etomica.species

Class SpeciesSpheresMono

java.lang.Object

etomica.species.Species

etomica.species.SpeciesSpheresMono

All Implemented Interfaces:

ISpecies, java.io.Serializable

Direct Known Subclasses:

SpeciesPolyhedron, SpeciesSpheresRotating, SpeciesSpheresRotatingMolecule

public class SpeciesSpheresMono
extends Species

Species in which molecules are each made of a single spherical atom. Does not permit multiatomic molecules. The advantage of this species over the multiatomic version (used with 1 atom), is that one layer of the atom hierarchy is eliminated in SpeciesSpheresMono. Each atom is the direct child of the species agent (i.e., each atom is at the "molecule" level in the hierarchy, without an intervening AtomGroup).

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected boolean	isDynamic
protected IAtomType	leafAtomType
protected ISpace	space

Fields inherited from class etomica.species.Species

childTypes, conformation, index

Constructor Summary

Constructors

Constructor and Description
SpeciesSpheresMono(ISpace space, IAtomType leafAtomType)
SpeciesSpheresMono(ISpace _space, IElement element)
SpeciesSpheresMono(Simulation sim, ISpace _space) Constructs instance with a default element

Method Summary

Modifier and Type	Method and Description
IAtomType	getLeafType()
int	getNumLeafAtoms()
boolean	isDynamic()
protected IAtom	makeLeafAtom()
IMolecule	makeMolecule() Constructs a new group.
void	setIsDynamic(boolean newIsDynamic)

Methods inherited from class etomica.species.Species

addChildType, getAtomType, getAtomTypeCount, getConformation, getIndex, getSpecies, initializeConformation, removeChildType, setConformation, setIndex

Methods inherited from class java.lang.Object

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

Field Detail

space

protected final ISpace space

isDynamic

protected boolean isDynamic

leafAtomType

protected final IAtomType leafAtomType

Constructor Detail

SpeciesSpheresMono

public SpeciesSpheresMono(Simulation sim,
                          ISpace _space)

Constructs instance with a default element

SpeciesSpheresMono

public SpeciesSpheresMono(ISpace _space,
                          IElement element)

SpeciesSpheresMono

public SpeciesSpheresMono(ISpace space,
                          IAtomType leafAtomType)

Method Detail

setIsDynamic

public void setIsDynamic(boolean newIsDynamic)

isDynamic

public boolean isDynamic()

getLeafType

public IAtomType getLeafType()

makeMolecule

public IMolecule makeMolecule()

Constructs a new group.

makeLeafAtom

protected IAtom makeLeafAtom()

getNumLeafAtoms

public int getNumLeafAtoms()