kineticMonteCarlo.lattice

Class AgLattice

java.lang.Object

kineticMonteCarlo.lattice.AbstractLattice

kineticMonteCarlo.lattice.AbstractGrowthLattice

kineticMonteCarlo.lattice.AgLattice

All Implemented Interfaces:

IDevitaLattice

Direct Known Subclasses:

AgUcLattice

public class AgLattice
extends AbstractGrowthLattice

Author:

N. Ferrando, J. Alberdi-Rodriguez

Field Summary

Fields

Modifier and Type	Field and Description
private Point2D	centralCartesianLocation

Fields inherited from class kineticMonteCarlo.lattice.AbstractGrowthLattice

Y_RATIO

Constructor Summary

Constructors

Constructor and Description
AgLattice(int hexaSizeI, int hexaSizeJ, ModifiedBuffer modified, HopsPerStep distancePerStep)

Method Summary

Modifier and Type	Method and Description
private void	addOccupiedNeighbour(AgAtom neighbourAtom, byte originType, boolean forceNucleation) Éste lo ejecutan los primeros vecinos.
void	changeOccupationByHand(double xMouse, double yMouse, int scale) Changes the occupation of the clicked atom from unoccupied to occupied, or vice versa.
private AbstractGrowthAtom	chooseClearAreaStep(short iHexaOrigin, short jHexaOrigin, int distance, double raw)
private AbstractGrowthAtom	chooseClearAreaTerrace(short iHexaOrigin, short jHexaOrigin, int distance, double raw)
private AgAtom[][]	createAtoms()
private int	createId(int i, int j)
void	deposit(AbstractGrowthAtom a, boolean forceNucleation)
double	extract(AbstractGrowthAtom a) Extract the given atom from the lattice.
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) The Cartesian X is the location I, plus the half of J.
double	getCartY(int jHexa) Simple relation between Y (Cartesian) and J (hexagonal), with Y_RATIO (=sin 60º).
AgAtom	getCentralAtom() Returns the atom that it is in the middle of single flake simulation.
Point2D	getCentralCartesianLocation()
private int	getClearAreaStep(short iHexaOrigin, short jHexaOrigin, int thresholdDistance)
private int	getClearAreaTerrace(short iHexaOrigin, short jHexaOrigin, int thresholdDistance)
AbstractGrowthAtom	getFarSite(AbstractGrowthAtom atom, int distance)
int[]	getHexagonalCoordinates(double xCart, double yCart)
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.
AbstractGrowthAtom	getNeighbour(int iHexa, int jHexa, int neighbour)
void	init()
private void	removeImmobilAddMobile(AgAtom atom)
private void	removeMobileAddImmobile(AgAtom atom, boolean forceNucleation)
private void	removeMobileOccupied(AgAtom neighbourAtom) Computes the removal of one mobile 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

centralCartesianLocation

private final Point2D centralCartesianLocation

Constructor Detail

AgLattice

public AgLattice(int hexaSizeI,
                 int hexaSizeJ,
                 ModifiedBuffer modified,
                 HopsPerStep distancePerStep)

Method Detail

getCentralAtom

public AgAtom 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.

getCentralCartesianLocation

public Point2D getCentralCartesianLocation()

Specified by:

getCentralCartesianLocation in class AbstractGrowthLattice

getCartSizeX

public float getCartSizeX()

Specified by:

getCartSizeX in class AbstractGrowthLattice

getCartSizeY

public float getCartSizeY()

Specified by:

getCartSizeY in class AbstractGrowthLattice

getCartesianLocation

public 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.

getHexagonalCoordinates

public int[] getHexagonalCoordinates(double xCart,
                                     double yCart)

getiHexa

public int getiHexa(double xCart,
                    double yCart)

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)

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.

getCartX

public double getCartX(int iHexa,
                       int jHexa)

The Cartesian X is the location I, plus the half of J. We have to do the module to ensure that fits in a rectangular Cartesian mesh.

Specified by:

getCartX in class AbstractGrowthLattice

Parameters:

iHexa -

jHexa -

Returns:

x Cartesian position.

getCartY

public double getCartY(int jHexa)

Simple relation between Y (Cartesian) and J (hexagonal), with Y_RATIO (=sin 60º).

Specified by:

getCartY in class AbstractGrowthLattice

Parameters:

jHexa -

Returns:

y Cartesian position.

getNeighbour

public AbstractGrowthAtom getNeighbour(int iHexa,
                                       int jHexa,
                                       int neighbour)

Specified by:

getNeighbour in class AbstractGrowthLattice

getAvailableDistance

public int getAvailableDistance(AbstractGrowthAtom atom,
                                int thresholdDistance)

getFarSite

public AbstractGrowthAtom getFarSite(AbstractGrowthAtom atom,
                                     int distance)

init

public void init()

deposit

public void deposit(AbstractGrowthAtom a,
                    boolean forceNucleation)

Specified by:

deposit in class AbstractGrowthLattice

extract

public double extract(AbstractGrowthAtom a)

Description copied from class: AbstractGrowthLattice

Extract the given atom from the lattice.

Specified by:

extract in class AbstractGrowthLattice

Parameters:

a - the atom to be extracted.

Returns:

probability change (positive value).

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 and only works with AgUc simulation mode. 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.

createAtoms

private AgAtom[][] createAtoms()

createId

private int createId(int i,
                     int j)

getClearAreaTerrace

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

chooseClearAreaTerrace

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

getClearAreaStep

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

chooseClearAreaStep

private AbstractGrowthAtom chooseClearAreaStep(short iHexaOrigin,
                                               short jHexaOrigin,
                                               int distance,
                                               double raw)

removeImmobilAddMobile

private void removeImmobilAddMobile(AgAtom atom)

removeMobileAddImmobile

private void removeMobileAddImmobile(AgAtom atom,
                                     boolean forceNucleation)

addOccupiedNeighbour

private void addOccupiedNeighbour(AgAtom neighbourAtom,
                                  byte originType,
                                  boolean forceNucleation)

Éste lo ejecutan los primeros vecinos.

Parameters:

neighbourAtom - neighbour atom of the original atom.

originType - type of the original atom.

forceNucleation -

removeMobileOccupied

private void removeMobileOccupied(AgAtom neighbourAtom)

Computes the removal of one mobile atom.

Parameters:

neighbourAtom - neighbour atom of the original atom.