* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+/*! \libinternal \file
+ * \brief
+ * Functionality for per-atom data in the nbnxm module
+ *
+ * \author Berk Hess <hess@kth.se>
+ * \ingroup module_nbnxm
+ * \inlibraryapi
+ */
+
#ifndef GMX_NBNXN_ATOMDATA_H
#define GMX_NBNXN_ATOMDATA_H
#include "gromacs/utility/bitmask.h"
#include "gromacs/utility/real.h"
-#include "gpu_types.h"
-
namespace gmx
{
class MDLogger;
}
+struct gmx_nbnxm_gpu_t;
struct nbnxn_atomdata_t;
struct nonbonded_verlet_t;
struct t_mdatoms;
enum class KernelType;
} // namespace Nbnxm
-/* Convenience type for vector with aligned memory */
+//! Convenience type for vector with aligned memory
template<typename T>
using AlignedVector = std::vector<T, gmx::AlignedAllocator<T>>;
AlignedVector<real> VSc; // Temporary SIMD Coulomb group energy storage
};
-/* Block size in atoms for the non-bonded thread force-buffer reduction,
- * should be a multiple of all cell and x86 SIMD sizes (i.e. 2, 4 and 8).
+/*! \brief Block size in atoms for the non-bonded thread force-buffer reduction.
+ *
+ * Should be a multiple of all cell and x86 SIMD sizes (i.e. 2, 4 and 8).
* Should be small to reduce the reduction and zeroing cost,
* but too small will result in overhead.
* Currently the block size is NBNXN_BUFFERFLAG_SIZE*3*sizeof(real)=192 bytes.
# define NBNXN_BUFFERFLAG_SIZE 16
#endif
-/* We store the reduction flags as gmx_bitmask_t.
+/*! \brief We store the reduction flags as gmx_bitmask_t.
* This limits the number of flags to BITMASK_SIZE.
*/
#define NBNXN_BUFFERFLAG_MAX_THREADS (BITMASK_SIZE)
-/* Flags for telling if threads write to force output buffers */
+/*! \internal
+ * \brief Flags for telling if threads write to force output buffers */
typedef struct
{
- int nflag; /* The number of flag blocks */
- gmx_bitmask_t* flag; /* Bit i is set when thread i writes to a cell-block */
- int flag_nalloc; /* Allocation size of cxy_flag */
+ //! The number of flag blocks
+ int nflag;
+ //! Bit i is set when thread i writes to a cell-block
+ gmx_bitmask_t* flag;
+ //! Allocation size of cxy_flag
+ int flag_nalloc;
} nbnxn_buffer_flags_t;
-/* LJ combination rules: geometric, Lorentz-Berthelot, none */
+/*! \brief LJ combination rules: geometric, Lorentz-Berthelot, none */
enum
{
ljcrGEOM,
ljcrNR
};
-/* Struct that stores atom related data for the nbnxn module
+/*! \internal
+ * \brief Struct that stores atom related data for the nbnxn module
*
* Note: performance would improve slightly when all std::vector containers
* in this struct would not initialize during resize().
gmx::HostVector<int> energrp;
};
- // Diagonal and topology exclusion helper data for all SIMD kernels
+ /*! \internal
+ * \brief Diagonal and topology exclusion helper data for all SIMD kernels. */
struct SimdMasks
{
SimdMasks();
- // Helper data for setting up diagonal exclusion masks in the SIMD 4xN kernels
+ //! Helper data for setting up diagonal exclusion masks in the SIMD 4xN kernels
AlignedVector<real> diagonal_4xn_j_minus_i;
- // Helper data for setting up diaginal exclusion masks in the SIMD 2xNN kernels
+ //! Helper data for setting up diaginal exclusion masks in the SIMD 2xNN kernels
AlignedVector<real> diagonal_2xnn_j_minus_i;
- // Filters for topology exclusion masks for the SIMD kernels
+ //! Filters for topology exclusion masks for the SIMD kernels
AlignedVector<uint32_t> exclusion_filter;
- // Filters for topology exclusion masks for double SIMD kernels without SIMD int32 logical support
+ //! Filters for topology exclusion masks for double SIMD kernels without SIMD int32 logical support
AlignedVector<uint64_t> exclusion_filter64;
- // Array of masks needed for exclusions
+ //! Array of masks needed for exclusions
AlignedVector<real> interaction_array;
};
- /* Constructor
+ /*! \brief Constructor
*
* \param[in] pinningPolicy Sets the pinning policy for all data that might be transfered to a GPU
*/
nbnxn_atomdata_t(gmx::PinningPolicy pinningPolicy);
- /* Returns a const reference to the parameters */
+ //! Returns a const reference to the parameters
const Params& params() const { return params_; }
- /* Returns a non-const reference to the parameters */
+ //! Returns a non-const reference to the parameters
Params& paramsDeprecated() { return params_; }
- /* Returns the current total number of atoms stored */
+ //! Returns the current total number of atoms stored
int numAtoms() const { return numAtoms_; }
- /* Return the coordinate buffer, and q with xFormat==nbatXYZQ */
+ //! Return the coordinate buffer, and q with xFormat==nbatXYZQ
gmx::ArrayRef<const real> x() const { return x_; }
- /* Return the coordinate buffer, and q with xFormat==nbatXYZQ */
+ //! Return the coordinate buffer, and q with xFormat==nbatXYZQ
gmx::ArrayRef<real> x() { return x_; }
- /* Resizes the coordinate buffer and sets the number of atoms */
+ //! Resizes the coordinate buffer and sets the number of atoms
void resizeCoordinateBuffer(int numAtoms);
- /* Resizes the force buffers for the current number of atoms */
+ //! Resizes the force buffers for the current number of atoms
void resizeForceBuffers();
private:
- // The LJ and charge parameters
+ //! The LJ and charge parameters
Params params_;
- // The total number of atoms currently stored
+ //! The total number of atoms currently stored
int numAtoms_;
public:
- int natoms_local; /* Number of local atoms */
- int XFormat; /* The format of x (and q), enum */
- int FFormat; /* The format of f, enum */
- gmx_bool bDynamicBox; /* Do we need to update shift_vec every step? */
- gmx::HostVector<gmx::RVec> shift_vec; /* Shift vectors, copied from t_forcerec */
- int xstride; /* stride for a coordinate in x (usually 3 or 4) */
- int fstride; /* stride for a coordinate in f (usually 3 or 4) */
+ //! Number of local atoms
+ int natoms_local;
+ //! The format of x (and q), enum
+ int XFormat;
+ //! The format of f, enum
+ int FFormat;
+ //! Do we need to update shift_vec every step?
+ gmx_bool bDynamicBox;
+ //! Shift vectors, copied from t_forcerec
+ gmx::HostVector<gmx::RVec> shift_vec;
+ //! stride for a coordinate in x (usually 3 or 4)
+ int xstride;
+ //! stride for a coordinate in f (usually 3 or 4)
+ int fstride;
+
private:
- gmx::HostVector<real> x_; /* x and possibly q, size natoms*xstride */
+ //! x and possibly q, size natoms*xstride
+ gmx::HostVector<real> x_;
public:
- // Masks for handling exclusions in the SIMD kernels
+ //! Masks for handling exclusions in the SIMD kernels
const SimdMasks simdMasks;
- /* Output data */
- std::vector<nbnxn_atomdata_output_t> out; /* Output data structures, 1 per thread */
-
- /* Reduction related data */
- gmx_bool bUseBufferFlags; /* Use the flags or operate on all atoms */
- nbnxn_buffer_flags_t buffer_flags; /* Flags for buffer zeroing+reduc. */
- gmx_bool bUseTreeReduce; /* Use tree for force reduction */
- tMPI_Atomic* syncStep; /* Synchronization step for tree reduce */
+ //! Output data structures, 1 per thread
+ std::vector<nbnxn_atomdata_output_t> out;
+
+ //! Reduction related data
+ //! \{
+ //! Use the flags or operate on all atoms
+ gmx_bool bUseBufferFlags;
+ //! Flags for buffer zeroing+reduc.
+ nbnxn_buffer_flags_t buffer_flags;
+ //! Use tree for force reduction
+ gmx_bool bUseTreeReduce;
+ //! Synchronization step for tree reduce
+ tMPI_Atomic* syncStep;
+ //! \}
};
-/* Copy na rvec elements from x to xnb using nbatFormat, start dest a0,
+/*! \brief Copy na rvec elements from x to xnb using nbatFormat, start dest a0,
* and fills up to na_round with coordinates that are far away.
*/
void copy_rvec_to_nbat_real(const int* a, int na, int na_round, const rvec* x, int nbatFormat, real* xnb, int a0);
+//! Describes the combination rule in use by this force field
enum
{
enbnxninitcombruleDETECT,
enbnxninitcombruleNONE
};
-/* Initialize the non-bonded atom data structure.
+/*! \brief Initialize the non-bonded atom data structure.
+ *
* The enum for nbatXFormat is in the file defining nbnxn_atomdata_t.
* Copy the ntypes*ntypes*2 sized nbfp non-bonded parameter list
* to the atom data structure.
int n_energygroups,
int nout);
+//! Sets the atomdata after pair search
void nbnxn_atomdata_set(nbnxn_atomdata_t* nbat,
const Nbnxm::GridSet& gridSet,
const t_mdatoms* mdatoms,
const int* atinfo);
-/* Copy the shift vectors to nbat */
+//! Copy the shift vectors to nbat
void nbnxn_atomdata_copy_shiftvec(gmx_bool dynamic_box, rvec* shift_vec, nbnxn_atomdata_t* nbat);
/*! \brief Transform coordinates to xbat layout
void nbnxn_atomdata_x_to_nbat_x_gpu(const Nbnxm::GridSet& gridSet,
gmx::AtomLocality locality,
bool fillLocal,
- gmx_nbnxn_gpu_t* gpu_nbv,
+ gmx_nbnxm_gpu_t* gpu_nbv,
DeviceBuffer<float> d_x,
GpuEventSynchronizer* xReadyOnDevice);
const Nbnxm::GridSet& gridSet,
void* pmeForcesDevice,
gmx::ArrayRef<GpuEventSynchronizer* const> dependencyList,
- gmx_nbnxn_gpu_t* gpu_nbv,
+ gmx_nbnxm_gpu_t* gpu_nbv,
bool useGpuFPmeReduction,
bool accumulateForce);
-/* Add the fshift force stored in nbat to fshift */
+//! Add the fshift force stored in nbat to fshift
void nbnxn_atomdata_add_nbat_fshift_to_fshift(const nbnxn_atomdata_t& nbat, gmx::ArrayRef<gmx::RVec> fshift);
-/* Get the atom start index and number of atoms for a given locality */
+//! Get the atom start index and number of atoms for a given locality
void nbnxn_get_atom_range(gmx::AtomLocality atomLocality,
const Nbnxm::GridSet& gridSet,
int* atomStart,
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff