Package etomica.nbr.list

Class AtomNeighborLists

java.lang.Object

etomica.nbr.list.AtomNeighborLists

public class AtomNeighborLists
extends java.lang.Object

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

Field Summary

Fields

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

Constructor Summary

Constructors

Constructor	Description
AtomNeighborLists()	Constructs sequencer for the given atom.

Method Summary

Modifier and Type	Method	Description
void	addDownNbr(IAtom a, int index)	Adds the given atom as a "down" neighbor interacting via the potential with the given index.
void	addUpNbr(IAtom 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 atoms.
IAtomList[]	getDownList()	Returns an array of downlist-neighbor-atom lists.
IAtomList[]	getUpList()	Returns an array of uplist-neighbor-atom 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 AtomArrayList[] upList

downList

protected AtomArrayList[] downList

Constructor Detail

AtomNeighborLists

public AtomNeighborLists()

Constructs sequencer for the given atom.

Method Detail

addUpNbr

public void addUpNbr(IAtom 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 atom

index - the of the potential between the atoms

addDownNbr

public void addDownNbr(IAtom 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 atom

index - the of the potential between the atoms

getUpList

public IAtomList[] getUpList()

Returns an array of uplist-neighbor-atom 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 IAtomList[] getDownList()

Returns an array of downlist-neighbor-atom 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 atoms.