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

P

P - Variable in class ratesLibrary.AgRatesFromPrbCox

p - Static variable in class samples.agAgGrowth.SimpleAgAgGrowthKmcSimulation

p - Static variable in class samples.grapheneCvdGrowth.SimpleGrapheneKmcSimulation

p - Variable in class utils.printByHandHelper

paint(Graphics) - Method in class graphicInterfaces.gaConvergence.ErrorPanel

paint(Graphics) - Method in class graphicInterfaces.growth.KmcCanvas

paintCanvas() - Method in class graphicInterfaces.MainInterface

paintCatalysis(Graphics) - Method in class graphicInterfaces.growth.KmcCanvas

paintComponent(Graphics) - Method in class graphicInterfaces.basic.BasicPanel

paintComponent(Graphics) - Method in class graphicInterfaces.surfaceViewer2D.Panel2D

PaintLoop() - Constructor for class basic.AbstractGrowthSimulation.PaintLoop

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

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

paintLoop() - Constructor for class utils.printByHandHelper.paintLoop

panel - Variable in class graphicInterfaces.gaConvergence.GaProgressFrame

panel - Variable in class graphicInterfaces.gaConvergence.GaProgressPanel

panel - Variable in class graphicInterfaces.growth.GrowthKmcFrame

Panel2D - Class in graphicInterfaces.surfaceViewer2D

Panel2D() - Constructor for class graphicInterfaces.surfaceViewer2D.Panel2D

panelMousePressed(MouseEvent) - Method in class graphicInterfaces.growth.GrowthKmcFrame

panelMouseReleased(MouseEvent) - Method in class graphicInterfaces.growth.GrowthKmcFrame

panelMouseWheelMoved(MouseWheelEvent) - Method in class graphicInterfaces.growth.GrowthKmcFrame

parallelEvaluator - Variable in class basic.Parser

Can be serial or threaded.

parent - Variable in class utils.list.AbstractList

parser - Variable in class basic.AbstractSimulation

Parser - Class in basic

This class will read an input file called "parameters" with all the parameters for the execution.

Parser() - Constructor for class basic.Parser

Constructor

parser - Variable in class geneticAlgorithm.AbstractGeneticAlgorithm

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

Pause() - Constructor for class graphicInterfaces.growth.GrowthKmcFrame.Pause

pauseButton - Variable in class graphicInterfaces.growth.GrowthKmcFrame

paused - Variable in class graphicInterfaces.growth.GrowthKmcFrame

paused - Variable in class graphicInterfaces.growth.KmcCanvas

paused - Variable in class kineticMonteCarlo.lattice.AbstractLattice

pauseIcon - Variable in class graphicInterfaces.growth.GrowthKmcFrame

pc - Variable in class geneticAlgorithm.recombination.DifferentialRecombination

P_c of sigma.

PcConfigurator - Class in main

PcConfigurator() - Constructor for class main.PcConfigurator

Pd - Variable in class ratesLibrary.AgRatesFromPrbCox

performConvergence() - Method in class samples.convergences.siEtching.SiEtchingKmcConvergence

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

Public drawing method, call this from your game loop for update image.

performDrawToImage(String) - Method in class graphicInterfaces.growth.KmcCanvas

This method prints the current canvas to a file.

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

This method prints the current canvas to a file.

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

This method prints the current canvas to a file.

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

Does the actual writing.

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

This method does the printing of the current canvas to a file.

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

This method prints the current canvas to a file

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

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

Performs a simulation step.

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

Performs a simulation step.

performSimulationStep() - Method in class kineticMonteCarlo.kmcCore.etching.BasicKmc

performSimulationStep() - Method in class kineticMonteCarlo.kmcCore.etching.SiKmc

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

Performs a simulation step.

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

Performs a simulation step.

perimeter - Variable in class graphicInterfaces.growth.KmcCanvas

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

perimeterMi - Variable in class graphicInterfaces.growth.GrowthKmcFrame

perimeterMustBeEnlarged(AbstractGrowthAtom) - Method in class kineticMonteCarlo.kmcCore.growth.AbstractGrowthKmc

perimeterStatistics - Variable in class kineticMonteCarlo.kmcCore.growth.RoundPerimeter

PerimeterStatistics - Class in kineticMonteCarlo.lattice.perimeterStatistics

PerimeterStatistics(Statistics, Statistics) - Constructor for class kineticMonteCarlo.lattice.perimeterStatistics.PerimeterStatistics

perimeterStatistics - Variable in class kineticMonteCarlo.lattice.perimeterStatistics.PerimeterStatisticsFactory

PerimeterStatisticsFactory - Class in kineticMonteCarlo.lattice.perimeterStatistics

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

perimeterType - Variable in class basic.Parser

See Parser.getPerimeterType().

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

periodicSingleFlake - Variable in class basic.Parser

See Parser.isPeriodicSingleFlake().

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

planeSurface(float[][]) - Static method in class utils.MathUtils

pngLastTmpFile - Variable in class graphicInterfaces.growth.GrowthKmcFrame

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

pngSave(String) - Method in class graphicInterfaces.growth.GrowthKmcFrame

pngSaveButton - Variable in class graphicInterfaces.growth.GrowthKmcFrame

Point2D - Class in java.awt.geom

The Point2D class defines a point representing a location in (x,y) coordinate space.

Point2D() - Constructor for class java.awt.geom.Point2D

This is an abstract class that cannot be instantiated directly.

Point2D.Double - Class in java.awt.geom

The Double class defines a point specified in double precision.

Point2D.Float - Class in java.awt.geom

The Float class defines a point specified in float precision.

Point3D - Class in javafx.geometry

A 3D geometric point that usually represents the x, y, z coordinates.

Point3D(double, double, double) - Constructor for class javafx.geometry.Point3D

Creates a new instance of Point3D.

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

Does nothing.

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

It goes through all nodes and recomputes sum of the rates.

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

populateAtom(Node) - Method in class utils.list.atoms.AtomsAvlTree

Populates tree with the sum of child rates to current node.

population - Variable in class geneticAlgorithm.AbstractGeneticAlgorithm

Population - Class in geneticAlgorithm

This class just model a Genetic Algorithm population, it can be the main population or an offspring

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

Population(int) - Constructor for class geneticAlgorithm.Population

populationReplacement - Variable in class basic.Parser

populationReplacements - Variable in class geneticAlgorithm.AbstractGeneticAlgorithm

populationSize - Variable in class basic.Parser

populationSize - Variable in class geneticAlgorithm.AbstractGeneticAlgorithm

pos - Variable in class kineticMonteCarlo.atom.AgAtom

Position within unit cell.

posI - Variable in class kineticMonteCarlo.unitCell.AgUc

posI - Variable in class kineticMonteCarlo.unitCell.CatalysisUc

posI - Variable in class kineticMonteCarlo.unitCell.Simple3dUc

posI - Variable in class kineticMonteCarlo.unitCell.SimpleUc

posJ - Variable in class kineticMonteCarlo.unitCell.AgUc

posJ - Variable in class kineticMonteCarlo.unitCell.CatalysisUc

posJ - Variable in class kineticMonteCarlo.unitCell.Simple3dUc

posJ - Variable in class kineticMonteCarlo.unitCell.SimpleUc

posK - Variable in class kineticMonteCarlo.unitCell.Simple3dUc

postRender() - Method in class graphicInterfaces.etching.Canvas3DOverlay

postRenderActions(Graphics2D) - Method in class graphicInterfaces.etching.Canvas3DOverlay

posX - Variable in class kineticMonteCarlo.unitCell.CatalysisUc

posX - Variable in class kineticMonteCarlo.unitCell.Simple3dUc

posX - Variable in class kineticMonteCarlo.unitCell.SimpleUc

posY - Variable in class kineticMonteCarlo.unitCell.CatalysisUc

posY - Variable in class kineticMonteCarlo.unitCell.Simple3dUc

posY - Variable in class kineticMonteCarlo.unitCell.SimpleUc

posZ - Variable in class kineticMonteCarlo.unitCell.Simple3dUc

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

powlaw(double, double) - Method in class utils.edu.cornell.lassp.houle.rngPack.RandomElement

generate a power-law distribution with exponent alpha and lower cutoff cut

PowOperation - Class in utils.akting.operations

PowOperation(double) - Constructor for class utils.akting.operations.PowOperation

predict(double) - Method in class utils.LinearRegression

Returns the expected response y given the value of the predictor variable x.

prefactor - Variable in class ratesLibrary.AbstractBasicGrowthRates

prefactor - Variable in class ratesLibrary.AgSimpleRates

prefactor - Variable in class ratesLibrary.CatalysisRates

prefactor - Variable in class ratesLibrary.concerted.AbstractConcertedRates

prefactor - Variable in class ratesLibrary.GrapheneGaillardOneNeighbourRates

prefactor - Variable in class ratesLibrary.GrapheneGaillardRates

prefactor - Variable in class ratesLibrary.GrapheneGaillardSimpleRates

prefactor - Variable in class ratesLibrary.GrapheneSchoenhalzRates

prefactor - Variable in class ratesLibrary.GrapheneSyntheticRates

prefactors - Variable in class ratesLibrary.AgRatesFromPrbCox

prefactors - Variable in class ratesLibrary.basic.RatesCase

prefactors - Variable in class ratesLibrary.SiRatesFromPreGosalvez

pressureCO - Variable in class basic.Parser

See Parser.getPressureO2() and Parser.getPressureCO().

pressureO2 - Variable in class basic.Parser

pressures - Variable in class ratesLibrary.CatalysisRates

Partial pressures in Pascal (Pa).

previous() - Method in class utils.list.BinnedListIterator

previousIndex() - Method in class utils.list.BinnedListIterator

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

previousTime - Variable in class basic.io.Restart

print() - Method in class basic.Parser

Prints all the parameters; either read from "parameter" file or the default value.

print(String) - Method in class geneticAlgorithm.Population

Prints to the standard output the current individuals, one line per individual with all its genes.

printAe(PrintWriter, float) - Method in class kineticMonteCarlo.kmcCore.growth.ActivationEnergy

printAe(PrintWriter[], double) - Method in class kineticMonteCarlo.kmcCore.growth.ActivationEnergy

printAeLow(PrintWriter, String, boolean, Object[][]) - Method in class kineticMonteCarlo.kmcCore.growth.ActivationEnergy

printAllIterations - Variable in class basic.Parser

See Parser.doPrintAllIterations()

printAvgToFile() - Method in class utils.psdAnalysis.PsdSignature2D

printByHand - Class in main

printByHand() - Constructor for class main.printByHand

printByHandHelper - Class in utils

printByHandHelper() - Constructor for class utils.printByHandHelper

printByHandHelper.paintLoop - Class in utils

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

printData(Integer) - Method in class kineticMonteCarlo.kmcCore.growth.AbstractGrowthKmc

Print current information to extra file.

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

Print current information to extra file.

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

printEnd() - Static method in class main.Morphokinetics

printFooter() - Method in class basic.AbstractSimulation

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

printHeader() - Static method in class basic.AbstractSimulation

printHeader(String) - Static method in class basic.AbstractSimulation

printId - Variable in class graphicInterfaces.growth.KmcCanvas

printIntermediatePngFiles - Variable in class basic.AbstractGrowthSimulation

printIslandCentres - Variable in class graphicInterfaces.growth.KmcCanvas

printIslandNumber - Variable in class graphicInterfaces.growth.KmcCanvas

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

printLattice() - Method in class kineticMonteCarlo.kmcCore.growth.AgUcKmc

printMultiAtom - Variable in class graphicInterfaces.growth.KmcCanvas

printOutput() - Method in class basic.AbstractSimulation

printPerimeter - Variable in class graphicInterfaces.growth.KmcCanvas

printRates(Parser) - Method in class basic.AbstractGrowthSimulation

printRates(Parser) - Method in class basic.AbstractSimulation

printRates(Parser) - Method in class basic.CatalysisSimulation

printRates(Parser) - Method in class basic.ConcertedSimulation

printRates(Parser) - Method in class basic.SiSimulation

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

Method to print rates.

printResult(Parser, IGeneticAlgorithm) - Static method in class main.Morphokinetics

printResult(IGeneticAlgorithm) - Static method in class samples.convergences.agAgGrowth.AgAgKmcConvergence

printResult(IGeneticAlgorithm) - Static method in class samples.convergences.agAgGrowth.AgAgKmcConvergenceDcmaEs

printResult(IGeneticAlgorithm) - Method in class samples.convergences.siEtching.SiEtchingKmcConvergence

printToImage(int) - Method in class basic.AbstractGrowthSimulation

Prints the current frame to a file.

printToImage(String, int) - Method in class basic.AbstractGrowthSimulation

Prints the current frame to a file.

printToImage(int) - Method in class basic.AbstractSimulation

Does nothing.

printToImage(String, int) - Method in class basic.AbstractSimulation

Does nothing.

printToImage - Variable in class basic.Parser

See Parser.printToImage().

printToImage() - Method in class basic.Parser

Selects to print the simulated system (the canvas of the frame) to a PNG file.

printToImage(int) - Method in class graphicInterfaces.growth.GrowthKmcFrame

Prints the current canvas to a png image in folder $PWD/results

printToImage(String, int) - Method in class graphicInterfaces.growth.GrowthKmcFrame

Prints the current canvas to a png image in folder $PWD/folder/results

printToImage(int) - Method in class graphicInterfaces.MainInterface

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

This method prints the current canvas to a file.

printToImage(String, int) - Method in class graphicInterfaces.surfaceViewer2D.Frame2D

This method prints the current canvas to a file.

printToImage(int) - Method in interface graphicInterfacesCommon.growth.IGrowthKmcFrame

printToImage(String, int) - Method in interface graphicInterfacesCommon.growth.IGrowthKmcFrame

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

This method prints the current canvas to a file.

printToImage(String, int) - Method in interface graphicInterfacesCommon.surfaceViewer2D.IFrame2D

This method prints the current canvas to a file.

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

probabilities - Variable in class kineticMonteCarlo.atom.AbstractAtom

probabilities - Variable in class kineticMonteCarlo.atom.AbstractGrowthAtom

Default rates to jump from one type to the other.

probabilities - Variable in class kineticMonteCarlo.atom.CatalysisAtom

Default rates to jump from one type to the other.

probability - Variable in class kineticMonteCarlo.atom.AbstractGrowthAtom

Should be the sum of neighbour probabilities.

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

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

probJumpToNeighbour(int, int) - Method in class kineticMonteCarlo.atom.AgAtomSimple

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

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

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

Probability to jump to given neighbour position.

probJumpToNeighbour(int, int) - Method in class kineticMonteCarlo.atom.GrapheneAtomGaillard

Probability to jump to given neighbour position.

probJumpToNeighbour(int, int) - Method in class kineticMonteCarlo.atom.GrapheneAtomGaillardSimple

probJumpToNeighbour(int, int) - Method in class kineticMonteCarlo.atom.GrapheneAtomSchoenhalz

Probability to jump to given neighbour position.

process - Variable in class kineticMonteCarlo.lattice.MultiAtom

process - Variable in class utils.list.atoms.AtomsArrayList

The "movements" that atom can do.

process - Variable in class utils.list.atoms.AtomsAvlTree

Adsorption, desorption, reaction or diffusion.

process - Variable in class utils.list.atoms.AvlTree.Itr

processes - Variable in class kineticMonteCarlo.atom.AbstractGrowthAtom

Different processes that atom can do.

processes - Variable in class kineticMonteCarlo.atom.CatalysisAtom

processes - Variable in class kineticMonteCarlo.atom.ConcertedAtom

processStimulus(Enumeration) - Method in class graphicInterfaces.etching.mouseBehaviors.MouseRocking

processStimulus(Enumeration) - Method in class graphicInterfaces.etching.mouseBehaviors.MouseRotate

processStimulus(Enumeration) - Method in class graphicInterfaces.etching.mouseBehaviors.MouseTranslate

processStimulus(Enumeration) - Method in class graphicInterfaces.etching.mouseBehaviors.MouseZoom

progressBar - Variable in class graphicInterfaces.growth.GrowthKmcFrame

progressPercent - Variable in class geneticAlgorithm.evaluationFunctions.BasicEvaluator

ProgressUpdater() - Constructor for class graphicInterfaces.gaConvergence.GaProgressFrame.ProgressUpdater

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

psd - Variable in class basic.AbstractSimulation

psd - Variable in class basic.Parser

See Parser.doPsd().

psd - Variable in class geneticAlgorithm.evaluationFunctions.AbstractPsdEvaluator

psd - Variable in class geneticAlgorithm.evaluationFunctions.AgBasicPsdEvaluator

psd - Variable in class geneticAlgorithm.evaluationFunctions.BasicGrowthPsdEvaluator

psd - Variable in class geneticAlgorithm.evaluationFunctions.SiBasicPsdEvaluator

psd - Variable in class graphicInterfaces.surfaceViewer2D.Panel2D

psd - Variable in class utils.psdAnalysis.PsdSignature2D

psdExtend - Variable in class basic.Parser

See Parser.getPsdExtend().

psdFromSurfaces(Parser) - Static method in class main.Morphokinetics

PsdFromSurfaces - Class in main

It does a PSD from a input binary mko file with format X Y value.

PsdFromSurfaces(Parser) - Constructor for class main.PsdFromSurfaces

psds - Variable in class geneticAlgorithm.evaluationFunctions.MultithreadedPsdEvaluator

psdScale - Variable in class basic.Parser

See Parser.getPsdScale().

PsdSignature2D - Class in utils.psdAnalysis

Every surface is associated with a 2D map where each location represents a harmonic frequency and the associated/displayed value represents the squared sum of the real and imaginary amplitudes for that harmonic component (i.e., the power for that frequency).

PsdSignature2D(int, int, double) - Constructor for class utils.psdAnalysis.PsdSignature2D

psdSizeX - Variable in class geneticAlgorithm.evaluationFunctions.AbstractPsdEvaluator

psdSizeX - Variable in class utils.psdAnalysis.PsdSignature2D

psdSizeY - Variable in class geneticAlgorithm.evaluationFunctions.AbstractPsdEvaluator

psdSizeY - Variable in class utils.psdAnalysis.PsdSignature2D

psdSymmetry - Variable in class basic.Parser

See Parser.isPsdSymmetric().

psdTmp - Variable in class utils.psdAnalysis.PsdSignature2D

psdVector - Variable in class utils.psdAnalysis.PsdSignature2D

pSigma - Variable in class geneticAlgorithm.recombination.DifferentialRecombination

P of sigma.

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