Package etomica.molecule.iterator

Class MoleculeIteratorAll

java.lang.Object

etomica.molecule.iterator.MoleculeIteratorAll

All Implemented Interfaces:

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

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

Iterator for all the molecules of a set of species in a box. Each iterate is all the molecules in a box, with each Atom as the first atom in the set. This class is used by PotentialMaster to iterate over molecules for N-body potentials. This class is designed to work and conform to the API... not to be efficient or pleasant to look at! Use neighbor lists.

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
protected Box	box
protected MoleculeArrayList	next
protected int	nextCursor
protected boolean	oneIterate
protected ISpecies[]	species

Constructor Summary

Constructors

Constructor	Description
MoleculeIteratorAll(ISpecies[] species)
MoleculeIteratorAll(ISpecies[] species, boolean oneIterate)

Method Summary

Modifier and Type	Method	Description
int	nBody()	Returns the number of atoms given in each iterate, i.e., the size of the atom array returned with each call to next().
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 newBox)	Sets the box containing the molecules for iteration.
void	setDirection(IteratorDirective.Direction newDirection)	Has no effect, but is included as part of the AtomsetIteratorPDT interface.
void	setTarget(IMolecule newTargetAtom)	Sets the target of iteration...
int	size()	Returns the number of iterates given by this iterator, if iterated after a call to reset().
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

species

protected final ISpecies[] species

box

protected Box box

nextCursor

protected int nextCursor

next

protected final MoleculeArrayList next

oneIterate

protected final boolean oneIterate

Constructor Detail

MoleculeIteratorAll

public MoleculeIteratorAll(ISpecies[] species)

MoleculeIteratorAll

public MoleculeIteratorAll(ISpecies[] species,
                           boolean oneIterate)

Parameters:

species - species for which molecules are returned as iterates. Only species[0] is relevant, and must not be null.

Method Detail

setBox

public void setBox(Box newBox)

Sets the box containing the molecules for iteration. A null box conditions iterator to give no iterates.

Specified by:

setBox in interface MoleculesetIteratorBoxDependent

setTarget

public void setTarget(IMolecule newTargetAtom)

Sets the target of iteration... has no actual effect since all iterates contain all Atoms.

Specified by:

setTarget in interface MoleculesetIteratorTargetable

setDirection

public void setDirection(IteratorDirective.Direction newDirection)

Has no effect, but is included as part of the AtomsetIteratorPDT interface. Besides, you didn't really want to iterate down, did you?

Specified by:

setDirection in interface AtomsetIteratorDirectable

reset

public void reset()

Description copied from interface: AtomsetIterator

Resets the iterator to loop through its iterates again.

Specified by:

reset in interface AtomsetIterator

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

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

nBody

public int nBody()

Description copied from interface: AtomsetIterator

Returns the number of atoms given in each iterate, i.e., the size of the atom array returned with each call to next().

Specified by:

nBody in interface AtomsetIterator

Returns:

size

public int size()

Returns the number of iterates given by this iterator, if iterated after a call to reset().

Specified by:

size in interface AtomsetIterator