src/gromacs/fileio/xtcio.c

   1 /*
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  37 #ifdef HAVE_CONFIG_H
  38 #include <config.h>
  39 #endif
  40
  41 #include <string.h>
  42 #include "typedefs.h"
  43 #include "xdrf.h"
  44 #include "gmxfio.h"
  45 #include "xtcio.h"
  46 #include "smalloc.h"
  47 #include "vec.h"
  48 #include "futil.h"
  49 #include "gmx_fatal.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 #ifdef 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, (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 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 void xtc_check_fat_err(const char *str, gmx_bool bResult, const char *file, int line)
 111 {
 112     if (!bResult)
 113     {
 114         gmx_fatal(FARGS, "XTC read/write of %s failed, "
 115                   "source file %s, line %d\n", str, file, line);
 116     }
 117 }
 118
 119 static int xtc_header(XDR *xd, int *magic, int *natoms, int *step, real *time,
 120                       gmx_bool bRead, gmx_bool *bOK)
 121 {
 122     int result;
 123
 124     if (xdr_int(xd, magic) == 0)
 125     {
 126         return 0;
 127     }
 128     result = XTC_CHECK("natoms", xdr_int(xd, natoms)); /* number of atoms */
 129     if (result)
 130     {
 131         result = XTC_CHECK("step",   xdr_int(xd, step)); /* frame number    */
 132     }
 133     if (result)
 134     {
 135         result = XTC_CHECK("time",   xdr_r2f(xd, time, bRead)); /* time */
 136     }
 137     *bOK = (result != 0);
 138
 139     return result;
 140 }
 141
 142 static int xtc_coord(XDR *xd, int *natoms, matrix box, rvec *x, real *prec, gmx_bool bRead)
 143 {
 144     int    i, j, result;
 145 #ifdef GMX_DOUBLE
 146     float *ftmp;
 147     float  fprec;
 148 #endif
 149
 150     /* box */
 151     result = 1;
 152     for (i = 0; ((i < DIM) && result); i++)
 153     {
 154         for (j = 0; ((j < DIM) && result); j++)
 155         {
 156             result = XTC_CHECK("box", xdr_r2f(xd, &(box[i][j]), bRead));
 157         }
 158     }
 159
 160     if (!result)
 161     {
 162         return result;
 163     }
 164
 165 #ifdef GMX_DOUBLE
 166     /* allocate temp. single-precision array */
 167     snew(ftmp, (*natoms)*DIM);
 168
 169     /* Copy data to temp. array if writing */
 170     if (!bRead)
 171     {
 172         for (i = 0; (i < *natoms); i++)
 173         {
 174             ftmp[DIM*i+XX] = x[i][XX];
 175             ftmp[DIM*i+YY] = x[i][YY];
 176             ftmp[DIM*i+ZZ] = x[i][ZZ];
 177         }
 178         fprec = *prec;
 179     }
 180     result = XTC_CHECK("x", xdr3dfcoord(xd, ftmp, natoms, &fprec));
 181
 182     /* Copy from temp. array if reading */
 183     if (bRead)
 184     {
 185         for (i = 0; (i < *natoms); i++)
 186         {
 187             x[i][XX] = ftmp[DIM*i+XX];
 188             x[i][YY] = ftmp[DIM*i+YY];
 189             x[i][ZZ] = ftmp[DIM*i+ZZ];
 190         }
 191         *prec = fprec;
 192     }
 193     sfree(ftmp);
 194 #else
 195     result = XTC_CHECK("x", xdr3dfcoord(xd, x[0], natoms, prec));
 196 #endif
 197
 198     return result;
 199 }
 200
 201
 202
 203 int write_xtc(t_fileio *fio,
 204               int natoms, int step, real time,
 205               matrix box, rvec *x, real prec)
 206 {
 207     int      magic_number = XTC_MAGIC;
 208     XDR     *xd;
 209     gmx_bool bDum;
 210     int      bOK;
 211
 212     if (!fio)
 213     {
 214         /* This means the fio object is not being used, e.g. because
 215            we are actually writing TNG output. We still have to return
 216            a pseudo-success value, to keep some callers happy. */
 217         return 1;
 218     }
 219
 220     xd = gmx_fio_getxdr(fio);
 221     /* write magic number and xtc identidier */
 222     if (xtc_header(xd, &magic_number, &natoms, &step, &time, FALSE, &bDum) == 0)
 223     {
 224         return 0;
 225     }
 226
 227     /* write data */
 228     bOK = xtc_coord(xd, &natoms, box, x, &prec, FALSE); /* bOK will be 1 if writing went well */
 229
 230     if (bOK)
 231     {
 232         if (gmx_fio_flush(fio) != 0)
 233         {
 234             bOK = 0;
 235         }
 236     }
 237     return bOK; /* 0 if bad, 1 if writing went well */
 238 }
 239
 240 int read_first_xtc(t_fileio *fio, int *natoms, int *step, real *time,
 241                    matrix box, rvec **x, real *prec, gmx_bool *bOK)
 242 {
 243     int  magic;
 244     XDR *xd;
 245
 246     *bOK = TRUE;
 247     xd   = gmx_fio_getxdr(fio);
 248
 249     /* read header and malloc x */
 250     if (!xtc_header(xd, &magic, natoms, step, time, TRUE, bOK))
 251     {
 252         return 0;
 253     }
 254
 255     /* Check magic number */
 256     check_xtc_magic(magic);
 257
 258     snew(*x, *natoms);
 259
 260     *bOK = xtc_coord(xd, natoms, box, *x, prec, TRUE);
 261
 262     return *bOK;
 263 }
 264
 265 int read_next_xtc(t_fileio* fio,
 266                   int natoms, int *step, real *time,
 267                   matrix box, rvec *x, real *prec, gmx_bool *bOK)
 268 {
 269     int  magic;
 270     int  n;
 271     XDR *xd;
 272
 273     *bOK = TRUE;
 274     xd   = gmx_fio_getxdr(fio);
 275
 276     /* read header */
 277     if (!xtc_header(xd, &magic, &n, step, time, TRUE, bOK))
 278     {
 279         return 0;
 280     }
 281
 282     /* Check magic number */
 283     check_xtc_magic(magic);
 284
 285     if (n > natoms)
 286     {
 287         gmx_fatal(FARGS, "Frame contains more atoms (%d) than expected (%d)",
 288                   n, natoms);
 289     }
 290
 291     *bOK = xtc_coord(xd, &natoms, box, x, prec, TRUE);
 292
 293     return *bOK;
 294 }