Package etomica.atom

Class Atom

java.lang.Object

etomica.atom.Atom

All Implemented Interfaces:

IAtom, java.io.Serializable

Direct Known Subclasses:

AtomLeafDynamic, AtomOriented, AtomOrientedQuaternion

public class Atom
extends java.lang.Object
implements IAtom, java.io.Serializable

Atom that represents a physical atom with a position.

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
protected int	index
protected int	leafIndex
protected IMolecule	parent
protected Vector	position
protected AtomType	type

Constructor Summary

Constructors

Constructor	Description
Atom(Space space)	Makes a simple atom for the given space.
Atom(Space space, AtomType type)

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 newIndex)	Informs the IAtom of its index within the atoms of its parent molecule.
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.
java.lang.String	signature()	Returns a string of digits that uniquely identifies this atom.
java.lang.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 AtomType type

position

protected final Vector position

index

protected int index

parent

protected IMolecule parent

leafIndex

protected int leafIndex

Constructor Detail

Atom

public Atom(Space space,
            AtomType type)

Atom

public Atom(Space 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 java.lang.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 java.lang.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 java.lang.Object

getIndex

public final int getIndex()

Specified by:

getIndex in interface IAtom

Returns:

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

setIndex

public final void setIndex(int newIndex)

Description copied from interface: IAtom

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

Specified by:

setIndex in interface IAtom

Parameters:

newIndex - the new index

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

Parameters:

newParent - the new parent molecule

getParentGroup

public IMolecule getParentGroup()

Specified by:

getParentGroup in interface IAtom

Returns:

the parent molecule of this IAtom.

getPosition

public Vector getPosition()

Specified by:

getPosition in interface IAtom

Returns:

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

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 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.

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 Box.

Specified by:

setLeafIndex in interface IAtom

getType

public final AtomType 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.