src/gromacs/fileio/trrio.cpp

   1 /*
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  37 #include "gmxpre.h"
  38
  39 #include "trrio.h"
  40
  41 #include <cstring>
  42
  43 #include "gromacs/fileio/gmxfio.h"
  44 #include "gromacs/fileio/gmxfio-xdr.h"
  45 #include "gromacs/mdtypes/md_enums.h"
  46 #include "gromacs/utility/fatalerror.h"
  47 #include "gromacs/utility/futil.h"
  48 #include "gromacs/utility/smalloc.h"
  49
  50 #define BUFSIZE     128
  51 #define GROMACS_MAGIC   1993
  52
  53 static int nFloatSize(gmx_trr_header_t *sh)
  54 {
  55     int nflsize = 0;
  56
  57     if (sh->box_size)
  58     {
  59         nflsize = sh->box_size/(DIM*DIM);
  60     }
  61     else if (sh->x_size)
  62     {
  63         nflsize = sh->x_size/(sh->natoms*DIM);
  64     }
  65     else if (sh->v_size)
  66     {
  67         nflsize = sh->v_size/(sh->natoms*DIM);
  68     }
  69     else if (sh->f_size)
  70     {
  71         nflsize = sh->f_size/(sh->natoms*DIM);
  72     }
  73     else
  74     {
  75         gmx_file("Can not determine precision of trr file");
  76     }
  77
  78     if (((nflsize != sizeof(float)) && (nflsize != sizeof(double))))
  79     {
  80         gmx_fatal(FARGS, "Float size %d. Maybe different CPU?", nflsize);
  81     }
  82
  83     return nflsize;
  84 }
  85
  86 static gmx_bool
  87 do_trr_frame_header(t_fileio *fio, bool bRead, gmx_trr_header_t *sh, gmx_bool *bOK)
  88 {
  89     int             magic  = GROMACS_MAGIC;
  90     static gmx_bool bFirst = TRUE;
  91     char            buf[256];
  92
  93     *bOK = TRUE;
  94
  95     if (!gmx_fio_do_int(fio, magic) || magic != GROMACS_MAGIC)
  96     {
  97         return FALSE;
  98     }
  99
 100     if (bRead)
 101     {
 102         *bOK = *bOK && gmx_fio_do_string(fio, buf);
 103         if (bFirst)
 104         {
 105             fprintf(stderr, "trr version: %s ", buf);
 106         }
 107     }
 108     else
 109     {
 110         sprintf(buf, "GMX_trn_file");
 111         *bOK = *bOK && gmx_fio_do_string(fio, buf);
 112     }
 113     *bOK = *bOK && gmx_fio_do_int(fio, sh->ir_size);
 114     *bOK = *bOK && gmx_fio_do_int(fio, sh->e_size);
 115     *bOK = *bOK && gmx_fio_do_int(fio, sh->box_size);
 116     *bOK = *bOK && gmx_fio_do_int(fio, sh->vir_size);
 117     *bOK = *bOK && gmx_fio_do_int(fio, sh->pres_size);
 118     *bOK = *bOK && gmx_fio_do_int(fio, sh->top_size);
 119     *bOK = *bOK && gmx_fio_do_int(fio, sh->sym_size);
 120     *bOK = *bOK && gmx_fio_do_int(fio, sh->x_size);
 121     *bOK = *bOK && gmx_fio_do_int(fio, sh->v_size);
 122     *bOK = *bOK && gmx_fio_do_int(fio, sh->f_size);
 123     *bOK = *bOK && gmx_fio_do_int(fio, sh->natoms);
 124
 125     if (!*bOK)
 126     {
 127         return *bOK;
 128     }
 129     sh->bDouble = (nFloatSize(sh) == sizeof(double));
 130     gmx_fio_setprecision(fio, sh->bDouble);
 131
 132     if (bRead && bFirst)
 133     {
 134         fprintf(stderr, "(%s precision)\n", sh->bDouble ? "double" : "single");
 135         bFirst = FALSE;
 136     }
 137
 138     *bOK = *bOK && gmx_fio_do_int(fio, sh->step);
 139     *bOK = *bOK && gmx_fio_do_int(fio, sh->nre);
 140     *bOK = *bOK && gmx_fio_do_real(fio, sh->t);
 141     *bOK = *bOK && gmx_fio_do_real(fio, sh->lambda);
 142
 143     return *bOK;
 144 }
 145
 146 static gmx_bool
 147 do_trr_frame_data(t_fileio *fio, gmx_trr_header_t *sh,
 148                   rvec *box, rvec *x, rvec *v, rvec *f)
 149 {
 150     matrix   pv;
 151     gmx_bool bOK;
 152
 153     bOK = TRUE;
 154     if (sh->box_size != 0)
 155     {
 156         bOK = bOK && gmx_fio_ndo_rvec(fio, box, DIM);
 157     }
 158     if (sh->vir_size != 0)
 159     {
 160         bOK = bOK && gmx_fio_ndo_rvec(fio, pv, DIM);
 161     }
 162     if (sh->pres_size != 0)
 163     {
 164         bOK = bOK && gmx_fio_ndo_rvec(fio, pv, DIM);
 165     }
 166     if (sh->x_size   != 0)
 167     {
 168         bOK = bOK && gmx_fio_ndo_rvec(fio, x, sh->natoms);
 169     }
 170     if (sh->v_size   != 0)
 171     {
 172         bOK = bOK && gmx_fio_ndo_rvec(fio, v, sh->natoms);
 173     }
 174     if (sh->f_size   != 0)
 175     {
 176         bOK = bOK && gmx_fio_ndo_rvec(fio, f, sh->natoms);
 177     }
 178
 179     return bOK;
 180 }
 181
 182 static gmx_bool
 183 do_trr_frame(t_fileio *fio, bool bRead, int *step, real *t, real *lambda,
 184              rvec *box, int *natoms, rvec *x, rvec *v, rvec *f)
 185 {
 186     gmx_trr_header_t *sh;
 187     gmx_bool          bOK;
 188
 189     snew(sh, 1);
 190     if (!bRead)
 191     {
 192         sh->box_size = (box) ? sizeof(matrix) : 0;
 193         sh->x_size   = ((x) ? (*natoms*sizeof(x[0])) : 0);
 194         sh->v_size   = ((v) ? (*natoms*sizeof(v[0])) : 0);
 195         sh->f_size   = ((f) ? (*natoms*sizeof(f[0])) : 0);
 196         sh->natoms   = *natoms;
 197         sh->step     = *step;
 198         sh->nre      = 0;
 199         sh->t        = *t;
 200         sh->lambda   = *lambda;
 201     }
 202     if (!do_trr_frame_header(fio, bRead, sh, &bOK))
 203     {
 204         return FALSE;
 205     }
 206     if (bRead)
 207     {
 208         *natoms = sh->natoms;
 209         *step   = sh->step;
 210         *t      = sh->t;
 211         *lambda = sh->lambda;
 212         if (sh->ir_size)
 213         {
 214             gmx_file("inputrec in trr file");
 215         }
 216         if (sh->e_size)
 217         {
 218             gmx_file("energies in trr file");
 219         }
 220         if (sh->top_size)
 221         {
 222             gmx_file("topology in trr file");
 223         }
 224         if (sh->sym_size)
 225         {
 226             gmx_file("symbol table in trr file");
 227         }
 228     }
 229     bOK = do_trr_frame_data(fio, sh, box, x, v, f);
 230
 231     sfree(sh);
 232
 233     return bOK;
 234 }
 235
 236 /************************************************************
 237  *
 238  *  The following routines are the exported ones
 239  *
 240  ************************************************************/
 241
 242 void gmx_trr_read_single_header(const char *fn, gmx_trr_header_t *header)
 243 {
 244     t_fileio *fio = gmx_trr_open(fn, "r");
 245     gmx_bool  bOK;
 246     if (!do_trr_frame_header(fio, true, header, &bOK))
 247     {
 248         gmx_fatal(FARGS, "Empty file %s", fn);
 249     }
 250     gmx_trr_close(fio);
 251 }
 252
 253 gmx_bool gmx_trr_read_frame_header(t_fileio *fio, gmx_trr_header_t *header, gmx_bool *bOK)
 254 {
 255     return do_trr_frame_header(fio, true, header, bOK);
 256 }
 257
 258 void gmx_trr_write_single_frame(const char *fn, int step, real t, real lambda,
 259                                 rvec *box, int natoms, rvec *x, rvec *v, rvec *f)
 260 {
 261     t_fileio *fio = gmx_trr_open(fn, "w");
 262     do_trr_frame(fio, false, &step, &t, &lambda, box, &natoms, x, v, f);
 263     gmx_trr_close(fio);
 264 }
 265
 266 void gmx_trr_read_single_frame(const char *fn, int *step, real *t, real *lambda,
 267                                rvec *box, int *natoms, rvec *x, rvec *v, rvec *f)
 268 {
 269     t_fileio *fio = gmx_trr_open(fn, "r");
 270     do_trr_frame(fio, true, step, t, lambda, box, natoms, x, v, f);
 271     gmx_trr_close(fio);
 272 }
 273
 274 void gmx_trr_write_frame(t_fileio *fio, int step, real t, real lambda,
 275                          rvec *box, int natoms, rvec *x, rvec *v, rvec *f)
 276 {
 277     if (!do_trr_frame(fio, false, &step, &t, &lambda, box, &natoms, x, v, f))
 278     {
 279         gmx_file("Cannot write trajectory frame; maybe you are out of disk space?");
 280     }
 281 }
 282
 283
 284 gmx_bool gmx_trr_read_frame(t_fileio *fio, int *step, real *t, real *lambda,
 285                             rvec *box, int *natoms, rvec *x, rvec *v, rvec *f)
 286 {
 287     return do_trr_frame(fio, true, step, t, lambda, box, natoms, x, v, f);
 288 }
 289
 290 gmx_bool gmx_trr_read_frame_data(t_fileio *fio, gmx_trr_header_t *header,
 291                                  rvec *box, rvec *x, rvec *v, rvec *f)
 292 {
 293     return do_trr_frame_data(fio, header, box, x, v, f);
 294 }
 295
 296 t_fileio *gmx_trr_open(const char *fn, const char *mode)
 297 {
 298     return gmx_fio_open(fn, mode);
 299 }
 300
 301 void gmx_trr_close(t_fileio *fio)
 302 {
 303     gmx_fio_close(fio);
 304 }