* The ShellFCElement manages the call to relax_shell_flexcon(...)
*/
class ShellFCElement final :
- public ISimulatorElement,
- public ITopologyHolderClient,
- public INeighborSearchSignallerClient,
- public IEnergySignallerClient
+ public ISimulatorElement,
+ public ITopologyHolderClient,
+ public INeighborSearchSignallerClient,
+ public IEnergySignallerClient
{
- public:
- //! Constructor
- ShellFCElement(
- StatePropagatorData *statePropagatorData,
- EnergyElement *energyElement,
- FreeEnergyPerturbationElement *freeEnergyPerturbationElement,
- bool isVerbose,
- bool isDynamicBox,
- FILE *fplog,
- const t_commrec *cr,
- const t_inputrec *inputrec,
- const MDAtoms *mdAtoms,
- t_nrnb *nrnb,
- t_forcerec *fr,
- t_fcdata *fcd,
- gmx_wallcycle *wcycle,
- MdrunScheduleWorkload *runScheduleWork,
- gmx_vsite_t *vsite,
- ImdSession *imdSession,
- pull_t *pull_work,
- Constraints *constr,
- const gmx_mtop_t *globalTopology,
- gmx_enfrot *enforcedRotation);
-
- /*! \brief Register shell / flex constraint calculation for step / time
- *
- * @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;
-
- //! Check that we got the local topology
- void elementSetup() override;
- //! Print some final output
- void elementTeardown() override;
-
- //! Whether either shells or flexible constraints are used
- static bool doShellsOrFlexConstraints(const gmx_mtop_t *mtop, int nflexcon);
-
- private:
- //! ITopologyHolderClient implementation
- void setTopology(const gmx_localtop_t *top) override;
- //! INeighborSearchSignallerClient implementation
- SignallerCallbackPtr registerNSCallback() override;
- //! IEnergySignallerClient implementation
- SignallerCallbackPtr registerEnergyCallback(EnergySignallerEvent event) override;
- //! The actual do_force call
- void run(Step step, Time time, unsigned int flags);
-
- //! The shell / FC helper struct
- gmx_shellfc_t *shellfc_;
-
- //! The next NS step
- Step nextNSStep_;
- //! The next energy calculation step
- Step nextEnergyCalculationStep_;
- //! The next energy calculation step
- Step nextVirialCalculationStep_;
- //! The next free energy calculation step
- Step nextFreeEnergyCalculationStep_;
-
- //! Pointer to the micro state
- StatePropagatorData *statePropagatorData_;
- //! Pointer to the energy element
- EnergyElement *energyElement_;
- //! The free energy perturbation element
- FreeEnergyPerturbationElement *freeEnergyPerturbationElement_;
-
- //! The local topology - updated by Topology via Client system
- const gmx_localtop_t *localTopology_;
-
- //! Whether we're having a dynamic box
- const bool isDynamicBox_;
- //! Whether we're being verbose
- const bool isVerbose_;
- //! The number of shell relaxation steps we did
- Step nSteps_;
-
- //! DD / DLB helper object
- const DDBalanceRegionHandler ddBalanceRegionHandler_;
-
- /* \brief The FEP lambda vector
- *
- * Used if FEP is off, since do_force
- * requires lambda to be allocated anyway
- */
- std::array<real, efptNR> lambda_;
-
- // Access to ISimulator data
- //! Handles logging.
- FILE *fplog_;
- //! Handles communication.
- const t_commrec *cr_;
- //! Contains user input mdp options.
- const t_inputrec *inputrec_;
- //! Atom parameters for this domain.
- const MDAtoms *mdAtoms_;
- //! Manages flop accounting.
- t_nrnb *nrnb_;
- //! Manages wall cycle accounting.
- gmx_wallcycle *wcycle_;
- //! Parameters for force calculations.
- t_forcerec *fr_;
- //! Handles virtual sites.
- gmx_vsite_t *vsite_;
- //! The Interactive Molecular Dynamics session.
- ImdSession *imdSession_;
- //! The pull work object.
- pull_t *pull_work_;
- //! Helper struct for force calculations.
- t_fcdata *fcd_;
- //! Schedule of work for each MD step for this task.
- MdrunScheduleWorkload *runScheduleWork_;
- //! Handles constraints.
- Constraints *constr_;
- //! Handles enforced rotation.
- gmx_enfrot *enforcedRotation_;
+public:
+ //! Constructor
+ ShellFCElement(StatePropagatorData* statePropagatorData,
+ EnergyElement* energyElement,
+ FreeEnergyPerturbationElement* freeEnergyPerturbationElement,
+ bool isVerbose,
+ bool isDynamicBox,
+ FILE* fplog,
+ const t_commrec* cr,
+ const t_inputrec* inputrec,
+ const MDAtoms* mdAtoms,
+ t_nrnb* nrnb,
+ t_forcerec* fr,
+ t_fcdata* fcd,
+ gmx_wallcycle* wcycle,
+ MdrunScheduleWorkload* runScheduleWork,
+ gmx_vsite_t* vsite,
+ ImdSession* imdSession,
+ pull_t* pull_work,
+ Constraints* constr,
+ const gmx_mtop_t* globalTopology,
+ gmx_enfrot* enforcedRotation);
+
+ /*! \brief Register shell / flex constraint calculation for step / time
+ *
+ * @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;
+
+ //! Check that we got the local topology
+ void elementSetup() override;
+ //! Print some final output
+ void elementTeardown() override;
+
+ //! Whether either shells or flexible constraints are used
+ static bool doShellsOrFlexConstraints(const gmx_mtop_t* mtop, int nflexcon);
+
+private:
+ //! ITopologyHolderClient implementation
+ void setTopology(const gmx_localtop_t* top) override;
+ //! INeighborSearchSignallerClient implementation
+ SignallerCallbackPtr registerNSCallback() override;
+ //! IEnergySignallerClient implementation
+ SignallerCallbackPtr registerEnergyCallback(EnergySignallerEvent event) override;
+ //! The actual do_force call
+ void run(Step step, Time time, unsigned int flags);
+
+ //! The shell / FC helper struct
+ gmx_shellfc_t* shellfc_;
+
+ //! The next NS step
+ Step nextNSStep_;
+ //! The next energy calculation step
+ Step nextEnergyCalculationStep_;
+ //! The next energy calculation step
+ Step nextVirialCalculationStep_;
+ //! The next free energy calculation step
+ Step nextFreeEnergyCalculationStep_;
+
+ //! Pointer to the micro state
+ StatePropagatorData* statePropagatorData_;
+ //! Pointer to the energy element
+ EnergyElement* energyElement_;
+ //! The free energy perturbation element
+ FreeEnergyPerturbationElement* freeEnergyPerturbationElement_;
+
+ //! The local topology - updated by Topology via Client system
+ const gmx_localtop_t* localTopology_;
+
+ //! Whether we're having a dynamic box
+ const bool isDynamicBox_;
+ //! Whether we're being verbose
+ const bool isVerbose_;
+ //! The number of shell relaxation steps we did
+ Step nSteps_;
+
+ //! DD / DLB helper object
+ const DDBalanceRegionHandler ddBalanceRegionHandler_;
+
+ /* \brief The FEP lambda vector
+ *
+ * Used if FEP is off, since do_force
+ * requires lambda to be allocated anyway
+ */
+ std::array<real, efptNR> lambda_;
+
+ // Access to ISimulator data
+ //! Handles logging.
+ FILE* fplog_;
+ //! Handles communication.
+ const t_commrec* cr_;
+ //! Contains user input mdp options.
+ const t_inputrec* inputrec_;
+ //! Atom parameters for this domain.
+ const MDAtoms* mdAtoms_;
+ //! Manages flop accounting.
+ t_nrnb* nrnb_;
+ //! Manages wall cycle accounting.
+ gmx_wallcycle* wcycle_;
+ //! Parameters for force calculations.
+ t_forcerec* fr_;
+ //! Handles virtual sites.
+ gmx_vsite_t* vsite_;
+ //! The Interactive Molecular Dynamics session.
+ ImdSession* imdSession_;
+ //! The pull work object.
+ pull_t* pull_work_;
+ //! Helper struct for force calculations.
+ t_fcdata* fcd_;
+ //! Schedule of work for each MD step for this task.
+ MdrunScheduleWorkload* runScheduleWork_;
+ //! Handles constraints.
+ Constraints* constr_;
+ //! Handles enforced rotation.
+ gmx_enfrot* enforcedRotation_;
};
-} // namespace gmx
+} // namespace gmx
#endif // GMX_MODULARSIMULATOR_SHELLFCELEMENT_H
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff