CatalysisKmc (Morphokinetics)

java.lang.Object
- kineticMonteCarlo.kmcCore.AbstractKmc
- - kineticMonteCarlo.kmcCore.growth.AbstractGrowthKmc
  - - kineticMonteCarlo.kmcCore.catalysis.CatalysisKmc

All Implemented Interfaces:

IKmc

Direct Known Subclasses:

CatalysisFarkasKmc
```
public class CatalysisKmc
extends AbstractGrowthKmc
```
Author:

K. Valencia, J. Alberdi-Rodriguez

Field Summary

Fields
Modifier and Type	Field and Description
`private ActivationEnergy`	`activationEnergy`
`private java.util.ArrayList<CatalysisData>`	`adsorptionData`
`private double`	`adsorptionRateCOPerSite`
`private double`	`adsorptionRateOPerSite`
`private boolean`	`automaticCollections`
`private long[]`	`co2`
`private int`	`co2max`
`private long`	`co2prv` Previous instant co2sum.
`private long`	`co2sum`
`(package private) AtomsCollection`	`col` Stores all collections of atoms; either in a tree or an array.
`private int`	`counterSitesWith4OccupiedNeighbours`
`(package private) double[]`	`desorptionRateCOPerSite`
`private double[]`	`desorptionRateOPerSite`
`(package private) double[]`	`diffusionRateCO`
`(package private) double[]`	`diffusionRateO`
`private boolean`	`doAdsorption`
`(package private) boolean`	`doDesorption`
`(package private) boolean`	`doDiffusion`
`private boolean`	`doO2Dissociation`
`(package private) boolean`	`doPrintAllIterations`
`(package private) boolean`	`doReaction`
`private double`	`goMultiplier`
`private float`	`maxCoverage` This attribute defines which is the maximum coverage for a multi-flake simulation.
`private long`	`maxSteps`
`private int`	`numGaps`
`private boolean`	`outputAe` Activation energy output during the execution
`private boolean`	`outputAeTotal`
`private boolean`	`outputData`
`private int`	`outputEvery`
`(package private) double[]`	`reactionRateCoO`
`private Restart`	`restart`
`private long`	`simulatedSteps`
`private IAtomsCollection[]`	`sites`
`private java.lang.String`	`start`
`private boolean`	`stationary`
`private long`	`stationaryStep`
`private long[]`	`steps`
`private double[]`	`totalRate`

Constructor Summary

Constructors
Constructor and Description

CatalysisKmc(Parser parser, java.lang.String restartFolder)

Constructors
Constructor and Description
`CatalysisKmc(Parser parser, java.lang.String restartFolder)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`private void`	`changeCollection(byte process, boolean toTree)` Changes current collection from array/tree to tree/array.
`private void`	`checkSizes()` If a process is stored in a array and it is too big, change to be a tree.
`private boolean`	`depositAtom(CatalysisAtom atom)`
`private CatalysisAtom`	`depositNewAtom()`
`void`	`depositSeed()`
`private void`	`desorpAtom()`
`private void`	`diffuseAtom()` Moves an atom.
`float`	`getCoverage()` Returns the coverage of the simulation.
`float`	`getCoverage(byte type)`
`float[]`	`getCoverages()`
`private double`	`getDesorptionProbability(CatalysisAtom atom, CatalysisAtom neighbour)` Computes desorption probability.
`(package private) double`	`getDesorptionRate(CatalysisAtom atom)` Computes desorption probability.
`(package private) double`	`getDiffusionRate(CatalysisAtom atom, CatalysisAtom neighbour)`
`float`	`getGapCoverage()`
`float[][]`	`getHexagonalPeriodicSurface(int binX, int binY)`
`double[][]`	`getOutputAdsorptionData()`
`(package private) double`	`getReactionRate(CatalysisAtom atom, CatalysisAtom neighbour)` One atom is O and the other CO, for sure.
`float[][]`	`getSampledSurface(int binX, int binY)` Returns a sampled topological measurement of the KMC surface
`private void`	`initAdsorptionProbability()` Iterates over all lattice sites and initialises adsorption probabilities.
`private void`	`initCovered()` Start with fully covered surface.
`protected boolean`	`performSimulationStep()` Performs a simulation step.
`void`	`printIteration()`
`void`	`printRates()` Method to print rates.
`private void`	`reactAtom()`
`private void`	`recomputeAdsorptionProbability(CatalysisAtom atom)`
`private void`	`recomputeCollection(byte process, CatalysisAtom atom, double oldRate)`
`private void`	`recomputeDesorptionProbability(CatalysisAtom atom)`
`private void`	`recomputeDiffusionProbability(CatalysisAtom atom)`
`private void`	`recomputeReactionProbability(CatalysisAtom atom)`
`void`	`reset()` Resets the lattice and the list of atoms.
`void`	`setRates(CatalysisRates rates)`
`int`	`simulate()` Does the actual simulation.
`private void`	`updateRateFromList(byte process)`
`private void`	`updateRates(CatalysisAtom atom)` Updates total adsorption, desorption, reaction and diffusion probabilities.

Methods inherited from class kineticMonteCarlo.kmcCore.growth.AbstractGrowthKmc
getAccelerator, getCurrentRadius, getLattice, getModifiedBuffer, getPerimeter, initialiseRates, isJustCentralFlake, setAccelerator, setArea, setDepositionRate, setLattice, setPerimeter, setTerraceToTerraceProbability

Methods inherited from class kineticMonteCarlo.kmcCore.AbstractKmc
getIterations, getList, getTime, setIterations, setLattice, simulate, simulate

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - outputData
```
private final boolean outputData
```
  - simulatedSteps
```
private long simulatedSteps
```
  - steps
```
private long[] steps
```
  - co2
```
private long[] co2
```
  - co2sum
```
private long co2sum
```
  - co2prv
```
private long co2prv
```
    Previous instant co2sum. For output
  - co2max
```
private final int co2max
```
  - maxSteps
```
private final long maxSteps
```
  - outputEvery
```
private int outputEvery
```
  - adsorptionData
```
private java.util.ArrayList<CatalysisData> adsorptionData
```
  - adsorptionRateCOPerSite
```
private double adsorptionRateCOPerSite
```
  - adsorptionRateOPerSite
```
private double adsorptionRateOPerSite
```
  - desorptionRateCOPerSite
```
double[] desorptionRateCOPerSite
```
  - desorptionRateOPerSite
```
private double[] desorptionRateOPerSite
```
  - reactionRateCoO
```
double[] reactionRateCoO
```
  - diffusionRateCO
```
double[] diffusionRateCO
```
  - diffusionRateO
```
double[] diffusionRateO
```
  - totalRate
```
private double[] totalRate
```
  - sites
```
private final IAtomsCollection[] sites
```
  - maxCoverage
```
private final float maxCoverage
```
    This attribute defines which is the maximum coverage for a multi-flake simulation.
  - doAdsorption
```
private final boolean doAdsorption
```
  - doDesorption
```
final boolean doDesorption
```
  - doReaction
```
final boolean doReaction
```
  - doDiffusion
```
final boolean doDiffusion
```
  - doPrintAllIterations
```
final boolean doPrintAllIterations
```
  - doO2Dissociation
```
private final boolean doO2Dissociation
```
  - start
```
private final java.lang.String start
```
  - restart
```
private final Restart restart
```
  - activationEnergy
```
private final ActivationEnergy activationEnergy
```
  - outputAe
```
private final boolean outputAe
```
    Activation energy output during the execution
  - outputAeTotal
```
private final boolean outputAeTotal
```
  - numGaps
```
private int numGaps
```
  - counterSitesWith4OccupiedNeighbours
```
private int counterSitesWith4OccupiedNeighbours
```
  - stationary
```
private boolean stationary
```
  - stationaryStep
```
private long stationaryStep
```
  - col
```
AtomsCollection col
```
    Stores all collections of atoms; either in a tree or an array.
  - automaticCollections
```
private final boolean automaticCollections
```
  - goMultiplier
```
private final double goMultiplier
```
- Constructor Detail
  - CatalysisKmc
```
public CatalysisKmc(Parser parser,
                    java.lang.String restartFolder)
```
- Method Detail
  - getHexagonalPeriodicSurface
```
public float[][] getHexagonalPeriodicSurface(int binX,
                                             int binY)
```
    Specified by:
    
    getHexagonalPeriodicSurface in interface IKmc
    
    Overrides:
    
    getHexagonalPeriodicSurface in class AbstractGrowthKmc
  - getSampledSurface
```
public float[][] getSampledSurface(int binX,
                                   int binY)
```
    Description copied from interface: IKmc
    
    Returns a sampled topological measurement of the KMC surface
    
    Specified by:
    
    getSampledSurface in interface IKmc
    
    Overrides:
    
    getSampledSurface in class AbstractGrowthKmc
    
    Returns:
    
    calculated surface
  - setRates
```
public void setRates(CatalysisRates rates)
```
  - getOutputAdsorptionData
```
public double[][] getOutputAdsorptionData()
```
  - getCoverage
```
public float getCoverage(byte type)
```
  - getCoverage
```
public float getCoverage()
```
    Description copied from class: AbstractGrowthKmc
    
    Returns the coverage of the simulation. Thus, the number of occupied locations divided by the total number of locations.
    
    Overrides:
    
    getCoverage in class AbstractGrowthKmc
    
    Returns:
    
    A value between 0 and 1.
  - getCoverages
```
public float[] getCoverages()
```
  - getGapCoverage
```
public float getGapCoverage()
```
  - performSimulationStep
```
protected boolean performSimulationStep()
```
    Performs a simulation step.
    
    Overrides:
    
    performSimulationStep in class AbstractGrowthKmc
    
    Returns:
    
    true if a stop condition happened (all atom etched, all surface covered).
  - simulate
```
public int simulate()
```
    Description copied from class: AbstractKmc
    
    Does the actual simulation. It has to be called after reset() and depositSeed().
    
    Specified by:
    
    simulate in interface IKmc
    
    Overrides:
    
    simulate in class AbstractGrowthKmc
    
    Returns:
    
    number of iterations that simulation took
  - depositSeed
```
public void depositSeed()
```
    Specified by:
    
    depositSeed in interface IKmc
    
    Overrides:
    
    depositSeed in class AbstractGrowthKmc
  - reset
```
public void reset()
```
    Description copied from class: AbstractKmc
    
    Resets the lattice and the list of atoms. This method has to be called just before depositSeed() and simulate().
    
    Specified by:
    
    reset in interface IKmc
    
    Overrides:
    
    reset in class AbstractGrowthKmc
  - depositAtom
```
private boolean depositAtom(CatalysisAtom atom)
```
  - depositNewAtom
```
private CatalysisAtom depositNewAtom()
```
  - desorpAtom
```
private void desorpAtom()
```
  - reactAtom
```
private void reactAtom()
```
  - diffuseAtom
```
private void diffuseAtom()
```
    Moves an atom.
  - initAdsorptionProbability
```
private void initAdsorptionProbability()
```
    Iterates over all lattice sites and initialises adsorption probabilities.
  - initCovered
```
private void initCovered()
```
    Start with fully covered surface.
    
    Parameters:
    
    randomTypes - if true, CO and O types randomly chosen. If false, only oxygen.
  - updateRates
```
private void updateRates(CatalysisAtom atom)
```
    Updates total adsorption, desorption, reaction and diffusion probabilities.
    
    Parameters:
    
    atom -
  - recomputeAdsorptionProbability
```
private void recomputeAdsorptionProbability(CatalysisAtom atom)
```
  - recomputeDesorptionProbability
```
private void recomputeDesorptionProbability(CatalysisAtom atom)
```
  - recomputeReactionProbability
```
private void recomputeReactionProbability(CatalysisAtom atom)
```
  - recomputeDiffusionProbability
```
private void recomputeDiffusionProbability(CatalysisAtom atom)
```
  - recomputeCollection
```
private void recomputeCollection(byte process,
                                 CatalysisAtom atom,
                                 double oldRate)
```
  - getDesorptionRate
```
double getDesorptionRate(CatalysisAtom atom)
```
    Computes desorption probability.
    
    Parameters:
    
    atom - CO molecule.
    
    Returns:
  - getDesorptionProbability
```
private double getDesorptionProbability(CatalysisAtom atom,
                                        CatalysisAtom neighbour)
```
    Computes desorption probability.
    
    Parameters:
    
    atom - O atom.
    
    neighbour - O atom.
    
    Returns:
  - getReactionRate
```
double getReactionRate(CatalysisAtom atom,
                       CatalysisAtom neighbour)
```
    One atom is O and the other CO, for sure.
    
    Parameters:
    
    atom -
    
    neighbour -
    
    Returns:
  - getDiffusionRate
```
double getDiffusionRate(CatalysisAtom atom,
                        CatalysisAtom neighbour)
```
  - updateRateFromList
```
private void updateRateFromList(byte process)
```
  - checkSizes
```
private void checkSizes()
```
    If a process is stored in a array and it is too big, change to be a tree. If a tree is too small, change it to be an array.
  - changeCollection
```
private void changeCollection(byte process,
                              boolean toTree)
```
    Changes current collection from array/tree to tree/array.
    
    Parameters:
    
    process - ADSORPTION, DESORPTION, REACTION, DIFFUSION.
    
    toTree - if true from array to tree, otherwise from tree to array.
  - printRates
```
public void printRates()
```
    Method to print rates. Equivalent to table 1 of Temel et al. J. Chem. Phys. 126 (2007).
  - printIteration
```
public void printIteration()
```

Class CatalysisKmc

Field Summary

Constructor Summary

Method Summary

Methods inherited from class kineticMonteCarlo.kmcCore.growth.AbstractGrowthKmc

Methods inherited from class kineticMonteCarlo.kmcCore.AbstractKmc

Methods inherited from class java.lang.Object

Field Detail

outputData

simulatedSteps

steps

co2

co2sum

co2prv

co2max

maxSteps

outputEvery

adsorptionData

adsorptionRateCOPerSite

adsorptionRateOPerSite

desorptionRateCOPerSite

desorptionRateOPerSite

reactionRateCoO

diffusionRateCO

diffusionRateO

totalRate

sites

maxCoverage

doAdsorption

doDesorption

doReaction

doDiffusion

doPrintAllIterations

doO2Dissociation

start

restart

activationEnergy

outputAe

outputAeTotal

numGaps

counterSitesWith4OccupiedNeighbours

stationary

stationaryStep

col

automaticCollections

goMultiplier

Constructor Detail

CatalysisKmc

Method Detail

getHexagonalPeriodicSurface

getSampledSurface

setRates

getOutputAdsorptionData

getCoverage

getCoverage

getCoverages

getGapCoverage

performSimulationStep

simulate

depositSeed

reset

depositAtom

depositNewAtom

desorpAtom

reactAtom

diffuseAtom

initAdsorptionProbability

initCovered

updateRates

recomputeAdsorptionProbability

recomputeDesorptionProbability

recomputeReactionProbability

recomputeDiffusionProbability

recomputeCollection

getDesorptionRate

getDesorptionProbability

getReactionRate

getDiffusionRate

updateRateFromList

checkSizes