Package etomica.nbr.list.molecule

Class NeighborListManagerSlantyMolecular

java.lang.Object

etomica.nbr.list.molecule.NeighborListManagerMolecular

etomica.nbr.list.molecule.NeighborListManagerSlantyMolecular

All Implemented Interfaces:

IntegratorListener, MoleculeAgentManager.MoleculeAgentSource

public class NeighborListManagerSlantyMolecular
extends NeighborListManagerMolecular

Implements neighbor listing for a slanty box. Because using slanty cells would be hard, we avoid them entirely. Neighbors are found by looping over all pairs of atoms. This is slow, but you're running a solid, right? So you don't really mind.

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	NeighborListManagerSlantyMolecular.NeighborListSlantyAgentSourceMolecular	Constructs instances of NeighborListManagerSlanty on behalf of the PotentialMaster

Nested classes/interfaces inherited from class etomica.nbr.list.molecule.NeighborListManagerMolecular

NeighborListManagerMolecular.MoleculePotential1ListSource

Field Summary

Fields

Modifier and Type	Field	Description
protected MoleculePair	pair

Fields inherited from class etomica.nbr.list.molecule.NeighborListManagerMolecular

agentManager1Body, agentManager2Body, box, doApplyPBC, initialized, moleculeSetSinglet, potentialMaster

Constructor Summary

Constructors

Constructor	Description
NeighborListManagerSlantyMolecular(PotentialMasterListMolecular potentialMasterList, double range, Box box, Space space)	Configures instance for use by the given PotentialMaster.

Method Summary

Modifier and Type	Method	Description
void	addMoleculeNotify(IMolecule molecule)	Constructs neighbor lists for the given molecule
protected void	neighborSetup()	Reassigns all interacting atoms to cells, then loops over all atom pairs, determines for each pair whether a potential applies to it, and if so, puts each in the other's neighbor list.

Methods inherited from class etomica.nbr.list.molecule.NeighborListManagerMolecular

dispose, getCriterion, getDoApplyPBC, getDownList, getEventManager, getPbcEnforcer, getPotential1BodyList, getRange, getUpdateInterval, getUpList, integratorInitialized, integratorStepFinished, integratorStepStarted, isQuiet, makeAgent, releaseAgent, reset, setDoApplyPBC, setPbcEnforcer, setQuiet, setRange, setUpdateInterval, updateLists, updateNbrsIfNeeded

Methods inherited from class java.lang.Object

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

Field Detail

pair

protected final MoleculePair pair

Constructor Detail

NeighborListManagerSlantyMolecular

public NeighborListManagerSlantyMolecular(PotentialMasterListMolecular potentialMasterList,
                                          double range,
                                          Box box,
                                          Space space)

Configures instance for use by the given PotentialMaster.

Method Detail

neighborSetup

protected void neighborSetup()

Reassigns all interacting atoms to cells, then loops over all atom pairs, determines for each pair whether a potential applies to it, and if so, puts each in the other's neighbor list. Called by updateNbrsIfNeeded, and by reset.

Overrides:

neighborSetup in class NeighborListManagerMolecular

addMoleculeNotify

public void addMoleculeNotify(IMolecule molecule)

Constructs neighbor lists for the given molecule

Overrides:

addMoleculeNotify in class NeighborListManagerMolecular