GrapheneAtom (Morphokinetics)

java.lang.Object
- kineticMonteCarlo.atom.AbstractAtom
- - kineticMonteCarlo.atom.AbstractGrowthAtom
  - - kineticMonteCarlo.atom.GrapheneAtom

All Implemented Interfaces:

java.lang.Comparable, IAtom, IElement

Direct Known Subclasses:

GrapheneAtomGaillard, GrapheneAtomGaillard1Neighbour, GrapheneAtomGaillardSimple, GrapheneAtomSchoenhalz
```
public class GrapheneAtom
extends AbstractGrowthAtom
```

Field Summary

Fields
Modifier and Type	Field and Description
`private boolean`	`allRatesTheSame`
`private HopsPerStep`	`distancePerStep`
`private int`	`n1` Total number of 1st neighbours. 0 <= n1 <= 3
`private int`	`n2` Total number of 2nd neighbours. 0 <= n2 <= 6
`private int`	`n3` Total number of 3rd neighbours. 0 <= n3 <= 3
`private GrapheneAtom[]`	`neighbours`
`private static GrapheneTypesTable`	`typesTable`

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

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

Constructors
Constructor and Description
`GrapheneAtom(int id, short iHexa, short jHexa, HopsPerStep distancePerStep)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`private boolean`	`areAllRatesTheSame()`
`boolean`	`areTwoTerracesTogether()`
`AbstractGrowthAtom`	`chooseRandomHop()` Decides to which position is going to jump.
`void`	`clear()` Resets current atom; TERRACE type, no neighbours, no occupied, no outside and no probability.
`java.util.List`	`getAllNeighbours()`
`HopsPerStep`	`getDistancePerStep()`
`int`	`getN1()` Total number of 1st neighbours.
`int`	`getN2()` Total number of 2nd neighbours.
`int`	`getN3()` Total number of 3rd neighbours.
`GrapheneAtom`	`getNeighbour(int pos)`
`int`	`getNeighbourCount()` Total number of neighbours.
`byte`	`getNewType(int neighbourPosition, int addOrRemove)` Calculates the new atom type when adding or removing a neighbour.
`int`	`getOrientation()`
`byte`	`getTypeWithoutNeighbour(int originPos)` saber que tipo de átomo sería si el vecino originPos estuviera vacío útil para saber el tipo de átomos que serás al saltar.
`boolean`	`isEligible()` KINK and BULK atom types are considered immobile atoms.
`boolean`	`isPartOfImmobilSubstrate()`
`void`	`obtainRateFromNeighbours()`
`double`	`probJumpToNeighbour(int originType, int pos)` Probability to jump to given neighbour position.
`void`	`setN1(int addOrRemove)`
`void`	`setNeighbour(AbstractGrowthAtom a, int pos)`
`void`	`setNeighbours(GrapheneAtom[] neighbours)`
`double`	`updateOneBound(int posNeighbour)`

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
  - typesTable
```
private static GrapheneTypesTable typesTable
```
  - allRatesTheSame
```
private boolean allRatesTheSame
```
  - neighbours
```
private GrapheneAtom[] neighbours
```
  - n1
```
private int n1
```
    Total number of 1st neighbours. 0 <= n1 <= 3
  - n2
```
private int n2
```
    Total number of 2nd neighbours. 0 <= n2 <= 6
  - n3
```
private int n3
```
    Total number of 3rd neighbours. 0 <= n3 <= 3
  - distancePerStep
```
private HopsPerStep distancePerStep
```
- Constructor Detail
  - GrapheneAtom
```
public GrapheneAtom(int id,
                    short iHexa,
                    short jHexa,
                    HopsPerStep distancePerStep)
```
- Method Detail
  - setNeighbours
```
public void setNeighbours(GrapheneAtom[] neighbours)
```
  - isEligible
```
public boolean isEligible()
```
    KINK and BULK atom types are considered immobile atoms.
    
    Returns:
    
    true if current atom can be moved, false otherwise.
  - isPartOfImmobilSubstrate
```
public boolean isPartOfImmobilSubstrate()
```
    Specified by:
    
    isPartOfImmobilSubstrate in class AbstractGrowthAtom
  - getN1
```
public int getN1()
```
    Total number of 1st neighbours.
    
    Returns:
    
    0 <= value <= 3
  - setN1
```
public void setN1(int addOrRemove)
```
  - getN2
```
public int getN2()
```
    Total number of 2nd neighbours.
    
    Returns:
    
    0 <= value <= 6
  - getN3
```
public int getN3()
```
    Total number of 3rd neighbours.
    
    Returns:
    
    0 <= value <= 3
  - getDistancePerStep
```
public HopsPerStep getDistancePerStep()
```
  - getNeighbourCount
```
public int getNeighbourCount()
```
    Total number of neighbours.
    
    Returns:
    
    0 <= value <= 12
  - setNeighbour
```
public void setNeighbour(AbstractGrowthAtom a,
                         int pos)
```
    Specified by:
    
    setNeighbour in class AbstractGrowthAtom
  - getNeighbour
```
public GrapheneAtom getNeighbour(int pos)
```
    Specified by:
    
    getNeighbour in class AbstractGrowthAtom
  - getAllNeighbours
```
public java.util.List getAllNeighbours()
```
    Specified by:
    
    getAllNeighbours in class AbstractGrowthAtom
  - getOrientation
```
public int getOrientation()
```
    Specified by:
    
    getOrientation 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
  - chooseRandomHop
```
public AbstractGrowthAtom chooseRandomHop()
```
    Decides to which position is going to jump.
    
    Specified by:
    
    chooseRandomHop in class AbstractGrowthAtom
    
    Returns:
    
    destination atom
  - areTwoTerracesTogether
```
public boolean areTwoTerracesTogether()
```
    Specified by:
    
    areTwoTerracesTogether in class AbstractGrowthAtom
  - getNewType
```
public byte getNewType(int neighbourPosition,
                       int addOrRemove)
```
    Calculates the new atom type when adding or removing a neighbour.
    
    Parameters:
    
    neighbourPosition - position of the neighbour. Must be 1, 2 or 3
    
    addOrRemove - add or remove one neighbour. Must be -1 or 1
    
    Returns:
    
    new atom type
  - obtainRateFromNeighbours
```
public void obtainRateFromNeighbours()
```
    Specified by:
    
    obtainRateFromNeighbours in class AbstractGrowthAtom
  - updateOneBound
```
public double updateOneBound(int posNeighbour)
```
    Specified by:
    
    updateOneBound in class AbstractGrowthAtom
  - probJumpToNeighbour
```
public double probJumpToNeighbour(int originType,
                                  int pos)
```
    Probability to jump to given neighbour position.
    
    Specified by:
    
    probJumpToNeighbour in class AbstractGrowthAtom
    
    Parameters:
    
    originType -
    
    pos -
    
    Returns:
    
    probability
  - getTypeWithoutNeighbour
```
public byte getTypeWithoutNeighbour(int originPos)
```
    saber que tipo de átomo sería si el vecino originPos estuviera vacío útil para saber el tipo de átomos que serás al saltar. sabiendo el tipo de átomo origen y destino puedes sacar la probabilidad de éxito origen ====> destino
    
    Specified by:
    
    getTypeWithoutNeighbour in class AbstractGrowthAtom
    
    Parameters:
    
    originPos -
    
    Returns:
    
    atom type without neighbour
  - areAllRatesTheSame
```
private boolean areAllRatesTheSame()
```

Class GrapheneAtom

Field Summary

Fields inherited from class kineticMonteCarlo.atom.AbstractAtom

Constructor Summary

Method Summary

Methods inherited from class kineticMonteCarlo.atom.AbstractGrowthAtom

Methods inherited from class kineticMonteCarlo.atom.AbstractAtom

Methods inherited from class java.lang.Object

Field Detail

typesTable

allRatesTheSame

neighbours

n1

n2

n3

distancePerStep

Constructor Detail

GrapheneAtom

Method Detail

setNeighbours

isEligible

isPartOfImmobilSubstrate

getN1

setN1

getN2

getN3

getDistancePerStep

getNeighbourCount

setNeighbour

getNeighbour

getAllNeighbours

getOrientation

clear

chooseRandomHop

areTwoTerracesTogether

getNewType

obtainRateFromNeighbours

updateOneBound

probJumpToNeighbour

getTypeWithoutNeighbour

areAllRatesTheSame