Package etomica.atom.iterator

Class ApiIntergroup

java.lang.Object

etomica.atom.iterator.ApiIntergroup

All Implemented Interfaces:

AtomLeafsetIterator, AtomsetIterator, AtomsetIteratorBasisDependent, AtomsetIteratorTargetable

Direct Known Subclasses:

ApiIntergroupCoupled, ApiIntergroupExchange, ApiIntergroupIntraSpecies

public class ApiIntergroup
extends java.lang.Object
implements AtomsetIteratorBasisDependent

Iterator that returns pairs formed using two different basis atoms, so that the iterates are taken from two different groups.

Field Summary

Fields

Modifier and Type	Field	Description
protected AtomIteratorBasisDependent	aiInner
protected AtomIteratorBasisDependent	aiOuter
protected MoleculeSetSinglet	atomSetSinglet
protected boolean	needSetupIterators
protected AtomPair	pair
protected IAtom	targetAtom

Constructor Summary

Constructors

Constructor	Description
ApiIntergroup()	Default iterator is an ApiInnerFixed formed from two AtomIteratorBasis instances.
ApiIntergroup(AtomIteratorBasisDependent outer, AtomIteratorBasisDependent inner)	Constructs a pair iterator that returns iterates from the given pairIterator, which is expected to contain two basis-dependent iterators.

Method Summary

Modifier and Type	Method	Description
int	basisSize()	Returns 2, indicating that the setBasis method expects an array of two atoms.
AtomIteratorBasisDependent	getInnerIterator()	Accessor method for the inner-loop atom iterator.
AtomIteratorBasisDependent	getOuterIterator()	Accessor method for the outer-loop atom iterator.
boolean	haveTarget(IAtom target)	Returns true if the iterator with its current basis would return an iterate for the given target.
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().
IAtomList	next()	Returns the next pair of atoms.
void	reset()	Resets the iterator to loop through its iterates again.
void	setBasis(IMoleculeList basisAtoms)	Specifies the basis, which identifies the atoms subject to iteration.
void	setTarget(IAtom newTargetAtom)	Specifies a target atom, which should appear in all iterates.
protected void	setupIterators()
int	size()	Returns the number of pairs given by this iterator.
void	unset()	Sets the iterator such that hasNext is false.

Methods inherited from class java.lang.Object

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

Field Detail

pair

protected final AtomPair pair

aiInner

protected final AtomIteratorBasisDependent aiInner

aiOuter

protected final AtomIteratorBasisDependent aiOuter

targetAtom

protected IAtom targetAtom

needSetupIterators

protected boolean needSetupIterators

atomSetSinglet

protected final MoleculeSetSinglet atomSetSinglet

Constructor Detail

ApiIntergroup

public ApiIntergroup()

Default iterator is an ApiInnerFixed formed from two AtomIteratorBasis instances.

ApiIntergroup

public ApiIntergroup(AtomIteratorBasisDependent outer,
                     AtomIteratorBasisDependent inner)

Constructs a pair iterator that returns iterates from the given pairIterator, which is expected to contain two basis-dependent iterators.

Method Detail

getOuterIterator

public AtomIteratorBasisDependent getOuterIterator()

Accessor method for the outer-loop atom iterator.

Returns:

the current outer-loop iterator

getInnerIterator

public AtomIteratorBasisDependent getInnerIterator()

Accessor method for the inner-loop atom iterator.

Returns:

the current inner-loop iterator

unset

public void unset()

Sets the iterator such that hasNext is false.

Specified by:

unset in interface AtomsetIterator

size

public int size()

Returns the number of pairs given by this iterator. Not dependent on state of hasNext.

Specified by:

size in interface AtomsetIterator

nBody

public final 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 IAtomList next()

Returns the next pair of atoms. The same AtomPair instance is returned every time, but the Atoms it holds are (of course) different for each iterate.

Specified by:

next in interface AtomLeafsetIterator

setTarget

public void setTarget(IAtom newTargetAtom)

Specifies a target atom, which should appear in all iterates. A null value removes any restriction on the iterates.

Specified by:

setTarget in interface AtomsetIteratorTargetable

haveTarget

public boolean haveTarget(IAtom target)

Description copied from interface: AtomsetIteratorBasisDependent

Returns true if the iterator with its current basis would return an iterate for the given target.

Specified by:

haveTarget in interface AtomsetIteratorBasisDependent

setupIterators

protected void setupIterators()

setBasis

public void setBasis(IMoleculeList basisAtoms)

Specifies the basis, which identifies the atoms subject to iteration. The given atomSet must be of length 2. The first atom in the set specifies the basis for the outer-loop iteration, and second atom specifies the basis for the inner-loop iteration. In each case, if the basis atom is not a leaf atom, its children will be the subject of iteration. If the basis atom is a leaf, it will itself be the iterate. If given atomset is null iterator will give no iterates until a proper basis is specified via another call to this method.

Specified by:

setBasis in interface AtomsetIteratorBasisDependent

Parameters:

basisAtoms - The basis atoms; a null basis will condition the iterator to give no iterates until a valid basis is specified via another call to this method.

reset

public void reset()

Description copied from interface: AtomsetIterator

Resets the iterator to loop through its iterates again.

Specified by:

reset in interface AtomsetIterator

basisSize

public int basisSize()

Returns 2, indicating that the setBasis method expects an array of two atoms.

Specified by:

basisSize in interface AtomsetIteratorBasisDependent

Returns:

the size of the basis for this iterator.