AbstractGrowthKmc (Morphokinetics)

java.lang.Object
- kineticMonteCarlo.kmcCore.AbstractKmc
- - kineticMonteCarlo.kmcCore.growth.AbstractGrowthKmc

All Implemented Interfaces:

IKmc

Direct Known Subclasses:

AgKmc, AgUcKmc, BasicGrowthKmc, CatalysisKmc, ConcertedKmc, GrapheneKmc
```
public abstract class AbstractGrowthKmc
extends AbstractKmc
```
Author:

N. Ferrando, J. Alberdi-Rodriguez, E. Sanchez

Field Summary

Fields
Modifier and Type	Field and Description
`private DevitaAccelerator`	`accelerator`
`private ActivationEnergy`	`activationEnergy`
`private boolean`	`aeOutput` Activation energy output at the end of execution
`private int`	`area` Total area of a single flake simulation.
`private int`	`currentArea` Attribute to store temporally the current area of the simulation.
`private double`	`depositionRatePerSite`
`private boolean`	`extraOutput` Attribute to control the output of data every 1% and nucleation.
`private boolean`	`extraOutput2` Attribute to control the output of extra data of delta time between two attachments and between an atom is deposited and attached to an island.
`private boolean`	`forceNucleation` If two terraces are together freeze them, in multi-flake simulation mode.
`private int`	`freeArea`
`private boolean`	`justCentralFlake`
`private AbstractGrowthLattice`	`lattice`
`private float`	`maxCoverage` This attribute defines which is the maximum coverage for a multi-flake simulation.
`private ModifiedBuffer`	`modifiedBuffer`
`private int`	`nucleations`
`private RoundPerimeter`	`perimeter`
`private short`	`perimeterType`
`private boolean`	`periodicSingleFlake`
`private Restart`	`restart`
`private long`	`simulatedSteps`
`private double`	`sumProbabilities`
`private double`	`terraceToTerraceProbability`
`private boolean`	`useMaxPerimeter`

Constructor Summary

Constructors
Constructor and Description

AbstractGrowthKmc(Parser parser)

Constructors
Constructor and Description
`AbstractGrowthKmc(Parser parser)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`private void`	`atomAttachedToIsland(AbstractGrowthAtom destination)` An atom has been attached to an island an so printing this to output files.
`private int`	`calculateAreaAsInKmcCanvas()` Calculates current area or, i.e. the number of current places that simulation has.
`private int`	`calculateAreaAsInLattice()` Calculates the total area of a single flake simulation.
`private AbstractGrowthAtom`	`chooseRandomHop(AbstractGrowthAtom originAtom, int times)` Selects the next step randomly.
`private boolean`	`depositAtom(AbstractGrowthAtom atom)`
`private AbstractGrowthAtom`	`depositNewAtom()`
`void`	`depositSeed()`
`private boolean`	`diffuseAtom(AbstractGrowthAtom originAtom, AbstractGrowthAtom destinationAtom)` Moves an atom from origin to destination.
`DevitaAccelerator`	`getAccelerator()`
`float`	`getCoverage()` Returns the coverage of the simulation.
`int`	`getCurrentRadius()` Takes the current radius from the perimeter attribute.
`private double`	`getEstimatedCoverage()` Method to obtain theoretical coverage from deposition flux and current time.
`float[][]`	`getHexagonalPeriodicSurface(int binX, int binY)`
`AbstractGrowthLattice`	`getLattice()`
`ModifiedBuffer`	`getModifiedBuffer()`
`RoundPerimeter`	`getPerimeter()`
`float[][]`	`getSampledSurface(int binX, int binY)` Returns a sampled topological measurement of the KMC surface
`void`	`initialiseRates(double[] rates)` Initialises the rates of the simulation.
`boolean`	`isJustCentralFlake()`
`protected boolean`	`performSimulationStep()` Performs a simulation step.
`private boolean`	`perimeterMustBeEnlarged(AbstractGrowthAtom destinationAtom)`
`private void`	`printData(java.lang.Integer coverage)` Print current information to extra file.
`void`	`reset()` Resets the lattice and the list of atoms.
`void`	`setAccelerator(DevitaAccelerator accelerator)`
`void`	`setArea(int area)`
`(package private) void`	`setAtomPerimeter()` Internal method to select the perimeter size and type.
`(package private) void`	`setCurrentOccupiedArea(int occupiedSize)` This has to be called only once from AgKmc or GrapheneKmc.
`void`	`setDepositionRate(double depositionRateML, double islandDensitySite)`
`void`	`setLattice(AbstractGrowthLattice lattice)`
`void`	`setPerimeter(RoundPerimeter perimeter)`
`void`	`setTerraceToTerraceProbability(double terraceToTerraceProbability)`
`int`	`simulate()` Does the actual simulation.

Methods inherited from class kineticMonteCarlo.kmcCore.AbstractKmc
getIterations, getList, getTime, setIterations, setLattice, simulate, simulate

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

- Field Detail
  - lattice
```
private AbstractGrowthLattice lattice
```
  - modifiedBuffer
```
private final ModifiedBuffer modifiedBuffer
```
  - justCentralFlake
```
private final boolean justCentralFlake
```
  - periodicSingleFlake
```
private final boolean periodicSingleFlake
```
  - perimeter
```
private RoundPerimeter perimeter
```
  - useMaxPerimeter
```
private final boolean useMaxPerimeter
```
  - perimeterType
```
private final short perimeterType
```
  - accelerator
```
private DevitaAccelerator accelerator
```
  - maxCoverage
```
private final float maxCoverage
```
    This attribute defines which is the maximum coverage for a multi-flake simulation.
  - area
```
private int area
```
    Total area of a single flake simulation.
  - currentArea
```
private int currentArea
```
    Attribute to store temporally the current area of the simulation.
  - depositionRatePerSite
```
private double depositionRatePerSite
```
  - freeArea
```
private int freeArea
```
  - nucleations
```
private int nucleations
```
  - extraOutput
```
private final boolean extraOutput
```
    Attribute to control the output of data every 1% and nucleation.
  - extraOutput2
```
private final boolean extraOutput2
```
    Attribute to control the output of extra data of delta time between two attachments and between an atom is deposited and attached to an island.
  - aeOutput
```
private final boolean aeOutput
```
    Activation energy output at the end of execution
  - activationEnergy
```
private final ActivationEnergy activationEnergy
```
  - forceNucleation
```
private final boolean forceNucleation
```
    If two terraces are together freeze them, in multi-flake simulation mode.
  - terraceToTerraceProbability
```
private double terraceToTerraceProbability
```
  - simulatedSteps
```
private long simulatedSteps
```
  - sumProbabilities
```
private double sumProbabilities
```
  - restart
```
private Restart restart
```
- Constructor Detail
  - AbstractGrowthKmc
```
public AbstractGrowthKmc(Parser parser)
```
- Method Detail
  - setDepositionRate
```
public final void setDepositionRate(double depositionRateML,
                                    double islandDensitySite)
```
    Specified by:
    
    setDepositionRate in interface IKmc
    
    Overrides:
    
    setDepositionRate in class AbstractKmc
    
    Parameters:
    
    depositionRateML - deposition rate per site (synonyms: deposition flux and diffusion mono layer).
    
    islandDensitySite - only used for single flake simulations to properly calculate deposition rate.
  - setTerraceToTerraceProbability
```
public void setTerraceToTerraceProbability(double terraceToTerraceProbability)
```
  - getCurrentRadius
```
public int getCurrentRadius()
```
    Takes the current radius from the perimeter attribute.
    
    Overrides:
    
    getCurrentRadius in class AbstractKmc
    
    Returns:
    
    current radius of the single flake simulation.
  - getHexagonalPeriodicSurface
```
public float[][] getHexagonalPeriodicSurface(int binX,
                                             int binY)
```
  - getSampledSurface
```
public float[][] getSampledSurface(int binX,
                                   int binY)
```
    Description copied from interface: IKmc
    
    Returns a sampled topological measurement of the KMC surface
    
    Returns:
    
    calculated surface
  - getCoverage
```
public float getCoverage()
```
    Returns the coverage of the simulation. Thus, the number of occupied locations divided by the total number of locations.
    
    Overrides:
    
    getCoverage in class AbstractKmc
    
    Returns:
    
    A value between 0 and 1.
  - getAccelerator
```
public DevitaAccelerator getAccelerator()
```
  - setAccelerator
```
public void setAccelerator(DevitaAccelerator accelerator)
```
  - setLattice
```
public final void setLattice(AbstractGrowthLattice lattice)
```
    Parameters:
    
    lattice - the lattice to set
  - getModifiedBuffer
```
public final ModifiedBuffer getModifiedBuffer()
```
    Returns:
    
    the modifiedBuffer
  - isJustCentralFlake
```
public boolean isJustCentralFlake()
```
    Returns:
    
    the justCentralFlake
  - getPerimeter
```
public RoundPerimeter getPerimeter()
```
  - setPerimeter
```
public final void setPerimeter(RoundPerimeter perimeter)
```
    Parameters:
    
    perimeter - the perimeter to set.
  - setArea
```
public void setArea(int area)
```
    Parameters:
    
    area - the area to set.
  - initialiseRates
```
public void initialiseRates(double[] rates)
```
    Description copied from class: AbstractKmc
    
    Initialises the rates of the simulation. It has to be called once, and only once (not within a loop.
    
    Specified by:
    
    initialiseRates in interface IKmc
    
    Specified by:
    
    initialiseRates in class AbstractKmc
  - reset
```
public void reset()
```
    Description copied from class: AbstractKmc
    
    Resets the lattice and the list of atoms. This method has to be called just before depositSeed() and simulate().
    
    Specified by:
    
    reset in interface IKmc
    
    Overrides:
    
    reset in class AbstractKmc
  - getLattice
```
public AbstractGrowthLattice getLattice()
```
    Specified by:
    
    getLattice in interface IKmc
    
    Overrides:
    
    getLattice in class AbstractKmc
    
    Returns:
    
    the lattice
  - simulate
```
public int simulate()
```
    Description copied from class: AbstractKmc
    
    Does the actual simulation. It has to be called after reset() and depositSeed().
    
    Specified by:
    
    simulate in interface IKmc
    
    Overrides:
    
    simulate in class AbstractKmc
    
    Returns:
    
    number of iterations that simulation took
  - depositSeed
```
public void depositSeed()
```
  - performSimulationStep
```
protected boolean performSimulationStep()
```
    Performs a simulation step.
    
    Specified by:
    
    performSimulationStep in class AbstractKmc
    
    Returns:
    
    true if a stop condition happened (all atom etched, all surface covered).
  - setCurrentOccupiedArea
```
void setCurrentOccupiedArea(int occupiedSize)
```
    This has to be called only once from AgKmc or GrapheneKmc.
    
    Parameters:
    
    occupiedSize - Size of the seed in atoms. Number to calculate free space.
  - setAtomPerimeter
```
void setAtomPerimeter()
```
    Internal method to select the perimeter size and type. Must be used in depositSeed() method just before depositing the seed.
  - depositAtom
```
private boolean depositAtom(AbstractGrowthAtom atom)
```
  - chooseRandomHop
```
private AbstractGrowthAtom chooseRandomHop(AbstractGrowthAtom originAtom,
                                           int times)
```
    Selects the next step randomly. If there is not accelerator, an neighbour atom of originAtom is chosen. With Devita accelerator many steps far away atom can be chosen.
    
    Parameters:
    
    originAtom - atom that has to be moved.
    
    times - how many times it has been called recursively
    
    Returns:
    
    destinationAtom.
  - printData
```
private void printData(java.lang.Integer coverage)
```
    Print current information to extra file.
    
    Parameters:
    
    coverage - used to have exactly the coverage and to be easily greppable.
  - calculateAreaAsInKmcCanvas
```
private int calculateAreaAsInKmcCanvas()
```
    Calculates current area or, i.e. the number of current places that simulation has. This total area changes with the current radius. It is calculated as is done in KmcCanvas class.
    
    Returns:
    
    simulated area.
  - calculateAreaAsInLattice
```
private int calculateAreaAsInLattice()
```
    Calculates the total area of a single flake simulation.
    
    Returns:
    
    total area.
  - diffuseAtom
```
private boolean diffuseAtom(AbstractGrowthAtom originAtom,
                            AbstractGrowthAtom destinationAtom)
```
    Moves an atom from origin to destination.
    
    Parameters:
    
    originAtom - origin atom.
    
    destinationAtom - destination atom.
    
    Returns:
    
    true if atom has moved, false otherwise.
  - atomAttachedToIsland
```
private void atomAttachedToIsland(AbstractGrowthAtom destination)
```
    An atom has been attached to an island an so printing this to output files.
    
    Parameters:
    
    destination - destination atom is required to compute time difference.
  - depositNewAtom
```
private AbstractGrowthAtom depositNewAtom()
```
  - perimeterMustBeEnlarged
```
private boolean perimeterMustBeEnlarged(AbstractGrowthAtom destinationAtom)
```
  - getEstimatedCoverage
```
private double getEstimatedCoverage()
```
    Method to obtain theoretical coverage from deposition flux and current time. This is beneficial to obtain better statistics for atom count (atoms with 0 neighbour, 1 neighbour and so on).
    
    Returns:
    
    estimated coverage.

Class AbstractGrowthKmc

Field Summary

Constructor Summary

Method Summary

Methods inherited from class kineticMonteCarlo.kmcCore.AbstractKmc

Methods inherited from class java.lang.Object

Field Detail

lattice

modifiedBuffer

justCentralFlake

periodicSingleFlake

perimeter

useMaxPerimeter

perimeterType

accelerator

maxCoverage

area

currentArea

depositionRatePerSite

freeArea

nucleations

extraOutput

extraOutput2

aeOutput

activationEnergy

forceNucleation

terraceToTerraceProbability

simulatedSteps

sumProbabilities

restart

Constructor Detail

AbstractGrowthKmc

Method Detail

setDepositionRate

setTerraceToTerraceProbability

getCurrentRadius

getHexagonalPeriodicSurface

getSampledSurface

getCoverage

getAccelerator

setAccelerator

setLattice

getModifiedBuffer

isJustCentralFlake

getPerimeter

setPerimeter

setArea

initialiseRates

reset

getLattice

simulate

depositSeed

performSimulationStep

setCurrentOccupiedArea

setAtomPerimeter

depositAtom

chooseRandomHop

printData

calculateAreaAsInKmcCanvas

calculateAreaAsInLattice

diffuseAtom

atomAttachedToIsland

depositNewAtom

perimeterMustBeEnlarged

getEstimatedCoverage