Package etomica.association

Class MCMoveVolumeAssociatedMolecule

java.lang.Object

etomica.integrator.mcmove.MCMove

etomica.integrator.mcmove.MCMoveBox

etomica.integrator.mcmove.MCMoveBoxStep

etomica.association.MCMoveVolumeAssociatedMolecule

All Implemented Interfaces:

MCMoveMolecular, MCMoveStepDependent, MoleculeAgentManager.MoleculeAgentSource

public class MCMoveVolumeAssociatedMolecule
extends MCMoveBoxStep
implements MoleculeAgentManager.MoleculeAgentSource, MCMoveMolecular

Monte Carlo volume-change move for associating fluids simulations in the NPT ensemble.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	MCMoveVolumeAssociatedMolecule.Agent

Field Summary

Fields

Modifier and Type	Field	Description
protected AtomIteratorLeafAtoms	affectedAtomIterator
protected IAssociationHelperMolecule	associationHelper
protected AssociationManagerMolecule	associationManager
static boolean	dodebug
protected Vector	dr
protected Vector	dr2
protected java.io.FileWriter	fileWriter
protected Vector	groupTranslationVector
protected MoleculeAgentManager	moleculeAgentManager
protected MoleculeIteratorAllMolecules	moleculeIterator
protected MoleculeChildAtomAction	moveMoleculeAction
protected int	numAssociatedMolecules
protected int	numMer
protected double	pressure
protected Vector	r
protected Simulation	sim
protected MoleculeArrayList	smerList

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
MCMoveVolumeAssociatedMolecule(Simulation sim, PotentialMaster potentialMaster, Space _space)
MCMoveVolumeAssociatedMolecule(Simulation sim, PotentialMaster potentialMaster, IRandom random, Space _space, double pressure)

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)
boolean	doTrial()	Method to perform trial move.
double	energyChange()
double	getChi(double temperature)	Chi is the parameter within standard Metropolis Monte Carlo.
double	getPressure()
Dimension	getPressureDimension()
java.lang.Object	makeAgent(IMolecule a)	Returns an agent for the given Atom.
Vector	positionDefinition(IMolecule molecule)
void	rejectNotify()	Method called by IntegratorMC in the event that the most recent trial move is rejected.
void	releaseAgent(java.lang.Object agent, IMolecule molecule)	This informs the agent source that the agent is going away and that the agent source should disconnect the agent from other elements
protected void	scaleAtoms(double rScale)
void	setAssociationManager(AssociationManagerMolecule associationManager, IAssociationHelperMolecule associationHelper)
void	setBox(Box p)	Sets the box on which this move acts.
void	setPressure(double p)
protected void	unscaleAtoms(double rScale)

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

pressure

protected double pressure

affectedAtomIterator

protected final AtomIteratorLeafAtoms affectedAtomIterator

moleculeIterator

protected final MoleculeIteratorAllMolecules moleculeIterator

r

protected final Vector r

dr

protected final Vector dr

dr2

protected final Vector dr2

associationManager

protected AssociationManagerMolecule associationManager

numAssociatedMolecules

protected int numAssociatedMolecules

numMer

protected int numMer

moleculeAgentManager

protected MoleculeAgentManager moleculeAgentManager

smerList

protected final MoleculeArrayList smerList

dodebug

public static boolean dodebug

fileWriter

protected java.io.FileWriter fileWriter

associationHelper

protected IAssociationHelperMolecule associationHelper

groupTranslationVector

protected Vector groupTranslationVector

moveMoleculeAction

protected MoleculeChildAtomAction moveMoleculeAction

sim

protected final Simulation sim

Constructor Detail

MCMoveVolumeAssociatedMolecule

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

MCMoveVolumeAssociatedMolecule

public MCMoveVolumeAssociatedMolecule(Simulation sim,
                                      PotentialMaster potentialMaster,
                                      IRandom random,
                                      Space _space,
                                      double pressure)

Parameters:

potentialMaster - an appropriate PotentialMaster instance for calculating energies

space - the governing space for the simulation

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

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

scaleAtoms

protected void scaleAtoms(double rScale)

unscaleAtoms

protected void unscaleAtoms(double rScale)

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

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

energyChange

public double energyChange()

Specified by:

energyChange in class MCMoveBox

affectedAtoms

public AtomIterator affectedAtoms()

Specified by:

affectedAtoms in class MCMoveBox

positionDefinition

public Vector positionDefinition(IMolecule molecule)

setPressure

public void setPressure(double p)

getPressure

public final double getPressure()

getPressureDimension

public Dimension getPressureDimension()

makeAgent

public java.lang.Object makeAgent(IMolecule a)

Description copied from interface: MoleculeAgentManager.MoleculeAgentSource

Returns an agent for the given Atom.

Specified by:

makeAgent in interface MoleculeAgentManager.MoleculeAgentSource

releaseAgent

public void releaseAgent(java.lang.Object agent,
                         IMolecule molecule)

Description copied from interface: MoleculeAgentManager.MoleculeAgentSource

This informs the agent source that the agent is going away and that the agent source should disconnect the agent from other elements

Specified by:

releaseAgent in interface MoleculeAgentManager.MoleculeAgentSource

affectedMolecules

public MoleculeIterator affectedMolecules(Box box)

Specified by:

affectedMolecules in interface MCMoveMolecular