Package etomica.integrator

Class IntegratorHard

java.lang.Object

etomica.integrator.Integrator

etomica.integrator.IntegratorBox

etomica.integrator.IntegratorMD

etomica.integrator.IntegratorHard

All Implemented Interfaces:

AtomLeafAgentManager.AgentSource<IntegratorHard.Agent>, BoxEventListener, INeighborListListener

Direct Known Subclasses:

IntegratorHardMDMC, IntegratorHardPiston

public class IntegratorHard
extends IntegratorMD
implements INeighborListListener, AtomLeafAgentManager.AgentSource<IntegratorHard.Agent>

Integrator for hard potentials. Integrates equations of motion through time by advancing atoms from one collision to the next. Determination of time of collision and implementation of collision dynamics is handled by the potential between the atoms and stored in an Agent.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	IntegratorHard.Agent	Agent defined by this integrator.
protected static class	IntegratorHard.CollisionHandlerUp
static interface	IntegratorHard.CollisionListener

Nested classes/interfaces inherited from class etomica.integrator.Integrator

Integrator.Forcible, Integrator.Torquable

Nested classes/interfaces inherited from class etomica.integrator.IntegratorMD

IntegratorMD.ThermostatType, IntegratorMD.VectorSource

Field Summary

Fields

Modifier and Type	Field	Description
protected AtomLeafAgentManager<IntegratorHard.Agent>	agentManager
protected double	collisionTimeStep
protected IteratorDirective	downList
protected TreeList	eventList
protected AtomArrayList	listToUpdate
protected IteratorDirective	upList

Fields inherited from class etomica.integrator.Integrator

eventManager, initialized, interval, stepCount

Fields inherited from class etomica.integrator.IntegratorBox

box, currentPotentialEnergy, isothermal, meterPE, potentialMaster, space, temperature

Fields inherited from class etomica.integrator.IntegratorMD

alwaysScaleMomenta, atomActionRandomizeVelocity, currentKineticEnergy, currentTime, integratorMC, mcSteps, meterKE, meterTemperature, momentum, nAccepted, nRejected, oldEnergy, oldPositionAgentManager, oldPotentialEnergy, random, temperatureVec, thermostat, thermostatCount, thermostatInterval, thermostatNoDrift, thermostatting, timeStep

Constructor Summary

Constructors

Constructor	Description
IntegratorHard(PotentialMaster potentialMaster, IRandom random, double timeStep, double temperature, Box box)
IntegratorHard(Simulation sim, PotentialMaster potentialMaster, Box box)

Method Summary

Modifier and Type	Method	Description
void	addCollisionListener(IntegratorHard.CollisionListener cl)	Registers an object that implements the CollisionListener interface.
protected void	advanceAcrossTimeStep(double tStep)	Advances all atom coordinates by tStep, without any intervening collisions.
void	boxMoleculeAdded(BoxMoleculeEvent e)	Called when a molecule is added to the box.
protected void	doStepInternal()	Steps all atoms across time interval timeStep, handling all intervening collisions.
long	getCollisionCount()
IntegratorHard.Agent	getLastColliderAgent()
PotentialHard	getNullPotential(AtomType atomType)
IntegratorHard.Agent	makeAgent(IAtom a, Box agentBox)	Produces the Agent for this integrator.
void	neighborListNeighborsUpdated()
protected void	processReverseList()	Recalculate collision times (up) for any atoms atoms in the "reverse" list of atoms that thought they would collide with an atom that's changed.
protected void	randomizeMomenta()	Updates collision times appropriately after randomizing momenta as part of the Andersen thermostat.
protected void	randomizeMomentum(IAtomKinetic atom)	Updates collision time appropriately after randomizing momentum as part of the Andersen thermostat.
protected void	randomizeTotalKE()	Updates collision times appropriately after randomizing momenta as part of the Andersen scaling thermostat.
void	releaseAgent(IntegratorHard.Agent 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	removeCollisionListener(IntegratorHard.CollisionListener cl)	De-registers an object from the list of collision listeners.
void	reset()	Performs superclass reset actions and recalculated currentPotentialEnergy
void	resetStepCount()	This method resets the step counter.
protected void	scaleMomenta()	Updates collision times appropriately after scaling momenta.
void	setNullPotential(PotentialHard nullPotential, AtomType type)	Sets the "null" potential for the given AtomType.
void	setTemperature(double temperature)
protected void	updateAtom(IAtom a)	updates collision time for a single atom (and any atom that might a collision with the atom)
protected void	updateAtoms(AtomPair colliders)	Updates collision times/partners for collider and partner, and for atoms that were to collide with one of them.

Methods inherited from class etomica.integrator.Integrator

doStep, getEventInterval, getEventManager, getStepCount, isInitialized, setEventInterval

Methods inherited from class etomica.integrator.IntegratorBox

getBox, getMeterPotentialEnergy, getPotentialEnergy, getPotentialMaster, getTemperature, getTemperatureDimension, isIsothermal, setBox, setMeterPotentialEnergy

Methods inherited from class etomica.integrator.IntegratorMD

boxAtomLeafIndexChanged, boxGlobalAtomLeafIndexChanged, boxMoleculeIndexChanged, boxMoleculeRemoved, boxNumberMolecules, doThermostat, doThermostatInternal, getAlwaysScaleRandomizedMomenta, getCurrentTime, getHybridAcceptance, getIntegratorMC, getKineticEnergy, getMeterTemperature, getThermostat, getThermostatInterval, getTimeStep, isThermostatNoDrift, resetHybridAcceptance, scaleMomenta, setAlwaysScaleRandomizedMomenta, setIntegratorMC, setIsothermal, setMeterTemperature, setThermostat, setThermostatInterval, setThermostatNoDrift, setTimeStep, setup, shiftMomenta

Methods inherited from class java.lang.Object

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

Field Detail

upList

protected final IteratorDirective upList

downList

protected final IteratorDirective downList

listToUpdate

protected final AtomArrayList listToUpdate

eventList

protected final TreeList eventList

collisionTimeStep

protected double collisionTimeStep

agentManager

protected final AtomLeafAgentManager<IntegratorHard.Agent> agentManager

Constructor Detail

IntegratorHard

public IntegratorHard(Simulation sim,
                      PotentialMaster potentialMaster,
                      Box box)

IntegratorHard

public IntegratorHard(PotentialMaster potentialMaster,
                      IRandom random,
                      double timeStep,
                      double temperature,
                      Box box)

Method Detail

setTemperature

public void setTemperature(double temperature)

Overrides:

setTemperature in class IntegratorMD

Parameters:

temperature - the new temperature

getLastColliderAgent

public IntegratorHard.Agent getLastColliderAgent()

doStepInternal

protected void doStepInternal()

Steps all atoms across time interval timeStep, handling all intervening collisions.

Overrides:

doStepInternal in class IntegratorMD

resetStepCount

public void resetStepCount()

Description copied from class: Integrator

This method resets the step counter.

Overrides:

resetStepCount in class IntegratorMD

getCollisionCount

public long getCollisionCount()

updateAtoms

protected void updateAtoms(AtomPair colliders)

Updates collision times/partners for collider and partner, and for atoms that were to collide with one of them. This method should not be called for 1-body collisions (call updateAtom).

updateAtom

protected void updateAtom(IAtom a)

updates collision time for a single atom (and any atom that might a collision with the atom)

processReverseList

protected void processReverseList()

Recalculate collision times (up) for any atoms atoms in the "reverse" list of atoms that thought they would collide with an atom that's changed.

advanceAcrossTimeStep

protected void advanceAcrossTimeStep(double tStep)

Advances all atom coordinates by tStep, without any intervening collisions. Uses free-flight kinematics.

reset

public void reset()

Description copied from class: IntegratorBox

Performs superclass reset actions and recalculated currentPotentialEnergy

Overrides:

reset in class IntegratorMD

neighborListNeighborsUpdated

public void neighborListNeighborsUpdated()

Specified by:

neighborListNeighborsUpdated in interface INeighborListListener

boxMoleculeAdded

public void boxMoleculeAdded(BoxMoleculeEvent e)

Description copied from interface: BoxEventListener

Called when a molecule is added to the box.

Specified by:

boxMoleculeAdded in interface BoxEventListener

Overrides:

boxMoleculeAdded in class IntegratorMD

Parameters:

e - the event, which contains the added molecule and the box to which it was added.

scaleMomenta

protected void scaleMomenta()

Updates collision times appropriately after scaling momenta.

Overrides:

scaleMomenta in class IntegratorMD

randomizeMomenta

protected void randomizeMomenta()

Updates collision times appropriately after randomizing momenta as part of the Andersen thermostat.

Overrides:

randomizeMomenta in class IntegratorMD

randomizeTotalKE

protected void randomizeTotalKE()

Updates collision times appropriately after randomizing momenta as part of the Andersen scaling thermostat.

Overrides:

randomizeTotalKE in class IntegratorMD

randomizeMomentum

protected void randomizeMomentum(IAtomKinetic atom)

Updates collision time appropriately after randomizing momentum as part of the Andersen thermostat.

Overrides:

randomizeMomentum in class IntegratorMD

Parameters:

atom - whose momenta is be randomized

addCollisionListener

public void addCollisionListener(IntegratorHard.CollisionListener cl)

Registers an object that implements the CollisionListener interface. This causes the collisionAction method of the object to be called after each collision. If the listener is already in the list, no action is taken to add it again.

removeCollisionListener

public void removeCollisionListener(IntegratorHard.CollisionListener cl)

De-registers an object from the list of collision listeners. No exception is generated if the listener is not in the list; method simply returns without taking any action.

getNullPotential

public PotentialHard getNullPotential(AtomType atomType)

Returns:

Returns the nullPotential.

setNullPotential

public void setNullPotential(PotentialHard nullPotential,
                             AtomType type)

Sets the "null" potential for the given AtomType. The null potential is a 1-body potential used by IntegratorHard to handle Atoms that wrap around periodic boundaries when neighbor listing is not used.

makeAgent

public IntegratorHard.Agent makeAgent(IAtom a,
                                      Box agentBox)

Produces the Agent for this integrator. This method gets called by the agentManager, which allocates/deallocates agents as needed.

Specified by:

makeAgent in interface AtomLeafAgentManager.AgentSource<IntegratorHard.Agent>

agentBox - TODO

releaseAgent

public void releaseAgent(IntegratorHard.Agent 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<IntegratorHard.Agent>