Package etomica.nbr

Class PotentialMasterNbr

java.lang.Object

etomica.potential.PotentialMaster

etomica.nbr.PotentialMasterNbr

Direct Known Subclasses:

PotentialMasterCell, PotentialMasterHybrid, PotentialMasterList, PotentialMasterSite

public abstract class PotentialMasterNbr
extends PotentialMaster

Nested Class Summary

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

PotentialMaster.AtomIterator0, PotentialMaster.MoleculeIterator0, PotentialMaster.PotentialLinker

Field Summary

Fields

Modifier and Type	Field	Description
protected NeighborCriterion[][]	criteria
protected java.util.List<NeighborCriterion>[]	criteria1Body
protected java.util.List<IPotentialAtomic>	potentials0body
protected IPotentialAtomic[][]	rangedPotentials
protected java.util.List<IPotentialAtomic>[]	rangedPotentials1Body
protected Simulation	simulation

Fields inherited from class etomica.potential.PotentialMaster

enabled, isPotentialHard, iteratorFactory, lrcMaster, potentialList

Constructor Summary

Constructors

Constructor	Description
PotentialMasterNbr(Simulation sim)

Method Summary

Modifier and Type	Method	Description
void	addPotential(IPotentialMolecular potential, ISpecies[] species)	Indicates to the PotentialMaster that the given potential should apply to the specified species.
protected void	addRangedPotentialForTypes(IPotentialAtomic subPotential, AtomType[] atomTypes)
abstract BoxCellManager	getBoxCellManager(Box box)
NeighborCriterion[]	getCriteria(AtomType type)
java.util.List<NeighborCriterion>	getCriteria1Body(AtomType type)
NeighborCriterion	getCriterion(AtomType type1, AtomType type2)
PotentialArray	getIntraPotentials(ISpecies species)
IPotentialAtomic[][]	getRangedPotentials()
IPotentialAtomic[]	getRangedPotentials(AtomType atomType)
java.util.List<IPotentialAtomic>	getRangedPotentials1Body(AtomType atomType)
PotentialGroup	makePotentialGroup(int nBody)	Returns an nBody PotentialGroup appropriate for this type of PotentialMaster.
void	potentialAddedNotify(IPotentialAtomic subPotential, PotentialGroup pGroup)	Notifies the PotentialMaster that the sub-potential has been added to the given PotentialGroup, which is associated (but not necessarily held by) this PotentialMaster.
void	removePotential(IPotentialAtomic potential)	Removes given potential from the group.
void	setBoxForCriteria(Box box)	Sets the box for all NeighborCriterions
protected void	setBoxForPotentials(Box box)	Sets the box for all ranged potentials
void	setCriterion(AtomType type1, AtomType type2, NeighborCriterion criterion)	Sets the criterion associated with the given pair of atom types, overriding the default provided by the PotentialMasterList.
void	setCriterion1Body(IPotentialAtomic potential, AtomType type, NeighborCriterion criterion)	Sets the criterion associated with the given 1-body potential, overriding the default provided by the PotentialMasterList.

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, calculate, getPotential, getPotentials, getSpecies, isEnabled, isEnabled, isEnabled, isPotentialHard, lrcMaster, removePotential, setEnabled, setEnabled, setEnabled, setPotentialHard

Field Detail

rangedPotentials

protected final IPotentialAtomic[][] rangedPotentials

rangedPotentials1Body

protected final java.util.List<IPotentialAtomic>[] rangedPotentials1Body

potentials0body

protected final java.util.List<IPotentialAtomic> potentials0body

criteria

protected final NeighborCriterion[][] criteria

criteria1Body

protected final java.util.List<NeighborCriterion>[] criteria1Body

simulation

protected final Simulation simulation

Constructor Detail

PotentialMasterNbr

public PotentialMasterNbr(Simulation sim)

Method Detail

makePotentialGroup

public PotentialGroup makePotentialGroup(int nBody)

Description copied from class: PotentialMaster

Returns an nBody PotentialGroup appropriate for this type of PotentialMaster.

Overrides:

makePotentialGroup in class PotentialMaster

addPotential

public void addPotential(IPotentialMolecular potential,
                         ISpecies[] species)

Description copied from class: PotentialMaster

Indicates to the PotentialMaster that the given potential should apply to the specified species. Exception is thrown if the potential.nBody() value is different from the length of the species array. Thus, for example, if giving a 2-body potential, then the array should contain exactly two species; the species may refer to the same instance (appropriate for an intra-species potential, defining the interactions between molecules of the same species).

Overrides:

addPotential in class PotentialMaster

potentialAddedNotify

public void potentialAddedNotify(IPotentialAtomic subPotential,
                                 PotentialGroup pGroup)

Description copied from class: PotentialMaster

Notifies the PotentialMaster that the sub-potential has been added to the given PotentialGroup, which is associated (but not necessarily held by) this PotentialMaster. This method is called by PotentialGroup and should not be called in other circumstances.

Overrides:

potentialAddedNotify in class PotentialMaster

addRangedPotentialForTypes

protected void addRangedPotentialForTypes(IPotentialAtomic subPotential,
                                          AtomType[] atomTypes)

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 PotentialMaster

getRangedPotentials

public final IPotentialAtomic[][] getRangedPotentials()

getRangedPotentials

public final IPotentialAtomic[] getRangedPotentials(AtomType atomType)

getRangedPotentials1Body

public final java.util.List<IPotentialAtomic> getRangedPotentials1Body(AtomType atomType)

getIntraPotentials

public final PotentialArray getIntraPotentials(ISpecies species)

getCriterion

public NeighborCriterion getCriterion(AtomType type1,
                                      AtomType type2)

Parameters:

type1 - the first atom type

type2 - the second atom type

Returns:

the criterion used to determine when atoms of the given type interact.

getCriteria

public NeighborCriterion[] getCriteria(AtomType type)

Parameters:

type - the atom type for which you want to know the NeighborCriteria

Returns:

an array of NeighborCrtieria for the given AtomType with each other AtomType.

getCriteria1Body

public java.util.List<NeighborCriterion> getCriteria1Body(AtomType type)

Parameters:

type - the atom type for which you want to know the NeighborCriteria

Returns:

aa List of 1-body NeighborCrtieria for the given AtomType with each other AtomType.

setCriterion

public void setCriterion(AtomType type1,
                         AtomType type2,
                         NeighborCriterion criterion)

Sets the criterion associated with the given pair of atom types, overriding the default provided by the PotentialMasterList. The criterion can be configured by calling getCriterion(Potential) and changing the criterion.

setCriterion1Body

public void setCriterion1Body(IPotentialAtomic potential,
                              AtomType type,
                              NeighborCriterion criterion)

Sets the criterion associated with the given 1-body 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.

setBoxForCriteria

public void setBoxForCriteria(Box box)

Sets the box for all NeighborCriterions

Parameters:

box - the box!

setBoxForPotentials

protected void setBoxForPotentials(Box box)

Sets the box for all ranged potentials

Parameters:

box - the box!

getBoxCellManager

public abstract BoxCellManager getBoxCellManager(Box box)