SiAtom (Morphokinetics)

java.lang.Object
- kineticMonteCarlo.atom.AbstractAtom
- - kineticMonteCarlo.atom.SiAtom

All Implemented Interfaces:

IAtom
```
public class SiAtom
extends AbstractAtom
```
Author:

N. Ferrando, J. Alberdi-Rodriguez

Field Summary

Fields
Modifier and Type	Field and Description
`private short`	`id`
`private float`	`limitX`
`private float`	`limitY`
`private float`	`limitZ`
`private byte`	`n1` Number of 1st neighbours.
`private byte`	`n2` Number of 2nd neighbours.
`private SiAtom`	`neighbour0`
`private SiAtom`	`neighbour1`
`private SiAtom`	`neighbour2`
`private SiAtom`	`neighbour3`
`private double`	`x`
`private double`	`y`
`private double`	`z`

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

SiAtom(double x, double y, double z)

Constructors
Constructor and Description
`SiAtom(double x, double y, double z)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`short`	`getId()`
`float`	`getLimitX()`
`float`	`getLimitY()`
`float`	`getLimitZ()`
`byte`	`getN1()` Number of 1st neighbours.
`byte`	`getN2()` Number of 2nd neighbours.
`SiAtom`	`getNeighbour(int pos)`
`Point3D`	`getPos()` Returns the position within the unit cell, (0,0) in this case.
`double`	`getProbability()`
`byte`	`getType()`
`double`	`getX()`
`double`	`getY()`
`double`	`getZ()`
`void`	`initialiseLimits(double limitX_a, double limitY_a, double limitZ_a)` Initialises limits in X, Y and Z.
`boolean`	`isEligible()`
`double`	`remove()`
`private double`	`remove1st()`
`private double`	`remove2nd()`
`void`	`setAsBulk()`
`void`	`setId(short id)`
`void`	`setNeighbour(AbstractAtom atom, int pos)`
`void`	`updateN1FromScratch()`
`void`	`updateN2FromScratch()`

Methods inherited from class kineticMonteCarlo.atom.AbstractAtom
getNumberOfNeighbours, getProbabilities, getRealType, isOccupied, isOnList, isRemoved, setList, setNumberOfNeighbours, setOccupied, setProbabilities, setRemoved, unRemove

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

Field Detail

neighbour0
```
private SiAtom neighbour0
```

neighbour1
```
private SiAtom neighbour1
```

neighbour2
```
private SiAtom neighbour2
```

neighbour3
```
private SiAtom neighbour3
```

n1
```
private byte n1
```
Number of 1st neighbours.

n2
```
private byte n2
```
Number of 2nd neighbours.

x
```
private final double x
```

y
```
private final double y
```

z
```
private final double z
```

limitX
```
private float limitX
```

limitY
```
private float limitY
```

limitZ
```
private float limitZ
```

id
```
private short id
```

Constructor Detail

SiAtom

public SiAtom(double x,
              double y,
              double z)

Method Detail

getX
```
public double getX()
```

getY
```
public double getY()
```

getZ
```
public double getZ()
```

getPos
```
public Point3D getPos()
```
Description copied from class: AbstractAtom

Returns the position within the unit cell, (0,0) in this case.

Specified by:

getPos in interface IAtom

Overrides:

getPos in class AbstractAtom

Returns:

coordinates in unit cell

getNeighbour
```
public SiAtom getNeighbour(int pos)
```

setNeighbour
```
public void setNeighbour(AbstractAtom atom,
                         int pos)
```
Specified by:

setNeighbour in interface IAtom

Overrides:

setNeighbour in class AbstractAtom

getType
```
public byte getType()
```

getN1
```
public byte getN1()
```
Number of 1st neighbours.

Returns:

number of 1st neighbours.

getN2
```
public byte getN2()
```
Number of 2nd neighbours.

Returns:

number of 2nd neighbours.

remove1st
```
private double remove1st()
```

remove2nd
```
private double remove2nd()
```

updateN1FromScratch
```
public void updateN1FromScratch()
```

updateN2FromScratch
```
public void updateN2FromScratch()
```

setAsBulk
```
public void setAsBulk()
```

remove
```
public double remove()
```

getProbability
```
public double getProbability()
```

isEligible
```
public boolean isEligible()
```

initialiseLimits

public void initialiseLimits(double limitX_a,
                             double limitY_a,
                             double limitZ_a)

Initialises limits in X, Y and Z.

Parameters:: limitX_a -; limitY_a -; limitZ_a -

getLimitX
```
public float getLimitX()
```

getLimitY
```
public float getLimitY()
```

getLimitZ
```
public float getLimitZ()
```

getId
```
public short getId()
```

setId
```
public void setId(short id)
```

Class SiAtom

Field Summary

Fields inherited from class kineticMonteCarlo.atom.AbstractAtom

Constructor Summary

Method Summary

Methods inherited from class kineticMonteCarlo.atom.AbstractAtom

Methods inherited from class java.lang.Object

Field Detail

neighbour0

neighbour1

neighbour2

neighbour3

n1

n2

x

y

z

limitX

limitY

limitZ

id

Constructor Detail

SiAtom

Method Detail

getX

getY

getZ

getPos

getNeighbour

setNeighbour

getType

getN1

getN2

remove1st

remove2nd

updateN1FromScratch

updateN2FromScratch

setAsBulk

remove

getProbability

isEligible

initialiseLimits

getLimitX

getLimitY

getLimitZ

getId

setId