Package etomica.association

Class AssociationManager

java.lang.Object

etomica.association.AssociationManager

All Implemented Interfaces:

AtomLeafAgentManager.AgentSource<AtomArrayList>, IListener

public class AssociationManager
extends java.lang.Object
implements AtomLeafAgentManager.AgentSource<AtomArrayList>, IListener

Class to define and track atom associations. Constructed given an iterator that defines the set of atoms that is managed, and an association definition that is used to determine if atoms are associated. Only pairwise associations are considered. To incorporate an instance of this class in a simulation, add an instance of this EnergySum inner class to the simulation:
sim.setEnergySum(associationManager.new EnergySum());

If a MC simulation, this should be done before any MCMove classes are instantiated. Also, register this as a listener to IntegratorMC:
integrator.addMCMoveListener(associationManager);

Constructor Summary

Constructors

Constructor	Description
AssociationManager(Box box, PotentialMasterCell potentialMaster, AssociationDefinition definition)

Method Summary

Modifier and Type	Method	Description
void	actionPerformed(IEvent evt)
IAtomList	getAssociatedAtoms()
IAtomList	getAssociatedAtoms(IAtom atom)	Returns the number of atoms on the list of associations of the given atom.
AssociationDefinition	getAssociationDefinition()
void	initialize()
AtomArrayList	makeAgent(IAtom a, Box agentBox)	Returns an agent for the given Atom.
void	releaseAgent(AtomArrayList agent, IAtom atom, Box agentBox)	This informs the agent source that the agent is going away and that the agent source should disconnect the agent from other elements.

Methods inherited from class java.lang.Object

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

Constructor Detail

AssociationManager

public AssociationManager(Box box,
                          PotentialMasterCell potentialMaster,
                          AssociationDefinition definition)

Method Detail

getAssociationDefinition

public AssociationDefinition getAssociationDefinition()

initialize

public void initialize()

getAssociatedAtoms

public IAtomList getAssociatedAtoms()

actionPerformed

public void actionPerformed(IEvent evt)

Specified by:

actionPerformed in interface IListener

getAssociatedAtoms

public IAtomList getAssociatedAtoms(IAtom atom)

Returns the number of atoms on the list of associations of the given atom.

makeAgent

public AtomArrayList makeAgent(IAtom a,
                               Box agentBox)

Description copied from interface: AtomLeafAgentManager.AgentSource

Returns an agent for the given Atom. The agentBox is provided for convenience for agent sources that handle multiple boxes.

Specified by:

makeAgent in interface AtomLeafAgentManager.AgentSource<AtomArrayList>

agentBox - TODO

releaseAgent

public void releaseAgent(AtomArrayList agent,
                         IAtom atom,
                         Box agentBox)

Description copied from interface: AtomLeafAgentManager.AgentSource

This informs the agent source that the agent is going away and that the agent source should disconnect the agent from other elements. The agentBox is provided for convenience for agent sources that handle multiple boxes.

Specified by:

releaseAgent in interface AtomLeafAgentManager.AgentSource<AtomArrayList>