* constraining are using this.
*/
class StatePropagatorData final :
- public ISimulatorElement,
- public ITrajectoryWriterClient,
- public ITrajectorySignallerClient,
- public ICheckpointHelperClient
+ public ISimulatorElement,
+ public ITrajectoryWriterClient,
+ public ITrajectorySignallerClient,
+ public ICheckpointHelperClient
{
- public:
- //! Constructor
- StatePropagatorData(
- int numAtoms,
- FILE *fplog,
- const t_commrec *cr,
- t_state *globalState,
- int nstxout,
- int nstvout,
- int nstfout,
- int nstxout_compressed,
- bool useGPU,
- FreeEnergyPerturbationElement *freeEnergyPerturbationElement,
- const t_inputrec *inputrec,
- const t_mdatoms *mdatoms);
+public:
+ //! Constructor
+ StatePropagatorData(int numAtoms,
+ FILE* fplog,
+ const t_commrec* cr,
+ t_state* globalState,
+ int nstxout,
+ int nstvout,
+ int nstfout,
+ int nstxout_compressed,
+ bool useGPU,
+ FreeEnergyPerturbationElement* freeEnergyPerturbationElement,
+ const t_inputrec* inputrec,
+ const t_mdatoms* mdatoms);
- // Allow access to state
- //! Get write access to position vector
- ArrayRefWithPadding<RVec> positionsView();
- //! Get read access to position vector
- ArrayRefWithPadding<const RVec> constPositionsView() const;
- //! Get write access to previous position vector
- ArrayRefWithPadding<RVec> previousPositionsView();
- //! Get read access to previous position vector
- ArrayRefWithPadding<const RVec> constPreviousPositionsView() const;
- //! Get write access to velocity vector
- ArrayRefWithPadding<RVec> velocitiesView();
- //! Get read access to velocity vector
- ArrayRefWithPadding<const RVec> constVelocitiesView() const;
- //! Get write access to force vector
- ArrayRefWithPadding<RVec> forcesView();
- //! Get read access to force vector
- ArrayRefWithPadding<const RVec> constForcesView() const;
- //! Get pointer to box
- rvec* box();
- //! Get const pointer to box
- const rvec* constBox();
- //! Get pointer to previous box
- rvec* previousBox();
- //! Get const pointer to previous box
- const rvec* constPreviousBox();
- //! Get the local number of atoms
- int localNumAtoms();
+ // Allow access to state
+ //! Get write access to position vector
+ ArrayRefWithPadding<RVec> positionsView();
+ //! Get read access to position vector
+ ArrayRefWithPadding<const RVec> constPositionsView() const;
+ //! Get write access to previous position vector
+ ArrayRefWithPadding<RVec> previousPositionsView();
+ //! Get read access to previous position vector
+ ArrayRefWithPadding<const RVec> constPreviousPositionsView() const;
+ //! Get write access to velocity vector
+ ArrayRefWithPadding<RVec> velocitiesView();
+ //! Get read access to velocity vector
+ ArrayRefWithPadding<const RVec> constVelocitiesView() const;
+ //! Get write access to force vector
+ ArrayRefWithPadding<RVec> forcesView();
+ //! Get read access to force vector
+ ArrayRefWithPadding<const RVec> constForcesView() const;
+ //! Get pointer to box
+ rvec* box();
+ //! Get const pointer to box
+ const rvec* constBox();
+ //! Get pointer to previous box
+ rvec* previousBox();
+ //! Get const pointer to previous box
+ const rvec* constPreviousBox();
+ //! Get the local number of atoms
+ int localNumAtoms();
- /*! \brief Register run function for step / time
- *
- * This needs to be called during the integration part of the simulator,
- * at the moment at which the state is at a full time step. Positioning
- * this element is the responsibility of the programmer writing the
- * integration algorithm! If the current step is a trajectory writing
- * step, StatePropagatorData will save a backup for later writeout.
- *
- * 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;
+ /*! \brief Register run function for step / time
+ *
+ * This needs to be called during the integration part of the simulator,
+ * at the moment at which the state is at a full time step. Positioning
+ * this element is the responsibility of the programmer writing the
+ * integration algorithm! If the current step is a trajectory writing
+ * step, StatePropagatorData will save a backup for later writeout.
+ *
+ * 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;
- /*! \brief Backup starting velocities
- *
- * This is only needed for vv, where the first (velocity) half step is only
- * used to compute the constraint virial, but the velocities need to be reset
- * after.
- * TODO: There must be a more elegant solution to this!
- */
- void elementSetup() override;
+ /*! \brief Backup starting velocities
+ *
+ * This is only needed for vv, where the first (velocity) half step is only
+ * used to compute the constraint virial, but the velocities need to be reset
+ * after.
+ * TODO: There must be a more elegant solution to this!
+ */
+ void elementSetup() override;
- //! No element teardown needed
- void elementTeardown() override {}
+ //! No element teardown needed
+ void elementTeardown() override {}
- //! @cond
- // (doxygen doesn't like these)
- // Classes which need access to legacy state
- friend class DomDecHelper;
- //! @endcond
+ //! @cond
+ // (doxygen doesn't like these)
+ // Classes which need access to legacy state
+ friend class DomDecHelper;
+ //! @endcond
- private:
- //! The total number of atoms in the system
- int totalNumAtoms_;
- //! The position writeout frequency
- int nstxout_;
- //! The velocity writeout frequency
- int nstvout_;
- //! The force writeout frequency
- int nstfout_;
- //! The compressed position writeout frequency
- int nstxout_compressed_;
+private:
+ //! The total number of atoms in the system
+ int totalNumAtoms_;
+ //! The position writeout frequency
+ int nstxout_;
+ //! The velocity writeout frequency
+ int nstvout_;
+ //! The force writeout frequency
+ int nstfout_;
+ //! The compressed position writeout frequency
+ int nstxout_compressed_;
- //! The local number of atoms
- int localNAtoms_;
- //! The position vector
- PaddedHostVector<RVec> x_;
- //! The position vector of the previous step
- PaddedHostVector<RVec> previousX_;
- //! The velocity vector
- PaddedHostVector<RVec> v_;
- //! The force vector
- PaddedHostVector<RVec> f_;
- //! The box matrix
- matrix box_;
- //! The box matrix of the previous step
- matrix previousBox_;
- //! The DD partitioning count for legacy t_state compatibility
- int ddpCount_;
+ //! The local number of atoms
+ int localNAtoms_;
+ //! The position vector
+ PaddedHostVector<RVec> x_;
+ //! The position vector of the previous step
+ PaddedHostVector<RVec> previousX_;
+ //! The velocity vector
+ PaddedHostVector<RVec> v_;
+ //! The force vector
+ PaddedHostVector<RVec> f_;
+ //! The box matrix
+ matrix box_;
+ //! The box matrix of the previous step
+ matrix previousBox_;
+ //! The DD partitioning count for legacy t_state compatibility
+ int ddpCount_;
- //! Move x_ to previousX_
- void copyPosition();
- //! OMP helper to move x_ to previousX_
- void copyPosition(int start, int end);
+ //! Move x_ to previousX_
+ void copyPosition();
+ //! OMP helper to move x_ to previousX_
+ void copyPosition(int start, int end);
- // Access to legacy state
- //! Get a deep copy of the current state in legacy format
- std::unique_ptr<t_state> localState();
- //! Update the current state with a state in legacy format
- void setLocalState(std::unique_ptr<t_state> state);
- //! Get a pointer to the global state
- t_state *globalState();
- //! Get a force pointer
- PaddedHostVector<gmx::RVec> *forcePointer();
+ // Access to legacy state
+ //! Get a deep copy of the current state in legacy format
+ std::unique_ptr<t_state> localState();
+ //! Update the current state with a state in legacy format
+ void setLocalState(std::unique_ptr<t_state> state);
+ //! Get a pointer to the global state
+ t_state* globalState();
+ //! Get a force pointer
+ PaddedHostVector<gmx::RVec>* forcePointer();
- //! Pointer to keep a backup of the state for later writeout
- std::unique_ptr<t_state> localStateBackup_;
- //! Step at which next writeout occurs
- Step writeOutStep_;
- //! Backup current state
- void saveState();
+ //! Pointer to keep a backup of the state for later writeout
+ std::unique_ptr<t_state> localStateBackup_;
+ //! Step at which next writeout occurs
+ Step writeOutStep_;
+ //! Backup current state
+ void saveState();
- //! ITrajectorySignallerClient implementation
- SignallerCallbackPtr
- registerTrajectorySignallerCallback(TrajectoryEvent event) override;
+ //! ITrajectorySignallerClient implementation
+ SignallerCallbackPtr registerTrajectorySignallerCallback(TrajectoryEvent event) override;
- //! ITrajectoryWriterClient implementation
- ITrajectoryWriterCallbackPtr
- registerTrajectoryWriterCallback(TrajectoryEvent event) override;
+ //! ITrajectoryWriterClient implementation
+ ITrajectoryWriterCallbackPtr registerTrajectoryWriterCallback(TrajectoryEvent event) override;
- //! ICheckpointHelperClient implementation
- void writeCheckpoint(t_state *localState, t_state *globalState) override;
+ //! ICheckpointHelperClient implementation
+ void writeCheckpoint(t_state* localState, t_state* globalState) override;
- //! Callback writing the state to file
- void write(gmx_mdoutf *outf, Step step, Time time);
+ //! Callback writing the state to file
+ void write(gmx_mdoutf* outf, Step step, Time time);
- //! Whether we're doing VV and need to reset velocities after the first half step
- bool vvResetVelocities_;
- //! Velocities backup for VV
- PaddedHostVector<RVec> velocityBackup_;
- //! Function resetting the velocities
- void resetVelocities();
+ //! Whether we're doing VV and need to reset velocities after the first half step
+ bool vvResetVelocities_;
+ //! Velocities backup for VV
+ PaddedHostVector<RVec> velocityBackup_;
+ //! Function resetting the velocities
+ void resetVelocities();
- //! Pointer to the free energy perturbation element (for trajectory writing only)
- FreeEnergyPerturbationElement *freeEnergyPerturbationElement_;
+ //! Pointer to the free energy perturbation element (for trajectory writing only)
+ FreeEnergyPerturbationElement* freeEnergyPerturbationElement_;
- // Access to ISimulator data
- //! Handles logging.
- FILE *fplog_;
- //! Handles communication.
- const t_commrec *cr_;
- //! Full simulation state (only non-nullptr on master rank).
- t_state *globalState_;
+ // Access to ISimulator data
+ //! Handles logging.
+ FILE* fplog_;
+ //! Handles communication.
+ const t_commrec* cr_;
+ //! Full simulation state (only non-nullptr on master rank).
+ t_state* globalState_;
- //! No trajectory writer setup needed
- void trajectoryWriterSetup(gmx_mdoutf gmx_unused *outf) override {}
- //! No trajectory writer teardown needed
- void trajectoryWriterTeardown(gmx_mdoutf gmx_unused *outf) override {}
+ //! No trajectory writer setup needed
+ void trajectoryWriterSetup(gmx_mdoutf gmx_unused* outf) override {}
+ //! No trajectory writer teardown needed
+ void trajectoryWriterTeardown(gmx_mdoutf gmx_unused* outf) override {}
};
-} // namespace gmx
+} // namespace gmx
#endif // GMX_MODULARSIMULATOR_STATEPROPAGATORDATA_H
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff