NeighborCellManager

java.lang.Object
- etomica.nbr.cell.NeighborCellManager

All Implemented Interfaces:

AtomLeafAgentManager.AgentSource<Cell>, BoxCellManager, BoundaryEventListener
```
public class NeighborCellManager
extends java.lang.Object
implements BoxCellManager, BoundaryEventListener, AtomLeafAgentManager.AgentSource<Cell>
```
Class that defines and manages construction and use of lattice of cells for cell-based neighbor listing. Before starting the simulation, it is necessary call makeMCMoveListener and register the result with the MCMoveEventManager of the Integrator.

Field Summary

Fields
Modifier and Type	Field	Description
`protected AtomLeafAgentManager<Cell>`	`agentManager`
`protected Box`	`box`
`protected int`	`cellRange`
`protected boolean`	`doApplyPBC`
`protected CellLattice`	`lattice`
`protected int[]`	`numCells`
`protected IMoleculePositionDefinition`	`positionDefinition`
`protected double`	`range`
`protected boolean`	`suppressBoxLengthWarning`
`protected Vector`	`v`

Constructor Summary

Constructors
Constructor	Description
`NeighborCellManager(Box box, double potentialRange)`	Constructs manager for neighbor cells in the given box.
`NeighborCellManager(Box box, double potentialRange, IMoleculePositionDefinition positionDefinition)`	Construct manager for neighbor cells in the given box.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`assignCell(IAtom atom)`	Assigns the cell for the given atom.
`void`	`assignCellAll()`	Assigns cells to all interacting atoms in the box.
`void`	`boundaryInflate(BoundaryEvent e)`	Informs the listener that the boundary shape and/or size has changed.
`protected boolean`	`checkDimensions()`	Checks the box's dimensions to make sure the number of cells is appropriate.
`Cell`	`getCell(IAtom atom)`
`int`	`getCellRange()`	Returns the cellRange.
`boolean`	`getDoApplyPBC()`
`CellLattice`	`getLattice()`	Returns the lattice that defines the cell arrangement.
`double`	`getPotentialRange()`	Returns the potential range.
`Cell`	`makeAgent(IAtom atom, Box agentBox)`	Returns the cell containing the given atom.
`IListener<MCMoveEvent>`	`makeMCMoveListener()`
`void`	`releaseAgent(Cell cell, IAtom atom, Box agentBox)`	Removes the given atom from the cell.
`void`	`setCellRange(int newCellRange)`	Sets the cell range to the given value.
`void`	`setDoApplyPBC(boolean newDoApplyPBC)`
`void`	`setPotentialRange(double newRange)`	Sets the potential range to the given value.
`void`	`setSuppressBoxLengthWarning(boolean doSuppress)`
`void`	`updateCell(IAtom atom)`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - lattice
```
protected final CellLattice lattice
```
  - positionDefinition
```
protected final IMoleculePositionDefinition positionDefinition
```
  - box
```
protected final Box box
```
  - cellRange
```
protected int cellRange
```
  - range
```
protected double range
```
  - agentManager
```
protected final AtomLeafAgentManager<Cell> agentManager
```
  - doApplyPBC
```
protected boolean doApplyPBC
```
  - v
```
protected final Vector v
```
  - numCells
```
protected final int[] numCells
```
  - suppressBoxLengthWarning
```
protected boolean suppressBoxLengthWarning
```
- Constructor Detail
  - NeighborCellManager
```
public NeighborCellManager(Box box,
                           double potentialRange)
```
    Constructs manager for neighbor cells in the given box. The number of cells in each dimension is given by nCells. Position definition for each atom is that given by its type (it is set to null in this class).
  - NeighborCellManager
```
public NeighborCellManager(Box box,
                           double potentialRange,
                           IMoleculePositionDefinition positionDefinition)
```
    Construct manager for neighbor cells in the given box. The number of cells in each dimension is given by nCells. Position definition is used to determine the cell a given atom is in; if null, the position definition given by the atom's type is used. Position definition is declared final.
- Method Detail
  - setSuppressBoxLengthWarning
```
public void setSuppressBoxLengthWarning(boolean doSuppress)
```
    Parameters:
    
    doSuppress - warnings about box length being too small. This is useful if the potential range is short enough, but the neighbor listing padding does not fit in the box.
  - setDoApplyPBC
```
public void setDoApplyPBC(boolean newDoApplyPBC)
```
  - getDoApplyPBC
```
public boolean getDoApplyPBC()
```
  - getLattice
```
public CellLattice getLattice()
```
    Description copied from interface: BoxCellManager
    
    Returns the lattice that defines the cell arrangement.
    
    Specified by:
    
    getLattice in interface BoxCellManager
  - setPotentialRange
```
public void setPotentialRange(double newRange)
```
    Sets the potential range to the given value. Cells are made large enough so that cellRange*cellSize > potentialRange.
  - getPotentialRange
```
public double getPotentialRange()
```
    Returns the potential range.
  - getCellRange
```
public int getCellRange()
```
    Returns the cellRange.
  - setCellRange
```
public void setCellRange(int newCellRange)
```
    Sets the cell range to the given value. Cells are made large enough so that cellRange*cellSize > potentialRange
  - boundaryInflate
```
public void boundaryInflate(BoundaryEvent e)
```
    Description copied from interface: BoundaryEventListener
    
    Informs the listener that the boundary shape and/or size has changed.
    
    Specified by:
    
    boundaryInflate in interface BoundaryEventListener
    
    Parameters:
    
    e - event, which can be used to determine the boundary that changed.
  - checkDimensions
```
protected boolean checkDimensions()
```
    Checks the box's dimensions to make sure the number of cells is appropriate.
  - assignCellAll
```
public void assignCellAll()
```
    Assigns cells to all interacting atoms in the box. Interacting atoms are those that have one or more potentials that act on them.
    
    Specified by:
    
    assignCellAll in interface BoxCellManager
  - getCell
```
public Cell getCell(IAtom atom)
```
  - assignCell
```
public void assignCell(IAtom atom)
```
    Assigns the cell for the given atom. The atom will be listed in the cell's atom list and the cell with be associated with the atom via agentManager.
  - updateCell
```
public void updateCell(IAtom atom)
```
  - makeMCMoveListener
```
public IListener<MCMoveEvent> makeMCMoveListener()
```
  - makeAgent
```
public Cell makeAgent(IAtom atom,
                      Box agentBox)
```
    Returns the cell containing the given atom. The atom is added to the cell's atom list.
    
    Specified by:
    
    makeAgent in interface AtomLeafAgentManager.AgentSource<Cell>
    
    agentBox - TODO
  - releaseAgent
```
public void releaseAgent(Cell cell,
                         IAtom atom,
                         Box agentBox)
```
    Removes the given atom from the cell.
    
    Specified by:
    
    releaseAgent in interface AtomLeafAgentManager.AgentSource<Cell>

Class NeighborCellManager

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

lattice

positionDefinition

box

cellRange

range

agentManager

doApplyPBC

v

numCells

suppressBoxLengthWarning

Constructor Detail

NeighborCellManager

NeighborCellManager

Method Detail

setSuppressBoxLengthWarning

setDoApplyPBC

getDoApplyPBC

getLattice

setPotentialRange

getPotentialRange

getCellRange

setCellRange

boundaryInflate

checkDimensions

assignCellAll

getCell

assignCell

updateCell

makeMCMoveListener

makeAgent

releaseAgent