Package etomica.nbr.cell.molecule

Class Mpi1ACell

java.lang.Object

etomica.nbr.cell.molecule.Mpi1ACell

All Implemented Interfaces:

AtomsetIterator, AtomsetIteratorDirectable, MoleculesetIterator, MoleculesetIteratorBoxDependent, MoleculesetIteratorPDT, MoleculesetIteratorTargetable, MoleculesetIteratorCellular, java.io.Serializable

public class Mpi1ACell
extends java.lang.Object
implements MoleculesetIteratorPDT, MoleculesetIteratorCellular, java.io.Serializable

Generates pairs that are cell-based neighbors of a specific Molecule. Iteration is performed using cell lists, which defines the neighboring molecules. Direction is related to ordering of cells and, within a cell, ordering of molecules in cell's occupant list.

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
protected boolean[]	periodicity

Constructor Summary

Constructors

Constructor	Description
Mpi1ACell(int D, double range, BoxAgentManager agentManager)	Constructor makes iterator that must have box specified and then be reset() before iteration.

Method Summary

Modifier and Type	Method	Description
CellLattice.NeighborIterator	getNbrCellIterator()
int	nBody()	Returns 2, indicating that this is a pair iterator.
IMoleculeList	next()	Returns the next AtomSet iterate, or null if hasNext() is false.
void	reset()	Resets the iterator to loop through its iterates again.
void	setBox(Box box)	Sets the Box to pull iterates from
void	setDirection(IteratorDirective.Direction direction)	Indicates allowed direction for iteration, relative to specified target atom.
void	setTarget(IMolecule newTargetMolecule)	Sets the target molecule with which all pairs are formed.
int	size()	Returns the number of atom pairs the iterator will return if reset and iterated in its present state.
void	unset()	Puts iterator in a state in which hasNext() returns false.

Methods inherited from class java.lang.Object

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

Field Detail

periodicity

protected final boolean[] periodicity

Constructor Detail

Mpi1ACell

public Mpi1ACell(int D,
                 double range,
                 BoxAgentManager agentManager)

Constructor makes iterator that must have box specified and then be reset() before iteration.

Parameters:

D - the dimension of the space of the simulation (used to construct cell iterators)

range - the distance within which pairs of atoms are considered neighbors. Used to define neighbor cells; some iterates may exceed this separation

Method Detail

setBox

public void setBox(Box box)

Description copied from interface: MoleculesetIteratorBoxDependent

Sets the Box to pull iterates from

Specified by:

setBox in interface MoleculesetIteratorBoxDependent

size

public int size()

Returns the number of atom pairs the iterator will return if reset and iterated in its present state.

Specified by:

size in interface AtomsetIterator

next

public IMoleculeList next()

Description copied from interface: MoleculesetIterator

Returns the next AtomSet iterate, or null if hasNext() is false.

Specified by:

next in interface MoleculesetIterator

unset

public void unset()

Description copied from interface: AtomsetIterator

Puts iterator in a state in which hasNext() returns false.

Specified by:

unset in interface AtomsetIterator

nBody

public int nBody()

Returns 2, indicating that this is a pair iterator.

Specified by:

nBody in interface AtomsetIterator

Returns:

reset

public void reset()

Description copied from interface: AtomsetIterator

Resets the iterator to loop through its iterates again.

Specified by:

reset in interface AtomsetIterator

setDirection

public void setDirection(IteratorDirective.Direction direction)

Indicates allowed direction for iteration, relative to specified target atom. Specification of a null direction indicates iteration in both directions relative to the target. Direction is determined by ordering within occupant list of cell of target atom, and then by the cell ordering of neighboring cells.

Specified by:

setDirection in interface AtomsetIteratorDirectable

setTarget

public void setTarget(IMolecule newTargetMolecule)

Sets the target molecule with which all pairs are formed. Molecule is determined from the first atom of the array, which may be the molecule itself or an atom that is part of it. If the atom is null or is not in one of the species given at construction, no iterates will be returned.

Specified by:

setTarget in interface MoleculesetIteratorTargetable

getNbrCellIterator

public CellLattice.NeighborIterator getNbrCellIterator()

Specified by:

getNbrCellIterator in interface MoleculesetIteratorCellular

Returns:

Returns the cellIterator.