Package etomica.virial

Class MCMoveClusterRingRegrow

java.lang.Object

etomica.integrator.mcmove.MCMove

etomica.integrator.mcmove.MCMoveBox

etomica.virial.MCMoveClusterRingRegrow

public class MCMoveClusterRingRegrow
extends MCMoveBox

MCMove that fully regrows the beads of a ring polymer, accepting or rejecting the move based on the sampling weight. The move can (optionally) regrow the beads such that the beads from multiple molecules are combined to form a larger ring.

Field Summary

Fields

Modifier and Type	Field	Description
protected Vector	com
protected Vector	com0
protected double	fac
protected AtomIteratorLeafAtoms	leafIterator
protected AtomArrayList	myAtoms
protected int	nTrial
protected Vector[][]	oldPositions
protected double[]	pkl
protected IRandom	random
protected Vector[]	rTrial
protected Space	space
protected int[][]	tangledMolecules
protected double	weightNew
protected double	weightOld
protected double	wNew
protected double	wOld

Fields inherited from class etomica.integrator.mcmove.MCMove

moveTracker, nominalFrequency, potential

Fields inherited from class etomica.integrator.mcmove.MCMoveBox

box, perParticleFrequency

Constructor Summary

Constructors

Constructor	Description
MCMoveClusterRingRegrow(IRandom random, Space _space)
MCMoveClusterRingRegrow(IRandom random, Space _space, int[][] tangledMolecules)

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.
int	getNumTrial()
void	rejectNotify()	Method called by IntegratorMC in the event that the most recent trial move is rejected.
void	setBox(Box p)	Sets the box on which this move acts.
void	setEnergyFactor(double factor)	sets the harmonic bond "energy" factor The probability of the bond have length x is proportional to exp(-factor*x^2) (there is no temperature involved here)
void	setNumTrial(int newNumTrial)	Sets the number of configurational bias trials

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 java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

space

protected final Space space

random

protected final IRandom random

oldPositions

protected Vector[][] oldPositions

rTrial

protected Vector[] rTrial

nTrial

protected int nTrial

pkl

protected double[] pkl

wOld

protected double wOld

wNew

protected double wNew

weightOld

protected double weightOld

weightNew

protected double weightNew

com

protected final Vector com

com0

protected final Vector com0

leafIterator

protected final AtomIteratorLeafAtoms leafIterator

fac

protected double fac

tangledMolecules

protected final int[][] tangledMolecules

myAtoms

protected final AtomArrayList myAtoms

Constructor Detail

MCMoveClusterRingRegrow

public MCMoveClusterRingRegrow(IRandom random,
                               Space _space)

MCMoveClusterRingRegrow

public MCMoveClusterRingRegrow(IRandom random,
                               Space _space,
                               int[][] tangledMolecules)

Method Detail

setNumTrial

public void setNumTrial(int newNumTrial)

Sets the number of configurational bias trials

getNumTrial

public int getNumTrial()

setEnergyFactor

public void setEnergyFactor(double factor)

sets the harmonic bond "energy" factor The probability of the bond have length x is proportional to exp(-factor*x^2) (there is no temperature involved here)

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

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

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

energyChange

public double energyChange()

Specified by:

energyChange in class MCMoveBox

affectedAtoms

public AtomIterator affectedAtoms()

Specified by:

affectedAtoms in class MCMoveBox