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
struct	gmx::IsSerializableType< T >
	Struct allowing to check if data is serializable through the KeyValueTree serializer. More...

struct	gmx::IsSerializableEnum< T, bool >
	Struct allowing to check if enum has a serializable underlying type. More...

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

struct	gmx::test::anonymous_namespace{checkpointdata.cpp}::IsVectorOfSerializableType< T >
	Struct allowing to check if type is vector of serializable data. More...

class	gmx::AndersenTemperatureCoupling
	Element implementing the Andersen thermostat. More...

class	gmx::CheckpointHelper
	Checkpoint helper. More...

class	gmx::CheckpointHelperBuilder
	Builder for the checkpoint helper. More...

class	gmx::CompositeSimulatorElement
	Composite simulator element. More...

class	gmx::ComputeGlobalsElement< algorithm >
	Encapsulate the calls to `compute_globals` More...

class	gmx::ConstraintsElement< variable >
	Constraints element. More...

class	gmx::DomDecHelper
	Infrastructure element responsible for domain decomposition. More...

class	gmx::DomDecHelperBuilder
	Builder for DomDecHelper. More...

class	gmx::EnergyData
	Data class managing energies. More...

class	gmx::EnergyData::Element
	Element for EnergyData. More...

class	gmx::ExpandedEnsembleElement
	The expanded ensemble element. More...

class	gmx::ForceElement
	Force element. More...

class	gmx::FreeEnergyPerturbationData
	The free energy perturbation data. More...

class	gmx::FepStateSetting
	Allows external clients to specify how to change the FEP state. More...

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

class	gmx::ISimulatorElement
	The general interface for elements of the modular simulator. More...

class	gmx::ISignaller
	The general Signaller interface. More...

class	gmx::INeighborSearchSignallerClient
	Interface for clients of the NeighborSearchSignaller. More...

class	gmx::ILastStepSignallerClient
	Interface for clients of the LastStepSignaller. More...

class	gmx::ILoggingSignallerClient
	Interface for clients of the LoggingSignaller. More...

class	gmx::IEnergySignallerClient
	Interface for clients of the EnergySignaller. More...

class	gmx::ITrajectorySignallerClient
	Interface for signaller clients of the TrajectoryElement. More...

class	gmx::ITrajectoryWriterClient
	Interface for writer clients of the TrajectoryElement. More...

class	gmx::ITopologyHolderClient
	Client requiring read access to the local topology. More...

class	gmx::ICheckpointHelperClient
	Client that needs to store data during checkpointing. 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...

struct	gmx::PropagatorTag
	Strong type used to name propagators. More...

struct	gmx::TimeStep
	Strong type used to denote propagation time steps. More...

struct	gmx::Offset
	Strong type used to denote scheduling offsets. More...

struct	gmx::PropagatorConnection
	Information needed to connect a propagator to a temperature and / or pressure coupling element. More...

class	gmx::IDomDecHelperClient
	Client interface of the DomDecHelper class. More...

class	gmx::ParrinelloRahmanBarostat
	Element implementing the Parrinello-Rahman barostat. More...

class	gmx::PmeLoadBalanceHelper
	Infrastructure element responsible for PME load balancing. More...

class	gmx::Propagator< integrationStage >
	Propagator element. More...

class	gmx::SignallerBuilder< Signaller >
	Builder for signallers. More...

class	gmx::NeighborSearchSignaller
	Element signalling a neighbor search step. More...

class	gmx::LastStepSignaller
	Element signalling the last step. More...

class	gmx::LoggingSignaller
	Element signalling a logging step. More...

class	gmx::TrajectorySignaller
	Element signalling trajectory writing. More...

class	gmx::EnergySignaller
	Element signalling energy related special steps. More...

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

class	gmx::StatePropagatorData
	StatePropagatorData and associated data. More...

class	gmx::TopologyHolder
	Object holding the topology. More...

class	gmx::TopologyHolder::Builder
	Builder for the topology holder. More...

class	gmx::TrajectoryElement
	Trajectory element signals and handles trajectory writing. More...

class	gmx::TrajectoryElementBuilder
	Build the `TrajectoryElement` More...

class	gmx::VelocityScalingTemperatureCoupling
	Element implementing the a velocity-scaling thermostat. 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<CheckpointDataOperation operation, typename T >
ArrayRef< std::conditional_t < operation==CheckpointDataOperation::Write\|\|std::is_const < T >::value, const typename T::value_type, typename T::value_type > >	gmx::makeCheckpointArrayRef (T &container)
	Get an ArrayRef whose const-ness is defined by the checkpointing operation. More...

template<CheckpointDataOperation operation, typename T >
ArrayRef< std::conditional_t < operation==CheckpointDataOperation::Write\|\|std::is_const < T >::value, const T, T > >	gmx::makeCheckpointArrayRefFromArray (T *begin, size_t size)
	Get an ArrayRef to a C array whose const-ness is defined by the checkpointing operation. More...

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	andersentemperaturecoupling.cpp
	Defines Andersen temperature coupling for the modular simulator.

file	andersentemperaturecoupling.h
	Declares Andersen temperature coupling for the modular simulator.

file	checkpointhelper.cpp
	Defines the checkpoint helper for the modular simulator.

file	checkpointhelper.h
	Declares the checkpoint helper for the modular simulator.

file	compositesimulatorelement.cpp
	Defines the composite element for the modular simulator.

file	compositesimulatorelement.h
	Declares the composite element for the modular simulator.

file	computeglobalselement.cpp
	Defines the global reduction element for the modular simulator.

file	computeglobalselement.h
	Declares the global reduction element for the modular simulator.

file	constraintelement.cpp
	Defines the constraint element for the modular simulator.

file	constraintelement.h
	Declares the constraint element for the modular simulator.

file	domdechelper.cpp
	Defines the domain decomposition helper for the modular simulator.

file	domdechelper.h
	Declares the domain decomposition helper for the modular simulator.

file	energydata.cpp
	Defines the microstate for the modular simulator.

file	energydata.h
	Declares the energy element for the modular simulator.

file	expandedensembleelement.cpp
	Defines the expanded ensemble element for the modular simulator.

file	expandedensembleelement.h
	Declares the expanded ensemble element for the modular simulator.

file	firstorderpressurecoupling.cpp
	Defines the element performing first-order pressure coupling for the modular simulator.

file	firstorderpressurecoupling.h
	Declares the element performing first-order pressure coupling for the modular simulator.

file	forceelement.cpp
	Defines the force element for the modular simulator.

file	forceelement.h
	Declares the force element for the modular simulator.

file	freeenergyperturbationdata.cpp
	Defines the free energy perturbation element for the modular simulator.

file	freeenergyperturbationdata.h
	Declares the free energy perturbation element for the modular simulator.

file	modularsimulator.cpp
	Defines the modular simulator.

file	modularsimulator.h
	Provides the modular simulator.

file	modularsimulatorinterfaces.h
	Declares the main interfaces used by the modular simulator.

file	mttk.cpp
	Defines classes related to MTTK pressure coupling.

file	mttk.h
	Declares classes related to MTTK pressure coupling.

file	nosehooverchains.cpp
	Defines classes related to Nose-Hoover chains for the modular simulator.

file	nosehooverchains.h
	Declares classes related to Nose-Hoover chains for the modular simulator.

file	parrinellorahmanbarostat.cpp
	Defines the Parrinello-Rahman barostat for the modular simulator.

file	parrinellorahmanbarostat.h
	Declares the Parrinello-Rahman barostat for the modular simulator.

file	pmeloadbalancehelper.cpp
	Declares the PME load balancing helper for the modular simulator.

file	pmeloadbalancehelper.h
	Declares the PME load balancing helper for the modular simulator.

file	propagator.cpp
	Defines the propagator element for the modular simulator.

file	propagator.h
	Declares the propagator element for the modular simulator.

file	pullelement.cpp
	Defines the pull element for the modular simulator.

file	pullelement.h
	Declares the pull element for the modular simulator.

file	referencetemperaturemanager.cpp
	Defines the a helper struct managing reference temperature changes.

file	referencetemperaturemanager.h
	Declares the a helper struct managing reference temperature changes.

file	signallers.cpp
	Defines the signallers for the modular simulator.

file	signallers.h
	Declares the signallers for the modular simulator.

file	simulatoralgorithm.cpp
	Defines the modular simulator algorithm.

file	simulatoralgorithm.h
	Provides the modular simulator algorithm.

file	statepropagatordata.cpp
	Defines the state for the modular simulator.

file	statepropagatordata.h
	Declares the state for the modular simulator.

file	topologyholder.cpp
	Defines the topology class for the modular simulator.

file	topologyholder.h
	Declares the topology class for the modular simulator.

file	trajectoryelement.cpp
	Defines the trajectory element for the modular simulator.

file	trajectoryelement.h
	Declares the trajectory element for the modular simulator.

file	trotterhelperfunctions.h
	Defines helper functions used by the Trotter decomposition algorithms (Nose-Hoover chains, MTTK)

file	velocityscalingtemperaturecoupling.cpp
	Defines a velocity-scaling temperature coupling element for the modular simulator.

file	velocityscalingtemperaturecoupling.h
	Declares a velocity-scaling temperature coupling element for 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.

template<CheckpointDataOperation operation, typename T >

ArrayRef<std::conditional_t<operation == CheckpointDataOperation::Write || std::is_const<T>::value, const typename T::value_type, typename T::value_type> > gmx::makeCheckpointArrayRef ( T & container )

Get an ArrayRef whose const-ness is defined by the checkpointing operation.

Template Parameters

operation	Whether we are reading or writing
T	The type of values stored in the ArrayRef

Parameters

container The container the ArrayRef is referencing to

Returns: The ArrayRef

See Also: ArrayRef

template<CheckpointDataOperation operation, typename T >

ArrayRef<std::conditional_t<operation == CheckpointDataOperation::Write \|\| std::is_const<T>::value, const T, T> > gmx::makeCheckpointArrayRefFromArray	(	T *	begin,
		size_t	size
	)

Get an ArrayRef to a C array whose const-ness is defined by the checkpointing operation.

Template Parameters

operation	Whether we are reading or writing
T	The type of values stored in the ArrayRef

Parameters

begin	Pointer to the beginning of array.
size	Number of elements in array.

Returns: The ArrayRef

See Also: ArrayRef

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.

Implemented in gmx::MttkBoxScaling, gmx::EnergyData::Element, gmx::StatePropagatorData::Element, gmx::MttkElement, gmx::NoseHooverChainsElement, gmx::FreeEnergyPerturbationData::Element, gmx::ComputeGlobalsElement< algorithm >, gmx::Propagator< integrationStage >, gmx::CheckpointHelper, gmx::ForceElement, gmx::VelocityScalingTemperatureCoupling, gmx::TrajectoryElement, gmx::ConstraintsElement< variable >, gmx::ParrinelloRahmanBarostat, gmx::AndersenTemperatureCoupling, gmx::CompositeSimulatorElement, gmx::FirstOrderPressureCoupling, gmx::ExpandedEnsembleElement, and gmx::PullElement.

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