Package etomica.molecule.iterator

Class MpiInterspecies1A

java.lang.Object

etomica.molecule.iterator.MpiInterspecies1A

All Implemented Interfaces:

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

public class MpiInterspecies1A
extends java.lang.Object
implements MoleculesetIteratorPDT, java.io.Serializable

Gives pairs formed from the molecules of two different species in a box, taking one molecule of one species with all molecules of the other. Species are specified at construction and cannot be changed afterwards. The 1-molecule species is identified via the setTarget method, and may be changed from one use of the iterator to the next.

Atoms in iterate pairs are ordered such that the first atom is of the first species given in the constructor, and the second atom is of the second species given in the constructor, regardless of the specification of the target.

Direction may be specified, and is interpreted as follows:

• For null direction, no restriction on iterates.
• For UP direction, iterates are given if index of target-atom species is less than index of other species.
• For DOWN direction, iterates are given if index of target-atom species is greater than index of other species.

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor	Description
MpiInterspecies1A(ISpecies[] species)	Sorts given array of species according to species index, then constructs iterator such that atom0 of the pair iterates is in (sorted) species[0], and atom1 is in (sorted) species[1], regardless of which is specified via setTarget.

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)	Configures iterator to return molecules from the set species in the given box.
void	setDirection(IteratorDirective.Direction direction)	Indicates allowed direction for iteration, relative to specified target atom.
void	setTarget(IMolecule newTargetAtom)	Sets the target molecule with which all pairs are formed.
int	size()	The number of iterates returned by this iterator in its current 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

Constructor Detail

MpiInterspecies1A

public MpiInterspecies1A(ISpecies[] species)

Sorts given array of species according to species index, then constructs iterator such that atom0 of the pair iterates is in (sorted) species[0], and atom1 is in (sorted) species[1], regardless of which is specified via setTarget. Thus the species index of atom0 is less than that of atom1, for all iterates.

Parameters:

species - array of two different, non-null species

Throws:

java.lang.IllegalArgumentException - is species array is not of length 2 or if species in array refer to the same instance

java.lang.NullPointerException - if species array is null or if either species in array is null

Method Detail

setBox

public void setBox(Box newBox)

Configures iterator to return molecules from the set species in the given box.

Specified by:

setBox in interface MoleculesetIteratorBoxDependent

setDirection

public void setDirection(IteratorDirective.Direction direction)

Indicates allowed direction for iteration, relative to specified target atom. If the specified direction is consisent with the direction from the target species to the non-target species (as given by their species index -- UP is direction from smaller index to larger index) direction, iteration is performed; if specified direction contradicts species direction, no iteration is performed. Specification of a null direction indicates no limitation, and iteration will be performed if a legitimate target atom is specified.

Specified by:

setDirection in interface AtomsetIteratorDirectable

setTarget

public void setTarget(IMolecule newTargetAtom)

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

Specified by:

setTarget in interface MoleculesetIteratorTargetable

Throws:

java.lang.NullPointerException - if targetAtom is null

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:

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

reset

public void reset()

Description copied from interface: AtomsetIterator

Resets the iterator to loop through its iterates again.

Specified by:

reset in interface AtomsetIterator

size

public int size()

Description copied from interface: AtomsetIterator

The number of iterates returned by this iterator in its current state.

Specified by:

size 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