etomica.nbr.list
Class PotentialMasterList

java.lang.Object
  etomica.potential.PotentialMaster
      etomica.nbr.PotentialMasterNbr
          etomica.nbr.list.PotentialMasterList

All Implemented Interfaces:

IPotentialMaster, AtomTypeAgentManager.AgentSource, SpeciesAgentManager.AgentSource, Serializable

public class PotentialMasterList
extends PotentialMasterNbr

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

See Also:

Serialized Form

Nested Class Summary

protected static class

PotentialMasterList.NeighborListAgentSource

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

PotentialMaster.AtomIterator0, PotentialMaster.PotentialLinker

Field Summary

protected NeighborCriterion[]	allCriteria
protected AtomPair	atomPair
protected AtomSetSinglet	atomSetSinglet
protected BoxAgentManager	neighborListAgentManager
protected PotentialMasterList.NeighborListAgentSource	neighborListAgentSource
protected double	range
protected ISpace	space

Fields inherited from class etomica.nbr.PotentialMasterNbr

allPotentials, boxAgentManager, boxAgentSource, intraAgentManager, intraPotentialIterator, rangedAgentManager, rangedPotentialIterator, simulation

Fields inherited from class etomica.potential.PotentialMaster

enabled, first, iteratorFactory, last, lrcMaster

Constructor Summary

PotentialMasterList(ISimulation sim, double range, BoxAgentSourceCellManagerList boxAgentSource, BoxAgentManager agentManager, ISpace _space)

PotentialMasterList(ISimulation sim, double range, BoxAgentSourceCellManagerList boxAgentSource, BoxAgentManager agentManager, PotentialMasterList.NeighborListAgentSource neighborListAgentSource, ISpace _space)

PotentialMasterList(ISimulation sim, double range, BoxAgentSourceCellManagerList boxAgentSource, ISpace _space)

PotentialMasterList(ISimulation sim, double range, IAtomPositionDefinition positionDefinition, ISpace _space)
Constructs class using given position definition for all atom cell assignments.

PotentialMasterList(ISimulation sim, double range, ISpace _space)
Constructor specifying space and range for neighbor listing; uses null AtomPositionDefinition.

PotentialMasterList(ISimulation sim, ISpace _space)
Default constructor uses range of 1.0.

Method Summary

protected void	addRangedPotentialForTypes(IPotentialAtomic potential, IAtomType[] atomType) Adds the potential as a ranged potential that applies to the given AtomTypes.
protected void	calculate(IAtom atom, IteratorDirective.Direction direction, PotentialCalculation pc, NeighborListManager neighborManager)
void	calculate(IBox 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, NeighborListManager neighborManager) Performs given PotentialCalculation using potentials/neighbors associated with the given atom (if any).
protected void	doNBodyStuff(IAtom atom, PotentialCalculation pc, int potentialIndex, IPotentialAtomic potential, NeighborListManager neighborManager) Invokes the PotentialCalculation for the given Atom with its up and down neighbors as a single AtomSet.
int	getCellRange()
NeighborCriterion	getCriterion(IPotentialAtomic 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
NeighborCellManager	getNbrCellManager(IBox box)
NeighborCriterion[]	getNeighborCriteria()
NeighborListManager	getNeighborManager(IBox 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(IPotentialAtomic 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(IPotentialAtomic potential, NeighborCriterion 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 etomica.nbr.PotentialMasterNbr

addPotential, addRangedPotential, getCellAgentManager, getIntraPotentials, getRangedPotentials, getSimulation, getSpeciesAgentClass, makeAgent, makeAgent, makePotentialGroup, potentialAddedNotify, releaseAgent, releaseAgent

Methods inherited from class etomica.potential.PotentialMaster

addModel, addPotential, addPotential, getPotential, getPotentials, getSpecies, isEnabled, isEnabled, isEnabled, lrcMaster, removePotential, setEnabled, setEnabled, setEnabled

Methods inherited from class java.lang.Object

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

Field Detail

space

protected final ISpace space

atomSetSinglet

protected final AtomSetSinglet atomSetSinglet

atomPair

protected final AtomPair atomPair

neighborListAgentSource

protected final PotentialMasterList.NeighborListAgentSource neighborListAgentSource

neighborListAgentManager

protected final BoxAgentManager neighborListAgentManager

range

protected double range

allCriteria

protected NeighborCriterion[] allCriteria

Constructor Detail

PotentialMasterList

public PotentialMasterList(ISimulation sim,
                           ISpace _space)

Default constructor uses range of 1.0.

PotentialMasterList

public PotentialMasterList(ISimulation sim,
                           double range,
                           ISpace _space)

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

PotentialMasterList

public PotentialMasterList(ISimulation sim,
                           double range,
                           IAtomPositionDefinition positionDefinition,
                           ISpace _space)

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

Parameters:

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

PotentialMasterList

public PotentialMasterList(ISimulation sim,
                           double range,
                           BoxAgentSourceCellManagerList boxAgentSource,
                           ISpace _space)

PotentialMasterList

public PotentialMasterList(ISimulation sim,
                           double range,
                           BoxAgentSourceCellManagerList boxAgentSource,
                           BoxAgentManager agentManager,
                           ISpace _space)

PotentialMasterList

public PotentialMasterList(ISimulation sim,
                           double range,
                           BoxAgentSourceCellManagerList boxAgentSource,
                           BoxAgentManager agentManager,
                           PotentialMasterList.NeighborListAgentSource neighborListAgentSource,
                           ISpace _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.

addRangedPotentialForTypes

protected void addRangedPotentialForTypes(IPotentialAtomic potential,
                                          IAtomType[] atomType)

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:

addRangedPotentialForTypes in class PotentialMasterNbr

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 NeighborCriterion getCriterion(IPotentialAtomic potential)

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

setCriterion

public void setCriterion(IPotentialAtomic potential,
                         NeighborCriterion 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(IPotentialAtomic potential)

Description copied from interface: IPotentialMaster

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

Specified by:

removePotential in interface IPotentialMaster

Overrides:

removePotential in class PotentialMasterNbr

getNeighborCriteria

public NeighborCriterion[] getNeighborCriteria()

calculate

public void calculate(IBox 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.

Specified by:

calculate in interface IPotentialMaster

Overrides:

calculate in class PotentialMaster

calculate

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

Performs given PotentialCalculation using potentials/neighbors associated with the given atom (if any). Then, if atom is not a leaf atom, iteration over child atoms is performed and process is repeated (recursively) with each on down the hierarchy until leaf atoms are reached.

calculate

protected void calculate(IAtom atom,
                         IteratorDirective.Direction direction,
                         PotentialCalculation pc,
                         NeighborListManager neighborManager)

doNBodyStuff

protected void doNBodyStuff(IAtom atom,
                            PotentialCalculation pc,
                            int potentialIndex,
                            IPotentialAtomic potential,
                            NeighborListManager neighborManager)

Invokes the PotentialCalculation for the given Atom with its up and down neighbors as a single AtomSet.

getNeighborManager

public NeighborListManager getNeighborManager(IBox box)

getNbrCellManager

public NeighborCellManager getNbrCellManager(IBox box)

setCellRange

public void setCellRange(int newCellRange)

getCellRange

public int getCellRange()