src/gromacs/mdlib/nbnxn_search.h

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  35
  36 #ifndef GMX_MDLIB_NBNXN_SEARCH_H
  37 #define GMX_MDLIB_NBNXN_SEARCH_H
  38
  39 #include "gromacs/mdlib/nbnxn_pairlist.h"
  40
  41 struct gmx_domdec_zones_t;
  42 struct gmx_groups_t;
  43 struct t_blocka;
  44 struct t_nrnb;
  45
  46 /* Tells if the pair-list corresponding to nb_kernel_type is simple.
  47  * Returns FALSE for super-sub type pair-list.
  48  */
  49 gmx_bool nbnxn_kernel_pairlist_simple(int nb_kernel_type);
  50
  51 /* Due to the cluster size the effective pair-list is longer than
  52  * that of a simple atom pair-list. This function gives the extra distance.
  53  */
  54 real nbnxn_get_rlist_effective_inc(int cluster_size, real atom_density);
  55
  56 /* Allocates and initializes a pair search data structure */
  57 void nbnxn_init_search(nbnxn_search_t           * nbs_ptr,
  58                        ivec                      *n_dd_cells,
  59                        struct gmx_domdec_zones_t *zones,
  60                        gmx_bool                   bFEP,
  61                        int                        nthread_max);
  62
  63 /* Initializes a set of pair lists stored in nbnxn_pairlist_set_t */
  64 void nbnxn_init_pairlist_set(nbnxn_pairlist_set_t *nbl_list,
  65                              gmx_bool simple, gmx_bool combined,
  66                              nbnxn_alloc_t *alloc,
  67                              nbnxn_free_t  *free);
  68
  69 /* Make a apir-list with radius rlist, store it in nbl.
  70  * The parameter min_ci_balanced sets the minimum required
  71  * number or roughly equally sized ci blocks in nbl.
  72  * When set >0 ci lists will be chopped up when the estimate
  73  * for the number of equally sized lists is below min_ci_balanced.
  74  * With perturbed particles, also a group scheme style nbl_fep list is made.
  75  */
  76 void nbnxn_make_pairlist(const nbnxn_search_t  nbs,
  77                          nbnxn_atomdata_t     *nbat,
  78                          const t_blocka       *excl,
  79                          real                  rlist,
  80                          int                   min_ci_balanced,
  81                          nbnxn_pairlist_set_t *nbl_list,
  82                          int                   iloc,
  83                          int                   nb_kernel_type,
  84                          t_nrnb               *nrnb);
  85
  86 #endif