Package etomica.association

Class AssociationHelperDouble

java.lang.Object

etomica.association.AssociationHelperDouble

All Implemented Interfaces:

IAssociationHelper

public class AssociationHelperDouble
extends java.lang.Object
implements IAssociationHelper

AssociationHelperDouble is capable of populating a list of atoms in an smer within a simulation with double-bonding (two bonding sites per atom). AssociationHelperDouble verifies that each atom has (at most) two bond, and that bonding information is consistent -- if B is listed as a bonding partner of A, then A is listed as a bonding parter of B. AssociationHelperDouble also verifies 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.

Field Summary

Fields

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

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
double	getMinBondedAtomDistance()
protected int	populate(AtomArrayList smerList, IAtom firstAtom, IAtom secondAtom, boolean mightBeBroken)
boolean	populateList(AtomArrayList smerList, IAtom atom, boolean mightBeBroken)	Populates smerList with all atoms in the smer that contains atom.
void	setMinBondedAtomDistance(double newDistance)
protected boolean	validateBondList(IAtom atom, IAtomList bondList, boolean mightBeBroken)

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

boundary

protected final Boundary boundary

minR2

protected double minR2

dr

protected final Vector dr

Constructor Detail

AssociationHelperDouble

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

Method Detail

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 int populate(AtomArrayList smerList,
                       IAtom firstAtom,
                       IAtom secondAtom,
                       boolean mightBeBroken)

validateBondList

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