src/gromacs/mdlib/nbnxn_grid.h

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  35
  36 #ifndef _nbnxn_grid_h
  37 #define _nbnxn_grid_h
  38
  39 #include "gromacs/math/vectypes.h"
  40 #include "gromacs/mdlib/nbnxn_consts.h"
  41 #include "gromacs/mdlib/nbnxn_internal.h"
  42 #include "gromacs/utility/real.h"
  43
  44 struct gmx_domdec_zones_t;
  45
  46 /* Allocate and initialize ngrid pair search grids in nbs */
  47 void nbnxn_grids_init(nbnxn_search_t nbs, int ngrid);
  48
  49 /* Put the atoms on the pair search grid.
  50  * Only atoms a0 to a1 in x are put on the grid.
  51  * The atom_density is used to determine the grid size.
  52  * When atom_density<=0, the density is determined from a1-a0 and the corners.
  53  * With domain decomposition part of the n particles might have migrated,
  54  * but have not been removed yet. This count is given by nmoved.
  55  * When move[i] < 0 particle i has migrated and will not be put on the grid.
  56  * Without domain decomposition move will be NULL.
  57  */
  58 void nbnxn_put_on_grid(nbnxn_search_t nbs,
  59                        int ePBC, matrix box,
  60                        int dd_zone,
  61                        rvec corner0, rvec corner1,
  62                        int a0, int a1,
  63                        real atom_density,
  64                        const int *atinfo,
  65                        rvec *x,
  66                        int nmoved, int *move,
  67                        int nb_kernel_type,
  68                        nbnxn_atomdata_t *nbat);
  69
  70 /* As nbnxn_put_on_grid, but for the non-local atoms
  71  * with domain decomposition. Should be called after calling
  72  * nbnxn_search_put_on_grid for the local atoms / home zone.
  73  */
  74 void nbnxn_put_on_grid_nonlocal(nbnxn_search_t                   nbs,
  75                                 const struct gmx_domdec_zones_t *zones,
  76                                 const int                       *atinfo,
  77                                 rvec                            *x,
  78                                 int                              nb_kernel_type,
  79                                 nbnxn_atomdata_t                *nbat);
  80
  81 /* Add simple grid type information to the local super/sub grid */
  82 void nbnxn_grid_add_simple(nbnxn_search_t    nbs,
  83                            nbnxn_atomdata_t *nbat);
  84
  85 /* Return the number of x and y cells in the local grid */
  86 void nbnxn_get_ncells(nbnxn_search_t nbs, int *ncx, int *ncy);
  87
  88 /* Return the order indices *a of the atoms on the ns grid, size n */
  89 void nbnxn_get_atomorder(const nbnxn_search_t nbs, const int **a, int *n);
  90
  91 /* Renumber the atom indices on the grid to consecutive order */
  92 void nbnxn_set_atomorder(nbnxn_search_t nbs);
  93
  94 #endif