Gromacs
2020
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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
docs/doxygen/lib/modularsimulator.md
?Typedefs | |
typedef std::function< void()> | gmx::CheckBondedInteractionsCallback |
The function type allowing to request a check of the number of bonded interactions. | |
typedef std::unique_ptr < CheckBondedInteractionsCallback > | gmx::CheckBondedInteractionsCallbackPtr |
Pointer to 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::unique_ptr < SimulatorRunFunction > | gmx::SimulatorRunFunctionPtr |
Pointer to the function type that can be scheduled to be run during the simulator run. | |
typedef std::function< void(SimulatorRunFunctionPtr)> | gmx::RegisterRunFunction |
The function type that allows to register run functions. | |
typedef std::unique_ptr < RegisterRunFunction > | gmx::RegisterRunFunctionPtr |
Pointer to the function type that allows to register run functions. | |
typedef std::function< void(Step, Time)> | gmx::SignallerCallback |
The function type that can be registered to signallers for callback. | |
typedef std::unique_ptr < SignallerCallback > | gmx::SignallerCallbackPtr |
Pointer to 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::unique_ptr < ITrajectoryWriterCallback > | gmx::ITrajectoryWriterCallbackPtr |
Pointer to the function type for trajectory writing clients. | |
typedef std::function< void(Step)> | gmx::PropagatorCallback |
Generic callback to the propagator. | |
typedef std::unique_ptr < PropagatorCallback > | gmx::PropagatorCallbackPtr |
Pointer to generic callback to the propagator. | |
Enumerations | |
enum | gmx::ComputeGlobalsAlgorithm { LeapFrog, VelocityVerletAtFullTimeStep, VelocityVerletAfterCoordinateUpdate } |
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::IntegrationStep { PositionsOnly, VelocitiesOnly, LeapFrog, VelocityVerletPositionsAndVelocities, Count } |
The different integration types we know about. 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::Full, Count } |
Sets the type of Parrinello-Rahman pressure scaling. More... | |
Functions | |
virtual void | gmx::ISimulatorElement::scheduleTask (Step, Time, const RegisterRunFunctionPtr &)=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::signallerSetup ()=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 SignallerCallbackPtr | gmx::INeighborSearchSignallerClient::registerNSCallback ()=0 |
Return callback to NeighborSearchSignaller. | |
virtual | gmx::ILastStepSignallerClient::~ILastStepSignallerClient ()=default |
Standard virtual destructor. | |
virtual SignallerCallbackPtr | gmx::ILastStepSignallerClient::registerLastStepCallback ()=0 |
Return callback to LastStepSignaller. | |
virtual | gmx::ILoggingSignallerClient::~ILoggingSignallerClient ()=default |
Standard virtual destructor. | |
virtual SignallerCallbackPtr | gmx::ILoggingSignallerClient::registerLoggingCallback ()=0 |
Return callback to LoggingSignaller. | |
virtual | gmx::IEnergySignallerClient::~IEnergySignallerClient ()=default |
Standard virtual destructor. | |
virtual SignallerCallbackPtr | gmx::IEnergySignallerClient::registerEnergyCallback (EnergySignallerEvent)=0 |
Return callback to EnergySignaller. | |
virtual | gmx::ITrajectorySignallerClient::~ITrajectorySignallerClient ()=default |
Standard virtual destructor. | |
virtual SignallerCallbackPtr | 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 ITrajectoryWriterCallbackPtr | 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::writeCheckpoint (t_state *localState, t_state *globalState)=0 |
Write checkpoint. | |
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strong |
The different integration types we know about.
PositionsOnly: Moves the position vector by the given time step VelocitiesOnly: Moves the velocity vector by the given time step LeapFrog: Is a manual fusion of the previous two propagators VelocityVerletPositionsAndVelocities: Is a manual fusion of VelocitiesOnly and PositionsOnly, where VelocitiesOnly is only propagated by half the time step of the positions.
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strong |
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strong |
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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.