class UpdateConstrainCuda::Impl
{
- public:
- /*! \brief Create Update-Constrain object.
- *
- * The constructor is given a non-nullptr \p commandStream, in which all the update and constrain
- * routines are executed. \p xUpdatedOnDevice should mark the completion of all kernels that modify
- * coordinates. The event is maintained outside this class and also passed to all (if any) consumers
- * of the updated coordinates. The \p xUpdatedOnDevice also can not be a nullptr because the
- * markEvent(...) method is called unconditionally.
- *
- * \param[in] ir Input record data: LINCS takes number of iterations and order of
- * projection from it.
- * \param[in] mtop Topology of the system: SETTLE gets the masses for O and H atoms
- * and target O-H and H-H distances from this object.
- * \param[in] commandStream GPU stream to use. Can be nullptr.
- * \param[in] xUpdatedOnDevice The event synchronizer to use to mark that update is done on the GPU.
- */
- Impl(const t_inputrec &ir,
- const gmx_mtop_t &mtop,
- const void *commandStream,
- GpuEventSynchronizer *xUpdatedOnDevice);
-
- ~Impl();
-
- /*! \brief Integrate
- *
- * Integrates the equation of motion using Leap-Frog algorithm and applies
- * LINCS and SETTLE constraints.
- * If computeVirial is true, constraints virial is written at the provided pointer.
- * doTempCouple should be true if:
- * 1. The temperature coupling is enabled.
- * 2. This is the temperature coupling step.
- * Parameters virial/lambdas can be nullptr if computeVirial/doTempCouple are false.
- *
- * \param[in] fReadyOnDevice Event synchronizer indicating that the forces are ready in the device memory.
- * \param[in] dt Timestep.
- * \param[in] updateVelocities If the velocities should be constrained.
- * \param[in] computeVirial If virial should be updated.
- * \param[out] virial Place to save virial tensor.
- * \param[in] doTempCouple If the temperature coupling should be performed.
- * \param[in] tcstat Temperature coupling data.
- * \param[in] doPressureCouple If the temperature coupling should be applied.
- * \param[in] dtPressureCouple Period between pressure coupling steps
- * \param[in] velocityScalingMatrix Parrinello-Rahman velocity scaling matrix
- */
- void integrate(GpuEventSynchronizer *fReadyOnDevice,
- real dt,
- bool updateVelocities,
- bool computeVirial,
- tensor virial,
- bool doTempCouple,
- gmx::ArrayRef<const t_grp_tcstat> tcstat,
- bool doPressureCouple,
- float dtPressureCouple,
- const matrix velocityScalingMatrix);
-
- /*! \brief Set the pointers and update data-structures (e.g. after NB search step).
- *
- * \param[in,out] d_x Device buffer with coordinates.
- * \param[in,out] d_v Device buffer with velocities.
- * \param[in] d_f Device buffer with forces.
- * \param[in] idef System topology
- * \param[in] md Atoms data.
- * \param[in] numTempScaleValues Number of temperature scaling groups. Set zero for no temperature coupling.
- */
- void set(DeviceBuffer<float> d_x,
- DeviceBuffer<float> d_v,
- const DeviceBuffer<float> d_f,
- const t_idef &idef,
- const t_mdatoms &md,
- const int numTempScaleValues);
-
- /*! \brief
- * Update PBC data.
- *
- * Converts PBC data from t_pbc into the PbcAiuc format and stores the latter.
- *
- * \param[in] pbc The PBC data in t_pbc format.
- */
- void setPbc(const t_pbc *pbc);
-
- /*! \brief Return the synchronizer associated with the event indicated that the coordinates are ready on the device.
- */
- GpuEventSynchronizer* getCoordinatesReadySync();
-
- private:
-
- //! CUDA stream
- CommandStream commandStream_ = nullptr;
-
- //! Periodic boundary data
- PbcAiuc pbcAiuc_;
-
- //! Number of atoms
- int numAtoms_;
-
- //! Local copy of the pointer to the device positions buffer
- float3 *d_x_;
- //! Local copy of the pointer to the device velocities buffer
- float3 *d_v_;
- //! Local copy of the pointer to the device forces buffer
- float3 *d_f_;
-
- //! Device buffer for intermediate positions (maintained internally)
- float3 *d_xp_;
- //! Number of elements in shifted coordinates buffer
- int numXp_ = -1;
- //! Allocation size for the shifted coordinates buffer
- int numXpAlloc_ = -1;
-
-
- //! 1/mass for all atoms (GPU)
- real *d_inverseMasses_;
- //! Number of elements in reciprocal masses buffer
- int numInverseMasses_ = -1;
- //! Allocation size for the reciprocal masses buffer
- int numInverseMassesAlloc_ = -1;
-
- //! Leap-Frog integrator
- std::unique_ptr<LeapFrogCuda> integrator_;
- //! LINCS CUDA object to use for non-water constraints
- std::unique_ptr<LincsCuda> lincsCuda_;
- //! SETTLE CUDA object for water constrains
- std::unique_ptr<SettleCuda> settleCuda_;
-
- //! An pointer to the event to indicate when the update of coordinates is complete
- GpuEventSynchronizer *coordinatesReady_;
+public:
+ /*! \brief Create Update-Constrain object.
+ *
+ * The constructor is given a non-nullptr \p commandStream, in which all the update and constrain
+ * routines are executed. \p xUpdatedOnDevice should mark the completion of all kernels that modify
+ * coordinates. The event is maintained outside this class and also passed to all (if any) consumers
+ * of the updated coordinates. The \p xUpdatedOnDevice also can not be a nullptr because the
+ * markEvent(...) method is called unconditionally.
+ *
+ * \param[in] ir Input record data: LINCS takes number of iterations and order of
+ * projection from it.
+ * \param[in] mtop Topology of the system: SETTLE gets the masses for O and H atoms
+ * and target O-H and H-H distances from this object.
+ * \param[in] commandStream GPU stream to use. Can be nullptr.
+ * \param[in] xUpdatedOnDevice The event synchronizer to use to mark that update is done on the GPU.
+ */
+ Impl(const t_inputrec& ir, const gmx_mtop_t& mtop, const void* commandStream, GpuEventSynchronizer* xUpdatedOnDevice);
+
+ ~Impl();
+
+ /*! \brief Integrate
+ *
+ * Integrates the equation of motion using Leap-Frog algorithm and applies
+ * LINCS and SETTLE constraints.
+ * If computeVirial is true, constraints virial is written at the provided pointer.
+ * doTempCouple should be true if:
+ * 1. The temperature coupling is enabled.
+ * 2. This is the temperature coupling step.
+ * Parameters virial/lambdas can be nullptr if computeVirial/doTempCouple are false.
+ *
+ * \param[in] fReadyOnDevice Event synchronizer indicating that the forces are ready in
+ * the device memory. \param[in] dt Timestep. \param[in] updateVelocities
+ * If the velocities should be constrained. \param[in] computeVirial If virial should
+ * be updated. \param[out] virial Place to save virial tensor. \param[in]
+ * doTempCouple If the temperature coupling should be performed. \param[in] tcstat
+ * Temperature coupling data. \param[in] doPressureCouple If the temperature coupling
+ * should be applied. \param[in] dtPressureCouple Period between pressure coupling steps
+ * \param[in] velocityScalingMatrix Parrinello-Rahman velocity scaling matrix
+ */
+ void integrate(GpuEventSynchronizer* fReadyOnDevice,
+ real dt,
+ bool updateVelocities,
+ bool computeVirial,
+ tensor virial,
+ bool doTempCouple,
+ gmx::ArrayRef<const t_grp_tcstat> tcstat,
+ bool doPressureCouple,
+ float dtPressureCouple,
+ const matrix velocityScalingMatrix);
+
+ /*! \brief Set the pointers and update data-structures (e.g. after NB search step).
+ *
+ * \param[in,out] d_x Device buffer with coordinates.
+ * \param[in,out] d_v Device buffer with velocities.
+ * \param[in] d_f Device buffer with forces.
+ * \param[in] idef System topology
+ * \param[in] md Atoms data.
+ * \param[in] numTempScaleValues Number of temperature scaling groups. Set zero for no temperature coupling.
+ */
+ void set(DeviceBuffer<float> d_x,
+ DeviceBuffer<float> d_v,
+ const DeviceBuffer<float> d_f,
+ const t_idef& idef,
+ const t_mdatoms& md,
+ const int numTempScaleValues);
+
+ /*! \brief
+ * Update PBC data.
+ *
+ * Converts PBC data from t_pbc into the PbcAiuc format and stores the latter.
+ *
+ * \param[in] pbc The PBC data in t_pbc format.
+ */
+ void setPbc(const t_pbc* pbc);
+
+ /*! \brief Return the synchronizer associated with the event indicated that the coordinates are ready on the device.
+ */
+ GpuEventSynchronizer* getCoordinatesReadySync();
+
+private:
+ //! CUDA stream
+ CommandStream commandStream_ = nullptr;
+
+ //! Periodic boundary data
+ PbcAiuc pbcAiuc_;
+
+ //! Number of atoms
+ int numAtoms_;
+
+ //! Local copy of the pointer to the device positions buffer
+ float3* d_x_;
+ //! Local copy of the pointer to the device velocities buffer
+ float3* d_v_;
+ //! Local copy of the pointer to the device forces buffer
+ float3* d_f_;
+
+ //! Device buffer for intermediate positions (maintained internally)
+ float3* d_xp_;
+ //! Number of elements in shifted coordinates buffer
+ int numXp_ = -1;
+ //! Allocation size for the shifted coordinates buffer
+ int numXpAlloc_ = -1;
+
+
+ //! 1/mass for all atoms (GPU)
+ real* d_inverseMasses_;
+ //! Number of elements in reciprocal masses buffer
+ int numInverseMasses_ = -1;
+ //! Allocation size for the reciprocal masses buffer
+ int numInverseMassesAlloc_ = -1;
+
+ //! Leap-Frog integrator
+ std::unique_ptr<LeapFrogCuda> integrator_;
+ //! LINCS CUDA object to use for non-water constraints
+ std::unique_ptr<LincsCuda> lincsCuda_;
+ //! SETTLE CUDA object for water constrains
+ std::unique_ptr<SettleCuda> settleCuda_;
+
+ //! An pointer to the event to indicate when the update of coordinates is complete
+ GpuEventSynchronizer* coordinatesReady_;
};
} // namespace gmx
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff