include/types/nbnxn_pairlist.h

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  35
  36 #ifndef _nbnxn_pairlist_h
  37 #define _nbnxn_pairlist_h
  38
  39 #ifdef __cplusplus
  40 extern "C" {
  41 #endif
  42
  43 /* A buffer data structure of 64 bytes
  44  * to be placed at the beginning and end of structs
  45  * to avoid cache invalidation of the real contents
  46  * of the struct by writes to neighboring memory.
  47  */
  48 typedef struct {
  49     int dummy[16];
  50 } gmx_cache_protect_t;
  51
  52 /* Abstract type for pair searching data */
  53 typedef struct nbnxn_search * nbnxn_search_t;
  54
  55 /* Function that should return a pointer *ptr to memory
  56  * of size nbytes.
  57  * Error handling should be done within this function.
  58  */
  59 typedef void gmx_nbat_alloc_t(void **ptr,size_t nbytes);
  60
  61 /* Function that should free the memory pointed to by *ptr.
  62  * NULL should not be passed to this function.
  63  */
  64 typedef void gmx_nbat_free_t(void *ptr);
  65
  66 typedef struct {
  67     int      cj;    /* The j-cluster                    */
  68     unsigned excl;  /* The exclusion (interaction) bits */
  69 } nbnxn_cj_t;
  70
  71 #define NBNXN_CI_SHIFT          127
  72 #define NBNXN_CI_DO_LJ(subc)    (1<<(7+3*(subc)))
  73 #define NBNXN_CI_HALF_LJ(subc)  (1<<(8+3*(subc)))
  74 #define NBNXN_CI_DO_COUL(subc)  (1<<(9+3*(subc)))
  75
  76 /* Simple pair-list i-unit */
  77 typedef struct {
  78     int ci;             /* i-cluster             */
  79     int shift;          /* Shift vector index plus possible flags */
  80     int cj_ind_start;   /* Start index into cj   */
  81     int cj_ind_end;     /* End index into cj     */
  82 } nbnxn_ci_t;
  83
  84 /* Grouped pair-list i-unit */
  85 typedef struct {
  86     int sci;            /* i-super-cluster       */
  87     int shift;          /* Shift vector index plus possible flags */
  88     int cj4_ind_start;  /* Start index into cj4  */
  89     int cj4_ind_end;    /* End index into cj4    */
  90 } nbnxn_sci_t;
  91
  92 typedef struct {
  93     unsigned imask;        /* The i-cluster interactions mask for 1 warp  */
  94     int excl_ind;          /* Index into the exclusion array for 1 warp   */
  95 } nbnxn_im_ei_t;
  96
  97 typedef struct {
  98     int cj[4];             /* The 4 j-clusters                            */
  99     nbnxn_im_ei_t imei[2]; /* The i-cluster mask data       for 2 warps   */
 100 } nbnxn_cj4_t;
 101
 102 typedef struct {
 103     unsigned pair[32];     /* Exclusion bits for one warp,                *
 104                             * each unsigned has bit for 4*8 i clusters    */
 105 } nbnxn_excl_t;
 106
 107 typedef struct {
 108     gmx_cache_protect_t cp0;
 109
 110     gmx_nbat_alloc_t *alloc;
 111     gmx_nbat_free_t  *free;
 112
 113     gmx_bool bSimple;      /* Simple list has na_sc=na_s and uses cj   *
 114                             * Complex list uses cj4                    */
 115
 116     int      na_ci;        /* The number of atoms per i-cluster        */
 117     int      na_cj;        /* The number of atoms per j-cluster        */
 118     int      na_sc;        /* The number of atoms per super cluster    */
 119     real     rlist;        /* The radius for constructing the list     */
 120     int      nci;          /* The number of i-clusters in the list     */
 121     nbnxn_ci_t *ci;        /* The i-cluster list, size nci             */
 122     int      ci_nalloc;    /* The allocation size of ci                */
 123     int      nsci;         /* The number of i-super-clusters in the list */
 124     nbnxn_sci_t *sci;      /* The i-super-cluster list                 */
 125     int      sci_nalloc;   /* The allocation size of sci               */
 126
 127     int      ncj;          /* The number of j-clusters in the list     */
 128     nbnxn_cj_t *cj;        /* The j-cluster list, size ncj             */
 129     int      cj_nalloc;    /* The allocation size of cj                */
 130
 131     int      ncj4;         /* The total number of 4*j clusters         */
 132     nbnxn_cj4_t *cj4;      /* The 4*j cluster list, size ncj4          */
 133     int      cj4_nalloc;   /* The allocation size of cj4               */
 134     int      nexcl;        /* The count for excl                       */
 135     nbnxn_excl_t *excl;    /* Atom interaction bits (non-exclusions)   */
 136     int      excl_nalloc;  /* The allocation size for excl             */
 137     int      nci_tot;      /* The total number of i clusters           */
 138
 139     struct nbnxn_list_work *work;
 140
 141     gmx_cache_protect_t cp1;
 142 } nbnxn_pairlist_t;
 143
 144 typedef struct {
 145     int          nnbl;      /* number of lists */
 146     nbnxn_pairlist_t **nbl; /* lists */
 147     gmx_bool     bCombined; /* TRUE if lists get combined into one (the 1st) */
 148     gmx_bool     bSimple;   /* TRUE if the list of of type "simple"
 149                                (na_sc=na_s, no super-clusters used) */
 150     int          natpair_ljq; /* Total number of atom pairs for LJ+Q kernel */
 151     int          natpair_lj;  /* Total number of atom pairs for LJ kernel   */
 152     int          natpair_q;   /* Total number of atom pairs for Q kernel    */
 153 } nbnxn_pairlist_set_t;
 154
 155 enum { nbatXYZ, nbatXYZQ, nbatX4, nbatX8 };
 156
 157 typedef struct {
 158     real *f;      /* f, size natoms*fstride                             */
 159     real *fshift; /* Shift force array, size SHIFTS*DIM                 */
 160     int  nV;      /* The size of *Vvdw and *Vc                          */
 161     real *Vvdw;   /* Temporary Van der Waals group energy storage       */
 162     real *Vc;     /* Temporary Coulomb group energy storage             */
 163     int  nVS;     /* The size of *VSvdw and *VSc                        */
 164     real *VSvdw;  /* Temporary SIMD Van der Waals group energy storage  */
 165     real *VSc;    /* Temporary SIMD Coulomb group energy storage        */
 166 } nbnxn_atomdata_output_t;
 167
 168 /* LJ combination rules: geometric, Lorentz-Berthelot, none */
 169 enum { ljcrGEOM, ljcrLB, ljcrNONE, ljcrNR };
 170
 171 typedef struct {
 172     gmx_nbat_alloc_t *alloc;
 173     gmx_nbat_free_t  *free;
 174     int  ntype;      /* The number of different atom types                 */
 175     real *nbfp;      /* Lennard-Jones 6*C6 and 12*C12 params, size ntype^2*2 */
 176     int  comb_rule;  /* Combination rule, see enum above                   */
 177     real *nbfp_comb; /* LJ parameter per atom type, size ntype*2           */
 178     real *nbfp_s4;   /* As nbfp, but with stride 4, size ntype^2*4         */
 179     int  natoms;     /* Number of atoms                                    */
 180     int  natoms_local;  /* Number of local atoms                           */
 181     int  *type;      /* Atom types                                         */
 182     real *lj_comb;   /* LJ parameters per atom for combining for pairs     */
 183     int  XFormat;    /* The format of x (and q), enum                      */
 184     int  FFormat;    /* The format of f, enum                              */
 185     real *q;         /* Charges, can be NULL if incorporated in x          */
 186     int  na_c;       /* The number of atoms per cluster                    */
 187     int  nenergrp;   /* The number of energy groups                        */
 188     int  neg_2log;   /* Log2 of nenergrp                                   */
 189     int  *energrp;   /* The energy groups per cluster, can be NULL         */
 190     gmx_bool bDynamicBox; /* Do we need to update shift_vec every step?    */
 191     rvec *shift_vec; /* Shift vectors, copied from t_forcerec              */
 192     int  xstride;    /* stride for a coordinate in x (usually 3 or 4)      */
 193     int  fstride;    /* stride for a coordinate in f (usually 3 or 4)      */
 194     real *x;         /* x and possibly q, size natoms*xstride              */
 195     int  nout;       /* The number of force arrays                         */
 196     nbnxn_atomdata_output_t *out;  /* Output data structures               */
 197     int  nalloc;     /* Allocation size of all arrays (for x/f *x/fstride) */
 198 } nbnxn_atomdata_t;
 199
 200 #ifdef __cplusplus
 201 }
 202 #endif
 203
 204 #endif