Package etomica.association

Class AssociationHelperBranched

java.lang.Object

etomica.association.AssociationHelperBranched

All Implemented Interfaces:

IAssociationHelper

public class AssociationHelperBranched
extends java.lang.Object
implements IAssociationHelper

AssociationHelperBranched is capable of populating a list of atoms in an smer within a simulation with multiple association sites per atom. The number of sites per atom can be set, but ought to be at least 3 (AssociationManagerSingle or AssociationManagerDouble are more efficient for single-site and double-site bonding). With at least 3 sites, branching can occur and is handled by this class. AssociationHelperBranched verifies that each atom has (at most) maxBonds bonds and that all atoms bonded to a single atom have a minimum distance from each other, which ensures that none of the atoms are bonded to the same site of the central atom. AssociationHelperBranched does not attempt to verify that bonding information is consistent.

Field Summary

Fields

Modifier and Type	Field	Description
protected AssociationManager	associationManager
protected Boundary	boundary
protected Vector	dr
protected int	maxBonds
protected double	minR2

Constructor Summary

Constructors

Constructor	Description
AssociationHelperBranched(Space space, Box box, AssociationManager associationManager)

Method Summary

Modifier and Type	Method	Description
int	getMaxBonds()
double	getMinBondedAtomDistance()
protected boolean	populate(AtomArrayList smerList, IAtom atom, boolean mightBeBroken)
boolean	populateList(AtomArrayList smerList, IAtom atom, boolean mightBeBroken)	Populates smerList with all atoms in the smer that contains atom.
void	setMaxBonds(int newMaxBonds)
void	setMinBondedAtomDistance(double newDistance)
protected boolean	validateBondList(IAtom atom, IAtomList bondList, boolean mightBeBroken)	Returns false if invalid bonding is recognized

Methods inherited from class java.lang.Object

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

Field Detail

associationManager

protected final AssociationManager associationManager

maxBonds

protected int maxBonds

boundary

protected final Boundary boundary

minR2

protected double minR2

dr

protected final Vector dr

Constructor Detail

AssociationHelperBranched

public AssociationHelperBranched(Space space,
                                 Box box,
                                 AssociationManager associationManager)

Method Detail

setMaxBonds

public void setMaxBonds(int newMaxBonds)

getMaxBonds

public int getMaxBonds()

setMinBondedAtomDistance

public void setMinBondedAtomDistance(double newDistance)

getMinBondedAtomDistance

public double getMinBondedAtomDistance()

populateList

public boolean populateList(AtomArrayList smerList,
                            IAtom atom,
                            boolean mightBeBroken)

Description copied from interface: IAssociationHelper

Populates smerList with all atoms in the smer that contains atom. If mightBeBroken is false, an exception is throw if any invalid bonding is encountered (along with potentially useful information about the invalid bonding). If mightBeBroken is true, then populateList returns true if any invalid bonding is encountered. populateList returns false if invalid bonding is not encountered.

Specified by:

populateList in interface IAssociationHelper

populate

protected boolean populate(AtomArrayList smerList,
                           IAtom atom,
                           boolean mightBeBroken)

validateBondList

protected boolean validateBondList(IAtom atom,
                                   IAtomList bondList,
                                   boolean mightBeBroken)

Returns false if invalid bonding is recognized