- g2g1 - Variable in class geneticAlgorithm.evaluationFunctions.AgBasicPsdEvaluator
-
- g2g1 - Variable in class geneticAlgorithm.evaluationFunctions.BasicGrowthPsdEvaluator
-
- g3g0 - Variable in class geneticAlgorithm.evaluationFunctions.AgBasicPsdEvaluator
-
- g3g0 - Variable in class geneticAlgorithm.evaluationFunctions.BasicGrowthPsdEvaluator
-
- g3g1 - Variable in class geneticAlgorithm.evaluationFunctions.AgBasicPsdEvaluator
-
- g3g1 - Variable in class geneticAlgorithm.evaluationFunctions.BasicGrowthPsdEvaluator
-
- g3g2 - Variable in class geneticAlgorithm.evaluationFunctions.AgBasicPsdEvaluator
-
- g3g2 - Variable in class geneticAlgorithm.evaluationFunctions.BasicGrowthPsdEvaluator
-
- g3g4 - Variable in class geneticAlgorithm.evaluationFunctions.AgBasicPsdEvaluator
-
- g3g4 - Variable in class geneticAlgorithm.evaluationFunctions.BasicGrowthPsdEvaluator
-
- g3g5 - Variable in class geneticAlgorithm.evaluationFunctions.AgBasicPsdEvaluator
-
- g4g0 - Variable in class geneticAlgorithm.evaluationFunctions.AgBasicPsdEvaluator
-
- g4g0 - Variable in class geneticAlgorithm.evaluationFunctions.BasicGrowthPsdEvaluator
-
- g4g1 - Variable in class geneticAlgorithm.evaluationFunctions.AgBasicPsdEvaluator
-
- g4g1 - Variable in class geneticAlgorithm.evaluationFunctions.BasicGrowthPsdEvaluator
-
- g5g0 - Variable in class geneticAlgorithm.evaluationFunctions.AgBasicPsdEvaluator
-
- g5g1 - Variable in class geneticAlgorithm.evaluationFunctions.AgBasicPsdEvaluator
-
- g5g4 - Variable in class geneticAlgorithm.evaluationFunctions.AgBasicPsdEvaluator
-
- GaProgressFrame - Class in graphicInterfaces.gaConvergence
-
- GaProgressFrame(IGeneticAlgorithm) - Constructor for class graphicInterfaces.gaConvergence.GaProgressFrame
-
- GaProgressFrame.ProgressUpdater - Class in graphicInterfaces.gaConvergence
-
- GaProgressPanel - Class in graphicInterfaces.gaConvergence
-
- GaProgressPanel() - Constructor for class graphicInterfaces.gaConvergence.GaProgressPanel
-
- gaProgressPanel - Variable in class graphicInterfaces.MainInterface
-
- GAUSSIAN - Static variable in class utils.edu.cornell.lassp.houle.rngPack.RandomApp
-
- gaussian() - Method in class utils.edu.cornell.lassp.houle.rngPack.RandomElement
-
gaussian() uses the Box-Muller algorithm to transform raw()'s into
gaussian deviates.
- gaussian(double) - Method in class utils.edu.cornell.lassp.houle.rngPack.RandomElement
-
- gaussian() - Method in class utils.edu.cornell.lassp.houle.rngPack.RandomSynchronized
-
Must be synchronized because state is stored in BMoutput
- genePosition - Variable in class geneticAlgorithm.restrictions.GeneRestriction
-
- genePositionToReplicate - Variable in class geneticAlgorithm.restrictions.ReplicatedGeneRestriction
-
- generatorA - Variable in class utils.edu.cornell.lassp.houle.rngPack.RandomShuffle
-
- generatorB - Variable in class utils.edu.cornell.lassp.houle.rngPack.RandomShuffle
-
- generators - Static variable in class utils.edu.cornell.lassp.houle.rngPack.RandomApp
-
- GeneRestriction - Class in geneticAlgorithm.restrictions
-
- GeneRestriction(int) - Constructor for class geneticAlgorithm.restrictions.GeneRestriction
-
- genes - Variable in class geneticAlgorithm.Individual
-
Individual genes.
- genesRestriction - Variable in class geneticAlgorithm.restrictions.RestrictionOperator
-
- geneticAlgorithm - package geneticAlgorithm
-
- GeneticAlgorithm - Class in geneticAlgorithm
-
- GeneticAlgorithm(Parser) - Constructor for class geneticAlgorithm.GeneticAlgorithm
-
- geneticAlgorithm - Variable in class graphicInterfaces.gaConvergence.GaProgressFrame
-
Creates new form NewJFrame
- geneticAlgorithm.evaluationFunctions - package geneticAlgorithm.evaluationFunctions
-
- geneticAlgorithm.mutation - package geneticAlgorithm.mutation
-
- geneticAlgorithm.populationInitialisation - package geneticAlgorithm.populationInitialisation
-
- geneticAlgorithm.recombination - package geneticAlgorithm.recombination
-
- geneticAlgorithm.reinsertion - package geneticAlgorithm.reinsertion
-
- geneticAlgorithm.restrictions - package geneticAlgorithm.restrictions
-
- geneticAlgorithm.selection - package geneticAlgorithm.selection
-
- GeneticAlgorithmDcmaEs - Class in geneticAlgorithm
-
- GeneticAlgorithmDcmaEs(Parser) - Constructor for class geneticAlgorithm.GeneticAlgorithmDcmaEs
-
- getAccelerator() - Method in class kineticMonteCarlo.kmcCore.growth.AbstractGrowthKmc
-
- getAdsorptionData() - Method in class basic.io.CatalysisData
-
- getAdsorptionRate(int) - Method in class ratesLibrary.CatalysisFarkasTestRates
-
Adsorption rate of 0.29, 0.15 or 0.03.
- getAdsorptionRate(int) - Method in class ratesLibrary.CatalysisRates
-
Adsorption rate for CO or O.
- getAllNeighbours() - Method in class kineticMonteCarlo.atom.AbstractGrowthAtom
-
- getAllNeighbours() - Method in class kineticMonteCarlo.atom.AgAtom
-
- getAllNeighbours() - Method in class kineticMonteCarlo.atom.BasicGrowthAtom
-
- getAllNeighbours() - Method in class kineticMonteCarlo.atom.CatalysisAtom
-
- getAllNeighbours() - Method in class kineticMonteCarlo.atom.GrapheneAtom
-
- getAngle() - Method in class kineticMonteCarlo.atom.AbstractGrowthAtom
-
- getAreaXY(double, double, double, double, double, double) - Method in class kineticMonteCarlo.unitCell.SiUnitCell
-
- getAreaXYPower(double, double, double, double, double, double) - Method in class kineticMonteCarlo.unitCell.SiUnitCell
-
- getAtom(int) - Method in class kineticMonteCarlo.lattice.AbstractGrowthLattice
-
Deprecated.
- getAtom(int, int) - Method in class kineticMonteCarlo.lattice.AbstractGrowthLattice
-
Deprecated.
- getAtom(int, int, int) - Method in class kineticMonteCarlo.lattice.AbstractGrowthLattice
-
- getAtom(int, int, int, int) - Method in class kineticMonteCarlo.lattice.AbstractGrowthLattice
-
- getAtom(int, int, int, int) - Method in class kineticMonteCarlo.lattice.AbstractLattice
-
Deprecated.
- getAtom(int, int) - Method in class kineticMonteCarlo.lattice.AgUcLattice
-
- getAtom(int, int, int) - Method in class kineticMonteCarlo.lattice.AgUcLattice
-
Returns an atom of given unit cell and lattice position.
- getAtom(int, int, int, int) - Method in class kineticMonteCarlo.lattice.BasicLattice
-
- getAtom(int, int, int, int) - Method in class kineticMonteCarlo.lattice.SiLattice
-
- getAtom(int) - Method in class kineticMonteCarlo.unitCell.AbstractGrowthUc
-
- getAtom(int) - Method in class kineticMonteCarlo.unitCell.AgUc
-
- getAtom(int) - Method in class kineticMonteCarlo.unitCell.CatalysisUc
-
Always returns the current atom
- getAtom(int) - Method in interface kineticMonteCarlo.unitCell.IUc
-
- getAtom(int) - Method in class kineticMonteCarlo.unitCell.Simple3dUc
-
Always returns the current atom.
- getAtom(int) - Method in class kineticMonteCarlo.unitCell.SimpleUc
-
Always returns the current atom.
- getAtomAt(int) - Method in class kineticMonteCarlo.lattice.Island
-
- getAtomAt(int) - Method in class utils.list.AbstractList
-
- getAtomAt(int) - Method in class utils.list.BinnedList
-
- getAtomAt(int) - Method in class utils.list.LinearList
-
- getAtomTypesCounter() - Method in class kineticMonteCarlo.lattice.AbstractGrowthLattice
-
- getAttributes() - Method in class kineticMonteCarlo.atom.AbstractGrowthAtom
-
- getAttributes() - Method in class kineticMonteCarlo.atom.CatalysisAtom
-
- getAvailableDistance(AbstractGrowthAtom, int) - Method in class kineticMonteCarlo.lattice.AgLattice
-
- getAvailableDistance(AbstractGrowthAtom, int) - Method in class kineticMonteCarlo.lattice.AgUcLattice
-
- getAvailableDistance(AbstractGrowthAtom, int) - Method in class kineticMonteCarlo.lattice.BasicGrowthLattice
-
- getAvailableDistance(AbstractGrowthAtom, int) - Method in class kineticMonteCarlo.lattice.CatalysisLattice
-
- getAvailableDistance(AbstractGrowthAtom, int) - Method in class kineticMonteCarlo.lattice.GrapheneLattice
-
- getAvailableDistance(AbstractGrowthAtom, int) - Method in interface kineticMonteCarlo.lattice.IDevitaLattice
-
- getAverageGyradius() - Method in class kineticMonteCarlo.lattice.AbstractGrowthLattice
-
Computes the average distances to the centre of mass for all islands.
- getAverageGyradius() - Method in class kineticMonteCarlo.lattice.AbstractLattice
-
Only defined in growth lattice.
- getAverageGyradius() - Method in class kineticMonteCarlo.lattice.BasicLattice
-
Gyradius is not implemented in etching.
- getAverageGyradius() - Method in class kineticMonteCarlo.lattice.SiLattice
-
Gyradius is not implemented in etching.
- getAvgDistance() - Method in class kineticMonteCarlo.lattice.Island
-
Equation (15) of Kinsner, A unified approach to fractal dimensions.
- getBestError() - Method in class geneticAlgorithm.Population
-
Returns the best error of the current population.
- getBestIndividual() - Method in class geneticAlgorithm.AbstractGeneticAlgorithm
-
- getBestIndividual() - Method in interface geneticAlgorithm.IGeneticAlgorithm
-
- getBestIndividual() - Method in class geneticAlgorithm.Population
-
Returns the best individual of the current population.
- getBins() - Method in class utils.list.BinnedList
-
- getBinsLevels() - Method in class basic.Parser
-
Selects the number of bin levels.
- getBondsProbability() - Method in class kineticMonteCarlo.atom.AbstractGrowthAtom
-
- getBondsProbability(int) - Method in class kineticMonteCarlo.atom.AbstractGrowthAtom
-
Get probability in the given neighbour position.
- getBondsProbability(int) - Method in class kineticMonteCarlo.atom.ConcertedAtom
-
Get probability in the given neighbour position.
- getBufferedReader(String) - Method in class main.Configurator
-
- getBufferedReader(String) - Method in interface main.IConfigurator
-
- getBufferedReader(String) - Method in class main.PcConfigurator
-
Returns proper reader for PC file.
- getCalculationMode() - Method in class basic.Parser
-
Selects the type of system to be calculated.
- getCalculationType() - Method in class basic.Parser
-
Morphokinetics has two main calculation modes: one called batch, for arbitrarily chosen input
parameters, and the other called evolutionary, which tries to find the best input parameters
for a target system.
- getCartesianLocation(int, int) - Method in class kineticMonteCarlo.lattice.AbstractGrowthLattice
-
Obtains the spatial location of certain atom, the distance between atoms is considered as 1
Returns the Cartesian position, given the hexagonal (lattice) location.
- getCartesianLocation(int, int) - Method in class kineticMonteCarlo.lattice.AgLattice
-
- getCartesianLocation(int, int) - Method in class kineticMonteCarlo.lattice.BasicGrowthLattice
-
- getCartesianLocation(int, int) - Method in class kineticMonteCarlo.lattice.CatalysisLattice
-
- getCartesianLocation(int, int) - Method in class kineticMonteCarlo.lattice.GrapheneLattice
-
- getCartesianPosition() - Method in class kineticMonteCarlo.atom.AbstractGrowthAtom
-
- getCartesianSuperCell() - Method in class kineticMonteCarlo.atom.AbstractGrowthAtom
-
- getCartSizeX() - Method in class basic.Parser
-
Selects the Cartesian size in X direction.
- getCartSizeX() - Method in class kineticMonteCarlo.lattice.AbstractGrowthLattice
-
- getCartSizeX() - Method in class kineticMonteCarlo.lattice.AgLattice
-
- getCartSizeX() - Method in class kineticMonteCarlo.lattice.AgUcLattice
-
- getCartSizeX() - Method in class kineticMonteCarlo.lattice.BasicGrowthLattice
-
- getCartSizeX() - Method in class kineticMonteCarlo.lattice.CatalysisLattice
-
- getCartSizeX() - Method in class kineticMonteCarlo.lattice.GrapheneLattice
-
- getCartSizeY() - Method in class basic.Parser
-
Selects the Cartesian size in Y direction.
- getCartSizeY() - Method in class kineticMonteCarlo.lattice.AbstractGrowthLattice
-
- getCartSizeY() - Method in class kineticMonteCarlo.lattice.AgLattice
-
- getCartSizeY() - Method in class kineticMonteCarlo.lattice.AgUcLattice
-
- getCartSizeY() - Method in class kineticMonteCarlo.lattice.BasicGrowthLattice
-
- getCartSizeY() - Method in class kineticMonteCarlo.lattice.CatalysisLattice
-
- getCartSizeY() - Method in class kineticMonteCarlo.lattice.GrapheneLattice
-
- getCartSizeZ() - Method in class basic.Parser
-
Selects the Cartesian size in Z direction.
- getCartX(int, int) - Method in class kineticMonteCarlo.lattice.AbstractGrowthLattice
-
- getCartX(int, int) - Method in class kineticMonteCarlo.lattice.AgLattice
-
The Cartesian X is the location I, plus the half of J.
- getCartX(int, int) - Method in class kineticMonteCarlo.lattice.BasicGrowthLattice
-
- getCartX(int, int) - Method in class kineticMonteCarlo.lattice.CatalysisLattice
-
- getCartX(int, int) - Method in class kineticMonteCarlo.lattice.GrapheneLattice
-
- getCartY(int) - Method in class kineticMonteCarlo.lattice.AbstractGrowthLattice
-
- getCartY(int) - Method in class kineticMonteCarlo.lattice.AgLattice
-
Simple relation between Y (Cartesian) and J (hexagonal), with Y_RATIO (=sin 60º).
- getCartY(int) - Method in class kineticMonteCarlo.lattice.BasicGrowthLattice
-
- getCartY(int) - Method in class kineticMonteCarlo.lattice.CatalysisLattice
-
- getCartY(int) - Method in class kineticMonteCarlo.lattice.GrapheneLattice
-
- getCatalysisData() - Method in class basic.io.CatalysisData
-
- getCellsP() - Method in class kineticMonteCarlo.unitCell.SiUnitCell
-
- getCentralAtom() - Method in class kineticMonteCarlo.lattice.AbstractGrowthLattice
-
Returns the atom that it is in the middle of single flake simulation.
- getCentralAtom() - Method in class kineticMonteCarlo.lattice.AgLattice
-
- getCentralAtom() - Method in class kineticMonteCarlo.lattice.AgUcLattice
-
- getCentralAtom() - Method in class kineticMonteCarlo.lattice.BasicGrowthLattice
-
- getCentralAtom() - Method in class kineticMonteCarlo.lattice.CatalysisLattice
-
- getCentralAtom() - Method in class kineticMonteCarlo.lattice.GrapheneLattice
-
- getCentralCartesianLocation() - Method in class kineticMonteCarlo.lattice.AbstractGrowthLattice
-
- getCentralCartesianLocation() - Method in class kineticMonteCarlo.lattice.AgLattice
-
- getCentralCartesianLocation() - Method in class kineticMonteCarlo.lattice.AgUcLattice
-
- getCentralCartesianLocation() - Method in class kineticMonteCarlo.lattice.BasicGrowthLattice
-
- getCentralCartesianLocation() - Method in class kineticMonteCarlo.lattice.CatalysisLattice
-
- getCentralCartesianLocation() - Method in class kineticMonteCarlo.lattice.GrapheneLattice
-
- getCentreOfMass() - Method in class kineticMonteCarlo.lattice.AbstractGrowthLattice
-
Calculates the centre of mass of each island.
- getCentreOfMass() - Method in class kineticMonteCarlo.lattice.Island
-
- getClearAreaArmchair(short, short, int, int[], double) - Method in class kineticMonteCarlo.lattice.GrapheneLattice
-
- getClearAreaStep(short, short, int) - Method in class kineticMonteCarlo.lattice.AgLattice
-
- getClearAreaStep(AbstractGrowthAtom, int) - Method in class kineticMonteCarlo.lattice.AgUcLattice
-
- getClearAreaStep(AbstractGrowthAtom, int) - Method in class kineticMonteCarlo.lattice.BasicGrowthLattice
-
- getClearAreaTerrace(short, short, int) - Method in class kineticMonteCarlo.lattice.AgLattice
-
- getClearAreaTerrace(AbstractGrowthAtom, int) - Method in class kineticMonteCarlo.lattice.AgUcLattice
-
We only care about the largest possible distance atoms.
- getClearAreaTerrace(AbstractGrowthAtom, int, boolean, int, int, int, byte) - Method in class kineticMonteCarlo.lattice.AgUcLattice
-
- getClearAreaTerrace(AbstractGrowthAtom, int) - Method in class kineticMonteCarlo.lattice.BasicGrowthLattice
-
We only care about the largest possible distance atoms.
- getClearAreaTerrace(short, short, int) - Method in class kineticMonteCarlo.lattice.GrapheneLattice
-
- getClearAreaZigzag(short, short, int, int[], double) - Method in class kineticMonteCarlo.lattice.GrapheneLattice
-
- getCmDistance() - Method in class kineticMonteCarlo.lattice.AbstractGrowthLattice
-
- getCoCusNeighbours() - Method in class kineticMonteCarlo.atom.CatalysisAtom
-
- getCode() - Method in class kineticMonteCarlo.atom.ConcertedAtom
-
Gets a BitSet of the current occupancy.
- getCollection(boolean, byte) - Method in class utils.list.atoms.AtomsCollection
-
- getColumns() - Method in class kineticMonteCarlo.lattice.perimeterStatistics.Statistics
-
- getConcertedDiffusionRate(int) - Method in class kineticMonteCarlo.kmcCore.growth.ConcertedKmc
-
- getConfigurator() - Static method in class main.Configurator
-
- getContext() - Method in class main.Configurator
-
- getContext() - Method in interface main.IConfigurator
-
- getContext() - Method in class main.PcConfigurator
-
It does not need any context.
- getContrastColor(Color) - Method in class graphicInterfaces.growth.KmcCanvas
-
Method taken from http://stackoverflow.com/questions/4672271/reverse-opposing-colors
- getCos3D(double, double, double, double, double, double) - Method in class kineticMonteCarlo.unitCell.SiUnitCell
-
- getCoverage() - Method in class basic.Parser
-
Returns the maximum coverage until a simulation is allowed to grow.
- getCoverage() - Method in class kineticMonteCarlo.kmcCore.AbstractKmc
-
Coverage is not defined in the etching.
- getCoverage(byte) - Method in class kineticMonteCarlo.kmcCore.catalysis.CatalysisKmc
-
- getCoverage() - Method in class kineticMonteCarlo.kmcCore.catalysis.CatalysisKmc
-
- getCoverage() - Method in class kineticMonteCarlo.kmcCore.growth.AbstractGrowthKmc
-
Returns the coverage of the simulation.
- getCoverage() - Method in class kineticMonteCarlo.lattice.AbstractGrowthLattice
-
- getCoverage() - Method in class kineticMonteCarlo.lattice.AgUcLattice
-
The area is the number of cells * 2.
- getCoverage(byte) - Method in class kineticMonteCarlo.lattice.CatalysisLattice
-
- getCoverage() - Method in class kineticMonteCarlo.lattice.CatalysisLattice
-
- getCoverages() - Method in class kineticMonteCarlo.kmcCore.catalysis.CatalysisKmc
-
- getCoverages() - Method in class kineticMonteCarlo.lattice.CatalysisLattice
-
Computes a partial coverage for CO and O in BR and CUS sites.
- getCrm() - Method in class geneticAlgorithm.Population
-
- getCurrentDifference() - Method in class geneticAlgorithm.evaluationFunctions.AbstractEvaluator
-
Undefined here
- getCurrentDifference() - Method in class geneticAlgorithm.evaluationFunctions.AbstractPsdEvaluator
-
- getCurrentDifference() - Method in interface geneticAlgorithm.evaluationFunctions.IEvaluation
-
- getCurrentError() - Method in class geneticAlgorithm.evaluationFunctions.AbstractEvaluator
-
Undefined here
- getCurrentError() - Method in class geneticAlgorithm.evaluationFunctions.AbstractPsdEvaluator
-
- getCurrentError() - Method in interface geneticAlgorithm.evaluationFunctions.IEvaluation
-
- getCurrentIteration() - Method in class geneticAlgorithm.AbstractGeneticAlgorithm
-
- getCurrentIteration() - Method in class geneticAlgorithm.evaluationFunctions.AbstractPsdEvaluator
-
- getCurrentIteration() - Method in interface geneticAlgorithm.IGeneticAlgorithm
-
- getCurrentPerimeter() - Method in class kineticMonteCarlo.kmcCore.growth.RoundPerimeter
-
- getCurrentPopulation() - Method in class geneticAlgorithm.evaluationFunctions.AbstractPsdEvaluator
-
- getCurrentProgress() - Method in class basic.AbstractSimulation
-
- getCurrentPsd() - Method in class geneticAlgorithm.evaluationFunctions.AbstractEvaluator
-
Undefined here
- getCurrentPsd() - Method in class geneticAlgorithm.evaluationFunctions.AbstractPsdEvaluator
-
- getCurrentPsd() - Method in interface geneticAlgorithm.evaluationFunctions.IEvaluation
-
- getCurrentRadius() - Method in class kineticMonteCarlo.kmcCore.AbstractKmc
-
- getCurrentRadius() - Method in class kineticMonteCarlo.kmcCore.growth.AbstractGrowthKmc
-
Takes the current radius from the perimeter attribute.
- getCurrentRadius() - Method in class kineticMonteCarlo.kmcCore.growth.RoundPerimeter
-
- getCurrentSimulation() - Method in class geneticAlgorithm.evaluationFunctions.AbstractPsdEvaluator
-
- getCurrentType(int, int) - Method in class kineticMonteCarlo.atom.AgTypesTable
-
Returns the type of the atom between TERRACE, CORNER, EDGE, KINK and ISLAND.
- getCurrentType(int) - Method in class kineticMonteCarlo.atom.BasicGrowthTypesTable
-
Returns the type of the atom between TERRACE, EDGE, KINK and ISLAND.
- getcurrXform() - Method in class graphicInterfaces.etching.mouseBehaviors.MouseRotate
-
- getcurrXform() - Method in class graphicInterfaces.etching.mouseBehaviors.MouseTranslate
-
- getcurrXform() - Method in class graphicInterfaces.etching.mouseBehaviors.MouseZoom
-
- getData(int, int) - Method in class kineticMonteCarlo.lattice.perimeterStatistics.Statistics
-
- getData() - Method in class utils.list.Node
-
- getDeltaTime(boolean) - Method in class utils.list.AbstractList
-
- getDepositionFlux() - Method in class basic.Parser
-
Number of atoms that is coming per second and per area.
- getDepositionPosition() - Method in class kineticMonteCarlo.atom.AbstractGrowthAtom
-
- getDepositionPosition() - Method in class kineticMonteCarlo.atom.AbstractGrowthAtomAttributes
-
- getDepositionProbability() - Method in class utils.list.AbstractList
-
- getDepositionRatePerSite() - Method in class ratesLibrary.AbstractBasicGrowthRates
-
- getDepositionRatePerSite() - Method in class ratesLibrary.AgRatesFromPrbCox
-
In principle, deposition rate is constant to 0.0035 ML/s.
- getDepositionRatePerSite() - Method in class ratesLibrary.AgSimpleRates
-
In principle, deposition rate is constant to 0.0035 ML/s.
- getDepositionRatePerSite() - Method in class ratesLibrary.basic.RatesCase
-
- getDepositionRatePerSite() - Method in class ratesLibrary.CatalysisRates
-
- getDepositionRatePerSite() - Method in class ratesLibrary.concerted.AbstractConcertedRates
-
In principle, deposition rate is constant to 0.0035 ML/s.
- getDepositionRatePerSite() - Method in class ratesLibrary.GrapheneGaillardOneNeighbourRates
-
- getDepositionRatePerSite() - Method in class ratesLibrary.GrapheneGaillardRates
-
- getDepositionRatePerSite() - Method in class ratesLibrary.GrapheneGaillardSimpleRates
-
- getDepositionRatePerSite() - Method in class ratesLibrary.GrapheneSchoenhalzRates
-
- getDepositionRatePerSite() - Method in class ratesLibrary.GrapheneSyntheticRates
-
- getDepositionRatePerSite() - Method in interface ratesLibrary.IRates
-
- getDepositionRatePerSite() - Method in class ratesLibrary.SiRatesFromPreGosalvez
-
- getDepositionTime() - Method in class kineticMonteCarlo.atom.AbstractGrowthAtom
-
- getDepositionTime() - Method in class kineticMonteCarlo.atom.AbstractGrowthAtomAttributes
-
- getDepth() - Method in class utils.list.Node
-
- getDesorptionProbability(CatalysisAtom, CatalysisAtom) - Method in class kineticMonteCarlo.kmcCore.catalysis.CatalysisKmc
-
Computes desorption probability.
- getDesorptionRate(CatalysisAtom) - Method in class kineticMonteCarlo.kmcCore.catalysis.CatalysisFarkasKmc
-
- getDesorptionRate(CatalysisAtom) - Method in class kineticMonteCarlo.kmcCore.catalysis.CatalysisKmc
-
Computes desorption probability.
- getDesorptionRate(byte, double) - Method in class ratesLibrary.CatalysisRates
-
mu_{A} = -K_{B} T log( k_{B} T / p_{A} * (2 pi m_{A} k_{B} T /
h^2)^(3/2) * (8 pi^2 I k_{B} T / sigma h^2) * 1/
( 1 - exp( -h v / k_{B} T ) )) )
- getDesorptionRates(int) - Method in class ratesLibrary.CatalysisFarkasTestRates
-
- getDesorptionRates(int) - Method in class ratesLibrary.CatalysisRates
-
- getDesorptionRates() - Method in class ratesLibrary.CatalysisRates
-
Only for Farkas and repulsion.
- getDetachedType(byte, int) - Method in class kineticMonteCarlo.atom.ConcertedAtom
-
When detaching from an island, the energy has to be different.
- getDiffusionProbability() - Method in class utils.list.AbstractList
-
Total hops probability.
- getDiffusionProbabilityFromList() - Method in class utils.list.AbstractList
-
- getDiffusionProbabilityFromList() - Method in class utils.list.BinnedList
-
- getDiffusionProbabilityFromList() - Method in class utils.list.LinearList
-
- getDiffusionRate(CatalysisAtom, CatalysisAtom) - Method in class kineticMonteCarlo.kmcCore.catalysis.CatalysisFarkasKmc
-
- getDiffusionRate(CatalysisAtom, CatalysisAtom) - Method in class kineticMonteCarlo.kmcCore.catalysis.CatalysisKmc
-
- getDiffusionRate(ConcertedAtom, ConcertedAtom, int) - Method in class kineticMonteCarlo.kmcCore.growth.ConcertedKmc
-
- getDiffusionRates(int) - Method in class ratesLibrary.CatalysisRates
-
- getDiffusionRates() - Method in class ratesLibrary.CatalysisRates
-
Only for Farkas and repulsion.
- getDiffusionRates() - Method in class ratesLibrary.concerted.AbstractConcertedRates
-
- getDirection() - Method in class kineticMonteCarlo.lattice.MultiAtom
-
- getDistance(int, int) - Method in class kineticMonteCarlo.atom.ConcertedAtom
-
Takes into account that maximum distance can be 3.
- getDistancePerStep() - Method in class kineticMonteCarlo.atom.GrapheneAtom
-
- getDistancePerStep(int, int) - Method in class kineticMonteCarlo.kmcCore.growth.devitaAccelerator.HopsPerStep
-
- getDistancesToCentre() - Method in class kineticMonteCarlo.lattice.AbstractGrowthLattice
-
Computes each atoms distance to the centre of mass.
- getDistanceToCenter(int, int) - Method in class kineticMonteCarlo.lattice.AbstractGrowthLattice
-
- getDistanceToCenter(double, double) - Method in class kineticMonteCarlo.lattice.AbstractGrowthLattice
-
Returns the distance of the given x,y point to the centre.
- getEdgeRate(byte, int) - Method in class kineticMonteCarlo.atom.AbstractGrowthAtom
-
- getEdgeRate(int) - Method in class kineticMonteCarlo.lattice.MultiAtom
-
- getEdgeRate(int) - Method in class kineticMonteCarlo.process.AbstractProcess
-
- getEdgeSubtype(BitSet) - Method in class kineticMonteCarlo.atom.ConcertedAtom
-
Two atoms are together, separated by one position or two positions.
- getEdgeType(int) - Method in class kineticMonteCarlo.lattice.MultiAtom
-
Edge 0 is the neighbour of atom 0, and
edge 1 is the neighbour of atom 1.
- getEmptyTypesCounter() - Method in class kineticMonteCarlo.lattice.AbstractGrowthLattice
-
- getEndTime() - Method in class basic.Parser
-
Returns the maximum simulation time that each run has to do or -1 if there is no time limit.
- getEnergy(int, int) - Method in class ratesLibrary.AbstractBasicGrowthRates
-
- getEnergy(int, int) - Method in class ratesLibrary.AgRatesFromPrbCox
-
- getEnergy(int, int) - Method in class ratesLibrary.AgSimpleRates
-
- getEnergy(int) - Method in interface ratesLibrary.basic.IBasicRates
-
- getEnergy(int) - Method in class ratesLibrary.basic.RatesCase
-
- getEnergy(int, int) - Method in class ratesLibrary.basic.RatesCase
-
- getEnergy(int, int) - Method in class ratesLibrary.CatalysisRates
-
- getEnergy(int, int) - Method in class ratesLibrary.concerted.AbstractConcertedRates
-
- getEnergy(int, int) - Method in class ratesLibrary.GrapheneGaillardOneNeighbourRates
-
- getEnergy(int, int) - Method in class ratesLibrary.GrapheneGaillardRates
-
- getEnergy(int, int) - Method in class ratesLibrary.GrapheneGaillardSimpleRates
-
- getEnergy(int, int) - Method in class ratesLibrary.GrapheneSchoenhalzRates
-
- getEnergy(int, int) - Method in class ratesLibrary.GrapheneSyntheticRates
-
- getEnergy(int, int) - Method in interface ratesLibrary.IRates
-
- getEnergy(int, int) - Method in class ratesLibrary.SiRatesFromPreGosalvez
-
- getError(int) - Method in class geneticAlgorithm.Individual
-
- getErrors() - Method in class geneticAlgorithm.Individual
-
- getErrorsSize() - Method in class geneticAlgorithm.Individual
-
- getEstimatedCoverage() - Method in class kineticMonteCarlo.kmcCore.growth.AbstractGrowthKmc
-
Method to obtain theoretical coverage from deposition flux and current time.
- getEvaluatorTypes() - Method in class basic.Parser
-
To have the possibility to choose between different evaluators in genetic algorithm runs.
- getEvolutionaryAlgorithm() - Method in class basic.Parser
-
- getEvolutionarySearchType() - Method in class basic.Parser
-
- getExtraLevels() - Method in class basic.Parser
-
- getExtraWriter() - Method in class basic.io.Restart
-
- getExtraWriters() - Method in class basic.io.Restart
-
- getFactor() - Method in class graphicInterfaces.etching.mouseBehaviors.MouseZoom
-
Return the y-axis movement multipler.
- getFarSite(AbstractGrowthAtom, int) - Method in class kineticMonteCarlo.lattice.AgLattice
-
- getFarSite(AbstractGrowthAtom, int) - Method in class kineticMonteCarlo.lattice.AgUcLattice
-
- getFarSite(AbstractGrowthAtom, int) - Method in class kineticMonteCarlo.lattice.BasicGrowthLattice
-
- getFarSite(AbstractGrowthAtom, int) - Method in class kineticMonteCarlo.lattice.CatalysisLattice
-
- getFarSite(AbstractGrowthAtom, int) - Method in class kineticMonteCarlo.lattice.GrapheneLattice
-
- getFarSite(AbstractGrowthAtom, int) - Method in interface kineticMonteCarlo.lattice.IDevitaLattice
-
- getFutureType(int, int) - Method in class kineticMonteCarlo.atom.AgTypesTable
-
- getFutureType(int) - Method in class kineticMonteCarlo.atom.BasicGrowthTypesTable
-
- getGapCoverage() - Method in class kineticMonteCarlo.kmcCore.catalysis.CatalysisKmc
-
- getGapCoverage() - Method in class kineticMonteCarlo.lattice.CatalysisLattice
-
- getGene(int) - Method in class geneticAlgorithm.Individual
-
- getGenePosition() - Method in class geneticAlgorithm.restrictions.GeneRestriction
-
- getGenes() - Method in class geneticAlgorithm.Individual
-
- getGeneSize() - Method in class geneticAlgorithm.Individual
-
Returns the number of genes
- getGitRevision() - Static method in class basic.io.Restart
-
- getGlobalProbability() - Method in class utils.list.AbstractList
-
Total hops probability plus deposition probability plus desorption probability plus reaction
probability.
- getGOMultiplier() - Method in class basic.Parser
-
GO multiplier for plotting resolution problem solving.
- getHexagonalCoordinates(double, double) - Method in class kineticMonteCarlo.lattice.AgLattice
-
- getHexagonalPeriodicSurface(int, int) - Method in class kineticMonteCarlo.kmcCore.catalysis.CatalysisKmc
-
- getHexagonalPeriodicSurface(int, int) - Method in class kineticMonteCarlo.kmcCore.etching.BasicKmc
-
- getHexagonalPeriodicSurface(int, int) - Method in class kineticMonteCarlo.kmcCore.etching.SiKmc
-
- getHexagonalPeriodicSurface(int, int) - Method in class kineticMonteCarlo.kmcCore.growth.AbstractGrowthKmc
-
- getHexagonalPeriodicSurface(int, int) - Method in class kineticMonteCarlo.kmcCore.growth.BasicGrowthKmc
-
- getHexagonalPeriodicSurface(int, int) - Method in interface kineticMonteCarlo.kmcCore.IKmc
-
- getHexaPosI(int, int, int, boolean) - Method in class kineticMonteCarlo.lattice.GrapheneLattice
-
- getHexaPosJ(int, int, int, boolean) - Method in class kineticMonteCarlo.lattice.GrapheneLattice
-
- getHexaSizeI() - Method in class basic.Parser
-
Selects the lattice size in I direction.
- getHexaSizeI() - Method in class kineticMonteCarlo.lattice.AbstractLattice
-
- getHexaSizeJ() - Method in class basic.Parser
-
Selects the lattice size in J direction.
- getHexaSizeJ() - Method in class kineticMonteCarlo.lattice.AbstractLattice
-
- getHexaSizeK() - Method in class kineticMonteCarlo.lattice.AbstractLattice
-
- getHierarchyEvaluator() - Method in class basic.Parser
-
If a hierarchy evaluator has been chosen, select the type of hierarchy evaluator.
- getHops() - Method in class kineticMonteCarlo.atom.AbstractGrowthAtom
-
- getHops() - Method in class kineticMonteCarlo.atom.AbstractGrowthAtomAttributes
-
- getHopsCount(int, int) - Method in class kineticMonteCarlo.lattice.perimeterStatistics.AbstractPerimeterStatistics
-
- getId() - Method in class kineticMonteCarlo.atom.AbstractGrowthAtom
-
- getId() - Method in class kineticMonteCarlo.atom.SiAtom
-
- getiHexa() - Method in class kineticMonteCarlo.atom.AbstractGrowthAtom
-
- getiHexa(double, double) - Method in class kineticMonteCarlo.lattice.AbstractGrowthLattice
-
Knowing the X and Y Cartesian location, returns closest atom hexagonal coordinate.
- getiHexa(double, double) - Method in class kineticMonteCarlo.lattice.AgLattice
-
Knowing the X and Y Cartesian location, returns closest atom hexagonal coordinate.
- getiHexa(double, double) - Method in class kineticMonteCarlo.lattice.BasicGrowthLattice
-
- getiHexa(double, double) - Method in class kineticMonteCarlo.lattice.CatalysisLattice
-
- getiHexa(double, double) - Method in class kineticMonteCarlo.lattice.GrapheneLattice
-
- getIndex(int, int) - Static method in class utils.MathUtils
-
- getIndividual(int) - Method in class geneticAlgorithm.AbstractGeneticAlgorithm
-
- getIndividual(int) - Method in interface geneticAlgorithm.IGeneticAlgorithm
-
- getIndividual(int) - Method in class geneticAlgorithm.Population
-
Return an population individual from position pos
- getIndividualCount() - Method in class geneticAlgorithm.evaluationFunctions.AbstractEvaluator
-
Undefined here
- getIndividualCount() - Method in class geneticAlgorithm.evaluationFunctions.AbstractPsdEvaluator
-
Calculates the count (number) of the current simulation.
- getIndividualCount() - Method in interface geneticAlgorithm.evaluationFunctions.IEvaluation
-
- getIndividuals() - Method in class geneticAlgorithm.Population
-
- getInnerPerimeterLenght() - Method in class kineticMonteCarlo.lattice.AbstractGrowthLattice
-
Inner perimeter is the sum of atoms that are occupied and have some neighbour not occupied.
- getIsland(int) - Method in class kineticMonteCarlo.lattice.AbstractGrowthLattice
-
- getIslandCount() - Method in class kineticMonteCarlo.lattice.AbstractGrowthLattice
-
- getIslandCount() - Method in class kineticMonteCarlo.lattice.AbstractLattice
-
Only defined in growth lattice.
- getIslandCount() - Method in class kineticMonteCarlo.lattice.BasicLattice
-
Number of islands has no sense in etching.
- getIslandCount() - Method in class kineticMonteCarlo.lattice.SiLattice
-
Number of islands has no sense in etching.
- getIslandDensity(double) - Method in class ratesLibrary.AbstractBasicGrowthRates
-
Returns the island density mono layer depending on the temperature.
- getIslandDensity(double) - Method in class ratesLibrary.AgRatesFromPrbCox
-
Returns the island density mono layer depending on the temperature.
- getIslandDensity(double) - Method in class ratesLibrary.AgSimpleRates
-
Returns the island density mono layer depending on the temperature.
- getIslandDensity(double) - Method in class ratesLibrary.basic.RatesCase
-
- getIslandDensity(double) - Method in class ratesLibrary.BasicGrowth2Rates
-
Returns the island density mono layer depending on the temperature.
- getIslandDensity(double) - Method in class ratesLibrary.BasicGrowth3Rates
-
Returns the island density mono layer depending on the temperature.
- getIslandDensity(double) - Method in class ratesLibrary.CatalysisRates
-
- getIslandDensity(double) - Method in class ratesLibrary.concerted.AbstractConcertedRates
-
Returns the island density mono layer depending on the temperature.
- getIslandDensity(double) - Method in class ratesLibrary.GrapheneGaillardOneNeighbourRates
-
Returns the island density mono layer depending on the temperature.
- getIslandDensity(double) - Method in class ratesLibrary.GrapheneGaillardRates
-
Returns the island density mono layer depending on the temperature.
- getIslandDensity(double) - Method in class ratesLibrary.GrapheneGaillardSimpleRates
-
Returns the island density mono layer depending on the temperature.
- getIslandDensity(double) - Method in class ratesLibrary.GrapheneSchoenhalzRates
-
Returns the island density mono layer depending on the temperature.
- getIslandDensity(double) - Method in class ratesLibrary.GrapheneSyntheticRates
-
Returns the island density mono layer depending on the temperature.
- getIslandDensity(double) - Method in interface ratesLibrary.IRates
-
Returns the island density mono layer depending on the temperature.
- getIslandDensity(double) - Method in class ratesLibrary.SiRatesFromPreGosalvez
-
- getIslandDiffusionRates() - Method in class ratesLibrary.concerted.AbstractConcertedRates
-
- getIslandIterator() - Method in class kineticMonteCarlo.lattice.AbstractGrowthLattice
-
- getIslandNumber() - Method in class kineticMonteCarlo.atom.AbstractGrowthAtom
-
- getIslandNumber() - Method in class kineticMonteCarlo.atom.AbstractGrowthAtomAttributes
-
- getIslandNumber() - Method in class kineticMonteCarlo.lattice.Island
-
- getIterationNumber() - Method in class geneticAlgorithm.Population
-
- getIterations() - Method in class kineticMonteCarlo.kmcCore.AbstractKmc
-
- getIterations() - Method in interface kineticMonteCarlo.kmcCore.IKmc
-
- getIterations() - Method in class kineticMonteCarlo.kmcCore.worker.KmcWorker
-
- getIterator() - Method in class utils.list.AbstractList
-
- getIterator() - Method in class utils.list.BinnedList
-
- getIterator() - Method in class utils.list.LinearList
-
- getJarBaseDir() - Static method in class basic.io.Restart
-
Returns the base location of the JAR file (or the main executable instead).
- getjHexa() - Method in class kineticMonteCarlo.atom.AbstractGrowthAtom
-
- getjHexa(double) - Method in class kineticMonteCarlo.lattice.AbstractGrowthLattice
-
Knowing the X and Y Cartesian location, returns closest atom hexagonal coordinate.
- getjHexa(double) - Method in class kineticMonteCarlo.lattice.AgLattice
-
Knowing the X and Y Cartesian location, returns closest atom hexagonal coordinate.
- getjHexa(double) - Method in class kineticMonteCarlo.lattice.BasicGrowthLattice
-
- getjHexa(double) - Method in class kineticMonteCarlo.lattice.CatalysisLattice
-
- getjHexa(double) - Method in class kineticMonteCarlo.lattice.GrapheneLattice
-
- getKinkSubtype(BitSet) - Method in class kineticMonteCarlo.atom.ConcertedAtom
-
If the given number from bits is multiple of 21 all atoms are separated,
other multiples of 7, all 3 atoms are together.
- getKmc() - Method in class basic.AbstractSimulation
-
- getKmc() - Method in class geneticAlgorithm.AbstractGeneticAlgorithm
-
- getKmc() - Method in class kineticMonteCarlo.kmcCore.worker.KmcWorker
-
- getLattice() - Method in class kineticMonteCarlo.kmcCore.AbstractKmc
-
- getLattice() - Method in class kineticMonteCarlo.kmcCore.growth.AbstractGrowthKmc
-
- getLattice() - Method in interface kineticMonteCarlo.kmcCore.IKmc
-
- getLattice() - Method in class kineticMonteCarlo.kmcCore.worker.KmcWorker
-
- getLatticeSite() - Method in class kineticMonteCarlo.atom.CatalysisAtom
-
- getLeft() - Method in class utils.list.Node
-
- getLevel() - Method in class utils.list.AbstractList
-
- getLevel() - Method in class utils.list.Node
-
- getLimitX() - Method in class kineticMonteCarlo.atom.SiAtom
-
- getLimitX() - Method in class kineticMonteCarlo.unitCell.SiUnitCell
-
- getLimitY() - Method in class kineticMonteCarlo.atom.SiAtom
-
- getLimitY() - Method in class kineticMonteCarlo.unitCell.SiUnitCell
-
- getLimitZ() - Method in class kineticMonteCarlo.atom.SiAtom
-
- getLimitZ() - Method in class kineticMonteCarlo.unitCell.SiUnitCell
-
- getList() - Method in class kineticMonteCarlo.kmcCore.AbstractKmc
-
- getList() - Method in interface kineticMonteCarlo.kmcCore.IKmc
-
- getListType() - Method in class basic.Parser
-
Selects the internal list type to be used between linear and binned.
- getLogY(int) - Method in class graphicInterfaces.gaConvergence.ErrorPanel
-
- getLogYSize() - Method in class graphicInterfaces.gaConvergence.ErrorPanel
-
- getMainEvaluator() - Method in class geneticAlgorithm.AbstractGeneticAlgorithm
-
- getMax() - Method in class graphicInterfaces.surfaceViewer2D.Frame2D
-
- getMax() - Method in class graphicInterfaces.surfaceViewer2D.Panel2D
-
- getMax() - Method in class graphicInterfaces.surfaceViewer2D.SurfaceViewerPanel2D
-
- getMax() - Method in interface graphicInterfacesCommon.surfaceViewer2D.IFrame2D
-
- getMax() - Method in class utils.psdAnalysis.PsdSignature2D
-
- getMaxAccumulatedSteps() - Method in class kineticMonteCarlo.kmcCore.growth.devitaAccelerator.DevitaHopsConfig
-
- getMaxDistance() - Method in class kineticMonteCarlo.lattice.Island
-
- getMaxDistanceHops() - Method in class kineticMonteCarlo.kmcCore.growth.devitaAccelerator.DevitaHopsConfig
-
- getMaximum() - Method in class utils.list.atoms.AvlTree
-
- getMaxIteration() - Method in class geneticAlgorithm.evaluationFunctions.AgBasicPsdEvaluator
-
- getMaxIteration() - Method in class geneticAlgorithm.evaluationFunctions.BasicGrowthPsdEvaluator
-
- getMaxValueGene() - Method in class basic.Parser
-
For evolutionary algorithm, maximum possible value of a gene.
- getMeasureInterval() - Method in class geneticAlgorithm.evaluationFunctions.AbstractPsdEvaluator
-
- getMillerX() - Method in class basic.Parser
-
- getMillerY() - Method in class basic.Parser
-
- getMillerZ() - Method in class basic.Parser
-
- getMin() - Method in class graphicInterfaces.surfaceViewer2D.Frame2D
-
- getMin() - Method in class graphicInterfaces.surfaceViewer2D.Panel2D
-
- getMin() - Method in class graphicInterfaces.surfaceViewer2D.SurfaceViewerPanel2D
-
- getMin() - Method in interface graphicInterfacesCommon.surfaceViewer2D.IFrame2D
-
- getMin() - Method in class utils.psdAnalysis.PsdSignature2D
-
- getMinAccumulatedSteps() - Method in class kineticMonteCarlo.kmcCore.growth.devitaAccelerator.DevitaHopsConfig
-
- getMinDistanceHops() - Method in class kineticMonteCarlo.kmcCore.growth.devitaAccelerator.DevitaHopsConfig
-
- getMinimum() - Method in class utils.list.atoms.AvlTree
-
- getMinimumNode() - Method in class utils.list.atoms.AvlTree
-
- getMinMax(float[][]) - Method in class graphicInterfaces.surfaceViewer2D.Panel2D
-
- getMinRadiusInSize() - Method in class kineticMonteCarlo.lattice.perimeterStatistics.AbstractPerimeterStatistics
-
Arbitrarily the minimum radius is 10
- getMinValueGene() - Method in class basic.Parser
-
For evolutionary algorithm, minimum possible value of a gene.
- getMobileAtoms() - Method in class kineticMonteCarlo.lattice.AbstractGrowthLattice
-
How many mobile atoms are.
- getModifiedBuffer() - Method in class kineticMonteCarlo.kmcCore.growth.AbstractGrowthKmc
-
- getMonomerCount() - Method in class kineticMonteCarlo.lattice.AbstractGrowthLattice
-
Monomers are atoms without neighbours.
- getMultiAtom(int) - Method in class kineticMonteCarlo.lattice.AbstractGrowthLattice
-
- getMultiAtomCount() - Method in class kineticMonteCarlo.lattice.AbstractGrowthLattice
-
- getMultiAtomDiffusionRate(MultiAtom) - Method in class kineticMonteCarlo.kmcCore.growth.ConcertedKmc
-
- getMultiAtomIterator() - Method in class kineticMonteCarlo.lattice.AbstractGrowthLattice
-
- getMultiAtomNumber() - Method in class kineticMonteCarlo.atom.AbstractGrowthAtom
-
- getMultiAtomNumber() - Method in class kineticMonteCarlo.atom.AbstractGrowthAtomAttributes
-
- getMultiAtomRate(int, double) - Method in class ratesLibrary.concerted.AbstractConcertedRates
-
Multi atom version.
- getMultiAtomRates() - Method in class ratesLibrary.concerted.AbstractConcertedRates
-
- getMultiAtomsIterator() - Method in class kineticMonteCarlo.lattice.AbstractGrowthLattice
-
- getMultiplier() - Method in class kineticMonteCarlo.atom.AbstractGrowthAtom
-
- getN1() - Method in class kineticMonteCarlo.atom.GrapheneAtom
-
Total number of 1st neighbours.
- getN1() - Method in class kineticMonteCarlo.atom.SiAtom
-
Number of 1st neighbours.
- getN2() - Method in class kineticMonteCarlo.atom.GrapheneAtom
-
Total number of 2nd neighbours.
- getN2() - Method in class kineticMonteCarlo.atom.SiAtom
-
Number of 2nd neighbours.
- getN3() - Method in class kineticMonteCarlo.atom.GrapheneAtom
-
Total number of 3rd neighbours.
- getNBlock() - Method in class kineticMonteCarlo.unitCell.SiUnitCell
-
- getNeededSteps() - Method in class kineticMonteCarlo.kmcCore.growth.RoundPerimeter
-
- getNeighbour(int) - Method in class kineticMonteCarlo.atom.AbstractGrowthAtom
-
- getNeighbour(int) - Method in class kineticMonteCarlo.atom.AgAtom
-
- getNeighbour(int) - Method in class kineticMonteCarlo.atom.BasicAtom
-
- getNeighbour(int) - Method in class kineticMonteCarlo.atom.BasicGrowthAtom
-
- getNeighbour(int) - Method in class kineticMonteCarlo.atom.CatalysisAtom
-
- getNeighbour(int) - Method in class kineticMonteCarlo.atom.GrapheneAtom
-
- getNeighbour(int) - Method in class kineticMonteCarlo.atom.GrapheneAtomSchoenhalz
-
- getNeighbour(int) - Method in class kineticMonteCarlo.atom.SiAtom
-
- getNeighbour(int, int, int) - Method in class kineticMonteCarlo.lattice.AbstractGrowthLattice
-
- getNeighbour(int, int, int) - Method in class kineticMonteCarlo.lattice.AgLattice
-
- getNeighbour(int, int, int) - Method in class kineticMonteCarlo.lattice.BasicGrowthLattice
-
- getNeighbour(int, int, int) - Method in class kineticMonteCarlo.lattice.CatalysisLattice
-
- getNeighbour(int, int, int) - Method in class kineticMonteCarlo.lattice.GrapheneLattice
-
- getNeighbourCount() - Method in class kineticMonteCarlo.atom.GrapheneAtom
-
Total number of neighbours.
- getNeighs() - Method in class kineticMonteCarlo.unitCell.SiUnitCell
-
- getNewType(int, int) - Method in class kineticMonteCarlo.atom.AgAtom
-
Calculates the new atom type when adding or removing a neighbour.
- getNewType(int) - Method in class kineticMonteCarlo.atom.BasicGrowthAtom
-
Calculates the new atom type when adding or removing a neighbour.
- getNewType(int, int) - Method in class kineticMonteCarlo.atom.GrapheneAtom
-
Calculates the new atom type when adding or removing a neighbour.
- getNewType(int, int) - Method in class kineticMonteCarlo.atom.GrapheneAtomGaillardSimple
-
Calculates the new atom type when adding or removing a neighbour.
- getNextRadiusInSize(int) - Method in class kineticMonteCarlo.lattice.perimeterStatistics.AbstractPerimeterStatistics
-
We increase the radius in 1 position, because it should be the most precise and agrees the best
with theory.
- getNImmobile() - Method in class kineticMonteCarlo.atom.AgAtom
-
- getNMobile() - Method in class kineticMonteCarlo.atom.AgAtom
-
- getNonFixedGenes(int) - Method in class geneticAlgorithm.restrictions.RestrictionOperator
-
- getNumberOfAtoms() - Method in class kineticMonteCarlo.lattice.Island
-
- getNumberOfCo2() - Method in class basic.Parser
-
Selects the number of CO2 molecules that will be created at most. -1 by default, which means that
it will run until another criteria is reached.
- getNumberOfNeighbours() - Method in class kineticMonteCarlo.atom.AbstractAtom
-
Number of neighbours that current atoms has, independently whether are occupied or not.
- getNumberOfNeighbours() - Method in interface kineticMonteCarlo.atom.IAtom
-
- getNumberOfSimulations() - Method in class basic.Parser
-
Selects the number of simulations that has to be done with the same parameters.
- getNumberOfSteps() - Method in class basic.Parser
-
Selects the number of steps that each simulation will at most. -1 by default, which means that
it will run until another criteria is reached.
- getOccupied() - Method in class kineticMonteCarlo.lattice.AbstractGrowthLattice
-
- getOccupiedNeighbours() - Method in class kineticMonteCarlo.atom.AbstractGrowthAtom
-
How many neighbours are occupied.
- getOffFitness() - Method in class geneticAlgorithm.Population
-
Objective function values for DCMA-ES algorithm.
- getOffspringGenes() - Method in class geneticAlgorithm.Population
-
- getOffspringSize() - Method in class basic.Parser
-
- getOrientation() - Method in class kineticMonteCarlo.atom.AbstractGrowthAtom
-
- getOrientation() - Method in class kineticMonteCarlo.atom.AgAtom
-
Computes the orientation with respect to the surface, for edges and kinks.
- getOrientation(AgAtom) - Method in class kineticMonteCarlo.atom.AgAtom
-
- getOrientation() - Method in class kineticMonteCarlo.atom.BasicGrowthAtom
-
For the orientation they are only available two position.
- getOrientation() - Method in class kineticMonteCarlo.atom.CatalysisAtom
-
For the orientation they are only available two position.
- getOrientation() - Method in class kineticMonteCarlo.atom.GrapheneAtom
-
- getOuterPerimeterLenght() - Method in class kineticMonteCarlo.lattice.AbstractGrowthLattice
-
Outer perimeter is the sum of atoms that are not occupied and are touching an occupied one.
- getOutputAdsorptionData() - Method in class kineticMonteCarlo.kmcCore.catalysis.CatalysisKmc
-
- getOutputEvery() - Method in class basic.Parser
-
How frequently should be printed extra file of catalysis.
- getOutputFormats() - Method in class basic.Parser
-
To have the possibility to output to different file formats.
- getParent() - Method in class utils.list.AbstractList
-
- getParser() - Method in class basic.AbstractSimulation
-
- getPerimeter() - Method in class kineticMonteCarlo.kmcCore.growth.AbstractGrowthKmc
-
- getPerimeterReentrance(AbstractGrowthAtom) - Method in class kineticMonteCarlo.kmcCore.growth.RoundPerimeter
-
- getPerimeterType() - Method in class basic.Parser
-
Input "parameters" variable: perimeterType.
- getPopulationReplacement() - Method in class basic.Parser
-
- getPopulationSize() - Method in class basic.Parser
-
- getPos() - Method in class kineticMonteCarlo.atom.AbstractAtom
-
Returns the position within the unit cell, (0,0) in this case.
- getPos() - Method in class kineticMonteCarlo.atom.AgAtom
-
Returns the position within the unit cell.
- getPos() - Method in class kineticMonteCarlo.atom.BasicAtom
-
- getPos() - Method in interface kineticMonteCarlo.atom.IAtom
-
- getPos() - Method in class kineticMonteCarlo.atom.SiAtom
-
- getPos() - Method in class kineticMonteCarlo.unitCell.AgUc
-
- getPos() - Method in class kineticMonteCarlo.unitCell.CatalysisUc
-
- getPos() - Method in interface kineticMonteCarlo.unitCell.IUc
-
Cartesian position of the origin of the unit cell.
- getPos() - Method in class kineticMonteCarlo.unitCell.Simple3dUc
-
- getPos() - Method in class kineticMonteCarlo.unitCell.SimpleUc
-
- getPosI() - Method in class kineticMonteCarlo.unitCell.AgUc
-
- getPosI() - Method in class kineticMonteCarlo.unitCell.CatalysisUc
-
- getPosI() - Method in interface kineticMonteCarlo.unitCell.IUc
-
- getPosI() - Method in class kineticMonteCarlo.unitCell.Simple3dUc
-
- getPosI() - Method in class kineticMonteCarlo.unitCell.SimpleUc
-
- getPosJ() - Method in class kineticMonteCarlo.unitCell.AgUc
-
- getPosJ() - Method in class kineticMonteCarlo.unitCell.CatalysisUc
-
- getPosJ() - Method in interface kineticMonteCarlo.unitCell.IUc
-
- getPosJ() - Method in class kineticMonteCarlo.unitCell.Simple3dUc
-
- getPosJ() - Method in class kineticMonteCarlo.unitCell.SimpleUc
-
- getPrefactor(int) - Method in interface ratesLibrary.basic.IBasicRates
-
- getPrefactor(int) - Method in class ratesLibrary.basic.RatesCase
-
- getPressureCO() - Method in class basic.Parser
-
Partial pressure for CO in atm.
- getPressureO2() - Method in class basic.Parser
-
Partial pressure for O2 in atm.
- getProbabilities() - Method in class kineticMonteCarlo.atom.AbstractAtom
-
- getProbabilities() - Method in interface kineticMonteCarlo.atom.IAtom
-
- getProbability() - Method in class kineticMonteCarlo.atom.AbstractGrowthAtom
-
- getProbability(int, int) - Method in class kineticMonteCarlo.atom.AbstractGrowthAtom
-
Returns the predefined probability (from rates) to jump from origin type to target type.
- getProbability(int) - Method in class kineticMonteCarlo.atom.AbstractGrowthAtom
-
- getProbability() - Method in class kineticMonteCarlo.atom.BasicAtom
-
- getProbability(int, int) - Method in class kineticMonteCarlo.atom.CatalysisAtom
-
Dummy method.
- getProbability() - Method in interface kineticMonteCarlo.atom.IAtom
-
- getProbability() - Method in class kineticMonteCarlo.atom.SiAtom
-
- getProbArray() - Method in class kineticMonteCarlo.atom.ArrayStack
-
- getProgressPercent() - Method in class geneticAlgorithm.AbstractGeneticAlgorithm
-
- getProgressPercent() - Method in class geneticAlgorithm.evaluationFunctions.AbstractEvaluator
-
- getProgressPercent() - Method in class geneticAlgorithm.evaluationFunctions.AbstractPsdEvaluator
-
- getProgressPercent() - Method in class geneticAlgorithm.evaluationFunctions.BasicEvaluator
-
- getProgressPercent() - Method in interface geneticAlgorithm.evaluationFunctions.IEvaluation
-
- getProgressPercent() - Method in interface geneticAlgorithm.IProgressable
-
- getPsd() - Method in class basic.AbstractSimulation
-
- getPsd() - Method in class utils.psdAnalysis.PsdSignature2D
-
- getPsdExtend() - Method in class basic.Parser
-
Factor which has to be added as empty area to the surface.
- getPsdFromSimulation(SiKmc, int) - Static method in class samples.silicon.SiliconPsdDifferencesBetweenTemperatures
-
- getPsdScale() - Method in class basic.Parser
-
Factor with which has to be multiplied the size of the surface to calculate the PSD.
- getPsdScript(String, String, float, float, int, int) - Method in class basic.io.Restart
-
- getPsdSizeX() - Method in class geneticAlgorithm.evaluationFunctions.AbstractPsdEvaluator
-
- getPsdSizeY() - Method in class geneticAlgorithm.evaluationFunctions.AbstractPsdEvaluator
-
- getPureArray() - Method in class utils.akting.RichArray
-
- getPureMatrix() - Method in class utils.akting.RichMatrix
-
- getR2() - Method in class kineticMonteCarlo.lattice.CatalysisLattice
-
- getRandomDirection() - Method in class kineticMonteCarlo.lattice.Island
-
Selects a random direction for the island to move.
- getRandomIsland() - Method in class kineticMonteCarlo.kmcCore.growth.ConcertedKmc
-
- getRandomMultiAtom() - Method in class kineticMonteCarlo.kmcCore.growth.ConcertedKmc
-
- getRandomMultiAtomDirection() - Method in class kineticMonteCarlo.lattice.MultiAtom
-
Selects a random direction for the multi atom to move.
- getRandomNeighbour(byte) - Method in class kineticMonteCarlo.atom.CatalysisAtom
-
- getRandomNeighbour(byte) - Method in class kineticMonteCarlo.atom.ConcertedAtom
-
- getRandomPerimeterAtom() - Method in class kineticMonteCarlo.kmcCore.growth.RoundPerimeter
-
- getRate(double) - Method in class geneticAlgorithm.evaluationFunctions.AgBasicPsdEvaluator
-
- getRate(double) - Method in class geneticAlgorithm.evaluationFunctions.BasicGrowthPsdEvaluator
-
- getRate(byte) - Method in class kineticMonteCarlo.atom.AbstractGrowthAtom
-
- getRate(byte) - Method in class kineticMonteCarlo.lattice.Island
-
- getRate() - Method in class kineticMonteCarlo.process.AbstractProcess
-
- getRate(byte) - Method in interface kineticMonteCarlo.process.IElement
-
- getRate(int, int, double) - Method in class ratesLibrary.AbstractBasicGrowthRates
-
- getRate(int, int, double) - Method in class ratesLibrary.AgRatesFromPrbCox
-
- getRate(double, double) - Static method in class ratesLibrary.AgRatesFromPrbCox
-
Giving energy it returns a rate with a prefactor of 1e13
- getRate(int, int, double) - Method in class ratesLibrary.AgSimpleRates
-
- getRate(int, int, int) - Method in class ratesLibrary.CatalysisRates
-
- getRate(int) - Method in class ratesLibrary.CatalysisRates
-
Only for Farkas and repulsion.
- getRate(int, int, double) - Method in class ratesLibrary.concerted.AbstractConcertedRates
-
- getRate(int, double) - Method in class ratesLibrary.concerted.AbstractConcertedRates
-
Concerted version.
- getRate(int, int, double) - Method in class ratesLibrary.GrapheneGaillardOneNeighbourRates
-
- getRate(int, int, int, int, double) - Method in class ratesLibrary.GrapheneGaillardRates
-
Rate is calculated with the formulas 8, 9 and 10 of the paper.
- getRate(int, int, double) - Method in class ratesLibrary.GrapheneGaillardSimpleRates
-
- getRate(int, int, int, int, boolean, double) - Method in class ratesLibrary.GrapheneSchoenhalzRates
-
Rate is calculated with the supporting info.
- getRate(int, int, double) - Method in class ratesLibrary.GrapheneSyntheticRates
-
- getRates() - Method in class basic.AbstractSimulation
-
- getRates(double[]) - Method in class geneticAlgorithm.evaluationFunctions.AgBasicPsdEvaluator
-
Calculates rates from the genes.
- getRates(double) - Method in class ratesLibrary.AbstractBasicGrowthRates
-
- getRates(double) - Method in class ratesLibrary.AgRatesFromPrbCox
-
- getRates(double) - Method in class ratesLibrary.AgSimpleRates
-
- getRates(double) - Method in class ratesLibrary.basic.RatesCase
-
- getRates(double) - Method in class ratesLibrary.CatalysisRates
-
- getRates(double) - Method in class ratesLibrary.concerted.AbstractConcertedRates
-
- getRates(double) - Method in class ratesLibrary.GrapheneGaillardOneNeighbourRates
-
We don't use the temperature by now.
- getRates(double) - Method in class ratesLibrary.GrapheneGaillardRates
-
Does nothing
- getRates(double) - Method in class ratesLibrary.GrapheneGaillardSimpleRates
-
We don't use the temperature by now.
- getRates(double) - Method in class ratesLibrary.GrapheneSchoenhalzRates
-
Does nothing
- getRates(double) - Method in class ratesLibrary.GrapheneSyntheticRates
-
We don't use the temperature by now.
- getRates(double) - Method in interface ratesLibrary.IRates
-
- getRates(double) - Method in class ratesLibrary.SiRatesFromPreGosalvez
-
- getRates5(double[]) - Method in class geneticAlgorithm.evaluationFunctions.BasicGrowthPsdEvaluator
-
Calculates rates from the genes.
- getRates6(double[]) - Method in class geneticAlgorithm.evaluationFunctions.AgBasicPsdEvaluator
-
Calculates rates from the genes.
- getRatesFactory() - Method in class basic.AbstractSimulation
-
- getRatesLibrary() - Method in class basic.Parser
-
Selects which rates are used for the simulation.
- getReactionRate(CatalysisAtom, CatalysisAtom) - Method in class kineticMonteCarlo.kmcCore.catalysis.CatalysisFarkasKmc
-
One atom is O and the other CO, for sure.
- getReactionRate(CatalysisAtom, CatalysisAtom) - Method in class kineticMonteCarlo.kmcCore.catalysis.CatalysisKmc
-
One atom is O and the other CO, for sure.
- getReactionRates() - Method in class ratesLibrary.CatalysisRates
-
- getReactionRates(boolean) - Method in class ratesLibrary.CatalysisRates
-
Only for Farkas and repulsion.
- getReadReference() - Method in class basic.Parser
-
Chooses between to read a reference PSD or doing an initial run to be the objective for the
Evolutionary run
- getRealType() - Method in class kineticMonteCarlo.atom.AbstractAtom
-
If not overridden, returns directly the type of current atom.
- getRealType() - Method in class kineticMonteCarlo.atom.AgAtom
-
Returns the real type of the current atom.
- getRealType() - Method in class kineticMonteCarlo.atom.AgAtomSimple
-
Returns the real type of the current atom.
- getRealType() - Method in class kineticMonteCarlo.atom.ConcertedAtom
-
Defines 11 atom types,subtypes:
0 -> 0
1 -> 1
2,0 -> 2
2,1 -> 3
2,2 -> 4
3,0 -> 5
3,1 -> 6
4,0 -> 7
4,1 -> 8
4,2 -> 9
5 -> 10
6 -> 16
with some of them as detaching destination.
- getRealType() - Method in interface kineticMonteCarlo.atom.IAtom
-
- getReduced5Energies() - Method in class ratesLibrary.AbstractBasicGrowthRates
-
- getReduced5Rates(float) - Method in class ratesLibrary.AbstractBasicGrowthRates
-
Calculates rates from the genes.
- getReduced6Energies() - Method in class ratesLibrary.AgRatesFromPrbCox
-
- getReduced6Rates(float) - Method in class ratesLibrary.AgRatesFromPrbCox
-
This is tuned to work with only 6 "genes".
- getReentranceCount(int, int) - Method in class kineticMonteCarlo.lattice.perimeterStatistics.AbstractPerimeterStatistics
-
- getRemovalsSinceLastCleanup() - Method in class utils.list.AbstractList
-
- getRepeats() - Method in class geneticAlgorithm.evaluationFunctions.AbstractPsdEvaluator
-
- getRepetitions() - Method in class basic.Parser
-
Number of repetitions or evaluations that a single Gene has to do.
- getRestartFolderName() - Method in class basic.AbstractSimulation
-
- getRestrictionType() - Method in class geneticAlgorithm.restrictions.BoundedGeneRestriction
-
- getRestrictionType() - Method in class geneticAlgorithm.restrictions.FixedGeneRestriction
-
- getRestrictionType() - Method in class geneticAlgorithm.restrictions.GeneRestriction
-
- getRestrictionType() - Method in class geneticAlgorithm.restrictions.ReplicatedGeneRestriction
-
- getResultPsd() - Method in class geneticAlgorithm.evaluationFunctions.BasicGrowthPsdEvaluator.Runner
-
- getRi_DeltaI() - Method in class utils.list.LinearList
-
- getRight() - Method in class utils.list.Node
-
- getRoot() - Method in class utils.list.atoms.AvlTree
-
- getRows() - Method in class kineticMonteCarlo.lattice.perimeterStatistics.Statistics
-
- getSampledSurface(int, int) - Method in class kineticMonteCarlo.kmcCore.catalysis.CatalysisKmc
-
- getSampledSurface(int, int) - Method in class kineticMonteCarlo.kmcCore.etching.BasicKmc
-
- getSampledSurface(int, int) - Method in class kineticMonteCarlo.kmcCore.etching.SiKmc
-
- getSampledSurface(int, int) - Method in class kineticMonteCarlo.kmcCore.growth.AbstractGrowthKmc
-
- getSampledSurface(int, int) - Method in interface kineticMonteCarlo.kmcCore.IKmc
-
Returns a sampled topological measurement of the KMC surface
- getSampledSurface(int, int) - Method in class kineticMonteCarlo.kmcCore.worker.KmcWorker
-
- getScale() - Method in class graphicInterfaces.etching.mouseBehaviors.MouseZoom
-
- getScale() - Method in class graphicInterfaces.growth.KmcCanvas
-
- getSeed() - Method in class utils.edu.cornell.lassp.houle.rngPack.Ranecu
-
- getSimulatedTime() - Method in class basic.AbstractSimulation
-
- getSimulationCount() - Method in class geneticAlgorithm.evaluationFunctions.AbstractEvaluator
-
Undefined here
- getSimulationCount() - Method in class geneticAlgorithm.evaluationFunctions.AbstractPsdEvaluator
-
Undefined here
- getSimulationCount() - Method in class geneticAlgorithm.evaluationFunctions.AgBasicPsdEvaluator
-
Method thought to be called from the main interface updater.
- getSimulationCount() - Method in class geneticAlgorithm.evaluationFunctions.BasicGrowthPsdEvaluator
-
Method thought to be called from the main interface updater.
- getSimulationCount() - Method in interface geneticAlgorithm.evaluationFunctions.IEvaluation
-
- getSimulationTime() - Method in class geneticAlgorithm.Individual
-
- getSin3D(double, double, double, double, double, double) - Method in class kineticMonteCarlo.unitCell.SiUnitCell
-
- getSize() - Method in class utils.list.AbstractList
-
- getSize() - Method in class utils.list.BinnedList
-
- getSize() - Method in class utils.list.LinearList
-
- getSizeX() - Method in class graphicInterfaces.growth.KmcCanvas
-
- getSizeX() - Static method in class kineticMonteCarlo.unitCell.AgUc
-
Cartesian size of the unit cell in X axis
- getSizeX() - Static method in class kineticMonteCarlo.unitCell.CatalysisUc
-
Cartesian size of the unit cell in X axis.
- getSizeX() - Static method in interface kineticMonteCarlo.unitCell.IUc
-
Cartesian size of the unit cell in X axis
- getSizeX() - Static method in class kineticMonteCarlo.unitCell.SimpleUc
-
Cartesian size of the unit cell in X axis.
- getSizeY() - Method in class graphicInterfaces.growth.KmcCanvas
-
- getSizeY() - Static method in class kineticMonteCarlo.unitCell.AgUc
-
Cartesian size of the unit cell in Y axis
- getSizeY() - Static method in class kineticMonteCarlo.unitCell.CatalysisUc
-
Cartesian size of the unit cell in Y axis.
- getSizeY() - Static method in interface kineticMonteCarlo.unitCell.IUc
-
Cartesian size of the unit cell in Y axis
- getSizeY() - Static method in class kineticMonteCarlo.unitCell.SimpleUc
-
Cartesian size of the unit cell in Y axis.
- getSizeZ() - Static method in interface kineticMonteCarlo.unitCell.IUc
-
Cartesian size of the unit cell in Z axis
- getStatistics() - Method in class kineticMonteCarlo.lattice.perimeterStatistics.PerimeterStatisticsFactory
-
- getStatusFlags(long) - Method in class basic.EvaluatorType
-
Translates a numeric status code into a Set of StatusFlag enums
- getStatusFlags(long) - Method in class basic.io.OutputType
-
Translates a numeric status code into a Set of StatusFlag enums
- getStatusFlagValue() - Method in enum basic.EvaluatorType.evaluatorFlag
-
- getStatusFlagValue() - Method in enum basic.io.OutputType.formatFlag
-
- getStatusValue(Set<EvaluatorType.evaluatorFlag>) - Method in class basic.EvaluatorType
-
Translates a set of StatusFlag enums into a numeric status code
- getStatusValue(Set<OutputType.formatFlag>) - Method in class basic.io.OutputType
-
Translates a set of StatusFlag enums into a numeric status code
- getStopError() - Method in class basic.Parser
-
For evolutionary algorithm run mode target minimum error
- getStopError() - Method in class geneticAlgorithm.AbstractGeneticAlgorithm
-
- getSumRate(byte) - Method in class kineticMonteCarlo.atom.AbstractGrowthAtom
-
- getSumRate(byte) - Method in class kineticMonteCarlo.lattice.Island
-
- getSumRate() - Method in class kineticMonteCarlo.process.AbstractProcess
-
- getSumRate(byte) - Method in interface kineticMonteCarlo.process.IElement
-
- getSurface() - Method in class geneticAlgorithm.evaluationFunctions.AbstractEvaluator
-
- getSurface() - Method in class geneticAlgorithm.evaluationFunctions.AgBasicPsdEvaluator
-
- getSurface() - Method in class geneticAlgorithm.evaluationFunctions.BasicGrowthPsdEvaluator
-
- getSurface() - Method in interface geneticAlgorithm.evaluationFunctions.IEvaluation
-
- getSurfaceList() - Method in class kineticMonteCarlo.kmcCore.worker.KmcWorker
-
- getSurfaceType() - Method in class basic.Parser
-
- getTemperature() - Method in class basic.Parser
-
Simulation temperature.
- getTime() - Method in class kineticMonteCarlo.kmcCore.AbstractKmc
-
- getTime() - Method in interface kineticMonteCarlo.kmcCore.IKmc
-
- getTime() - Method in class kineticMonteCarlo.kmcCore.worker.KmcWorker
-
- getTime() - Method in class utils.list.AbstractList
-
- getTotalAtoms() - Method in class utils.list.AbstractList
-
- getTotalCount(int) - Method in class kineticMonteCarlo.lattice.perimeterStatistics.AbstractPerimeterStatistics
-
- getTotalCount(int) - Method in class kineticMonteCarlo.lattice.perimeterStatistics.Statistics
-
Returns the total value of analysed atoms used to do the statistics, which is stores in the last position (for every radius).
- getTotalError() - Method in class geneticAlgorithm.Individual
-
- getTotalHops() - Method in class kineticMonteCarlo.lattice.AbstractGrowthLattice
-
How many steps has been moved all the atoms.
- getTotalIterations() - Method in class basic.Parser
-
Total number of iterations that the evolutionary algorithm has to do.
- getTotalIterations() - Method in class geneticAlgorithm.AbstractGeneticAlgorithm
-
- getTotalIterations() - Method in interface geneticAlgorithm.IGeneticAlgorithm
-
- getTotalRate(byte) - Method in class utils.list.atoms.AtomsArrayList
-
- getTotalRate(byte) - Method in class utils.list.atoms.AtomsAvlTree
-
- getTotalRate(byte) - Method in interface utils.list.atoms.IAtomsCollection
-
- getTracerDistance() - Method in class kineticMonteCarlo.lattice.AbstractGrowthLattice
-
How far in average is an atom from where it was deposited.
- getTranslation() - Method in class graphicInterfaces.etching.mouseBehaviors.MouseZoom
-
- getTranslationX() - Method in class graphicInterfaces.etching.mouseBehaviors.MouseTranslate
-
- getTranslationY() - Method in class graphicInterfaces.etching.mouseBehaviors.MouseTranslate
-
- getType() - Method in class kineticMonteCarlo.atom.AbstractGrowthAtom
-
- getType() - Method in class kineticMonteCarlo.atom.BasicAtom
-
- getType() - Method in class kineticMonteCarlo.atom.CatalysisAtomAttributes
-
- getType(int, int, int) - Method in class kineticMonteCarlo.atom.GrapheneTypesTable
-
- getType() - Method in interface kineticMonteCarlo.atom.IAtom
-
- getType() - Method in class kineticMonteCarlo.atom.SiAtom
-
- getType() - Method in class kineticMonteCarlo.kmcCore.growth.RoundPerimeter
-
- getType4Subtype(BitSet) - Method in class kineticMonteCarlo.atom.ConcertedAtom
-
It is just the complementary of the edge one.
- getTypeCode(byte, BitSet) - Method in class kineticMonteCarlo.atom.ConcertedAtom
-
- getTypeWithoutNeighbour(int) - Method in class kineticMonteCarlo.atom.AbstractGrowthAtom
-
Returns the type of the neighbour atom if current one would not exist.
- getTypeWithoutNeighbour(int) - Method in class kineticMonteCarlo.atom.AgAtom
-
Returns the type of the neighbour atom if current one would not exist.
- getTypeWithoutNeighbour(int) - Method in class kineticMonteCarlo.atom.AgAtomSimple
-
Returns the type of the neighbour atom if current one would not exist.
- getTypeWithoutNeighbour(int) - Method in class kineticMonteCarlo.atom.BasicGrowthAtom
-
Returns the type of the neighbour atom if current one would not exist.
- getTypeWithoutNeighbour(int) - Method in class kineticMonteCarlo.atom.CatalysisAtom
-
Returns the type of the neighbour atom if current one would not exist.
- getTypeWithoutNeighbour(int) - Method in class kineticMonteCarlo.atom.ConcertedAtom
-
Returns the type of the neighbour atom if current one would not exist.
- getTypeWithoutNeighbour(int) - Method in class kineticMonteCarlo.atom.GrapheneAtom
-
saber que tipo de átomo sería si el vecino originPos estuviera vacío
útil para saber el tipo de átomos que serás al saltar.
- getTypeWithoutNeighbour(int) - Method in class kineticMonteCarlo.atom.GrapheneAtomGaillardSimple
-
Returns the type of the neighbour atom if current one would not exist.
- getUc(int) - Method in class kineticMonteCarlo.lattice.AbstractGrowthLattice
-
- getUc(int, int) - Method in class kineticMonteCarlo.lattice.AbstractGrowthLattice
-
- getUc(int) - Method in class kineticMonteCarlo.lattice.AbstractLattice
-
- getUc(int) - Method in class kineticMonteCarlo.lattice.AgUcLattice
-
- getUc(int, int) - Method in class kineticMonteCarlo.lattice.AgUcLattice
-
- getUc(int) - Method in class kineticMonteCarlo.lattice.BasicLattice
-
- getUc(int) - Method in class kineticMonteCarlo.lattice.SiLattice
-
- getUnitCell() - Method in class kineticMonteCarlo.lattice.SiLattice
-
- getUnitCellSize() - Method in class kineticMonteCarlo.lattice.AbstractLattice
-
- getWheight() - Method in class geneticAlgorithm.evaluationFunctions.AbstractEvaluator
-
- getWheight() - Method in interface geneticAlgorithm.evaluationFunctions.IEvaluation
-
- getWholeData() - Method in class kineticMonteCarlo.lattice.perimeterStatistics.Statistics
-
Returns the entire data matrix that is working on.
- getWorkerId() - Method in class kineticMonteCarlo.kmcCore.worker.KmcWorker
-
- getX() - Method in class java.awt.geom.Point2D.Double
-
Returns the X coordinate of this Point2D in
double precision.
- getX() - Method in class java.awt.geom.Point2D.Float
-
Returns the X coordinate of this Point2D in
double precision.
- getX() - Method in class java.awt.geom.Point2D
-
Returns the X coordinate of this Point2D in
double precision.
- getX() - Method in class javafx.geometry.Point3D
-
The x coordinate.
- getX() - Method in class kineticMonteCarlo.atom.BasicAtom
-
- getX() - Method in class kineticMonteCarlo.atom.SiAtom
-
- getXFactor() - Method in class graphicInterfaces.etching.mouseBehaviors.MouseRocking
-
- getXFactor() - Method in class graphicInterfaces.etching.mouseBehaviors.MouseRotate
-
- getY() - Method in class java.awt.geom.Point2D.Double
-
Returns the Y coordinate of this Point2D in
double precision.
- getY() - Method in class java.awt.geom.Point2D.Float
-
Returns the Y coordinate of this Point2D in
double precision.
- getY() - Method in class java.awt.geom.Point2D
-
Returns the Y coordinate of this Point2D in
double precision.
- getY() - Method in class javafx.geometry.Point3D
-
The y coordinate.
- getY() - Method in class kineticMonteCarlo.atom.BasicAtom
-
- getY() - Method in class kineticMonteCarlo.atom.SiAtom
-
- getYFactor() - Method in class graphicInterfaces.etching.mouseBehaviors.MouseRocking
-
- getYFactor() - Method in class graphicInterfaces.etching.mouseBehaviors.MouseRotate
-
- getZ() - Method in class javafx.geometry.Point3D
-
The z coordinate.
- getZ() - Method in class kineticMonteCarlo.atom.SiAtom
-
- GOLD - Static variable in class graphicInterfaces.growth.KmcCanvas
-
- goMultiplier - Variable in class basic.Parser
-
Gets O desorption rate multiplied by a factor for plotting resolution problems.
- goMultiplier - Variable in class kineticMonteCarlo.kmcCore.catalysis.CatalysisKmc
-
- goToNextRadius() - Method in class kineticMonteCarlo.kmcCore.growth.RoundPerimeter
-
Enlarge the perimeter; i.e. go to the next radius in the perimeter.
- gradientPaint_bulk - Variable in class graphicInterfaces.basic.BasicPanel
-
- gradientPaint_etched - Variable in class graphicInterfaces.basic.BasicPanel
-
- GrapheneAtom - Class in kineticMonteCarlo.atom
-
- GrapheneAtom(int, short, short, HopsPerStep) - Constructor for class kineticMonteCarlo.atom.GrapheneAtom
-
- GrapheneAtomGaillard - Class in kineticMonteCarlo.atom
-
Based on paper P.
- GrapheneAtomGaillard(int, short, short, HopsPerStep) - Constructor for class kineticMonteCarlo.atom.GrapheneAtomGaillard
-
- GrapheneAtomGaillard1Neighbour - Class in kineticMonteCarlo.atom
-
Based on paper P.
- GrapheneAtomGaillard1Neighbour(int, short, short, HopsPerStep) - Constructor for class kineticMonteCarlo.atom.GrapheneAtomGaillard1Neighbour
-
- GrapheneAtomGaillardSimple - Class in kineticMonteCarlo.atom
-
Based on paper P.
- GrapheneAtomGaillardSimple(int, short, short, HopsPerStep) - Constructor for class kineticMonteCarlo.atom.GrapheneAtomGaillardSimple
-
- GrapheneAtomSchoenhalz - Class in kineticMonteCarlo.atom
-
Based on paper P.
- GrapheneAtomSchoenhalz(int, short, short, HopsPerStep) - Constructor for class kineticMonteCarlo.atom.GrapheneAtomSchoenhalz
-
- GrapheneGaillardOneNeighbourRates - Class in ratesLibrary
-
Rates based on paper P.
- GrapheneGaillardOneNeighbourRates() - Constructor for class ratesLibrary.GrapheneGaillardOneNeighbourRates
-
- GrapheneGaillardRates - Class in ratesLibrary
-
Rates based on paper Gaillard, P., Chanier, T., Henrard, L., Moskovkin, P., & Lucas, S. (2015).
- GrapheneGaillardRates() - Constructor for class ratesLibrary.GrapheneGaillardRates
-
- GrapheneGaillardSimpleRates - Class in ratesLibrary
-
Rates based on paper P.
- GrapheneGaillardSimpleRates() - Constructor for class ratesLibrary.GrapheneGaillardSimpleRates
-
- GrapheneKmc - Class in kineticMonteCarlo.kmcCore.growth
-
- GrapheneKmc(Parser) - Constructor for class kineticMonteCarlo.kmcCore.growth.GrapheneKmc
-
- GrapheneLattice - Class in kineticMonteCarlo.lattice
-
- GrapheneLattice(int, int, ModifiedBuffer, HopsPerStep, Class<?>) - Constructor for class kineticMonteCarlo.lattice.GrapheneLattice
-
- GrapheneLatticeSimple - Class in kineticMonteCarlo.lattice
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- GrapheneLatticeSimple(int, int, ModifiedBuffer, HopsPerStep, Class<?>) - Constructor for class kineticMonteCarlo.lattice.GrapheneLatticeSimple
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- GrapheneSchoenhalzRates - Class in ratesLibrary
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Based on paper P.
- GrapheneSchoenhalzRates() - Constructor for class ratesLibrary.GrapheneSchoenhalzRates
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- GrapheneSimulation - Class in basic
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- GrapheneSimulation(Parser) - Constructor for class basic.GrapheneSimulation
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- GrapheneSyntheticRates - Class in ratesLibrary
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- GrapheneSyntheticRates() - Constructor for class ratesLibrary.GrapheneSyntheticRates
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- GrapheneTypesTable - Class in kineticMonteCarlo.atom
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- GrapheneTypesTable() - Constructor for class kineticMonteCarlo.atom.GrapheneTypesTable
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- graphicInterfaces - package graphicInterfaces
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- graphicInterfaces.basic - package graphicInterfaces.basic
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- graphicInterfaces.etching - package graphicInterfaces.etching
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- graphicInterfaces.etching.mouseBehaviors - package graphicInterfaces.etching.mouseBehaviors
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- graphicInterfaces.gaConvergence - package graphicInterfaces.gaConvergence
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- graphicInterfaces.growth - package graphicInterfaces.growth
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- graphicInterfaces.surfaceViewer2D - package graphicInterfaces.surfaceViewer2D
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- graphicInterfacesCommon.growth - package graphicInterfacesCommon.growth
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- graphicInterfacesCommon.surfaceViewer2D - package graphicInterfacesCommon.surfaceViewer2D
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- graphics - Variable in class geneticAlgorithm.AbstractGeneticAlgorithm
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- GRAY - Static variable in class graphicInterfaces.growth.KmcCanvas
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- GREEN - Static variable in class graphicInterfaces.growth.KmcCanvas
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- growCanvas - Variable in class graphicInterfaces.MainInterface
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- growPanel - Variable in class graphicInterfaces.MainInterface
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- GrowthKmcFrame - Class in graphicInterfaces.growth
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- GrowthKmcFrame(AbstractGrowthLattice, RoundPerimeter, int) - Constructor for class graphicInterfaces.growth.GrowthKmcFrame
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Creates new form frame for growth.
- GrowthKmcFrame.MenuItemHandler - Class in graphicInterfaces.growth
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- GrowthKmcFrame.Pause - Class in graphicInterfaces.growth
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- growthLayout - Variable in class graphicInterfaces.MainInterface
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- gyradius - Variable in class basic.AbstractSimulation
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