src/gromacs/fileio/trrio.cpp

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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
  52 static int nFloatSize(gmx_trr_header_t *sh)
  53 {
  54     int nflsize = 0;
  55
  56     if (sh->box_size)
  57     {
  58         nflsize = sh->box_size/(DIM*DIM);
  59     }
  60     else if (sh->x_size)
  61     {
  62         nflsize = sh->x_size/(sh->natoms*DIM);
  63     }
  64     else if (sh->v_size)
  65     {
  66         nflsize = sh->v_size/(sh->natoms*DIM);
  67     }
  68     else if (sh->f_size)
  69     {
  70         nflsize = sh->f_size/(sh->natoms*DIM);
  71     }
  72     else
  73     {
  74         gmx_file("Can not determine precision of trr file");
  75     }
  76
  77     if (((nflsize != sizeof(float)) && (nflsize != sizeof(double))))
  78     {
  79         gmx_fatal(FARGS, "Float size %d. Maybe different CPU?", nflsize);
  80     }
  81
  82     return nflsize;
  83 }
  84
  85 /* Returns whether a valid frame header was read. Upon exit, *bOK is
  86    TRUE if a normal outcome resulted. Usually that is the same thing,
  87    but encountering the end of the file before reading the magic
  88    integer is a normal outcome for TRR reading, and it does not
  89    produce a valid frame header, so the values differ in that case.
  90    That does not exclude the possibility of a reading error between
  91    frames, but the trajectory-handling infrastructure needs an
  92    overhaul before we can handle that. */
  93 static gmx_bool
  94 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, "Failed to find GROMACS magic number in trr frame header, so this is not a trr file!\n");
 115         return *bOK;
 116     }
 117
 118     if (bRead)
 119     {
 120         *bOK = *bOK && gmx_fio_do_string(fio, buf);
 121         if (bFirst)
 122         {
 123             fprintf(stderr, "trr version: %s ", buf);
 124         }
 125     }
 126     else
 127     {
 128         sprintf(buf, "GMX_trn_file");
 129         *bOK = *bOK && gmx_fio_do_string(fio, buf);
 130     }
 131     *bOK = *bOK && gmx_fio_do_int(fio, sh->ir_size);
 132     *bOK = *bOK && gmx_fio_do_int(fio, sh->e_size);
 133     *bOK = *bOK && gmx_fio_do_int(fio, sh->box_size);
 134     *bOK = *bOK && gmx_fio_do_int(fio, sh->vir_size);
 135     *bOK = *bOK && gmx_fio_do_int(fio, sh->pres_size);
 136     *bOK = *bOK && gmx_fio_do_int(fio, sh->top_size);
 137     *bOK = *bOK && gmx_fio_do_int(fio, sh->sym_size);
 138     *bOK = *bOK && gmx_fio_do_int(fio, sh->x_size);
 139     *bOK = *bOK && gmx_fio_do_int(fio, sh->v_size);
 140     *bOK = *bOK && gmx_fio_do_int(fio, sh->f_size);
 141     *bOK = *bOK && gmx_fio_do_int(fio, sh->natoms);
 142
 143     if (!*bOK)
 144     {
 145         return *bOK;
 146     }
 147     sh->bDouble = (nFloatSize(sh) == sizeof(double));
 148     gmx_fio_setprecision(fio, sh->bDouble);
 149
 150     if (bRead && bFirst)
 151     {
 152         fprintf(stderr, "(%s precision)\n", sh->bDouble ? "double" : "single");
 153         bFirst = FALSE;
 154     }
 155
 156     /* Note that TRR wasn't defined to be extensible, so we can't fix
 157      * the fact that we used a default int for the step number, which
 158      * is typically defined to be signed and 32 bit. */
 159     int intStep = sh->step;
 160     *bOK     = *bOK && gmx_fio_do_int(fio, intStep);
 161     sh->step = intStep;
 162     *bOK     = *bOK && gmx_fio_do_int(fio, sh->nre);
 163     *bOK     = *bOK && gmx_fio_do_real(fio, sh->t);
 164     *bOK     = *bOK && gmx_fio_do_real(fio, sh->lambda);
 165
 166     return *bOK;
 167 }
 168
 169 static gmx_bool
 170 do_trr_frame_data(t_fileio *fio, gmx_trr_header_t *sh,
 171                   rvec *box, rvec *x, rvec *v, rvec *f)
 172 {
 173     matrix   pv;
 174     gmx_bool bOK;
 175
 176     bOK = TRUE;
 177     if (sh->box_size != 0)
 178     {
 179         bOK = bOK && gmx_fio_ndo_rvec(fio, box, DIM);
 180     }
 181     if (sh->vir_size != 0)
 182     {
 183         bOK = bOK && gmx_fio_ndo_rvec(fio, pv, DIM);
 184     }
 185     if (sh->pres_size != 0)
 186     {
 187         bOK = bOK && gmx_fio_ndo_rvec(fio, pv, DIM);
 188     }
 189     if (sh->x_size   != 0)
 190     {
 191         bOK = bOK && gmx_fio_ndo_rvec(fio, x, sh->natoms);
 192     }
 193     if (sh->v_size   != 0)
 194     {
 195         bOK = bOK && gmx_fio_ndo_rvec(fio, v, sh->natoms);
 196     }
 197     if (sh->f_size   != 0)
 198     {
 199         bOK = bOK && gmx_fio_ndo_rvec(fio, f, sh->natoms);
 200     }
 201
 202     return bOK;
 203 }
 204
 205 static gmx_bool
 206 do_trr_frame(t_fileio *fio, bool bRead, gmx_int64_t *step, real *t, real *lambda,
 207              rvec *box, int *natoms, rvec *x, rvec *v, rvec *f)
 208 {
 209     gmx_trr_header_t *sh;
 210     gmx_bool          bOK;
 211
 212     snew(sh, 1);
 213     if (!bRead)
 214     {
 215         sh->box_size = (box) ? sizeof(matrix) : 0;
 216         sh->x_size   = ((x) ? (*natoms*sizeof(x[0])) : 0);
 217         sh->v_size   = ((v) ? (*natoms*sizeof(v[0])) : 0);
 218         sh->f_size   = ((f) ? (*natoms*sizeof(f[0])) : 0);
 219         sh->natoms   = *natoms;
 220         sh->step     = *step;
 221         sh->nre      = 0;
 222         sh->t        = *t;
 223         sh->lambda   = *lambda;
 224     }
 225     if (!do_trr_frame_header(fio, bRead, sh, &bOK))
 226     {
 227         return FALSE;
 228     }
 229     if (bRead)
 230     {
 231         *natoms = sh->natoms;
 232         *step   = sh->step;
 233         *t      = sh->t;
 234         *lambda = sh->lambda;
 235         if (sh->ir_size)
 236         {
 237             gmx_file("inputrec in trr file");
 238         }
 239         if (sh->e_size)
 240         {
 241             gmx_file("energies in trr file");
 242         }
 243         if (sh->top_size)
 244         {
 245             gmx_file("topology in trr file");
 246         }
 247         if (sh->sym_size)
 248         {
 249             gmx_file("symbol table in trr file");
 250         }
 251     }
 252     bOK = do_trr_frame_data(fio, sh, box, x, v, f);
 253
 254     sfree(sh);
 255
 256     return bOK;
 257 }
 258
 259 /************************************************************
 260  *
 261  *  The following routines are the exported ones
 262  *
 263  ************************************************************/
 264
 265 void gmx_trr_read_single_header(const char *fn, gmx_trr_header_t *header)
 266 {
 267     t_fileio *fio = gmx_trr_open(fn, "r");
 268     gmx_bool  bOK;
 269     if (!do_trr_frame_header(fio, true, header, &bOK))
 270     {
 271         gmx_fatal(FARGS, "Empty file %s", fn);
 272     }
 273     gmx_trr_close(fio);
 274 }
 275
 276 gmx_bool gmx_trr_read_frame_header(t_fileio *fio, gmx_trr_header_t *header, gmx_bool *bOK)
 277 {
 278     return do_trr_frame_header(fio, true, header, bOK);
 279 }
 280
 281 void gmx_trr_write_single_frame(const char *fn, gmx_int64_t step, real t, real lambda,
 282                                 const rvec *box, int natoms, const rvec *x, const rvec *v, const rvec *f)
 283 {
 284     t_fileio *fio = gmx_trr_open(fn, "w");
 285     do_trr_frame(fio, false, &step, &t, &lambda, const_cast<rvec *>(box), &natoms, const_cast<rvec *>(x), const_cast<rvec *>(v), const_cast<rvec *>(f));
 286     gmx_trr_close(fio);
 287 }
 288
 289 void gmx_trr_read_single_frame(const char *fn, gmx_int64_t *step, real *t, real *lambda,
 290                                rvec *box, int *natoms, rvec *x, rvec *v, rvec *f)
 291 {
 292     t_fileio *fio = gmx_trr_open(fn, "r");
 293     do_trr_frame(fio, true, step, t, lambda, box, natoms, x, v, f);
 294     gmx_trr_close(fio);
 295 }
 296
 297 void gmx_trr_write_frame(t_fileio *fio, gmx_int64_t step, real t, real lambda,
 298                          const rvec *box, int natoms, const rvec *x, const rvec *v, const rvec *f)
 299 {
 300     if (!do_trr_frame(fio, false, &step, &t, &lambda, const_cast<rvec *>(box), &natoms, const_cast<rvec *>(x), const_cast<rvec *>(v), const_cast<rvec *>(f)))
 301     {
 302         gmx_file("Cannot write trajectory frame; maybe you are out of disk space?");
 303     }
 304 }
 305
 306
 307 gmx_bool gmx_trr_read_frame(t_fileio *fio, gmx_int64_t *step, real *t, real *lambda,
 308                             rvec *box, int *natoms, rvec *x, rvec *v, rvec *f)
 309 {
 310     return do_trr_frame(fio, true, step, t, lambda, box, natoms, x, v, f);
 311 }
 312
 313 gmx_bool gmx_trr_read_frame_data(t_fileio *fio, gmx_trr_header_t *header,
 314                                  rvec *box, rvec *x, rvec *v, rvec *f)
 315 {
 316     return do_trr_frame_data(fio, header, box, x, v, f);
 317 }
 318
 319 t_fileio *gmx_trr_open(const char *fn, const char *mode)
 320 {
 321     return gmx_fio_open(fn, mode);
 322 }
 323
 324 void gmx_trr_close(t_fileio *fio)
 325 {
 326     gmx_fio_close(fio);
 327 }