Package etomica.virial

Class MCMoveClusterAngleBendAceticAcid

java.lang.Object

etomica.integrator.mcmove.MCMove

etomica.integrator.mcmove.MCMoveBox

etomica.integrator.mcmove.MCMoveBoxStep

etomica.virial.MCMoveClusterAngleBendAceticAcid

All Implemented Interfaces:

MCMoveStepDependent

public class MCMoveClusterAngleBendAceticAcid
extends MCMoveBoxStep

An MC Move for cluster simulations that bends the bond angle for 3-atom molecule. The COM is not moved and both end atoms are moved by the same amount such that the move does not alter the orientation of the molecule.

Field Summary

Fields

Modifier and Type	Field	Description
protected AtomIteratorArrayListSimple	affectedAtomIterator
protected double[]	dTheta
protected MeterPotentialEnergy	energyMeter
protected MoleculeSource	moleculeSource
protected IRandom	random
protected Space	space
protected ISpecies	species
protected double	uNew
protected double	uOld
protected double	wNew
protected double	wOld
protected Vector	work1
protected Vector	work2
protected Vector	work3

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
MCMoveClusterAngleBendAceticAcid(PotentialMaster potentialMaster, IRandom random, double stepSize, Space _space)
MCMoveClusterAngleBendAceticAcid(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()
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)
void	setSpecies(ISpecies newSpecies)
protected void	transform(IMolecule molecule, double dt)

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

energyMeter

protected final MeterPotentialEnergy energyMeter

work1

protected final Vector work1

work2

protected final Vector work2

work3

protected final Vector work3

dTheta

protected double[] dTheta

wOld

protected double wOld

wNew

protected double wNew

space

protected final Space space

species

protected ISpecies species

uOld

protected double uOld

uNew

protected double uNew

random

protected final IRandom random

moleculeSource

protected MoleculeSource moleculeSource

Constructor Detail

MCMoveClusterAngleBendAceticAcid

public MCMoveClusterAngleBendAceticAcid(Simulation sim,
                                        PotentialMaster potentialMaster,
                                        Space _space)

MCMoveClusterAngleBendAceticAcid

public MCMoveClusterAngleBendAceticAcid(PotentialMaster potentialMaster,
                                        IRandom random,
                                        double stepSize,
                                        Space _space)

Method Detail

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

setSpecies

public void setSpecies(ISpecies newSpecies)

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

transform

protected void transform(IMolecule molecule,
                         double dt)

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

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

affectedAtoms

public AtomIterator affectedAtoms()

Specified by:

affectedAtoms in class MCMoveBox

getAtomSource

public MoleculeSource getAtomSource()

Returns:

Returns the atomSource.

setMoleculeSource

public void setMoleculeSource(MoleculeSource source)

Parameters:

source - The atomSource to set.