Package etomica.kmc

Class SimKMCLJadatom

java.lang.Object

etomica.simulation.Simulation

etomica.kmc.SimKMCLJadatom

public class SimKMCLJadatom
extends Simulation

Simulation using Henkelman's Dimer method to find a saddle point for an adatom on a surface, modeled with LJ.

Field Summary

Fields

Modifier and Type	Field	Description
Vector	adAtomPos
Box	box
SpeciesGeneral	fixed
IntegratorDimerRT	integratorDimer
IntegratorKMC	integratorKMC
IntegratorKMCCluster	integratorKMCCluster
SpeciesGeneral	movable
IMoleculeList	movableSet
PotentialMaster	potentialMaster

Fields inherited from class etomica.simulation.Simulation

eventManager, random, seeds, space

Constructor Summary

Constructors

Constructor	Description
SimKMCLJadatom()

Method Summary

Modifier and Type	Method	Description
void	enableDimerSearch(java.lang.String fileName, long maxSteps)
void	initializeConfiguration(java.lang.String fileName)
void	integratorKMC()
void	integratorKMCCluster(double temp, int steps, int totalSearch)
static void	main(java.lang.String[] args)
void	randomizePositions()
void	removeAtoms(double distance, Vector center)
void	setMovableAtoms(double distance, Vector center)

Methods inherited from class java.lang.Object

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

Methods inherited from class etomica.simulation.Simulation

addBox, addSpecies, box, getBox, getBoxCount, getBoxes, getController, getEventManager, getIntegrator, getRandom, getRandomSeeds, getSpace, getSpecies, getSpeciesCount, getSpeciesList, makeBox, makeBox, makeUniqueElementSymbol, removeBox, setRandom, species

Field Detail

potentialMaster

public final PotentialMaster potentialMaster

integratorKMC

public IntegratorKMC integratorKMC

integratorKMCCluster

public IntegratorKMCCluster integratorKMCCluster

integratorDimer

public IntegratorDimerRT integratorDimer

box

public Box box

fixed

public SpeciesGeneral fixed

movable

public SpeciesGeneral movable

movableSet

public IMoleculeList movableSet

adAtomPos

public Vector adAtomPos

Constructor Detail

SimKMCLJadatom

public SimKMCLJadatom()

Method Detail

main

public static void main(java.lang.String[] args)

setMovableAtoms

public void setMovableAtoms(double distance,
                            Vector center)

removeAtoms

public void removeAtoms(double distance,
                        Vector center)

randomizePositions

public void randomizePositions()

initializeConfiguration

public void initializeConfiguration(java.lang.String fileName)

integratorKMC

public void integratorKMC()

integratorKMCCluster

public void integratorKMCCluster(double temp,
                                 int steps,
                                 int totalSearch)

enableDimerSearch

public void enableDimerSearch(java.lang.String fileName,
                              long maxSteps)