Package etomica.virial

Class MCMoveClusterTorsionAlkaneEH

java.lang.Object

etomica.integrator.mcmove.MCMove

etomica.integrator.mcmove.MCMoveBox

etomica.integrator.mcmove.MCMoveBoxStep

etomica.integrator.mcmove.MCMoveMolecule

etomica.virial.MCMoveClusterTorsionAlkaneEH

All Implemented Interfaces:

MCMoveMolecular, MCMoveStepDependent

public class MCMoveClusterTorsionAlkaneEH
extends MCMoveMolecule

MC move for alkane-TraPPE-EH torsion pick up carbons in the box only, but move update all the atoms(carbons and hydrogens)

Field Summary

Fields

Modifier and Type	Field	Description
protected double	bias
protected double[]	binSize
protected double	bondLength
protected Vector	dr21
protected Vector	dr23
protected Vector	dr34
protected MeterPotentialEnergy	energyMeter
protected Vector	oldCenter
protected Vector[][]	oldPositions
protected IMoleculePositionDefinition	positionDefinition
protected double[]	probabilityBins
protected int[]	probabilityReverseMap
protected MoleculeArrayList	selectedMolecules
protected ISpecies	species
protected P4BondTorsion	torsionPotential
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, space, uNew, uOld

Constructor Summary

Constructors

Constructor	Description
MCMoveClusterTorsionAlkaneEH(PotentialMaster potentialMaster, Space space, IRandom random, double stepSize, P4BondTorsion torsionPotential, int nBins)
MCMoveClusterTorsionAlkaneEH(Simulation sim, PotentialMaster potentialMaster, Space space, P4BondTorsion torsionPotential)

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.
protected void	selectMolecules()
void	setBondLength(double b)
void	setBox(Box p)	Sets the box on which this move acts.
void	setSpecies(ISpecies newSpecies)
void	setTemperature(double temperature)

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

torsionPotential

protected final P4BondTorsion torsionPotential

positionDefinition

protected IMoleculePositionDefinition positionDefinition

probabilityBins

protected final double[] probabilityBins

binSize

protected final double[] binSize

probabilityReverseMap

protected final int[] probabilityReverseMap

selectedMolecules

protected MoleculeArrayList selectedMolecules

bondLength

protected double bondLength

work1

protected final Vector work1

work2

protected final Vector work2

work3

protected final Vector work3

dr21

protected final Vector dr21

dr23

protected final Vector dr23

dr34

protected final Vector dr34

oldPositions

protected Vector[][] oldPositions

oldCenter

protected final Vector oldCenter

wOld

protected double wOld

wNew

protected double wNew

bias

protected double bias

species

protected ISpecies species

Constructor Detail

MCMoveClusterTorsionAlkaneEH

public MCMoveClusterTorsionAlkaneEH(Simulation sim,
                                    PotentialMaster potentialMaster,
                                    Space space,
                                    P4BondTorsion torsionPotential)

MCMoveClusterTorsionAlkaneEH

public MCMoveClusterTorsionAlkaneEH(PotentialMaster potentialMaster,
                                    Space space,
                                    IRandom random,
                                    double stepSize,
                                    P4BondTorsion torsionPotential,
                                    int nBins)

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

setTemperature

public void setTemperature(double temperature)

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

setBondLength

public void setBondLength(double b)

selectMolecules

protected void selectMolecules()

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