NeighborListManager

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

All Implemented Interfaces:

AtomLeafAgentManager.AgentSource<AtomNeighborLists>, IntegratorListener

Direct Known Subclasses:

NeighborListManagerColloid, NeighborListManagerSlanty
```
public class NeighborListManager
extends java.lang.Object
implements IntegratorListener, AtomLeafAgentManager.AgentSource<AtomNeighborLists>
```
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.

Nested Class Summary

Nested Classes
Modifier and Type Class Description

static class NeighborListManager.AtomPotential1ListSource

Nested Classes
Modifier and Type	Class	Description
`static class`	`NeighborListManager.AtomPotential1ListSource`

Field Summary

Fields
Modifier and Type	Field	Description
`protected AtomLeafAgentManager<AtomPotentialList>`	`agentManager1Body`
`protected AtomLeafAgentManager<AtomNeighborLists>`	`agentManager2Body`
`protected Box`	`box`
`protected boolean`	`initialized`
`protected PotentialMasterList`	`potentialMaster`

Constructor Summary

Constructors
Constructor	Description
`NeighborListManager(PotentialMasterList potentialMasterList, double range, Box box)`
`NeighborListManager(PotentialMasterList potentialMasterList, NeighborCellManager neighborCellManager, double range, Box box)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`addAtomNotify(IAtom atom)`	Constructs neighbor lists for the given atom
`void`	`dispose()`
`void`	`ensureDownLists()`
`boolean`	`getDoApplyPBC()`
`IAtomList[]`	`getDownList(IAtom atom)`
`NeighborListEventManager`	`getEventManager()`
`NeighborCellManager`	`getNeighborCellManager()`
`int`	`getNumUpdates()`	Returns the number of times the neighbor lists have been updated.
`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(IntegratorEvent e)`	Invoked when integration begins.
`void`	`integratorStepFinished(IntegratorEvent e)`	Invoked at the end of each integrator step.
`void`	`integratorStepStarted(IntegratorEvent e)`	Invoked at the beginning of each integrator step.
`boolean`	`isQuiet()`
`AtomNeighborLists`	`makeAgent(IAtom atom, Box agentBox)`	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(AtomNeighborLists nbrLists, 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.
`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`	`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`	`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
  - potentialMaster
```
protected final PotentialMasterList potentialMaster
```
  - agentManager2Body
```
protected final AtomLeafAgentManager<AtomNeighborLists> agentManager2Body
```
  - agentManager1Body
```
protected final AtomLeafAgentManager<AtomPotentialList> agentManager1Body
```
  - box
```
protected Box box
```
  - initialized
```
protected boolean initialized
```
- Constructor Detail
  - NeighborListManager
```
public NeighborListManager(PotentialMasterList potentialMasterList,
                           double range,
                           Box box)
```
  - NeighborListManager
```
public NeighborListManager(PotentialMasterList potentialMasterList,
                           NeighborCellManager neighborCellManager,
                           double range,
                           Box box)
```
- Method Detail
  - getNeighborCellManager
```
public NeighborCellManager getNeighborCellManager()
```
  - getDoApplyPBC
```
public boolean getDoApplyPBC()
```
  - setDoApplyPBC
```
public void setDoApplyPBC(boolean newDoApplyPBC)
```
  - integratorInitialized
```
public void integratorInitialized(IntegratorEvent e)
```
    Description copied from interface: IntegratorListener
    
    Invoked when integration begins.
    
    Specified by:
    
    integratorInitialized in interface IntegratorListener
  - integratorStepFinished
```
public void integratorStepFinished(IntegratorEvent e)
```
    Description copied from interface: IntegratorListener
    
    Invoked at the end of each integrator step.
    
    Specified by:
    
    integratorStepFinished in interface IntegratorListener
  - integratorStepStarted
```
public void integratorStepStarted(IntegratorEvent e)
```
    Description copied from interface: IntegratorListener
    
    Invoked at the beginning of each integrator step.
    
    Specified by:
    
    integratorStepStarted in interface IntegratorListener
  - 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.
  - getNumUpdates
```
public int getNumUpdates()
```
    Returns the number of times the neighbor lists have been updated.
  - getPbcEnforcer
```
public BoxImposePbc getPbcEnforcer()
```
    Returns:
    
    Returns the pbcEnforcer.
  - 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.
  - ensureDownLists
```
public void ensureDownLists()
```
  - addAtomNotify
```
public void addAtomNotify(IAtom atom)
```
    Constructs neighbor lists for the given atom
  - getRange
```
public double getRange()
```
  - 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.
  - 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()
```
  - makeAgent
```
public AtomNeighborLists makeAgent(IAtom atom,
                                   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<AtomNeighborLists>
    
    agentBox - TODO
  - releaseAgent
```
public void releaseAgent(AtomNeighborLists nbrLists,
                         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<AtomNeighborLists>

Class NeighborListManager

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

potentialMaster

agentManager2Body

agentManager1Body

box

initialized

Constructor Detail

NeighborListManager

NeighborListManager

Method Detail

getNeighborCellManager

getDoApplyPBC

setDoApplyPBC

integratorInitialized

integratorStepFinished

integratorStepStarted

reset

updateNbrsIfNeeded

getUpdateInterval

setUpdateInterval

getNumUpdates

getPbcEnforcer

neighborSetup

ensureDownLists

addAtomNotify

getRange

setRange

isQuiet

setQuiet

getUpList

getDownList

getPotential1BodyList

dispose

getEventManager

makeAgent

releaseAgent