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38 * \brief Declares internal nbnxm module details
40 * \author Berk Hess <hess@kth.se>
42 * \ingroup module_nbnxm
45 #ifndef GMX_NBNXM_INTERNAL_H
46 #define GMX_NBNXM_INTERNAL_H
51 #include "gromacs/domdec/domdec.h"
52 #include "gromacs/math/vectypes.h"
53 #include "gromacs/nbnxm/pairlist.h"
54 #include "gromacs/simd/simd.h"
55 #include "gromacs/timing/cyclecounter.h"
56 #include "gromacs/utility/alignedallocator.h"
57 #include "gromacs/utility/arrayref.h"
58 #include "gromacs/utility/real.h"
60 struct gmx_domdec_zones_t;
64 // TODO Document after refactoring
67 /* Strides for x/f with xyz and xyzq coordinate (and charge) storage */
70 /* Size of packs of x, y or z with SIMD packed coords/forces */
71 static const int c_packX4 = 4;
72 static const int c_packX8 = 8;
73 /* Strides for a pack of 4 and 8 coordinates/forces */
74 #define STRIDE_P4 (DIM*c_packX4)
75 #define STRIDE_P8 (DIM*c_packX8)
77 /* Returns the index in a coordinate array corresponding to atom a */
78 template<int packSize> static inline int atom_to_x_index(int a)
80 return DIM*(a & ~(packSize - 1)) + (a & (packSize - 1));
85 /* Memory alignment in bytes as required by SIMD aligned loads/stores */
86 #define NBNXN_MEM_ALIGN (GMX_SIMD_REAL_WIDTH*sizeof(real))
88 /* No alignment required, but set it so we can call the same routines */
89 #define NBNXN_MEM_ALIGN 32
95 /*! \brief Convenience declaration for an std::vector with aligned memory */
97 using AlignedVector = std::vector < T, gmx::AlignedAllocator < T>>;
100 /* Local cycle count struct for profiling */
107 /* Local cycle count enum for profiling */
109 enbsCCgrid, enbsCCsearch, enbsCCcombine, enbsCCreducef, enbsCCnr
112 /* Thread-local work struct, contains part of nbnxn_grid_t */
113 struct nbnxn_search_work_t
115 nbnxn_search_work_t();
117 ~nbnxn_search_work_t();
119 gmx_cache_protect_t cp0; /* Buffer to avoid cache polution */
121 std::vector<int> cxy_na; /* Grid column atom counts temporary buffer */
123 std::vector<int> sortBuffer; /* Temporary buffer for sorting atoms within a grid column */
125 nbnxn_buffer_flags_t buffer_flags; /* Flags for force buffer access */
127 int ndistc; /* Number of distance checks for flop counting */
130 std::unique_ptr<t_nblist> nbl_fep; /* Temporary FEP list for load balancing */
132 nbnxn_cycle_t cc[enbsCCnr]; /* Counters for thread-local cycles */
134 gmx_cache_protect_t cp1; /* Buffer to avoid cache polution */
137 /* Main pair-search struct, contains the grid(s), not the pair-list(s) */
140 /* \brief Constructor
142 * \param[in] n_dd_cells The number of domain decomposition cells per dimension, without DD nullptr should be passed
143 * \param[in] zones The domain decomposition zone setup, without DD nullptr should be passed
144 * \param[in] bFEP Tells whether non-bonded interactions are perturbed
145 * \param[in] nthread_max The maximum number of threads used in the search
148 nbnxn_search(const ivec *n_dd_cells,
149 const gmx_domdec_zones_t *zones,
153 gmx_bool bFEP; /* Do we have perturbed atoms? */
154 int ePBC; /* PBC type enum */
155 matrix box; /* The periodic unit-cell */
157 gmx_bool DomDec; /* Are we doing domain decomposition? */
158 ivec dd_dim; /* Are we doing DD in x,y,z? */
159 const gmx_domdec_zones_t *zones; /* The domain decomposition zones */
161 std::vector<nbnxn_grid_t> grid; /* Array of grids, size ngrid */
162 std::vector<int> cell; /* Actual allocated cell array for all grids */
163 std::vector<int> a; /* Atom index for grid, the inverse of cell */
165 int natoms_local; /* The local atoms run from 0 to natoms_local */
166 int natoms_nonlocal; /* The non-local atoms run from natoms_local
167 * to natoms_nonlocal */
169 gmx_bool print_cycles;
171 nbnxn_cycle_t cc[enbsCCnr];
173 /* Thread-local work data */
174 mutable std::vector<nbnxn_search_work_t> work; /* Work array, one entry for each thread */
178 /*! \brief Start an nbnxn cycle counter */
179 static inline void nbs_cycle_start(nbnxn_cycle_t *cc)
181 cc->start = gmx_cycles_read();
184 /*! \brief Stop an nbnxn cycle counter */
185 static inline void nbs_cycle_stop(nbnxn_cycle_t *cc)
187 cc->c += gmx_cycles_read() - cc->start;