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.
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typedef std::function< void()> | gmx::CheckBondedInteractionsCallback |
| | The function type allowing to request a check of the number of bonded interactions.
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using | gmx::Step = int64_t |
| | Step number.
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using | gmx::Time = double |
| | Simulation time.
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typedef std::function< void()> | gmx::SimulatorRunFunction |
| | The function type that can be scheduled to be run during the simulator run.
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typedef std::function< void(SimulatorRunFunction)> | gmx::RegisterRunFunction |
| | The function type that allows to register run functions.
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typedef std::function< void(Step,
Time, const
RegisterRunFunction &)> | gmx::SchedulingFunction |
| | The function type scheduling run functions for a step / time using a RegisterRunFunction reference.
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typedef std::function< void(Step,
Time)> | gmx::SignallerCallback |
| | The function type that can be registered to signallers for callback.
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typedef std::function< void(gmx_mdoutf
*, Step, Time, bool, bool)> | gmx::ITrajectoryWriterCallback |
| | Function type for trajectory writing clients.
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typedef std::function< void(Step)> | gmx::PropagatorCallback |
| | Generic callback to the propagator.
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typedef std::function< void()> | gmx::DomDecCallback |
| | Callback used by the DomDecHelper object to inform clients about system re-partitioning.
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using | gmx::ReferenceTemperatureCallback = std::function< void(ArrayRef< const real >, ReferenceTemperatureChangeAlgorithm algorithm)> |
| | Callback updating the reference temperature.
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| enum | gmx::ComputeGlobalsAlgorithm { LeapFrog,
VelocityVerlet
} |
| | The different global reduction schemes we know about.
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| enum | gmx::EnergySignallerEvent { EnergyCalculationStep,
VirialCalculationStep,
FreeEnergyCalculationStep
} |
| | The energy events signalled by the EnergySignaller.
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| enum | gmx::TrajectoryEvent { StateWritingStep,
EnergyWritingStep
} |
| | The trajectory writing events.
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| enum | gmx::ModularSimulatorBuilderState { AcceptingClientRegistrations,
NotAcceptingClientRegistrations
} |
| | Enum allowing builders to store whether they can accept client registrations.
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| enum | gmx::ReportPreviousStepConservedEnergy { Yes,
No,
Count
} |
| | Enum describing whether an element is reporting conserved energy from the previous step.
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| enum | gmx::ScaleVelocities { PreStepOnly,
PreStepAndPostStep
} |
| | Which velocities the thermostat scales.
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| 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...
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| enum | gmx::NumPositionScalingValues { gmx::NumPositionScalingValues::None,
gmx::NumPositionScalingValues::Single,
gmx::NumPositionScalingValues::Multiple,
gmx::NumPositionScalingValues::Count
} |
| | Sets the number of different position scaling values. More...
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| enum | gmx::NumVelocityScalingValues { gmx::NumVelocityScalingValues::None,
gmx::NumVelocityScalingValues::Single,
gmx::NumVelocityScalingValues::Multiple,
Count
} |
| | Sets the number of different velocity scaling values. More...
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| enum | gmx::ParrinelloRahmanVelocityScaling { gmx::ParrinelloRahmanVelocityScaling::No,
gmx::ParrinelloRahmanVelocityScaling::Diagonal,
gmx::ParrinelloRahmanVelocityScaling::Anisotropic,
Count
} |
| | Describes the properties of the Parrinello-Rahman pressure scaling matrix. More...
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| virtual void | gmx::ISimulatorElement::scheduleTask (Step, Time, const RegisterRunFunction &)=0 |
| | Query whether element wants to run at step / time. More...
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virtual void | gmx::ISimulatorElement::elementSetup ()=0 |
| | Method guaranteed to be called after construction, before simulator run.
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virtual void | gmx::ISimulatorElement::elementTeardown ()=0 |
| | Method guaranteed to be called after simulator run, before deconstruction.
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virtual | gmx::ISimulatorElement::~ISimulatorElement ()=default |
| | Standard virtual destructor.
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virtual void | gmx::ISignaller::signal (Step, Time)=0 |
| | Function run before every step of scheduling.
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virtual void | gmx::ISignaller::setup ()=0 |
| | Method guaranteed to be called after construction, before simulator run.
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virtual | gmx::ISignaller::~ISignaller ()=default |
| | Standard virtual destructor.
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virtual | gmx::INeighborSearchSignallerClient::~INeighborSearchSignallerClient ()=default |
| | Standard virtual destructor.
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virtual std::optional
< SignallerCallback > | gmx::INeighborSearchSignallerClient::registerNSCallback ()=0 |
| | Return callback to NeighborSearchSignaller.
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virtual | gmx::ILastStepSignallerClient::~ILastStepSignallerClient ()=default |
| | Standard virtual destructor.
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virtual std::optional
< SignallerCallback > | gmx::ILastStepSignallerClient::registerLastStepCallback ()=0 |
| | Return callback to LastStepSignaller.
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virtual | gmx::ILoggingSignallerClient::~ILoggingSignallerClient ()=default |
| | Standard virtual destructor.
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virtual std::optional
< SignallerCallback > | gmx::ILoggingSignallerClient::registerLoggingCallback ()=0 |
| | Return callback to LoggingSignaller.
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virtual | gmx::IEnergySignallerClient::~IEnergySignallerClient ()=default |
| | Standard virtual destructor.
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virtual std::optional
< SignallerCallback > | gmx::IEnergySignallerClient::registerEnergyCallback (EnergySignallerEvent)=0 |
| | Return callback to EnergySignaller.
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virtual | gmx::ITrajectorySignallerClient::~ITrajectorySignallerClient ()=default |
| | Standard virtual destructor.
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virtual std::optional
< SignallerCallback > | gmx::ITrajectorySignallerClient::registerTrajectorySignallerCallback (TrajectoryEvent)=0 |
| | Return callback to TrajectoryElement.
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virtual | gmx::ITrajectoryWriterClient::~ITrajectoryWriterClient ()=default |
| | Standard virtual destructor.
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virtual void | gmx::ITrajectoryWriterClient::trajectoryWriterSetup (gmx_mdoutf *outf)=0 |
| | Setup method with valid output pointer.
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virtual void | gmx::ITrajectoryWriterClient::trajectoryWriterTeardown (gmx_mdoutf *outf)=0 |
| | Teardown method with valid output pointer.
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virtual std::optional
< ITrajectoryWriterCallback > | gmx::ITrajectoryWriterClient::registerTrajectoryWriterCallback (TrajectoryEvent)=0 |
| | Return callback to TrajectoryElement.
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virtual | gmx::ITopologyHolderClient::~ITopologyHolderClient ()=default |
| | Standard virtual destructor.
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virtual void | gmx::ITopologyHolderClient::setTopology (const gmx_localtop_t *)=0 |
| | Pass pointer to new local topology.
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virtual | gmx::ICheckpointHelperClient::~ICheckpointHelperClient ()=default |
| | Standard virtual destructor.
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virtual void | gmx::ICheckpointHelperClient::saveCheckpointState (std::optional< WriteCheckpointData > checkpointData, const MpiComm &mpiComm, gmx_domdec_t *dd)=0 |
| | Write checkpoint (CheckpointData object only passed on main rank)
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virtual void | gmx::ICheckpointHelperClient::restoreCheckpointState (std::optional< ReadCheckpointData > checkpointData, const MpiComm &mpiComm, gmx_domdec_t *dd)=0 |
| | Read checkpoint (CheckpointData object only passed on main rank)
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virtual const std::string & | gmx::ICheckpointHelperClient::clientID ()=0 |
| | Get unique client id.
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| | gmx::ElementNotFoundError::ElementNotFoundError (const ExceptionInitializer &details) |
| | Creates an exception object with the provided initializer/reason. More...
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| | gmx::MissingElementConnectionError::MissingElementConnectionError (const ExceptionInitializer &details) |
| | Creates an exception object with the provided initializer/reason. More...
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| | gmx::SimulationAlgorithmSetupError::SimulationAlgorithmSetupError (const ExceptionInitializer &details) |
| | Creates an exception object with the provided initializer/reason. More...
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| | gmx::CheckpointError::CheckpointError (const ExceptionInitializer &details) |
| | Creates an exception object with the provided initializer/reason. More...
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| gmx::PropagatorTag::PropagatorTag (std::string_view name) |
| | Explicit constructor.
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| gmx::PropagatorTag::operator const std::string & () const |
| | Can be used as string.
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bool | gmx::PropagatorTag::operator== (const PropagatorTag &other) const |
| | Equality operator.
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bool | gmx::PropagatorTag::operator!= (const PropagatorTag &other) const |
| | Inequality operator.
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| gmx::TimeStep::TimeStep (real timeStep) |
| | Explicit constructor.
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| gmx::TimeStep::operator const real & () const |
| | Can be used as underlying type.
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| gmx::Offset::Offset (int offset) |
| | Explicit constructor.
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| gmx::Offset::operator const int & () const |
| | Can be used as underlying type.
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bool | gmx::PropagatorConnection::hasStartVelocityScaling () const |
| | Whether the propagator offers start velocity scaling.
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bool | gmx::PropagatorConnection::hasEndVelocityScaling () const |
| | Whether the propagator offers end velocity scaling.
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bool | gmx::PropagatorConnection::hasPositionScaling () const |
| | Whether the propagator offers position scaling.
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bool | gmx::PropagatorConnection::hasParrinelloRahmanScaling () const |
| | Whether the propagator offers Parrinello-Rahman scaling.
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virtual | gmx::IDomDecHelperClient::~IDomDecHelperClient ()=default |
| | Standard virtual destructor.
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virtual DomDecCallback | gmx::IDomDecHelperClient::registerDomDecCallback ()=0 |
| | Register function to be informed about system re-partitioning.
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1.8.5