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36 #ifndef _nbnxn_search_h
37 #define _nbnxn_search_h
45 /* Returns the j-cluster size for kernel of type nb_kernel_type */
46 int nbnxn_kernel_to_cj_size(int nb_kernel_type);
48 /* Tells if the pair-list corresponding to nb_kernel_type is simple.
49 * Returns FALSE for super-sub type pair-list.
51 gmx_bool nbnxn_kernel_pairlist_simple(int nb_kernel_type);
53 /* Due to the cluster size the effective pair-list is longer than
54 * that of a simple atom pair-list. This function gives the extra distance.
56 real nbnxn_get_rlist_effective_inc(int cluster_size, real atom_density);
58 /* Allocates and initializes a pair search data structure */
59 void nbnxn_init_search(nbnxn_search_t * nbs_ptr,
61 gmx_domdec_zones_t *zones,
65 /* Put the atoms on the pair search grid.
66 * Only atoms a0 to a1 in x are put on the grid.
67 * The atom_density is used to determine the grid size.
68 * When atom_density<=0, the density is determined from a1-a0 and the corners.
69 * With domain decomposition part of the n particles might have migrated,
70 * but have not been removed yet. This count is given by nmoved.
71 * When move[i] < 0 particle i has migrated and will not be put on the grid.
72 * Without domain decomposition move will be NULL.
74 void nbnxn_put_on_grid(nbnxn_search_t nbs,
77 rvec corner0, rvec corner1,
82 int nmoved, int *move,
84 nbnxn_atomdata_t *nbat);
86 /* As nbnxn_put_on_grid, but for the non-local atoms
87 * with domain decomposition. Should be called after calling
88 * nbnxn_search_put_on_grid for the local atoms / home zone.
90 void nbnxn_put_on_grid_nonlocal(nbnxn_search_t nbs,
91 const gmx_domdec_zones_t *zones,
95 nbnxn_atomdata_t *nbat);
97 /* Add simple grid type information to the local super/sub grid */
98 void nbnxn_grid_add_simple(nbnxn_search_t nbs,
99 nbnxn_atomdata_t *nbat);
101 /* Return the number of x and y cells in the local grid */
102 void nbnxn_get_ncells(nbnxn_search_t nbs, int *ncx, int *ncy);
104 /* Return the order indices *a of the atoms on the ns grid, size n */
105 void nbnxn_get_atomorder(nbnxn_search_t nbs, int **a, int *n);
107 /* Renumber the atom indices on the grid to consecutive order */
108 void nbnxn_set_atomorder(nbnxn_search_t nbs);
110 /* Initializes a set of pair lists stored in nbnxn_pairlist_set_t */
111 void nbnxn_init_pairlist_set(nbnxn_pairlist_set_t *nbl_list,
112 gmx_bool simple, gmx_bool combined,
113 nbnxn_alloc_t *alloc,
116 /* Make a apir-list with radius rlist, store it in nbl.
117 * The parameter min_ci_balanced sets the minimum required
118 * number or roughly equally sized ci blocks in nbl.
119 * When set >0 ci lists will be chopped up when the estimate
120 * for the number of equally sized lists is below min_ci_balanced.
121 * With perturbed particles, also a group scheme style nbl_fep list is made.
123 void nbnxn_make_pairlist(const nbnxn_search_t nbs,
124 nbnxn_atomdata_t *nbat,
125 const t_blocka *excl,
128 nbnxn_pairlist_set_t *nbl_list,