kineticMonteCarlo.atom

Class AgAtom

java.lang.Object

kineticMonteCarlo.atom.AbstractAtom

kineticMonteCarlo.atom.AbstractGrowthAtom

kineticMonteCarlo.atom.AgAtom

All Implemented Interfaces:

java.lang.Comparable, IAtom, IElement

Direct Known Subclasses:

AgAtomSimple

public class AgAtom
extends AbstractGrowthAtom

Author:

N. Ferrando, J. Alberdi-Rodriguez

Field Summary

Fields

Modifier and Type	Field and Description
static byte	CORNER
static byte	EDGE
static byte	EDGE_A
static byte	EDGE_B
static byte	ISLAND
static byte	KINK
static byte	KINK_A
static byte	KINK_B
private AgAtom[]	neighbours
private int	nImmobile Number of immobile neighbours.
private int	nMobile Number of mobile neighbours.
private int	pos Position within unit cell.
static byte	TERRACE
private static AgTypesTable	typesTable

Fields inherited from class kineticMonteCarlo.atom.AbstractAtom

ARMCHAIR_EDGE, BULK, SICK, ZIGZAG_EDGE, ZIGZAG_WITH_EXTRA

Constructor Summary

Constructors

Constructor and Description
AgAtom(int id, int pos) Constructor for unit cell.
AgAtom(int id, short iHexa, short jHexa)

Method Summary

Modifier and Type	Method and Description
void	addNImmobile(int quantity) Adds the given number to the number of immobile neighbours.
void	addNMobile(int quantity) Adds the given number to the number of mobile neighbours.
private AgAtom	ahead2CornersAtom(int cornerPosition) This should be called when a edge jumps to a corner (instead of expected edge).
private AgAtom	aheadCornerAtom(int cornerPosition) When the current atom's destination is a corner, it jumps over it to the different type edge.
boolean	areTwoTerracesTogether() This method tells if two terraces are going to form a dimer.
private int	calculateEdgeType(int code) This atom is an edge (it has two neighbours).
private int	calculateKinkType(int code) This atom is a kink (it has three neighbours).
AbstractGrowthAtom	chooseRandomHop() It chooses one neighbour atom randomly.
void	clear() Resets current atom; TERRACE type, no neighbours, no occupied, no outside and no probability.
java.util.List	getAllNeighbours()
AgAtom	getNeighbour(int pos)
byte	getNewType(int addToImmobile, int addToMobile) Calculates the new atom type when adding or removing a neighbour.
int	getNImmobile()
int	getNMobile()
int	getOrientation() Computes the orientation with respect to the surface, for edges and kinks.
int	getOrientation(AgAtom atom) See getOrientation().
Point3D	getPos() Returns the position within the unit cell.
byte	getRealType() Returns the real type of the current atom.
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)
void	setNImmobile(int nImmobile)
void	setNMobile(int nMobile)
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, getProbabilities, 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

CORNER

public static final byte CORNER

See Also:

Constant Field Values

EDGE_A

public static final byte EDGE_A

See Also:

Constant Field Values

KINK_A

public static final byte KINK_A

See Also:

Constant Field Values

ISLAND

public static final byte ISLAND

See Also:

Constant Field Values

EDGE_B

public static final byte EDGE_B

See Also:

Constant Field Values

KINK_B

public static final byte KINK_B

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

typesTable

private static AgTypesTable typesTable

neighbours

private final AgAtom[] neighbours

nImmobile

private int nImmobile

Number of immobile neighbours.

nMobile

private int nMobile

Number of mobile neighbours.

pos

private final int pos

Position within unit cell.

Constructor Detail

AgAtom

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

AgAtom

public AgAtom(int id,
              int pos)

Constructor for unit cell.

Parameters:

id - atom identifier.

pos - position within the unit cell

Method Detail

getPos

public Point3D getPos()

Returns the position within the unit cell.

Specified by:

getPos in interface IAtom

Overrides:

getPos in class AbstractAtom

Returns:

coordinates in unit cell

setNeighbour

public void setNeighbour(AbstractGrowthAtom a,
                         int pos)

Specified by:

setNeighbour in class AbstractGrowthAtom

getNeighbour

public AgAtom getNeighbour(int pos)

Specified by:

getNeighbour in class AbstractGrowthAtom

getAllNeighbours

public java.util.List getAllNeighbours()

Specified by:

getAllNeighbours in class AbstractGrowthAtom

isEligible

public boolean isEligible()

isPartOfImmobilSubstrate

public boolean isPartOfImmobilSubstrate()

Specified by:

isPartOfImmobilSubstrate in class AbstractGrowthAtom

getNImmobile

public int getNImmobile()

Returns:

the number of immobile neighbours.

getNMobile

public int getNMobile()

Returns:

the number of mobile neighbours.

setNImmobile

public void setNImmobile(int nImmobile)

setNMobile

public void setNMobile(int nMobile)

addNMobile

public void addNMobile(int quantity)

Adds the given number to the number of mobile neighbours.

Parameters:

quantity -

addNImmobile

public void addNImmobile(int quantity)

Adds the given number to the number of immobile neighbours.

Parameters:

quantity -

getNewType

public byte getNewType(int addToImmobile,
                       int addToMobile)

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

Parameters:

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

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

Returns:

new type

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

getOrientation

public int getOrientation()

Computes the orientation with respect to the surface, for edges and kinks.

 A type: _
        \ /
 B type:
        /_\
 (central area would be island)
 

Specified by:

getOrientation in class AbstractGrowthAtom

Returns:

a number between 0 and 5 inclusive. Even number if A type or odd if B type.

getOrientation

public int getOrientation(AgAtom atom)

See getOrientation().

Parameters:

atom - atom to be excluded to compute the orientation. If null, none is excluded.

Returns:

a number between 0 and 5 inclusive. Even number if A type or odd if B type.

chooseRandomHop

public AbstractGrowthAtom chooseRandomHop()

It chooses one neighbour atom randomly.

Specified by:

chooseRandomHop in class AbstractGrowthAtom

Returns:

atom to be moved.

areTwoTerracesTogether

public boolean areTwoTerracesTogether()

This method tells if two terraces are going to form a dimer. This method should be called from an empty lattice location where atom is going to jump. In affirmative case, generally, it has two terrace neighbours. It only detects step-by-step collisions (it is not valid for Devita or perimeter reentrance).

Specified by:

areTwoTerracesTogether in class AbstractGrowthAtom

Returns:

true if two terraces are going to be together.

obtainRateFromNeighbours

public void obtainRateFromNeighbours()

Specified by:

obtainRateFromNeighbours 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.

getRealType

public byte getRealType()

Returns the real type of the current atom. This means, that is able to determine whether edge or kink is of type A or B. If the orientation number is odd the type is B.

Specified by:

getRealType in interface IAtom

Overrides:

getRealType in class AbstractAtom

Returns:

real type of the current atom.

probJumpToNeighbour

public double probJumpToNeighbour(int ignored,
                                  int position)

Specified by:

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

Returns:

the type.

calculateEdgeType

private int calculateEdgeType(int code)

This atom is an edge (it has two neighbours). There are 6 possible positions for the edge, depending on its neighbours. In the next "figure" the current atom is [] and the numbers are its neighbours:

    0  1
   5 [] 2
    4  3
 

A proper image of the positions is documented here: https://bitbucket.org/Nesferjo/ekmc-project/wiki/Relationship%20between%20Cartesian%20and%20hexagonal%20representations

Parameters:

code - binary code with the occupied neighbours.

Returns:

orientation (a number between 0 and 5 inclusive).

calculateKinkType

private int calculateKinkType(int code)

This atom is a kink (it has three neighbours). There are 6 possible positions for the kink, depending on its neighbours. In the next "figure" the current atom is [] and the numbers are its neighbours:

    0  1
   5 [] 2
    4  3
 

A proper image of the positions is documented here: https://bitbucket.org/Nesferjo/ekmc-project/wiki/Relationship%20between%20Cartesian%20and%20hexagonal%20representations

Parameters:

code - binary code with the occupied neighbours.

Returns:

orientation (a number between 0 and 5 inclusive).

aheadCornerAtom

private AgAtom aheadCornerAtom(int cornerPosition)

When the current atom's destination is a corner, it jumps over it to the different type edge.

Parameters:

cornerPosition - position of the neighbour, from current atom

Returns:

other type edge

ahead2CornersAtom

private AgAtom ahead2CornersAtom(int cornerPosition)

This should be called when a edge jumps to a corner (instead of expected edge). It happens when a sharp vertex is found in the island geometry and the atom has to jump over two corners and finish in the same type of edge (or any other type: ISLAND, KINK).

Parameters:

cornerPosition - position of the neighbour, from current atom

Returns:

any other type (EDGE, KINK or BULK)