src/gromacs/domdec/dump.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2018,2019, by the GROMACS development team, led by
   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   6  * and including many others, as listed in the AUTHORS file in the
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  35 /*! \internal \file
  36  *
  37  * \brief This file definees functions for DD to write PDB files
  38  * e.g. when reporting problems.
  39  *
  40  * \author Berk Hess <hess@kth.se>
  41  * \ingroup module_domdec
  42  */
  43
  44 #include "gmxpre.h"
  45
  46 #include "dump.h"
  47
  48 #include "gromacs/domdec/domdec_network.h"
  49 #include "gromacs/fileio/gmxfio.h"
  50 #include "gromacs/fileio/pdbio.h"
  51 #include "gromacs/math/vec.h"
  52 #include "gromacs/mdtypes/commrec.h"
  53 #include "gromacs/pbcutil/pbc.h"
  54 #include "gromacs/topology/mtop_lookup.h"
  55 #include "gromacs/utility/cstringutil.h"
  56
  57 #include "domdec_internal.h"
  58
  59 void write_dd_grid_pdb(const char *fn, int64_t step,
  60                        gmx_domdec_t *dd, matrix box, gmx_ddbox_t *ddbox)
  61 {
  62     rvec   grid_s[2], *grid_r = nullptr, cx, r;
  63     char   fname[STRLEN], buf[22];
  64     FILE  *out;
  65     int    a, i, d, z, y, x;
  66     matrix tric;
  67     real   vol;
  68
  69     copy_rvec(dd->comm->cell_x0, grid_s[0]);
  70     copy_rvec(dd->comm->cell_x1, grid_s[1]);
  71
  72     if (DDMASTER(dd))
  73     {
  74         snew(grid_r, 2*dd->nnodes);
  75     }
  76
  77     dd_gather(dd, 2*sizeof(rvec), grid_s, DDMASTER(dd) ? grid_r : nullptr);
  78
  79     if (DDMASTER(dd))
  80     {
  81         for (d = 0; d < DIM; d++)
  82         {
  83             for (i = 0; i < DIM; i++)
  84             {
  85                 if (d == i)
  86                 {
  87                     tric[d][i] = 1;
  88                 }
  89                 else
  90                 {
  91                     if (d < ddbox->npbcdim && dd->nc[d] > 1)
  92                     {
  93                         tric[d][i] = box[i][d]/box[i][i];
  94                     }
  95                     else
  96                     {
  97                         tric[d][i] = 0;
  98                     }
  99                 }
 100             }
 101         }
 102         sprintf(fname, "%s_%s.pdb", fn, gmx_step_str(step, buf));
 103         out = gmx_fio_fopen(fname, "w");
 104         gmx_write_pdb_box(out, dd->bScrewPBC ? epbcSCREW : epbcXYZ, box);
 105         a = 1;
 106         for (i = 0; i < dd->nnodes; i++)
 107         {
 108             vol = dd->nnodes/(box[XX][XX]*box[YY][YY]*box[ZZ][ZZ]);
 109             for (d = 0; d < DIM; d++)
 110             {
 111                 vol *= grid_r[i*2+1][d] - grid_r[i*2][d];
 112             }
 113             for (z = 0; z < 2; z++)
 114             {
 115                 for (y = 0; y < 2; y++)
 116                 {
 117                     for (x = 0; x < 2; x++)
 118                     {
 119                         cx[XX] = grid_r[i*2+x][XX];
 120                         cx[YY] = grid_r[i*2+y][YY];
 121                         cx[ZZ] = grid_r[i*2+z][ZZ];
 122                         mvmul(tric, cx, r);
 123                         gmx_fprintf_pdb_atomline(out, epdbATOM, a++, "CA", ' ', "GLY", ' ', i+1, ' ',
 124                                                  10*r[XX], 10*r[YY], 10*r[ZZ], 1.0, vol, "");
 125                     }
 126                 }
 127             }
 128             for (d = 0; d < DIM; d++)
 129             {
 130                 for (x = 0; x < 4; x++)
 131                 {
 132                     switch (d)
 133                     {
 134                         case 0: y = 1 + i*8 + 2*x; break;
 135                         case 1: y = 1 + i*8 + 2*x - (x % 2); break;
 136                         case 2: y = 1 + i*8 + x; break;
 137                     }
 138                     fprintf(out, "%6s%5d%5d\n", "CONECT", y, y+(1<<d));
 139                 }
 140             }
 141         }
 142         gmx_fio_fclose(out);
 143         sfree(grid_r);
 144     }
 145 }
 146
 147 void write_dd_pdb(const char *fn, int64_t step, const char *title,
 148                   const gmx_mtop_t *mtop, const t_commrec *cr,
 149                   int natoms, const rvec x[], const matrix box)
 150 {
 151     char          fname[STRLEN], buf[22];
 152     FILE         *out;
 153     int           resnr;
 154     const char   *atomname, *resname;
 155     gmx_domdec_t *dd;
 156
 157     dd = cr->dd;
 158     if (natoms == -1)
 159     {
 160         natoms = dd->comm->atomRanges.end(DDAtomRanges::Type::Vsites);
 161     }
 162
 163     sprintf(fname, "%s_%s_n%d.pdb", fn, gmx_step_str(step, buf), cr->sim_nodeid);
 164
 165     out = gmx_fio_fopen(fname, "w");
 166
 167     fprintf(out, "TITLE     %s\n", title);
 168     gmx_write_pdb_box(out, dd->bScrewPBC ? epbcSCREW : epbcXYZ, box);
 169     int molb = 0;
 170     for (int i = 0; i < natoms; i++)
 171     {
 172         int  ii = dd->globalAtomIndices[i];
 173         mtopGetAtomAndResidueName(mtop, ii, &molb, &atomname, &resnr, &resname, nullptr);
 174         int  c;
 175         real b;
 176         if (i < dd->comm->atomRanges.end(DDAtomRanges::Type::Zones))
 177         {
 178             c = 0;
 179             while (i >= dd->comm->zones.cg_range[c + 1])
 180             {
 181                 c++;
 182             }
 183             b = c;
 184         }
 185         else if (i < dd->comm->atomRanges.end(DDAtomRanges::Type::Vsites))
 186         {
 187             b = dd->comm->zones.n;
 188         }
 189         else
 190         {
 191             b = dd->comm->zones.n + 1;
 192         }
 193         gmx_fprintf_pdb_atomline(out, epdbATOM, ii+1, atomname, ' ', resname, ' ', resnr, ' ',
 194                                  10*x[i][XX], 10*x[i][YY], 10*x[i][ZZ], 1.0, b, "");
 195     }
 196     fprintf(out, "TER\n");
 197
 198     gmx_fio_fclose(out);
 199 }