NeighborListManagerMolecular

java.lang.Object
- etomica.nbr.list.molecule.NeighborListManagerMolecular

All Implemented Interfaces:

IntegratorListener, MoleculeAgentManager.MoleculeAgentSource, java.io.Serializable

Direct Known Subclasses:

NeighborListManagerSlantyMolecular
```
public class NeighborListManagerMolecular
extends java.lang.Object
implements IntegratorListener, MoleculeAgentManager.MoleculeAgentSource, java.io.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

Nested Classes
Modifier and Type Class Description

static class NeighborListManagerMolecular.MoleculePotential1ListSource

Nested Classes
Modifier and Type	Class	Description
`static class`	`NeighborListManagerMolecular.MoleculePotential1ListSource`

Field Summary

Fields
Modifier and Type	Field	Description
`protected MoleculeAgentManager`	`agentManager1Body`
`protected MoleculeAgentManager`	`agentManager2Body`
`protected Box`	`box`
`protected boolean`	`doApplyPBC`
`protected boolean`	`initialized`
`protected MoleculeSetSinglet`	`moleculeSetSinglet`
`protected PotentialMasterListMolecular`	`potentialMaster`

Constructor Summary

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

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`addMoleculeNotify(IMolecule molecule)`	Constructs neighbor lists for the given atom
`void`	`dispose()`
`NeighborCriterionMolecular[]`	`getCriterion(ISpecies species)`
`boolean`	`getDoApplyPBC()`
`IMoleculeList[]`	`getDownList(IMolecule molecule)`
`NeighborListEventManagerMolecular`	`getEventManager()`
`BoxImposePbc`	`getPbcEnforcer()`
`MoleculePotentialList`	`getPotential1BodyList(IMolecule molecule)`
`double`	`getRange()`
`int`	`getUpdateInterval()`	Returns the interval for which neighbor update checks are performed.
`IMoleculeList[]`	`getUpList(IMolecule molecule)`
`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()`
`java.lang.Object`	`makeAgent(IMolecule molecule)`	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(java.lang.Object agent, IMolecule molecule)`	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
  - moleculeSetSinglet
```
protected final MoleculeSetSinglet moleculeSetSinglet
```
  - potentialMaster
```
protected final PotentialMasterListMolecular potentialMaster
```
  - agentManager2Body
```
protected final MoleculeAgentManager agentManager2Body
```
  - agentManager1Body
```
protected final MoleculeAgentManager agentManager1Body
```
  - box
```
protected Box box
```
  - initialized
```
protected boolean initialized
```
  - doApplyPBC
```
protected boolean doApplyPBC
```
- Constructor Detail
  - NeighborListManagerMolecular
```
public NeighborListManagerMolecular(PotentialMasterListMolecular potentialMasterList,
                                    double range,
                                    Box box,
                                    Space 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(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.
  - getCriterion
```
public NeighborCriterionMolecular[] getCriterion(ISpecies species)
```
  - 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.
  - addMoleculeNotify
```
public void addMoleculeNotify(IMolecule molecule)
```
    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 IMoleculeList[] getUpList(IMolecule molecule)
```
  - getDownList
```
public IMoleculeList[] getDownList(IMolecule molecule)
```
  - getPotential1BodyList
```
public MoleculePotentialList getPotential1BodyList(IMolecule molecule)
```
  - dispose
```
public void dispose()
```
  - getEventManager
```
public NeighborListEventManagerMolecular getEventManager()
```
  - makeAgent
```
public java.lang.Object makeAgent(IMolecule molecule)
```
    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 molecule)
```
    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

Class NeighborListManagerMolecular

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

moleculeSetSinglet

potentialMaster

agentManager2Body

agentManager1Body

box

initialized

doApplyPBC

Constructor Detail

NeighborListManagerMolecular

Method Detail

setDoApplyPBC

getDoApplyPBC

updateLists

integratorInitialized

integratorStepFinished

integratorStepStarted

reset

updateNbrsIfNeeded

getUpdateInterval

setUpdateInterval

getCriterion

getPbcEnforcer

setPbcEnforcer

neighborSetup

addMoleculeNotify

setRange

getRange

isQuiet

setQuiet

getUpList

getDownList

getPotential1BodyList

dispose

getEventManager

makeAgent

releaseAgent