Package etomica.virial

Class MCMoveClusterAtomHSTree

java.lang.Object

etomica.integrator.mcmove.MCMove

etomica.integrator.mcmove.MCMoveBox

etomica.integrator.mcmove.MCMoveBoxStep

etomica.integrator.mcmove.MCMoveAtom

etomica.virial.MCMoveClusterAtomHSTree

All Implemented Interfaces:

MCMoveStepDependent

Direct Known Subclasses:

MCMoveClusterAtomHSTreeMix, MCMoveClusterAtomSQWTree

public class MCMoveClusterAtomHSTree
extends MCMoveAtom

Class that samples molecule positions based on a tree of hard spheres of diameter sigma. The tree structure is chosen randomly as a Prüfer sequence.

https://en.wikipedia.org/wiki/Pr%C3%BCfer_sequence#Algorithm_to_convert_a_Pr.C3.BCfer_sequence_into_a_tree

Field Summary

Fields

Modifier and Type	Field	Description
protected int[]	a
protected int[][]	bonds
protected int[]	degree
protected boolean	forceInBox
protected int[]	inserted
protected double	sigma

Fields inherited from class etomica.integrator.mcmove.MCMove

moveTracker, nominalFrequency, potential

Fields inherited from class etomica.integrator.mcmove.MCMoveAtom

affectedAtomIterator, atom, atomSource, energyMeter, fixOverlap, random, space, translationVector, uNew, uOld

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
MCMoveClusterAtomHSTree(IRandom random, Space _space, double sigma)

Method Summary

Modifier and Type	Method	Description
void	acceptNotify()	Method called by IntegratorMC in the event that the most recent trial is accepted.
boolean	doTrial()	Method to perform trial move.
double	getChi(double temperature)	Chi is the parameter within standard Metropolis Monte Carlo.
protected double	getSigma(int i, int j)
void	rejectNotify()	Method called by IntegratorMC in the event that the most recent trial move is rejected.
void	setBox(Box box)	Sets the box on which this move acts.
void	setForceInBox(boolean forceInBox)

Methods inherited from class etomica.integrator.mcmove.MCMove

getNominalFrequency, getTracker, setTracker

Methods inherited from class etomica.integrator.mcmove.MCMoveAtom

affectedAtoms, energyChange, getAtomSource, setAtomSource

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

sigma

protected final double sigma

bonds

protected int[][] bonds

degree

protected int[] degree

a

protected int[] a

inserted

protected int[] inserted

forceInBox

protected boolean forceInBox

Constructor Detail

MCMoveClusterAtomHSTree

public MCMoveClusterAtomHSTree(IRandom random,
                               Space _space,
                               double sigma)

Method Detail

setForceInBox

public void setForceInBox(boolean forceInBox)

setBox

public void setBox(Box box)

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 MCMoveAtom

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.

Overrides:

doTrial in class MCMoveAtom

getSigma

protected double getSigma(int i,
                          int j)

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).

Overrides:

getChi in class MCMoveAtom

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.

Overrides:

rejectNotify in class MCMoveAtom

acceptNotify

public void acceptNotify()

Description copied from class: MCMove

Method called by IntegratorMC in the event that the most recent trial is accepted.

Overrides:

acceptNotify in class MCMoveAtom