Package etomica.integrator

Class IntegratorRigidMatrixIterative

java.lang.Object

etomica.integrator.Integrator

etomica.integrator.IntegratorBox

etomica.integrator.IntegratorMD

etomica.integrator.IntegratorRigidMatrixIterative

All Implemented Interfaces:

BoxEventListener, MoleculeAgentManager.MoleculeAgentSource, SpeciesAgentManager.AgentSource

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

Integrator implementation of Omelyan's leapfrog integrator for rotational motion. Molecular Simulation, 22 (1999) 213-236.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	IntegratorRigidMatrixIterative.BoxImposePbcMolecule

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 MoleculePositionCOM	atomPositionCOM
protected RotationTensor3D	axesTensor
protected AtomLeafAgentManager<Vector>	forces
protected int	maxIterations
protected MoleculeAgentManager	moleculeAgentManager
protected Tensor	omegaTensor
protected double	omegaTolerance
protected Tensor	pressureTensor
int	printInterval
protected RotationTensor3D	rotationTensor
protected double	rotationTolerance
protected Simulation	sim
protected Vector	tempAngularVelocity
protected RotationTensor3D	tempAxesTensor
protected OrientationFull3D	tempOrientation
protected PotentialCalculationTorqueSum	torqueSum
protected AtomActionTranslateBy	translateBy
protected MoleculeChildAtomAction	translator
protected SpeciesAgentManager	typeAgentManager
protected Tensor	workTensor
protected Vector	xWork
protected Vector	yWork

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
IntegratorRigidMatrixIterative(Simulation sim, PotentialMaster potentialMaster, double timeStep, double temperature, Box box)
IntegratorRigidMatrixIterative(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.
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	randomizeMomentum(IAtomKinetic atom)	Randomizes the velocities of the given atom using value chosen from a Maxwell-Boltzmann distribution, as in the Andersen thermostat.
void	releaseAgent(java.lang.Object agent, IMolecule molecule)	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	setMaxIterations(int newMaxIterations)
void	setOrientationCalc(ISpecies species, OrientationCalc 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, 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

torqueSum

protected PotentialCalculationTorqueSum torqueSum

pressureTensor

protected final Tensor pressureTensor

workTensor

protected final Tensor workTensor

rotationTensor

protected final RotationTensor3D rotationTensor

xWork

protected final Vector xWork

yWork

protected final Vector yWork

typeAgentManager

protected final SpeciesAgentManager typeAgentManager

tempAngularVelocity

protected final Vector tempAngularVelocity

atomPositionCOM

protected final MoleculePositionCOM atomPositionCOM

translateBy

protected final AtomActionTranslateBy translateBy

translator

protected final MoleculeChildAtomAction translator

tempOrientation

protected final OrientationFull3D tempOrientation

printInterval

public int printInterval

maxIterations

protected int maxIterations

omegaTolerance

protected double omegaTolerance

rotationTolerance

protected double rotationTolerance

axesTensor

protected final RotationTensor3D axesTensor

tempAxesTensor

protected final RotationTensor3D tempAxesTensor

omegaTensor

protected final Tensor omegaTensor

sim

protected final Simulation sim

forces

protected AtomLeafAgentManager<Vector> forces

moleculeAgentManager

protected MoleculeAgentManager moleculeAgentManager

Constructor Detail

IntegratorRigidMatrixIterative

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

IntegratorRigidMatrixIterative

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

Method Detail

setOrientationCalc

public void setOrientationCalc(ISpecies species,
                               OrientationCalc calcer)

setMaxIterations

public void setMaxIterations(int newMaxIterations)

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

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

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

randomizeMomentum

public void randomizeMomentum(IAtomKinetic atom)

Description copied from class: IntegratorMD

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).

Overrides:

randomizeMomentum in class IntegratorMD

Parameters:

atom - whose momenta is be randomized

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 molecule)

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