Package etomica.virial

Class MCMoveClusterWiggleAceticAcid

java.lang.Object

etomica.integrator.mcmove.MCMove

etomica.integrator.mcmove.MCMoveBox

etomica.integrator.mcmove.MCMoveBoxStep

etomica.integrator.mcmove.MCMoveMolecule

etomica.virial.MCMoveClusterWiggleAceticAcid

All Implemented Interfaces:

MCMoveMolecular, MCMoveStepDependent

public class MCMoveClusterWiggleAceticAcid
extends MCMoveMolecule

An MC Move for cluster simulations that "wiggles" a chain molecule. If the first or last atom in the chain is chosen, it is moved to a new position with the same bond length as before, but perturbed by some angle from its original position. If an Atom in the middle of the chain is chosen, a crankshaft move is performed that maintains its distances with its neighbors. If a middle Atom has a bond angle too close to 180 degrees (such that rotation does nothing) the Atom is not moved at all. In each doTrial, wiggle moves are attempted on all molecules in the box.

Field Summary

Fields

Modifier and Type	Field	Description
protected int[]	bondedAtoms
protected MeterPotentialEnergy	energyMeter
protected int[]	selectedAtoms
protected Space	space
protected ISpecies	species
protected Vector[]	translationVectors
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

Fields inherited from class etomica.integrator.mcmove.MCMoveMolecule

affectedAtomIterator, affectedMoleculeIterator, groupTranslationVector, molecule, moleculeSource, moveMoleculeAction, random, uNew, uOld

Constructor Summary

Constructors

Constructor	Description
MCMoveClusterWiggleAceticAcid(PotentialMaster potentialMaster, IRandom random, double stepSize, Space _space)
MCMoveClusterWiggleAceticAcid(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.
boolean	doTrial()	Method to perform trial move.
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	setSpecies(ISpecies newSpecies)

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 etomica.integrator.mcmove.MCMoveMolecule

affectedAtoms, affectedMolecules, energyChange, getAtomSource, setMoleculeSource

Methods inherited from class java.lang.Object

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

Field Detail

energyMeter

protected final MeterPotentialEnergy energyMeter

selectedAtoms

protected int[] selectedAtoms

bondedAtoms

protected int[] bondedAtoms

work1

protected final Vector work1

work2

protected final Vector work2

work3

protected final Vector work3

translationVectors

protected Vector[] translationVectors

wOld

protected double wOld

wNew

protected double wNew

space

protected final Space space

species

protected ISpecies species

Constructor Detail

MCMoveClusterWiggleAceticAcid

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

MCMoveClusterWiggleAceticAcid

public MCMoveClusterWiggleAceticAcid(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 MCMoveMolecule

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.

Overrides:

doTrial in class MCMoveMolecule

acceptNotify

public void acceptNotify()

Description copied from class: MCMoveMolecule

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

Overrides:

acceptNotify in class MCMoveMolecule

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.

Overrides:

rejectNotify in class MCMoveMolecule

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 MCMoveMolecule

Parameters:

temperature - used to compute chi

Returns:

chi