Package etomica.nbr.list.molecule

Class PotentialMasterListMolecular

java.lang.Object

etomica.potential.PotentialMaster

etomica.nbr.molecule.PotentialMasterNbrMolecular

etomica.nbr.list.molecule.PotentialMasterListMolecular

public class PotentialMasterListMolecular
extends PotentialMasterNbrMolecular

PotentialMaster used to implement neighbor listing. Instance of this class is given as an argument to the Simulation constructor.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	PotentialMasterListMolecular.NeighborListAgentSourceMolecular

Nested classes/interfaces inherited from class etomica.potential.PotentialMaster

PotentialMaster.AtomIterator0, PotentialMaster.MoleculeIterator0, PotentialMaster.PotentialLinker

Field Summary

Fields

Modifier and Type	Field	Description
protected NeighborCriterionMolecular[]	allCriteria
protected MoleculePair	moleculePair
protected MoleculeSetSinglet	moleculeSetSinglet
protected BoxAgentManager<NeighborListManagerMolecular>	neighborListAgentManager
protected PotentialMasterListMolecular.NeighborListAgentSourceMolecular	neighborListAgentSource
protected double	range
protected Space	space

Fields inherited from class etomica.potential.PotentialMaster

enabled, isPotentialHard, iteratorFactory, lrcMaster, potentialList

Fields inherited from class etomica.nbr.molecule.PotentialMasterNbrMolecular

allPotentials, boxAgentManager, boxAgentSource, rangedAgentManager, simulation, speciesAgentManager

Constructor Summary

Constructors

Constructor	Description
PotentialMasterListMolecular(Simulation sim, double range, IMoleculePositionDefinition positionDefinition, Space _space)	Constructs class using given position definition for all atom cell assignments.
PotentialMasterListMolecular(Simulation sim, double range, BoxAgentSourceCellManagerListMolecular boxAgentSource, BoxAgentManager<? extends BoxCellManager> agentManager, PotentialMasterListMolecular.NeighborListAgentSourceMolecular neighborListAgentSource, Space _space)
PotentialMasterListMolecular(Simulation sim, double range, BoxAgentSourceCellManagerListMolecular boxAgentSource, BoxAgentManager<? extends BoxCellManager> agentManager, Space _space)
PotentialMasterListMolecular(Simulation sim, double range, BoxAgentSourceCellManagerListMolecular boxAgentSource, Space _space)
PotentialMasterListMolecular(Simulation sim, double range, Space _space)	Constructor specifying space and range for neighbor listing; uses null AtomPositionDefinition.
PotentialMasterListMolecular(Simulation sim, Space _space)	Default constructor uses range of 1.0.

Method Summary

Modifier and Type	Method	Description
protected void	addRangedPotentialForSpecies(IPotentialMolecular potential, ISpecies[] species)	Adds the potential as a ranged potential that applies to the given AtomTypes.
void	calculate(Box box, IteratorDirective id, PotentialCalculation pc)	Overrides superclass method to enable direct neighbor-list iteration instead of iteration via species/potential hierarchy.
protected void	calculate(IMolecule molecule, IteratorDirective.Direction direction, PotentialCalculation pc, NeighborListManagerMolecular neighborManager)
protected void	doNBodyStuff(IMolecule molecule, PotentialCalculation pc, int potentialIndex, IPotentialMolecular potential, NeighborListManagerMolecular neighborManager)	Invokes the PotentialCalculationMolecular for the given Molecule with its up and down neighbors as a single MoleculeSet.
int	getCellRange()
NeighborCriterionMolecular	getCriterion(IPotentialMolecular potential)	Returns the criterion used by to determine what atoms interact with the given potential.
double	getMaxPotentialRange()	Returns the maximum range of any potential held by this potential master
NeighborCellManagerMolecular	getNbrCellManager(Box box)
NeighborCriterionMolecular[]	getNeighborCriteria()
NeighborListManagerMolecular	getNeighborManager(Box box)
double	getRange()	Returns the range that determines how far to look for neighbors.
double	getSafetyFactor()	Returns the safety factor.
void	recomputeCriteriaRanges()	Recomputes the range for all criterion based on our own range.
void	removePotential(IPotentialMolecular potential)	Removes given potential from the group.
void	reset()	Recomputes the maximum potential range (which might change without this class receiving notification) and readjust cell lists
void	setCellRange(int newCellRange)
void	setCriterion(IPotentialMolecular potential, NeighborCriterionMolecular criterion)	Sets the criterion associated with the given potential, overriding the default provided by the PotentialMasterList.
void	setRange(double newRange)	Sets the range that determines how far to look for neighbors.
void	setSafetyFactor(double newSafetyFactor)	Sets the safety factor.

Methods inherited from class java.lang.Object

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

Methods inherited from class etomica.potential.PotentialMaster

addPotential, addPotential, getPotential, getPotentials, getSpecies, isEnabled, isEnabled, isEnabled, isPotentialHard, lrcMaster, potentialAddedNotify, removePotential, setEnabled, setEnabled, setEnabled, setPotentialHard

Methods inherited from class etomica.nbr.molecule.PotentialMasterNbrMolecular

addPotential, addRangedPotential, getCellAgentManager, getIntraPotentials, getRangedPotentials, getSimulation, makePotentialGroup

Field Detail

space

protected final Space space

moleculeSetSinglet

protected final MoleculeSetSinglet moleculeSetSinglet

moleculePair

protected final MoleculePair moleculePair

neighborListAgentSource

protected final PotentialMasterListMolecular.NeighborListAgentSourceMolecular neighborListAgentSource

neighborListAgentManager

protected final BoxAgentManager<NeighborListManagerMolecular> neighborListAgentManager

range

protected double range

allCriteria

protected NeighborCriterionMolecular[] allCriteria

Constructor Detail

PotentialMasterListMolecular

public PotentialMasterListMolecular(Simulation sim,
                                    Space _space)

Default constructor uses range of 1.0.

PotentialMasterListMolecular

public PotentialMasterListMolecular(Simulation sim,
                                    double range,
                                    Space _space)

Constructor specifying space and range for neighbor listing; uses null AtomPositionDefinition.

PotentialMasterListMolecular

public PotentialMasterListMolecular(Simulation sim,
                                    double range,
                                    IMoleculePositionDefinition positionDefinition,
                                    Space _space)

Constructs class using given position definition for all atom cell assignments.

Parameters:

positionDefinition - if null, specifies use of atom type's position definition

PotentialMasterListMolecular

public PotentialMasterListMolecular(Simulation sim,
                                    double range,
                                    BoxAgentSourceCellManagerListMolecular boxAgentSource,
                                    Space _space)

PotentialMasterListMolecular

public PotentialMasterListMolecular(Simulation sim,
                                    double range,
                                    BoxAgentSourceCellManagerListMolecular boxAgentSource,
                                    BoxAgentManager<? extends BoxCellManager> agentManager,
                                    Space _space)

PotentialMasterListMolecular

public PotentialMasterListMolecular(Simulation sim,
                                    double range,
                                    BoxAgentSourceCellManagerListMolecular boxAgentSource,
                                    BoxAgentManager<? extends BoxCellManager> agentManager,
                                    PotentialMasterListMolecular.NeighborListAgentSourceMolecular neighborListAgentSource,
                                    Space _space)

Method Detail

setRange

public void setRange(double newRange)

Sets the range that determines how far to look for neighbors. This range must be greater than the range of the longest-range potential.

getRange

public double getRange()

Returns the range that determines how far to look for neighbors.

getMaxPotentialRange

public double getMaxPotentialRange()

Returns the maximum range of any potential held by this potential master

setSafetyFactor

public void setSafetyFactor(double newSafetyFactor)

Sets the safety factor. The default value, 0.4, is appropriate for most simulations. Valid values range from 0 to 0.5 (non-inclusive). The safety factor determines how far an atom can travel from its original position before the neighbor lists are reconstructed. 0.5 means the atom can travel half of its neighbor range. If another atom also travels half-way then the Atoms could interact without the PotentialMaster recognizing they are neighbors. High values of the safetyFactor make it more probable that an Atom will move too far between checks and interact without the PotentialMaster knowing. Smaller values make it less probable, but slow down the simulation due to more frequent neighbor list constructing.

getSafetyFactor

public double getSafetyFactor()

Returns the safety factor.

addRangedPotentialForSpecies

protected void addRangedPotentialForSpecies(IPotentialMolecular potential,
                                            ISpecies[] species)

Adds the potential as a ranged potential that applies to the given AtomTypes. This method creates a criterion for the potential and notifies the NeighborListManager of its existence.

Specified by:

addRangedPotentialForSpecies in class PotentialMasterNbrMolecular

reset

public void reset()

Recomputes the maximum potential range (which might change without this class receiving notification) and readjust cell lists

recomputeCriteriaRanges

public void recomputeCriteriaRanges()

Recomputes the range for all criterion based on our own range. The range for each criterion is set so that they all have an equal max displacement. Our nominal neighbor range is used for the criterion with the longest potential range.

getCriterion

public NeighborCriterionMolecular getCriterion(IPotentialMolecular potential)

Returns the criterion used by to determine what atoms interact with the given potential.

setCriterion

public void setCriterion(IPotentialMolecular potential,
                         NeighborCriterionMolecular criterion)

Sets the criterion associated with the given potential, overriding the default provided by the PotentialMasterList. The criterion can be configured by calling getCriterion(Potential) and changing the criterion. The potential passed to this method must be a potential handled by this instance.

removePotential

public void removePotential(IPotentialMolecular potential)

Description copied from class: PotentialMaster

Removes given potential from the group. No error is generated if potential is not in group.

Overrides:

removePotential in class PotentialMasterNbrMolecular

getNeighborCriteria

public NeighborCriterionMolecular[] getNeighborCriteria()

calculate

public void calculate(Box box,
                      IteratorDirective id,
                      PotentialCalculation pc)

Overrides superclass method to enable direct neighbor-list iteration instead of iteration via species/potential hierarchy. If no target atoms are specified in directive, neighborlist iteration is begun with speciesMaster of box, and repeated recursively down species hierarchy; if one atom is specified, neighborlist iteration is performed on it and down species hierarchy from it; if two or more atoms are specified, superclass method is invoked.

Overrides:

calculate in class PotentialMaster

calculate

protected void calculate(IMolecule molecule,
                         IteratorDirective.Direction direction,
                         PotentialCalculation pc,
                         NeighborListManagerMolecular neighborManager)

doNBodyStuff

protected void doNBodyStuff(IMolecule molecule,
                            PotentialCalculation pc,
                            int potentialIndex,
                            IPotentialMolecular potential,
                            NeighborListManagerMolecular neighborManager)

Invokes the PotentialCalculationMolecular for the given Molecule with its up and down neighbors as a single MoleculeSet.

getNeighborManager

public NeighborListManagerMolecular getNeighborManager(Box box)

getNbrCellManager

public NeighborCellManagerMolecular getNbrCellManager(Box box)

setCellRange

public void setCellRange(int newCellRange)

getCellRange

public int getCellRange()