kineticMonteCarlo.kmcCore.growth

Class ActivationEnergy

java.lang.Object

kineticMonteCarlo.kmcCore.growth.ActivationEnergy

public class ActivationEnergy
extends java.lang.Object

Author:

J. Alberdi-Rodriguez

Field Summary

Fields

Modifier and Type	Field and Description
private boolean	aeOutput
private boolean	doActivationEnergyStudy
private java.lang.Double[][]	histogramPossible
private java.lang.Double[]	histogramPossibleAdsorption
private java.lang.Long[][]	histogramPossibleCounter
private java.lang.Long[][]	histogramPossibleCounterTmp
private java.lang.Double[][][]	histogramPossibleDesorption
private java.lang.Double[][][][]	histogramPossibleDiffusion CO|O, from BR|CUS to BR|CUS.
private java.lang.Double[]	histogramPossibleIsland
private java.lang.Double[]	histogramPossibleIslandTmp
private java.lang.Double[]	histogramPossibleMultiAtom
private java.lang.Double[]	histogramPossibleReactionCoCus
private java.lang.Double[][]	histogramPossibleTmp
private java.lang.Integer[][]	histogramSuccess Attribute to count processes that happened.
private int	lengthI
private int	lengthJ
private int	numberOfNeighbours
private double	previousProbability
private double[][]	rates
private java.util.ArrayList<AbstractAtom>	surface

Constructor Summary

Constructors

Constructor and Description
ActivationEnergy(Parser parser)

Method Summary

Modifier and Type	Method and Description
private java.lang.Double[][]	initDouble()
private java.lang.Double[]	initDouble1(int length)
private java.lang.Double[][][]	initDouble3()
private java.lang.Double[][][][]	initDouble4()
private java.lang.Integer[][]	initInt()
private java.lang.Long[][]	initLong()
void	printAe(java.io.PrintWriter[] print, double time)
void	printAe(java.io.PrintWriter print, float coverage)
private void	printAeLow(java.io.PrintWriter print, java.lang.String name, boolean printLineBreak, java.lang.Object[][] histogram)
void	reset()
void	setRates(double[][] rates)
void	update(java.util.ArrayList<AbstractAtom> surface)
void	updatePossibles(CatalysisLattice lattice, double elapsedTime, boolean stationary) Computes possibles for catalysis for all kind of processes
void	updatePossibles(java.util.Iterator<AbstractAtom> surface, double totalAndDepositionProbability, double elapsedTime)
void	updatePossibles(java.util.Iterator<CatalysisAtom> surface, double elapsedTime, boolean stationary) Computes possibles for catalysis.
void	updatePossiblesIslands(java.util.Iterator<Island> islands, double totalAndDepositionProbability, double elapsedTime)
void	updatePossiblesMultiAtoms(java.util.Iterator<MultiAtom> islands, double totalAndDepositionProbability, double elapsedTime)
void	updateSuccess(int oldType, int newType)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

histogramSuccess

private java.lang.Integer[][] histogramSuccess

Attribute to count processes that happened. Used to compute activation energy per each rate.

histogramPossible

private java.lang.Double[][] histogramPossible

histogramPossibleReactionCoCus

private java.lang.Double[] histogramPossibleReactionCoCus

histogramPossibleAdsorption

private java.lang.Double[] histogramPossibleAdsorption

histogramPossibleDesorption

private java.lang.Double[][][] histogramPossibleDesorption

histogramPossibleDiffusion

private java.lang.Double[][][][] histogramPossibleDiffusion

CO|O, from BR|CUS to BR|CUS. For Farkas, number of CO^C with CO^C neighbours

histogramPossibleCounter

private java.lang.Long[][] histogramPossibleCounter

histogramPossibleTmp

private java.lang.Double[][] histogramPossibleTmp

histogramPossibleCounterTmp

private java.lang.Long[][] histogramPossibleCounterTmp

histogramPossibleIsland

private java.lang.Double[] histogramPossibleIsland

histogramPossibleIslandTmp

private java.lang.Double[] histogramPossibleIslandTmp

histogramPossibleMultiAtom

private java.lang.Double[] histogramPossibleMultiAtom

surface

private final java.util.ArrayList<AbstractAtom> surface

aeOutput

private final boolean aeOutput

doActivationEnergyStudy

private boolean doActivationEnergyStudy

previousProbability

private double previousProbability

lengthI

private int lengthI

lengthJ

private int lengthJ

numberOfNeighbours

private int numberOfNeighbours

rates

private double[][] rates

Constructor Detail

ActivationEnergy

public ActivationEnergy(Parser parser)

Method Detail

setRates

public void setRates(double[][] rates)

updatePossibles

public void updatePossibles(CatalysisLattice lattice,
                            double elapsedTime,
                            boolean stationary)

Computes possibles for catalysis for all kind of processes

Parameters:

lattice -

elapsedTime -

stationary -

updatePossibles

public void updatePossibles(java.util.Iterator<CatalysisAtom> surface,
                            double elapsedTime,
                            boolean stationary)

Computes possibles for catalysis.

Parameters:

surface -

elapsedTime -

stationary -

updatePossibles

public void updatePossibles(java.util.Iterator<AbstractAtom> surface,
                            double totalAndDepositionProbability,
                            double elapsedTime)

updatePossiblesIslands

public void updatePossiblesIslands(java.util.Iterator<Island> islands,
                                   double totalAndDepositionProbability,
                                   double elapsedTime)

updatePossiblesMultiAtoms

public void updatePossiblesMultiAtoms(java.util.Iterator<MultiAtom> islands,
                                      double totalAndDepositionProbability,
                                      double elapsedTime)

updateSuccess

public void updateSuccess(int oldType,
                          int newType)

update

public void update(java.util.ArrayList<AbstractAtom> surface)

reset

public void reset()

printAe

public void printAe(java.io.PrintWriter print,
                    float coverage)

printAe

public void printAe(java.io.PrintWriter[] print,
                    double time)

printAeLow

private void printAeLow(java.io.PrintWriter print,
                        java.lang.String name,
                        boolean printLineBreak,
                        java.lang.Object[][] histogram)

initDouble1

private java.lang.Double[] initDouble1(int length)

initDouble3

private java.lang.Double[][][] initDouble3()

initDouble4

private java.lang.Double[][][][] initDouble4()

initDouble

private java.lang.Double[][] initDouble()

initLong

private java.lang.Long[][] initLong()

initInt

private java.lang.Integer[][] initInt()