etomica.integrator
Class IntegratorRigidIterative

java.lang.Object
  etomica.integrator.Integrator
      etomica.integrator.IntegratorBox
          etomica.integrator.IntegratorMD
              etomica.integrator.IntegratorRigidIterative

All Implemented Interfaces:

IBoxListener, IIntegrator, AtomLeafAgentManager.AgentSource, MoleculeAgentManager.MoleculeAgentSource, SpeciesAgentManager.AgentSource, Serializable

public class IntegratorRigidIterative
extends IntegratorMD
implements AtomLeafAgentManager.AgentSource, SpeciesAgentManager.AgentSource, MoleculeAgentManager.MoleculeAgentSource

See Also:

Serialized Form

Nested Class Summary

static class

IntegratorRigidIterative.MoleculeAgent

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

IntegratorMD.ThermostatType

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

Integrator.Forcible, Integrator.Torquable

Field Summary

protected AtomPositionCOM	atomPositionCOM
protected AtomLeafAgentManager	leafAgentManager
protected int	maxIterations
protected MoleculeAgentManager	moleculeAgentManager
protected double	omegaTolerance
protected Tensor	pressureTensor
int	printInterval
protected RotationTensor3D	rotationTensor
protected ISimulation	sim
protected boolean	storeAngularMomentum
protected IVectorMutable	tempAngularVelocity
protected OrientationFull3D	tempOrientation
protected RotationTensor3D	tempRotationTensor
protected PotentialCalculationTorqueSum	torqueSum
protected AtomActionTranslateBy	translateBy
protected MoleculeChildAtomAction	translator
protected SpeciesAgentManager	typeAgentManager
protected Tensor	workTensor
protected IVectorMutable	xWork

Fields inherited from class etomica.integrator.IntegratorMD

atomActionRandomizeVelocity, currentKineticEnergy, currentTime, meterKE, meterTemperature, momentum, random, space, thermostat, thermostatCount, thermostatInterval, timeStep

Fields inherited from class etomica.integrator.IntegratorBox

box, currentPotentialEnergy, isothermal, meterPE, potentialMaster, temperature

Fields inherited from class etomica.integrator.Integrator

eventManager, initialized, interval, stepCount

Constructor Summary

IntegratorRigidIterative(ISimulation sim, IPotentialMaster potentialMaster, double timeStep, double temperature, ISpace _space)

IntegratorRigidIterative(ISimulation sim, IPotentialMaster potentialMaster, ISpace _space)

Method Summary

void	doStepInternal() Performs the elementary integration step, such as a molecular dynamics time step, or a Monte Carlo trial.
Class	getAgentClass() Returns the Class of the agent.
static EtomicaInfo	getEtomicaInfo()
Class	getMoleculeAgentClass() Returns the Class of the agent.
Tensor	getPressureTensor() Returns the pressure tensor based on the forces calculated during the last time step.
Class	getSpeciesAgentClass() Returns the Class of the agent.
static void	main(String[] args)
Object	makeAgent(IAtom a) Returns an agent for the given Atom.
Object	makeAgent(IMolecule a) Returns an agent for the given Atom.
Object	makeAgent(ISpecies type) Returns an agent for the given AtomType.
void	randomizeMomenta() randomizes the velocities for the given box using velocities chosen form a Maxwell-Boltzmann distribution as in the Andersen thermostat.
void	randomizeMomentum(IAtomKinetic atom) randomizes the velocity of an atom in the given box using velocities chosen form a Maxwell-Boltzmann distribution as in the Andersen thermostat.
void	releaseAgent(Object agent, IAtom 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(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(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() reset the integrator's kinetic energy tracker
void	scaleMomenta() Crude method to enforce constant-temperature constraint Scales momenta of all atoms by a constant factor so that box adheres to setpoint temperature.
void	setBox(IBox p) Performs activities needed to set up integrator to work on given box.
void	setMaxIterations(int newMaxIterations)
void	setOrientationCalc(ISpecies moleculeType, OrientationCalc calcer)
void	setTorqueSum(PotentialCalculationTorqueSum pc)

Methods inherited from class etomica.integrator.IntegratorMD

boxAtomAdded, boxAtomLeafIndexChanged, boxAtomRemoved, boxGlobalAtomIndexChanged, boxGlobalAtomLeafIndexChanged, boxMoleculeAdded, boxMoleculeIndexChanged, boxMoleculeRemoved, boxNumberMolecules, doThermostat, getCurrentTime, getKineticEnergy, getMeterTemperature, getThermostat, getTimeStep, getTimeStepDimension, resetStepCount, setIsothermal, setMeterTemperature, setTemperature, setThermostat, setThermostatInterval, setTimeStep, setup, shiftMomenta

Methods inherited from class etomica.integrator.IntegratorBox

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

Methods inherited from class etomica.integrator.Integrator

doStep, getEventInterval, getEventManager, getStepCount, setEventInterval

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

tempRotationTensor

protected final RotationTensor3D tempRotationTensor

xWork

protected final IVectorMutable xWork

typeAgentManager

protected final SpeciesAgentManager typeAgentManager

tempAngularVelocity

protected final IVectorMutable tempAngularVelocity

atomPositionCOM

protected final AtomPositionCOM 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

storeAngularMomentum

protected final boolean storeAngularMomentum

See Also:

Constant Field Values

sim

protected final ISimulation sim

leafAgentManager

protected AtomLeafAgentManager leafAgentManager

moleculeAgentManager

protected MoleculeAgentManager moleculeAgentManager

Constructor Detail

IntegratorRigidIterative

public IntegratorRigidIterative(ISimulation sim,
                                IPotentialMaster potentialMaster,
                                ISpace _space)

IntegratorRigidIterative

public IntegratorRigidIterative(ISimulation sim,
                                IPotentialMaster potentialMaster,
                                double timeStep,
                                double temperature,
                                ISpace _space)

Method Detail

getEtomicaInfo

public static EtomicaInfo getEtomicaInfo()

setBox

public void setBox(IBox p)

Description copied from class: IntegratorBox

Performs activities needed to set up integrator to work on given box.

Overrides:

setBox in class IntegratorMD

setTorqueSum

public void setTorqueSum(PotentialCalculationTorqueSum pc)

setOrientationCalc

public void setOrientationCalc(ISpecies moleculeType,
                               OrientationCalc calcer)

setMaxIterations

public void setMaxIterations(int newMaxIterations)

doStepInternal

public 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 Scales 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 for the given box using velocities chosen form a Maxwell-Boltzmann distribution as in the Andersen thermostat. The state of the integrator needs to be updated after calling this method.

Overrides:

randomizeMomenta in class IntegratorMD

randomizeMomentum

public void randomizeMomentum(IAtomKinetic atom)

Description copied from class: IntegratorMD

randomizes the velocity of an atom in the given box using velocities chosen form a Maxwell-Boltzmann distribution as in the Andersen thermostat. The state of the integrator needs to be updated after calling this method.

Overrides:

randomizeMomentum in class IntegratorMD

Parameters:

atom - whose momenta is be randomized

reset

public void reset()

Description copied from class: IntegratorMD

reset the integrator's kinetic energy tracker

Specified by:

reset in interface IIntegrator

Overrides:

reset in class IntegratorMD

getMoleculeAgentClass

public Class getMoleculeAgentClass()

Description copied from interface: MoleculeAgentManager.MoleculeAgentSource

Returns the Class of the agent. This is used to create an array of the appropriate Class.

Specified by:

getMoleculeAgentClass in interface MoleculeAgentManager.MoleculeAgentSource

makeAgent

public final 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(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

getAgentClass

public Class getAgentClass()

Description copied from interface: AtomLeafAgentManager.AgentSource

Returns the Class of the agent. This is used to create an array of the appropriate Class.

Specified by:

getAgentClass in interface AtomLeafAgentManager.AgentSource

makeAgent

public final Object makeAgent(IAtom a)

Description copied from interface: AtomLeafAgentManager.AgentSource

Returns an agent for the given Atom.

Specified by:

makeAgent in interface AtomLeafAgentManager.AgentSource

releaseAgent

public void releaseAgent(Object agent,
                         IAtom atom)

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

Specified by:

releaseAgent in interface AtomLeafAgentManager.AgentSource

getSpeciesAgentClass

public Class getSpeciesAgentClass()

Description copied from interface: SpeciesAgentManager.AgentSource

Returns the Class of the agent. This is used to create an array of the appropriate Class.

Specified by:

getSpeciesAgentClass in interface SpeciesAgentManager.AgentSource

makeAgent

public 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(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

main

public static void main(String[] args)