Package etomica.rotation

Class IntegratorVelocityVerletQuaternion

java.lang.Object

etomica.integrator.Integrator

etomica.integrator.IntegratorBox

etomica.integrator.IntegratorMD

etomica.rotation.IntegratorVelocityVerletQuaternion

All Implemented Interfaces:

BoxEventListener, MoleculeAgentManager.MoleculeAgentSource, SpeciesAgentManager.AgentSource

public class IntegratorVelocityVerletQuaternion
extends IntegratorMD
implements SpeciesAgentManager.AgentSource, MoleculeAgentManager.MoleculeAgentSource

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	IntegratorVelocityVerletQuaternion.MoleculeAgent
static class	IntegratorVelocityVerletQuaternion.MyTypeAgent

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 Vector	angularVelocity
protected MoleculePositionCOM	atomPositionCOM
protected PotentialCalculationForceSum	forceSum
protected AtomLeafAgentManager<Vector>	leafAgentManager
protected MoleculeAgentManager	moleculeAgentManager
protected Tensor	pressureTensor
int	printInterval
protected double[]	quatVelocity
protected RotationTensor3D	rotationTensor
protected Simulation	sim
protected double[]	tempQuat
protected AtomActionTranslateBy	translateBy
protected MoleculeChildAtomAction	translator
protected SpeciesAgentManager	typeAgentManager
protected Tensor	workTensor
protected Vector	xWork

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
IntegratorVelocityVerletQuaternion(Simulation sim, PotentialMaster potentialMaster, double timeStep, double temperature, Box box)
IntegratorVelocityVerletQuaternion(Simulation sim, PotentialMaster potentialMaster, Box box)

Method Summary

Modifier and Type	Method	Description
protected void	doStepInternal()	Performs the elementary integration step, such as a molecular dynamics time step, or a Monte Carlo trial.
Tensor	getPressureTensor()	Returns the pressure tensor based on the forces calculated during the last time step.
static void	main(java.lang.String[] args)
java.lang.Object	makeAgent(IMolecule a)	Returns an agent for the given Atom.
java.lang.Object	makeAgent(ISpecies type)	Returns an agent for the given AtomType.
void	randomizeMomenta()	Randomizes the velocities of all atoms in the box using values chosen from a Maxwell-Boltzmann distribution, as in the Andersen thermostat.
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	releaseAgent(java.lang.Object agent, ISpecies type)	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()	Performs superclass reset actions and recalculated currentPotentialEnergy
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.
void	setOrientationCalc(ISpecies species, OrientationCalcQuaternion calcer)
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 etomica.integrator.IntegratorMD

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

Methods inherited from class java.lang.Object

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

Field Detail

pressureTensor

protected final Tensor pressureTensor

workTensor

protected final Tensor workTensor

rotationTensor

protected final RotationTensor3D rotationTensor

xWork

protected final Vector xWork

typeAgentManager

protected final SpeciesAgentManager typeAgentManager

angularVelocity

protected final Vector angularVelocity

quatVelocity

protected final double[] quatVelocity

tempQuat

protected final double[] tempQuat

atomPositionCOM

protected final MoleculePositionCOM atomPositionCOM

translateBy

protected final AtomActionTranslateBy translateBy

translator

protected final MoleculeChildAtomAction translator

sim

protected final Simulation sim

printInterval

public int printInterval

forceSum

protected PotentialCalculationForceSum forceSum

leafAgentManager

protected AtomLeafAgentManager<Vector> leafAgentManager

moleculeAgentManager

protected MoleculeAgentManager moleculeAgentManager

Constructor Detail

IntegratorVelocityVerletQuaternion

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

IntegratorVelocityVerletQuaternion

public IntegratorVelocityVerletQuaternion(Simulation sim,
                                          PotentialMaster potentialMaster,
                                          double timeStep,
                                          double temperature,
                                          Box box)

Method Detail

main

public static void main(java.lang.String[] args)

setOrientationCalc

public void setOrientationCalc(ISpecies species,
                               OrientationCalcQuaternion calcer)

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.

Overrides:

doStepInternal in class IntegratorMD

getPressureTensor

public Tensor getPressureTensor()

Returns the pressure tensor based on the forces calculated during the last time step.

scaleMomenta

public void scaleMomenta()

Description copied from class: IntegratorMD

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.

Overrides:

scaleMomenta in class IntegratorMD

randomizeMomenta

public void randomizeMomenta()

Description copied from class: IntegratorMD

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).

Overrides:

randomizeMomenta in class IntegratorMD

shiftMomenta

public void shiftMomenta()

Description copied from class: IntegratorMD

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

Overrides:

shiftMomenta in class IntegratorMD

reset

public void reset()

Description copied from class: IntegratorBox

Performs superclass reset actions and recalculated currentPotentialEnergy

Overrides:

reset in class IntegratorMD

makeAgent

public final 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

makeAgent

public java.lang.Object makeAgent(ISpecies type)

Description copied from interface: SpeciesAgentManager.AgentSource

Returns an agent for the given AtomType.

Specified by:

makeAgent in interface SpeciesAgentManager.AgentSource

releaseAgent

public void releaseAgent(java.lang.Object agent,
                         ISpecies type)

Description copied from interface: SpeciesAgentManager.AgentSource

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 SpeciesAgentManager.AgentSource