ConcertedKmc (Morphokinetics)

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

All Implemented Interfaces:

IKmc
```
public class ConcertedKmc
extends AbstractGrowthKmc
```
Author:

J. Alberdi-Rodriguez

Field Summary

Fields
Modifier and Type	Field and Description
`private ActivationEnergy`	`activationEnergy`
`private double`	`adsorptionRatePerSite`
`private boolean`	`aeOutput` Activation energy output at the end of execution
`private boolean`	`automaticCollections`
`private AtomsCollection`	`col` Stores all collections of atoms; either in a tree or an array.
`private double[]`	`diffusionRateMultiAtom`
`private double[][]`	`diffusionRatePerAtom`
`private double[]`	`diffusionRatePerIslandSize`
`private boolean`	`doIslandDiffusion`
`private boolean`	`doMultiAtomDiffusion`
`private boolean`	`extraOutput` Attribute to control the output of data every 1% and nucleation.
`private float`	`maxCoverage` This attribute defines which is the maximum coverage for a multi-flake simulation.
`private long`	`maxSteps`
`private Restart`	`restart`
`private long`	`simulatedSteps`
`private int`	`simulationNumber`
`private IAtomsCollection[]`	`sites`
`private double[]`	`totalRate`

Constructor Summary

Constructors
Constructor and Description

ConcertedKmc(Parser parser, java.lang.String restartFolder)

Constructors
Constructor and Description
`ConcertedKmc(Parser parser, java.lang.String restartFolder)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`private java.util.Set<ConcertedAtom>`	`addModifiedAtoms(java.util.Set<ConcertedAtom> modifiedAtoms, ConcertedAtom atom)` Includes all the first and second neighbourhood of the current atom in a list without repeated elements.
`private void`	`changeCollection(byte process, boolean toTree)` Changes current collection from array/tree to tree/array.
`private void`	`checkMergeIslands(AbstractGrowthAtom atom)`
`private void`	`checkMergeIslands(Island island)`
`private void`	`checkSizes()` If a process is stored in a array and it is too big, change to be a tree.
`private boolean`	`depositAtom(ConcertedAtom atom)`
`private ConcertedAtom`	`depositNewAtom()`
`private ConcertedAtom`	`depositNewAtom(int id)` Deposit new atom in with the given label.
`void`	`depositSeed()`
`private void`	`diffuseAtom()` Moves an atom.
`private void`	`diffuseIsland()` Moves an island.
`private void`	`diffuseMultiAtom()`
`private double`	`getConcertedDiffusionRate(int islandNumber)`
`private double`	`getDiffusionRate(ConcertedAtom atom, ConcertedAtom neighbour, int position)`
`private double`	`getMultiAtomDiffusionRate(MultiAtom multiAtom)`
`private int`	`getRandomIsland()`
`private MultiAtom`	`getRandomMultiAtom()`
`private void`	`initRates()` Iterates over all lattice sites and initialises adsorption probabilities.
`private void`	`mergeIslands()`
`private Island`	`moveIsland(Island originIsland, int direction)` Moves an island and recomputes all the neighbourhood.
`private Island`	`moveMultiAtom(MultiAtom originMultiAtom, int direction)` A copy of moveIsland(): Moves an island and recomputes all the neighbourhood.
`protected boolean`	`performSimulationStep()` Performs a simulation step.
`private void`	`printData()` Print current information to extra file.
`private void`	`recomputeAdsorptionProbability(ConcertedAtom atom)`
`private void`	`recomputeCollection(byte process, ConcertedAtom atom, double oldRate)`
`private void`	`recomputeConcertedDiffusionProbability(ConcertedAtom atom)` Doesn't work yet!!
`private void`	`recomputeDiffusionProbability(ConcertedAtom atom)`
`private void`	`recomputeMultiAtomProbability(ConcertedAtom atom)`
`void`	`reset()` Resets the lattice and the list of atoms.
`void`	`setRates(AbstractConcertedRates rates)`
`int`	`simulate()` Does the actual simulation.
`private void`	`updatePossibles()`
`private void`	`updateRateFromList(byte process)`
`private void`	`updateRates(java.util.Set<ConcertedAtom> modifiedAtoms)` Updates total adsorption and diffusion probabilities.
`private void`	`updateRatesIslands(ConcertedAtom origin, ConcertedAtom destination, boolean wasDimer)`

Methods inherited from class kineticMonteCarlo.kmcCore.growth.AbstractGrowthKmc
getAccelerator, getCoverage, getCurrentRadius, getHexagonalPeriodicSurface, getLattice, getModifiedBuffer, getPerimeter, getSampledSurface, initialiseRates, isJustCentralFlake, setAccelerator, setArea, setAtomPerimeter, setCurrentOccupiedArea, setDepositionRate, setLattice, setPerimeter, setTerraceToTerraceProbability

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
  - simulatedSteps
```
private long simulatedSteps
```
  - simulationNumber
```
private int simulationNumber
```
  - sites
```
private final IAtomsCollection[] sites
```
  - col
```
private AtomsCollection col
```
    Stores all collections of atoms; either in a tree or an array.
  - automaticCollections
```
private final boolean automaticCollections
```
  - maxSteps
```
private final long maxSteps
```
  - maxCoverage
```
private final float maxCoverage
```
    This attribute defines which is the maximum coverage for a multi-flake simulation.
  - adsorptionRatePerSite
```
private double adsorptionRatePerSite
```
  - diffusionRatePerAtom
```
private double[][] diffusionRatePerAtom
```
  - diffusionRatePerIslandSize
```
private double[] diffusionRatePerIslandSize
```
  - diffusionRateMultiAtom
```
private double[] diffusionRateMultiAtom
```
  - totalRate
```
private double[] totalRate
```
  - extraOutput
```
private final boolean extraOutput
```
    Attribute to control the output of data every 1% and nucleation.
  - aeOutput
```
private final boolean aeOutput
```
    Activation energy output at the end of execution
  - activationEnergy
```
private final ActivationEnergy activationEnergy
```
  - restart
```
private final Restart restart
```
  - doIslandDiffusion
```
private final boolean doIslandDiffusion
```
  - doMultiAtomDiffusion
```
private final boolean doMultiAtomDiffusion
```
- Constructor Detail
  - ConcertedKmc
```
public ConcertedKmc(Parser parser,
                    java.lang.String restartFolder)
```
- Method Detail
  - setRates
```
public void setRates(AbstractConcertedRates rates)
```
  - performSimulationStep
```
protected boolean performSimulationStep()
```
    Performs a simulation step.
    
    Overrides:
    
    performSimulationStep in class AbstractGrowthKmc
    
    Returns:
    
    true if a stop condition happened (all atom etched, all surface covered).
  - 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 AbstractGrowthKmc
    
    Returns:
    
    number of iterations that simulation took
  - depositSeed
```
public void depositSeed()
```
    Specified by:
    
    depositSeed in interface IKmc
    
    Overrides:
    
    depositSeed in class AbstractGrowthKmc
  - 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 AbstractGrowthKmc
  - depositAtom
```
private boolean depositAtom(ConcertedAtom atom)
```
  - depositNewAtom
```
private ConcertedAtom depositNewAtom()
```
  - depositNewAtom
```
private ConcertedAtom depositNewAtom(int id)
```
    Deposit new atom in with the given label.
    
    Parameters:
    
    id - if negative, random number is chosen.
    
    Returns:
  - diffuseAtom
```
private void diffuseAtom()
```
    Moves an atom.
  - getRandomIsland
```
private int getRandomIsland()
```
  - moveIsland
```
private Island moveIsland(Island originIsland,
                          int direction)
```
    Moves an island and recomputes all the neighbourhood.
    
    Parameters:
    
    originIsland - Island to be moved.
    
    direction - Moving direction.
    
    Returns:
    
    New island with the number of the original one.
  - moveMultiAtom
```
private Island moveMultiAtom(MultiAtom originMultiAtom,
                             int direction)
```
    A copy of moveIsland(): Moves an island and recomputes all the neighbourhood. Should be merged in the future.
    
    Parameters:
    
    originMultiAtom - Island to be moved.
    
    direction - Moving direction.
    
    Returns:
    
    New island with the number of the original one.
  - diffuseIsland
```
private void diffuseIsland()
```
    Moves an island.
  - getRandomMultiAtom
```
private MultiAtom getRandomMultiAtom()
```
  - diffuseMultiAtom
```
private void diffuseMultiAtom()
```
  - checkMergeIslands
```
private void checkMergeIslands(Island island)
```
  - checkMergeIslands
```
private void checkMergeIslands(AbstractGrowthAtom atom)
```
  - mergeIslands
```
private void mergeIslands()
```
  - initRates
```
private void initRates()
```
    Iterates over all lattice sites and initialises adsorption probabilities.
  - addModifiedAtoms
```
private java.util.Set<ConcertedAtom> addModifiedAtoms(java.util.Set<ConcertedAtom> modifiedAtoms,
                                                      ConcertedAtom atom)
```
    Includes all the first and second neighbourhood of the current atom in a list without repeated elements.
    
    Parameters:
    
    modifiedAtoms - previously added atoms, can be null.
    
    atom - current central atom.
    
    Returns:
    
    A list with of atoms that should be recomputed their rate.
  - updateRates
```
private void updateRates(java.util.Set<ConcertedAtom> modifiedAtoms)
```
    Updates total adsorption and diffusion probabilities.
    
    Parameters:
    
    atom -
  - updateRatesIslands
```
private void updateRatesIslands(ConcertedAtom origin,
                                ConcertedAtom destination,
                                boolean wasDimer)
```
  - recomputeAdsorptionProbability
```
private void recomputeAdsorptionProbability(ConcertedAtom atom)
```
  - recomputeDiffusionProbability
```
private void recomputeDiffusionProbability(ConcertedAtom atom)
```
  - recomputeConcertedDiffusionProbability
```
private void recomputeConcertedDiffusionProbability(ConcertedAtom atom)
```
    Doesn't work yet!!
    
    Parameters:
    
    atom -
  - recomputeMultiAtomProbability
```
private void recomputeMultiAtomProbability(ConcertedAtom atom)
```
  - recomputeCollection
```
private void recomputeCollection(byte process,
                                 ConcertedAtom atom,
                                 double oldRate)
```
  - getDiffusionRate
```
private double getDiffusionRate(ConcertedAtom atom,
                                ConcertedAtom neighbour,
                                int position)
```
  - getConcertedDiffusionRate
```
private double getConcertedDiffusionRate(int islandNumber)
```
  - getMultiAtomDiffusionRate
```
private double getMultiAtomDiffusionRate(MultiAtom multiAtom)
```
  - updateRateFromList
```
private void updateRateFromList(byte process)
```
  - checkSizes
```
private void checkSizes()
```
    If a process is stored in a array and it is too big, change to be a tree. If a tree is too small, change it to be an array.
  - changeCollection
```
private void changeCollection(byte process,
                              boolean toTree)
```
    Changes current collection from array/tree to tree/array.
    
    Parameters:
    
    process - ADSORPTION, SINGLE diffusion, CONCERTED island diffusion or MULTI atom diffusion.
    
    toTree - if true from array to tree, otherwise from tree to array.
  - updatePossibles
```
private void updatePossibles()
```
  - printData
```
private void printData()
```
    Print current information to extra file.
    
    Parameters:
    
    coverage - used to have exactly the coverage and to be easily greppable.

Class ConcertedKmc

Field Summary

Constructor Summary

Method Summary

Methods inherited from class kineticMonteCarlo.kmcCore.growth.AbstractGrowthKmc

Methods inherited from class kineticMonteCarlo.kmcCore.AbstractKmc

Methods inherited from class java.lang.Object

Field Detail

simulatedSteps

simulationNumber

sites

col

automaticCollections

maxSteps

maxCoverage

adsorptionRatePerSite

diffusionRatePerAtom

diffusionRatePerIslandSize

diffusionRateMultiAtom

totalRate

extraOutput

aeOutput

activationEnergy

restart

doIslandDiffusion

doMultiAtomDiffusion

Constructor Detail

ConcertedKmc

Method Detail

setRates

performSimulationStep

simulate

depositSeed

reset

depositAtom

depositNewAtom

depositNewAtom

diffuseAtom

getRandomIsland

moveIsland

moveMultiAtom

diffuseIsland

getRandomMultiAtom

diffuseMultiAtom

checkMergeIslands

checkMergeIslands

mergeIslands

initRates

addModifiedAtoms

updateRates

updateRatesIslands

recomputeAdsorptionProbability

recomputeDiffusionProbability

recomputeConcertedDiffusionProbability

recomputeMultiAtomProbability

recomputeCollection

getDiffusionRate

getConcertedDiffusionRate

getMultiAtomDiffusionRate

updateRateFromList

checkSizes

changeCollection

updatePossibles

printData