Package etomica.integrator.mcmove

Class MCMoveAtom

java.lang.Object

etomica.integrator.mcmove.MCMove

etomica.integrator.mcmove.MCMoveBox

etomica.integrator.mcmove.MCMoveBoxStep

etomica.integrator.mcmove.MCMoveAtom

All Implemented Interfaces:

MCMoveStepDependent

Direct Known Subclasses:

MCMoveAtomDimer, MCMoveAtomInRegion, MCMoveAtomMonomer, MCMoveAtomNbr, MCMoveAtomNoSmer, MCMoveAtomNPath, MCMoveAtomSmer, MCMoveClusterAtom, MCMoveClusterAtomChainHSTail, MCMoveClusterAtomDiscrete, MCMoveClusterAtomHSChain, MCMoveClusterAtomHSRing, MCMoveClusterAtomHSTree, MCMoveClusterAtomInBox, MCMoveClusterAtomMulti, MCMoveClusterAtomQ, MCMoveClusterAtomRotateMulti, MCMoveClusterPolyhedraChain, MCMoveClusterPolyhedraTree, MCMoveRotate, MCMoveRotateAssociated

public class MCMoveAtom
extends MCMoveBoxStep

Standard Monte Carlo atom-displacement trial move. Selects an atom at random, displaces it to a new position selected at random on a cube centered on its current position. The set of atoms subject to the trial can be configured; default is all leaf-atoms.

Field Summary

Fields

Modifier and Type	Field	Description
protected AtomIteratorSinglet	affectedAtomIterator
protected IAtom	atom
protected AtomSource	atomSource
protected MeterPotentialEnergy	energyMeter
protected boolean	fixOverlap
protected IRandom	random
protected Space	space
protected Vector	translationVector
protected double	uNew
protected double	uOld

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
MCMoveAtom(IRandom random, PotentialMaster potentialMaster, Space space)	Constructs the move with default stepSize = 1.0, stepSizeMax = 15.0, fixOverlap = false
MCMoveAtom(IRandom random, PotentialMaster potentialMaster, Space space, double stepSize, double stepSizeMax, boolean fixOverlap)
MCMoveAtom(IRandom random, PotentialMaster potentialMaster, Space space, double stepSize, double stepSizeMax, boolean fixOverlap, MeterPotentialEnergy meterPE)	Constructs with specification of special-purpose energy meter.

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()
AtomSource	getAtomSource()	The AtomSource is used to select the atom at the beginning of the trial
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	setAtomSource(AtomSource source)
void	setBox(Box p)	Sets the box on which this move acts.

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

affectedAtomIterator

protected final AtomIteratorSinglet affectedAtomIterator

energyMeter

protected final MeterPotentialEnergy energyMeter

translationVector

protected final Vector translationVector

random

protected final IRandom random

fixOverlap

protected final boolean fixOverlap

space

protected final Space space

atom

protected IAtom atom

uOld

protected double uOld

uNew

protected double uNew

atomSource

protected AtomSource atomSource

Constructor Detail

MCMoveAtom

public MCMoveAtom(IRandom random,
                  PotentialMaster potentialMaster,
                  Space space)

Constructs the move with default stepSize = 1.0, stepSizeMax = 15.0, fixOverlap = false

Parameters:

random - random number generator used to select the atom and its displacement

potentialMaster - used to construct MeterPotentialEnergy required by full constructor

space - space of the simulation

MCMoveAtom

public MCMoveAtom(IRandom random,
                  PotentialMaster potentialMaster,
                  Space space,
                  double stepSize,
                  double stepSizeMax,
                  boolean fixOverlap)

Parameters:

random - random number generator used to select the atom and its displacement

potentialMaster - used to construct MeterPotentialEnergy required by full constructor

space - space of the simulation

stepSize - starting step size for the trial

stepSizeMax - maximum allowable value of stepSize

fixOverlap - flag specifying whether trial throws an exception if the configuration at the start of the trial has an overlap

MCMoveAtom

public MCMoveAtom(IRandom random,
                  PotentialMaster potentialMaster,
                  Space space,
                  double stepSize,
                  double stepSizeMax,
                  boolean fixOverlap,
                  MeterPotentialEnergy meterPE)

Constructs with specification of special-purpose energy meter.

Parameters:

random - random number generator used to select the atom and its displacement

potentialMaster - not directly used

space - space of the simulation

stepSize - starting step size for the trial

stepSizeMax - maximum allowable value of stepSize

fixOverlap - if false, throws an exception if the configuration at the start of the trial has an overlap

meterPE - used to compute energies before and after displacement

Method Detail

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

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

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

affectedAtoms

public AtomIterator affectedAtoms()

Specified by:

affectedAtoms in class MCMoveBox

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

getAtomSource

public AtomSource getAtomSource()

The AtomSource is used to select the atom at the beginning of the trial

Returns:

the atomSource.

setAtomSource

public void setAtomSource(AtomSource source)

Parameters:

source - The atomSource to set.