Package etomica.models.nitrogen

Class MCMoveMoleculeCoupledInitPert

java.lang.Object

etomica.integrator.mcmove.MCMove

etomica.integrator.mcmove.MCMoveBox

etomica.integrator.mcmove.MCMoveBoxStep

etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert

All Implemented Interfaces:

MCMoveStepDependent

public class MCMoveMoleculeCoupledInitPert
extends MCMoveBoxStep

Standard Monte Carlo molecule-displacement trial move. Two molecules are moved at a time in such a way that the geometric center of the system is not changed. Specifically for no-rotational energy perturbation - before calculating the translational energy for the molecule, the molecule is rotated to its nominal orientation and later it's rotated back to its orientation

Field Summary

Fields

Modifier and Type	Field	Description
protected AtomIteratorArrayListSimple	affectedMoleculeIterator
protected AtomArrayList	affectedMoleculeList
protected CoordinateDefinitionNitrogen	coordinateDef
protected boolean	doExcludeNonNeighbors
protected boolean	doIncludePair
protected MeterPotentialEnergy	energyMeter
protected Vector	groupTransVect
protected double[]	initU
protected IMolecule	molecule0
protected IMolecule	molecule1
protected MoleculeSource	moleculeSource
protected MoleculeChildAtomAction	moveMoleculeAction
protected MoleculePair	pair
protected IPotentialMolecular	pairPotential
protected IRandom	random
protected AtomActionTranslateBy	singleAction
protected double[]	tempU
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
MCMoveMoleculeCoupledInitPert(PotentialMaster potentialMaster, IRandom nRandom, Space _space, CoordinateDefinitionNitrogen coordinateDef)

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.
boolean	getDoExcludeNonNeighbors()	Returns true if the move does not explicitly calculate the potential for atom pairs that are not neighbors (as determined by the potentialMaster).
void	rejectNotify()	Method called by IntegratorMC in the event that the most recent trial move is rejected.
void	setBox(Box newBox)	Sets the box on which this move acts.
void	setDoExcludeNonNeighbors(boolean newDoExcludeNonNeighbors)	Configures the move to not explicitly calculate the potential for atom pairs that are not neighbors (as determined by the potentialMaster).
void	setPotential(IPotentialMolecular newPotential)

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

moveMoleculeAction

protected final MoleculeChildAtomAction moveMoleculeAction

groupTransVect

protected final Vector groupTransVect

molecule0

protected IMolecule molecule0

molecule1

protected IMolecule molecule1

energyMeter

protected final MeterPotentialEnergy energyMeter

moleculeSource

protected MoleculeSource moleculeSource

uOld

protected double uOld

uNew

protected double uNew

random

protected final IRandom random

affectedMoleculeIterator

protected final AtomIteratorArrayListSimple affectedMoleculeIterator

affectedMoleculeList

protected final AtomArrayList affectedMoleculeList

singleAction

protected final AtomActionTranslateBy singleAction

pair

protected final MoleculePair pair

pairPotential

protected IPotentialMolecular pairPotential

doExcludeNonNeighbors

protected boolean doExcludeNonNeighbors

doIncludePair

protected boolean doIncludePair

coordinateDef

protected CoordinateDefinitionNitrogen coordinateDef

initU

protected double[] initU

tempU

protected double[] tempU

Constructor Detail

MCMoveMoleculeCoupledInitPert

public MCMoveMoleculeCoupledInitPert(PotentialMaster potentialMaster,
                                     IRandom nRandom,
                                     Space _space,
                                     CoordinateDefinitionNitrogen coordinateDef)

Method Detail

setBox

public void setBox(Box newBox)

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

setPotential

public void setPotential(IPotentialMolecular newPotential)

affectedAtoms

public AtomIterator affectedAtoms()

Specified by:

affectedAtoms in class MCMoveBox

energyChange

public double energyChange()

Specified by:

energyChange 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

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

setDoExcludeNonNeighbors

public void setDoExcludeNonNeighbors(boolean newDoExcludeNonNeighbors)

Configures the move to not explicitly calculate the potential for atom pairs that are not neighbors (as determined by the potentialMaster). Setting this has an effect only if the potentialMaster is an instance of PotentialMasterList

getDoExcludeNonNeighbors

public boolean getDoExcludeNonNeighbors()

Returns true if the move does not explicitly calculate the potential for atom pairs that are not neighbors (as determined by the potentialMaster).