src/gromacs/fileio/xtcio.cpp

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