Package etomica.species

Interface ISpecies

All Known Implementing Classes:

SpeciesGeneral, SpeciesGeneralMutable

public interface ISpecies

An ISpecies holds information about how to construct a molecule, and creates molecules on demand. In addition to actually creating molecules, ISpecies objects are often used as keys to pass and designate which species is of interest (for assigning potentials or setting the number of molecules in the box, for instance).

See Also:

Box, PotentialMaster

Method Summary

Modifier and Type	Method	Description
int	getAtomByTypeName(java.lang.String name)	Get the index within the molecule of the first atom of a given AtomType name.
int	getAtomByTypeName(java.lang.String name, int number)	Get the index within the molecule of the nth atom of given AtomType name.
AtomType	getAtomType(int index)	Returns the child type of this Species for the specified index.
int	getAtomTypeCount()	Returns the number of unique AtomTypes that make up this Species.
java.util.List<AtomType>	getAtomTypes()	Get the list of AtomTypes that make up this Species.
int	getByName(java.lang.String atomName)	Get the index within a molecule instance of a named atom for this Species.
IConformation	getConformation()
int	getIndex()	Returns the index for this ISpecies, within the context of an Simulation.
int	getLeafAtomCount()
AtomType	getLeafType()
double	getMass()
Vector	getMomentOfInertia()
Space	getSpace()
AtomType	getTypeByName(java.lang.String typeName)	Get the AtomType with a given name used in this Species.
void	initializeConformation(IMolecule molecule)	Initializes the molecule's IAtoms in their standard arrangement.
boolean	isDynamic()	Returns whether the Species is dynamic.
IMolecule	makeMolecule()	Builds and returns the IMolecule of this ISpecies.
void	setIndex(int newIndex)	Informs the ISpecies what its index should be.

Method Detail

getIndex

int getIndex()

Returns the index for this ISpecies, within the context of an Simulation. The index is the ISpecies' position in the array returned by SpeciesManager.getSpecies().

setIndex

void setIndex(int newIndex)

Informs the ISpecies what its index should be. This should only be called by the SpeciesManager.

makeMolecule

IMolecule makeMolecule()

Builds and returns the IMolecule of this ISpecies.

isDynamic

boolean isDynamic()

Returns whether the Species is dynamic. If a Species is dynamic and has oriented molecules, then the molecules will have a velocity component. If a Species is dynamic and is not oriented, its atoms will have a velocity component.

Returns:

whether the Species is dynamic

getSpace

Space getSpace()

Returns:

the Space of the Species. This is the Space that molecules and atoms are constructed with.

getAtomTypeCount

int getAtomTypeCount()

Returns the number of unique AtomTypes that make up this Species.

getLeafAtomCount

int getLeafAtomCount()

Returns:

the total number of atoms in this Species.

getAtomType

AtomType getAtomType(int index)

Returns the child type of this Species for the specified index.

getLeafType

AtomType getLeafType()

Returns:

the singular AtomType that makes up this Species.

getAtomTypes

java.util.List<AtomType> getAtomTypes()

Get the list of AtomTypes that make up this Species.

The returned list should not be modified.

initializeConformation

void initializeConformation(IMolecule molecule)

Initializes the molecule's IAtoms in their standard arrangement. The overall position of the molecule may be changed by this method.

getConformation

IConformation getConformation()

Returns:

the Conformation used by this Species to initialize positions of atoms within a molecule.

getByName

int getByName(java.lang.String atomName)

Get the index within a molecule instance of a named atom for this Species.

Parameters:

atomName - the name for a specific Atom in this Species.

Returns:

an index for use in IMolecule.getChildList()

getAtomByTypeName

int getAtomByTypeName(java.lang.String name,
                      int number)

Get the index within the molecule of the nth atom of given AtomType name.

Parameters:

name - String matching the name for the AtomType.

number - The nth atom with that type to get, starting at 1.

Returns:

the index of that atom within a molecule of this species.

getAtomByTypeName

int getAtomByTypeName(java.lang.String name)

Get the index within the molecule of the first atom of a given AtomType name.

Parameters:

name - String matching the name for the AtomType.

Returns:

the index of that atom within a molecule of this species.

getTypeByName

AtomType getTypeByName(java.lang.String typeName)

Get the AtomType with a given name used in this Species.

Parameters:

typeName - String matching the name for the AtomType.

Returns:

AtomType with the given name.

getMomentOfInertia

Vector getMomentOfInertia()

Returns:

the moment of inertia for a molecule of this Species.

getMass

double getMass()

Returns:

the total mass of all the atoms in a molecule of this Species.