src/gromacs/mdlib/nbnxn_pairlist.h

   1 /*
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  35
  36 #ifndef _nbnxn_pairlist_h
  37 #define _nbnxn_pairlist_h
  38
  39 #include <cstddef>
  40
  41 #include "thread_mpi/atomic.h"
  42
  43 #include "gromacs/math/vectypes.h"
  44 #include "gromacs/mdtypes/nblist.h"
  45 #include "gromacs/utility/basedefinitions.h"
  46 #include "gromacs/utility/bitmask.h"
  47 #include "gromacs/utility/real.h"
  48
  49 /* A buffer data structure of 64 bytes
  50  * to be placed at the beginning and end of structs
  51  * to avoid cache invalidation of the real contents
  52  * of the struct by writes to neighboring memory.
  53  */
  54 typedef struct {
  55     int dummy[16];
  56 } gmx_cache_protect_t;
  57
  58 /* Abstract type for pair searching data */
  59 typedef struct nbnxn_search * nbnxn_search_t;
  60
  61 /* Function that should return a pointer *ptr to memory
  62  * of size nbytes.
  63  * Error handling should be done within this function.
  64  */
  65 typedef void nbnxn_alloc_t (void **ptr, size_t nbytes);
  66
  67 /* Function that should free the memory pointed to by *ptr.
  68  * NULL should not be passed to this function.
  69  */
  70 typedef void nbnxn_free_t (void *ptr);
  71
  72 /* This is the actual cluster-pair list j-entry.
  73  * cj is the j-cluster.
  74  * The interaction bits in excl are indexed i-major, j-minor.
  75  * The cj entries are sorted such that ones with exclusions come first.
  76  * This means that once a full mask (=NBNXN_INTERACTION_MASK_ALL)
  77  * is found, all subsequent j-entries in the i-entry also have full masks.
  78  */
  79 typedef struct {
  80     int          cj;    /* The j-cluster                    */
  81     unsigned int excl;  /* The exclusion (interaction) bits */
  82 } nbnxn_cj_t;
  83
  84 /* In nbnxn_ci_t the integer shift contains the shift in the lower 7 bits.
  85  * The upper bits contain information for non-bonded kernel optimization.
  86  * Simply calculating LJ and Coulomb for all pairs in a cluster pair is fine.
  87  * But three flags can be used to skip interactions, currently only for subc=0
  88  * !(shift & NBNXN_CI_DO_LJ(subc))   => we can skip LJ for all pairs
  89  * shift & NBNXN_CI_HALF_LJ(subc)    => we can skip LJ for the second half of i
  90  * !(shift & NBNXN_CI_DO_COUL(subc)) => we can skip Coulomb for all pairs
  91  */
  92 #define NBNXN_CI_SHIFT          127
  93 #define NBNXN_CI_DO_LJ(subc)    (1<<(7+3*(subc)))
  94 #define NBNXN_CI_HALF_LJ(subc)  (1<<(8+3*(subc)))
  95 #define NBNXN_CI_DO_COUL(subc)  (1<<(9+3*(subc)))
  96
  97 /* Simple pair-list i-unit */
  98 typedef struct {
  99     int ci;             /* i-cluster             */
 100     int shift;          /* Shift vector index plus possible flags, see above */
 101     int cj_ind_start;   /* Start index into cj   */
 102     int cj_ind_end;     /* End index into cj     */
 103 } nbnxn_ci_t;
 104
 105 /* Grouped pair-list i-unit */
 106 typedef struct {
 107     int sci;            /* i-super-cluster       */
 108     int shift;          /* Shift vector index plus possible flags */
 109     int cj4_ind_start;  /* Start index into cj4  */
 110     int cj4_ind_end;    /* End index into cj4    */
 111 } nbnxn_sci_t;
 112
 113 typedef struct {
 114     unsigned int imask;    /* The i-cluster interactions mask for 1 warp  */
 115     int          excl_ind; /* Index into the exclusion array for 1 warp   */
 116 } nbnxn_im_ei_t;
 117
 118 typedef struct {
 119     int           cj[4];   /* The 4 j-clusters                            */
 120     nbnxn_im_ei_t imei[2]; /* The i-cluster mask data       for 2 warps   */
 121 } nbnxn_cj4_t;
 122
 123 typedef struct {
 124     unsigned int pair[32]; /* Topology exclusion interaction bits for one warp,
 125                             * each unsigned has bitS for 4*8 i clusters
 126                             */
 127 } nbnxn_excl_t;
 128
 129 typedef struct nbnxn_pairlist_t {
 130     gmx_cache_protect_t cp0;
 131
 132     nbnxn_alloc_t      *alloc;
 133     nbnxn_free_t       *free;
 134
 135     gmx_bool            bSimple;         /* Simple list has na_sc=na_s and uses cj   *
 136                                           * Complex list uses cj4                    */
 137
 138     int                     na_ci;       /* The number of atoms per i-cluster        */
 139     int                     na_cj;       /* The number of atoms per j-cluster        */
 140     int                     na_sc;       /* The number of atoms per super cluster    */
 141     real                    rlist;       /* The radius for constructing the list     */
 142     int                     nci;         /* The number of i-clusters in the list     */
 143     nbnxn_ci_t             *ci;          /* The i-cluster list, size nci             */
 144     int                     ci_nalloc;   /* The allocation size of ci                */
 145     int                     nsci;        /* The number of i-super-clusters in the list */
 146     nbnxn_sci_t            *sci;         /* The i-super-cluster list                 */
 147     int                     sci_nalloc;  /* The allocation size of sci               */
 148
 149     int                     ncj;         /* The number of j-clusters in the list     */
 150     nbnxn_cj_t             *cj;          /* The j-cluster list, size ncj             */
 151     int                     cj_nalloc;   /* The allocation size of cj                */
 152
 153     int                     ncj4;        /* The total number of 4*j clusters         */
 154     nbnxn_cj4_t            *cj4;         /* The 4*j cluster list, size ncj4          */
 155     int                     cj4_nalloc;  /* The allocation size of cj4               */
 156     int                     nexcl;       /* The count for excl                       */
 157     nbnxn_excl_t           *excl;        /* Atom interaction bits (non-exclusions)   */
 158     int                     excl_nalloc; /* The allocation size for excl             */
 159     int                     nci_tot;     /* The total number of i clusters           */
 160
 161     struct nbnxn_list_work *work;
 162
 163     gmx_cache_protect_t     cp1;
 164 } nbnxn_pairlist_t;
 165
 166 typedef struct {
 167     int                nnbl;        /* number of lists */
 168     nbnxn_pairlist_t **nbl;         /* lists */
 169     gmx_bool           bCombined;   /* TRUE if lists get combined into one (the 1st) */
 170     gmx_bool           bSimple;     /* TRUE if the list of of type "simple"
 171                                        (na_sc=na_s, no super-clusters used) */
 172     int                natpair_ljq; /* Total number of atom pairs for LJ+Q kernel */
 173     int                natpair_lj;  /* Total number of atom pairs for LJ kernel   */
 174     int                natpair_q;   /* Total number of atom pairs for Q kernel    */
 175     t_nblist         **nbl_fep;
 176 } nbnxn_pairlist_set_t;
 177
 178 enum {
 179     nbatXYZ, nbatXYZQ, nbatX4, nbatX8
 180 };
 181
 182 typedef struct {
 183     real *f;      /* f, size natoms*fstride                             */
 184     real *fshift; /* Shift force array, size SHIFTS*DIM                 */
 185     int   nV;     /* The size of *Vvdw and *Vc                          */
 186     real *Vvdw;   /* Temporary Van der Waals group energy storage       */
 187     real *Vc;     /* Temporary Coulomb group energy storage             */
 188     int   nVS;    /* The size of *VSvdw and *VSc                        */
 189     real *VSvdw;  /* Temporary SIMD Van der Waals group energy storage  */
 190     real *VSc;    /* Temporary SIMD Coulomb group energy storage        */
 191 } nbnxn_atomdata_output_t;
 192
 193 /* Block size in atoms for the non-bonded thread force-buffer reduction,
 194  * should be a multiple of all cell and x86 SIMD sizes (i.e. 2, 4 and 8).
 195  * Should be small to reduce the reduction and zeroing cost,
 196  * but too small will result in overhead.
 197  * Currently the block size is NBNXN_BUFFERFLAG_SIZE*3*sizeof(real)=192 bytes.
 198  */
 199 #ifdef GMX_DOUBLE
 200 #define NBNXN_BUFFERFLAG_SIZE   8
 201 #else
 202 #define NBNXN_BUFFERFLAG_SIZE  16
 203 #endif
 204
 205 /* We store the reduction flags as gmx_bitmask_t.
 206  * This limits the number of flags to BITMASK_SIZE.
 207  */
 208 #define NBNXN_BUFFERFLAG_MAX_THREADS  (BITMASK_SIZE)
 209
 210 /* Flags for telling if threads write to force output buffers */
 211 typedef struct {
 212     int               nflag;       /* The number of flag blocks                         */
 213     gmx_bitmask_t    *flag;        /* Bit i is set when thread i writes to a cell-block */
 214     int               flag_nalloc; /* Allocation size of cxy_flag                       */
 215 } nbnxn_buffer_flags_t;
 216
 217 /* LJ combination rules: geometric, Lorentz-Berthelot, none */
 218 enum {
 219     ljcrGEOM, ljcrLB, ljcrNONE, ljcrNR
 220 };
 221
 222 typedef struct nbnxn_atomdata_t {
 223     nbnxn_alloc_t           *alloc;
 224     nbnxn_free_t            *free;
 225     int                      ntype;           /* The number of different atom types                 */
 226     real                    *nbfp;            /* Lennard-Jones 6*C6 and 12*C12 params, size ntype^2*2 */
 227     int                      comb_rule;       /* Combination rule, see enum above                   */
 228     real                    *nbfp_comb;       /* LJ parameter per atom type, size ntype*2           */
 229     real                    *nbfp_aligned;    /* As nbfp, but with an alignment (stride) suitable
 230                                                * for the present SIMD architectures
 231                                                */
 232     int                      natoms;          /* Number of atoms                                    */
 233     int                      natoms_local;    /* Number of local atoms                           */
 234     int                     *type;            /* Atom types                                         */
 235     real                    *lj_comb;         /* LJ parameters per atom for combining for pairs     */
 236     int                      XFormat;         /* The format of x (and q), enum                      */
 237     int                      FFormat;         /* The format of f, enum                              */
 238     real                    *q;               /* Charges, can be NULL if incorporated in x          */
 239     int                      na_c;            /* The number of atoms per cluster                    */
 240     int                      nenergrp;        /* The number of energy groups                        */
 241     int                      neg_2log;        /* Log2 of nenergrp                                   */
 242     int                     *energrp;         /* The energy groups per cluster, can be NULL         */
 243     gmx_bool                 bDynamicBox;     /* Do we need to update shift_vec every step?    */
 244     rvec                    *shift_vec;       /* Shift vectors, copied from t_forcerec              */
 245     int                      xstride;         /* stride for a coordinate in x (usually 3 or 4)      */
 246     int                      fstride;         /* stride for a coordinate in f (usually 3 or 4)      */
 247     real                    *x;               /* x and possibly q, size natoms*xstride              */
 248
 249     /* j-atom minus i-atom index for generating self and Newton exclusions
 250      * cluster-cluster pairs of the diagonal, for 4xn and 2xnn kernels.
 251      */
 252     real                    *simd_4xn_diagonal_j_minus_i;
 253     real                    *simd_2xnn_diagonal_j_minus_i;
 254     /* Filters for topology exclusion masks for the SIMD kernels. */
 255     gmx_uint32_t            *simd_exclusion_filter;
 256     gmx_uint64_t            *simd_exclusion_filter64; //!< Used for double w/o SIMD int32 logical support
 257     real                    *simd_interaction_array;  /* Array of masks needed for exclusions */
 258     int                      nout;                    /* The number of force arrays                         */
 259     nbnxn_atomdata_output_t *out;                     /* Output data structures               */
 260     int                      nalloc;                  /* Allocation size of all arrays (for x/f *x/fstride) */
 261     gmx_bool                 bUseBufferFlags;         /* Use the flags or operate on all atoms     */
 262     nbnxn_buffer_flags_t     buffer_flags;            /* Flags for buffer zeroing+reduc.  */
 263     gmx_bool                 bUseTreeReduce;          /* Use tree for force reduction */
 264     tMPI_Atomic_t           *syncStep;                /* Synchronization step for tree reduce */
 265 } nbnxn_atomdata_t;
 266
 267 #endif