Package etomica.association

Class AssociationManagerMolecule

java.lang.Object

etomica.association.AssociationManagerMolecule

All Implemented Interfaces:

MoleculeAgentManager.MoleculeAgentSource, IListener

public class AssociationManagerMolecule
extends java.lang.Object
implements MoleculeAgentManager.MoleculeAgentSource, IListener

Class to define and track molecule associations. Constructed given an iterator that defines the set of molecules that is managed, and an association definition that is used to determine if molecules are associated. 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
AssociationManagerMolecule(Simulation sim, Box box, BoxAgentManager<NeighborCellManagerMolecular> cellAgentManager, AssociationDefinitionMolecule definition, double range)

Method Summary

Modifier and Type	Method	Description
void	actionPerformed(IEvent evt)
IMoleculeList	getAssociatedMolecules()
IMoleculeList	getAssociatedMolecules(IMolecule molecule)	Returns the number of atoms on the list of associations of the given atom.
AssociationDefinitionMolecule	getAssociationDefinition()
void	initialize()
java.lang.Object	makeAgent(IMolecule a)	Returns an agent for the given Atom.
void	releaseAgent(java.lang.Object agent, IMolecule atom)	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

AssociationManagerMolecule

public AssociationManagerMolecule(Simulation sim,
                                  Box box,
                                  BoxAgentManager<NeighborCellManagerMolecular> cellAgentManager,
                                  AssociationDefinitionMolecule definition,
                                  double range)

Method Detail

getAssociationDefinition

public AssociationDefinitionMolecule getAssociationDefinition()

initialize

public void initialize()

getAssociatedMolecules

public IMoleculeList getAssociatedMolecules()

actionPerformed

public void actionPerformed(IEvent evt)

Specified by:

actionPerformed in interface IListener

getAssociatedMolecules

public IMoleculeList getAssociatedMolecules(IMolecule molecule)

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

makeAgent

public java.lang.Object makeAgent(IMolecule a)

Description copied from interface: MoleculeAgentManager.MoleculeAgentSource

Returns an agent for the given Atom.

Specified by:

makeAgent in interface MoleculeAgentManager.MoleculeAgentSource

releaseAgent

public void releaseAgent(java.lang.Object agent,
                         IMolecule atom)

Description copied from interface: MoleculeAgentManager.MoleculeAgentSource

This informs the agent source that the agent is going away and that the agent source should disconnect the agent from other elements

Specified by:

releaseAgent in interface MoleculeAgentManager.MoleculeAgentSource