Package etomica.atom

Interface IAtom

All Known Subinterfaces:

IAtomKinetic, IAtomOriented, IAtomOrientedKinetic

All Known Implementing Classes:

Atom, AtomHydrogen, AtomLeafDynamic, AtomOriented, AtomOrientedDynamic, AtomOrientedQuaternion

public interface IAtom

IAtom is an interface for atoms in the simulation. Atoms have a type (IAtomType), a position (IVectorMutable) and a parent molecule (IMolecule). Atoms also have indices (one for the list of atoms in the box, one for the list of atoms in a molecule).

Method Summary

Modifier and Type	Method	Description
int	getIndex()
int	getLeafIndex()	Returns the global index (within the Box) of this Atom.
IMolecule	getParentGroup()
Vector	getPosition()
AtomType	getType()
void	setIndex(int index)	Informs the IAtom of its index within the atoms of its parent molecule.
void	setLeafIndex(int newGlobalIndex)	Sets the atom's global index to the give value.
void	setParent(IMolecule newParent)	Informs the Atom that the given IMolecule is its parent.

Method Detail

getIndex

int getIndex()

Returns:

this IAtom's index, which is its place in the parent AtomGroup's list of child IAtoms.

setIndex

void setIndex(int index)

Informs the IAtom of its index within the atoms of its parent molecule. This should only be called by the parent molecule.

Parameters:

index - the new index

getLeafIndex

int getLeafIndex()

Returns the global index (within the Box) of this Atom. The global index is unique to the IAtom in the Box. The IAtom's global index may change over the course of a simulation due to addition or removal of other IAtoms in the Box. An BoxGlobalAtomIndexEvent is fired by the Box's event manager when an Atom's global index changes.

setLeafIndex

void setLeafIndex(int newGlobalIndex)

Sets the atom's global index to the give value. This method should only be called by the Box.

setParent

void setParent(IMolecule newParent)

Informs the Atom that the given IMolecule is its parent. This method should only be called by the parent molecule.

Parameters:

newParent - the new parent molecule

getParentGroup

IMolecule getParentGroup()

Returns:

the parent molecule of this IAtom.

getType

AtomType getType()

Returns:

the Atom type, holding properties held in common with other atoms of the same type.

getPosition

Vector getPosition()

Returns:

the position of the IAtom. Modifying the returned vector will alter the IAtom's position.