteCarlo.atom.AgAtom

ISLAND - Static variable in class kineticMonteCarlo.atom.BasicGrowthAtom

Island - Class in kineticMonteCarlo.lattice

Island(int) - Constructor for class kineticMonteCarlo.lattice.Island

Island(Island) - Constructor for class kineticMonteCarlo.lattice.Island

To clone.

islandCount - Variable in class kineticMonteCarlo.lattice.AbstractGrowthLattice

islandDensity - Variable in class geneticAlgorithm.AbstractGeneticAlgorithm

islandDensityPerSite - Variable in class ratesLibrary.GrapheneGaillardOneNeighbourRates

islandDensityPerSite - Variable in class ratesLibrary.GrapheneGaillardRates

islandDensityPerSite - Variable in class ratesLibrary.GrapheneGaillardSimpleRates

islandDensityPerSite - Variable in class ratesLibrary.GrapheneSchoenhalzRates

islandDensityPerSite - Variable in class ratesLibrary.GrapheneSyntheticRates

islandNumber - Variable in class kineticMonteCarlo.atom.AbstractGrowthAtomAttributes

If current atom belong to an island, its number is stored, otherwise is 0.

islandNumber - Variable in class kineticMonteCarlo.lattice.Island

islands - Variable in class basic.AbstractSimulation

islands - Variable in class kineticMonteCarlo.lattice.AbstractGrowthLattice

islandsMi - Variable in class graphicInterfaces.growth.GrowthKmcFrame

isLeaf() - Method in class utils.list.Node

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

isMultithreaded() - Method in class basic.Parser

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

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

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

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

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

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

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

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

isPartOfImmobilSubstrate() - Method in class kineticMonteCarlo.atom.AgAtom

isPartOfImmobilSubstrate() - Method in class kineticMonteCarlo.atom.AgAtomSimple

isPartOfImmobilSubstrate() - Method in class kineticMonteCarlo.atom.BasicGrowthAtom

isPartOfImmobilSubstrate() - Method in class kineticMonteCarlo.atom.BasicGrowthSimpleAtom

isPartOfImmobilSubstrate() - Method in class kineticMonteCarlo.atom.CatalysisAtom

isPartOfImmobilSubstrate() - Method in class kineticMonteCarlo.atom.GrapheneAtom

isPaused() - Method in class graphicInterfaces.growth.KmcCanvas

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

isPeriodicSingleFlake() - Method in class basic.Parser

Returns if single-flake simulation is periodic.

isPsdSymmetric() - Method in class basic.Parser

Returns if the PSD (Parser.doPsd()) has to be symmetrised.

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

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

isStationary(double) - Method in class kineticMonteCarlo.lattice.CatalysisLattice

Identifies stationary situation, when sufficient number of previous steps are saved and their R² is lower than 0.1 for all the species.

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

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

itemStateChanged(ItemEvent) - Method in class graphicInterfaces.growth.GrowthKmcFrame.MenuItemHandler

Do not allow to have both id and island number at the same time selected.

iterate() - Method in class geneticAlgorithm.AbstractGeneticAlgorithm

iterate() - Method in interface geneticAlgorithm.IGeneticAlgorithm

iterateOneStep() - Method in class geneticAlgorithm.AbstractGeneticAlgorithm

iterateOneStep() - Method in interface geneticAlgorithm.IGeneticAlgorithm

iteration - Variable in class basic.io.Restart

iterationNumber - Variable in class geneticAlgorithm.Population

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

iterationsForLastSimulation - Variable in class kineticMonteCarlo.kmcCore.AbstractKmc

iterationStartTime - Variable in class basic.AbstractSimulation

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

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

iterator(byte) - Method in class utils.list.atoms.AvlTree

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

iterators - Variable in class utils.list.BinnedListIterator

Itr(byte) - Constructor for class utils.list.atoms.AvlTree.Itr

itwo24 - Static variable in class utils.edu.cornell.lassp.houle.rngPack.Ranlux

IUc - Interface in kineticMonteCarlo.unitCell

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