Package etomica.potential

Class P2HardBondedList

java.lang.Object

etomica.potential.Potential

etomica.potential.Potential2

etomica.potential.P2HardBondedList

All Implemented Interfaces:

AtomLeafAgentManager.AgentSource<P2HardBondedList.BondArrayList>, IPotential, IPotentialAtomic, PotentialHard

public class P2HardBondedList
extends Potential2
implements PotentialHard, AtomLeafAgentManager.AgentSource<P2HardBondedList.BondArrayList>

Hard potential that wraps two others. One potential applies to atoms that are found on each other's list of bonded atoms, and the other applies for pairs not on each other's list. The list of bonded atoms must be configured externally to this class, using the setBonded method.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
class	P2HardBondedList.BondArrayList

Field Summary

Fields inherited from class etomica.potential.Potential

space

Constructor Summary

Constructors

Constructor	Description
P2HardBondedList(Simulation sim, PotentialHard bondedPotential, PotentialHard nonBondedPotential)

Method Summary

Modifier and Type	Method	Description
void	bump(IAtomList pair, double falseTime)	Implements the collision dynamics.
double	collisionTime(IAtomList pair, double falseTime)	Computes the time of collision of the given atom(s) with the hard potential, assuming no intervening collisions.
double	energy(IAtomList pair)	Returns the interaction energy between the given atoms.
double	energyChange()	returns change in potential energy due to the last collision
P2HardBondedList.BondArrayList	getBondedList(IAtom atom)	Returns the list containing the bonds for the given atom.
double	getRange()	Returns the range over which the potential applies.
boolean	isBonded(IAtomList pair)
boolean	isBonded(IAtom atom0, IAtom atom1)	Returns true if the pair of atoms are on each others' bonded list; false otherwise.
double	lastCollisionVirial()	Value of the virial from the most recent collision.
Tensor	lastCollisionVirialTensor()	Value of the virial from the most recent collision, decomposed into it tensoral elements.
P2HardBondedList.BondArrayList	makeAgent(IAtom a, Box agentBox)	Returns an agent for the given Atom.
void	releaseAgent(P2HardBondedList.BondArrayList agent, IAtom atom, Box agentBox)	This informs the agent source that the agent is going away and that the agent source should disconnect the agent from other elements.
void	setBonded(boolean bonding, IAtom atom0, IAtom atom1, double bondLengthSquared)	Adds/removes the pair of atoms to/from each other's bonded list.
void	setBox(Box box)	Informs the potential of the box on which it acts.

Methods inherited from interface etomica.potential.IPotential

nBody

Methods inherited from class java.lang.Object

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

Methods inherited from class etomica.potential.Potential

nBody

Constructor Detail

P2HardBondedList

public P2HardBondedList(Simulation sim,
                        PotentialHard bondedPotential,
                        PotentialHard nonBondedPotential)

Method Detail

getRange

public double getRange()

Description copied from interface: IPotential

Returns the range over which the potential applies. IAtoms with a greater separation do not interact.

Specified by:

getRange in interface IPotential

Specified by:

getRange in class Potential

bump

public void bump(IAtomList pair,
                 double falseTime)

Description copied from interface: PotentialHard

Implements the collision dynamics. The given atom(s) is assumed to be at the point of collision. This method is called to change their momentum according to the action of the collision. Extensions can be defined to instead implement other, perhaps unphysical changes.

Specified by:

bump in interface PotentialHard

collisionTime

public double collisionTime(IAtomList pair,
                            double falseTime)

Description copied from interface: PotentialHard

Computes the time of collision of the given atom(s) with the hard potential, assuming no intervening collisions. Usually assumes free-flight between collisions.

Specified by:

collisionTime in interface PotentialHard

energyChange

public double energyChange()

Description copied from interface: PotentialHard

returns change in potential energy due to the last collision

Specified by:

energyChange in interface PotentialHard

lastCollisionVirial

public double lastCollisionVirial()

Description copied from interface: PotentialHard

Value of the virial from the most recent collision.

Specified by:

lastCollisionVirial in interface PotentialHard

Returns:

double virial value

lastCollisionVirialTensor

public Tensor lastCollisionVirialTensor()

Description copied from interface: PotentialHard

Value of the virial from the most recent collision, decomposed into it tensoral elements.

Specified by:

lastCollisionVirialTensor in interface PotentialHard

Returns:

Tensor

energy

public double energy(IAtomList pair)

Description copied from class: Potential

Returns the interaction energy between the given atoms. There might be 0, 1, 2 or more atoms in the AtomSet.

Specified by:

energy in interface IPotentialAtomic

Specified by:

energy in class Potential

setBox

public void setBox(Box box)

Description copied from class: Potential

Informs the potential of the box on which it acts. Typically this requires at least that it update the nearestImageTransformer of its coordinatePair (if it uses one), e.g.: cPair.setNearestImageTransformer(box.boundary());

Specified by:

setBox in interface IPotential

Specified by:

setBox in class Potential

isBonded

public boolean isBonded(IAtom atom0,
                        IAtom atom1)

Returns true if the pair of atoms are on each others' bonded list; false otherwise.

isBonded

public boolean isBonded(IAtomList pair)

setBonded

public void setBonded(boolean bonding,
                      IAtom atom0,
                      IAtom atom1,
                      double bondLengthSquared)

Adds/removes the pair of atoms to/from each other's bonded list. Adding a bond to bonded atoms does not cause an error, and has no effect. Remove a bond from unbonded atoms causes an exception.

Parameters:

bonding - true for adding to bonded list; false for removing

Throws:

java.lang.IndexOutOfBoundsException - if specifying unbonding, and atoms are not bonded already

getBondedList

public P2HardBondedList.BondArrayList getBondedList(IAtom atom)

Returns the list containing the bonds for the given atom.

makeAgent

public P2HardBondedList.BondArrayList makeAgent(IAtom a,
                                                Box agentBox)

Description copied from interface: AtomLeafAgentManager.AgentSource

Returns an agent for the given Atom. The agentBox is provided for convenience for agent sources that handle multiple boxes.

Specified by:

makeAgent in interface AtomLeafAgentManager.AgentSource<P2HardBondedList.BondArrayList>

agentBox - TODO

releaseAgent

public void releaseAgent(P2HardBondedList.BondArrayList agent,
                         IAtom atom,
                         Box agentBox)

Description copied from interface: AtomLeafAgentManager.AgentSource

This informs the agent source that the agent is going away and that the agent source should disconnect the agent from other elements. The agentBox is provided for convenience for agent sources that handle multiple boxes.

Specified by:

releaseAgent in interface AtomLeafAgentManager.AgentSource<P2HardBondedList.BondArrayList>