*
* @tparam algorithm The global reduction scheme
*/
-template <ComputeGlobalsAlgorithm algorithm>
+template<ComputeGlobalsAlgorithm algorithm>
class ComputeGlobalsElement final :
- public ISimulatorElement,
- public IEnergySignallerClient,
- public ITrajectorySignallerClient,
- public ITopologyHolderClient
+ public ISimulatorElement,
+ public IEnergySignallerClient,
+ public ITrajectorySignallerClient,
+ public ITopologyHolderClient
{
- public:
- //! Constructor
- ComputeGlobalsElement(
- StatePropagatorData *statePropagatorData,
- EnergyElement *energyElement,
- FreeEnergyPerturbationElement *freeEnergyPerturbationElement,
- SimulationSignals *signals,
- int nstglobalcomm,
- FILE *fplog,
- const MDLogger &mdlog,
- t_commrec *cr,
- t_inputrec *inputrec,
- const MDAtoms *mdAtoms,
- t_nrnb *nrnb,
- gmx_wallcycle *wcycle,
- t_forcerec *fr,
- const gmx_mtop_t *global_top,
- Constraints *constr,
- bool hasReadEkinState);
-
- //! Destructor
- ~ComputeGlobalsElement() override;
-
- /*! \brief Element setup - first call to compute_globals
- *
- */
- void elementSetup() override;
-
- /*! \brief Register run function for step / time
- *
- * This registers the call to compute_globals when needed.
- *
- * @param step The step number
- * @param time The time
- * @param registerRunFunction Function allowing to register a run function
- */
- void scheduleTask(
- Step step, Time time,
- const RegisterRunFunctionPtr ®isterRunFunction) override;
-
- //! Get callback to request checking of bonded interactions
- CheckBondedInteractionsCallbackPtr getCheckNumberOfBondedInteractionsCallback();
-
- //! No element teardown needed
- void elementTeardown() override {}
-
- private:
- //! ITopologyClient implementation
- void setTopology(const gmx_localtop_t *top) override;
- //! IEnergySignallerClient implementation
- SignallerCallbackPtr registerEnergyCallback(EnergySignallerEvent event) override;
- //! ITrajectorySignallerClient implementation
- SignallerCallbackPtr registerTrajectorySignallerCallback(TrajectoryEvent event) override;
- //! The compute_globals call
- void compute(
- Step step, unsigned int flags,
- SimulationSignaller *signaller, bool useLastBox,
- bool isInit = false);
-
- //! Next step at which energy needs to be reduced
- Step energyReductionStep_;
- //! Next step at which virial needs to be reduced
- Step virialReductionStep_;
-
- //! Whether center of mass motion stopping is enabled
- const bool doStopCM_;
- //! Number of steps after which center of mass motion is removed
- int nstcomm_;
- //! Compute globals communication period
- int nstglobalcomm_;
- //! The last (planned) step (only used for LF)
- const Step lastStep_;
- //! The initial step (only used for VV)
- const Step initStep_;
- //! A dummy signaller (used for setup and VV)
- std::unique_ptr<SimulationSignaller> nullSignaller_;
- //! Whether we read kinetic energy from checkpoint
- const bool hasReadEkinState_;
-
- /*! \brief Check that DD doesn't miss bonded interactions
- *
- * Domain decomposition could incorrectly miss a bonded
- * interaction, but checking for that requires a global
- * communication stage, which does not otherwise happen in DD
- * code. So we do that alongside the first global energy reduction
- * after a new DD is made. These variables handle whether the
- * check happens, and the result it returns.
- */
- //! @{
- int totalNumberOfBondedInteractions_;
- bool shouldCheckNumberOfBondedInteractions_;
- //! @}
-
- /*! \brief Signal to ComputeGlobalsElement that it should check for DD errors
- *
- * Note that this should really be the responsibility of the DD element.
- * MDLogger, global and local topology are only needed due to the call to
- * checkNumberOfBondedInteractions(...).
- *
- * The DD element should have a single variable which gets reduced, and then
- * be responsible for the checking after a global reduction has happened.
- * This would, however, require a new approach for the compute_globals calls,
- * which is not yet implemented. So for now, we're leaving this here.
- */
- void needToCheckNumberOfBondedInteractions();
-
- //! Global reduction struct
- gmx_global_stat *gstat_;
-
- //! Pointer to the microstate
- StatePropagatorData *statePropagatorData_;
- //! Pointer to the energy element (needed for the tensors and mu_tot)
- EnergyElement *energyElement_;
- //! Pointer to the local topology (only needed for checkNumberOfBondedInteractions)
- const gmx_localtop_t *localTopology_;
- //! Pointer to the free energy perturbation element
- FreeEnergyPerturbationElement *freeEnergyPerturbationElement_;
-
- //! Center of mass motion removal
- t_vcm vcm_;
- //! Signals
- SimulationSignals *signals_;
-
- // Access to ISimulator data
- //! Handles logging.
- FILE *fplog_;
- //! Handles logging.
- const MDLogger &mdlog_;
- //! Handles communication.
- t_commrec *cr_;
- //! Contains user input mdp options.
- t_inputrec *inputrec_;
- //! Full system topology - only needed for checkNumberOfBondedInteractions.
- const gmx_mtop_t *top_global_;
- //! Atom parameters for this domain.
- const MDAtoms *mdAtoms_;
- //! Handles constraints.
- Constraints *constr_;
- //! Manages flop accounting.
- t_nrnb *nrnb_;
- //! Manages wall cycle accounting.
- gmx_wallcycle *wcycle_;
- //! Parameters for force calculations.
- t_forcerec *fr_;
+public:
+ //! Constructor
+ ComputeGlobalsElement(StatePropagatorData* statePropagatorData,
+ EnergyElement* energyElement,
+ FreeEnergyPerturbationElement* freeEnergyPerturbationElement,
+ SimulationSignals* signals,
+ int nstglobalcomm,
+ FILE* fplog,
+ const MDLogger& mdlog,
+ t_commrec* cr,
+ t_inputrec* inputrec,
+ const MDAtoms* mdAtoms,
+ t_nrnb* nrnb,
+ gmx_wallcycle* wcycle,
+ t_forcerec* fr,
+ const gmx_mtop_t* global_top,
+ Constraints* constr,
+ bool hasReadEkinState);
+
+ //! Destructor
+ ~ComputeGlobalsElement() override;
+
+ /*! \brief Element setup - first call to compute_globals
+ *
+ */
+ void elementSetup() override;
+
+ /*! \brief Register run function for step / time
+ *
+ * This registers the call to compute_globals when needed.
+ *
+ * @param step The step number
+ * @param time The time
+ * @param registerRunFunction Function allowing to register a run function
+ */
+ void scheduleTask(Step step, Time time, const RegisterRunFunctionPtr& registerRunFunction) override;
+
+ //! Get callback to request checking of bonded interactions
+ CheckBondedInteractionsCallbackPtr getCheckNumberOfBondedInteractionsCallback();
+
+ //! No element teardown needed
+ void elementTeardown() override {}
+
+private:
+ //! ITopologyClient implementation
+ void setTopology(const gmx_localtop_t* top) override;
+ //! IEnergySignallerClient implementation
+ SignallerCallbackPtr registerEnergyCallback(EnergySignallerEvent event) override;
+ //! ITrajectorySignallerClient implementation
+ SignallerCallbackPtr registerTrajectorySignallerCallback(TrajectoryEvent event) override;
+ //! The compute_globals call
+ void compute(Step step, unsigned int flags, SimulationSignaller* signaller, bool useLastBox, bool isInit = false);
+
+ //! Next step at which energy needs to be reduced
+ Step energyReductionStep_;
+ //! Next step at which virial needs to be reduced
+ Step virialReductionStep_;
+
+ //! Whether center of mass motion stopping is enabled
+ const bool doStopCM_;
+ //! Number of steps after which center of mass motion is removed
+ int nstcomm_;
+ //! Compute globals communication period
+ int nstglobalcomm_;
+ //! The last (planned) step (only used for LF)
+ const Step lastStep_;
+ //! The initial step (only used for VV)
+ const Step initStep_;
+ //! A dummy signaller (used for setup and VV)
+ std::unique_ptr<SimulationSignaller> nullSignaller_;
+ //! Whether we read kinetic energy from checkpoint
+ const bool hasReadEkinState_;
+
+ /*! \brief Check that DD doesn't miss bonded interactions
+ *
+ * Domain decomposition could incorrectly miss a bonded
+ * interaction, but checking for that requires a global
+ * communication stage, which does not otherwise happen in DD
+ * code. So we do that alongside the first global energy reduction
+ * after a new DD is made. These variables handle whether the
+ * check happens, and the result it returns.
+ */
+ //! @{
+ int totalNumberOfBondedInteractions_;
+ bool shouldCheckNumberOfBondedInteractions_;
+ //! @}
+
+ /*! \brief Signal to ComputeGlobalsElement that it should check for DD errors
+ *
+ * Note that this should really be the responsibility of the DD element.
+ * MDLogger, global and local topology are only needed due to the call to
+ * checkNumberOfBondedInteractions(...).
+ *
+ * The DD element should have a single variable which gets reduced, and then
+ * be responsible for the checking after a global reduction has happened.
+ * This would, however, require a new approach for the compute_globals calls,
+ * which is not yet implemented. So for now, we're leaving this here.
+ */
+ void needToCheckNumberOfBondedInteractions();
+
+ //! Global reduction struct
+ gmx_global_stat* gstat_;
+
+ //! Pointer to the microstate
+ StatePropagatorData* statePropagatorData_;
+ //! Pointer to the energy element (needed for the tensors and mu_tot)
+ EnergyElement* energyElement_;
+ //! Pointer to the local topology (only needed for checkNumberOfBondedInteractions)
+ const gmx_localtop_t* localTopology_;
+ //! Pointer to the free energy perturbation element
+ FreeEnergyPerturbationElement* freeEnergyPerturbationElement_;
+
+ //! Center of mass motion removal
+ t_vcm vcm_;
+ //! Signals
+ SimulationSignals* signals_;
+
+ // Access to ISimulator data
+ //! Handles logging.
+ FILE* fplog_;
+ //! Handles logging.
+ const MDLogger& mdlog_;
+ //! Handles communication.
+ t_commrec* cr_;
+ //! Contains user input mdp options.
+ t_inputrec* inputrec_;
+ //! Full system topology - only needed for checkNumberOfBondedInteractions.
+ const gmx_mtop_t* top_global_;
+ //! Atom parameters for this domain.
+ const MDAtoms* mdAtoms_;
+ //! Handles constraints.
+ Constraints* constr_;
+ //! Manages flop accounting.
+ t_nrnb* nrnb_;
+ //! Manages wall cycle accounting.
+ gmx_wallcycle* wcycle_;
+ //! Parameters for force calculations.
+ t_forcerec* fr_;
};
//! \}
-} // namespace gmx
+} // namespace gmx
#endif // GMX_MODULARSIMULATOR_COMPUTEGLOBALSELEMENT_H
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff