src/gromacs/mdlib/nsgrid.h

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  37 #ifndef GMX_MDLIB_NSGRID_H
  38 #define GMX_MDLIB_NSGRID_H
  39
  40 #include <cstdio>
  41
  42 #include "gromacs/math/vectypes.h"
  43 #include "gromacs/utility/real.h"
  44
  45 struct gmx_domdec_t;
  46 struct gmx_domdec_zones_t;
  47 struct gmx_ddbox_t;
  48 struct t_forcerec;
  49 struct t_grid;
  50
  51 typedef struct t_grid {
  52     int     nr;           // Total number of charge groups
  53     int     nboundeddim;  // The number of bounded dimensions
  54     int     npbcdim;      // The number of dimensions with pbc
  55     int     ncg_ideal;    // The ideal number of cg's per cell
  56     ivec    n;            // The dimension of the grid
  57     int     ncells;       // Total number of cells
  58     int     cells_nalloc; // Allocation size of index and nra
  59     ivec    ncpddc;       // The number of cells per DD cell
  60     rvec    cell_size;    // The size of the cells
  61     rvec    cell_offset;  // The offset of the cell (0,0,0)
  62     int    *cell_index;   // The cell number of each cg
  63     int    *index;        // The index into a for each cell
  64                           // The location of the cell in the index
  65                           // array can be found by calling xyz2ci
  66     int    *nra;          // The number of entries in a cell
  67     int     icg0;         // The start of the i-cg range
  68     int     icg1;         // The end of the i-cg range
  69     rvec   *os0;
  70     rvec   *os1;
  71     int    *a;            // The grid of cgs
  72     int     nr_alloc;     // Allocation size of cell_index and a
  73     real   *dcx2;         // Squared distance from atom to j-cell
  74     real   *dcy2;         // Squared distance from atom to j-cell
  75     real   *dcz2;         // Squared distance from atom to j-cell
  76     int     dc_nalloc;    // Allocation size of dcx2, dyc2, dcz2
  77 } t_grid;
  78
  79 /*! \brief Used when estimating the interaction density.
  80  *
  81  * GRID_STDDEV_FAC * stddev estimates the interaction density. The
  82  * value sqrt(3) == 1.73205080757 gives a uniform load for a
  83  * rectangular 3D block of charge groups. For a sphere, it is not a
  84  * bad approximation for 4x1x1 up to 4x2x2.
  85  *
  86  * \todo It would be nicer to use sqrt(3) here, when all code that
  87  * includes this file is in C++, which will let us cope with the
  88  * std::sqrt<T> on Windows. */
  89 static const real GRID_STDDEV_FAC = 1.73205080757;
  90
  91 /*! \brief The extent of the neighborsearch grid is a bit larger than sqrt(3)
  92  * to account for less dense regions at the edges of the system.
  93  */
  94 static const real NSGRID_STDDEV_FAC = 2.0;
  95
  96 #define NSGRID_SIGNAL_MOVED_FAC  4
  97 /* A cell index of NSGRID_SIGNAL_MOVED_FAC*ncells signals
  98  * that a charge group moved to another DD domain.
  99  */
 100
 101 t_grid *init_grid(FILE *fplog, t_forcerec *fr);
 102
 103 void done_grid(t_grid *grid);
 104
 105 void get_nsgrid_boundaries(int nboundeddim, matrix box,
 106                            struct gmx_domdec_t *dd,
 107                            gmx_ddbox_t *ddbox,
 108                            rvec *gr0, rvec *gr1,
 109                            int ncg, rvec *cgcm,
 110                            rvec grid_x0, rvec grid_x1,
 111                            real *grid_density);
 112 /* Return the ns grid boundaries grid_x0 and grid_x1
 113  * and the estimate for the grid density.
 114  * For non-bounded dimensions the boundaries are determined
 115  * from the average and std.dev. of cgcm.
 116  * The are determined from box, unless gr0!=NULL or gr1!=NULL,
 117  * then they are taken from gr0 or gr1.
 118  * With dd and unbounded dimensions, the proper grid borders for cells
 119  * on the edges are determined from cgcm.
 120  */
 121
 122 void grid_first(FILE *log, t_grid *grid,
 123                 struct gmx_domdec_t *dd, const gmx_ddbox_t *ddbox, matrix box, rvec izones_x0, rvec izones_x1,
 124                 real rlong, real grid_density);
 125
 126 void fill_grid(struct gmx_domdec_zones_t *dd_zones,
 127                t_grid *grid, int ncg_tot,
 128                int cg0, int cg1, rvec cg_cm[]);
 129 /* Allocates space on the grid for ncg_tot cg's.
 130  * Fills the grid with cg's from cg0 to cg1.
 131  * When cg0 is -1, contiues filling from grid->nr to cg1.
 132  */
 133
 134 void calc_elemnr(t_grid *grid, int cg0, int cg1, int ncg);
 135
 136 void calc_ptrs(t_grid *grid);
 137
 138 void grid_last(t_grid *grid, int cg0, int cg1, int ncg);
 139
 140 int xyz2ci_(int nry, int nrz, int x, int y, int z);
 141 #define xyz2ci(nry, nrz, x, y, z) ((nry)*(nrz)*(x)+(nrz)*(y)+(z))
 142 /* Return the cell index */
 143
 144 void ci2xyz(t_grid *grid, int i, int *x, int *y, int *z);
 145
 146 void check_grid(t_grid *grid);
 147
 148 void print_grid(FILE *log, t_grid *grid);
 149
 150 #endif