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)", magic, XTC_MAGIC);
  92     }
  93 }
  94
  95 static int xtc_check(const char* str, gmx_bool bResult, const char* file, int line)
  96 {
  97     if (!bResult)
  98     {
  99         if (debug)
 100         {
 101             fprintf(debug,
 102                     "\nXTC error: read/write of %s failed, "
 103                     "source file %s, line %d\n",
 104                     str, file, line);
 105         }
 106         return 0;
 107     }
 108     return 1;
 109 }
 110
 111 #define XTC_CHECK(s, b) xtc_check(s, b, __FILE__, __LINE__)
 112
 113 static int xtc_header(XDR* xd, int* magic, int* natoms, int64_t* step, real* time, 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 int write_xtc(t_fileio* fio, int natoms, int64_t step, real time, const rvec* box, const rvec* x, real prec)
 201 {
 202     int      magic_number = XTC_MAGIC;
 203     XDR*     xd;
 204     gmx_bool bDum;
 205     int      bOK;
 206
 207     if (!fio)
 208     {
 209         /* This means the fio object is not being used, e.g. because
 210            we are actually writing TNG output. We still have to return
 211            a pseudo-success value, to keep some callers happy. */
 212         return 1;
 213     }
 214
 215     xd = gmx_fio_getxdr(fio);
 216     /* write magic number and xtc identidier */
 217     if (xtc_header(xd, &magic_number, &natoms, &step, &time, FALSE, &bDum) == 0)
 218     {
 219         return 0;
 220     }
 221
 222     /* write data */
 223     bOK = xtc_coord(xd, &natoms, const_cast<rvec*>(box), const_cast<rvec*>(x), &prec,
 224                     FALSE); /* bOK will be 1 if writing went well */
 225
 226     if (bOK)
 227     {
 228         if (gmx_fio_flush(fio) != 0)
 229         {
 230             bOK = 0;
 231         }
 232     }
 233     return bOK; /* 0 if bad, 1 if writing went well */
 234 }
 235
 236 int read_first_xtc(t_fileio* fio, int* natoms, int64_t* step, real* time, matrix box, rvec** x, real* prec, gmx_bool* bOK)
 237 {
 238     int  magic;
 239     XDR* xd;
 240
 241     *bOK = TRUE;
 242     xd   = gmx_fio_getxdr(fio);
 243
 244     /* read header and malloc x */
 245     if (!xtc_header(xd, &magic, natoms, step, time, TRUE, bOK))
 246     {
 247         return 0;
 248     }
 249
 250     /* Check magic number */
 251     check_xtc_magic(magic);
 252
 253     snew(*x, *natoms);
 254
 255     *bOK = (xtc_coord(xd, natoms, box, *x, prec, TRUE) != 0);
 256
 257     return static_cast<int>(*bOK);
 258 }
 259
 260 int read_next_xtc(t_fileio* fio, int natoms, int64_t* step, real* time, matrix box, rvec* x, real* prec, gmx_bool* bOK)
 261 {
 262     int  magic;
 263     int  n;
 264     XDR* xd;
 265
 266     *bOK = TRUE;
 267     xd   = gmx_fio_getxdr(fio);
 268
 269     /* read header */
 270     if (!xtc_header(xd, &magic, &n, step, time, TRUE, bOK))
 271     {
 272         return 0;
 273     }
 274
 275     /* Check magic number */
 276     check_xtc_magic(magic);
 277
 278     if (n > natoms)
 279     {
 280         gmx_fatal(FARGS, "Frame contains more atoms (%d) than expected (%d)", n, natoms);
 281     }
 282
 283     *bOK = (xtc_coord(xd, &natoms, box, x, prec, TRUE) != 0);
 284
 285     return static_cast<int>(*bOK);
 286 }