kineticMonteCarlo.lattice

Class GrapheneLattice

java.lang.Object

kineticMonteCarlo.lattice.AbstractLattice

kineticMonteCarlo.lattice.AbstractGrowthLattice

kineticMonteCarlo.lattice.GrapheneLattice

All Implemented Interfaces:

IDevitaLattice

Direct Known Subclasses:

GrapheneLatticeSimple

public class GrapheneLattice
extends AbstractGrowthLattice

Author:

N. Ferrando, J. Alberdi-Rodriguez

Field Summary

Fields

Modifier and Type	Field and Description
private Point2D	centralCartesianLocation
private static double	COS30
private static double	COS60
private static int[]	latticeNeighborhoodData

Fields inherited from class kineticMonteCarlo.lattice.AbstractGrowthLattice

Y_RATIO

Constructor Summary

Constructors

Constructor and Description
GrapheneLattice(int hexaSizeI, int hexaSizeJ, ModifiedBuffer modified, HopsPerStep distancePerStep, java.lang.Class<?> inputClass)

Method Summary

Modifier and Type	Method and Description
private void	add1stNeighbour(GrapheneAtom atom, boolean forceNucleation)
private void	add2ndNeighbour(GrapheneAtom atom)
private void	add3rdNeighbour(GrapheneAtom atom)
void	changeOccupationByHand(double xMouse, double yMouse, int scale) Changes the occupation of the clicked atom from unoccupied to occupied, or vice versa.
private AbstractGrowthAtom	chooseClearAreaTerrace(short iHexaOrigin, short jHexaOrigin, int thresholdDistance, double raw)
private GrapheneAtom[][]	createAtoms(int hexaSizeI, int hexaSizeJ, HopsPerStep distancePerStep, java.lang.Class<?> inputClass) Creates the atom array for graphene.
private int	createId(int i, int j)
void	deposit(AbstractGrowthAtom a, boolean forceNucleation)
private void	evaluateModifiedWhenAddNeigh(GrapheneAtom atom, byte newType)
private void	evaluateModifiedWhenRemNeigh(GrapheneAtom atom, byte newType)
double	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)
int	getAvailableDistance(AbstractGrowthAtom atom, int thresholdDistance)
Point2D	getCartesianLocation(int iHexa, int jHexa) Obtains the spatial location of certain atom, the distance between atoms is considered as 1 Returns the Cartesian position, given the hexagonal (lattice) location.
float	getCartSizeX()
float	getCartSizeY()
double	getCartX(int iHexa, int jHexa)
double	getCartY(int jHexa)
GrapheneAtom	getCentralAtom() Returns the atom that it is in the middle of single flake simulation.
Point2D	getCentralCartesianLocation()
private int	getClearAreaArmchair(short iHexaOrigin, short jHexaOrigin, int thresholdDistance, int[] destinationIndex, double raw)
private int	getClearAreaTerrace(short iHexaOrigin, short jHexaOrigin, int thresholdDistance)
private int	getClearAreaZigzag(short iHexaOrigin, short jHexaOrigin, int thresholdDistance, int[] destinationIndex, double raw)
AbstractGrowthAtom	getFarSite(AbstractGrowthAtom atom, int distance)
int	getHexaPosI(int iHexa, int jHexa, int pos, boolean type0)
int	getHexaPosJ(int iHexa, int jHexa, int pos, boolean type0)
int	getiHexa(double xCart, double yCart) Knowing the X and Y Cartesian location, returns closest atom hexagonal coordinate.
int	getjHexa(double yCart) Knowing the X and Y Cartesian location, returns closest atom hexagonal coordinate.
GrapheneAtom	getNeighbour(int xCart, int yCart, int neighbour)
private static void	initialiseNeighborHoodCache()
private void	remove1stNeighbour(GrapheneAtom atom)
private void	remove2ndNeighbour(GrapheneAtom atom)
private void	remove3rdNeighbour(GrapheneAtom atom)

Methods inherited from class kineticMonteCarlo.lattice.AbstractGrowthLattice

addAtom, addBondAtom, addOccupied, countIslands, countPerimeter, getAtom, getAtom, getAtom, getAtom, getAtomTypesCounter, getAverageGyradius, getCentreOfMass, getCmDistance, getCoverage, getDistancesToCentre, getDistanceToCenter, getDistanceToCenter, getEmptyTypesCounter, getInnerPerimeterLenght, getIsland, getIslandCount, getIslandIterator, getMobileAtoms, getMonomerCount, getMultiAtom, getMultiAtomCount, getMultiAtomIterator, getMultiAtomsIterator, getOccupied, getOuterPerimeterLenght, getTotalHops, getTracerDistance, getUc, getUc, identifyAddMultiAtom, identifyIsland, identifyRemoveMultiAtomIsland, initialiseRates, printDistances, reset, resetOccupied, setAngles, setAtoms, setAtomsTypesCounter, setInsideCircle, setInsideSquare, size, subtractOccupied, swapAtomsInMultiAtom, swapIsland

Methods inherited from class kineticMonteCarlo.lattice.AbstractLattice

getHexaSizeI, getHexaSizeJ, getHexaSizeK, getUnitCellSize, isPaused, setHexaSizeI, setHexaSizeJ, setHexaSizeK, setPaused, setProbabilities, setUnitCellSize

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

latticeNeighborhoodData

private static int[] latticeNeighborhoodData

COS60

private static final double COS60

COS30

private static final double COS30

centralCartesianLocation

private final Point2D centralCartesianLocation

Constructor Detail

GrapheneLattice

public GrapheneLattice(int hexaSizeI,
                       int hexaSizeJ,
                       ModifiedBuffer modified,
                       HopsPerStep distancePerStep,
                       java.lang.Class<?> inputClass)

Method Detail

getCentralAtom

public GrapheneAtom getCentralAtom()

Description copied from class: AbstractGrowthLattice

Returns the atom that it is in the middle of single flake simulation.

Specified by:

getCentralAtom in class AbstractGrowthLattice

Returns:

central atom.

getNeighbour

public GrapheneAtom getNeighbour(int xCart,
                                 int yCart,
                                 int neighbour)

Specified by:

getNeighbour in class AbstractGrowthLattice

getHexaPosI

public int getHexaPosI(int iHexa,
                       int jHexa,
                       int pos,
                       boolean type0)

getHexaPosJ

public int getHexaPosJ(int iHexa,
                       int jHexa,
                       int pos,
                       boolean type0)

getAvailableDistance

public int getAvailableDistance(AbstractGrowthAtom atom,
                                int thresholdDistance)

getFarSite

public AbstractGrowthAtom getFarSite(AbstractGrowthAtom atom,
                                     int distance)

getCartSizeX

public float getCartSizeX()

Specified by:

getCartSizeX in class AbstractGrowthLattice

getCartSizeY

public float getCartSizeY()

Specified by:

getCartSizeY in class AbstractGrowthLattice

getCentralCartesianLocation

public Point2D getCentralCartesianLocation()

Specified by:

getCentralCartesianLocation in class AbstractGrowthLattice

getCartesianLocation

public final Point2D getCartesianLocation(int iHexa,
                                          int jHexa)

Description copied from class: AbstractGrowthLattice

Obtains the spatial location of certain atom, the distance between atoms is considered as 1 Returns the Cartesian position, given the hexagonal (lattice) location.

Specified by:

getCartesianLocation in class AbstractGrowthLattice

Parameters:

iHexa - i index in the hexagonal mesh.

jHexa - j index in the hexagonal mesh.

Returns:

spatial location in Cartesian.

getCartX

public double getCartX(int iHexa,
                       int jHexa)

Specified by:

getCartX in class AbstractGrowthLattice

getCartY

public double getCartY(int jHexa)

Specified by:

getCartY in class AbstractGrowthLattice

getiHexa

public int getiHexa(double xCart,
                    double yCart)

Description copied from class: AbstractGrowthLattice

Knowing the X and Y Cartesian location, returns closest atom hexagonal coordinate.

Specified by:

getiHexa in class AbstractGrowthLattice

Parameters:

xCart - Cartesian X coordinate.

yCart - Cartesian Y coordinate.

Returns:

i hexagonal position.

getjHexa

public int getjHexa(double yCart)

Description copied from class: AbstractGrowthLattice

Knowing the X and Y Cartesian location, returns closest atom hexagonal coordinate.

Specified by:

getjHexa in class AbstractGrowthLattice

Parameters:

yCart - Cartesian Y coordinate.

Returns:

j hexagonal position.

deposit

public void deposit(AbstractGrowthAtom a,
                    boolean forceNucleation)

Specified by:

deposit in class AbstractGrowthLattice

extract

public double 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)

Specified by:

extract in class AbstractGrowthLattice

Parameters:

a - atom to be extracted.

Returns:

the previous probability of the extracted atom (in positive).

changeOccupationByHand

public void changeOccupationByHand(double xMouse,
                                   double yMouse,
                                   int scale)

Changes the occupation of the clicked atom from unoccupied to occupied, or vice versa. It is experimental. If fails, the execution continues normally.

Specified by:

changeOccupationByHand in class AbstractGrowthLattice

Parameters:

xMouse - absolute X location of the pressed point

yMouse - absolute Y location of the pressed point

scale - zoom level

initialiseNeighborHoodCache

private static void initialiseNeighborHoodCache()

createId

private int createId(int i,
                     int j)

createAtoms

private GrapheneAtom[][] createAtoms(int hexaSizeI,
                                     int hexaSizeJ,
                                     HopsPerStep distancePerStep,
                                     java.lang.Class<?> inputClass)

Creates the atom array for graphene. It only allows even parameters.

Parameters:

hexaSizeI - even number of the size in hexagonal lattice points. Currently it is represented vertically starting from the top

hexaSizeJ - even number of the size in hexagonal lattice points. Currently it is represented horizontally starting from the left

distancePerStep -

Returns:

just created atoms in a 2D matrix.

chooseClearAreaTerrace

private AbstractGrowthAtom chooseClearAreaTerrace(short iHexaOrigin,
                                                  short jHexaOrigin,
                                                  int thresholdDistance,
                                                  double raw)

getClearAreaTerrace

private int getClearAreaTerrace(short iHexaOrigin,
                                short jHexaOrigin,
                                int thresholdDistance)

getClearAreaZigzag

private int getClearAreaZigzag(short iHexaOrigin,
                               short jHexaOrigin,
                               int thresholdDistance,
                               int[] destinationIndex,
                               double raw)

getClearAreaArmchair

private int getClearAreaArmchair(short iHexaOrigin,
                                 short jHexaOrigin,
                                 int thresholdDistance,
                                 int[] destinationIndex,
                                 double raw)

add1stNeighbour

private void add1stNeighbour(GrapheneAtom atom,
                             boolean forceNucleation)

add2ndNeighbour

private void add2ndNeighbour(GrapheneAtom atom)

add3rdNeighbour

private void add3rdNeighbour(GrapheneAtom atom)

remove1stNeighbour

private void remove1stNeighbour(GrapheneAtom atom)

remove2ndNeighbour

private void remove2ndNeighbour(GrapheneAtom atom)

remove3rdNeighbour

private void remove3rdNeighbour(GrapheneAtom atom)

evaluateModifiedWhenRemNeigh

private void evaluateModifiedWhenRemNeigh(GrapheneAtom atom,
                                          byte newType)

evaluateModifiedWhenAddNeigh

private void evaluateModifiedWhenAddNeigh(GrapheneAtom atom,
                                          byte newType)