Open Qmin: velocityVerlet Class Reference

#include <velocityVerlet.h>

Inheritance diagram for velocityVerlet:

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Collaboration diagram for velocityVerlet:

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Public Member Functions
virtual void	integrateEOMGPU ()

virtual void	integrateEOMCPU ()

virtual void	performUpdate ()
	The function which performs the update. More...

virtual void	integrateEquationOfMotion ()

virtual void	initializeFromModel ()
	by default, set Ndof More...

virtual scalar	getClassSize ()

virtual void	Update (int timestep)
	The fundamental function that a controlling Simulation can call. More...

void	setSimulation (shared_ptr< basicSimulation > _sim)
	set the simulation More...

virtual void	setModel (shared_ptr< simpleModel > _model)
	virtual function to allow the model to be a derived class More...

void	setPeriod (int _p)
	set the period More...

void	setPhase (int _p)
	set the phase More...

virtual void	spatialSorting ()
	allow for spatial sorting to be called if necessary... More...

virtual void	setReproducible (bool rep)
	Allow for a reproducibility call to be made. More...

virtual void	setGPU (bool _useGPU=true)
	Enforce GPU operation. More...

int	getNdof ()
	Get the number of degrees of freedom of the equation of motion. More...

void	setNdof (int _n)
	Set the number of degrees of freedom of the equation of motion. More...

virtual void	setDeltaT (scalar dt)
	allow all updaters to potentially implement an internal time scale More...

virtual void	setNThreads (int n)
	allow for setting multiple threads More...

virtual scalar	getMaxForce ()

void	setMaximumIterations (int maxIt)
	Set the maximum number of iterations before terminating (or set to -1 to ignore) More...

int	getCurrentIterations ()

int	getMaxIterations ()

void	setCurrentIterations (int newIterations)

int	getNTotal ()
	communicate the number of non-object sites across ranks More...

Public Attributes
GPUArray< dVec >	displacement
	an array of displacements More...

shared_ptr< basicSimulation >	sim
	A pointer to the governing simulation. More...

shared_ptr< simpleModel >	model
	A pointer to a simpleModel that the updater acts on. More...

vector< scalar >	updaterData

int	iterations
	The number of iterations performed. More...

Protected Attributes
int	nThreads =1
	number of threads to use More...

int	Period
	The period of the updater... the updater will work every Period timesteps. More...

int	Phase
	The phase of the updater... the updater will work every Period timesteps offset by a phase. More...

bool	useGPU
	whether the updater does its work on the GPU or not More...

bool	neverGPU
	whether the updater never does work on the GPU More...

int	Ndof
	some measure of the number of degrees of freedom the equations of motion might need to know about locally More...

int	nTotal
	the total number of non-object sites across all ranks More...

bool	reproducible
	whether the RNGs give reproducible results More...

scalar	deltaT
	The internal time step size. More...

int	maxIterations
	The maximum number of iterations allowed. More...

Member Function Documentation

◆ integrateEOMGPU()

void velocityVerlet::integrateEOMGPU ( )

virtual

Reimplemented from equationOfMotion.

References ArrayHandle< T >::data, updater::deltaT, access_location::device, equationOfMotion::displacement, gpu_displacement_velocity_verlet(), gpu_update_velocity(), updater::model, updater::Ndof, access_mode::overwrite, access_mode::read, access_mode::readwrite, and updater::sim.

◆ integrateEOMCPU()

void velocityVerlet::integrateEOMCPU ( )

virtual

Reimplemented from equationOfMotion.

References ArrayHandle< T >::data, updater::deltaT, equationOfMotion::displacement, updater::model, updater::Ndof, and updater::sim.

◆ performUpdate()

virtual void equationOfMotion::performUpdate ( )

inlinevirtualinherited

The function which performs the update.

Reimplemented from updater.

Reimplemented in energyMinimizerFIRE, energyMinimizerGradientDescent, energyMinimizerLoLBFGS, energyMinimizerNesterovAG, and energyMinimizerAdam.

References equationOfMotion::integrateEquationOfMotion().

◆ integrateEquationOfMotion()

virtual void equationOfMotion::integrateEquationOfMotion ( )

inlinevirtualinherited

References equationOfMotion::initializeFromModel(), equationOfMotion::integrateEOMCPU(), equationOfMotion::integrateEOMGPU(), updater::model, updater::Ndof, and updater::useGPU.

Referenced by energyMinimizerFIRE::minimize(), and equationOfMotion::performUpdate().

◆ initializeFromModel()

virtual void equationOfMotion::initializeFromModel ( )

inlinevirtualinherited

by default, set Ndof

Reimplemented from updater.

Reimplemented in energyMinimizerFIRE, energyMinimizerGradientDescent, energyMinimizerLoLBFGS, energyMinimizerNesterovAG, and energyMinimizerAdam.

References equationOfMotion::displacement, updater::model, updater::Ndof, updater::neverGPU, GPUArray< T >::noGPU, and GPUArray< T >::resize().

Referenced by equationOfMotion::integrateEquationOfMotion().

◆ getClassSize()

virtual scalar equationOfMotion::getClassSize ( )

inlinevirtualinherited

Reimplemented from updater.

Reimplemented in energyMinimizerFIRE, energyMinimizerLoLBFGS, and energyMinimizerGradientDescent.

References equationOfMotion::displacement, updater::getClassSize(), GPUArray< T >::getNumElements(), and scalar.

Referenced by energyMinimizerGradientDescent::getClassSize(), energyMinimizerLoLBFGS::getClassSize(), and energyMinimizerFIRE::getClassSize().

◆ Update()

virtual void updater::Update ( int timestep )

inlinevirtualinherited

The fundamental function that a controlling Simulation can call.

References updater::performUpdate(), updater::Period, and updater::Phase.

◆ setSimulation()

void updater::setSimulation ( shared_ptr< basicSimulation > _sim )

inlineinherited

set the simulation

References updater::sim.

◆ setModel()

virtual void updater::setModel ( shared_ptr< simpleModel > _model )

inlinevirtualinherited

virtual function to allow the model to be a derived class

References updater::initializeFromModel(), and updater::model.

Referenced by energyMinimizerFIRE::energyMinimizerFIRE(), energyMinimizerGradientDescent::energyMinimizerGradientDescent(), energyMinimizerLoLBFGS::energyMinimizerLoLBFGS(), and energyMinimizerNesterovAG::energyMinimizerNesterovAG().

◆ setPeriod()

void updater::setPeriod ( int _p )

inlineinherited

set the period

References updater::Period.

◆ setPhase()

void updater::setPhase ( int _p )

inlineinherited

set the phase

References updater::Phase.

◆ spatialSorting()

virtual void updater::spatialSorting ( )

inlinevirtualinherited

allow for spatial sorting to be called if necessary...

◆ setReproducible()

virtual void updater::setReproducible ( bool rep )

inlinevirtualinherited

Allow for a reproducibility call to be made.

References updater::reproducible.

◆ setGPU()

virtual void updater::setGPU ( bool _useGPU = true )

inlinevirtualinherited

Enforce GPU operation.

References updater::useGPU.

Referenced by energyMinimizerNesterovAG::initializeParameters(), energyMinimizerLoLBFGS::initializeParameters(), energyMinimizerGradientDescent::initializeParameters(), and energyMinimizerFIRE::initializeParameters().

◆ getNdof()

int updater::getNdof ( )

inlineinherited

Get the number of degrees of freedom of the equation of motion.

References updater::Ndof.

◆ setNdof()

void updater::setNdof ( int _n )

inlineinherited

Set the number of degrees of freedom of the equation of motion.

References updater::Ndof.

◆ setDeltaT()

virtual void updater::setDeltaT ( scalar dt )

inlinevirtualinherited

allow all updaters to potentially implement an internal time scale

Reimplemented in energyMinimizerFIRE.

References updater::deltaT.

Referenced by energyMinimizerGradientDescent::initializeParameters(), and energyMinimizerGradientDescent::setGradientDescentParameters().

◆ setNThreads()

virtual void updater::setNThreads ( int n )

inlinevirtualinherited

allow for setting multiple threads

References n, and updater::nThreads.

◆ getMaxForce()

virtual scalar updater::getMaxForce ( )

inlinevirtualinherited

Reimplemented in energyMinimizerFIRE, energyMinimizerGradientDescent, energyMinimizerLoLBFGS, energyMinimizerNesterovAG, and energyMinimizerAdam.

◆ setMaximumIterations()

void updater::setMaximumIterations ( int maxIt )

inlineinherited

Set the maximum number of iterations before terminating (or set to -1 to ignore)

References updater::maxIterations.

◆ getCurrentIterations()

int updater::getCurrentIterations ( )

inlineinherited

References updater::iterations.

◆ getMaxIterations()

int updater::getMaxIterations ( )

inlineinherited

References updater::maxIterations.

◆ setCurrentIterations()

void updater::setCurrentIterations ( int newIterations )

inlineinherited

References updater::iterations.

◆ getNTotal()

int updater::getNTotal ( )

inherited

communicate the number of non-object sites across ranks

References access_location::host, updater::model, updater::Ndof, updater::nTotal, access_mode::read, updater::sim, and updater::updaterData.

Member Data Documentation

◆ displacement

GPUArray<dVec> equationOfMotion::displacement

inherited

an array of displacements

Referenced by energyMinimizerAdam::adamStepCPU(), energyMinimizerAdam::adamStepGPU(), equationOfMotion::getClassSize(), energyMinimizerAdam::initializeFromModel(), equationOfMotion::initializeFromModel(), energyMinimizerGradientDescent::initializeFromModel(), energyMinimizerFIRE::initializeFromModel(), integrateEOMCPU(), and integrateEOMGPU().

◆ sim

shared_ptr<basicSimulation> updater::sim

inherited

◆ model

shared_ptr<simpleModel> updater::model

inherited

A pointer to a simpleModel that the updater acts on.

Referenced by energyMinimizerAdam::adamStepCPU(), energyMinimizerAdam::adamStepGPU(), energyMinimizerFIRE::fireStepCPU(), energyMinimizerFIRE::fireStepGPU(), updater::getNTotal(), energyMinimizerGradientDescent::gradientDescentCPU(), energyMinimizerGradientDescent::gradientDescentGPU(), energyMinimizerAdam::initializeFromModel(), energyMinimizerNesterovAG::initializeFromModel(), energyMinimizerLoLBFGS::initializeFromModel(), equationOfMotion::initializeFromModel(), energyMinimizerGradientDescent::initializeFromModel(), energyMinimizerFIRE::initializeFromModel(), updater::initializeFromModel(), integrateEOMCPU(), integrateEOMGPU(), equationOfMotion::integrateEquationOfMotion(), energyMinimizerLoLBFGS::lineSearchCPU(), energyMinimizerLoLBFGS::LoLBFGSStepCPU(), energyMinimizerLoLBFGS::LoLBFGSStepGPU(), energyMinimizerAdam::minimize(), energyMinimizerNesterovAG::minimize(), energyMinimizerLoLBFGS::minimize(), energyMinimizerGradientDescent::minimize(), energyMinimizerFIRE::minimize(), energyMinimizerNesterovAG::nesterovStepCPU(), energyMinimizerNesterovAG::nesterovStepGPU(), and updater::setModel().

◆ updaterData

vector<scalar> updater::updaterData

inherited

Referenced by energyMinimizerFIRE::fireStepCPU(), energyMinimizerFIRE::fireStepGPU(), updater::getNTotal(), energyMinimizerGradientDescent::gradientDescentCPU(), energyMinimizerGradientDescent::gradientDescentGPU(), energyMinimizerGradientDescent::initializeParameters(), and energyMinimizerFIRE::initializeParameters().

◆ iterations

int updater::iterations

inherited

The number of iterations performed.

Referenced by energyMinimizerFIRE::fireStepCPU(), energyMinimizerFIRE::fireStepGPU(), updater::getCurrentIterations(), energyMinimizerAdam::initializeFromModel(), energyMinimizerNesterovAG::initializeParameters(), energyMinimizerLoLBFGS::initializeParameters(), energyMinimizerGradientDescent::initializeParameters(), energyMinimizerFIRE::initializeParameters(), energyMinimizerLoLBFGS::LoLBFGSStepCPU(), energyMinimizerLoLBFGS::LoLBFGSStepGPU(), energyMinimizerAdam::minimize(), energyMinimizerNesterovAG::minimize(), energyMinimizerLoLBFGS::minimize(), energyMinimizerGradientDescent::minimize(), energyMinimizerFIRE::minimize(), and updater::setCurrentIterations().

◆ nThreads

int updater::nThreads =1

protectedinherited

number of threads to use

Referenced by updater::setNThreads().

◆ Period

int updater::Period

protectedinherited

The period of the updater... the updater will work every Period timesteps.

Referenced by updater::setPeriod(), updater::Update(), and updater::updater().

◆ Phase

int updater::Phase

protectedinherited

The phase of the updater... the updater will work every Period timesteps offset by a phase.

Referenced by updater::setPhase(), updater::Update(), and updater::updater().

◆ useGPU

bool updater::useGPU

protectedinherited

whether the updater does its work on the GPU or not

Referenced by energyMinimizerFIRE::fireStep(), energyMinimizerGradientDescent::gradientDescentStep(), equationOfMotion::integrateEquationOfMotion(), energyMinimizerAdam::minimize(), energyMinimizerNesterovAG::minimize(), energyMinimizerLoLBFGS::minimize(), updater::setGPU(), and updater::updater().

◆ neverGPU

bool updater::neverGPU

protectedinherited

whether the updater never does work on the GPU

Referenced by equationOfMotion::initializeFromModel(), energyMinimizerGradientDescent::initializeFromModel(), and energyMinimizerFIRE::initializeFromModel().

◆ Ndof

int updater::Ndof

protectedinherited

some measure of the number of degrees of freedom the equations of motion might need to know about locally

Referenced by energyMinimizerAdam::adamStepCPU(), energyMinimizerAdam::adamStepGPU(), energyMinimizerFIRE::fireStepCPU(), energyMinimizerFIRE::fireStepGPU(), updater::getNdof(), updater::getNTotal(), energyMinimizerGradientDescent::gradientDescentCPU(), energyMinimizerGradientDescent::gradientDescentGPU(), energyMinimizerAdam::initializeFromModel(), energyMinimizerNesterovAG::initializeFromModel(), energyMinimizerLoLBFGS::initializeFromModel(), equationOfMotion::initializeFromModel(), energyMinimizerGradientDescent::initializeFromModel(), energyMinimizerFIRE::initializeFromModel(), updater::initializeFromModel(), energyMinimizerFIRE::initializeParameters(), integrateEOMCPU(), integrateEOMGPU(), equationOfMotion::integrateEquationOfMotion(), energyMinimizerLoLBFGS::lineSearchCPU(), energyMinimizerLoLBFGS::LoLBFGSStepCPU(), energyMinimizerLoLBFGS::LoLBFGSStepGPU(), energyMinimizerAdam::minimize(), energyMinimizerNesterovAG::minimize(), energyMinimizerLoLBFGS::minimize(), energyMinimizerGradientDescent::minimize(), energyMinimizerFIRE::minimize(), energyMinimizerNesterovAG::nesterovStepCPU(), energyMinimizerNesterovAG::nesterovStepGPU(), and updater::setNdof().

◆ nTotal

int updater::nTotal

protectedinherited

the total number of non-object sites across all ranks

◆ reproducible

bool updater::reproducible

protectedinherited

whether the RNGs give reproducible results

Referenced by updater::setReproducible(), and updater::updater().

◆ deltaT

scalar updater::deltaT

protectedinherited

The internal time step size.

Referenced by energyMinimizerAdam::adamStepCPU(), energyMinimizerAdam::adamStepGPU(), energyMinimizerFIRE::fireStepCPU(), energyMinimizerFIRE::fireStepGPU(), energyMinimizerGradientDescent::gradientDescentCPU(), energyMinimizerGradientDescent::gradientDescentGPU(), integrateEOMCPU(), integrateEOMGPU(), energyMinimizerLoLBFGS::minimize(), energyMinimizerFIRE::minimize(), energyMinimizerNesterovAG::nesterovStepCPU(), energyMinimizerNesterovAG::nesterovStepGPU(), energyMinimizerAdam::setAdamParameters(), energyMinimizerFIRE::setDeltaT(), updater::setDeltaT(), energyMinimizerFIRE::setFIREParameters(), energyMinimizerGradientDescent::setGradientDescentParameters(), energyMinimizerLoLBFGS::setLoLBFGSParameters(), and energyMinimizerNesterovAG::setNesterovAGParameters().

◆ maxIterations

int updater::maxIterations

protectedinherited

The maximum number of iterations allowed.

Referenced by updater::getMaxIterations(), energyMinimizerAdam::minimize(), energyMinimizerNesterovAG::minimize(), energyMinimizerLoLBFGS::minimize(), and updater::setMaximumIterations().

The documentation for this class was generated from the following files:

Public Member Functions

Public Attributes

Protected Attributes

Member Function Documentation

◆ integrateEOMGPU()

◆ integrateEOMCPU()

◆ performUpdate()

◆ integrateEquationOfMotion()

◆ initializeFromModel()

◆ getClassSize()

◆ Update()

◆ setSimulation()

◆ setModel()

◆ setPeriod()

◆ setPhase()

◆ spatialSorting()

◆ setReproducible()

◆ setGPU()

◆ getNdof()

◆ setNdof()

◆ setDeltaT()

◆ setNThreads()

◆ getMaxForce()

◆ setMaximumIterations()

◆ getCurrentIterations()

◆ getMaxIterations()

◆ setCurrentIterations()

◆ getNTotal()

Member Data Documentation

◆ displacement

◆ sim

◆ model

◆ updaterData

◆ iterations

◆ nThreads

◆ Period

◆ Phase

◆ useGPU

◆ neverGPU

◆ Ndof

◆ nTotal

◆ reproducible

◆ deltaT

◆ maxIterations