Package etomica.integrator.mcmove

Class MCMoveMolecule

java.lang.Object

etomica.integrator.mcmove.MCMove

etomica.integrator.mcmove.MCMoveBox

etomica.integrator.mcmove.MCMoveBoxStep

etomica.integrator.mcmove.MCMoveMolecule

All Implemented Interfaces:

MCMoveMolecular, MCMoveStepDependent

Direct Known Subclasses:

MCMoveBondLength, MCMoveClusterMolecule, MCMoveClusterMoleculeHSChain, MCMoveClusterMoleculeHSChain, MCMoveClusterMoleculeHSChainB3, MCMoveClusterMoleculeMulti, MCMoveClusterRotateCH3, MCMoveClusterTorsionAceticAcid, MCMoveClusterTorsionAlkaneEH, MCMoveClusterTorsionMulti, MCMoveClusterWiggleAceticAcid, MCMoveClusterWiggleAlkaneEH, MCMoveClusterWiggleMulti, MCMoveMoleculeMonomer, MCMoveMoleculeSmer, MCMoveRotateArm, MCMoveRotateMolecule3D, MCMoveRotateMolecule3DConstraint, MCMoveRotateMolecule3DFixedAngle, MCMoveRotateMolecule3DN2AveCosThetaConstraint, MCMoveRotateMolecule3DSuperBox, MCMoveTorsionAceticAcid, MCMoveWiggle, MCMoveWiggleAceticAcid

public class MCMoveMolecule
extends MCMoveBoxStep
implements MCMoveMolecular

Standard Monte Carlo molecule-displacement trial move.

Field Summary

Fields

Modifier and Type	Field	Description
protected AtomIteratorArrayListSimple	affectedAtomIterator
protected MoleculeIteratorSinglet	affectedMoleculeIterator
protected MeterPotentialEnergy	energyMeter
protected Vector	groupTranslationVector
protected IMolecule	molecule
protected MoleculeSource	moleculeSource
protected MoleculeChildAtomAction	moveMoleculeAction
protected IRandom	random
protected Space	space
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
MCMoveMolecule(PotentialMaster potentialMaster, IRandom random, Space space, double stepSize, double stepSizeMax)
MCMoveMolecule(Simulation sim, PotentialMaster potentialMaster, Space space)

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()
MoleculeIterator	affectedMolecules(Box box)
boolean	doTrial()	Method to perform trial move.
double	energyChange()
MoleculeSource	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	setBox(Box p)	Sets the box on which this move acts.
void	setMoleculeSource(MoleculeSource source)

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

affectedMoleculeIterator

protected final MoleculeIteratorSinglet affectedMoleculeIterator

energyMeter

protected final MeterPotentialEnergy energyMeter

uOld

protected double uOld

uNew

protected double uNew

random

protected final IRandom random

space

protected final Space space

moveMoleculeAction

protected final MoleculeChildAtomAction moveMoleculeAction

groupTranslationVector

protected final Vector groupTranslationVector

moleculeSource

protected MoleculeSource moleculeSource

molecule

protected IMolecule molecule

Constructor Detail

MCMoveMolecule

public MCMoveMolecule(Simulation sim,
                      PotentialMaster potentialMaster,
                      Space space)

MCMoveMolecule

public MCMoveMolecule(PotentialMaster potentialMaster,
                      IRandom random,
                      Space space,
                      double stepSize,
                      double stepSizeMax)

Method Detail

doTrial

public boolean doTrial()

Description copied from class: MCMove

Method to perform trial move. Returns false if the trial could not be attempted, for example if there were no molecules in the box and the trial is designed to displace an atom; returns true otherwise.

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()

Description copied from class: MCMove

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

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

affectedAtoms

public AtomIterator affectedAtoms()

Specified by:

affectedAtoms in class MCMoveBox

affectedMolecules

public MoleculeIterator affectedMolecules(Box box)

Specified by:

affectedMolecules in interface MCMoveMolecular

getAtomSource

public MoleculeSource getAtomSource()

Returns:

Returns the atomSource.

setMoleculeSource

public void setMoleculeSource(MoleculeSource source)

Parameters:

source - The atomSource to set.