Package etomica.association

Class MCMoveVolumeAssociated

java.lang.Object

etomica.integrator.mcmove.MCMove

etomica.integrator.mcmove.MCMoveBox

etomica.integrator.mcmove.MCMoveBoxStep

etomica.association.MCMoveVolumeAssociated

All Implemented Interfaces:

AtomLeafAgentManager.AgentSource<MCMoveVolumeAssociated.Agent>, MCMoveStepDependent

public class MCMoveVolumeAssociated
extends MCMoveBoxStep
implements AtomLeafAgentManager.AgentSource<MCMoveVolumeAssociated.Agent>

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

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	MCMoveVolumeAssociated.Agent

Field Summary

Fields

Modifier and Type	Field	Description
protected AtomIteratorLeafAtoms	affectedAtomIterator
protected AssociationManager	associationManager
protected AtomLeafAgentManager<MCMoveVolumeAssociated.Agent>	atomLeafAgentManager
static boolean	dodebug
protected Vector	dr
protected Vector	dr2
protected java.io.FileWriter	fileWriter
protected int	numAssociatedAtoms
protected int	numMer
protected double	pressure
protected Vector	r
protected AtomArrayList	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
MCMoveVolumeAssociated(PotentialMaster potentialMaster, IRandom random, Space _space, double pressure)
MCMoveVolumeAssociated(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()
double	getChi(double temperature)	Chi is the parameter within standard Metropolis Monte Carlo.
double	getPressure()
Dimension	getPressureDimension()
MCMoveVolumeAssociated.Agent	makeAgent(IAtom a, Box agentBox)	Returns an agent for the given Atom.
protected int	populateList(AtomArrayList mySmerList, IAtom atom)
void	rejectNotify()	Method called by IntegratorMC in the event that the most recent trial move is rejected.
void	releaseAgent(MCMoveVolumeAssociated.Agent agent, IAtom atom, Box agentBox)	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(AssociationManager associationManager)
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

r

protected final Vector r

dr

protected final Vector dr

dr2

protected final Vector dr2

associationManager

protected AssociationManager associationManager

numAssociatedAtoms

protected int numAssociatedAtoms

numMer

protected int numMer

atomLeafAgentManager

protected AtomLeafAgentManager<MCMoveVolumeAssociated.Agent> atomLeafAgentManager

smerList

protected final AtomArrayList smerList

dodebug

public static boolean dodebug

fileWriter

protected java.io.FileWriter fileWriter

Constructor Detail

MCMoveVolumeAssociated

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

MCMoveVolumeAssociated

public MCMoveVolumeAssociated(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

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)

populateList

protected int populateList(AtomArrayList mySmerList,
                           IAtom atom)

setAssociationManager

public void setAssociationManager(AssociationManager associationManager)

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

setPressure

public void setPressure(double p)

getPressure

public final double getPressure()

getPressureDimension

public Dimension getPressureDimension()

makeAgent

public MCMoveVolumeAssociated.Agent makeAgent(IAtom a,
                                              Box agentBox)

Description copied from interface: AtomLeafAgentManager.AgentSource

Returns an agent for the given Atom. The agentBox is provided for convenience for agent sources that handle multiple boxes.

Specified by:

makeAgent in interface AtomLeafAgentManager.AgentSource<MCMoveVolumeAssociated.Agent>

agentBox - TODO

releaseAgent

public void releaseAgent(MCMoveVolumeAssociated.Agent agent,
                         IAtom atom,
                         Box agentBox)

Description copied from interface: AtomLeafAgentManager.AgentSource

This informs the agent source that the agent is going away and that the agent source should disconnect the agent from other elements. The agentBox is provided for convenience for agent sources that handle multiple boxes.

Specified by:

releaseAgent in interface AtomLeafAgentManager.AgentSource<MCMoveVolumeAssociated.Agent>