kineticMonteCarlo.atom

Class GrapheneAtomGaillardSimple

java.lang.Object

kineticMonteCarlo.atom.AbstractAtom

kineticMonteCarlo.atom.AbstractGrowthAtom

kineticMonteCarlo.atom.GrapheneAtom

kineticMonteCarlo.atom.GrapheneAtomGaillardSimple

All Implemented Interfaces:

java.lang.Comparable, IAtom, IElement

public class GrapheneAtomGaillardSimple
extends GrapheneAtom

Based on paper P. Gaillard, T. Chanier, L. Henrard, P. Moskovkin, S. Lucas. Surface Science, Volumes 637–638, July–August 2015, Pages 11-18, http://dx.doi.org/10.1016/j.susc.2015.02.014.

Author:

J. Alberdi-Rodriguez

Field Summary

Fields

Modifier and Type	Field and Description
static byte	NEIGH0
static byte	NEIGH1
static byte	NEIGH2
static byte	NEIGH3

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
GrapheneAtomGaillardSimple(int id, short iHexa, short jHexa, HopsPerStep distancePerStep)

Method Summary

Modifier and Type	Method and Description
byte	getNewType(int neighbourPosition, int addOrRemove) Calculates the new atom type when adding or removing a neighbour.
byte	getTypeWithoutNeighbour(int position) Returns the type of the neighbour atom if current one would not exist.
boolean	isEligible() Only BULK atom types are considered immobile atoms.
double	probJumpToNeighbour(int ignored, int position) Probability to jump to given neighbour position.

Methods inherited from class kineticMonteCarlo.atom.GrapheneAtom

areTwoTerracesTogether, chooseRandomHop, clear, getAllNeighbours, getDistancePerStep, getN1, getN2, getN3, getNeighbour, getNeighbourCount, getOrientation, isPartOfImmobilSubstrate, obtainRateFromNeighbours, setN1, setNeighbour, setNeighbours, updateOneBound

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

NEIGH0

public static final byte NEIGH0

See Also:

Constant Field Values

NEIGH1

public static final byte NEIGH1

See Also:

Constant Field Values

NEIGH2

public static final byte NEIGH2

See Also:

Constant Field Values

NEIGH3

public static final byte NEIGH3

See Also:

Constant Field Values

Constructor Detail

GrapheneAtomGaillardSimple

public GrapheneAtomGaillardSimple(int id,
                                  short iHexa,
                                  short jHexa,
                                  HopsPerStep distancePerStep)

Method Detail

isEligible

public boolean isEligible()

Only BULK atom types are considered immobile atoms. From page 15 of the paper.

Specified by:

isEligible in interface IAtom

Overrides:

isEligible in class GrapheneAtom

Returns:

true if current atom can be moved, false otherwise.

probJumpToNeighbour

public double probJumpToNeighbour(int ignored,
                                  int position)

Description copied from class: GrapheneAtom

Probability to jump to given neighbour position.

Overrides:

probJumpToNeighbour in class GrapheneAtom

Returns:

probability

getTypeWithoutNeighbour

public byte getTypeWithoutNeighbour(int position)

Returns the type of the neighbour atom if current one would not exist. Essentially, it has one less neighbour.

Overrides:

getTypeWithoutNeighbour in class GrapheneAtom

Parameters:

position - ignored.

Returns:

the type.

getNewType

public byte getNewType(int neighbourPosition,
                       int addOrRemove)

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

Overrides:

getNewType in class GrapheneAtom

Parameters:

neighbourPosition - position of the neighbour. Must be always 1. Ignored

addOrRemove - add or remove one neighbour. Must be -1 or 1

Returns:

new atom type