Package etomica.association

Class MCMoveDimer

java.lang.Object

etomica.integrator.mcmove.MCMove

etomica.integrator.mcmove.MCMoveBox

etomica.integrator.mcmove.MCMoveBoxStep

etomica.association.MCMoveDimer

All Implemented Interfaces:

MCMoveStepDependent

public class MCMoveDimer
extends MCMoveBoxStep

Standard Monte Carlo atom-displacement trial move of dimer

Field Summary

Fields

Modifier and Type	Field	Description
protected AtomIteratorArrayListSimple	affectedAtomIterator
protected AtomArrayList	affectedAtoms
protected AssociationManager	associationManager
protected IAtom	atom
protected IAtom	atom1
protected AtomSource	atomSource
protected IPotentialAtomic	dimerPotential
protected Vector	dr
protected MeterPotentialEnergy	energyMeter
protected boolean	fixOverlap
protected PotentialMasterCell	potentialMaster
protected IRandom	random
protected Space	space
protected Vector	translationVector
protected double	uNew
protected double	uOld

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.MCMoveBoxStep

stepSize, stepSizeMax, stepSizeMin

Constructor Summary

Constructors

Constructor	Description
MCMoveDimer(PotentialMasterCell potentialMaster, IRandom random, Space _space, double stepSize, double stepSizeMax, boolean fixOverlap, IPotentialAtomic dimerPotential)
MCMoveDimer(Simulation sim, PotentialMasterCell potentialMaster, Space _space, IPotentialAtomic dimerPotential)

Method Summary

Modifier and Type	Method	Description
void	acceptNotify()	Method called by IntegratorMC in the event that the most recent trial is accepted.
AtomIterator	affectedAtoms()
boolean	doTrial()	Method to perform trial move.
double	energyChange()
AtomSource	getAtomSource()
double	getChi(double temperature)	Chi is the parameter within standard Metropolis Monte Carlo.
void	rejectNotify()	Method called by IntegratorMC in the event that the most recent trial move is rejected.
void	setAssociationManager(AssociationManager associationManager)
void	setAtomSource(AtomSource source)
void	setBox(Box p)	Sets the box on which this move acts.

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.MCMoveBoxStep

getStepSize, getStepSizeDimension, getStepSizeMax, getStepSizeMaxDimension, getStepSizeMin, getStepSizeMinDimension, setStepSize, setStepSizeMax, setStepSizeMin

Methods inherited from class java.lang.Object

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

Field Detail

affectedAtomIterator

protected final AtomIteratorArrayListSimple affectedAtomIterator

affectedAtoms

protected final AtomArrayList affectedAtoms

energyMeter

protected final MeterPotentialEnergy energyMeter

translationVector

protected final Vector translationVector

atom

protected IAtom atom

uOld

protected double uOld

uNew

protected double uNew

atomSource

protected AtomSource atomSource

fixOverlap

protected boolean fixOverlap

random

protected final IRandom random

space

protected Space space

potentialMaster

protected final PotentialMasterCell potentialMaster

dr

protected final Vector dr

dimerPotential

protected final IPotentialAtomic dimerPotential

atom1

protected IAtom atom1

associationManager

protected AssociationManager associationManager

Constructor Detail

MCMoveDimer

public MCMoveDimer(Simulation sim,
                   PotentialMasterCell potentialMaster,
                   Space _space,
                   IPotentialAtomic dimerPotential)

MCMoveDimer

public MCMoveDimer(PotentialMasterCell potentialMaster,
                   IRandom random,
                   Space _space,
                   double stepSize,
                   double stepSizeMax,
                   boolean fixOverlap,
                   IPotentialAtomic dimerPotential)

Method Detail

setAssociationManager

public void setAssociationManager(AssociationManager associationManager)

doTrial

public boolean doTrial()

Method to perform trial move.

Specified by:

doTrial in class MCMove

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).

Specified by:

getChi in class MCMove

Parameters:

temperature - used to compute chi

Returns:

chi

energyChange

public double energyChange()

Specified by:

energyChange in class MCMoveBox

acceptNotify

public void acceptNotify()

Method called by IntegratorMC in the event that the most recent trial is accepted.

Specified by:

acceptNotify in class MCMove

rejectNotify

public void rejectNotify()

Method called by IntegratorMC in the event that the most recent trial move is rejected. This method should cause the system to be restored to the condition before the most recent call to doTrial.

Specified by:

rejectNotify in class MCMove

affectedAtoms

public AtomIterator affectedAtoms()

Specified by:

affectedAtoms in class MCMoveBox

setBox

public void setBox(Box p)

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 MCMoveBox

getAtomSource

public AtomSource getAtomSource()

Returns:

Returns the atomSource.

setAtomSource

public void setAtomSource(AtomSource source)

Parameters:

source - The atomSource to set.