src/gromacs/fileio/trrio.cpp

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  38 #include "gmxpre.h"
  39
  40 #include "trrio.h"
  41
  42 #include <cstring>
  43
  44 #include "gromacs/fileio/gmxfio.h"
  45 #include "gromacs/fileio/gmxfio_xdr.h"
  46 #include "gromacs/mdtypes/md_enums.h"
  47 #include "gromacs/utility/fatalerror.h"
  48 #include "gromacs/utility/futil.h"
  49 #include "gromacs/utility/smalloc.h"
  50
  51 #define BUFSIZE 128
  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 /* Returns whether a valid frame header was read. Upon exit, *bOK is
  87    TRUE if a normal outcome resulted. Usually that is the same thing,
  88    but encountering the end of the file before reading the magic
  89    integer is a normal outcome for TRR reading, and it does not
  90    produce a valid frame header, so the values differ in that case.
  91    That does not exclude the possibility of a reading error between
  92    frames, but the trajectory-handling infrastructure needs an
  93    overhaul before we can handle that. */
  94 static gmx_bool do_trr_frame_header(t_fileio* fio, bool bRead, gmx_trr_header_t* sh, gmx_bool* bOK)
  95 {
  96     const int       magicValue = 1993;
  97     int             magic      = magicValue;
  98     static gmx_bool bFirst     = TRUE;
  99     char            buf[256];
 100
 101     *bOK = TRUE;
 102
 103     if (!gmx_fio_do_int(fio, magic))
 104     {
 105         /* Failed to read an integer, which should be the magic
 106            number, which usually means we've reached the end
 107            of the file (but could be an I/O error that we now
 108            might mishandle). */
 109         return FALSE;
 110     }
 111     if (magic != magicValue)
 112     {
 113         *bOK = FALSE;
 114         gmx_fatal(FARGS,
 115                   "Failed to find GROMACS magic number in trr frame header, so this is not a trr "
 116                   "file!\n");
 117     }
 118
 119     if (bRead)
 120     {
 121         *bOK = *bOK && gmx_fio_do_string(fio, buf);
 122         if (bFirst)
 123         {
 124             fprintf(stderr, "trr version: %s ", buf);
 125         }
 126     }
 127     else
 128     {
 129         sprintf(buf, "GMX_trn_file");
 130         *bOK = *bOK && gmx_fio_do_string(fio, buf);
 131     }
 132     *bOK = *bOK && gmx_fio_do_int(fio, sh->ir_size);
 133     *bOK = *bOK && gmx_fio_do_int(fio, sh->e_size);
 134     *bOK = *bOK && gmx_fio_do_int(fio, sh->box_size);
 135     *bOK = *bOK && gmx_fio_do_int(fio, sh->vir_size);
 136     *bOK = *bOK && gmx_fio_do_int(fio, sh->pres_size);
 137     *bOK = *bOK && gmx_fio_do_int(fio, sh->top_size);
 138     *bOK = *bOK && gmx_fio_do_int(fio, sh->sym_size);
 139     *bOK = *bOK && gmx_fio_do_int(fio, sh->x_size);
 140     *bOK = *bOK && gmx_fio_do_int(fio, sh->v_size);
 141     *bOK = *bOK && gmx_fio_do_int(fio, sh->f_size);
 142     *bOK = *bOK && gmx_fio_do_int(fio, sh->natoms);
 143
 144     if (!*bOK)
 145     {
 146         return *bOK;
 147     }
 148     sh->bDouble = (nFloatSize(sh) == sizeof(double));
 149     gmx_fio_setprecision(fio, sh->bDouble);
 150
 151     if (bRead && bFirst)
 152     {
 153         fprintf(stderr, "(%s precision)\n", sh->bDouble ? "double" : "single");
 154         bFirst = FALSE;
 155     }
 156
 157     /* Note that TRR wasn't defined to be extensible, so we can't fix
 158      * the fact that we used a default int for the step number, which
 159      * is typically defined to be signed and 32 bit. */
 160     int intStep = sh->step;
 161     *bOK        = *bOK && gmx_fio_do_int(fio, intStep);
 162     sh->step    = intStep;
 163     *bOK        = *bOK && gmx_fio_do_int(fio, sh->nre);
 164     *bOK        = *bOK && gmx_fio_do_real(fio, sh->t);
 165     *bOK        = *bOK && gmx_fio_do_real(fio, sh->lambda);
 166
 167     return *bOK;
 168 }
 169
 170 static gmx_bool do_trr_frame_data(t_fileio* fio, gmx_trr_header_t* sh, rvec* box, rvec* x, rvec* v, rvec* f)
 171 {
 172     matrix   pv;
 173     gmx_bool bOK;
 174
 175     bOK = TRUE;
 176     if (sh->box_size != 0)
 177     {
 178         bOK = bOK && gmx_fio_ndo_rvec(fio, box, DIM);
 179     }
 180     if (sh->vir_size != 0)
 181     {
 182         bOK = bOK && gmx_fio_ndo_rvec(fio, pv, DIM);
 183     }
 184     if (sh->pres_size != 0)
 185     {
 186         bOK = bOK && gmx_fio_ndo_rvec(fio, pv, DIM);
 187     }
 188     if (sh->x_size != 0)
 189     {
 190         bOK = bOK && gmx_fio_ndo_rvec(fio, x, sh->natoms);
 191     }
 192     if (sh->v_size != 0)
 193     {
 194         bOK = bOK && gmx_fio_ndo_rvec(fio, v, sh->natoms);
 195     }
 196     if (sh->f_size != 0)
 197     {
 198         bOK = bOK && gmx_fio_ndo_rvec(fio, f, sh->natoms);
 199     }
 200
 201     return bOK;
 202 }
 203
 204 static gmx_bool do_trr_frame(t_fileio* fio,
 205                              bool      bRead,
 206                              int64_t*  step,
 207                              real*     t,
 208                              real*     lambda,
 209                              rvec*     box,
 210                              int*      natoms,
 211                              rvec*     x,
 212                              rvec*     v,
 213                              rvec*     f)
 214 {
 215     gmx_trr_header_t* sh;
 216     gmx_bool          bOK;
 217
 218     snew(sh, 1);
 219     if (!bRead)
 220     {
 221         sh->box_size = (box) ? sizeof(matrix) : 0;
 222         sh->x_size   = ((x) ? (*natoms * sizeof(x[0])) : 0);
 223         sh->v_size   = ((v) ? (*natoms * sizeof(v[0])) : 0);
 224         sh->f_size   = ((f) ? (*natoms * sizeof(f[0])) : 0);
 225         sh->natoms   = *natoms;
 226         sh->step     = *step;
 227         sh->nre      = 0;
 228         sh->t        = *t;
 229         sh->lambda   = *lambda;
 230     }
 231     if (!do_trr_frame_header(fio, bRead, sh, &bOK))
 232     {
 233         return FALSE;
 234     }
 235     if (bRead)
 236     {
 237         *natoms = sh->natoms;
 238         *step   = sh->step;
 239         *t      = sh->t;
 240         *lambda = sh->lambda;
 241         if (sh->ir_size)
 242         {
 243             gmx_file("inputrec in trr file");
 244         }
 245         if (sh->e_size)
 246         {
 247             gmx_file("energies in trr file");
 248         }
 249         if (sh->top_size)
 250         {
 251             gmx_file("topology in trr file");
 252         }
 253         if (sh->sym_size)
 254         {
 255             gmx_file("symbol table in trr file");
 256         }
 257     }
 258     bOK = do_trr_frame_data(fio, sh, box, x, v, f);
 259
 260     sfree(sh);
 261
 262     return bOK;
 263 }
 264
 265 /************************************************************
 266  *
 267  *  The following routines are the exported ones
 268  *
 269  ************************************************************/
 270
 271 void gmx_trr_read_single_header(const char* fn, gmx_trr_header_t* header)
 272 {
 273     t_fileio* fio = gmx_trr_open(fn, "r");
 274     gmx_bool  bOK;
 275     if (!do_trr_frame_header(fio, true, header, &bOK))
 276     {
 277         gmx_fatal(FARGS, "Empty file %s", fn);
 278     }
 279     gmx_trr_close(fio);
 280 }
 281
 282 gmx_bool gmx_trr_read_frame_header(t_fileio* fio, gmx_trr_header_t* header, gmx_bool* bOK)
 283 {
 284     return do_trr_frame_header(fio, true, header, bOK);
 285 }
 286
 287 void gmx_trr_write_single_frame(const char* fn,
 288                                 int64_t     step,
 289                                 real        t,
 290                                 real        lambda,
 291                                 const rvec* box,
 292                                 int         natoms,
 293                                 const rvec* x,
 294                                 const rvec* v,
 295                                 const rvec* f)
 296 {
 297     t_fileio* fio = gmx_trr_open(fn, "w");
 298     do_trr_frame(fio, false, &step, &t, &lambda, const_cast<rvec*>(box), &natoms,
 299                  const_cast<rvec*>(x), const_cast<rvec*>(v), const_cast<rvec*>(f));
 300     gmx_trr_close(fio);
 301 }
 302
 303 void gmx_trr_read_single_frame(const char* fn,
 304                                int64_t*    step,
 305                                real*       t,
 306                                real*       lambda,
 307                                rvec*       box,
 308                                int*        natoms,
 309                                rvec*       x,
 310                                rvec*       v,
 311                                rvec*       f)
 312 {
 313     t_fileio* fio = gmx_trr_open(fn, "r");
 314     do_trr_frame(fio, true, step, t, lambda, box, natoms, x, v, f);
 315     gmx_trr_close(fio);
 316 }
 317
 318 void gmx_trr_write_frame(t_fileio*   fio,
 319                          int64_t     step,
 320                          real        t,
 321                          real        lambda,
 322                          const rvec* box,
 323                          int         natoms,
 324                          const rvec* x,
 325                          const rvec* v,
 326                          const rvec* f)
 327 {
 328     if (!do_trr_frame(fio, false, &step, &t, &lambda, const_cast<rvec*>(box), &natoms,
 329                       const_cast<rvec*>(x), const_cast<rvec*>(v), const_cast<rvec*>(f)))
 330     {
 331         gmx_file("Cannot write trajectory frame; maybe you are out of disk space?");
 332     }
 333 }
 334
 335
 336 gmx_bool gmx_trr_read_frame(t_fileio* fio,
 337                             int64_t*  step,
 338                             real*     t,
 339                             real*     lambda,
 340                             rvec*     box,
 341                             int*      natoms,
 342                             rvec*     x,
 343                             rvec*     v,
 344                             rvec*     f)
 345 {
 346     return do_trr_frame(fio, true, step, t, lambda, box, natoms, x, v, f);
 347 }
 348
 349 gmx_bool gmx_trr_read_frame_data(t_fileio* fio, gmx_trr_header_t* header, rvec* box, rvec* x, rvec* v, rvec* f)
 350 {
 351     return do_trr_frame_data(fio, header, box, x, v, f);
 352 }
 353
 354 t_fileio* gmx_trr_open(const char* fn, const char* mode)
 355 {
 356     return gmx_fio_open(fn, mode);
 357 }
 358
 359 void gmx_trr_close(t_fileio* fio)
 360 {
 361     gmx_fio_close(fio);
 362 }