Package etomica.modules.sam

Class CriterionTether3

java.lang.Object

etomica.modules.sam.CriterionTether3

All Implemented Interfaces:

MoleculeAgentManager.MoleculeAgentSource, NeighborCriterion

public class CriterionTether3
extends java.lang.Object
implements NeighborCriterion, MoleculeAgentManager.MoleculeAgentSource

Returns first leaf atom of each polymer molecule and the atom its bonded to.

Field Summary

Fields

Modifier and Type	Field	Description
protected MoleculeAgentManager	bondManager
protected Box	box
protected int	cursor
protected IMoleculeList	polymerList
protected ISpecies	polymerSpecies
protected Simulation	sim
protected int	surfaceCursor
protected AtomType	surfaceType
protected IMolecule	targetMolecule

Constructor Summary

Constructors

Constructor	Description
CriterionTether3(Simulation sim, ISpecies polymerSpecies, AtomType surfaceType)

Method Summary

Modifier and Type	Method	Description
boolean	accept(IAtom atom1, IAtom atom2)
java.lang.Object	makeAgent(IMolecule a)	Returns an agent for the given Atom.
boolean	needUpdate(IAtom atom)	Indicates whether the neighbor list for the given atom should be updated, according to this criterion.
void	releaseAgent(java.lang.Object agent, IMolecule atom)	This informs the agent source that the agent is going away and that the agent source should disconnect the agent from other elements
void	reset(IAtom atom)	Indicates to criterion that given atom's neighbor list has just been updated, and that properties (e.g., record of atom's position) used by needUpdate and unsafe() methods should be reset.
void	setBondedSurfaceAtoms(IMolecule polymerMolecule, IAtomList surfaceAtoms)
void	setBox(Box newBox)	Specifies the box where the criterion is being applied.
boolean	unsafe()	Indicates whether the atom has changed (e.g.

Methods inherited from class java.lang.Object

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

Field Detail

sim

protected final Simulation sim

polymerSpecies

protected final ISpecies polymerSpecies

surfaceType

protected final AtomType surfaceType

box

protected Box box

polymerList

protected IMoleculeList polymerList

bondManager

protected MoleculeAgentManager bondManager

cursor

protected int cursor

surfaceCursor

protected int surfaceCursor

targetMolecule

protected IMolecule targetMolecule

Constructor Detail

CriterionTether3

public CriterionTether3(Simulation sim,
                        ISpecies polymerSpecies,
                        AtomType surfaceType)

Method Detail

setBox

public void setBox(Box newBox)

Description copied from interface: NeighborCriterion

Specifies the box where the criterion is being applied. Sometimes needed if the criterion depends on features of the box, such as the boundary.

Specified by:

setBox in interface NeighborCriterion

setBondedSurfaceAtoms

public void setBondedSurfaceAtoms(IMolecule polymerMolecule,
                                  IAtomList surfaceAtoms)

accept

public boolean accept(IAtom atom1,
                      IAtom atom2)

Specified by:

accept in interface NeighborCriterion

needUpdate

public boolean needUpdate(IAtom atom)

Description copied from interface: NeighborCriterion

Indicates whether the neighbor list for the given atom should be updated, according to this criterion.

Specified by:

needUpdate in interface NeighborCriterion

Returns:

true if the atom's list should be updated.

reset

public void reset(IAtom atom)

Description copied from interface: NeighborCriterion

Indicates to criterion that given atom's neighbor list has just been updated, and that properties (e.g., record of atom's position) used by needUpdate and unsafe() methods should be reset.

Specified by:

reset in interface NeighborCriterion

unsafe

public boolean unsafe()

Description copied from interface: NeighborCriterion

Indicates whether the atom has changed (e.g. moved) by an amount that might have caused its neighbor list to be invalid. If this method returns true, a neighbor list failure may have introduced errors in the calculation.

Specified by:

unsafe in interface NeighborCriterion

makeAgent

public java.lang.Object makeAgent(IMolecule a)

Description copied from interface: MoleculeAgentManager.MoleculeAgentSource

Returns an agent for the given Atom.

Specified by:

makeAgent in interface MoleculeAgentManager.MoleculeAgentSource

releaseAgent

public void releaseAgent(java.lang.Object agent,
                         IMolecule atom)

Description copied from interface: MoleculeAgentManager.MoleculeAgentSource

This informs the agent source that the agent is going away and that the agent source should disconnect the agent from other elements

Specified by:

releaseAgent in interface MoleculeAgentManager.MoleculeAgentSource