src/gromacs/fileio/xtcio.cpp

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  37 #include "gmxpre.h"
  38
  39 #include "xtcio.h"
  40
  41 #include <cstring>
  42
  43 #include "gromacs/fileio/gmxfio.h"
  44 #include "gromacs/fileio/gmxfio_xdr.h"
  45 #include "gromacs/fileio/xdrf.h"
  46 #include "gromacs/math/vec.h"
  47 #include "gromacs/utility/fatalerror.h"
  48 #include "gromacs/utility/futil.h"
  49 #include "gromacs/utility/smalloc.h"
  50
  51 #define XTC_MAGIC 1995
  52
  53
  54 static int xdr_r2f(XDR *xdrs, real *r, gmx_bool gmx_unused bRead)
  55 {
  56 #if GMX_DOUBLE
  57     float f;
  58     int   ret;
  59
  60     if (!bRead)
  61     {
  62         f = *r;
  63     }
  64     ret = xdr_float(xdrs, &f);
  65     if (bRead)
  66     {
  67         *r = f;
  68     }
  69
  70     return ret;
  71 #else
  72     return xdr_float(xdrs, static_cast<float *>(r));
  73 #endif
  74 }
  75
  76
  77 t_fileio *open_xtc(const char *fn, const char *mode)
  78 {
  79     return gmx_fio_open(fn, mode);
  80 }
  81
  82 void close_xtc(t_fileio *fio)
  83 {
  84     gmx_fio_close(fio);
  85 }
  86
  87 static void check_xtc_magic(int magic)
  88 {
  89     if (magic != XTC_MAGIC)
  90     {
  91         gmx_fatal(FARGS, "Magic Number Error in XTC file (read %d, should be %d)",
  92                   magic, XTC_MAGIC);
  93     }
  94 }
  95
  96 static int xtc_check(const char *str, gmx_bool bResult, const char *file, int line)
  97 {
  98     if (!bResult)
  99     {
 100         if (debug)
 101         {
 102             fprintf(debug, "\nXTC error: read/write of %s failed, "
 103                     "source file %s, line %d\n", str, file, line);
 104         }
 105         return 0;
 106     }
 107     return 1;
 108 }
 109
 110 #define XTC_CHECK(s, b) xtc_check(s, b, __FILE__, __LINE__)
 111
 112 static int xtc_header(XDR *xd, int *magic, int *natoms, int64_t *step, real *time,
 113                       gmx_bool bRead, gmx_bool *bOK)
 114 {
 115     int result;
 116
 117     if (xdr_int(xd, magic) == 0)
 118     {
 119         return 0;
 120     }
 121     result = XTC_CHECK("natoms", xdr_int(xd, natoms)); /* number of atoms */
 122     if (result)
 123     {
 124         /* Note that XTC wasn't defined to be extensible, so we can't
 125          * fix the fact that we used xdr_int for the step number,
 126          * which is defined to be signed and 32 bit. */
 127         int intStep = *step;
 128         result = XTC_CHECK("step",   xdr_int(xd, &intStep)); /* frame number    */
 129         *step  = intStep;
 130     }
 131     if (result)
 132     {
 133         result = XTC_CHECK("time",   xdr_r2f(xd, time, bRead)); /* time */
 134     }
 135     *bOK = (result != 0);
 136
 137     return result;
 138 }
 139
 140 static int xtc_coord(XDR *xd, int *natoms, rvec *box, rvec *x, real *prec, gmx_bool bRead)
 141 {
 142     int    i, j, result;
 143 #if GMX_DOUBLE
 144     float *ftmp;
 145     float  fprec;
 146 #endif
 147
 148     /* box */
 149     result = 1;
 150     for (i = 0; ((i < DIM) && result); i++)
 151     {
 152         for (j = 0; ((j < DIM) && result); j++)
 153         {
 154             result = XTC_CHECK("box", xdr_r2f(xd, &(box[i][j]), bRead));
 155         }
 156     }
 157
 158     if (!result)
 159     {
 160         return result;
 161     }
 162
 163 #if GMX_DOUBLE
 164     /* allocate temp. single-precision array */
 165     snew(ftmp, (*natoms)*DIM);
 166
 167     /* Copy data to temp. array if writing */
 168     if (!bRead)
 169     {
 170         for (i = 0; (i < *natoms); i++)
 171         {
 172             ftmp[DIM*i+XX] = x[i][XX];
 173             ftmp[DIM*i+YY] = x[i][YY];
 174             ftmp[DIM*i+ZZ] = x[i][ZZ];
 175         }
 176         fprec = *prec;
 177     }
 178     result = XTC_CHECK("x", xdr3dfcoord(xd, ftmp, natoms, &fprec));
 179
 180     /* Copy from temp. array if reading */
 181     if (bRead)
 182     {
 183         for (i = 0; (i < *natoms); i++)
 184         {
 185             x[i][XX] = ftmp[DIM*i+XX];
 186             x[i][YY] = ftmp[DIM*i+YY];
 187             x[i][ZZ] = ftmp[DIM*i+ZZ];
 188         }
 189         *prec = fprec;
 190     }
 191     sfree(ftmp);
 192 #else
 193     result = XTC_CHECK("x", xdr3dfcoord(xd, x[0], natoms, prec));
 194 #endif
 195
 196     return result;
 197 }
 198
 199
 200
 201 int write_xtc(t_fileio *fio,
 202               int natoms, int64_t step, real time,
 203               const rvec *box, const rvec *x, real prec)
 204 {
 205     int      magic_number = XTC_MAGIC;
 206     XDR     *xd;
 207     gmx_bool bDum;
 208     int      bOK;
 209
 210     if (!fio)
 211     {
 212         /* This means the fio object is not being used, e.g. because
 213            we are actually writing TNG output. We still have to return
 214            a pseudo-success value, to keep some callers happy. */
 215         return 1;
 216     }
 217
 218     xd = gmx_fio_getxdr(fio);
 219     /* write magic number and xtc identidier */
 220     if (xtc_header(xd, &magic_number, &natoms, &step, &time, FALSE, &bDum) == 0)
 221     {
 222         return 0;
 223     }
 224
 225     /* write data */
 226     bOK = xtc_coord(xd, &natoms, const_cast<rvec *>(box), const_cast<rvec *>(x), &prec, FALSE); /* bOK will be 1 if writing went well */
 227
 228     if (bOK)
 229     {
 230         if (gmx_fio_flush(fio) != 0)
 231         {
 232             bOK = 0;
 233         }
 234     }
 235     return bOK; /* 0 if bad, 1 if writing went well */
 236 }
 237
 238 int read_first_xtc(t_fileio *fio, int *natoms, int64_t *step, real *time,
 239                    matrix box, rvec **x, real *prec, gmx_bool *bOK)
 240 {
 241     int  magic;
 242     XDR *xd;
 243
 244     *bOK = TRUE;
 245     xd   = gmx_fio_getxdr(fio);
 246
 247     /* read header and malloc x */
 248     if (!xtc_header(xd, &magic, natoms, step, time, TRUE, bOK))
 249     {
 250         return 0;
 251     }
 252
 253     /* Check magic number */
 254     check_xtc_magic(magic);
 255
 256     snew(*x, *natoms);
 257
 258     *bOK = (xtc_coord(xd, natoms, box, *x, prec, TRUE) != 0);
 259
 260     return static_cast<int>(*bOK);
 261 }
 262
 263 int read_next_xtc(t_fileio* fio,
 264                   int natoms, int64_t *step, real *time,
 265                   matrix box, rvec *x, real *prec, gmx_bool *bOK)
 266 {
 267     int  magic;
 268     int  n;
 269     XDR *xd;
 270
 271     *bOK = TRUE;
 272     xd   = gmx_fio_getxdr(fio);
 273
 274     /* read header */
 275     if (!xtc_header(xd, &magic, &n, step, time, TRUE, bOK))
 276     {
 277         return 0;
 278     }
 279
 280     /* Check magic number */
 281     check_xtc_magic(magic);
 282
 283     if (n > natoms)
 284     {
 285         gmx_fatal(FARGS, "Frame contains more atoms (%d) than expected (%d)",
 286                   n, natoms);
 287     }
 288
 289     *bOK = (xtc_coord(xd, &natoms, box, x, prec, TRUE) != 0);
 290
 291     return static_cast<int>(*bOK);
 292 }