C-Index (Morphokinetics)

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

C

C - Variable in class geneticAlgorithm.recombination.DifferentialRecombination: Covariance matrix C.
c - Variable in class graphicInterfaces.gaConvergence.ErrorPanel
C - Static variable in class kineticMonteCarlo.atom.CatalysisAtom
c - Variable in class utils.edu.cornell.lassp.houle.rngPack.Ranmar
c1 - Variable in class geneticAlgorithm.recombination.DifferentialRecombination
calculateAreaAsInKmcCanvas() - Method in class kineticMonteCarlo.kmcCore.growth.AbstractGrowthKmc: Calculates current area or, i.e. the number of current places that simulation has.
calculateAreaAsInLattice() - Method in class kineticMonteCarlo.kmcCore.growth.AbstractGrowthKmc: Calculates the total area of a single flake simulation.
calculateDifferenceWithRealPsd() - Method in class geneticAlgorithm.evaluationFunctions.MultithreadedPsdEvaluator
calculateEdgeType(int) - Method in class kineticMonteCarlo.atom.AgAtom: This atom is an edge (it has two neighbours).
calculateFrobeniusNorm(float[][]) - Method in class geneticAlgorithm.evaluationFunctions.AbstractPsdEvaluator: It calculates Frobenius norm with the next formula: ||A||_F = (SUM(|A_ij|^2))^1/2 It is useful to measure the difference among two matrices.
calculateFrobeniusNormErrorMatrix(float[][]) - Method in class geneticAlgorithm.evaluationFunctions.AbstractPsdEvaluator
calculateHierarchyError(Individual) - Method in class geneticAlgorithm.evaluationFunctions.AbstractPsdEvaluator
calculateHierarchyError(Individual) - Method in class geneticAlgorithm.evaluationFunctions.AgBasicPsdEvaluator: Calculates the hierarchy error based on the rates of Cox et al.
calculateHierarchyError(Individual) - Method in class geneticAlgorithm.evaluationFunctions.AgThreadedPsdEvaluator: Calculates the hierarchy error based on the rates of Cox et al.
calculateHierarchyError(Individual) - Method in class geneticAlgorithm.evaluationFunctions.BasicGrowthPsdEvaluator: Calculates the hierarchy error based on the rates of Cox et al.
calculateHierarchyError(Individual) - Method in class geneticAlgorithm.evaluationFunctions.SiBasicPsdEvaluator: It is not implemented
calculateHierarchyError(Individual) - Method in class geneticAlgorithm.evaluationFunctions.SiThreadedPsdEvaluator: It is not implemented
calculateHierarchyErrorDiscrete(Individual) - Method in class geneticAlgorithm.evaluationFunctions.AbstractPsdEvaluator
calculateHierarchyErrorDiscrete(Individual) - Method in class geneticAlgorithm.evaluationFunctions.AgBasicPsdEvaluator: If the difference is lower than 1, error is not added; otherwise, error is added by one.
calculateHierarchyErrorDiscrete(Individual) - Method in class geneticAlgorithm.evaluationFunctions.AgThreadedPsdEvaluator
calculateHierarchyErrorDiscrete(Individual) - Method in class geneticAlgorithm.evaluationFunctions.BasicGrowthPsdEvaluator: If the difference is lower than 1, error is not added; otherwise, error is added by one.
calculateHierarchyErrorDiscrete(Individual) - Method in class geneticAlgorithm.evaluationFunctions.SiBasicPsdEvaluator
calculateHierarchyErrorDiscrete(Individual) - Method in class geneticAlgorithm.evaluationFunctions.SiThreadedPsdEvaluator
calculateHierarchyErrorFrobenius(Individual) - Method in class geneticAlgorithm.evaluationFunctions.AgBasicPsdEvaluator
calculateHierarchyErrorFrobenius(Individual) - Method in class geneticAlgorithm.evaluationFunctions.BasicGrowthPsdEvaluator
calculateHierarchyErrorFromReference(Individual) - Method in class geneticAlgorithm.evaluationFunctions.AbstractPsdEvaluator
calculateHierarchyErrorFromReference(Individual) - Method in class geneticAlgorithm.evaluationFunctions.AgBasicPsdEvaluator: Calculates the hierarchy error based on the rates of Cox et al.
calculateHierarchyErrorFromReference(Individual) - Method in class geneticAlgorithm.evaluationFunctions.AgThreadedPsdEvaluator
calculateHierarchyErrorFromReference(Individual) - Method in class geneticAlgorithm.evaluationFunctions.BasicGrowthPsdEvaluator: Calculates the hierarchy error based on the rates of Cox et al.
calculateHierarchyErrorFromReference(Individual) - Method in class geneticAlgorithm.evaluationFunctions.SiBasicPsdEvaluator: It is not implemented
calculateHierarchyErrorFromReference(Individual) - Method in class geneticAlgorithm.evaluationFunctions.SiThreadedPsdEvaluator: It is not implemented
calculateHierarchyErrorOrder(Individual) - Method in class geneticAlgorithm.evaluationFunctions.AgBasicPsdEvaluator: Adds the error if the next condition is not fulfilled: E_f > E_b > E_a > E_d > E_e > E_c g(3) > g(5) > g(4) > g(0) > g(2) > g(1)
calculateHierarchyErrorOrder(Individual) - Method in class geneticAlgorithm.evaluationFunctions.BasicGrowthPsdEvaluator: Adds the error if the next condition is not fulfilled: E_f > E_b > E_a > E_d > E_e > E_c g(3) > g(5) > g(4) > g(0) > g(2) > g(1)
calculateKinkType(int) - Method in class kineticMonteCarlo.atom.AgAtom: This atom is a kink (it has three neighbours).
calculatePsdFromIndividual(Individual) - Method in class geneticAlgorithm.evaluationFunctions.AbstractPsdEvaluator
calculatePsdFromIndividual(Individual) - Method in class geneticAlgorithm.evaluationFunctions.AgBasicPsdEvaluator
calculatePsdFromIndividual(Individual) - Method in class geneticAlgorithm.evaluationFunctions.BasicGrowthPsdEvaluator
calculatePsdFromIndividual(Individual) - Method in class geneticAlgorithm.evaluationFunctions.MultithreadedPsdEvaluator
calculatePsdFromIndividual(Individual) - Method in class geneticAlgorithm.evaluationFunctions.SiBasicPsdEvaluator
calculatePsdOfPopulation(Population) - Method in class geneticAlgorithm.evaluationFunctions.MultithreadedPsdEvaluator
calculationMode - Variable in class basic.Parser: See Parser.getCalculationMode().
calculationType - Variable in class basic.Parser: See Parser.getCalculationType().
callback - Variable in class graphicInterfaces.etching.mouseBehaviors.MouseRocking
callback - Variable in class graphicInterfaces.etching.mouseBehaviors.MouseRotate
callback - Variable in class graphicInterfaces.etching.mouseBehaviors.MouseTranslate
callback - Variable in class graphicInterfaces.etching.mouseBehaviors.MouseZoom
canvas - Variable in class graphicInterfaces.growth.GrowthKmcFrame
Canvas3DOverlay - Class in graphicInterfaces.etching: Esto es un simple canvas3D: elemento donde se renderiza el universo creado con Java3D Tiene operaciones de post-Render para dibujar el GUI por encima del entorno 3D.
Canvas3DOverlay(GraphicsConfiguration) - Constructor for class graphicInterfaces.etching.Canvas3DOverlay
capacity - Variable in class utils.akting.RichArray
capacity - Variable in class utils.akting.RichMatrix
carry - Variable in class utils.edu.cornell.lassp.houle.rngPack.Ranlux
cartesianPosition - Variable in class kineticMonteCarlo.atom.AbstractGrowthAtom
cartesianSuperCell - Variable in class kineticMonteCarlo.atom.AbstractGrowthAtom
cartSizeX - Variable in class basic.Parser: See Parser.getCartSizeX().
cartSizeY - Variable in class basic.Parser: See Parser.getCartSizeY().
cartSizeZ - Variable in class basic.Parser: See Parser.getCartSizeZ().
catalysisAdsorption - Variable in class basic.Parser: See Parser.doCatalysisAdsorption()
CatalysisAtom - Class in kineticMonteCarlo.atom
CatalysisAtom(int, short, short) - Constructor for class kineticMonteCarlo.atom.CatalysisAtom
CatalysisAtomAttributes - Class in kineticMonteCarlo.atom
CatalysisAtomAttributes() - Constructor for class kineticMonteCarlo.atom.CatalysisAtomAttributes
CatalysisData - Class in basic.io
CatalysisData(int, int, double) - Constructor for class basic.io.CatalysisData
CatalysisData(float, double, float, float, float) - Constructor for class basic.io.CatalysisData
CatalysisData(float, double, float, float, float, float) - Constructor for class basic.io.CatalysisData
catalysisDesorption - Variable in class basic.Parser: See Parser.doCatalysisDesorption()
catalysisDiffusion - Variable in class basic.Parser: See Parser.doCatalysisDiffusion()
CatalysisFarkasKmc - Class in kineticMonteCarlo.kmcCore.catalysis
CatalysisFarkasKmc(Parser, String) - Constructor for class kineticMonteCarlo.kmcCore.catalysis.CatalysisFarkasKmc
CatalysisFarkasRates - Class in ratesLibrary: Farkas, Hess, Over J Phys.
CatalysisFarkasRates(float) - Constructor for class ratesLibrary.CatalysisFarkasRates
CatalysisFarkasTestRates - Class in ratesLibrary: Farkas, Hess, Over J Phys.
CatalysisFarkasTestRates(float) - Constructor for class ratesLibrary.CatalysisFarkasTestRates
CatalysisKiejnaRates - Class in ratesLibrary: F.
CatalysisKiejnaRates(float) - Constructor for class ratesLibrary.CatalysisKiejnaRates
CatalysisKmc - Class in kineticMonteCarlo.kmcCore.catalysis
CatalysisKmc(Parser, String) - Constructor for class kineticMonteCarlo.kmcCore.catalysis.CatalysisKmc
CatalysisLattice - Class in kineticMonteCarlo.lattice
CatalysisLattice(int, int, String) - Constructor for class kineticMonteCarlo.lattice.CatalysisLattice
catalysisO2Dissociation - Variable in class basic.Parser: See Parser.doCatalysisO2Dissociation()
CatalysisProcess - Class in kineticMonteCarlo.process: Class to store a process of catalysis.
CatalysisProcess() - Constructor for class kineticMonteCarlo.process.CatalysisProcess
CatalysisRates - Class in ratesLibrary
CatalysisRates(float) - Constructor for class ratesLibrary.CatalysisRates
catalysisReaction - Variable in class basic.Parser: See Parser.doCatalysisReaction()
CatalysisReuterOverRates - Class in ratesLibrary: F.
CatalysisReuterOverRates(float) - Constructor for class ratesLibrary.CatalysisReuterOverRates
CatalysisReuterRates - Class in ratesLibrary
CatalysisReuterRates(float) - Constructor for class ratesLibrary.CatalysisReuterRates
CatalysisSeitsonenRates - Class in ratesLibrary: F.
CatalysisSeitsonenRates(float) - Constructor for class ratesLibrary.CatalysisSeitsonenRates
CatalysisSimulation - Class in basic
CatalysisSimulation(Parser) - Constructor for class basic.CatalysisSimulation
catalysisStart - Variable in class basic.Parser: See #calalysisStart()
catalysisStart() - Method in class basic.Parser: Starts a catalysis run given coverage.
catalysisTree - Variable in class basic.Parser: Attribute to control the use of trees for catalysis.
CatalysisUc - Class in kineticMonteCarlo.unitCell: Really simple unit cell, which will contain only one atom.
CatalysisUc(int, int, CatalysisAtom) - Constructor for class kineticMonteCarlo.unitCell.CatalysisUc
cc - Variable in class geneticAlgorithm.recombination.DifferentialRecombination
cd - Variable in class utils.edu.cornell.lassp.houle.rngPack.Ranmar
cellsPointer - Variable in class kineticMonteCarlo.unitCell.SiUnitCell
centralCartesianLocation - Variable in class kineticMonteCarlo.lattice.AgLattice
centralCartesianLocation - Variable in class kineticMonteCarlo.lattice.AgUcLattice
centralCartesianLocation - Variable in class kineticMonteCarlo.lattice.GrapheneLattice
centreButton - Variable in class graphicInterfaces.growth.GrowthKmcFrame
centreMassDistance - Variable in class kineticMonteCarlo.lattice.AbstractGrowthLattice
centreOfMass - Variable in class kineticMonteCarlo.lattice.Island
centresMi - Variable in class graphicInterfaces.growth.GrowthKmcFrame
changeBlackAndWhite() - Method in class graphicInterfaces.growth.KmcCanvas
changeCollection(byte, boolean) - Method in class kineticMonteCarlo.kmcCore.catalysis.CatalysisKmc: Changes current collection from array/tree to tree/array.
changeCollection(byte, boolean) - Method in class kineticMonteCarlo.kmcCore.growth.ConcertedKmc: Changes current collection from array/tree to tree/array.
changeOccupationByHand(double, double) - Method in class graphicInterfaces.growth.KmcCanvas: Changes the occupation of the clicked atom from unoccupied to occupied, or vice versa.
changeOccupationByHand(double, double, int) - Method in class kineticMonteCarlo.lattice.AbstractGrowthLattice
changeOccupationByHand(double, double, int) - Method in class kineticMonteCarlo.lattice.AgLattice: Changes the occupation of the clicked atom from unoccupied to occupied, or vice versa.
changeOccupationByHand(double, double, int) - Method in class kineticMonteCarlo.lattice.AgUcLattice: Changes the occupation of the clicked atom from unoccupied to occupied, or vice versa.
changeOccupationByHand(double, double, int) - Method in class kineticMonteCarlo.lattice.BasicGrowthLattice: Changes the occupation of the clicked atom from unoccupied to occupied, or vice versa.
changeOccupationByHand(double, double, int) - Method in class kineticMonteCarlo.lattice.CatalysisLattice: Changes the occupation of the clicked atom from unoccupied to occupied, or vice versa.
changeOccupationByHand(double, double, int) - Method in class kineticMonteCarlo.lattice.GrapheneLattice: Changes the occupation of the clicked atom from unoccupied to occupied, or vice versa.
changePrintIslandCentres() - Method in class graphicInterfaces.growth.KmcCanvas
changePrintPerimeter() - Method in class graphicInterfaces.growth.KmcCanvas
checkForComodification() - Method in class utils.list.atoms.AvlTree.Itr
checkImmobile() - Method in class kineticMonteCarlo.atom.CatalysisAtom: Makes this atom "immobile" if it is surrounded by 4 neighbours.
checkMergeIslands(Island) - Method in class kineticMonteCarlo.kmcCore.growth.ConcertedKmc
checkMergeIslands(AbstractGrowthAtom) - Method in class kineticMonteCarlo.kmcCore.growth.ConcertedKmc
checkSizes() - Method in class kineticMonteCarlo.kmcCore.catalysis.CatalysisKmc: If a process is stored in a array and it is too big, change to be a tree.
checkSizes() - Method in class kineticMonteCarlo.kmcCore.growth.ConcertedKmc: If a process is stored in a array and it is too big, change to be a tree.
checkTableSize(Individual) - Method in class graphicInterfaces.gaConvergence.GaProgressFrame
chiN - Variable in class geneticAlgorithm.recombination.DifferentialRecombination: Expectation of ||N(0,I)|| == norm(randn(N,1)).
choose(int) - Method in class utils.edu.cornell.lassp.houle.rngPack.RandomElement
choose(int, int) - Method in class utils.edu.cornell.lassp.houle.rngPack.RandomElement
choose(int, int) - Method in class utils.edu.cornell.lassp.houle.rngPack.RandomSynchronized: Wrapped so generators can override.
CHOOSE1 - Static variable in class utils.edu.cornell.lassp.houle.rngPack.RandomApp
CHOOSE2 - Static variable in class utils.edu.cornell.lassp.houle.rngPack.RandomApp
chooseClearAreaStep(short, short, int, double) - Method in class kineticMonteCarlo.lattice.AgLattice
chooseClearAreaStep(AbstractGrowthAtom, int) - Method in class kineticMonteCarlo.lattice.AgUcLattice
chooseClearAreaStep(AbstractGrowthAtom, int) - Method in class kineticMonteCarlo.lattice.BasicGrowthLattice
chooseClearAreaTerrace(short, short, int, double) - Method in class kineticMonteCarlo.lattice.AgLattice
chooseClearAreaTerrace(AbstractGrowthAtom, int) - Method in class kineticMonteCarlo.lattice.AgUcLattice
chooseClearAreaTerrace(AbstractGrowthAtom, int) - Method in class kineticMonteCarlo.lattice.BasicGrowthLattice: Chooses the randomly a far atom.
chooseClearAreaTerrace(short, short, int, double) - Method in class kineticMonteCarlo.lattice.GrapheneLattice
chooseRandomHop() - Method in class kineticMonteCarlo.atom.AbstractGrowthAtom
chooseRandomHop() - Method in class kineticMonteCarlo.atom.AgAtom: It chooses one neighbour atom randomly.
chooseRandomHop() - Method in class kineticMonteCarlo.atom.AgAtomSimple: Simpler implementation than AgAtom.chooseRandomHop().
chooseRandomHop() - Method in class kineticMonteCarlo.atom.BasicGrowthAtom
chooseRandomHop() - Method in class kineticMonteCarlo.atom.CatalysisAtom
chooseRandomHop() - Method in class kineticMonteCarlo.atom.GrapheneAtom: Decides to which position is going to jump.
chooseRandomHop(AbstractGrowthAtom, int) - Method in class kineticMonteCarlo.kmcCore.growth.AbstractGrowthKmc: Selects the next step randomly.
chooseRandomHop(AbstractGrowthAtom) - Method in class kineticMonteCarlo.kmcCore.growth.devitaAccelerator.DevitaAccelerator
CIRCLE - Static variable in class kineticMonteCarlo.kmcCore.growth.RoundPerimeter
clean - Variable in class utils.list.BinnedList: Stores if the current totalProbability and the probability calculated from the list are the same.
clean - Variable in class utils.list.LinearList: Stores if the current totalProbability and the probability calculated from the list are the same.
cleanCoCusNeighbours() - Method in class kineticMonteCarlo.atom.CatalysisAtom
cleanup() - Method in class utils.list.AbstractList
cleanup() - Method in class utils.list.BinnedList
cleanup() - Method in class utils.list.LinearList
clear() - Method in class graphicInterfaces.gaConvergence.ErrorPanel
clear() - Method in class graphicInterfaces.gaConvergence.GaProgressFrame
clear() - Method in class graphicInterfaces.gaConvergence.GaProgressPanel
clear() - Method in interface graphicInterfaces.gaConvergence.IgaProgressFrame
clear() - Method in class kineticMonteCarlo.atom.AbstractGrowthAtom: Resets current atom; TERRACE type, no neighbours, no occupied, no outside and no probability.
clear() - Method in class kineticMonteCarlo.atom.AbstractGrowthAtomAttributes
clear() - Method in class kineticMonteCarlo.atom.AgAtom: Resets current atom; TERRACE type, no neighbours, no occupied, no outside and no probability.
clear() - Method in class kineticMonteCarlo.atom.BasicGrowthAtom: Resets current atom; TERRACE type, no neighbours, no occupied, no outside and no probability.
clear() - Method in class kineticMonteCarlo.atom.CatalysisAtom: Resets current atom; TERRACE type, no neighbours, no occupied, no outside and no probability.
clear() - Method in class kineticMonteCarlo.atom.ConcertedAtom: Resets current atom; TERRACE type, no occupied, no outside and no probability.
clear() - Method in class kineticMonteCarlo.atom.GrapheneAtom: Resets current atom; TERRACE type, no neighbours, no occupied, no outside and no probability.
clear() - Method in class kineticMonteCarlo.atom.ModifiedBuffer: Empties current modified buffer.
clear() - Method in class kineticMonteCarlo.lattice.Island
clear() - Method in class kineticMonteCarlo.process.AbstractProcess
clear() - Method in interface kineticMonteCarlo.process.IElement
clear() - Method in class utils.list.atoms.AtomsArrayList
clear() - Method in class utils.list.atoms.AtomsAvlTree: Used to recompute the tree/total rate.
clear(Node) - Method in class utils.list.atoms.AtomsAvlTree
clear() - Method in interface utils.list.atoms.IAtomsCollection: Used to recompute the collection.
clearGraphics() - Method in class geneticAlgorithm.AbstractGeneticAlgorithm
ClockSeed(Date) - Static method in class utils.edu.cornell.lassp.houle.rngPack.RandomSeedable: Return a long integer seed given a date
ClockSeed() - Static method in class utils.edu.cornell.lassp.houle.rngPack.RandomSeedable: Return a long integer seed calculated from the date.
clone() - Method in class java.awt.geom.Point2D: Creates a new object of the same class and with the same contents as this object.
clone() - Method in class utils.edu.cornell.lassp.houle.rngPack.RandomElement
cm - Variable in class utils.edu.cornell.lassp.houle.rngPack.Ranmar
cmu - Variable in class geneticAlgorithm.recombination.DifferentialRecombination
CO - Static variable in class kineticMonteCarlo.atom.CatalysisAtom
co2 - Variable in class kineticMonteCarlo.kmcCore.catalysis.CatalysisKmc
co2C - Variable in class basic.io.Restart: Current moment CO2 amount.
co2max - Variable in class kineticMonteCarlo.kmcCore.catalysis.CatalysisKmc
co2P - Variable in class basic.io.Restart: Previous moment CO2 amount.
co2prv - Variable in class kineticMonteCarlo.kmcCore.catalysis.CatalysisKmc: Previous instant co2sum.
co2sum - Variable in class kineticMonteCarlo.kmcCore.catalysis.CatalysisKmc
coCusWithCoCus - Variable in class kineticMonteCarlo.atom.CatalysisAtom: Current atom is CO^CUS and it has as many CO^CUS neighbours.
coin() - Method in class utils.edu.cornell.lassp.houle.rngPack.RandomElement
coin(double) - Method in class utils.edu.cornell.lassp.houle.rngPack.RandomElement
COIN1 - Static variable in class utils.edu.cornell.lassp.houle.rngPack.RandomApp
COIN2 - Static variable in class utils.edu.cornell.lassp.houle.rngPack.RandomApp
col - Variable in class kineticMonteCarlo.kmcCore.catalysis.CatalysisKmc: Stores all collections of atoms; either in a tree or an array.
col - Variable in class kineticMonteCarlo.kmcCore.growth.ConcertedKmc: Stores all collections of atoms; either in a tree or an array.
COLOR_BW - Static variable in class graphicInterfaces.surfaceViewer2D.Frame2D
COLOR_BW - Static variable in class graphicInterfaces.surfaceViewer2D.Panel2D
COLOR_HSV - Static variable in class graphicInterfaces.surfaceViewer2D.Frame2D
COLOR_HSV - Static variable in class graphicInterfaces.surfaceViewer2D.Panel2D
colormap - Variable in class graphicInterfaces.surfaceViewer2D.Panel2D
colours - Variable in class graphicInterfaces.growth.KmcCanvas
compare(Integer, Integer) - Method in class utils.akting.RichArrayComparator
compareTo(Object) - Method in class kineticMonteCarlo.atom.AbstractGrowthAtom: Compares IDs of two atoms.
compareTo(Object) - Method in class kineticMonteCarlo.lattice.Island: Compares island numbers of two islands.
compareTo(Node<T>) - Method in class utils.list.Node
computeAdsorptionRate(int) - Method in class ratesLibrary.CatalysisRates: Equation (3) of Reuter & Scheffler, PRB 73, 2006.
computeAdsorptionRates() - Method in class ratesLibrary.CatalysisRates: Compute all adsorptions.
computeDiffusivity() - Method in class kineticMonteCarlo.lattice.AbstractGrowthLattice
computeTime - Variable in class utils.list.AbstractList
computeTree() - Method in class basic.Parser
CONCERTED - Static variable in class kineticMonteCarlo.process.ConcertedProcess
Concerted6LatticeSimple - Class in kineticMonteCarlo.lattice
Concerted6LatticeSimple(int, int, ModifiedBuffer, HopsPerStep) - Constructor for class kineticMonteCarlo.lattice.Concerted6LatticeSimple
ConcertedAgAgRates - Class in ratesLibrary.concerted
ConcertedAgAgRates(float) - Constructor for class ratesLibrary.concerted.ConcertedAgAgRates
ConcertedAtom - Class in kineticMonteCarlo.atom
ConcertedAtom(int, int) - Constructor for class kineticMonteCarlo.atom.ConcertedAtom
ConcertedCuCuRates - Class in ratesLibrary.concerted
ConcertedCuCuRates(float) - Constructor for class ratesLibrary.concerted.ConcertedCuCuRates
ConcertedCuNiRates - Class in ratesLibrary.concerted
ConcertedCuNiRates(float) - Constructor for class ratesLibrary.concerted.ConcertedCuNiRates
concertedEnergies - Variable in class ratesLibrary.concerted.AbstractConcertedRates
ConcertedKmc - Class in kineticMonteCarlo.kmcCore.growth
ConcertedKmc(Parser, String) - Constructor for class kineticMonteCarlo.kmcCore.growth.ConcertedKmc
ConcertedKmcAction - Class in kineticMonteCarlo.kmcCore.growth
ConcertedKmcAction() - Constructor for class kineticMonteCarlo.kmcCore.growth.ConcertedKmcAction
ConcertedKmcUpdate - Class in kineticMonteCarlo.kmcCore.growth
ConcertedKmcUpdate() - Constructor for class kineticMonteCarlo.kmcCore.growth.ConcertedKmcUpdate
ConcertedNiCuRates - Class in ratesLibrary.concerted
ConcertedNiCuRates(float) - Constructor for class ratesLibrary.concerted.ConcertedNiCuRates
ConcertedNiNiRates - Class in ratesLibrary.concerted
ConcertedNiNiRates(float) - Constructor for class ratesLibrary.concerted.ConcertedNiNiRates
ConcertedPdPdRates - Class in ratesLibrary.concerted
ConcertedPdPdRates(float) - Constructor for class ratesLibrary.concerted.ConcertedPdPdRates
ConcertedProcess - Class in kineticMonteCarlo.process
ConcertedProcess() - Constructor for class kineticMonteCarlo.process.ConcertedProcess
ConcertedSimulation - Class in basic
ConcertedSimulation(Parser) - Constructor for class basic.ConcertedSimulation
concreteConfigurator - Static variable in class main.Configurator
Configurator - Class in main: Configurator singleton class chooses between Android and PC executions.
Configurator() - Constructor for class main.Configurator
configurator - Static variable in class main.Configurator
configureDevitaAccelerator(HopsPerStep) - Method in class kineticMonteCarlo.kmcCore.growth.AgKmc
configureDevitaAccelerator(HopsPerStep) - Method in class kineticMonteCarlo.kmcCore.growth.AgUcKmc
configureDevitaAccelerator(HopsPerStep) - Method in class kineticMonteCarlo.kmcCore.growth.BasicGrowthKmc
configureDevitaAccelerator(HopsPerStep) - Method in class kineticMonteCarlo.kmcCore.growth.GrapheneKmc
configureSiKmc() - Method in class geneticAlgorithm.AbstractGeneticAlgorithm
contains(AbstractGrowthAtom) - Method in class kineticMonteCarlo.kmcCore.growth.RoundPerimeter
copy() - Method in class utils.akting.RichArray
CORNER - Static variable in class kineticMonteCarlo.atom.AbstractAtom
CORNER - Static variable in class kineticMonteCarlo.atom.AgAtom
CORNFLOWERBLUE - Static variable in class graphicInterfaces.growth.KmcCanvas
correctionFactor - Variable in class ratesLibrary.CatalysisRates
cos() - Static method in class utils.akting.operations.OperationFactory
COS30 - Static variable in class kineticMonteCarlo.lattice.GrapheneLattice
COS30 - Static variable in class samples.grapheneCvdGrowth.SimpleGrapheneKmcSimulation
COS60 - Static variable in class kineticMonteCarlo.lattice.GrapheneLattice
CosOperation - Class in utils.akting.operations
CosOperation() - Constructor for class utils.akting.operations.CosOperation
counterCo2 - Variable in class basic.io.Restart
counterSitesWith4OccupiedNeighbours - Variable in class kineticMonteCarlo.kmcCore.catalysis.CatalysisKmc
counteval - Variable in class geneticAlgorithm.recombination.DifferentialRecombination: Counter for the number of evaluations.
countIslands(PrintWriter) - Method in class kineticMonteCarlo.lattice.AbstractGrowthLattice: Counts the number of islands that the simulation has.
countIslands(PrintWriter) - Method in class kineticMonteCarlo.lattice.CatalysisLattice: There are no islands in catalysis.
countPerimeter(PrintWriter) - Method in class kineticMonteCarlo.lattice.AbstractGrowthLattice: Counts the sum of all islands perimeters.
Couple - Class in geneticAlgorithm
Couple() - Constructor for class geneticAlgorithm.Couple
covariance(RichMatrix, RichArray) - Static method in class utils.akting.RichMatrix
coverage - Variable in class basic.AbstractSimulation
coverage - Variable in class basic.io.CatalysisData
coverage - Variable in class basic.Parser: See Parser.getCoverage().
coverage - Variable in class kineticMonteCarlo.lattice.CatalysisLattice: Current CO and O coverages, for sites BR, CUS.
coverageCO - Variable in class basic.io.CatalysisData
coverageGaps - Variable in class basic.io.CatalysisData
coverageLakes - Variable in class basic.io.CatalysisData
coverageO - Variable in class basic.io.CatalysisData
create(int, int, double) - Static method in class utils.akting.RichMatrix
createArrayInRange(int) - Static method in class utils.akting.RichArray
createArrayInRange(int, int) - Static method in class utils.akting.RichArray
createAtoms() - Method in class kineticMonteCarlo.lattice.AgLattice
createAtoms(int) - Method in class kineticMonteCarlo.lattice.AgUcLattice: Creates all atoms and assigns it neighbours.
createAtoms() - Method in class kineticMonteCarlo.lattice.BasicGrowthLattice
createAtoms(int, int) - Method in class kineticMonteCarlo.lattice.BasicLattice
createAtoms() - Method in class kineticMonteCarlo.lattice.CatalysisLattice
createAtoms(int, int, HopsPerStep, Class<?>) - Method in class kineticMonteCarlo.lattice.GrapheneLattice: Creates the atom array for graphene.
createAtoms(float[], SiUnitCell) - Method in class kineticMonteCarlo.lattice.SiLattice: Atoms creation.
createAtoms() - Method in class kineticMonteCarlo.unitCell.SiUnitCell
createBorderLayout(JComponent...) - Method in class graphicInterfaces.MainInterface
createExperimentalData(Parser, AbstractGeneticAlgorithm) - Static method in class main.Morphokinetics
createFolder(String) - Method in class basic.io.Restart
createFrame() - Method in class basic.AbstractGrowthSimulation
createFrame() - Method in class basic.AbstractSimulation: Creates the simulation frame.
createFrame() - Method in class basic.SiSimulation: Does nothing.
createGraphicsFrame(AgKmc) - Static method in class geneticAlgorithm.evaluationFunctions.AgThreadedPsdEvaluator
createGraphicsFrame(AgKmc) - Static method in class samples.agAgGrowth.AgAgPsdTest
createGraphicsFrame(AgKmc) - Static method in class samples.agAgGrowth.SimpleAgAgGrowthKmcSimulation
createGraphicsFrame(GrapheneKmc) - Static method in class samples.grapheneCvdGrowth.SimpleGrapheneKmcSimulation
createId(int, int) - Method in class kineticMonteCarlo.lattice.AgLattice
createId(int, int) - Method in class kineticMonteCarlo.lattice.BasicGrowthLattice
createId(int, int) - Method in class kineticMonteCarlo.lattice.CatalysisLattice
createId(int, int) - Method in class kineticMonteCarlo.lattice.GrapheneLattice
createIndexArray() - Method in class utils.akting.RichArrayComparator
createList(String) - Method in class utils.list.atoms.AvlTree: Creates a list inside the tree.
createMainEvaluator() - Method in class geneticAlgorithm.AbstractGeneticAlgorithm: Evaluator evaluation
createMainJPanel() - Method in class graphicInterfaces.MainInterface
createMaterialAppearance() - Method in class graphicInterfaces.etching.SiFrame
createMenuBar() - Method in class graphicInterfaces.growth.GrowthKmcFrame
createMenuBar() - Method in class graphicInterfaces.MainInterface
createRandomPopulation(int, int, double, double, boolean) - Method in class geneticAlgorithm.populationInitialisation.AbstractInitialisator: Initialises the population with random numbers, with linear or logarithmic distribution.
createRandomPopulation(int) - Method in class geneticAlgorithm.populationInitialisation.AgInitialisator: Robust initialisation methods, it uses a logarithmic distribution of process rates, more similar to what is expected from a real system.
createRandomPopulation(int) - Method in class geneticAlgorithm.populationInitialisation.AgReduced6Initialisator: Initialises all the rates between 1 and 1e12
createRandomPopulation(int) - Method in class geneticAlgorithm.populationInitialisation.AgReducedInitialisator: Initialises all the rates between 1 and 1e12
createRandomPopulation(int) - Method in class geneticAlgorithm.populationInitialisation.BasicGrowthInitialisator: Initialises all the rates between 1e-6 and 1e9.
createRandomPopulation(int) - Method in interface geneticAlgorithm.populationInitialisation.IInitialisator
createRandomPopulation(int, int, double, double, boolean) - Method in interface geneticAlgorithm.populationInitialisation.IInitialisator
createRandomPopulation(int) - Method in class geneticAlgorithm.populationInitialisation.SiInitialisator: Simplest way of initialisation, a pure random value.
createSceneGraph(float) - Method in class graphicInterfaces.etching.SiFrame
createSiliconPanel(float) - Method in class graphicInterfaces.etching.SiFrame
createTableModel(int, int) - Method in class graphicInterfaces.gaConvergence.GaProgressFrame
createUnitCell(int, int, int) - Method in class kineticMonteCarlo.unitCell.SiUnitCell
createWeightsArray() - Method in class geneticAlgorithm.recombination.DifferentialRecombination
crm - Variable in class geneticAlgorithm.Population: Crossover mean.
CrossoverMutator - Class in geneticAlgorithm.mutation
CrossoverMutator() - Constructor for class geneticAlgorithm.mutation.CrossoverMutator
crossProduct(double, double, double) - Method in class javafx.geometry.Point3D: Computes cross product of the vector represented by this instance and the specified vector.
crossProduct(Point3D) - Method in class javafx.geometry.Point3D: Computes cross product of the vector represented by this instance and the specified vector.
crs - Variable in class geneticAlgorithm.mutation.CrossoverMutator: Crossover standard deviation.
cSigma - Variable in class geneticAlgorithm.recombination.DifferentialRecombination: C_sigma.
current - Variable in class utils.list.atoms.AvlTree
currentArea - Variable in class kineticMonteCarlo.kmcCore.growth.AbstractGrowthKmc: Attribute to store temporally the current area of the simulation.
currentBin - Variable in class utils.list.BinnedList
currentEvaluator - Variable in class geneticAlgorithm.evaluationFunctions.BasicEvaluator
currentIteration - Variable in class geneticAlgorithm.AbstractGeneticAlgorithm
currentIterator - Variable in class utils.list.BinnedListIterator
currentPerimeter - Variable in class kineticMonteCarlo.kmcCore.growth.RoundPerimeter: Atoms vector belonging to the perimeter.
currentPerimeterTreeMap - Variable in class kineticMonteCarlo.kmcCore.growth.RoundPerimeter
currentPopulation - Variable in class geneticAlgorithm.evaluationFunctions.AbstractPsdEvaluator
currentProgress - Variable in class basic.AbstractSimulation
currentRadius - Variable in class kineticMonteCarlo.kmcCore.growth.RoundPerimeter: Current size of the radius (in units).
currentRun - Variable in class geneticAlgorithm.evaluationFunctions.BasicGrowthPsdEvaluator: Current thread, responsible to run many KMCs to compute a PSD.
currentSimulation - Variable in class geneticAlgorithm.evaluationFunctions.AbstractPsdEvaluator
currentTime - Variable in class basic.io.Restart
CUS - Static variable in class kineticMonteCarlo.atom.CatalysisAtom
customPi() - Static method in class utils.akting.operations.OperationFactory
CustomPiOperation - Class in utils.akting.operations
CustomPiOperation() - Constructor for class utils.akting.operations.CustomPiOperation

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