struct LincsCudaKernelParameters
{
//! Periodic boundary data
- PbcAiuc pbcAiuc;
+ PbcAiuc pbcAiuc;
//! Order of expansion when inverting the matrix
- int expansionOrder;
+ int expansionOrder;
//! Number of iterations used to correct the projection
- int numIterations;
+ int numIterations;
//! 1/mass for all atoms (GPU)
- float *d_inverseMasses;
+ float* d_inverseMasses;
//! Scaled virial tensor (6 floats: [XX, XY, XZ, YY, YZ, ZZ], GPU)
- float *d_virialScaled;
+ float* d_virialScaled;
/*! \brief Total number of threads.
*
* This covers all constraints and gaps in the ends of the thread blocks
* that are necessary to avoid inter-block synchronizations.
* Should be a multiple of block size (the last block is filled with dummy to the end).
*/
- int numConstraintsThreads;
+ int numConstraintsThreads;
//! List of constrained atoms (GPU memory)
- int2 *d_constraints;
+ int2* d_constraints;
//! Equilibrium distances for the constraints (GPU)
- float *d_constraintsTargetLengths;
+ float* d_constraintsTargetLengths;
//! Number of constraints, coupled with the current one (GPU)
- int *d_coupledConstraintsCounts;
+ int* d_coupledConstraintsCounts;
//! List of coupled with the current one (GPU)
- int *d_coupledConstraintsIndices;
+ int* d_coupledConstraintsIndices;
//! Elements of the coupling matrix.
- float *d_matrixA;
+ float* d_matrixA;
//! Mass factors (GPU)
- float *d_massFactors;
+ float* d_massFactors;
};
/*! \internal \brief Class with interfaces and data for CUDA version of LINCS. */
class LincsCuda
{
- public:
-
- /*! \brief Constructor.
- *
- * \param[in] numIterations Number of iteration for the correction of the projection.
- * \param[in] expansionOrder Order of the matrix inversion algorithm.
- * \param[in] commandStream Device command stream.
- */
- LincsCuda(int numIterations,
- int expansionOrder,
- CommandStream commandStream);
- /*! \brief Destructor.*/
- ~LincsCuda();
-
- /*! \brief Apply LINCS.
- *
- * Applies LINCS to coordinates and velocities, stored on GPU.
- * The results are not automatically copied back to the CPU memory.
- * Method uses this class data structures which should be updated
- * when needed using set() and setPbc() method.
- *
- * \param[in] d_x Coordinates before timestep (in GPU memory)
- * \param[in,out] d_xp Coordinates after timestep (in GPU memory). The
- * resulting constrained coordinates will be saved here.
- * \param[in] updateVelocities If the velocities should be updated.
- * \param[in,out] d_v Velocities to update (in GPU memory, can be nullptr
- * if not updated)
- * \param[in] invdt Reciprocal timestep (to scale Lagrange
- * multipliers when velocities are updated)
- * \param[in] computeVirial If virial should be updated.
- * \param[in,out] virialScaled Scaled virial tensor to be updated.
- */
- void apply(const float3 *d_x,
- float3 *d_xp,
- const bool updateVelocities,
- float3 *d_v,
- const real invdt,
- const bool computeVirial,
- tensor virialScaled);
-
- /*! \brief
- * Update data-structures (e.g. after NB search step).
- *
- * Updates the constraints data and copies it to the GPU. Should be
- * called if the particles were sorted, redistributed between domains, etc.
- * This version uses common data formats so it can be called from anywhere
- * in the code. Does not recycle the data preparation routines from the CPU
- * version. Works only with simple case when all the constraints in idef are
- * are handled by a single GPU. Triangles are not handled as special case.
- *
- * Information about constraints is taken from:
- * idef.il[F_CONSTR].iatoms --- type (T) of constraint and two atom indexes (i1, i2)
- * idef.iparams[T].constr.dA --- target length for constraint of type T
- * From t_mdatom, the code takes:
- * md.invmass --- array of inverse square root of masses for each atom in the system.
- *
- * \param[in] idef Local topology data to get information on constraints from.
- * \param[in] md Atoms data to get atom masses from.
- */
- void set(const t_idef &idef,
- const t_mdatoms &md);
-
- /*! \brief
- * Update PBC data.
- *
- * Converts pbc data from t_pbc into the PbcAiuc format and stores the latter.
- *
- * \todo Remove this method. LINCS should not manage PBC.
- *
- * \param[in] pbc The PBC data in t_pbc format.
- */
- void setPbc(const t_pbc *pbc);
-
-
- private:
-
- //! CUDA stream
- CommandStream commandStream_;
-
- //! Parameters and pointers, passed to the CUDA kernel
- LincsCudaKernelParameters kernelParams_;
-
- //! Scaled virial tensor (6 floats: [XX, XY, XZ, YY, YZ, ZZ])
- std::vector<float> h_virialScaled_;
-
- /*! \brief Maximum total number of constraints so far.
- *
- * If the new number of constraints is larger then previous maximum, the GPU data arrays are
- * reallocated.
- */
- int numConstraintsThreadsAlloc_;
-
- /*! \brief Maximum total number of atoms so far.
- *
- * If the new number of atoms is larger then previous maximum, the GPU array with masses is
- * reallocated.
- */
- int numAtomsAlloc_;
+public:
+ /*! \brief Constructor.
+ *
+ * \param[in] numIterations Number of iteration for the correction of the projection.
+ * \param[in] expansionOrder Order of the matrix inversion algorithm.
+ * \param[in] commandStream Device command stream.
+ */
+ LincsCuda(int numIterations, int expansionOrder, CommandStream commandStream);
+ /*! \brief Destructor.*/
+ ~LincsCuda();
+
+ /*! \brief Apply LINCS.
+ *
+ * Applies LINCS to coordinates and velocities, stored on GPU.
+ * The results are not automatically copied back to the CPU memory.
+ * Method uses this class data structures which should be updated
+ * when needed using set() and setPbc() method.
+ *
+ * \param[in] d_x Coordinates before timestep (in GPU memory)
+ * \param[in,out] d_xp Coordinates after timestep (in GPU memory). The
+ * resulting constrained coordinates will be saved here.
+ * \param[in] updateVelocities If the velocities should be updated.
+ * \param[in,out] d_v Velocities to update (in GPU memory, can be nullptr
+ * if not updated)
+ * \param[in] invdt Reciprocal timestep (to scale Lagrange
+ * multipliers when velocities are updated)
+ * \param[in] computeVirial If virial should be updated.
+ * \param[in,out] virialScaled Scaled virial tensor to be updated.
+ */
+ void apply(const float3* d_x,
+ float3* d_xp,
+ const bool updateVelocities,
+ float3* d_v,
+ const real invdt,
+ const bool computeVirial,
+ tensor virialScaled);
+
+ /*! \brief
+ * Update data-structures (e.g. after NB search step).
+ *
+ * Updates the constraints data and copies it to the GPU. Should be
+ * called if the particles were sorted, redistributed between domains, etc.
+ * This version uses common data formats so it can be called from anywhere
+ * in the code. Does not recycle the data preparation routines from the CPU
+ * version. Works only with simple case when all the constraints in idef are
+ * are handled by a single GPU. Triangles are not handled as special case.
+ *
+ * Information about constraints is taken from:
+ * idef.il[F_CONSTR].iatoms --- type (T) of constraint and two atom indexes (i1, i2)
+ * idef.iparams[T].constr.dA --- target length for constraint of type T
+ * From t_mdatom, the code takes:
+ * md.invmass --- array of inverse square root of masses for each atom in the system.
+ *
+ * \param[in] idef Local topology data to get information on constraints from.
+ * \param[in] md Atoms data to get atom masses from.
+ */
+ void set(const t_idef& idef, const t_mdatoms& md);
+
+ /*! \brief
+ * Update PBC data.
+ *
+ * Converts pbc data from t_pbc into the PbcAiuc format and stores the latter.
+ *
+ * \todo Remove this method. LINCS should not manage PBC.
+ *
+ * \param[in] pbc The PBC data in t_pbc format.
+ */
+ void setPbc(const t_pbc* pbc);
+
+
+private:
+ //! CUDA stream
+ CommandStream commandStream_;
+
+ //! Parameters and pointers, passed to the CUDA kernel
+ LincsCudaKernelParameters kernelParams_;
+ //! Scaled virial tensor (6 floats: [XX, XY, XZ, YY, YZ, ZZ])
+ std::vector<float> h_virialScaled_;
+
+ /*! \brief Maximum total number of constraints so far.
+ *
+ * If the new number of constraints is larger then previous maximum, the GPU data arrays are
+ * reallocated.
+ */
+ int numConstraintsThreadsAlloc_;
+
+ /*! \brief Maximum total number of atoms so far.
+ *
+ * If the new number of atoms is larger then previous maximum, the GPU array with masses is
+ * reallocated.
+ */
+ int numAtomsAlloc_;
};
-} // namespace gmx
+} // namespace gmx
#endif // GMX_MDLIB_LINCS_CUDA_CUH
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