Collaboration diagram for The modular simulator:

Description

The modular simulator improves extensibility, adds Monte Carlo capabilities, promotes data locality and communication via interfaces, supports multi-stepping integrators, and paves the way for some task parallelism.

For more information, see page_modularsimulator

Todo:: Can we link to docs/doxygen/lib/modularsimulator.md?

Author: Pascal Merz pasca.nosp@m.l.me.nosp@m.rz@me.nosp@m..com

Classes
class	gmx::CheckpointData< operation >
	} More...

class	gmx::ModularSimulator
	The modular simulator. More...

class	gmx::ElementNotFoundError
	Exception class signalling that a requested element was not found. More...

class	gmx::MissingElementConnectionError
	Exception class signalling that elements were not connected properly. More...

class	gmx::SimulationAlgorithmSetupError
	Exception class signalling that the ModularSimulatorAlgorithm was set up in an incompatible way. More...

class	gmx::CheckpointError
	Exception class signalling an error in reading or writing modular checkpoints. More...

Typedefs
typedef std::function< void()>	gmx::CheckBondedInteractionsCallback
	The function type allowing to request a check of the number of bonded interactions.

using	gmx::Step = int64_t
	Step number.

using	gmx::Time = double
	Simulation time.

typedef std::function< void()>	gmx::SimulatorRunFunction
	The function type that can be scheduled to be run during the simulator run.

typedef std::function< void(SimulatorRunFunction)>	gmx::RegisterRunFunction
	The function type that allows to register run functions.

typedef std::function< void(Step, Time, const RegisterRunFunction &)>	gmx::SchedulingFunction
	The function type scheduling run functions for a step / time using a RegisterRunFunction reference.

typedef std::function< void(Step, Time)>	gmx::SignallerCallback
	The function type that can be registered to signallers for callback.

typedef std::function< void(gmx_mdoutf *, Step, Time, bool, bool)>	gmx::ITrajectoryWriterCallback
	Function type for trajectory writing clients.

typedef std::function< void(Step)>	gmx::PropagatorCallback
	Generic callback to the propagator.

typedef std::function< void()>	gmx::DomDecCallback
	Callback used by the DomDecHelper object to inform clients about system re-partitioning.

using	gmx::ReferenceTemperatureCallback = std::function< void(ArrayRef< const real >, ReferenceTemperatureChangeAlgorithm algorithm)>
	Callback updating the reference temperature.

Enumerations
enum	gmx::CheckpointDataOperation { Read, Write, Count }
	The operations on CheckpointData. More...

enum	gmx::ComputeGlobalsAlgorithm { LeapFrog, VelocityVerlet }
	The different global reduction schemes we know about.

enum	gmx::EnergySignallerEvent { EnergyCalculationStep, VirialCalculationStep, FreeEnergyCalculationStep }
	The energy events signalled by the EnergySignaller.

enum	gmx::TrajectoryEvent { StateWritingStep, EnergyWritingStep }
	The trajectory writing events.

enum	gmx::ModularSimulatorBuilderState { AcceptingClientRegistrations, NotAcceptingClientRegistrations }
	Enum allowing builders to store whether they can accept client registrations.

enum	gmx::ReportPreviousStepConservedEnergy { Yes, No, Count }
	Enum describing whether an element is reporting conserved energy from the previous step.

enum	gmx::ScaleVelocities { PreStepOnly, PreStepAndPostStep }
	Which velocities the thermostat scales.

enum	gmx::IntegrationStage { gmx::IntegrationStage::PositionsOnly, gmx::IntegrationStage::VelocitiesOnly, gmx::IntegrationStage::LeapFrog, gmx::IntegrationStage::VelocityVerletPositionsAndVelocities, gmx::IntegrationStage::ScaleVelocities, gmx::IntegrationStage::ScalePositions, gmx::IntegrationStage::Count }
	The different integration types we know about. More...

enum	gmx::NumPositionScalingValues { gmx::NumPositionScalingValues::None, gmx::NumPositionScalingValues::Single, gmx::NumPositionScalingValues::Multiple, gmx::NumPositionScalingValues::Count }
	Sets the number of different position scaling values. More...

enum	gmx::NumVelocityScalingValues { gmx::NumVelocityScalingValues::None, gmx::NumVelocityScalingValues::Single, gmx::NumVelocityScalingValues::Multiple, Count }
	Sets the number of different velocity scaling values. More...

enum	gmx::ParrinelloRahmanVelocityScaling { gmx::ParrinelloRahmanVelocityScaling::No, gmx::ParrinelloRahmanVelocityScaling::Diagonal, gmx::ParrinelloRahmanVelocityScaling::Anisotropic, Count }
	Describes the properties of the Parrinello-Rahman pressure scaling matrix. More...

Functions
template<typename... Ts>
auto	gmx::checkUseModularSimulator (Ts &&...args) -> decltype(ModularSimulator::isInputCompatible(std::forward< Ts >(args)...))
	Whether or not to use the ModularSimulator. More...

virtual void	gmx::ISimulatorElement::scheduleTask (Step, Time, const RegisterRunFunction &)=0
	Query whether element wants to run at step / time. More...

virtual void	gmx::ISimulatorElement::elementSetup ()=0
	Method guaranteed to be called after construction, before simulator run.

virtual void	gmx::ISimulatorElement::elementTeardown ()=0
	Method guaranteed to be called after simulator run, before deconstruction.

virtual	gmx::ISimulatorElement::~ISimulatorElement ()=default
	Standard virtual destructor.

virtual void	gmx::ISignaller::signal (Step, Time)=0
	Function run before every step of scheduling.

virtual void	gmx::ISignaller::setup ()=0
	Method guaranteed to be called after construction, before simulator run.

virtual	gmx::ISignaller::~ISignaller ()=default
	Standard virtual destructor.

virtual	gmx::INeighborSearchSignallerClient::~INeighborSearchSignallerClient ()=default
	Standard virtual destructor.

virtual std::optional < SignallerCallback >	gmx::INeighborSearchSignallerClient::registerNSCallback ()=0
	Return callback to NeighborSearchSignaller.

virtual	gmx::ILastStepSignallerClient::~ILastStepSignallerClient ()=default
	Standard virtual destructor.

virtual std::optional < SignallerCallback >	gmx::ILastStepSignallerClient::registerLastStepCallback ()=0
	Return callback to LastStepSignaller.

virtual	gmx::ILoggingSignallerClient::~ILoggingSignallerClient ()=default
	Standard virtual destructor.

virtual std::optional < SignallerCallback >	gmx::ILoggingSignallerClient::registerLoggingCallback ()=0
	Return callback to LoggingSignaller.

virtual	gmx::IEnergySignallerClient::~IEnergySignallerClient ()=default
	Standard virtual destructor.

virtual std::optional < SignallerCallback >	gmx::IEnergySignallerClient::registerEnergyCallback (EnergySignallerEvent)=0
	Return callback to EnergySignaller.

virtual	gmx::ITrajectorySignallerClient::~ITrajectorySignallerClient ()=default
	Standard virtual destructor.

virtual std::optional < SignallerCallback >	gmx::ITrajectorySignallerClient::registerTrajectorySignallerCallback (TrajectoryEvent)=0
	Return callback to TrajectoryElement.

virtual	gmx::ITrajectoryWriterClient::~ITrajectoryWriterClient ()=default
	Standard virtual destructor.

virtual void	gmx::ITrajectoryWriterClient::trajectoryWriterSetup (gmx_mdoutf *outf)=0
	Setup method with valid output pointer.

virtual void	gmx::ITrajectoryWriterClient::trajectoryWriterTeardown (gmx_mdoutf *outf)=0
	Teardown method with valid output pointer.

virtual std::optional < ITrajectoryWriterCallback >	gmx::ITrajectoryWriterClient::registerTrajectoryWriterCallback (TrajectoryEvent)=0
	Return callback to TrajectoryElement.

virtual	gmx::ITopologyHolderClient::~ITopologyHolderClient ()=default
	Standard virtual destructor.

virtual void	gmx::ITopologyHolderClient::setTopology (const gmx_localtop_t *)=0
	Pass pointer to new local topology.

virtual	gmx::ICheckpointHelperClient::~ICheckpointHelperClient ()=default
	Standard virtual destructor.

virtual void	gmx::ICheckpointHelperClient::saveCheckpointState (std::optional< WriteCheckpointData > checkpointData, const t_commrec *cr)=0
	Write checkpoint (CheckpointData object only passed on main rank)

virtual void	gmx::ICheckpointHelperClient::restoreCheckpointState (std::optional< ReadCheckpointData > checkpointData, const t_commrec *cr)=0
	Read checkpoint (CheckpointData object only passed on main rank)

virtual const std::string &	gmx::ICheckpointHelperClient::clientID ()=0
	Get unique client id.

	gmx::ElementNotFoundError::ElementNotFoundError (const ExceptionInitializer &details)
	Creates an exception object with the provided initializer/reason. More...

	gmx::MissingElementConnectionError::MissingElementConnectionError (const ExceptionInitializer &details)
	Creates an exception object with the provided initializer/reason. More...

	gmx::SimulationAlgorithmSetupError::SimulationAlgorithmSetupError (const ExceptionInitializer &details)
	Creates an exception object with the provided initializer/reason. More...

	gmx::CheckpointError::CheckpointError (const ExceptionInitializer &details)
	Creates an exception object with the provided initializer/reason. More...

	gmx::PropagatorTag::PropagatorTag (std::string_view name)
	Explicit constructor.

	gmx::PropagatorTag::operator const std::string & () const
	Can be used as string.

bool	gmx::PropagatorTag::operator== (const PropagatorTag &other) const
	Equality operator.

bool	gmx::PropagatorTag::operator!= (const PropagatorTag &other) const
	Inequality operator.

	gmx::TimeStep::TimeStep (real timeStep)
	Explicit constructor.

	gmx::TimeStep::operator const real & () const
	Can be used as underlying type.

	gmx::Offset::Offset (int offset)
	Explicit constructor.

	gmx::Offset::operator const int & () const
	Can be used as underlying type.

bool	gmx::PropagatorConnection::hasStartVelocityScaling () const
	Whether the propagator offers start velocity scaling.

bool	gmx::PropagatorConnection::hasEndVelocityScaling () const
	Whether the propagator offers end velocity scaling.

bool	gmx::PropagatorConnection::hasPositionScaling () const
	Whether the propagator offers position scaling.

bool	gmx::PropagatorConnection::hasParrinelloRahmanScaling () const
	Whether the propagator offers Parrinello-Rahman scaling.

virtual	gmx::IDomDecHelperClient::~IDomDecHelperClient ()=default
	Standard virtual destructor.

virtual DomDecCallback	gmx::IDomDecHelperClient::registerDomDecCallback ()=0
	Register function to be informed about system re-partitioning.

Variables
PropagatorTag	gmx::PropagatorConnection::tag
	The tag of the creating propagator.

std::function< void(int, ScaleVelocities)>	gmx::PropagatorConnection::setNumVelocityScalingVariables
	Function object for setting velocity scaling variables.

std::function< void(int)>	gmx::PropagatorConnection::setNumPositionScalingVariables
	Function object for setting velocity scaling variables.

std::function< ArrayRef< real >)>	gmx::PropagatorConnection::getViewOnStartVelocityScaling
	Function object for receiving view on velocity scaling (before step)

std::function< ArrayRef< real >)>	gmx::PropagatorConnection::getViewOnEndVelocityScaling
	Function object for receiving view on velocity scaling (after step)

std::function< ArrayRef< real >)>	gmx::PropagatorConnection::getViewOnPositionScaling
	Function object for receiving view on position scaling.

std::function < PropagatorCallback()>	gmx::PropagatorConnection::getVelocityScalingCallback
	Function object to request callback allowing to signal a velocity scaling step.

std::function < PropagatorCallback()>	gmx::PropagatorConnection::getPositionScalingCallback
	Function object to request callback allowing to signal a position scaling step.

std::function< Matrix3x3 *()>	gmx::PropagatorConnection::getViewOnPRScalingMatrix
	Function object for receiving view on pressure scaling matrix.

std::function < PropagatorCallback()>	gmx::PropagatorConnection::getPRScalingCallback
	Function object to request callback allowing to signal a Parrinello-Rahman scaling step.

Files
file	modularsimulator.h
	Provides the modular simulator.

Enumeration Type Documentation

enum gmx::CheckpointDataOperation

strong

The operations on CheckpointData.

This enum defines the two modes of operation on CheckpointData objects, reading and writing. This allows to template all access functions, which in turn enables clients to write a single function for read and write access, eliminating the risk of having read and write functions getting out of sync.

enum gmx::IntegrationStage

strong

The different integration types we know about.

Enumerator
PositionsOnly	Moves the position vector by the given time step.
VelocitiesOnly	Moves the velocity vector by the given time step.
LeapFrog	Manual fusion of the previous two propagators.
VelocityVerletPositionsAndVelocities	Manual position (full dt) and velocity (half dt) fusion.
ScaleVelocities	Only scale velocities, don't propagate.
ScalePositions	Only scale positions, don't propagate.
Count	The number of enum entries.

enum gmx::NumPositionScalingValues

strong

Sets the number of different position scaling values.

Enumerator
None	No position scaling (either this step or ever)
Single	Single scaling value (either one group or all values =1)
Multiple	Multiple scaling values, need to use T-group indices.
Count	The number of enum entries.

enum gmx::NumVelocityScalingValues

strong

Sets the number of different velocity scaling values.

Enumerator
None	No velocity scaling (either this step or ever)
Single	Single T-scaling value (either one group or all values =1)
Multiple	Multiple T-scaling values, need to use T-group indices.

enum gmx::ParrinelloRahmanVelocityScaling

strong

Describes the properties of the Parrinello-Rahman pressure scaling matrix.

Enumerator
No	Do not apply velocity scaling (not a PR-coupling run or step)
Diagonal	Apply velocity scaling using a diagonal matrix.
Anisotropic	Apply velocity scaling using a matrix with off-diagonal elements.

Function Documentation

gmx::CheckpointError::CheckpointError ( const ExceptionInitializer & details )

inlineexplicit

Creates an exception object with the provided initializer/reason.

Parameters

[in] details Initializer for the exception.

Exceptions

std::bad_alloc if out of memory.

It is possible to call this constructor either with an explicit ExceptionInitializer object (useful for more complex cases), or a simple string if only a reason string needs to be provided.

template<typename... Ts>

auto gmx::checkUseModularSimulator ( Ts &&... args ) -> decltype(ModularSimulator::isInputCompatible(std::forward<Ts>(args)...))

Whether or not to use the ModularSimulator.

GMX_DISABLE_MODULAR_SIMULATOR environment variable allows to disable modular simulator for all uses.

See ModularSimulator::isInputCompatible() for function signature.

gmx::ElementNotFoundError::ElementNotFoundError ( const ExceptionInitializer & details )

inlineexplicit

Creates an exception object with the provided initializer/reason.

Parameters

[in] details Initializer for the exception.

Exceptions

std::bad_alloc if out of memory.

It is possible to call this constructor either with an explicit ExceptionInitializer object (useful for more complex cases), or a simple string if only a reason string needs to be provided.

gmx::MissingElementConnectionError::MissingElementConnectionError ( const ExceptionInitializer & details )

inlineexplicit

Creates an exception object with the provided initializer/reason.

Parameters

[in] details Initializer for the exception.

Exceptions

std::bad_alloc if out of memory.

It is possible to call this constructor either with an explicit ExceptionInitializer object (useful for more complex cases), or a simple string if only a reason string needs to be provided.

virtual void gmx::ISimulatorElement::scheduleTask	(	Step	,
		Time	,
		const RegisterRunFunction &
	)

pure virtual

Query whether element wants to run at step / time.

Element can register one or more functions to be run at that step through the registration pointer.

gmx::SimulationAlgorithmSetupError::SimulationAlgorithmSetupError ( const ExceptionInitializer & details )

inlineexplicit

Creates an exception object with the provided initializer/reason.

Parameters

[in] details Initializer for the exception.

Exceptions

std::bad_alloc if out of memory.

It is possible to call this constructor either with an explicit ExceptionInitializer object (useful for more complex cases), or a simple string if only a reason string needs to be provided.

Description

Classes

Typedefs

Enumerations

Functions

Variables

Files

Enumeration Type Documentation

Function Documentation