src/gromacs/domdec/dump.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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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, gmx_domdec_t* dd, matrix box, gmx_ddbox_t* ddbox)
  60 {
  61     rvec   grid_s[2], *grid_r = nullptr, cx, r;
  62     char   fname[STRLEN], buf[22];
  63     FILE*  out;
  64     int    a, i, d, z, y, x;
  65     matrix tric;
  66     real   vol;
  67
  68     copy_rvec(dd->comm->cell_x0, grid_s[0]);
  69     copy_rvec(dd->comm->cell_x1, grid_s[1]);
  70
  71     if (DDMASTER(dd))
  72     {
  73         snew(grid_r, 2 * dd->nnodes);
  74     }
  75
  76     dd_gather(dd, 2 * sizeof(rvec), grid_s, DDMASTER(dd) ? grid_r : nullptr);
  77
  78     if (DDMASTER(dd))
  79     {
  80         for (d = 0; d < DIM; d++)
  81         {
  82             for (i = 0; i < DIM; i++)
  83             {
  84                 if (d == i)
  85                 {
  86                     tric[d][i] = 1;
  87                 }
  88                 else
  89                 {
  90                     if (d < ddbox->npbcdim && dd->numCells[d] > 1)
  91                     {
  92                         tric[d][i] = box[i][d] / box[i][i];
  93                     }
  94                     else
  95                     {
  96                         tric[d][i] = 0;
  97                     }
  98                 }
  99             }
 100         }
 101         sprintf(fname, "%s_%s.pdb", fn, gmx_step_str(step, buf));
 102         out = gmx_fio_fopen(fname, "w");
 103         gmx_write_pdb_box(out, dd->unitCellInfo.haveScrewPBC ? PbcType::Screw : PbcType::Xyz, box);
 104         a = 1;
 105         for (i = 0; i < dd->nnodes; i++)
 106         {
 107             vol = dd->nnodes / (box[XX][XX] * box[YY][YY] * box[ZZ][ZZ]);
 108             for (d = 0; d < DIM; d++)
 109             {
 110                 vol *= grid_r[i * 2 + 1][d] - grid_r[i * 2][d];
 111             }
 112             for (z = 0; z < 2; z++)
 113             {
 114                 for (y = 0; y < 2; y++)
 115                 {
 116                     for (x = 0; x < 2; x++)
 117                     {
 118                         cx[XX] = grid_r[i * 2 + x][XX];
 119                         cx[YY] = grid_r[i * 2 + y][YY];
 120                         cx[ZZ] = grid_r[i * 2 + z][ZZ];
 121                         mvmul(tric, cx, r);
 122                         gmx_fprintf_pdb_atomline(out, epdbATOM, a++, "CA", ' ', "GLY", ' ', i + 1, ' ',
 123                                                  10 * r[XX], 10 * r[YY], 10 * r[ZZ], 1.0, vol, "");
 124                     }
 125                 }
 126             }
 127             for (d = 0; d < DIM; d++)
 128             {
 129                 for (x = 0; x < 4; x++)
 130                 {
 131                     switch (d)
 132                     {
 133                         case 0: y = 1 + i * 8 + 2 * x; break;
 134                         case 1: y = 1 + i * 8 + 2 * x - (x % 2); break;
 135                         case 2: y = 1 + i * 8 + x; break;
 136                     }
 137                     fprintf(out, "%6s%5d%5d\n", "CONECT", y, y + (1 << d));
 138                 }
 139             }
 140         }
 141         gmx_fio_fclose(out);
 142         sfree(grid_r);
 143     }
 144 }
 145
 146 void write_dd_pdb(const char*       fn,
 147                   int64_t           step,
 148                   const char*       title,
 149                   const gmx_mtop_t* mtop,
 150                   const t_commrec*  cr,
 151                   int               natoms,
 152                   const rvec        x[],
 153                   const matrix      box)
 154 {
 155     char          fname[STRLEN], buf[22];
 156     FILE*         out;
 157     int           resnr;
 158     const char *  atomname, *resname;
 159     gmx_domdec_t* dd;
 160
 161     dd = cr->dd;
 162     if (natoms == -1)
 163     {
 164         natoms = dd->comm->atomRanges.end(DDAtomRanges::Type::Vsites);
 165     }
 166
 167     sprintf(fname, "%s_%s_n%d.pdb", fn, gmx_step_str(step, buf), cr->sim_nodeid);
 168
 169     out = gmx_fio_fopen(fname, "w");
 170
 171     fprintf(out, "TITLE     %s\n", title);
 172     gmx_write_pdb_box(out, dd->unitCellInfo.haveScrewPBC ? PbcType::Screw : PbcType::Xyz, box);
 173     int molb = 0;
 174     for (int i = 0; i < natoms; i++)
 175     {
 176         int ii = dd->globalAtomIndices[i];
 177         mtopGetAtomAndResidueName(mtop, ii, &molb, &atomname, &resnr, &resname, nullptr);
 178         int  c;
 179         real b;
 180         if (i < dd->comm->atomRanges.end(DDAtomRanges::Type::Zones))
 181         {
 182             c = 0;
 183             while (i >= dd->comm->zones.cg_range[c + 1])
 184             {
 185                 c++;
 186             }
 187             b = c;
 188         }
 189         else if (i < dd->comm->atomRanges.end(DDAtomRanges::Type::Vsites))
 190         {
 191             b = dd->comm->zones.n;
 192         }
 193         else
 194         {
 195             b = dd->comm->zones.n + 1;
 196         }
 197         gmx_fprintf_pdb_atomline(out, epdbATOM, ii + 1, atomname, ' ', resname, ' ', resnr, ' ',
 198                                  10 * x[i][XX], 10 * x[i][YY], 10 * x[i][ZZ], 1.0, b, "");
 199     }
 200     fprintf(out, "TER\n");
 201
 202     gmx_fio_fclose(out);
 203 }