* dipole vector, and the legacy energy data structures.
*/
class EnergyElement final :
- public ISimulatorElement,
- public ITrajectoryWriterClient,
- public ITrajectorySignallerClient,
- public IEnergySignallerClient,
- public ICheckpointHelperClient
+ public ISimulatorElement,
+ public ITrajectoryWriterClient,
+ public ITrajectorySignallerClient,
+ public IEnergySignallerClient,
+ public ICheckpointHelperClient
{
- public:
- //! Constructor
- EnergyElement(
- StatePropagatorData *statePropagatorData,
- FreeEnergyPerturbationElement *freeEnergyPerturbationElement,
- const gmx_mtop_t *globalTopology,
- const t_inputrec *inputrec,
- const MDAtoms *mdAtoms,
- gmx_enerdata_t *enerd,
- gmx_ekindata_t *ekind,
- const Constraints *constr,
- FILE *fplog,
- t_fcdata *fcd,
- const MdModulesNotifier &mdModulesNotifier,
- bool isMasterRank,
- ObservablesHistory *observablesHistory,
- StartingBehavior startingBehavior);
-
- /*! \brief Register run function for step / time
- *
- * This needs to be called when the energies are at a full time step.
- * Positioning this element is the responsibility of the programmer.
- *
- * This is also the place at which the current state becomes the previous
- * state.
- *
- * @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;
-
- //! No element setup needed
- void elementSetup() override {}
-
- /*! \brief Final output
- *
- * Prints the averages to log.
- */
- void elementTeardown() override;
-
- /*! \brief Add contribution to force virial
- *
- * This automatically resets the tensor if the step is higher
- * than the current step, starting the tensor calculation for
- * a new step at zero. Otherwise, it adds the new contribution
- * to the existing virial.
- */
- void addToForceVirial(const tensor virial, Step step);
-
- /*! \brief Add contribution to constraint virial
- *
- * This automatically resets the tensor if the step is higher
- * than the current step, starting the tensor calculation for
- * a new step at zero. Otherwise, it adds the new contribution
- * to the existing virial.
- */
- void addToConstraintVirial(const tensor virial, Step step);
-
- /*! \brief Get pointer to force virial tensor
- *
- * Allows access to the raw pointer to the tensor.
- */
- rvec* forceVirial(Step step);
-
- /*! \brief Get pointer to constraint virial tensor
- *
- * Allows access to the raw pointer to the tensor.
- */
- rvec* constraintVirial(Step step);
-
- /*! \brief Get pointer to total virial tensor
- *
- * Allows access to the raw pointer to the tensor.
- */
- rvec* totalVirial(Step step);
-
- /*! \brief Get pointer to pressure tensor
- *
- * Allows access to the raw pointer to the tensor.
- */
- rvec* pressure(Step step);
-
- /*! \brief Get pointer to mu_tot
- *
- * Allows access to the raw pointer to the dipole vector.
- */
- real* muTot();
-
- /*! \brief Get pointer to energy structure
- *
- */
- gmx_enerdata_t* enerdata();
-
- /*! \brief Get pointer to kinetic energy structure
- *
- */
- gmx_ekindata_t* ekindata();
-
- /*! \brief Get pointer to needToSumEkinhOld
- *
- */
- bool* needToSumEkinhOld();
-
- /*! \brief set vrescale thermostat
- *
- * This allows to set a pointer to the vrescale thermostat used to
- * print the thermostat integral.
- * TODO: This should be made obsolete my a more modular energy element
- */
- void setVRescaleThermostat(const VRescaleThermostat* vRescaleThermostat);
-
- /*! \brief set Parrinello-Rahman barostat
- *
- * This allows to set a pointer to the Parrinello-Rahman barostat used to
- * print the box velocities.
- * TODO: This should be made obsolete my a more modular energy element
- */
- void setParrinelloRahamnBarostat(const ParrinelloRahmanBarostat* parrinelloRahmanBarostat);
-
- /*! \brief Initialize energy history
- *
- * Kept as a static function to allow usage from legacy code
- * \todo Make member function once legacy use is not needed anymore
- */
- static void initializeEnergyHistory(
- StartingBehavior startingBehavior,
- ObservablesHistory *observablesHistory,
- EnergyOutput *energyOutput);
-
- private:
- /*! \brief Setup (needs file pointer)
- *
- * ITrajectoryWriterClient implementation.
- *
- * Initializes the EnergyOutput object, and does some logging output.
- *
- * @param mdoutf File pointer
- */
- void trajectoryWriterSetup(gmx_mdoutf *mdoutf) override;
- //! No trajectory writer teardown needed
- void trajectoryWriterTeardown(gmx_mdoutf gmx_unused *outf) override {}
-
- //! ITrajectoryWriterClient implementation.
- SignallerCallbackPtr
- registerTrajectorySignallerCallback(TrajectoryEvent event) override;
- //! ITrajectorySignallerClient implementation
- ITrajectoryWriterCallbackPtr
- registerTrajectoryWriterCallback(TrajectoryEvent event) override;
- //! IEnergySignallerClient implementation
- SignallerCallbackPtr registerEnergyCallback(EnergySignallerEvent event) override;
-
- /*! \brief Save data at energy steps
- *
- * @param time The current time
- * @param isEnergyCalculationStep Whether the current step is an energy calculation step
- * @param isFreeEnergyCalculationStep Whether the current step is a free energy calculation step
- */
- void doStep(
- Time time,
- bool isEnergyCalculationStep,
- bool isFreeEnergyCalculationStep);
-
- /*! \brief Write to energy trajectory
- *
- * This is only called by master - writes energy to trajectory and to log.
- */
- void write(
- gmx_mdoutf *outf,
- Step step, Time time,
- bool writeTrajectory, bool writeLog);
-
- //! ICheckpointHelperClient implementation
- void writeCheckpoint(t_state *localState, t_state *globalState) override;
-
- /*
- * Data owned by EnergyElement
- */
- //! The energy output object
- std::unique_ptr<EnergyOutput> energyOutput_;
-
- //! Whether this is the master rank
- const bool isMasterRank_;
- //! The next communicated energy writing step
- Step energyWritingStep_;
- //! The next communicated energy calculation step
- Step energyCalculationStep_;
- //! The next communicated free energy calculation step
- Step freeEnergyCalculationStep_;
-
- //! The force virial tensor
- tensor forceVirial_;
- //! The constraint virial tensor
- tensor shakeVirial_;
- //! The total virial tensor
- tensor totalVirial_;
- //! The pressure tensor
- tensor pressure_;
- //! The total dipole moment
- rvec muTot_;
-
- //! The step number of the current force virial tensor
- Step forceVirialStep_;
- //! The step number of the current constraint virial tensor
- Step shakeVirialStep_;
- //! The step number of the current total virial tensor
- Step totalVirialStep_;
- //! The step number of the current pressure tensor
- Step pressureStep_;
-
- //! Whether ekinh_old needs to be summed up (set by compute globals)
- bool needToSumEkinhOld_;
-
- //! Describes how the simulation (re)starts
- const StartingBehavior startingBehavior_;
-
- //! Legacy state object used to communicate with energy output
- t_state dummyLegacyState_;
-
- /*
- * Pointers to Simulator data
- */
- //! Pointer to the state propagator data
- StatePropagatorData *statePropagatorData_;
- //! Pointer to the free energy perturbation element
- FreeEnergyPerturbationElement *freeEnergyPerturbationElement_;
- //! Pointer to the vrescale thermostat
- const VRescaleThermostat *vRescaleThermostat_;
- //! Pointer to the Parrinello-Rahman barostat
- const ParrinelloRahmanBarostat *parrinelloRahmanBarostat_;
- //! Contains user input mdp options.
- const t_inputrec *inputrec_;
- //! Full system topology.
- const gmx_mtop_t *top_global_;
- //! Atom parameters for this domain.
- const MDAtoms *mdAtoms_;
- //! Energy data structure
- gmx_enerdata_t *enerd_;
- //! Kinetic energy data
- gmx_ekindata_t *ekind_;
- //! Handles constraints.
- const Constraints *constr_;
- //! Handles logging.
- FILE *fplog_;
- //! Helper struct for force calculations.
- t_fcdata *fcd_;
- //! Notification to MD modules
- const MdModulesNotifier &mdModulesNotifier_;
- //! Global topology groups
- const SimulationGroups *groups_;
- //! History of simulation observables.
- ObservablesHistory *observablesHistory_;
+public:
+ //! Constructor
+ EnergyElement(StatePropagatorData* statePropagatorData,
+ FreeEnergyPerturbationElement* freeEnergyPerturbationElement,
+ const gmx_mtop_t* globalTopology,
+ const t_inputrec* inputrec,
+ const MDAtoms* mdAtoms,
+ gmx_enerdata_t* enerd,
+ gmx_ekindata_t* ekind,
+ const Constraints* constr,
+ FILE* fplog,
+ t_fcdata* fcd,
+ const MdModulesNotifier& mdModulesNotifier,
+ bool isMasterRank,
+ ObservablesHistory* observablesHistory,
+ StartingBehavior startingBehavior);
+
+ /*! \brief Register run function for step / time
+ *
+ * This needs to be called when the energies are at a full time step.
+ * Positioning this element is the responsibility of the programmer.
+ *
+ * This is also the place at which the current state becomes the previous
+ * state.
+ *
+ * @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;
+
+ //! No element setup needed
+ void elementSetup() override {}
+
+ /*! \brief Final output
+ *
+ * Prints the averages to log.
+ */
+ void elementTeardown() override;
+
+ /*! \brief Add contribution to force virial
+ *
+ * This automatically resets the tensor if the step is higher
+ * than the current step, starting the tensor calculation for
+ * a new step at zero. Otherwise, it adds the new contribution
+ * to the existing virial.
+ */
+ void addToForceVirial(const tensor virial, Step step);
+
+ /*! \brief Add contribution to constraint virial
+ *
+ * This automatically resets the tensor if the step is higher
+ * than the current step, starting the tensor calculation for
+ * a new step at zero. Otherwise, it adds the new contribution
+ * to the existing virial.
+ */
+ void addToConstraintVirial(const tensor virial, Step step);
+
+ /*! \brief Get pointer to force virial tensor
+ *
+ * Allows access to the raw pointer to the tensor.
+ */
+ rvec* forceVirial(Step step);
+
+ /*! \brief Get pointer to constraint virial tensor
+ *
+ * Allows access to the raw pointer to the tensor.
+ */
+ rvec* constraintVirial(Step step);
+
+ /*! \brief Get pointer to total virial tensor
+ *
+ * Allows access to the raw pointer to the tensor.
+ */
+ rvec* totalVirial(Step step);
+
+ /*! \brief Get pointer to pressure tensor
+ *
+ * Allows access to the raw pointer to the tensor.
+ */
+ rvec* pressure(Step step);
+
+ /*! \brief Get pointer to mu_tot
+ *
+ * Allows access to the raw pointer to the dipole vector.
+ */
+ real* muTot();
+
+ /*! \brief Get pointer to energy structure
+ *
+ */
+ gmx_enerdata_t* enerdata();
+
+ /*! \brief Get pointer to kinetic energy structure
+ *
+ */
+ gmx_ekindata_t* ekindata();
+
+ /*! \brief Get pointer to needToSumEkinhOld
+ *
+ */
+ bool* needToSumEkinhOld();
+
+ /*! \brief set vrescale thermostat
+ *
+ * This allows to set a pointer to the vrescale thermostat used to
+ * print the thermostat integral.
+ * TODO: This should be made obsolete my a more modular energy element
+ */
+ void setVRescaleThermostat(const VRescaleThermostat* vRescaleThermostat);
+
+ /*! \brief set Parrinello-Rahman barostat
+ *
+ * This allows to set a pointer to the Parrinello-Rahman barostat used to
+ * print the box velocities.
+ * TODO: This should be made obsolete my a more modular energy element
+ */
+ void setParrinelloRahamnBarostat(const ParrinelloRahmanBarostat* parrinelloRahmanBarostat);
+
+ /*! \brief Initialize energy history
+ *
+ * Kept as a static function to allow usage from legacy code
+ * \todo Make member function once legacy use is not needed anymore
+ */
+ static void initializeEnergyHistory(StartingBehavior startingBehavior,
+ ObservablesHistory* observablesHistory,
+ EnergyOutput* energyOutput);
+
+private:
+ /*! \brief Setup (needs file pointer)
+ *
+ * ITrajectoryWriterClient implementation.
+ *
+ * Initializes the EnergyOutput object, and does some logging output.
+ *
+ * @param mdoutf File pointer
+ */
+ void trajectoryWriterSetup(gmx_mdoutf* mdoutf) override;
+ //! No trajectory writer teardown needed
+ void trajectoryWriterTeardown(gmx_mdoutf gmx_unused* outf) override {}
+
+ //! ITrajectoryWriterClient implementation.
+ SignallerCallbackPtr registerTrajectorySignallerCallback(TrajectoryEvent event) override;
+ //! ITrajectorySignallerClient implementation
+ ITrajectoryWriterCallbackPtr registerTrajectoryWriterCallback(TrajectoryEvent event) override;
+ //! IEnergySignallerClient implementation
+ SignallerCallbackPtr registerEnergyCallback(EnergySignallerEvent event) override;
+
+ /*! \brief Save data at energy steps
+ *
+ * @param time The current time
+ * @param isEnergyCalculationStep Whether the current step is an energy calculation step
+ * @param isFreeEnergyCalculationStep Whether the current step is a free energy calculation step
+ */
+ void doStep(Time time, bool isEnergyCalculationStep, bool isFreeEnergyCalculationStep);
+
+ /*! \brief Write to energy trajectory
+ *
+ * This is only called by master - writes energy to trajectory and to log.
+ */
+ void write(gmx_mdoutf* outf, Step step, Time time, bool writeTrajectory, bool writeLog);
+
+ //! ICheckpointHelperClient implementation
+ void writeCheckpoint(t_state* localState, t_state* globalState) override;
+
+ /*
+ * Data owned by EnergyElement
+ */
+ //! The energy output object
+ std::unique_ptr<EnergyOutput> energyOutput_;
+
+ //! Whether this is the master rank
+ const bool isMasterRank_;
+ //! The next communicated energy writing step
+ Step energyWritingStep_;
+ //! The next communicated energy calculation step
+ Step energyCalculationStep_;
+ //! The next communicated free energy calculation step
+ Step freeEnergyCalculationStep_;
+
+ //! The force virial tensor
+ tensor forceVirial_;
+ //! The constraint virial tensor
+ tensor shakeVirial_;
+ //! The total virial tensor
+ tensor totalVirial_;
+ //! The pressure tensor
+ tensor pressure_;
+ //! The total dipole moment
+ rvec muTot_;
+
+ //! The step number of the current force virial tensor
+ Step forceVirialStep_;
+ //! The step number of the current constraint virial tensor
+ Step shakeVirialStep_;
+ //! The step number of the current total virial tensor
+ Step totalVirialStep_;
+ //! The step number of the current pressure tensor
+ Step pressureStep_;
+
+ //! Whether ekinh_old needs to be summed up (set by compute globals)
+ bool needToSumEkinhOld_;
+
+ //! Describes how the simulation (re)starts
+ const StartingBehavior startingBehavior_;
+
+ //! Legacy state object used to communicate with energy output
+ t_state dummyLegacyState_;
+
+ /*
+ * Pointers to Simulator data
+ */
+ //! Pointer to the state propagator data
+ StatePropagatorData* statePropagatorData_;
+ //! Pointer to the free energy perturbation element
+ FreeEnergyPerturbationElement* freeEnergyPerturbationElement_;
+ //! Pointer to the vrescale thermostat
+ const VRescaleThermostat* vRescaleThermostat_;
+ //! Pointer to the Parrinello-Rahman barostat
+ const ParrinelloRahmanBarostat* parrinelloRahmanBarostat_;
+ //! Contains user input mdp options.
+ const t_inputrec* inputrec_;
+ //! Full system topology.
+ const gmx_mtop_t* top_global_;
+ //! Atom parameters for this domain.
+ const MDAtoms* mdAtoms_;
+ //! Energy data structure
+ gmx_enerdata_t* enerd_;
+ //! Kinetic energy data
+ gmx_ekindata_t* ekind_;
+ //! Handles constraints.
+ const Constraints* constr_;
+ //! Handles logging.
+ FILE* fplog_;
+ //! Helper struct for force calculations.
+ t_fcdata* fcd_;
+ //! Notification to MD modules
+ const MdModulesNotifier& mdModulesNotifier_;
+ //! Global topology groups
+ const SimulationGroups* groups_;
+ //! History of simulation observables.
+ ObservablesHistory* observablesHistory_;
};
-} // namespace gmx
+} // namespace gmx
#endif // GMX_ENERGYELEMENT_MICROSTATE_H
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff