kineticMonteCarlo.atom

Class CatalysisAtom

java.lang.Object

kineticMonteCarlo.atom.AbstractAtom

kineticMonteCarlo.atom.AbstractGrowthAtom

kineticMonteCarlo.atom.CatalysisAtom

All Implemented Interfaces:

java.lang.Comparable, IAtom, IElement

public class CatalysisAtom
extends AbstractGrowthAtom

Author:

K. Valencia, J. Alberdi-Rodriguez

Field Summary

Fields

Modifier and Type	Field and Description
private CatalysisAtomAttributes	attributes
static byte	BR
static byte	C
static byte	CO
private int	coCusWithCoCus Current atom is CO^CUS and it has as many CO^CUS neighbours.
static byte	CUS
private boolean	eligible
private byte	latticeSite Bridge or CUS.
private CatalysisAtom[]	neighbours
static byte	O
static byte	O2
private int	occupiedNeighbours
private double[][][]	probabilities Default rates to jump from one type to the other.
private CatalysisProcess[]	processes
private static BasicGrowthTypesTable	TYPE_TABLE

Fields inherited from class kineticMonteCarlo.atom.AbstractAtom

ARMCHAIR_EDGE, BULK, CORNER, EDGE, KINK, SICK, TERRACE, ZIGZAG_EDGE, ZIGZAG_WITH_EXTRA

Constructor Summary

Constructors

Constructor and Description
CatalysisAtom(int id, short iHexa, short jHexa)

Method Summary

Modifier and Type	Method and Description
void	addCoCusNeighbours(int value)
boolean	areTwoTerracesTogether()
void	checkImmobile() Makes this atom "immobile" if it is surrounded by 4 neighbours.
AbstractGrowthAtom	chooseRandomHop()
void	cleanCoCusNeighbours()
void	clear() Resets current atom; TERRACE type, no neighbours, no occupied, no outside and no probability.
java.util.List	getAllNeighbours()
AbstractGrowthAtomAttributes	getAttributes()
int	getCoCusNeighbours()
byte	getLatticeSite()
CatalysisAtom	getNeighbour(int pos)
int	getOrientation() For the orientation they are only available two position.
double	getProbability(int originType, int targetType) Dummy method.
CatalysisAtom	getRandomNeighbour(byte process)
byte	getTypeWithoutNeighbour(int position) Returns the type of the neighbour atom if current one would not exist.
void	initialiseRates(double[][][] probabilities) Default rates to jump from one type to the other.
boolean	isEligible()
boolean	isIsolated() Tells when current atom is completely surrounded.
boolean	isPartOfImmobilSubstrate()
void	obtainRateFromNeighbours()
double	probJumpToNeighbour(int ignored, int position)
void	setAttributes(AbstractGrowthAtomAttributes attributes)
void	setNeighbour(AbstractGrowthAtom a, int pos)
void	swapAttributes(AbstractGrowthAtom a)
java.lang.String	toString()
double	updateOneBound(int pos)

Methods inherited from class kineticMonteCarlo.atom.AbstractGrowthAtom

addOccupiedNeighbour, addProbability, addRate, addToSumRate, areTwoTerracesTogetherInPerimeter, compareTo, equalRate, equals, getAngle, getBondsProbability, getBondsProbability, getCartesianPosition, getCartesianSuperCell, getDepositionPosition, getDepositionTime, getEdgeRate, getHops, getId, getiHexa, getIslandNumber, getjHexa, getMultiAtomNumber, getMultiplier, getOccupiedNeighbours, getProbability, getProbability, getRate, getSumRate, getType, hashCode, initialiseRates, isInnerPerimeter, isOnList, isOuterPerimeter, isOutside, isVisited, remove, removeMultiAtomNumber, removeMultiAtoms, resetPerimeter, resetProbability, setAngle, setBondsProbability, setBondsProbability, setCartesianPosition, setCartesianSuperCell, setDepositionPosition, setDepositionTime, setHops, setInnerPerimeter, setIslandNumber, setMultiAtomNumber, setMultiplier, setOnList, setOuterPerimeter, setOutside, setProcceses, setRate, setSumRate, setType, setVisited, updateRate

Methods inherited from class kineticMonteCarlo.atom.AbstractAtom

getNumberOfNeighbours, getPos, getProbabilities, getRealType, isOccupied, isOnList, isRemoved, setList, setNeighbour, setNumberOfNeighbours, setOccupied, setProbabilities, setRemoved, unRemove

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

CO

public static final byte CO

See Also:

Constant Field Values

O

public static final byte O

See Also:

Constant Field Values

C

public static final byte C

See Also:

Constant Field Values

O2

public static final byte O2

See Also:

Constant Field Values

BR

public static final byte BR

See Also:

Constant Field Values

CUS

public static final byte CUS

See Also:

Constant Field Values

TYPE_TABLE

private static final BasicGrowthTypesTable TYPE_TABLE

occupiedNeighbours

private int occupiedNeighbours

neighbours

private final CatalysisAtom[] neighbours

latticeSite

private final byte latticeSite

Bridge or CUS.

eligible

private boolean eligible

processes

private final CatalysisProcess[] processes

probabilities

private 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.

attributes

private CatalysisAtomAttributes attributes

coCusWithCoCus

private int coCusWithCoCus

Current atom is CO^CUS and it has as many CO^CUS neighbours.

Constructor Detail

CatalysisAtom

public CatalysisAtom(int id,
                     short iHexa,
                     short jHexa)

Method Detail

getAttributes

public AbstractGrowthAtomAttributes getAttributes()

Overrides:

getAttributes in class AbstractGrowthAtom

setAttributes

public void setAttributes(AbstractGrowthAtomAttributes attributes)

Overrides:

setAttributes in class AbstractGrowthAtom

getLatticeSite

public byte getLatticeSite()

isIsolated

public boolean isIsolated()

Tells when current atom is completely surrounded.

Overrides:

isIsolated in class AbstractGrowthAtom

Returns:

true if it has 4 occupied neighbours.

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.

getProbability

public double getProbability(int originType,
                             int targetType)

Dummy method. Just to run.

Overrides:

getProbability in class AbstractGrowthAtom

Parameters:

originType -

targetType -

Returns:

getOrientation

public int getOrientation()

For the orientation they are only available two position. Orientation is either | or _. It is assumed that current atom is of type EDGE.

Specified by:

getOrientation in class AbstractGrowthAtom

Returns:

horizontal (0) or vertical (1).

setNeighbour

public void setNeighbour(AbstractGrowthAtom a,
                         int pos)

Specified by:

setNeighbour in class AbstractGrowthAtom

getAllNeighbours

public java.util.List getAllNeighbours()

Specified by:

getAllNeighbours in class AbstractGrowthAtom

getNeighbour

public CatalysisAtom getNeighbour(int pos)

Specified by:

getNeighbour in class AbstractGrowthAtom

getRandomNeighbour

public CatalysisAtom getRandomNeighbour(byte process)

addCoCusNeighbours

public void addCoCusNeighbours(int value)

cleanCoCusNeighbours

public void cleanCoCusNeighbours()

getCoCusNeighbours

public int getCoCusNeighbours()

updateOneBound

public double updateOneBound(int pos)

Specified by:

updateOneBound in class AbstractGrowthAtom

Parameters:

pos - position of the neighbour

Returns:

change in the probability

isEligible

public boolean isEligible()

isPartOfImmobilSubstrate

public boolean isPartOfImmobilSubstrate()

Specified by:

isPartOfImmobilSubstrate in class AbstractGrowthAtom

getTypeWithoutNeighbour

public byte getTypeWithoutNeighbour(int position)

Returns the type of the neighbour atom if current one would not exist.

Specified by:

getTypeWithoutNeighbour in class AbstractGrowthAtom

Parameters:

position - position is the original one; has to be inverted.

Returns:

the type.

areTwoTerracesTogether

public boolean areTwoTerracesTogether()

Specified by:

areTwoTerracesTogether in class AbstractGrowthAtom

checkImmobile

public void checkImmobile()

Makes this atom "immobile" if it is surrounded by 4 neighbours. Thus, it will not be eligible for diffusion.

chooseRandomHop

public AbstractGrowthAtom chooseRandomHop()

Specified by:

chooseRandomHop in class AbstractGrowthAtom

obtainRateFromNeighbours

public void obtainRateFromNeighbours()

Specified by:

obtainRateFromNeighbours in class AbstractGrowthAtom

probJumpToNeighbour

public double probJumpToNeighbour(int ignored,
                                  int position)

Specified by:

probJumpToNeighbour in class AbstractGrowthAtom

clear

public void clear()

Resets current atom; TERRACE type, no neighbours, no occupied, no outside and no probability.

Specified by:

clear in interface IElement

Overrides:

clear in class AbstractGrowthAtom

swapAttributes

public void swapAttributes(AbstractGrowthAtom a)

Overrides:

swapAttributes in class AbstractGrowthAtom

toString

public java.lang.String toString()

Overrides:

toString in class AbstractGrowthAtom