AbstractAtom (Morphokinetics)

java.lang.Object
- kineticMonteCarlo.atom.AbstractAtom

All Implemented Interfaces:

IAtom

Direct Known Subclasses:

AbstractGrowthAtom, BasicAtom, SiAtom
```
public abstract class AbstractAtom
extends java.lang.Object
implements IAtom
```
Author:

N. Ferrando, J. Alberdi-Rodriguez

Field Summary

Fields
Modifier and Type	Field and Description
`static byte`	`ARMCHAIR_EDGE`
`static byte`	`BULK`
`static byte`	`CORNER`
`static byte`	`EDGE`
`static byte`	`KINK`
`private java.lang.Boolean`	`list`
`private int`	`numberOfNeighbours`
`private boolean`	`occupied`
`private double[]`	`probabilities`
`private boolean`	`removed`
`static byte`	`SICK`
`static byte`	`TERRACE`
`static byte`	`ZIGZAG_EDGE`
`static byte`	`ZIGZAG_WITH_EXTRA`

Constructor Summary

Constructors
Constructor and Description

AbstractAtom()

Constructors
Constructor and Description
`AbstractAtom()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`int`	`getNumberOfNeighbours()` Number of neighbours that current atoms has, independently whether are occupied or not.
`Point3D`	`getPos()` Returns the position within the unit cell, (0,0) in this case.
`double[]`	`getProbabilities()`
`byte`	`getRealType()` If not overridden, returns directly the type of current atom.
`boolean`	`isOccupied()`
`boolean`	`isOnList()`
`boolean`	`isRemoved()`
`void`	`setList(java.lang.Boolean list)`
`void`	`setNeighbour(AbstractAtom lattice, int i)`
`void`	`setNumberOfNeighbours(int numberOfNeighbours)`
`void`	`setOccupied(boolean occupied)`
`void`	`setProbabilities(double[] probabilities)`
`void`	`setRemoved()`
`void`	`unRemove()`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface kineticMonteCarlo.atom.IAtom
getProbability, getType, isEligible, remove

- 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
```
public static final byte EDGE
```
    See Also:
    
    Constant Field Values
  - ZIGZAG_EDGE
```
public static final byte ZIGZAG_EDGE
```
    See Also:
    
    Constant Field Values
  - ARMCHAIR_EDGE
```
public static final byte ARMCHAIR_EDGE
```
    See Also:
    
    Constant Field Values
  - ZIGZAG_WITH_EXTRA
```
public static final byte ZIGZAG_WITH_EXTRA
```
    See Also:
    
    Constant Field Values
  - SICK
```
public static final byte SICK
```
    See Also:
    
    Constant Field Values
  - KINK
```
public static final byte KINK
```
    See Also:
    
    Constant Field Values
  - BULK
```
public static final byte BULK
```
    See Also:
    
    Constant Field Values
  - list
```
private java.lang.Boolean list
```
  - probabilities
```
private double[] probabilities
```
  - numberOfNeighbours
```
private int numberOfNeighbours
```
  - removed
```
private boolean removed
```
  - occupied
```
private boolean occupied
```
- Constructor Detail
  - AbstractAtom
```
public AbstractAtom()
```
- Method Detail
  - setProbabilities
```
public void setProbabilities(double[] probabilities)
```
    Specified by:
    
    setProbabilities in interface IAtom
  - getProbabilities
```
public double[] getProbabilities()
```
    Specified by:
    
    getProbabilities in interface IAtom
  - setList
```
public void setList(java.lang.Boolean list)
```
    Specified by:
    
    setList in interface IAtom
  - isOnList
```
public boolean isOnList()
```
    Specified by:
    
    isOnList in interface IAtom
  - isRemoved
```
public boolean isRemoved()
```
    Specified by:
    
    isRemoved in interface IAtom
  - unRemove
```
public void unRemove()
```
    Specified by:
    
    unRemove in interface IAtom
  - setRemoved
```
public void setRemoved()
```
    Specified by:
    
    setRemoved in interface IAtom
  - isOccupied
```
public final boolean isOccupied()
```
    Specified by:
    
    isOccupied in interface IAtom
  - setOccupied
```
public final void setOccupied(boolean occupied)
```
  - getNumberOfNeighbours
```
public final int getNumberOfNeighbours()
```
    Number of neighbours that current atoms has, independently whether are occupied or not.
    
    Specified by:
    
    getNumberOfNeighbours in interface IAtom
    
    Returns:
    
    fixed number of neighbours.
  - setNumberOfNeighbours
```
public final void setNumberOfNeighbours(int numberOfNeighbours)
```
    Specified by:
    
    setNumberOfNeighbours in interface IAtom
  - setNeighbour
```
public void setNeighbour(AbstractAtom lattice,
                         int i)
```
    Specified by:
    
    setNeighbour in interface IAtom
  - getRealType
```
public byte getRealType()
```
    If not overridden, returns directly the type of current atom.
    
    Specified by:
    
    getRealType in interface IAtom
    
    Returns:
    
    atom type of current atom.
  - getPos
```
public Point3D getPos()
```
    Returns the position within the unit cell, (0,0) in this case.
    
    Specified by:
    
    getPos in interface IAtom
    
    Returns:
    
    coordinates in unit cell

Class AbstractAtom

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface kineticMonteCarlo.atom.IAtom

Field Detail

TERRACE

CORNER

EDGE

ZIGZAG_EDGE

ARMCHAIR_EDGE

ZIGZAG_WITH_EXTRA

SICK

KINK

BULK

list

probabilities

numberOfNeighbours

removed

occupied

Constructor Detail

AbstractAtom

Method Detail

setProbabilities

getProbabilities

setList

isOnList

isRemoved

unRemove

setRemoved

isOccupied

setOccupied

getNumberOfNeighbours

setNumberOfNeighbours

setNeighbour

getRealType

getPos