Package etomica.atom

Class AtomType

java.lang.Object

etomica.atom.AtomType

All Implemented Interfaces:

java.lang.Comparable<AtomType>

Direct Known Subclasses:

AtomTypeOriented, AtomTypeSpheroPolyhedron

public class AtomType
extends java.lang.Object
implements java.lang.Comparable<AtomType>

Identifies a set of atoms and defines properties of those atoms. Properties include indices used for tracking, mass and element.

Field Summary

Fields

Modifier and Type	Field	Description
protected IElement	element
protected int	index
protected ISpecies	species

Constructor Summary

Constructors

Constructor	Description
AtomType(IElement element)
AtomType(IElement element, java.lang.String name)

Method Summary

Modifier and Type	Method	Description
int	compareTo(AtomType otherAtomType)
static AtomType	element(IElement element)
static AtomType	element(IElement element, java.lang.String name)
IElement	getElement()
int	getIndex()
double	getMass()
Dimension	getMassDimension()
java.lang.String	getName()
ISpecies	getSpecies()
double	rm()
void	setIndex(int newIndex)	Informs the IAtomType what its index should be.
void	setSpecies(ISpecies newSpecies)	Informs the atom type what species contains the atom types.
static AtomType	simple(java.lang.String symbol)
static AtomType	simple(java.lang.String symbol, double mass)	Convenience factory method for creating an AtomType with a one-off ElementSimple.
static AtomType	simpleFromSim(Simulation sim)
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

element

protected final IElement element

index

protected int index

species

protected ISpecies species

Constructor Detail

AtomType

public AtomType(IElement element)

AtomType

public AtomType(IElement element,
                java.lang.String name)

Method Detail

simple

public static AtomType simple(java.lang.String symbol,
                              double mass)

Convenience factory method for creating an AtomType with a one-off ElementSimple.

Parameters:

symbol - symbol for the element of this AtomType

mass - mass for the element of this AtomType

Returns:

an AtomType with an ElementSimple

simple

public static AtomType simple(java.lang.String symbol)

simpleFromSim

public static AtomType simpleFromSim(Simulation sim)

element

public static AtomType element(IElement element)

element

public static AtomType element(IElement element,
                               java.lang.String name)

getIndex

public int getIndex()

Returns:

the index for this IAtomType, within the context of an Simulation. The index is the IAtomType's position in the list of atom types in the simulation.

getName

public java.lang.String getName()

Returns:

the name of this AtomType. The name is by default the symbol of the element, but must be unique within a Species.

setIndex

public void setIndex(int newIndex)

Informs the IAtomType what its index should be. This should only be called by the species.

Parameters:

newIndex - the atom type's new index

getSpecies

public ISpecies getSpecies()

Returns:

the species that contains the atom type

setSpecies

public void setSpecies(ISpecies newSpecies)

Informs the atom type what species contains the atom types. This should only be called by the species.

Parameters:

newSpecies - the atom type's new species

getMass

public final double getMass()

Returns:

the value of the mass.

rm

public final double rm()

Returns:

the reciprocal of the mass, 1.0/mass

getMassDimension

public final Dimension getMassDimension()

getElement

public final IElement getElement()

Returns:

the element for this atom type

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

compareTo

public int compareTo(AtomType otherAtomType)

Specified by:

compareTo in interface java.lang.Comparable<AtomType>