include/nsgrid.h

   1 /*
   2  *
   3  *                This source code is part of
   4  *
   5  *                 G   R   O   M   A   C   S
   6  *
   7  *          GROningen MAchine for Chemical Simulations
   8  *
   9  *                        VERSION 3.2.0
  10  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  11  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  12  * Copyright (c) 2001-2004, The GROMACS development team,
  13  * check out http://www.gromacs.org for more information.
  14
  15  * This program is free software; you can redistribute it and/or
  16  * modify it under the terms of the GNU General Public License
  17  * as published by the Free Software Foundation; either version 2
  18  * of the License, or (at your option) any later version.
  19  *
  20  * If you want to redistribute modifications, please consider that
  21  * scientific software is very special. Version control is crucial -
  22  * bugs must be traceable. We will be happy to consider code for
  23  * inclusion in the official distribution, but derived work must not
  24  * be called official GROMACS. Details are found in the README & COPYING
  25  * files - if they are missing, get the official version at www.gromacs.org.
  26  *
  27  * To help us fund GROMACS development, we humbly ask that you cite
  28  * the papers on the package - you can find them in the top README file.
  29  *
  30  * For more info, check our website at http://www.gromacs.org
  31  *
  32  * And Hey:
  33  * Gromacs Runs On Most of All Computer Systems
  34  */
  35
  36 #ifdef HAVE_CONFIG_H
  37 #include <config.h>
  38 #endif
  39
  40 #include "typedefs.h"
  41
  42 #define   GRID_STDDEV_FAC  sqrt(3)
  43 #define NSGRID_STDDEV_FAC  2.0
  44 /*
  45  * GRID_STDDEV_FAC * stddev is used to estimate the interaction density.
  46  * sqrt(3) gives a uniform load for a rectangular block of cg's.
  47  * For a sphere it is not a bad approximation for 4x1x1 up to 4x2x2.
  48  *
  49  * The extent of the neighborsearch grid is a bit larger than sqrt(3)
  50  * to account for less dense regions at the edges of the system.
  51  */
  52
  53 extern t_grid *init_grid(FILE *fplog,t_forcerec *fr);
  54
  55 extern void done_grid(t_grid *grid);
  56
  57 extern void get_nsgrid_boundaries(t_grid *grid,
  58                                   gmx_domdec_t *dd,
  59                                   matrix box,gmx_ddbox_t *ddbox,
  60                                   rvec *gr0,rvec *gr1,
  61                                   int ncg,rvec *cgcm,
  62                                   rvec grid_x0,rvec grid_x1,
  63                                   real *grid_density);
  64 /* Return the ns grid boundaries grid_x0 and grid_x1
  65  * and the estimate for the grid density.
  66  * For non-bounded dimensions the boundaries are determined
  67  * from the average and std.dev. of cgcm.
  68  * The are determined from box, unless gr0!=NULL or gr1!=NULL,
  69  * then they are taken from gr0 or gr1.
  70  * With dd and unbounded dimensions, the proper grid borders for cells
  71  * on the edges are determined from cgcm.
  72  */
  73
  74 extern void grid_first(FILE *log,t_grid *grid,
  75                        gmx_domdec_t *dd,const gmx_ddbox_t *ddbox,
  76                        int ePBC,matrix box,rvec izones_x0,rvec izones_x1,
  77                        real rlong,real grid_density);
  78
  79 extern void fill_grid(FILE *log,
  80                       gmx_domdec_zones_t *dd_zones,
  81                       t_grid *grid,int ncg_tot,
  82                       int cg0,int cg1,rvec cg_cm[]);
  83 /* Allocates space on the grid for ncg_tot cg's.
  84  * Fills the grid with cg's from cg0 to cg1.
  85  * When cg0 is -1, contiues filling from grid->nr to cg1.
  86  */
  87
  88 extern void calc_elemnr(FILE *log,t_grid *grid,int cg0,int cg1,int ncg);
  89
  90 extern void calc_ptrs(t_grid *grid);
  91
  92 extern void grid_last(FILE *log,t_grid *grid,int cg0,int cg1,int ncg);
  93
  94 extern int xyz2ci_(int nry,int nrz,int x,int y,int z);
  95 #define xyz2ci(nry,nrz,x,y,z) ((nry)*(nrz)*(x)+(nrz)*(y)+(z))
  96 /* Return the cell index */
  97
  98 extern void ci2xyz(t_grid *grid,int i,int *x,int *y,int *z);
  99
 100 extern void check_grid(FILE *log,t_grid *grid);
 101
 102 extern void print_grid(FILE *log,t_grid *grid);
 103
 104 extern void mv_grid(t_commrec *cr,t_grid *grid);
 105 /* Move the grid over processors */
 106
 107