kineticMonteCarlo.lattice

Class AgUcLattice

java.lang.Object

kineticMonteCarlo.lattice.AbstractLattice

kineticMonteCarlo.lattice.AbstractGrowthLattice

kineticMonteCarlo.lattice.AgLattice

kineticMonteCarlo.lattice.AgUcLattice

All Implemented Interfaces:

IDevitaLattice

Direct Known Subclasses:

AgUcLatticeSimple

public class AgUcLattice
extends AgLattice

Ag lattice with unit cell

Author:

J. Alberdi-Rodriguez

Field Summary

Fields

Modifier and Type	Field and Description
private Point2D	centralCartesianLocation
private int[]	shift List to store free area that current atom has.
private int	sizeI How many unit cells are in X axis.
private int	sizeJ How many unit cells are in Y axis.
private AgUc[][]	ucArray Unit cell array.
private java.util.List<AgUc>	ucList Unit cell list.

Fields inherited from class kineticMonteCarlo.lattice.AbstractGrowthLattice

Y_RATIO

Constructor Summary

Constructors

Constructor and Description
AgUcLattice(int hexaSizeI, int hexaSizeJ, ModifiedBuffer modified, HopsPerStep distancePerStep, int type) Creates a lattice to work with hexagonal Ag simulation, based on unit cells (UC).

Method Summary

Modifier and Type	Method and Description
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)
private void	createAtoms(int type) Creates all atoms and assigns it neighbours.
AgAtom	getAtom(int iHexa, int jHexa) We ignore the unitCellPos by now, we get directly the atom of i,j hexagonal location.
AgAtom	getAtom(int iHexa, int jHexa, int pos) Returns an atom of given unit cell and lattice position.
int	getAvailableDistance(AbstractGrowthAtom atom, int thresholdDistance)
float	getCartSizeX()
float	getCartSizeY()
AgAtom	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.
private int	getClearAreaTerrace(AbstractGrowthAtom atom, int thresholdDistance, boolean changeLevel, int currentLevel, int position, int turnDirection, byte errorCode)
float	getCoverage() The area is the number of cells * 2.
AbstractGrowthAtom	getFarSite(AbstractGrowthAtom atom, int distance)
AgUc	getUc(int pos)
AgUc	getUc(int i, int j)
int	size()

Methods inherited from class kineticMonteCarlo.lattice.AgLattice

deposit, extract, getCartesianLocation, getCartX, getCartY, getHexagonalCoordinates, getiHexa, getjHexa, getNeighbour, init

Methods inherited from class kineticMonteCarlo.lattice.AbstractGrowthLattice

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

sizeI

private int sizeI

How many unit cells are in X axis.

sizeJ

private int sizeJ

How many unit cells are in Y axis.

ucList

private java.util.List<AgUc> ucList

Unit cell list.

ucArray

private AgUc[][] ucArray

Unit cell array.

shift

private final int[] shift

List to store free area that current atom has.

Constructor Detail

AgUcLattice

public AgUcLattice(int hexaSizeI,
                   int hexaSizeJ,
                   ModifiedBuffer modified,
                   HopsPerStep distancePerStep,
                   int type)

Creates a lattice to work with hexagonal Ag simulation, based on unit cells (UC).

Parameters:

hexaSizeI - size in I direction. How many points horizontally.

hexaSizeJ - size in J direction. How many points vertically.

modified - temporary buffer.

distancePerStep - auxiliary class for Devita.

type - whether to use Ag simple, normal or concerted

Method Detail

getCartSizeX

public float getCartSizeX()

Overrides:

getCartSizeX in class AgLattice

getCartSizeY

public float getCartSizeY()

Overrides:

getCartSizeY in class AgLattice

getUc

public AgUc getUc(int pos)

Overrides:

getUc in class AbstractGrowthLattice

getUc

public AgUc getUc(int i,
                  int j)

Overrides:

getUc in class AbstractGrowthLattice

getCoverage

public float getCoverage()

The area is the number of cells * 2.

Overrides:

getCoverage in class AbstractGrowthLattice

Returns:

the coverage of the lattice.

size

public int size()

Overrides:

size in class AbstractGrowthLattice

getAtom

public AgAtom getAtom(int iHexa,
                      int jHexa)

Description copied from class: AbstractGrowthLattice

We ignore the unitCellPos by now, we get directly the atom of i,j hexagonal location.

Overrides:

getAtom in class AbstractGrowthLattice

Returns:

required atom.

getAtom

public AgAtom getAtom(int iHexa,
                      int jHexa,
                      int pos)

Returns an atom of given unit cell and lattice position.

Overrides:

getAtom in class AbstractGrowthLattice

Parameters:

iHexa -

jHexa -

pos -

Returns:

an atom.

getCentralAtom

public AgAtom getCentralAtom()

Description copied from class: AbstractGrowthLattice

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

Overrides:

getCentralAtom in class AgLattice

Returns:

central atom.

getCentralCartesianLocation

public Point2D getCentralCartesianLocation()

Overrides:

getCentralCartesianLocation in class AgLattice

getAvailableDistance

public int getAvailableDistance(AbstractGrowthAtom atom,
                                int thresholdDistance)

Specified by:

getAvailableDistance in interface IDevitaLattice

Overrides:

getAvailableDistance in class AgLattice

getFarSite

public AbstractGrowthAtom getFarSite(AbstractGrowthAtom atom,
                                     int distance)

Specified by:

getFarSite in interface IDevitaLattice

Overrides:

getFarSite in class AgLattice

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.

Overrides:

changeOccupationByHand in class AgLattice

Parameters:

xMouse - absolute X location of the pressed point

yMouse - absolute Y location of the pressed point

scale - zoom level

createAtoms

private void createAtoms(int type)

Creates all atoms and assigns it neighbours. How are computed the neighbours is documented here: https://bitbucket.org/Nesferjo/ekmc-project/wiki/Relationship%20between%20Cartesian%20and%20hexagonal%20representations

Parameters:

type - 0 = AgAtomSimple, type 1 = AgAtom, type 2 = ConcertedAtom.

getClearAreaTerrace

private int getClearAreaTerrace(AbstractGrowthAtom atom,
                                int thresholdDistance)

We only care about the largest possible distance atoms.

Parameters:

atom -

thresholdDistance -

Returns:

clear distance.

getClearAreaTerrace

private int getClearAreaTerrace(AbstractGrowthAtom atom,
                                int thresholdDistance,
                                boolean changeLevel,
                                int currentLevel,
                                int position,
                                int turnDirection,
                                byte errorCode)

chooseClearAreaTerrace

private AbstractGrowthAtom chooseClearAreaTerrace(AbstractGrowthAtom atom,
                                                  int distance)

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)