Package etomica.nbr.cell.molecule

Class NeighborCellManagerMolecular

java.lang.Object

etomica.nbr.cell.molecule.NeighborCellManagerMolecular

All Implemented Interfaces:

BoxCellManager, MoleculeAgentManager.MoleculeAgentSource, BoundaryEventListener, java.io.Serializable

Direct Known Subclasses:

NeighborCellManagerListMolecular

public class NeighborCellManagerMolecular
extends java.lang.Object
implements BoxCellManager, BoundaryEventListener, MoleculeAgentManager.MoleculeAgentSource, java.io.Serializable

Class that defines and manages construction and use of lattice of cells for cell-based neighbor listing.

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
protected MoleculeAgentManager	agentManager
protected Box	box
protected int	cellRange
protected boolean	doApplyPBC
protected CellLattice	lattice
protected IMoleculePositionDefinition	moleculeSite
protected int[]	numCells
protected IMoleculePositionDefinition	positionDefinition
protected double	range
protected Simulation	sim
protected Space	space
protected Vector	v

Constructor Summary

Constructors

Constructor	Description
NeighborCellManagerMolecular(Simulation sim, Box box, double potentialRange, IMoleculePositionDefinition positionDefinition, Space space)	Construct manager for neighbor cells in the given box.
NeighborCellManagerMolecular(Simulation sim, Box box, double potentialRange, Space _space)	Constructs manager for neighbor cells in the given box.

Method Summary

Modifier and Type	Method	Description
void	assignCell(IMolecule molecule)	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.
CellMolecular	getCell(IMolecule molecule)
int	getCellRange()	Returns the cellRange.
boolean	getDoApplyPBC()
CellLattice	getLattice()	Returns the lattice that defines the cell arrangement.
double	getPotentialRange()	Returns the potential range.
java.lang.Object	makeAgent(IMolecule molecule)	Returns the cell containing the given atom.
IListener	makeMCMoveListener()
void	releaseAgent(java.lang.Object cell, IMolecule molecule)	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.

Methods inherited from class java.lang.Object

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

Field Detail

sim

protected final Simulation sim

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 MoleculeAgentManager agentManager

doApplyPBC

protected boolean doApplyPBC

v

protected final Vector v

numCells

protected final int[] numCells

moleculeSite

protected IMoleculePositionDefinition moleculeSite

space

protected Space space

Constructor Detail

NeighborCellManagerMolecular

public NeighborCellManagerMolecular(Simulation sim,
                                    Box box,
                                    double potentialRange,
                                    Space _space)

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).

NeighborCellManagerMolecular

public NeighborCellManagerMolecular(Simulation sim,
                                    Box box,
                                    double potentialRange,
                                    IMoleculePositionDefinition positionDefinition,
                                    Space space)

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

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 CellMolecular getCell(IMolecule molecule)

assignCell

public void assignCell(IMolecule molecule)

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.

makeMCMoveListener

public IListener makeMCMoveListener()

makeAgent

public java.lang.Object makeAgent(IMolecule molecule)

Returns the cell containing the given atom. The atom is added to the cell's atom list.

Specified by:

makeAgent in interface MoleculeAgentManager.MoleculeAgentSource

releaseAgent

public void releaseAgent(java.lang.Object cell,
                         IMolecule molecule)

Removes the given atom from the cell.

Specified by:

releaseAgent in interface MoleculeAgentManager.MoleculeAgentSource