Package etomica.models.nitrogen

Class MCMoveMoleculeCoupledSuperBox

java.lang.Object

etomica.integrator.mcmove.MCMove

etomica.integrator.mcmove.MCMoveBox

etomica.integrator.mcmove.MCMoveBoxStep

etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox

All Implemented Interfaces:

MCMoveMolecular, MCMoveStepDependent

public class MCMoveMoleculeCoupledSuperBox
extends MCMoveBoxStep
implements MCMoveMolecular

Standard Monte Carlo molecule-displacement trial move for superbox. Two molecules are moved at a time in such a way that the geometric center of the system is not changed. When move one molecule in the center cell; the same molecule in the other 26 unit cells will move too! The potential master that being passed in this class is a "full-strength" potential without multiplying by 0.5 for the speciesA and speciesB interaction.

Field Summary

Fields

Modifier and Type	Field	Description
protected MoleculeIteratorArrayListSimple	affectedMoleculeIterator
protected MoleculeArrayList	affectedMoleculeList
protected CoordinateDefinition.BasisCell[]	basisCell
protected MeterPotentialEnergy	energyMeter
protected Vector	groupTransVect
protected IMolecule	molecule0
protected IMolecule	molecule1
protected MoleculeSource	moleculeSource
protected int[][]	molIndex
protected IMolecule	molSpeciesA
protected IMolecule	molSpeciesB
protected MoleculeChildAtomAction	moveMoleculeAction
protected int	nA
protected MoleculePair	pair
protected MoleculePair	pairAB
protected IPotentialMolecular	potential
protected IRandom	random
protected int	randomMol0
protected int	randomMol1
protected AtomActionTranslateBy	singleAction
protected double	uCorrect
protected double	uNew
protected double	uOld

Fields inherited from class etomica.integrator.mcmove.MCMove

moveTracker, nominalFrequency

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
MCMoveMoleculeCoupledSuperBox(PotentialMaster potentialMaster, IRandom nRandom, Space _space, Box box, int nC, int basis, CoordinateDefinitionNitrogenSuperBox coordinateDef)

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 aBox)
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	setBox(Box newBox)	Sets the box on which this move acts.
void	setPotential(IPotentialMolecular newPotential)

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

moveMoleculeAction

protected final MoleculeChildAtomAction moveMoleculeAction

groupTransVect

protected final Vector groupTransVect

molecule0

protected IMolecule molecule0

molecule1

protected IMolecule molecule1

energyMeter

protected final MeterPotentialEnergy energyMeter

moleculeSource

protected MoleculeSource moleculeSource

uOld

protected double uOld

uNew

protected double uNew

random

protected final IRandom random

affectedMoleculeIterator

protected MoleculeIteratorArrayListSimple affectedMoleculeIterator

affectedMoleculeList

protected MoleculeArrayList affectedMoleculeList

singleAction

protected final AtomActionTranslateBy singleAction

pair

protected final MoleculePair pair

pairAB

protected final MoleculePair pairAB

potential

protected IPotentialMolecular potential

molIndex

protected int[][] molIndex

randomMol0

protected int randomMol0

randomMol1

protected int randomMol1

molSpeciesA

protected IMolecule molSpeciesA

molSpeciesB

protected IMolecule molSpeciesB

nA

protected int nA

basisCell

protected CoordinateDefinition.BasisCell[] basisCell

uCorrect

protected double uCorrect

Constructor Detail

MCMoveMoleculeCoupledSuperBox

public MCMoveMoleculeCoupledSuperBox(PotentialMaster potentialMaster,
                                     IRandom nRandom,
                                     Space _space,
                                     Box box,
                                     int nC,
                                     int basis,
                                     CoordinateDefinitionNitrogenSuperBox coordinateDef)

Method Detail

setBox

public void setBox(Box newBox)

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

setPotential

public void setPotential(IPotentialMolecular newPotential)

affectedAtoms

public AtomIterator affectedAtoms()

Specified by:

affectedAtoms in class MCMoveBox

affectedMolecules

public MoleculeIterator affectedMolecules(Box aBox)

Specified by:

affectedMolecules in interface MCMoveMolecular

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

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

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