* scaling factor, and
* * scales the box and the positions of the system.
*/
-class ParrinelloRahmanBarostat final :
- public ISimulatorElement,
- public ICheckpointHelperClient
+class ParrinelloRahmanBarostat final : public ISimulatorElement, public ICheckpointHelperClient
{
- public:
- //! Constructor
- ParrinelloRahmanBarostat(
- int nstpcouple,
- int offset,
- real couplingTimeStep,
- Step initStep,
- ArrayRef<rvec> scalingTensor,
- PropagatorCallbackPtr propagatorCallback,
- StatePropagatorData *statePropagatorData,
- EnergyElement *energyElement,
- FILE *fplog,
- const t_inputrec *inputrec,
- const MDAtoms *mdAtoms,
- const t_state *globalState,
- t_commrec *cr,
- bool isRestart);
-
- /*! \brief Register run function 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;
-
- //! Fix relative box shape
- void elementSetup() override;
- //! No element teardown needed
- void elementTeardown() override {}
-
- //! Getter for the box velocities
- const rvec* boxVelocities() const;
-
- private:
- //! The frequency at which the barostat is applied
- const int nstpcouple_;
- //! If != 0, offset the step at which the barostat is applied
- const int offset_;
- //! The coupling time step - simulation time step x nstcouple_
- const real couplingTimeStep_;
- //! The first step of the simulation
- const Step initStep_;
-
- //! Whether this is the first step
- bool isInitStep_;
-
- //! View on the velocity scaling tensor (owned by the propagator)
- ArrayRef<rvec> scalingTensor_;
- //! Callback to let propagator know that we updated lambda
- PropagatorCallbackPtr propagatorCallback_;
-
- //! Relative change in box before - after barostatting
- matrix mu_;
- //! Relative box shape
- tensor boxRel_;
- //! Box velocity
- tensor boxVelocity_;
-
- //! Pointer to the micro state
- StatePropagatorData *statePropagatorData_;
- //! Pointer to the energy element
- EnergyElement *energyElement_;
-
- //! Integrate the PR box vector equations of motion - does not alter state
- void integrateBoxVelocityEquations(Step step);
- //! Scale box and positions
- void scaleBoxAndPositions();
-
- //! ICheckpointHelperClient implementation
- void writeCheckpoint(t_state *localState, t_state *globalState) override;
-
- // Access to ISimulator data
- //! Handles logging.
- FILE *fplog_;
- //! Contains user input mdp options.
- const t_inputrec *inputrec_;
- //! Atom parameters for this domain.
- const MDAtoms *mdAtoms_;
+public:
+ //! Constructor
+ ParrinelloRahmanBarostat(int nstpcouple,
+ int offset,
+ real couplingTimeStep,
+ Step initStep,
+ ArrayRef<rvec> scalingTensor,
+ PropagatorCallbackPtr propagatorCallback,
+ StatePropagatorData* statePropagatorData,
+ EnergyElement* energyElement,
+ FILE* fplog,
+ const t_inputrec* inputrec,
+ const MDAtoms* mdAtoms,
+ const t_state* globalState,
+ t_commrec* cr,
+ bool isRestart);
+
+ /*! \brief Register run function 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;
+
+ //! Fix relative box shape
+ void elementSetup() override;
+ //! No element teardown needed
+ void elementTeardown() override {}
+
+ //! Getter for the box velocities
+ const rvec* boxVelocities() const;
+
+private:
+ //! The frequency at which the barostat is applied
+ const int nstpcouple_;
+ //! If != 0, offset the step at which the barostat is applied
+ const int offset_;
+ //! The coupling time step - simulation time step x nstcouple_
+ const real couplingTimeStep_;
+ //! The first step of the simulation
+ const Step initStep_;
+
+ //! Whether this is the first step
+ bool isInitStep_;
+
+ //! View on the velocity scaling tensor (owned by the propagator)
+ ArrayRef<rvec> scalingTensor_;
+ //! Callback to let propagator know that we updated lambda
+ PropagatorCallbackPtr propagatorCallback_;
+
+ //! Relative change in box before - after barostatting
+ matrix mu_;
+ //! Relative box shape
+ tensor boxRel_;
+ //! Box velocity
+ tensor boxVelocity_;
+
+ //! Pointer to the micro state
+ StatePropagatorData* statePropagatorData_;
+ //! Pointer to the energy element
+ EnergyElement* energyElement_;
+
+ //! Integrate the PR box vector equations of motion - does not alter state
+ void integrateBoxVelocityEquations(Step step);
+ //! Scale box and positions
+ void scaleBoxAndPositions();
+
+ //! ICheckpointHelperClient implementation
+ void writeCheckpoint(t_state* localState, t_state* globalState) override;
+
+ // Access to ISimulator data
+ //! Handles logging.
+ FILE* fplog_;
+ //! Contains user input mdp options.
+ const t_inputrec* inputrec_;
+ //! Atom parameters for this domain.
+ const MDAtoms* mdAtoms_;
};
-} // namespace gmx
+} // namespace gmx
#endif // GMX_MODULARSIMULATOR_PARRINELLORAHMANBAROSTAT_H
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff