kineticMonteCarlo.lattice

Class CatalysisLattice

java.lang.Object

kineticMonteCarlo.lattice.AbstractLattice

kineticMonteCarlo.lattice.AbstractGrowthLattice

kineticMonteCarlo.lattice.CatalysisLattice

All Implemented Interfaces:

IDevitaLattice

public class CatalysisLattice
extends AbstractGrowthLattice

Author:

K. Valencia, J. Alberdi-Rodriguez

Field Summary

Fields

Modifier and Type	Field and Description
private int[][]	coverage Current CO and O coverages, for sites BR, CUS.
private java.util.List<double[][]>	last1000events
private java.util.List<java.lang.Double>	last1000eventsTime
private int	MAX
private java.lang.String	ratesLibrary
(package private) java.util.ArrayList<LinearRegression>	regressions

Fields inherited from class kineticMonteCarlo.lattice.AbstractGrowthLattice

Y_RATIO

Constructor Summary

Constructors

Constructor and Description
CatalysisLattice(int hexaSizeI, int hexaSizeJ, java.lang.String ratesLibrary)

Method Summary

Modifier and Type	Method and Description
void	changeOccupationByHand(double xMouse, double yMouse, int scale) Changes the occupation of the clicked atom from unoccupied to occupied, or vice versa.
int	countIslands(java.io.PrintWriter print) There are no islands in catalysis.
private CatalysisAtom[][]	createAtoms()
private int	createId(int i, int j)
void	deposit(AbstractGrowthAtom a, boolean forceNucleation)
double	extract(AbstractGrowthAtom a) Extract the given atom from the lattice.
int	getAvailableDistance(AbstractGrowthAtom atom, int thresholdDistance)
Point2D	getCartesianLocation(int iHexa, int jHexa) Obtains the spatial location of certain atom, the distance between atoms is considered as 1 Returns the Cartesian position, given the hexagonal (lattice) location.
float	getCartSizeX()
float	getCartSizeY()
double	getCartX(int iHexa, int jHexa)
double	getCartY(int jHexa)
CatalysisAtom	getCentralAtom() Returns the atom that it is in the middle of single flake simulation.
Point2D	getCentralCartesianLocation()
float	getCoverage()
float	getCoverage(byte type)
float[]	getCoverages() Computes a partial coverage for CO and O in BR and CUS sites.
AbstractGrowthAtom	getFarSite(AbstractGrowthAtom atom, int distance)
float	getGapCoverage()
int	getiHexa(double xCart, double yCart) Knowing the X and Y Cartesian location, returns closest atom hexagonal coordinate.
int	getjHexa(double yCart) Knowing the X and Y Cartesian location, returns closest atom hexagonal coordinate.
AbstractGrowthAtom	getNeighbour(int iHexa, int jHexa, int neighbour)
double[]	getR2()
void	init()
void	initialiseRates(double[][][] probabilities) Default rates to jump from one type to the other.
boolean	isStationary(double time) Identifies stationary situation, when sufficient number of previous steps are saved and their R² is lower than 0.1 for all the species.
void	reset()
private void	updateCoCus(CatalysisAtom atom) Check whether two CO^CUS atoms are together.

Methods inherited from class kineticMonteCarlo.lattice.AbstractGrowthLattice

addAtom, addBondAtom, addOccupied, countPerimeter, getAtom, getAtom, getAtom, getAtom, getAtomTypesCounter, getAverageGyradius, getCentreOfMass, getCmDistance, getDistancesToCentre, getDistanceToCenter, getDistanceToCenter, getEmptyTypesCounter, getInnerPerimeterLenght, getIsland, getIslandCount, getIslandIterator, getMobileAtoms, getMonomerCount, getMultiAtom, getMultiAtomCount, getMultiAtomIterator, getMultiAtomsIterator, getOccupied, getOuterPerimeterLenght, getTotalHops, getTracerDistance, getUc, getUc, identifyAddMultiAtom, identifyIsland, identifyRemoveMultiAtomIsland, initialiseRates, printDistances, resetOccupied, setAngles, setAtoms, setAtomsTypesCounter, setInsideCircle, setInsideSquare, size, subtractOccupied, swapAtomsInMultiAtom, swapIsland

Methods inherited from class kineticMonteCarlo.lattice.AbstractLattice

getHexaSizeI, getHexaSizeJ, getHexaSizeK, getUnitCellSize, isPaused, setHexaSizeI, setHexaSizeJ, setHexaSizeK, setPaused, setProbabilities, setUnitCellSize

Methods inherited from class java.lang.Object

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

Field Detail

ratesLibrary

private final java.lang.String ratesLibrary

coverage

private final int[][] coverage

Current CO and O coverages, for sites BR, CUS.

last1000events

private final java.util.List<double[][]> last1000events

last1000eventsTime

private final java.util.List<java.lang.Double> last1000eventsTime

MAX

private final int MAX

regressions

java.util.ArrayList<LinearRegression> regressions

Constructor Detail

CatalysisLattice

public CatalysisLattice(int hexaSizeI,
                        int hexaSizeJ,
                        java.lang.String ratesLibrary)

Method Detail

isStationary

public boolean isStationary(double time)

Identifies stationary situation, when sufficient number of previous steps are saved and their R² is lower than 0.1 for all the species.

Parameters:

time -

Returns:

getR2

public double[] getR2()

getCentralAtom

public CatalysisAtom getCentralAtom()

Description copied from class: AbstractGrowthLattice

Returns the atom that it is in the middle of single flake simulation.

Specified by:

getCentralAtom in class AbstractGrowthLattice

Returns:

central atom.

getNeighbour

public AbstractGrowthAtom getNeighbour(int iHexa,
                                       int jHexa,
                                       int neighbour)

Specified by:

getNeighbour in class AbstractGrowthLattice

getCartSizeX

public float getCartSizeX()

Specified by:

getCartSizeX in class AbstractGrowthLattice

getCartSizeY

public float getCartSizeY()

Specified by:

getCartSizeY in class AbstractGrowthLattice

getCartX

public double getCartX(int iHexa,
                       int jHexa)

Specified by:

getCartX in class AbstractGrowthLattice

getCartY

public double getCartY(int jHexa)

Specified by:

getCartY in class AbstractGrowthLattice

getiHexa

public int getiHexa(double xCart,
                    double yCart)

Description copied from class: AbstractGrowthLattice

Knowing the X and Y Cartesian location, returns closest atom hexagonal coordinate.

Specified by:

getiHexa in class AbstractGrowthLattice

Parameters:

xCart - Cartesian X coordinate.

yCart - Cartesian Y coordinate.

Returns:

i hexagonal position.

getjHexa

public int getjHexa(double yCart)

Description copied from class: AbstractGrowthLattice

Knowing the X and Y Cartesian location, returns closest atom hexagonal coordinate.

Specified by:

getjHexa in class AbstractGrowthLattice

Parameters:

yCart - Cartesian Y coordinate.

Returns:

j hexagonal position.

getCartesianLocation

public Point2D getCartesianLocation(int iHexa,
                                    int jHexa)

Description copied from class: 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.

Specified by:

getCartesianLocation in class AbstractGrowthLattice

Parameters:

iHexa - i index in the hexagonal mesh.

jHexa - j index in the hexagonal mesh.

Returns:

spatial location in Cartesian.

getCentralCartesianLocation

public Point2D getCentralCartesianLocation()

Specified by:

getCentralCartesianLocation in class AbstractGrowthLattice

getCoverage

public float getCoverage(byte type)

getCoverages

public float[] getCoverages()

Computes a partial coverage for CO and O in BR and CUS sites.

Returns:

coverage CO^BR, CO^CUS, O^BR, CO^CUS

initialiseRates

public void initialiseRates(double[][][] probabilities)

Default rates to jump from one type to the other. For example, this matrix stores the rates to jump from terrace to edge.

Parameters:

probabilities - Default rates.

init

public void init()

deposit

public void deposit(AbstractGrowthAtom a,
                    boolean forceNucleation)

Specified by:

deposit in class AbstractGrowthLattice

extract

public double extract(AbstractGrowthAtom a)

Description copied from class: AbstractGrowthLattice

Extract the given atom from the lattice.

Specified by:

extract in class AbstractGrowthLattice

Parameters:

a - the atom to be extracted.

Returns:

probability change (positive value).

reset

public void reset()

Overrides:

reset in class AbstractGrowthLattice

getCoverage

public float getCoverage()

Overrides:

getCoverage in class AbstractGrowthLattice

Returns:

the coverage of the lattice.

getGapCoverage

public float getGapCoverage()

changeOccupationByHand

public void changeOccupationByHand(double xMouse,
                                   double yMouse,
                                   int scale)

Changes the occupation of the clicked atom from unoccupied to occupied, or vice versa. It is experimental and only works with AgUc simulation mode. If fails, the execution continues normally.

Specified by:

changeOccupationByHand in class AbstractGrowthLattice

Parameters:

xMouse - absolute X location of the pressed point

yMouse - absolute Y location of the pressed point

scale - zoom level

countIslands

public int countIslands(java.io.PrintWriter print)

There are no islands in catalysis.

Overrides:

countIslands in class AbstractGrowthLattice

Parameters:

print -

Returns:

-1

getAvailableDistance

public int getAvailableDistance(AbstractGrowthAtom atom,
                                int thresholdDistance)

getFarSite

public AbstractGrowthAtom getFarSite(AbstractGrowthAtom atom,
                                     int distance)

createId

private int createId(int i,
                     int j)

createAtoms

private CatalysisAtom[][] createAtoms()

updateCoCus

private void updateCoCus(CatalysisAtom atom)

Check whether two CO^CUS atoms are together. Only for Farkas

Parameters:

atom -