etomica.atom
Class Atom

java.lang.Object
  etomica.atom.Atom

All Implemented Interfaces:

IAtom, Serializable

Direct Known Subclasses:

AtomLeafDynamic, AtomOriented

public class Atom
extends Object
implements IAtom, Serializable

Atom that represents a physical atom with a position.

See Also:

Serialized Form

Field Summary

protected int	index
protected int	leafIndex
protected IMolecule	parent
protected IVectorMutable	position
protected IAtomType	type

Constructor Summary

Atom(ISpace space)
Makes a simple atom for the given space.

Atom(ISpace space, IAtomType type)

Method Summary

int	getIndex() Returns this IAtom's index, which is its place in the parent AtomGroup's list of child IAtoms.
int	getLeafIndex() Returns the global index (within the Box) of this Atom.
IMolecule	getParentGroup() Returns the parent AtomGruop of this IAtom.
IVectorMutable	getPosition() Returns the position of the IAtom.
IAtomType	getType()
void	setIndex(int newIndex) Informs the IAtom of its index, which is used to construct the address.
void	setLeafIndex(int newLeafIndex) Sets the atom's global index to the give value.
void	setParent(IMolecule newParent) Informs the Atom that the given AtomGroup is its parent.
String	signature() Returns a string of digits that uniquely identifies this atom.
String	toString() Returns a string formed by concatenating the signature of this atom to a string that identifies it as a species master, species agent, molecule, group, or (leaf) atom.

Methods inherited from class java.lang.Object

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

Field Detail

type

protected final IAtomType type

index

protected int index

position

protected final IVectorMutable position

parent

protected IMolecule parent

leafIndex

protected int leafIndex

Constructor Detail

Atom

public Atom(ISpace space,
            IAtomType type)

Atom

public Atom(ISpace space)

Makes a simple atom for the given space. Coordinate is non-kinetic sphere; node is for a leaf atom; type is a sphere with unit mass and unit size, unique to the new atom; depth is 0.

Method Detail

signature

public String signature()

Returns a string of digits that uniquely identifies this atom. String is formed by concatenating the ordinal of this atom to the signature given by the parent of this atom. If atom has no parent, forms a string from only the ordinal.

toString

public final String toString()

Returns a string formed by concatenating the signature of this atom to a string that identifies it as a species master, species agent, molecule, group, or (leaf) atom.

Overrides:

toString in class Object

setIndex

public final void setIndex(int newIndex)

Description copied from interface: IAtom

Informs the IAtom of its index, which is used to construct the address.

Specified by:

setIndex in interface IAtom

getIndex

public final int getIndex()

Description copied from interface: IAtom

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

Specified by:

getIndex in interface IAtom

setParent

public void setParent(IMolecule newParent)

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

Specified by:

setParent in interface IAtom

getParentGroup

public IMolecule getParentGroup()

Description copied from interface: IAtom

Returns the parent AtomGruop of this IAtom.

Specified by:

getParentGroup in interface IAtom

getPosition

public IVectorMutable getPosition()

Description copied from interface: IAtom

Returns the position of the IAtom. Modifying the returned IVector will alter the IAtom's position.

Specified by:

getPosition in interface IAtom

getLeafIndex

public int getLeafIndex()

Description copied from interface: IAtom

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 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.

Specified by:

getLeafIndex in interface IAtom

setLeafIndex

public void setLeafIndex(int newLeafIndex)

Description copied from interface: IAtom

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

Specified by:

setLeafIndex in interface IAtom

getType

public final IAtomType getType()

Specified by:

getType in interface IAtom

Returns:

the Atom type, holding properties held in common with other atoms made by this atom's factory.