Package etomica.association

Class MCMoveBiasUBMolecule

java.lang.Object

etomica.integrator.mcmove.MCMove

etomica.integrator.mcmove.MCMoveBox

etomica.association.MCMoveBiasUBMolecule

All Implemented Interfaces:

MCMoveMolecular

public class MCMoveBiasUBMolecule
extends MCMoveBox
implements MCMoveMolecular

Field Summary

Fields

Modifier and Type	Field	Description
protected MoleculeIteratorSinglet	affectedMoleculeIterator
protected Vector	groupTranslationVector
protected MoleculeChildAtomAction	moveMoleculeAction
protected RotationTensor3D	rotationTensor
protected MoleculeArrayList	smerList
protected Space	space

Fields inherited from class etomica.integrator.mcmove.MCMove

moveTracker, nominalFrequency, potential

Fields inherited from class etomica.integrator.mcmove.MCMoveBox

box, perParticleFrequency

Constructor Summary

Constructors

Constructor	Description
MCMoveBiasUBMolecule(PotentialMaster potentialMaster, BiasVolumeMolecule bv, IRandom random, 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)
protected void	doTransform(IMolecule molecule, Vector r0)
boolean	doTrial()	Method to perform trial move.
double	energyChange()
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(AssociationManagerMolecule associationManager, IAssociationHelperMolecule associationHelper)
void	setBox(Box box)	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 java.lang.Object

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

Field Detail

affectedMoleculeIterator

protected final MoleculeIteratorSinglet affectedMoleculeIterator

smerList

protected final MoleculeArrayList smerList

space

protected final Space space

rotationTensor

protected final RotationTensor3D rotationTensor

groupTranslationVector

protected Vector groupTranslationVector

moveMoleculeAction

protected MoleculeChildAtomAction moveMoleculeAction

Constructor Detail

MCMoveBiasUBMolecule

public MCMoveBiasUBMolecule(PotentialMaster potentialMaster,
                            BiasVolumeMolecule bv,
                            IRandom random,
                            Space space)

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 MCMoveBox

setAssociationManager

public void setAssociationManager(AssociationManagerMolecule associationManager,
                                  IAssociationHelperMolecule associationHelper)

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

affectedAtoms

public AtomIterator affectedAtoms()

Specified by:

affectedAtoms in class MCMoveBox

doTransform

protected void doTransform(IMolecule molecule,
                           Vector r0)

energyChange

public double energyChange()

Specified by:

energyChange in class MCMoveBox

acceptNotify

public void acceptNotify()

Description copied from class: MCMove

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

affectedMolecules

public MoleculeIterator affectedMolecules(Box box)

Specified by:

affectedMolecules in interface MCMoveMolecular