Package etomica.nbr.list

Class PotentialMasterList

java.lang.Object

etomica.potential.PotentialMaster

etomica.nbr.PotentialMasterNbr

etomica.nbr.list.PotentialMasterList

public class PotentialMasterList
extends PotentialMasterNbr

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

Nested Class Summary

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

PotentialMaster.AtomIterator0, PotentialMaster.MoleculeIterator0, PotentialMaster.PotentialLinker

Field Summary

Fields inherited from class etomica.potential.PotentialMaster

enabled, isPotentialHard, iteratorFactory, lrcMaster, potentialList

Fields inherited from class etomica.nbr.PotentialMasterNbr

criteria, criteria1Body, potentials0body, rangedPotentials, rangedPotentials1Body, simulation

Constructor Summary

Constructors

Constructor	Description
PotentialMasterList(Simulation sim, double range, NeighborListAgentSource neighborListAgentSource, Space _space)
PotentialMasterList(Simulation sim, double range, Space _space)
PotentialMasterList(Simulation sim, Space _space)	Default constructor uses range of 1.0.

Method Summary

Modifier and Type	Method	Description
void	addPotentialNbrList(IPotentialAtomic potential, AtomType[] atomTypes, NeighborCriterion criterion)	Add the given potential to be used for the given atom types and the given criterion.
protected void	addRangedPotentialForTypes(IPotentialAtomic potential, AtomType[] atomType)	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.
void	calculate(Box box, PotentialCalculation pc, boolean includeLrc)
BoxCellManager	getBoxCellManager(Box box)
int	getCellRange()
double	getMaxPotentialRange()	Returns the maximum range of any potential held by this potential master
NeighborCellManager	getNbrCellManager(Box box)
NeighborListManager	getNeighborManager(Box box)
double	getRange()	Returns the range that determines how far to look for neighbors.
double	getSafetyFactor()	Returns the safety factor.
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	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, removePotential, setEnabled, setEnabled, setEnabled, setPotentialHard

Methods inherited from class etomica.nbr.PotentialMasterNbr

addPotential, getCriteria, getCriteria1Body, getCriterion, getIntraPotentials, getRangedPotentials, getRangedPotentials, getRangedPotentials1Body, makePotentialGroup, potentialAddedNotify, setBoxForCriteria, setBoxForPotentials, setCriterion, setCriterion1Body

Constructor Detail

PotentialMasterList

public PotentialMasterList(Simulation sim,
                           Space _space)

Default constructor uses range of 1.0.

PotentialMasterList

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

PotentialMasterList

public PotentialMasterList(Simulation sim,
                           double range,
                           NeighborListAgentSource neighborListAgentSource,
                           Space _space)

Method Detail

getRange

public double getRange()

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

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.

getMaxPotentialRange

public double getMaxPotentialRange()

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

getSafetyFactor

public double getSafetyFactor()

Returns the safety factor.

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.

getCellRange

public int getCellRange()

setCellRange

public void setCellRange(int newCellRange)

getNeighborManager

public NeighborListManager getNeighborManager(Box box)

getNbrCellManager

public NeighborCellManager getNbrCellManager(Box box)

addPotentialNbrList

public void addPotentialNbrList(IPotentialAtomic potential,
                                AtomType[] atomTypes,
                                NeighborCriterion criterion)

Add the given potential to be used for the given atom types and the given criterion. If multiple types are given, then the potential will be used for any set of atoms containing only the atom types listed; if types A and B are passed, then the potential will be used for A-A, A-B, B-A and B-B. The criterion must handle any additional filtering.

The given potential will not be held by a PotentialGroup.

addRangedPotentialForTypes

protected void addRangedPotentialForTypes(IPotentialAtomic potential,
                                          AtomType[] 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.

Overrides:

addRangedPotentialForTypes in class PotentialMasterNbr

removePotential

public void removePotential(IPotentialAtomic 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 PotentialMasterNbr

getBoxCellManager

public BoxCellManager getBoxCellManager(Box box)

Specified by:

getBoxCellManager in class PotentialMasterNbr

reset

public void reset()

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

calculate

public void calculate(Box box,
                      PotentialCalculation pc,
                      boolean includeLrc)

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