kineticMonteCarlo.atom

Class BasicGrowthAtom

java.lang.Object

kineticMonteCarlo.atom.AbstractAtom

kineticMonteCarlo.atom.AbstractGrowthAtom

kineticMonteCarlo.atom.BasicGrowthAtom

All Implemented Interfaces:

java.lang.Comparable, IAtom, IElement

Direct Known Subclasses:

BasicGrowthSimpleAtom

public class BasicGrowthAtom
extends AbstractGrowthAtom

Author:

J. Alberdi-Rodriguez

Field Summary

Fields

Modifier and Type	Field and Description
static byte	EDGE
static byte	ISLAND
static byte	KINK
private BasicGrowthAtom[]	neighbours
static byte	TERRACE
private static BasicGrowthTypesTable	TYPE_TABLE

Fields inherited from class kineticMonteCarlo.atom.AbstractAtom

ARMCHAIR_EDGE, BULK, CORNER, SICK, ZIGZAG_EDGE, ZIGZAG_WITH_EXTRA

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method and Description
boolean	areTwoTerracesTogether()
AbstractGrowthAtom	chooseRandomHop()
void	clear() Resets current atom; TERRACE type, no neighbours, no occupied, no outside and no probability.
java.util.List	getAllNeighbours()
BasicGrowthAtom	getNeighbour(int pos)
byte	getNewType(int addToNeighbour) Calculates the new atom type when adding or removing a neighbour.
int	getOrientation() For the orientation they are only available two position.
byte	getTypeWithoutNeighbour(int position) Returns the type of the neighbour atom if current one would not exist.
boolean	isEligible()
boolean	isPartOfImmobilSubstrate()
void	obtainRateFromNeighbours()
double	probJumpToNeighbour(int ignored, int position)
void	setNeighbour(AbstractGrowthAtom a, int pos)
double	updateOneBound(int pos)

Methods inherited from class kineticMonteCarlo.atom.AbstractGrowthAtom

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

TERRACE

public static final byte TERRACE

See Also:

Constant Field Values

EDGE

public static final byte EDGE

See Also:

Constant Field Values

KINK

public static final byte KINK

See Also:

Constant Field Values

ISLAND

public static final byte ISLAND

See Also:

Constant Field Values

TYPE_TABLE

private static final BasicGrowthTypesTable TYPE_TABLE

neighbours

private final BasicGrowthAtom[] neighbours

Constructor Detail

BasicGrowthAtom

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

Method Detail

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

getNeighbour

public BasicGrowthAtom getNeighbour(int pos)

Specified by:

getNeighbour in class AbstractGrowthAtom

getAllNeighbours

public java.util.List getAllNeighbours()

Specified by:

getAllNeighbours in class AbstractGrowthAtom

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

getNewType

public byte getNewType(int addToNeighbour)

Calculates the new atom type when adding or removing a neighbour.

Parameters:

addToNeighbour - variation of the number of the number of neighbours. Must be -1, 0 or 1

Returns:

new type

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

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