etomica.nbr.cell
Class Api1ACell

java.lang.Object
  etomica.nbr.cell.Api1ACell

All Implemented Interfaces:

AtomLeafsetIterator, AtomsetIterator, AtomsetIteratorBoxDependent, AtomsetIteratorDirectable, AtomsetIteratorPDT, AtomsetIteratorTargetable, AtomsetIteratorCellular, Serializable

public class Api1ACell
extends Object
implements AtomsetIteratorPDT, AtomsetIteratorCellular, Serializable

Generates pairs that are cell-based neighbors of a specific Atom. 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

protected boolean[]

periodicity

Constructor Summary

Api1ACell(int D, double range, BoxAgentManager agentManager)
Constructor makes iterator that must have box specified and then be reset() before iteration.

Method Summary

CellLattice.NeighborIterator	getNbrCellIterator()
int	nBody() Returns 2, indicating that this is a pair iterator.
IAtomList	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(IBox 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(IAtom newTargetAtom) 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

Api1ACell

public Api1ACell(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(IBox box)

Description copied from interface: AtomsetIteratorBoxDependent

Sets the Box to pull iterates from

Specified by:

setBox in interface AtomsetIteratorBoxDependent

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 IAtomList next()

Description copied from interface: AtomLeafsetIterator

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

Specified by:

next in interface AtomLeafsetIterator

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(IAtom newTargetAtom)

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 AtomsetIteratorTargetable

getNbrCellIterator

public CellLattice.NeighborIterator getNbrCellIterator()

Specified by:

getNbrCellIterator in interface AtomsetIteratorCellular

Returns:

Returns the cellIterator.