kineticMonteCarlo.lattice

Class BasicGrowthLattice

java.lang.Object

kineticMonteCarlo.lattice.AbstractLattice

kineticMonteCarlo.lattice.AbstractGrowthLattice

kineticMonteCarlo.lattice.BasicGrowthLattice

All Implemented Interfaces:

IDevitaLattice

public class BasicGrowthLattice
extends AbstractGrowthLattice

Author:

J. Alberdi-Rodriguez

Field Summary

Fields

Modifier and Type	Field and Description
private boolean	simple

Fields inherited from class kineticMonteCarlo.lattice.AbstractGrowthLattice

Y_RATIO

Constructor Summary

Constructors

Constructor and Description
BasicGrowthLattice(int hexaSizeI, int hexaSizeJ, ModifiedBuffer modified, boolean simple)

Method Summary

Modifier and Type	Method and Description
private void	addNeighbour(BasicGrowthAtom neighbourAtom, int neighbourPosition, boolean forceNucleation) A new occupied atom was added before calling this method, here, updating the first and the second neighbourhood.
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(AbstractGrowthAtom atom, int distance)
private AbstractGrowthAtom	chooseClearAreaTerrace(AbstractGrowthAtom atom, int distance) Chooses the randomly a far atom.
private BasicGrowthAtom[][]	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)
double	getCartY(int jHexa)
BasicGrowthAtom	getCentralAtom() Returns the atom that it is in the middle of single flake simulation.
Point2D	getCentralCartesianLocation()
private int	getClearAreaStep(AbstractGrowthAtom atom, int thresholdDistance)
private int	getClearAreaTerrace(AbstractGrowthAtom atom, int thresholdDistance) We only care about the largest possible distance atoms.
AbstractGrowthAtom	getFarSite(AbstractGrowthAtom atom, int distance)
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	removeNeighbour(BasicGrowthAtom neighbourAtom, int neighbourPosition) Computes the removal of one atom.
private void	updateSecondNeighbour(BasicGrowthAtom secondNeighbourAtom)

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

simple

private final boolean simple

Constructor Detail

BasicGrowthLattice

public BasicGrowthLattice(int hexaSizeI,
                          int hexaSizeJ,
                          ModifiedBuffer modified,
                          boolean simple)

Method Detail

getCentralAtom

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

Specified by:

getNeighbour in class AbstractGrowthLattice

getCartSizeX

public float getCartSizeX()

Specified by:

getCartSizeX in class AbstractGrowthLattice

getCartSizeY

public float getCartSizeY()

Specified by:

getCartSizeY in class AbstractGrowthLattice

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.

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.

getCentralCartesianLocation

public Point2D getCentralCartesianLocation()

Specified by:

getCentralCartesianLocation 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

createId

private int createId(int i,
                     int j)

createAtoms

private BasicGrowthAtom[][] createAtoms()

getClearAreaTerrace

private int getClearAreaTerrace(AbstractGrowthAtom atom,
                                int thresholdDistance)

We only care about the largest possible distance atoms.

Parameters:

atom -

thresholdDistance -

Returns:

clear distance.

chooseClearAreaTerrace

private AbstractGrowthAtom chooseClearAreaTerrace(AbstractGrowthAtom atom,
                                                  int distance)

Chooses the randomly a far atom. Firstly, it goes to the given distance and secondly, it navigates throw the perimeter.

Parameters:

atom - origin atom.

distance - how far we have to move.

Returns:

destination atom.

getClearAreaStep

private int getClearAreaStep(AbstractGrowthAtom atom,
                             int thresholdDistance)

chooseClearAreaStep

private AbstractGrowthAtom chooseClearAreaStep(AbstractGrowthAtom atom,
                                               int distance)

addNeighbour

private void addNeighbour(BasicGrowthAtom neighbourAtom,
                          int neighbourPosition,
                          boolean forceNucleation)

A new occupied atom was added before calling this method, here, updating the first and the second neighbourhood.

Parameters:

neighbourAtom - current atom.

neighbourPosition - the position of the neighbour.

forceNucleation -

updateSecondNeighbour

private void updateSecondNeighbour(BasicGrowthAtom secondNeighbourAtom)

removeNeighbour

private void removeNeighbour(BasicGrowthAtom neighbourAtom,
                             int neighbourPosition)

Computes the removal of one atom.

Parameters:

neighbourAtom - neighbour atom of the original atom.