Package etomica.integrator.mcmove

Class MCMoveInsertDeleteLatticeVacancy

java.lang.Object

etomica.integrator.mcmove.MCMove

etomica.integrator.mcmove.MCMoveBox

etomica.integrator.mcmove.MCMoveInsertDelete

etomica.integrator.mcmove.MCMoveInsertDeleteBiased

etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy

All Implemented Interfaces:

IListener

public class MCMoveInsertDeleteLatticeVacancy
extends MCMoveInsertDeleteBiased
implements IListener

Looks for atoms without a full set of first nearest neighbors and attempts insertions adjacent to one of those atoms. Hoops are jumped through to ensure detailed balance. Neighbor lists are used to find insertion points and candidates for deletion. Internal lists are constructed (relatively expensive) and then reconstructed when a move is accepted or when some other part of the simulation moves atoms (this part is somewhat hardcoded; enjoy).

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	MCMoveInsertDeleteLatticeVacancy.AtomIteratorBruteForce
static class	MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbr
static class	MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbrCell

Field Summary

Fields

Modifier and Type	Field	Description
protected AtomIteratorAtomDependent	atomIterator
protected java.util.List<java.lang.Integer>	deleteCandidates
protected int[]	deleteCandidateTimes
protected Vector	dest
protected boolean	dirty
protected Vector	dr
protected int	forced
protected java.util.List<java.lang.Integer>	insertCandidates
protected Integrator	integrator
protected long	lastStepCount
protected double	maxDistance
protected double	maxInsertDistance
protected double	nbrDistance
protected Vector[]	nbrVectors
protected double	newLnA
protected int[]	numDeleteCandidateNbrs
protected int[]	numNeighborCandidatesOnDelete
protected int[]	numNeighbors
protected int	numNewDeleteCandidates
protected double	oldB
protected double	oldBoxSize
protected double	oldLnA
protected Vector	oldPosition
protected PotentialMasterNbr	potentialMaster
protected Space	space
protected int	totalDeleteCandidateTimes

Fields inherited from class etomica.integrator.mcmove.MCMove

moveTracker, nominalFrequency, potential

Fields inherited from class etomica.integrator.mcmove.MCMoveBox

box, perParticleFrequency

Fields inherited from class etomica.integrator.mcmove.MCMoveInsertDelete

affectedAtomIterator, atomTranslator, energyMeter, insert, moleculeList, mu, positionSource, random, reservoir, species, testMolecule, uNew, uOld

Fields inherited from class etomica.integrator.mcmove.MCMoveInsertDeleteBiased

lnbias, maxN, minN

Constructor Summary

Constructors

Constructor	Description
MCMoveInsertDeleteLatticeVacancy(PotentialMasterNbr potentialMaster, IRandom random, Space _space, Integrator integrator, double maxDistance, int maxN, int maxVacancy)

Method Summary

Modifier and Type	Method	Description
void	actionPerformed(IEvent event)
boolean	doTrial()	Chooses and performs with equal probability an elementary molecule insertion or deletion.
protected void	findCandidates()
double	getChi(double temperature)	Chi is the parameter within standard Metropolis Monte Carlo.
double	getMaxDistance()
void	makeFccVectors(double newNbrDistance)
void	makeHcpVectors(double newNbrDistance)
void	myAcceptNotify()
void	reset()
void	setBox(Box box)	Sets the box on which this move acts.
void	setFluidNbrDistance(double newNbrDistance)
void	setLnBias(int n, double nBias)
void	setMaxDistance(double maxDistance)
void	setMaxInsertDistance(double maxInsertDistance)

Methods inherited from class etomica.integrator.mcmove.MCMove

getNominalFrequency, getTracker, setTracker

Methods inherited from class etomica.integrator.mcmove.MCMoveBox

affectedAtoms, energyChange, getBox, isNominallyPerParticleFrequency, toString

Methods inherited from class etomica.integrator.mcmove.MCMoveInsertDelete

affectedAtoms, energyChange, getMu, getMuDimension, getPositionSource, getSpecies, lastMoveInsert, setPositionSource, setSpecies

Methods inherited from class etomica.integrator.mcmove.MCMoveInsertDeleteBiased

acceptNotify, getLnBias, getLnBiasDiff, myRejectNotify, rejectNotify, setMinMax, setMu

Methods inherited from class java.lang.Object

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

Field Detail

dest

protected final Vector dest

dr

protected final Vector dr

integrator

protected Integrator integrator

lastStepCount

protected long lastStepCount

dirty

protected boolean dirty

maxDistance

protected double maxDistance

maxInsertDistance

protected double maxInsertDistance

nbrDistance

protected double nbrDistance

insertCandidates

protected java.util.List<java.lang.Integer> insertCandidates

deleteCandidates

protected java.util.List<java.lang.Integer> deleteCandidates

numNeighbors

protected int[] numNeighbors

numNeighborCandidatesOnDelete

protected int[] numNeighborCandidatesOnDelete

deleteCandidateTimes

protected int[] deleteCandidateTimes

numDeleteCandidateNbrs

protected int[] numDeleteCandidateNbrs

totalDeleteCandidateTimes

protected int totalDeleteCandidateTimes

potentialMaster

protected PotentialMasterNbr potentialMaster

numNewDeleteCandidates

protected int numNewDeleteCandidates

forced

protected int forced

oldLnA

protected double oldLnA

oldB

protected double oldB

newLnA

protected double newLnA

oldPosition

protected final Vector oldPosition

nbrVectors

protected Vector[] nbrVectors

space

protected final Space space

oldBoxSize

protected double oldBoxSize

atomIterator

protected AtomIteratorAtomDependent atomIterator

Constructor Detail

MCMoveInsertDeleteLatticeVacancy

public MCMoveInsertDeleteLatticeVacancy(PotentialMasterNbr potentialMaster,
                                        IRandom random,
                                        Space _space,
                                        Integrator integrator,
                                        double maxDistance,
                                        int maxN,
                                        int maxVacancy)

Method Detail

setBox

public void setBox(Box box)

Description copied from class: MCMoveBox

Sets the box on which this move acts. The box itself can be changed via this method, if desired.

Overrides:

setBox in class MCMoveInsertDeleteBiased

setFluidNbrDistance

public void setFluidNbrDistance(double newNbrDistance)

makeFccVectors

public void makeFccVectors(double newNbrDistance)

makeHcpVectors

public void makeHcpVectors(double newNbrDistance)

setMaxDistance

public void setMaxDistance(double maxDistance)

getMaxDistance

public double getMaxDistance()

setMaxInsertDistance

public void setMaxInsertDistance(double maxInsertDistance)

reset

public void reset()

setLnBias

public void setLnBias(int n,
                      double nBias)

Overrides:

setLnBias in class MCMoveInsertDeleteBiased

doTrial

public boolean doTrial()

Description copied from class: MCMoveInsertDelete

Chooses and performs with equal probability an elementary molecule insertion or deletion.

Overrides:

doTrial in class MCMoveInsertDelete

findCandidates

protected void findCandidates()

getChi

public double getChi(double temperature)

Description copied from class: MCMove

Chi is the parameter within standard Metropolis Monte Carlo. The probability of accepting the move is given by min(1,chi).

Overrides:

getChi in class MCMoveInsertDeleteBiased

Parameters:

temperature - used to compute chi

Returns:

chi

myAcceptNotify

public void myAcceptNotify()

Overrides:

myAcceptNotify in class MCMoveInsertDeleteBiased

actionPerformed

public void actionPerformed(IEvent event)

Specified by:

actionPerformed in interface IListener