Uses of Class
kineticMonteCarlo.atom.AbstractGrowthAtom

Packages that use AbstractGrowthAtom

Package	Description
basic.io
kineticMonteCarlo.atom
kineticMonteCarlo.kmcCore.growth
kineticMonteCarlo.kmcCore.growth.devitaAccelerator
kineticMonteCarlo.lattice
kineticMonteCarlo.unitCell
utils

Uses of AbstractGrowthAtom in basic.io

Methods in basic.io with parameters of type AbstractGrowthAtom

Modifier and Type	Method and Description
void	Restart.writeExtra2Output(AbstractGrowthLattice lattice, AbstractGrowthAtom atom, float coverage, double time, double diffusionRate)

Uses of AbstractGrowthAtom in kineticMonteCarlo.atom

Subclasses of AbstractGrowthAtom in kineticMonteCarlo.atom

Modifier and Type	Class and Description
class	AgAtom
class	AgAtomSimple
class	BasicGrowthAtom
class	BasicGrowthSimpleAtom
class	CatalysisAtom
class	ConcertedAtom
class	GrapheneAtom
class	GrapheneAtomGaillard Based on paper P.
class	GrapheneAtomGaillard1Neighbour Based on paper P.
class	GrapheneAtomGaillardSimple Based on paper P.
class	GrapheneAtomSchoenhalz Based on paper P.

Fields in kineticMonteCarlo.atom with type parameters of type AbstractGrowthAtom

Modifier and Type	Field and Description
private java.util.List<AbstractGrowthAtom>	ModifiedBuffer.buffer
private java.util.List<AbstractGrowthAtom>	ModifiedBuffer.bufferL

Methods in kineticMonteCarlo.atom that return AbstractGrowthAtom

Modifier and Type	Method and Description
abstract AbstractGrowthAtom	AbstractGrowthAtom.chooseRandomHop()
AbstractGrowthAtom	AgAtom.chooseRandomHop() It chooses one neighbour atom randomly.
AbstractGrowthAtom	AgAtomSimple.chooseRandomHop() Simpler implementation than AgAtom.chooseRandomHop().
AbstractGrowthAtom	BasicGrowthAtom.chooseRandomHop()
AbstractGrowthAtom	CatalysisAtom.chooseRandomHop()
AbstractGrowthAtom	GrapheneAtom.chooseRandomHop() Decides to which position is going to jump.
abstract AbstractGrowthAtom	AbstractGrowthAtom.getNeighbour(int pos)

Methods in kineticMonteCarlo.atom with parameters of type AbstractGrowthAtom

Modifier and Type	Method and Description
void	ModifiedBuffer.addBondAtom(AbstractGrowthAtom atom) Adds a bond atom to the current modified buffer list.
void	ModifiedBuffer.addOwnAtom(AbstractGrowthAtom atom) Adds an atom to the current modified buffer list.
boolean	AbstractGrowthAtom.areTwoTerracesTogetherInPerimeter(AbstractGrowthAtom originAtom) It has one neighbour.
abstract void	AbstractGrowthAtom.setNeighbour(AbstractGrowthAtom a, int pos)
void	AgAtom.setNeighbour(AbstractGrowthAtom a, int pos)
void	BasicGrowthAtom.setNeighbour(AbstractGrowthAtom a, int pos)
void	CatalysisAtom.setNeighbour(AbstractGrowthAtom a, int pos)
void	GrapheneAtom.setNeighbour(AbstractGrowthAtom a, int pos)
void	AbstractGrowthAtom.swapAttributes(AbstractGrowthAtom atom)
void	CatalysisAtom.swapAttributes(AbstractGrowthAtom a)
private void	ModifiedBuffer.updateAllNeighbours(AbstractGrowthAtom atom, AbstractList list)
private void	ModifiedBuffer.updateAllRates(AbstractGrowthAtom atom, AbstractList list)

Uses of AbstractGrowthAtom in kineticMonteCarlo.kmcCore.growth

Fields in kineticMonteCarlo.kmcCore.growth with type parameters of type AbstractGrowthAtom

Modifier and Type	Field and Description
private java.util.List<AbstractGrowthAtom>	RoundPerimeter.currentPerimeter Atoms vector belonging to the perimeter.
private java.util.TreeMap<java.lang.Integer,AbstractGrowthAtom>	RoundPerimeter.currentPerimeterTreeMap

Methods in kineticMonteCarlo.kmcCore.growth that return AbstractGrowthAtom

Modifier and Type	Method and Description
private AbstractGrowthAtom	AbstractGrowthKmc.chooseRandomHop(AbstractGrowthAtom originAtom, int times) Selects the next step randomly.
private AbstractGrowthAtom	AbstractGrowthKmc.depositNewAtom()
AbstractGrowthAtom	RoundPerimeter.getPerimeterReentrance(AbstractGrowthAtom originAtom)
AbstractGrowthAtom	RoundPerimeter.getRandomPerimeterAtom()

Methods in kineticMonteCarlo.kmcCore.growth that return types with arguments of type AbstractGrowthAtom

Modifier and Type	Method and Description
java.util.List<AbstractGrowthAtom>	RoundPerimeter.getCurrentPerimeter()

Methods in kineticMonteCarlo.kmcCore.growth with parameters of type AbstractGrowthAtom

Modifier and Type	Method and Description
private void	AbstractGrowthKmc.atomAttachedToIsland(AbstractGrowthAtom destination) An atom has been attached to an island an so printing this to output files.
private void	ConcertedKmc.checkMergeIslands(AbstractGrowthAtom atom)
private AbstractGrowthAtom	AbstractGrowthKmc.chooseRandomHop(AbstractGrowthAtom originAtom, int times) Selects the next step randomly.
boolean	RoundPerimeter.contains(AbstractGrowthAtom atom)
private boolean	AbstractGrowthKmc.depositAtom(AbstractGrowthAtom atom)
private boolean	AbstractGrowthKmc.diffuseAtom(AbstractGrowthAtom originAtom, AbstractGrowthAtom destinationAtom) Moves an atom from origin to destination.
AbstractGrowthAtom	RoundPerimeter.getPerimeterReentrance(AbstractGrowthAtom originAtom)
private boolean	AbstractGrowthKmc.perimeterMustBeEnlarged(AbstractGrowthAtom destinationAtom)

Method parameters in kineticMonteCarlo.kmcCore.growth with type arguments of type AbstractGrowthAtom

Modifier and Type	Method and Description
void	RoundPerimeter.setCurrentPerimeter(java.util.List<AbstractGrowthAtom> perimeter)

Uses of AbstractGrowthAtom in kineticMonteCarlo.kmcCore.growth.devitaAccelerator

Methods in kineticMonteCarlo.kmcCore.growth.devitaAccelerator that return AbstractGrowthAtom

Modifier and Type	Method and Description
AbstractGrowthAtom	DevitaAccelerator.chooseRandomHop(AbstractGrowthAtom originAtom)

Methods in kineticMonteCarlo.kmcCore.growth.devitaAccelerator with parameters of type AbstractGrowthAtom

Modifier and Type	Method and Description
AbstractGrowthAtom	DevitaAccelerator.chooseRandomHop(AbstractGrowthAtom originAtom)

Uses of AbstractGrowthAtom in kineticMonteCarlo.lattice

Fields in kineticMonteCarlo.lattice with type parameters of type AbstractGrowthAtom

Modifier and Type	Field and Description
private java.util.ArrayList<AbstractGrowthAtom>	Island.atoms

Methods in kineticMonteCarlo.lattice that return AbstractGrowthAtom

Modifier and Type	Method and Description
private AbstractGrowthAtom	AgUcLattice.chooseClearAreaStep(AbstractGrowthAtom atom, int distance)
private AbstractGrowthAtom	BasicGrowthLattice.chooseClearAreaStep(AbstractGrowthAtom atom, int distance)
private AbstractGrowthAtom	AgLattice.chooseClearAreaStep(short iHexaOrigin, short jHexaOrigin, int distance, double raw)
private AbstractGrowthAtom	AgUcLattice.chooseClearAreaTerrace(AbstractGrowthAtom atom, int distance)
private AbstractGrowthAtom	BasicGrowthLattice.chooseClearAreaTerrace(AbstractGrowthAtom atom, int distance) Chooses the randomly a far atom.
private AbstractGrowthAtom	AgLattice.chooseClearAreaTerrace(short iHexaOrigin, short jHexaOrigin, int distance, double raw)
private AbstractGrowthAtom	GrapheneLattice.chooseClearAreaTerrace(short iHexaOrigin, short jHexaOrigin, int thresholdDistance, double raw)
AbstractGrowthAtom	AbstractGrowthLattice.getAtom(int index) Deprecated.
AbstractGrowthAtom	AbstractGrowthLattice.getAtom(int iHexa, int jHexa) Deprecated.
AbstractGrowthAtom	AbstractGrowthLattice.getAtom(int iHexa, int jHexa, int unitCellPos)
AbstractGrowthAtom	Island.getAtomAt(int i)
abstract AbstractGrowthAtom	AbstractGrowthLattice.getCentralAtom() Returns the atom that it is in the middle of single flake simulation.
AbstractGrowthAtom	AgLattice.getFarSite(AbstractGrowthAtom atom, int distance)
AbstractGrowthAtom	AgUcLattice.getFarSite(AbstractGrowthAtom atom, int distance)
AbstractGrowthAtom	BasicGrowthLattice.getFarSite(AbstractGrowthAtom atom, int distance)
AbstractGrowthAtom	CatalysisLattice.getFarSite(AbstractGrowthAtom atom, int distance)
AbstractGrowthAtom	GrapheneLattice.getFarSite(AbstractGrowthAtom atom, int distance)
AbstractGrowthAtom	IDevitaLattice.getFarSite(AbstractGrowthAtom atom, int distance)
abstract AbstractGrowthAtom	AbstractGrowthLattice.getNeighbour(int iHexa, int jHexa, int neighbour)
AbstractGrowthAtom	AgLattice.getNeighbour(int iHexa, int jHexa, int neighbour)
AbstractGrowthAtom	BasicGrowthLattice.getNeighbour(int iHexa, int jHexa, int neighbour)
AbstractGrowthAtom	CatalysisLattice.getNeighbour(int iHexa, int jHexa, int neighbour)

Methods in kineticMonteCarlo.lattice that return types with arguments of type AbstractGrowthAtom

Modifier and Type	Method and Description
java.util.List<AbstractGrowthAtom>	AbstractGrowthLattice.setInsideCircle(int radius, boolean periodicSingleFlake) Defines which atoms are inside from the current position (centre) and given radius.
java.util.List<AbstractGrowthAtom>	AbstractGrowthLattice.setInsideSquare(int radius) Defines which atoms are inside from the current position.

Methods in kineticMonteCarlo.lattice with parameters of type AbstractGrowthAtom

Modifier and Type	Method and Description
(package private) void	AbstractGrowthLattice.addAtom(AbstractGrowthAtom atom)
void	Island.addAtom(AbstractGrowthAtom atom)
(package private) void	AbstractGrowthLattice.addBondAtom(AbstractGrowthAtom atom)
private MultiAtom	AbstractGrowthLattice.addMultiAtomIsland(AbstractGrowthAtom atom, AbstractGrowthAtom neighbour, int i)
private void	Concerted6LatticeSimple.addNeighbour(AbstractGrowthAtom neighbourAtom) Éste lo ejecutan los primeros vecinos
private boolean	AbstractGrowthLattice.allMultiAtomsDifferent(AbstractGrowthAtom atom, AbstractGrowthAtom neighbour)
private AbstractGrowthAtom	AgUcLattice.chooseClearAreaStep(AbstractGrowthAtom atom, int distance)
private AbstractGrowthAtom	BasicGrowthLattice.chooseClearAreaStep(AbstractGrowthAtom atom, int distance)
private AbstractGrowthAtom	AgUcLattice.chooseClearAreaTerrace(AbstractGrowthAtom atom, int distance)
private AbstractGrowthAtom	BasicGrowthLattice.chooseClearAreaTerrace(AbstractGrowthAtom atom, int distance) Chooses the randomly a far atom.
abstract void	AbstractGrowthLattice.deposit(AbstractGrowthAtom atom, boolean forceNucleation)
void	AgLattice.deposit(AbstractGrowthAtom a, boolean forceNucleation)
void	AgUcLatticeSimple.deposit(AbstractGrowthAtom a, boolean forceNucleation)
void	BasicGrowthLattice.deposit(AbstractGrowthAtom a, boolean forceNucleation)
void	CatalysisLattice.deposit(AbstractGrowthAtom a, boolean forceNucleation)
void	Concerted6LatticeSimple.deposit(AbstractGrowthAtom atom, boolean forceNucleation)
void	GrapheneLattice.deposit(AbstractGrowthAtom a, boolean forceNucleation)
void	GrapheneLatticeSimple.deposit(AbstractGrowthAtom a, boolean forceNucleation)
abstract double	AbstractGrowthLattice.extract(AbstractGrowthAtom atom) Extract the given atom from the lattice.
double	AgLattice.extract(AbstractGrowthAtom a)
double	AgUcLatticeSimple.extract(AbstractGrowthAtom a)
double	BasicGrowthLattice.extract(AbstractGrowthAtom a)
double	CatalysisLattice.extract(AbstractGrowthAtom a)
double	Concerted6LatticeSimple.extract(AbstractGrowthAtom atom)
double	GrapheneLattice.extract(AbstractGrowthAtom a) Extrae el átomo de este lugar (pásalo a no occupied y reduce la vecindad de los átomos vecinos, si cambia algún tipo, recalcula probabilidades)
double	GrapheneLatticeSimple.extract(AbstractGrowthAtom a)
int	AgLattice.getAvailableDistance(AbstractGrowthAtom atom, int thresholdDistance)
int	AgUcLattice.getAvailableDistance(AbstractGrowthAtom atom, int thresholdDistance)
int	BasicGrowthLattice.getAvailableDistance(AbstractGrowthAtom atom, int thresholdDistance)
int	CatalysisLattice.getAvailableDistance(AbstractGrowthAtom atom, int thresholdDistance)
int	GrapheneLattice.getAvailableDistance(AbstractGrowthAtom atom, int thresholdDistance)
int	IDevitaLattice.getAvailableDistance(AbstractGrowthAtom atom, int thresholdDistance)
private int	AgUcLattice.getClearAreaStep(AbstractGrowthAtom atom, int thresholdDistance)
private int	BasicGrowthLattice.getClearAreaStep(AbstractGrowthAtom atom, int thresholdDistance)
private int	AgUcLattice.getClearAreaTerrace(AbstractGrowthAtom atom, int thresholdDistance) We only care about the largest possible distance atoms.
private int	BasicGrowthLattice.getClearAreaTerrace(AbstractGrowthAtom atom, int thresholdDistance) We only care about the largest possible distance atoms.
private int	AgUcLattice.getClearAreaTerrace(AbstractGrowthAtom atom, int thresholdDistance, boolean changeLevel, int currentLevel, int position, int turnDirection, byte errorCode)
AbstractGrowthAtom	AgLattice.getFarSite(AbstractGrowthAtom atom, int distance)
AbstractGrowthAtom	AgUcLattice.getFarSite(AbstractGrowthAtom atom, int distance)
AbstractGrowthAtom	BasicGrowthLattice.getFarSite(AbstractGrowthAtom atom, int distance)
AbstractGrowthAtom	CatalysisLattice.getFarSite(AbstractGrowthAtom atom, int distance)
AbstractGrowthAtom	GrapheneLattice.getFarSite(AbstractGrowthAtom atom, int distance)
AbstractGrowthAtom	IDevitaLattice.getFarSite(AbstractGrowthAtom atom, int distance)
java.util.ArrayList<MultiAtom>	AbstractGrowthLattice.identifyAddMultiAtom(AbstractGrowthAtom atom) Counts the number of islands from current atom.
void	AbstractGrowthLattice.identifyIsland(AbstractGrowthAtom atom, boolean first, boolean fromNeighbour) Counts the number of islands from current atom.
private void	AbstractGrowthLattice.identifyIsland(AbstractGrowthAtom atom, boolean fromNeighbour, int xDiference, int yDiference) Counts the number of islands that the simulation has.
double	AbstractGrowthLattice.identifyRemoveMultiAtomIsland(AbstractGrowthAtom atom)
private boolean	AbstractGrowthLattice.onlyOneNeighbourInCommon(AbstractGrowthAtom atom, AbstractGrowthAtom neighbour) Edge diffusion can only happen when two atoms are in an edge.
void	Island.removeAtom(AbstractGrowthAtom atom)
private double	AbstractGrowthLattice.removeMultiAtom(AbstractGrowthAtom atom)
private void	Concerted6LatticeSimple.removeNeighbour(AbstractGrowthAtom neighbourAtom) Computes the removal of one mobile atom.
void	AbstractGrowthLattice.setAtoms(AbstractGrowthAtom[][] atoms)
void	AbstractGrowthLattice.swapAtomsInMultiAtom(AbstractGrowthAtom origin, AbstractGrowthAtom destination)

Uses of AbstractGrowthAtom in kineticMonteCarlo.unitCell

Fields in kineticMonteCarlo.unitCell declared as AbstractGrowthAtom

Modifier and Type	Field and Description
private AbstractGrowthAtom	SimpleUc.atom

Methods in kineticMonteCarlo.unitCell that return AbstractGrowthAtom

Modifier and Type	Method and Description
abstract AbstractGrowthAtom	AbstractGrowthUc.getAtom(int pos)
AbstractGrowthAtom	SimpleUc.getAtom(int pos) Always returns the current atom.

Constructors in kineticMonteCarlo.unitCell with parameters of type AbstractGrowthAtom

Constructor and Description
SimpleUc(int posI, int posJ, AbstractGrowthAtom atom)

Uses of AbstractGrowthAtom in utils

Method parameters in utils with type arguments of type AbstractGrowthAtom

Modifier and Type	Method and Description
static void	QuickSort.orderByAngle(java.util.List<AbstractGrowthAtom> a, int sizeEvent)
private static void	QuickSort.orderByAngle(java.util.List<AbstractGrowthAtom> atom, int left, int right)