Package etomica.box

Class Box

java.lang.Object

etomica.box.Box

Direct Known Subclasses:

BoxCluster

public class Box
extends java.lang.Object

A Box collects all atoms that interact with one another; atoms in different boxes do not interact. These are the important features of a Box:

• It holds lists of the molecules in the box, including a list of all molecules, and an array of lists that can be selected by Species. It contains methods to add and remove molecules.
• It holds a list of all atoms in the box.
• It holds a Boundary object that defines the volume of the box and the behavior of atoms as they move into or across the boundary of the box.
• It maintains a list of listeners that are informed when significant events happen in the box (such as when molecules are added or removed).
• Each Box has a unique index assigned when it is constructed. The index assignment begins at 0 and is incremented after each Box construction. This index is useful when collecting things in reference to the box.

The box maintains index values for each molecule and each atom. These values are held as integer fields by the corresponding Molecule and Atom instances. The indices are assigned when molecule (and its atoms) are added to the box via the addMolecule method. The indices are assigned to match the index in the list holding the molecule/atom.
A box is acted upon by an Integrator instance to move its atoms around and generate configurations.
A simulation may involve more than one box. All Box instances should be registered with the simulation via Simulation.addBox(Box) and may be accessed via the simulation's getBox method.

See Also:

Boundary, BoxEventManager

Field Summary

Fields

Modifier and Type	Field	Description
protected AtomSetAllMolecules	allMoleculeList
protected AtomArrayList	leafList	List of leaf atoms in box
protected MoleculeArrayList[]	moleculeLists

Constructor Summary

Constructors

Constructor	Description
Box(Boundary boundary, Space space)	Constructs box with the given Boundary, which specifies the size and shape of the Box and specifies what happens to atoms as they cross the box boundary e.g.
Box(Space space)	Constructs box with default rectangular periodic boundary.

Method Summary

Modifier and Type	Method	Description
void	addMolecule(IMolecule molecule)	Adds the given molecule to the this Box.
IMolecule	addNewMolecule(ISpecies species)	Creates a molecule of the given species and adds it to the box
void	addSpeciesNotify(ISpecies species)	Notifies the Box that the given species has been added to the simulation.
Boundary	getBoundary()
BoxEventManager	getEventManager()
int	getIndex()
IAtomList	getLeafList()
IMoleculeList	getMoleculeList()
IMoleculeList	getMoleculeList(ISpecies species)	Returns the list of molecules of the given species.
int	getNMolecules(ISpecies species)
Space	getSpace()
protected void	notifyNewMolecules(ISpecies species, int numNewMolecules, int moleculeLeafAtoms)
void	removeMolecule(IMolecule molecule)	Removes the given molecule from this Box.
void	removeSpeciesNotify(ISpecies species)	Notifies the Box that a Species has been removed.
void	setDensity(double rho)	Uses BoxInflate to adjust the volume to the specified density.
void	setIndex(int newIndex)	Informs the Box what its index is.
void	setNMolecules(ISpecies species, int n)	Sets the number of molecules in this box of the given Species to n.
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

leafList

protected final AtomArrayList leafList

List of leaf atoms in box

allMoleculeList

protected final AtomSetAllMolecules allMoleculeList

moleculeLists

protected MoleculeArrayList[] moleculeLists

Constructor Detail

Box

public Box(Space space)

Constructs box with default rectangular periodic boundary.

Parameters:

space - space governing the simulation

Box

public Box(Boundary boundary,
           Space space)

Constructs box with the given Boundary, which specifies the size and shape of the Box and specifies what happens to atoms as they cross the box boundary e.g. periodic boundaries.

Parameters:

boundary - the specified Boundary

space - space governing the simulation

Method Detail

getSpace

public Space getSpace()

getIndex

public int getIndex()

Returns:

the Box's index. The index corresponds to the box's position in the simulation's list of Boxes. The index of the first Box is 0. The index of the last Box is n-1, where n is the number of Boxes.

setIndex

public void setIndex(int newIndex)

Informs the Box what its index is. This should only be called by the Simulation.

Parameters:

newIndex - the Box's new index

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

Returns:

the String "Box" with the box index appended

addNewMolecule

public IMolecule addNewMolecule(ISpecies species)

Creates a molecule of the given species and adds it to the box

Parameters:

species - the given species

Returns:

the new molecule

addMolecule

public void addMolecule(IMolecule molecule)

Adds the given molecule to the this Box. The molecule should not already be in this Box and should not be in another Box. The molecule should be a member of an ISpecies which has been added to the Simulation. No exceptions are thrown if these conditions are violated.

Parameters:

molecule - the molecule to be added to the Box

removeMolecule

public void removeMolecule(IMolecule molecule)

Removes the given molecule from this Box.

Parameters:

molecule - the molecule to be removed from the Box

Throws:

java.lang.IllegalArgumentException - if the given molecule is not in the Box

setNMolecules

public void setNMolecules(ISpecies species,
                          int n)

Sets the number of molecules in this box of the given Species to n. Molecules are added to or removed from the box to achieve the desired number.

Parameters:

species - the species whose number of molecules should be changed

n - the desired number of molecules

Throws:

java.lang.IllegalArgumentException - if n < 0.

getNMolecules

public int getNMolecules(ISpecies species)

Returns:

the number of molecules in this box of the given ISpecies.

getMoleculeList

public IMoleculeList getMoleculeList(ISpecies species)

Returns the list of molecules of the given species.

Parameters:

species - the species

Returns:

the requested list of molecules

getMoleculeList

public IMoleculeList getMoleculeList()

Returns:

a list of all molecules in this box.

getBoundary

public final Boundary getBoundary()

Returns:

the box's boundary.

setDensity

public void setDensity(double rho)

Uses BoxInflate to adjust the volume to the specified density. New volume is set such that N/V = rho, where N is the number of molecules in the box.

Parameters:

rho - the specified density

getEventManager

public BoxEventManager getEventManager()

Returns:

the event manager for this box.

addSpeciesNotify

public void addSpeciesNotify(ISpecies species)

Notifies the Box that the given species has been added to the simulation. This method should only be called by the simulation.

Parameters:

species - the added species

removeSpeciesNotify

public void removeSpeciesNotify(ISpecies species)

Notifies the Box that a Species has been removed. This method should only be called by the simulation. This triggers the removal of all molecules of the given species from this box.

Parameters:

species - the removed species

getLeafList

public IAtomList getLeafList()

Returns:

the list of atoms contained in this box.

notifyNewMolecules

protected void notifyNewMolecules(ISpecies species,
                                  int numNewMolecules,
                                  int moleculeLeafAtoms)