etomica.nbr.list
Class NeighborListManager

java.lang.Object
  etomica.nbr.list.NeighborListManager

All Implemented Interfaces:

IIntegratorListener, AtomLeafAgentManager.AgentSource, Serializable

public class NeighborListManager
extends Object
implements IIntegratorListener, AtomLeafAgentManager.AgentSource, Serializable

Initiates the process of updating the neighbor lists. Instance is constructed by PotentialMasterNbr constructor. Acts as a listener of the integrator(s), and performs the update at regular intervals upon receiving interval events. Each event causes the manager to loop through all boxs acted upon by the integrator (as given by the integrator's getBox method), and check each atom against any neighbor criteria that apply to it, seeing if it has changed (e.g., moved) in a way that requires its neighbor lists to be updated. When this is found for any atom, all atom neighbor lists are updated via a call to the calculate method of PotentialMasterNbr, passing a PotentialCalculationCellAssign instance as the PotentialCalculation.

See Also:

Serialized Form

Nested Class Summary

static class

NeighborListManager.AtomPotential1ListSource

Field Summary

protected AtomSetSinglet	atomSetSinglet
protected IBox	box
protected boolean	doApplyPBC
protected boolean	initialized
protected PotentialMasterList	potentialMaster

Constructor Summary

NeighborListManager(PotentialMasterList potentialMasterList, double range, IBox box, ISpace space)
Configures instance for use by the given PotentialMaster.

Method Summary

void	addAtomNotify(IAtom atom) Constructs neighbor lists for the given atom
void	dispose()
Class	getAgentClass() Returns the Class of the agent.
NeighborCriterion[]	getCriterion(IAtomType atomType)
boolean	getDoApplyPBC()
IAtomList[]	getDownList(IAtom atom)
NeighborListEventManager	getEventManager()
BoxImposePbc	getPbcEnforcer()
AtomPotentialList	getPotential1BodyList(IAtom atom)
double	getRange()
int	getUpdateInterval() Returns the interval for which neighbor update checks are performed.
IAtomList[]	getUpList(IAtom atom)
void	integratorInitialized(IIntegratorEvent e) Invoked when integration begins.
void	integratorStepFinished(IIntegratorEvent e) Invoked at the end of each integrator step.
void	integratorStepStarted(IIntegratorEvent e) Invoked at the beginning of each integrator step.
boolean	isQuiet()
Object	makeAgent(IAtom atom) Returns an agent for the given Atom.
protected void	neighborSetup() Reassigns all interacting atoms to cells, then loops over all cell-list neighbor pairs, determines for each pair whether a potential applies to it, and if so, puts each in the other's neighbor list.
void	releaseAgent(Object agent, IAtom atom) This informs the agent source that the agent is going away and that the agent source should disconnect the agent from other elements
void	reset() For each box in the array, applies central image, resets neighbors of all atoms, and sets up all neighbor lists.
void	setDoApplyPBC(boolean newDoApplyPBC)
void	setPbcEnforcer(BoxImposePbc pbcEnforcer)
void	setQuiet(boolean quiet) Sets the quiet flag, indicating if unsafe-neighbor conditions should generate an error message (would not want this if atoms were inserted in a MC move, for example).
void	setRange(double d) Sets the interaction range, which affects the cell-list neighbor iteration used to generate candidate neighbors for neighbor listing.
void	setUpdateInterval(int updateInterval) Sets the interval for which neighbor update checks are performed.
void	updateLists()
void	updateNbrsIfNeeded() Checks whether any atom needs neighbor list updating, and if one is found, performs neighbor list updates of all atom neighbor lists.

Methods inherited from class java.lang.Object

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

Field Detail

atomSetSinglet

protected final AtomSetSinglet atomSetSinglet

potentialMaster

protected final PotentialMasterList potentialMaster

box

protected IBox box

initialized

protected boolean initialized

doApplyPBC

protected boolean doApplyPBC

Constructor Detail

NeighborListManager

public NeighborListManager(PotentialMasterList potentialMasterList,
                           double range,
                           IBox box,
                           ISpace space)

Configures instance for use by the given PotentialMaster.

Method Detail

setDoApplyPBC

public void setDoApplyPBC(boolean newDoApplyPBC)

getDoApplyPBC

public boolean getDoApplyPBC()

updateLists

public void updateLists()

integratorInitialized

public void integratorInitialized(IIntegratorEvent e)

Description copied from interface: IIntegratorListener

Invoked when integration begins.

Specified by:

integratorInitialized in interface IIntegratorListener

integratorStepFinished

public void integratorStepFinished(IIntegratorEvent e)

Description copied from interface: IIntegratorListener

Invoked at the end of each integrator step.

Specified by:

integratorStepFinished in interface IIntegratorListener

integratorStepStarted

public void integratorStepStarted(IIntegratorEvent e)

Description copied from interface: IIntegratorListener

Invoked at the beginning of each integrator step.

Specified by:

integratorStepStarted in interface IIntegratorListener

reset

public void reset()

For each box in the array, applies central image, resets neighbors of all atoms, and sets up all neighbor lists.

updateNbrsIfNeeded

public void updateNbrsIfNeeded()

Checks whether any atom needs neighbor list updating, and if one is found, performs neighbor list updates of all atom neighbor lists. Performs this action on all boxs acted on by given integrator.

getUpdateInterval

public int getUpdateInterval()

Returns the interval for which neighbor update checks are performed. After receiving this number of interval events, updateNbrsIfNeeded is invoked.

setUpdateInterval

public void setUpdateInterval(int updateInterval)

Sets the interval for which neighbor update checks are performed. After receiving this number of interval events, updateNbrsIfNeeded is invoked.

getCriterion

public NeighborCriterion[] getCriterion(IAtomType atomType)

getPbcEnforcer

public BoxImposePbc getPbcEnforcer()

Returns:

Returns the pbcEnforcer.

setPbcEnforcer

public void setPbcEnforcer(BoxImposePbc pbcEnforcer)

Parameters:

pbcEnforcer - The pbcEnforcer to set.

neighborSetup

protected void neighborSetup()

Reassigns all interacting atoms to cells, then loops over all cell-list neighbor 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.

Parameters:

box - box in which neighbor setup is performed.

addAtomNotify

public void addAtomNotify(IAtom atom)

Constructs neighbor lists for the given atom

setRange

public void setRange(double d)

Sets the interaction range, which affects the cell-list neighbor iteration used to generate candidate neighbors for neighbor listing.

getRange

public double getRange()

isQuiet

public boolean isQuiet()

Returns:

quiet flag, indicating if unsafe-neighbor conditions should generate an error message (would not want this if atoms were inserted in a MC move, for example).

setQuiet

public void setQuiet(boolean quiet)

Sets the quiet flag, indicating if unsafe-neighbor conditions should generate an error message (would not want this if atoms were inserted in a MC move, for example).

Parameters:

quiet - if true, no error will be generated; default is false

getUpList

public IAtomList[] getUpList(IAtom atom)

getDownList

public IAtomList[] getDownList(IAtom atom)

getPotential1BodyList

public AtomPotentialList getPotential1BodyList(IAtom atom)

dispose

public void dispose()

getEventManager

public NeighborListEventManager getEventManager()

getAgentClass

public Class getAgentClass()

Description copied from interface: AtomLeafAgentManager.AgentSource

Returns the Class of the agent. This is used to create an array of the appropriate Class.

Specified by:

getAgentClass in interface AtomLeafAgentManager.AgentSource

makeAgent

public Object makeAgent(IAtom atom)

Description copied from interface: AtomLeafAgentManager.AgentSource

Returns an agent for the given Atom.

Specified by:

makeAgent in interface AtomLeafAgentManager.AgentSource

releaseAgent

public void releaseAgent(Object agent,
                         IAtom atom)

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

Specified by:

releaseAgent in interface AtomLeafAgentManager.AgentSource