Package etomica.nbr.list.molecule

Class MoleculeNeighborLists

java.lang.Object

etomica.nbr.list.molecule.MoleculeNeighborLists

All Implemented Interfaces:

java.io.Serializable

public class MoleculeNeighborLists
extends java.lang.Object
implements java.io.Serializable

Class used to maintain neighbor lists. Holds lists of molecules that were elsewhere deemed to be neighbors of the another molecule. A separate MoleculeArrayList is kept for each potential (potential => MoleculeArrayList mapping is the responsibility of the consumer).

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
protected MoleculeArrayList[]	downList
protected MoleculeArrayList[]	upList

Constructor Summary

Constructors

Constructor	Description
MoleculeNeighborLists()	Constructs sequencer for the given molecule.

Method Summary

Modifier and Type	Method	Description
void	addDownNbr(IMolecule a, int index)	Adds the given atom as a "down" neighbor interacting via the potential with the given index.
void	addUpNbr(IMolecule a, int index)	Adds the given atom as a "down" neighbor interacting via the potential with the given index.
void	clearNbrs()	Clears neighbor lists, removing all listed neighbor molecules.
IMoleculeList[]	getDownList()	Returns an array of downlist-neighbor-molecule lists.
IMoleculeList[]	getUpList()	Returns an array of uplist-neighbor-molecule lists.
protected void	setCapacity(int newCapacity)	Sets the number of up and down lists maintained by this instance.

Methods inherited from class java.lang.Object

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

Field Detail

upList

protected MoleculeArrayList[] upList

downList

protected MoleculeArrayList[] downList

Constructor Detail

MoleculeNeighborLists

public MoleculeNeighborLists()

Constructs sequencer for the given molecule.

Method Detail

addUpNbr

public void addUpNbr(IMolecule a,
                     int index)

Adds the given atom as a "down" neighbor interacting via the potential with the given index.

Parameters:

a - the new downlist neighbor molecule

index - the of the potential between the molecules

addDownNbr

public void addDownNbr(IMolecule a,
                       int index)

Adds the given atom as a "down" neighbor interacting via the potential with the given index.

Parameters:

a - the new downlist neighbor molecule

index - the of the potential between the molecules

getUpList

public IMoleculeList[] getUpList()

Returns an array of uplist-neighbor-molecule lists. Each list in the array corresponds to a specific potential. A zero-length list indicates that no concrete potentials apply to the atom.

getDownList

public IMoleculeList[] getDownList()

Returns an array of downlist-neighbor-molecule lists. Each list in the array corresponds to a specific potential. A zero-length list indicates that no concrete potentials apply to the atom.

setCapacity

protected void setCapacity(int newCapacity)

Sets the number of up and down lists maintained by this instance.

clearNbrs

public void clearNbrs()

Clears neighbor lists, removing all listed neighbor molecules.