Package etomica.integrator

Class IntegratorMD

java.lang.Object

etomica.integrator.Integrator

etomica.integrator.IntegratorBox

etomica.integrator.IntegratorMD

All Implemented Interfaces:

BoxEventListener

Direct Known Subclasses:

IntegratorDroplet, IntegratorGear4, IntegratorHard, IntegratorHarmonic, IntegratorPolymer, IntegratorRigidIterative, IntegratorRigidMatrixIterative, IntegratorVelocityVerlet, IntegratorVelocityVerletQuaternion, IntegratorVelocityVerletShake, IntegratorVerlet

public abstract class IntegratorMD
extends IntegratorBox
implements BoxEventListener

Superclass of all molecular-dynamics integrators.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	IntegratorMD.ThermostatType
static class	IntegratorMD.VectorSource	An AgentSource that permits another vector to be associated with each atom.

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

Integrator.Forcible, Integrator.Torquable

Field Summary

Fields

Modifier and Type	Field	Description
protected boolean	alwaysScaleMomenta
protected AtomActionRandomizeVelocity	atomActionRandomizeVelocity
protected double	currentKineticEnergy
protected double	currentTime
protected IntegratorMC	integratorMC
protected int	mcSteps
protected DataSourceScalar	meterKE
protected MeterTemperature	meterTemperature
protected Vector	momentum
protected long	nAccepted
protected long	nRejected
protected double	oldEnergy
protected AtomLeafAgentManager<Vector>	oldPositionAgentManager
protected double	oldPotentialEnergy
protected IRandom	random
protected Vector	temperatureVec
protected IntegratorMD.ThermostatType	thermostat
protected int	thermostatCount
protected int	thermostatInterval
protected boolean	thermostatNoDrift
protected boolean	thermostatting
protected double	timeStep

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

Constructor Summary

Constructors

Constructor	Description
IntegratorMD(PotentialMaster potentialMaster, IRandom random, double timeStep, double temperature, Box box)	Constructs integrator with a default for non-isothermal sampling.

Method Summary

Modifier and Type	Method	Description
void	boxAtomLeafIndexChanged(BoxAtomIndexEvent e)	Called when an atom's global (leaf) index has changed.
void	boxGlobalAtomLeafIndexChanged(BoxIndexEvent e)	Called when the maximum leaf index in the box has changed.
void	boxMoleculeAdded(BoxMoleculeEvent e)	Called when a molecule is added to the box.
void	boxMoleculeIndexChanged(BoxMoleculeIndexEvent e)	Called when an molecule's index has changed.
void	boxMoleculeRemoved(BoxMoleculeEvent e)	Called when a molecule is removed from the box.
void	boxNumberMolecules(BoxMoleculeCountEvent e)	Called when the number of molecules of a particular species has changed in the box.
protected void	doStepInternal()	Performs the elementary integration step, such as a molecular dynamics time step, or a Monte Carlo trial.
void	doThermostat()	Invokes thermostat, modifying velocities according to specified temperature and algorithm of thermostat specified via setThermostat.
protected void	doThermostatInternal()	Fires the thermostat if the appropriate interval has been reached.
boolean	getAlwaysScaleRandomizedMomenta()	Returns true if the thermostat is set to always scale randomized momenta to match the set temperature
double	getCurrentTime()
double	getHybridAcceptance()
IntegratorMC	getIntegratorMC()
double	getKineticEnergy()
DataSourceScalar	getMeterTemperature()
IntegratorMD.ThermostatType	getThermostat()
int	getThermostatInterval()
double	getTimeStep()
boolean	isThermostatNoDrift()
protected void	randomizeMomenta()	Randomizes the velocities of all atoms in the box using values chosen from a Maxwell-Boltzmann distribution, as in the Andersen thermostat.
protected void	randomizeMomentum(IAtomKinetic atom)	Randomizes the velocities of the given atom using value chosen from a Maxwell-Boltzmann distribution, as in the Andersen thermostat.
protected void	randomizeTotalKE()	Scales all velocities so that the total kinetic energy matches a value selected at random for the previously specified temperature.
void	reset()	Performs superclass reset actions and recalculated currentPotentialEnergy
void	resetHybridAcceptance()	Zeros counters used to track acceptance fraction of HYBRID_MC thermostat.
void	resetStepCount()	This method resets the step counter.
protected void	scaleMomenta()	Crude method to enforce constant-temperature constraint, by scaling momenta of all atoms by a constant factor so that box adheres to setpoint temperature.
protected void	scaleMomenta(Vector t)
void	setAlwaysScaleRandomizedMomenta(boolean alwaysScale)	Configure thermostat to always scale randomized momenta to match the set temperature
void	setIntegratorMC(IntegratorMC integratorMC, int mcSteps)	A Monte Carlo integrator is employed with this MD integrator when performing hybrid MD/MC sampling.
void	setIsothermal(boolean b)
void	setMeterTemperature(MeterTemperature meter)	Sets the temperature meter used to calculate temperature for velocity rescaling.
void	setTemperature(double t)
void	setThermostat(IntegratorMD.ThermostatType aThermostat)	Sets the type of thermostat used by the integrator for isothermal sampling.
void	setThermostatInterval(int interval)	Sets the number of integrator steps between thermostat actions (for thermostats such as velocity scaling and Andersen).
void	setThermostatNoDrift(boolean newNoDrift)	Configures the thermostat to remove any net momenta imparted to the system after use of the thermostat.
void	setTimeStep(double t)
protected void	setup()	Perform initialization.
protected void	shiftMomenta()	Subtracts velocity from all atoms such that the new net momentum of the whole system is zero.

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 java.lang.Object

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

Field Detail

random

protected final IRandom random

momentum

protected final Vector momentum

temperatureVec

protected final Vector temperatureVec

timeStep

protected double timeStep

currentKineticEnergy

protected double currentKineticEnergy

thermostat

protected IntegratorMD.ThermostatType thermostat

thermostatCount

protected int thermostatCount

thermostatInterval

protected int thermostatInterval

meterKE

protected DataSourceScalar meterKE

atomActionRandomizeVelocity

protected AtomActionRandomizeVelocity atomActionRandomizeVelocity

meterTemperature

protected MeterTemperature meterTemperature

currentTime

protected double currentTime

thermostatting

protected boolean thermostatting

thermostatNoDrift

protected boolean thermostatNoDrift

alwaysScaleMomenta

protected boolean alwaysScaleMomenta

oldEnergy

protected double oldEnergy

oldPotentialEnergy

protected double oldPotentialEnergy

nRejected

protected long nRejected

nAccepted

protected long nAccepted

oldPositionAgentManager

protected AtomLeafAgentManager<Vector> oldPositionAgentManager

integratorMC

protected IntegratorMC integratorMC

mcSteps

protected int mcSteps

Constructor Detail

IntegratorMD

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

Constructs integrator with a default for non-isothermal sampling.

Parameters:

potentialMaster - PotentialMaster instance used to compute the energy and forces

random - random number generator used for initial velocities and some thermostats

timeStep - time step for integration

temperature - used by thermostat and/or to initialize velocities

Method Detail

getTimeStep

public final double getTimeStep()

Returns:

the integration time step

setTimeStep

public void setTimeStep(double t)

Parameters:

t - the new integration time step

setup

protected void setup()

Description copied from class: Integrator

Perform initialization. Subclasses can override this method to set up before integration begins.

Overrides:

setup in class Integrator

resetStepCount

public void resetStepCount()

Description copied from class: Integrator

This method resets the step counter.

Overrides:

resetStepCount in class Integrator

reset

public void reset()

Description copied from class: IntegratorBox

Performs superclass reset actions and recalculated currentPotentialEnergy

Overrides:

reset in class IntegratorBox

doStepInternal

protected void doStepInternal()

Description copied from class: Integrator

Performs the elementary integration step, such as a molecular dynamics time step, or a Monte Carlo trial.

Specified by:

doStepInternal in class Integrator

getCurrentTime

public double getCurrentTime()

Returns:

the amount of simulation time that has elapsed since construction or since last call to resetStepCount

getKineticEnergy

public double getKineticEnergy()

Returns:

the current kinetic energy as tracked by the integrator

setIsothermal

public void setIsothermal(boolean b)

Overrides:

setIsothermal in class IntegratorBox

Parameters:

b - specifies whether the Integrator should (if true) sample according to a specified temperature

setTemperature

public void setTemperature(double t)

Overrides:

setTemperature in class IntegratorBox

Parameters:

t - the new temperature

setIntegratorMC

public void setIntegratorMC(IntegratorMC integratorMC,
                            int mcSteps)

A Monte Carlo integrator is employed with this MD integrator when performing hybrid MD/MC sampling. The HYBRIC_MC thermostat will accept/reject a segment of the MD trajectory, and then, optionally, the IntegratorMC will perform additional sampling (e.g., grand-canonical), leaving the system in a state ready for the next MD segment.

Parameters:

integratorMC - the Monte Carlo integrator to be used for hybrid MC/MD

mcSteps - number of Monte Carlo trial steps to perform after MD segment

Throws:

java.lang.RuntimeException - if HYBRID_MC thermostat is not enabled or if isothermal is false

getIntegratorMC

public IntegratorMC getIntegratorMC()

Returns:

the Monte Carlo integrator used to enable hybrid MD/MC sampling. Will be null if not previously set via setIntegratorMC.

setThermostatNoDrift

public void setThermostatNoDrift(boolean newNoDrift)

Configures the thermostat to remove any net momenta imparted to the system after use of the thermostat.

Parameters:

newNoDrift - if true, will remove net momentum after thermostat use

isThermostatNoDrift

public boolean isThermostatNoDrift()

Returns:

flag specifying whether net momentum should be removed after application of thermostat

setAlwaysScaleRandomizedMomenta

public void setAlwaysScaleRandomizedMomenta(boolean alwaysScale)

Configure thermostat to always scale randomized momenta to match the set temperature

getAlwaysScaleRandomizedMomenta

public boolean getAlwaysScaleRandomizedMomenta()

Returns true if the thermostat is set to always scale randomized momenta to match the set temperature

getThermostat

public IntegratorMD.ThermostatType getThermostat()

Returns:

the type of thermostat used to implement isothermal sampling.

setThermostat

public void setThermostat(IntegratorMD.ThermostatType aThermostat)

Sets the type of thermostat used by the integrator for isothermal sampling. The default at construction is ANDERSEN.

Parameters:

aThermostat - the desired thermostat

getThermostatInterval

public int getThermostatInterval()

Returns:

the value of the thermostat interval

setThermostatInterval

public void setThermostatInterval(int interval)

Sets the number of integrator steps between thermostat actions (for thermostats such as velocity scaling and Andersen).

Parameters:

interval - number of integrator steps between thermostat activity

doThermostatInternal

protected void doThermostatInternal()

Fires the thermostat if the appropriate interval has been reached.

doThermostat

public void doThermostat()

Invokes thermostat, modifying velocities according to specified temperature and algorithm of thermostat specified via setThermostat.

getHybridAcceptance

public double getHybridAcceptance()

Returns:

fraction of Monte Carlo trials that were accepted when using HYBRID_MC thermostat, since construction, or since last call to resetHybridAcceptance.

resetHybridAcceptance

public void resetHybridAcceptance()

Zeros counters used to track acceptance fraction of HYBRID_MC thermostat.

randomizeTotalKE

protected void randomizeTotalKE()

Scales all velocities so that the total kinetic energy matches a value selected at random for the previously specified temperature.

randomizeMomenta

protected void randomizeMomenta()

Randomizes the velocities of all atoms in the box using values chosen from a Maxwell-Boltzmann distribution, as in the Andersen thermostat. Does not reset or otherwise updated integrator for new velocities (some integrators, e.g. IntegratorHard, will need to be reset after calling this method).

randomizeMomentum

protected void randomizeMomentum(IAtomKinetic atom)

Randomizes the velocities of the given atom using value chosen from a Maxwell-Boltzmann distribution, as in the Andersen thermostat. Does not reset or otherwise updated integrator for new velocities (some integrators, e.g. IntegratorHard, will need to be reset after calling this method).

Parameters:

atom - whose momenta is be randomized

shiftMomenta

protected void shiftMomenta()

Subtracts velocity from all atoms such that the new net momentum of the whole system is zero.

scaleMomenta

protected void scaleMomenta()

Crude method to enforce constant-temperature constraint, by scaling momenta of all atoms by a constant factor so that box adheres to setpoint temperature. The state of the integrator may need to be updated after calling this method.

scaleMomenta

protected void scaleMomenta(Vector t)

getMeterTemperature

public DataSourceScalar getMeterTemperature()

Returns:

the temperature meter used for velocity rescaling.

setMeterTemperature

public void setMeterTemperature(MeterTemperature meter)

Sets the temperature meter used to calculate temperature for velocity rescaling. You only need to call this method if the standard MeterTemperature won't work.

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

Parameters:

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

boxMoleculeRemoved

public void boxMoleculeRemoved(BoxMoleculeEvent e)

Description copied from interface: BoxEventListener

Called when a molecule is removed from the box.

Specified by:

boxMoleculeRemoved in interface BoxEventListener

Parameters:

e - the event, which contains the removed molecule and the box from which it was removed.

boxGlobalAtomLeafIndexChanged

public void boxGlobalAtomLeafIndexChanged(BoxIndexEvent e)

Description copied from interface: BoxEventListener

Called when the maximum leaf index in the box has changed.

Specified by:

boxGlobalAtomLeafIndexChanged in interface BoxEventListener

Parameters:

e - the event, which contains the box and the new maximum global index

boxAtomLeafIndexChanged

public void boxAtomLeafIndexChanged(BoxAtomIndexEvent e)

Description copied from interface: BoxEventListener

Called when an atom's global (leaf) index has changed. This typically happens after one molecule is removed and the indices of other atoms are renumbered to fill in the gap left by the removed atoms.

Specified by:

boxAtomLeafIndexChanged in interface BoxEventListener

Parameters:

e - the event, which contains the box, the atom whose index changed and the atom's old leaf index. The atom's new leaf index can be obtained from the atom.

boxMoleculeIndexChanged

public void boxMoleculeIndexChanged(BoxMoleculeIndexEvent e)

Description copied from interface: BoxEventListener

Called when an molecule's index has changed. This typically happens after one molecule is removed and the indices of another molecule is changed to fill in the gap.

Specified by:

boxMoleculeIndexChanged in interface BoxEventListener

Parameters:

e - the event, which contains the box, the molecule whose index changed and the molecule's old index. The molecule's new index can be obtained from the atom.

boxNumberMolecules

public void boxNumberMolecules(BoxMoleculeCountEvent e)

Description copied from interface: BoxEventListener

Called when the number of molecules of a particular species has changed in the box. This method is called before the new molecules have been added to the box.

Specified by:

boxNumberMolecules in interface BoxEventListener

Parameters:

e - the event, which contains the box, the species and the new number of molecules of that species.