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38 #ifndef GMX_FILEIO_GMXFIO_H
39 #define GMX_FILEIO_GMXFIO_H
43 #include "../utility/cstringutil.h"
44 #include "../utility/futil.h"
45 #include "../utility/real.h"
46 #include "../math/vectypes.h"
54 /* Enumerated for different items in files */
56 eitemHEADER, eitemIR, eitemBOX,
57 eitemTOP, eitemX, eitemV, eitemF, eitemNR
60 /* Enumerated for data types in files */
62 eioREAL, eioFLOAT, eioDOUBLE, eioINT, eioINT64,
63 eioUCHAR, eioNUCHAR, eioUSHORT,
64 eioRVEC, eioNRVEC, eioIVEC, eioSTRING, eioNR
67 typedef struct t_fileio t_fileio;
69 /* NOTE ABOUT THREAD SAFETY:
71 The functions are all thread-safe, provided that two threads don't
72 do something silly like closing the same file, or one thread
73 accesses a file that has been closed by another.
76 /********************************************************
78 ********************************************************/
80 t_fileio *gmx_fio_open(const char *fn, const char *mode);
81 /* Open a new file for reading or writing.
82 * The file type will be deduced from the file name.
85 int gmx_fio_close(t_fileio *fp);
86 /* Close the file corresponding to fp (if not stdio)
87 * The routine will exit when an invalid fio is handled.
88 * Returns 0 on success.
91 int gmx_fio_fp_close(t_fileio *fp);
92 /* Close the file corresponding to fp without closing the FIO entry
93 * Needed e.g. for trxio because the FIO entries are used to store
95 * NOTE that the fp still needs to be properly closed with gmx_fio_close().
96 * The routine will exit when an invalid fio is handled.
97 * Returns 0 on success.
101 /* Open a file, return a stream, record the entry in internal FIO object */
102 FILE* gmx_fio_fopen(const char *fn, const char *mode);
104 /* Close a file previously opened with gmx_fio_fopen.
105 * Do not mix these calls with standard fopen/fclose ones!
106 * Returns 0 on success. */
107 int gmx_fio_fclose(FILE *fp);
111 /********************************************************
112 * Change properties of the open file
113 ********************************************************/
115 void gmx_fio_setprecision(t_fileio *fio, gmx_bool bDouble);
116 /* Select the floating point precision for reading and writing files */
118 char *gmx_fio_getname(t_fileio *fio);
119 /* Return the filename corresponding to the fio index */
121 int gmx_fio_getftp(t_fileio *fio);
122 /* Return the filetype corresponding to the fio index.
123 There is as of now no corresponding setftp function because the file
124 was opened as a specific file type and changing that midway is most
125 likely an evil hack. */
127 void gmx_fio_setdebug(t_fileio *fio, gmx_bool bDebug);
128 /* Set the debug mode */
130 gmx_bool gmx_fio_getdebug(t_fileio *fio);
131 /* Return whether debug mode is on in fio */
133 gmx_bool gmx_fio_getread(t_fileio *fio);
134 /* Return whether read mode is on in fio */
137 void gmx_fio_checktype(t_fileio *fio);
138 /* Check whether the fio is of a sane type */
140 /***************************************************
142 ***************************************************/
144 void gmx_fio_rewind(t_fileio *fio);
145 /* Rewind the file in fio */
147 int gmx_fio_flush(t_fileio *fio);
148 /* Flush the fio, returns 0 on success */
150 int gmx_fio_fsync(t_fileio *fio);
151 /* fsync the fio, returns 0 on success.
152 NOTE: don't use fsync function unless you're absolutely sure you need it
153 because it deliberately interferes with the OS's caching mechanisms and
154 can cause dramatically slowed down IO performance. Some OSes (Linux,
155 for example), may implement fsync as a full sync() point. */
157 gmx_off_t gmx_fio_ftell(t_fileio *fio);
158 /* Return file position if possible */
160 int gmx_fio_seek(t_fileio *fio, gmx_off_t fpos);
161 /* Set file position if possible, quit otherwise */
163 FILE *gmx_fio_getfp(t_fileio *fio);
164 /* Return the file pointer itself */
167 /* Element with information about position in a currently open file.
168 * gmx_off_t should be defined by autoconf if your system does not have it.
169 * If you do not have it on some other platform you do not have largefile
170 * support at all, and you can define it to int (or better, find out how to
171 * enable large files). */
174 char filename[STRLEN];
176 unsigned char chksum[16];
181 int gmx_fio_get_output_file_positions(gmx_file_position_t ** outputfiles,
183 /* Return the name and file pointer positions for all currently open
184 * output files. This is used for saving in the checkpoint files, so we
185 * can truncate output files upon restart-with-appending.
187 * For the first argument you should use a pointer, which will be set to
188 * point to a list of open files.
191 t_fileio *gmx_fio_all_output_fsync(void);
192 /* fsync all open output files. This is used for checkpointing, where
193 we need to ensure that all output is actually written out to
195 This is most important in the case of some networked file systems,
196 where data is not synced with the file server until close() or
197 fsync(), so data could remain in cache for days.
198 Note the caveats reported with gmx_fio_fsync().
200 returns: NULL if no error occurred, or a pointer to the first file that
201 failed if an error occurred
205 int gmx_fio_get_file_md5(t_fileio *fio, gmx_off_t offset,
206 unsigned char digest[]);
209 int xtc_seek_frame(t_fileio *fio, int frame, int natoms);
211 int xtc_seek_time(t_fileio *fio, real time, int natoms, gmx_bool bSeekForwardOnly);
214 /* Add this to the comment string for debugging */
215 void gmx_fio_set_comment(t_fileio *fio, const char *comment);
217 /* Remove previously set comment */
218 void gmx_fio_unset_comment(t_fileio *fio);
223 /********************************************************
225 ********************************************************/
228 /* basic reading & writing */
229 gmx_bool gmx_fio_reade_real(t_fileio *fio, real *item,
230 const char *desc, const char *srcfile, int line);
231 gmx_bool gmx_fio_reade_float(t_fileio *fio, float *item,
232 const char *desc, const char *srcfile, int line);
233 gmx_bool gmx_fio_reade_double(t_fileio *fio, double *item,
234 const char *desc, const char *srcfile, int line);
235 gmx_bool gmx_fio_reade_int(t_fileio *fio, int *item,
236 const char *desc, const char *srcfile, int line);
237 gmx_bool gmx_fio_reade_int64(t_fileio *fio, gmx_int64_t *item,
238 const char *desc, const char *srcfile, int line);
239 gmx_bool gmx_fio_reade_uchar(t_fileio *fio, unsigned char *item,
240 const char *desc, const char *srcfile, int line);
241 gmx_bool gmx_fio_reade_ushort(t_fileio *fio, unsigned short *item,
242 const char *desc, const char *srcfile, int line);
243 gmx_bool gmx_fio_reade_rvec(t_fileio *fio, rvec *item,
244 const char *desc, const char *srcfile, int line);
245 gmx_bool gmx_fio_reade_ivec(t_fileio *fio, ivec *item,
246 const char *desc, const char *srcfile, int line);
247 gmx_bool gmx_fio_reade_string(t_fileio *fio, char *item,
248 const char *desc, const char *srcfile, int line);
250 gmx_bool gmx_fio_writee_real(t_fileio *fio, real item,
251 const char *desc, const char *srcfile, int line);
252 gmx_bool gmx_fio_writee_float(t_fileio *fio, float item,
253 const char *desc, const char *srcfile, int line);
254 gmx_bool gmx_fio_writee_double(t_fileio *fio, double item,
255 const char *desc, const char *srcfile, int line);
256 gmx_bool gmx_fio_writee_int(t_fileio *fio, int item,
257 const char *desc, const char *srcfile, int line);
258 gmx_bool gmx_fio_writee_int64(t_fileio *fio, gmx_int64_t item,
259 const char *desc, const char *srcfile, int line);
260 gmx_bool gmx_fio_writee_uchar(t_fileio *fio, unsigned char item,
261 const char *desc, const char *srcfile, int line);
262 gmx_bool gmx_fio_writee_ushort(t_fileio *fio, unsigned short item,
263 const char *desc, const char *srcfile, int line);
264 gmx_bool gmx_fio_writee_rvec(t_fileio *fio, rvec *item,
265 const char *desc, const char *srcfile, int line);
266 gmx_bool gmx_fio_writee_ivec(t_fileio *fio, ivec *item,
267 const char *desc, const char *srcfile, int line);
268 gmx_bool gmx_fio_writee_string(t_fileio *fio, const char *item,
269 const char *desc, const char *srcfile, int line);
271 /* reading or writing, depending on the file's opening mode string */
272 gmx_bool gmx_fio_doe_real(t_fileio *fio, real *item,
273 const char *desc, const char *srcfile, int line);
274 gmx_bool gmx_fio_doe_float(t_fileio *fio, float *item,
275 const char *desc, const char *srcfile, int line);
276 gmx_bool gmx_fio_doe_double(t_fileio *fio, double *item,
277 const char *desc, const char *srcfile, int line);
278 gmx_bool gmx_fio_doe_gmx_bool(t_fileio *fio, gmx_bool *item,
279 const char *desc, const char *srcfile, int line);
280 gmx_bool gmx_fio_doe_int(t_fileio *fio, int *item,
281 const char *desc, const char *srcfile, int line);
282 gmx_bool gmx_fio_doe_int64(t_fileio *fio, gmx_int64_t *item,
283 const char *desc, const char *srcfile, int line);
284 gmx_bool gmx_fio_doe_uchar(t_fileio *fio, unsigned char *item,
285 const char *desc, const char *srcfile, int line);
286 gmx_bool gmx_fio_doe_ushort(t_fileio *fio, unsigned short *item,
287 const char *desc, const char *srcfile, int line);
288 gmx_bool gmx_fio_doe_rvec(t_fileio *fio, rvec *item,
289 const char *desc, const char *srcfile, int line);
290 gmx_bool gmx_fio_doe_ivec(t_fileio *fio, ivec *item,
291 const char *desc, const char *srcfile, int line);
292 gmx_bool gmx_fio_doe_string(t_fileio *fio, char *item,
293 const char *desc, const char *srcfile, int line);
298 /* array reading & writing */
299 gmx_bool gmx_fio_nreade_real(t_fileio *fio, real *item, int n,
300 const char *desc, const char *srcfile, int line);
301 gmx_bool gmx_fio_nreade_float(t_fileio *fio, float *item, int n,
302 const char *desc, const char *srcfile, int line);
303 gmx_bool gmx_fio_nreade_double(t_fileio *fio, double *item, int n,
304 const char *desc, const char *srcfile, int line);
305 gmx_bool gmx_fio_nreade_int(t_fileio *fio, int *item, int n,
306 const char *desc, const char *srcfile, int line);
307 gmx_bool gmx_fio_nreade_int64(t_fileio *fio, gmx_int64_t *item, int n,
308 const char *desc, const char *srcfile,
310 gmx_bool gmx_fio_nreade_uchar(t_fileio *fio, unsigned char *item, int n,
311 const char *desc, const char *srcfile, int line);
312 gmx_bool gmx_fio_nreade_ushort(t_fileio *fio, unsigned short *item, int n,
313 const char *desc, const char *srcfile, int line);
314 gmx_bool gmx_fio_nreade_rvec(t_fileio *fio, rvec *item, int n,
315 const char *desc, const char *srcfile, int line);
316 gmx_bool gmx_fio_nreade_ivec(t_fileio *fio, ivec *item, int n,
317 const char *desc, const char *srcfile, int line);
318 gmx_bool gmx_fio_nreade_string(t_fileio *fio, char *item[], int n,
319 const char *desc, const char *srcfile, int line);
321 gmx_bool gmx_fio_nwritee_real(t_fileio *fio, const real *item, int n,
322 const char *desc, const char *srcfile, int line);
323 gmx_bool gmx_fio_nwritee_float(t_fileio *fio, const float *item, int n,
324 const char *desc, const char *srcfile, int line);
325 gmx_bool gmx_fio_nwritee_double(t_fileio *fio, const double *item, int n,
326 const char *desc, const char *srcfile, int line);
327 gmx_bool gmx_fio_nwritee_int(t_fileio *fio, const int *item, int n,
328 const char *desc, const char *srcfile, int line);
329 gmx_bool gmx_fio_nwritee_int64(t_fileio *fio,
330 const gmx_int64_t *item, int n,
331 const char *desc, const char *srcfile,
333 gmx_bool gmx_fio_nwritee_uchar(t_fileio *fio, const unsigned char *item, int n,
334 const char *desc, const char *srcfile, int line);
335 gmx_bool gmx_fio_nwritee_ushort(t_fileio *fio, const unsigned short *item, int n,
336 const char *desc, const char *srcfile, int line);
337 gmx_bool gmx_fio_nwritee_rvec(t_fileio *fio, const rvec *item, int n,
338 const char *desc, const char *srcfile, int line);
339 gmx_bool gmx_fio_nwritee_ivec(t_fileio *fio, const ivec *item, int n,
340 const char *desc, const char *srcfile, int line);
341 gmx_bool gmx_fio_nwritee_string(t_fileio *fio, const char *item[], int n,
342 const char *desc, const char *srcfile, int line);
344 gmx_bool gmx_fio_ndoe_real(t_fileio *fio, real *item, int n,
345 const char *desc, const char *srcfile, int line);
346 gmx_bool gmx_fio_ndoe_float(t_fileio *fio, float *item, int n,
347 const char *desc, const char *srcfile, int line);
348 gmx_bool gmx_fio_ndoe_double(t_fileio *fio, double *item, int n,
349 const char *desc, const char *srcfile, int line);
350 gmx_bool gmx_fio_ndoe_gmx_bool(t_fileio *fio, gmx_bool *item, int n,
351 const char *desc, const char *srcfile, int line);
352 gmx_bool gmx_fio_ndoe_int(t_fileio *fio, int *item, int n,
353 const char *desc, const char *srcfile, int line);
354 gmx_bool gmx_fio_ndoe_int64(t_fileio *fio, gmx_int64_t *item, int n,
355 const char *desc, const char *srcfile,
357 gmx_bool gmx_fio_ndoe_uchar(t_fileio *fio, unsigned char *item, int n,
358 const char *desc, const char *srcfile, int line);
359 gmx_bool gmx_fio_ndoe_ushort(t_fileio *fio, unsigned short *item, int n,
360 const char *desc, const char *srcfile, int line);
361 gmx_bool gmx_fio_ndoe_rvec(t_fileio *fio, rvec *item, int n,
362 const char *desc, const char *srcfile, int line);
363 gmx_bool gmx_fio_ndoe_ivec(t_fileio *fio, ivec *item, int n,
364 const char *desc, const char *srcfile, int line);
365 gmx_bool gmx_fio_ndoe_string(t_fileio *fio, char *item[], int n,
366 const char *desc, const char *srcfile, int line);
370 /* convenience macros */
371 #define gmx_fio_read_real(fio, item) gmx_fio_reade_real(fio, &item, (#item), __FILE__, __LINE__)
372 #define gmx_fio_read_float(fio, item) gmx_fio_reade_float(fio, &item, (#item), __FILE__, __LINE__)
373 #define gmx_fio_read_double(fio, item) gmx_fio_reade_double(fio, &item, (#item), __FILE__, __LINE__)
374 #define gmx_fio_read_int(fio, item) gmx_fio_reade_int(fio, &item, (#item), __FILE__, __LINE__)
375 #define gmx_fio_read_int64(fio, item) gmx_fio_reade_int64(fio, &item, (#item), __FILE__, __LINE__)
376 #define gmx_fio_read_uchar(fio, item) gmx_fio_reade_uchar(fio, &item, (#item), __FILE__, __LINE__)
377 #define gmx_fio_read_ushort(fio, item) gmx_fio_reade_ushort(fio, &item, (#item), __FILE__, __LINE__)
378 #define gmx_fio_read_rvec(fio, item) gmx_fio_reade_rvec(fio, item, (#item), __FILE__, __LINE__)
379 #define gmx_fio_read_ivec(fio, item) gmx_fio_reade_ivec(fio, item, (#item), __FILE__, __LINE__)
380 #define gmx_fio_read_string(fio, item) gmx_fio_reade_string(fio, item, (#item), __FILE__, __LINE__)
382 #define gmx_fio_write_real(fio, item) gmx_fio_writee_real(fio, item, (#item), __FILE__, __LINE__)
383 #define gmx_fio_write_float(fio, item) gmx_fio_writee_float(fio, item, (#item), __FILE__, __LINE__)
384 #define gmx_fio_write_double(fio, item) gmx_fio_writee_double(fio, item, (#item), __FILE__, __LINE__)
385 #define gmx_fio_write_int(fio, item) gmx_fio_writee_int(fio, item, (#item), __FILE__, __LINE__)
386 #define gmx_fio_write_int64(fio, item) gmx_fio_writee_int64(fio, item, (#item), __FILE__, __LINE__)
387 #define gmx_fio_write_uchar(fio, item) gmx_fio_writee_uchar(fio, item, (#item), __FILE__, __LINE__)
388 #define gmx_fio_write_ushort(fio, item) gmx_fio_writee_ushort(fio, item, (#item), __FILE__, __LINE__)
389 #define gmx_fio_write_rvec(fio, item) gmx_fio_writee_rvec(fio, item, (#item), __FILE__, __LINE__)
390 #define gmx_fio_write_ivec(fio, item) gmx_fio_writee_ivec(fio, item, (#item), __FILE__, __LINE__)
391 #define gmx_fio_write_string(fio, item) gmx_fio_writee_string(fio, item, (#item), __FILE__, __LINE__)
393 #define gmx_fio_do_real(fio, item) gmx_fio_doe_real(fio, &item, (#item), __FILE__, __LINE__)
394 #define gmx_fio_do_float(fio, item) gmx_fio_doe_float(fio, &item, (#item), __FILE__, __LINE__)
395 #define gmx_fio_do_double(fio, item) gmx_fio_doe_double(fio, &item, (#item), __FILE__, __LINE__)
396 #define gmx_fio_do_gmx_bool(fio, item) gmx_fio_doe_gmx_bool(fio, &item, (#item), __FILE__, __LINE__)
397 #define gmx_fio_do_int(fio, item) gmx_fio_doe_int(fio, &item, (#item), __FILE__, __LINE__)
398 #define gmx_fio_do_int64(fio, item) gmx_fio_doe_int64(fio, &item, (#item), __FILE__, __LINE__)
399 #define gmx_fio_do_uchar(fio, item) gmx_fio_doe_uchar(fio, &item, (#item), __FILE__, __LINE__)
400 #define gmx_fio_do_ushort(fio, item) gmx_fio_doe_ushort(fio, &item, (#item), __FILE__, __LINE__)
401 #define gmx_fio_do_rvec(fio, item) gmx_fio_doe_rvec(fio, &item, (#item), __FILE__, __LINE__)
402 #define gmx_fio_do_ivec(fio, item) gmx_fio_doe_ivec(fio, &item, (#item), __FILE__, __LINE__)
403 #define gmx_fio_do_string(fio, item) gmx_fio_doe_string(fio, item, (#item), __FILE__, __LINE__)
408 #define gmx_fio_nread_real(fio, item, n) gmx_fio_nreade_real(fio, item, n, (#item), __FILE__, __LINE__)
409 #define gmx_fio_nread_float(fio, item, n) gmx_fio_nreade_float(fio, item, n, (#item), __FILE__, __LINE__)
410 #define gmx_fio_nread_double(fio, item, n) gmx_fio_nreade_double(fio, item, n, (#item), __FILE__, __LINE__)
411 #define gmx_fio_nread_int(fio, item, n) gmx_fio_nreade_int(fio, item, n, (#item), __FILE__, __LINE__)
412 #define gmx_fio_nread_int64(fio, item, n) gmx_fio_nreade_int64(fio, item, n, (#item), __FILE__, __LINE__)
413 #define gmx_fio_nread_uchar(fio, item, n) gmx_fio_nreade_uchar(fio, item, n, (#item), __FILE__, __LINE__)
414 #define gmx_fio_nread_ushort(fio, item, n) gmx_fio_nreade_ushort(fio, item, n, (#item), __FILE__, __LINE__)
415 #define gmx_fio_nread_rvec(fio, item, n) gmx_fio_nreade_rvec(fio, item, n, (#item), __FILE__, __LINE__)
416 #define gmx_fio_nread_ivec(fio, item, n) gmx_fio_nreade_ivec(fio, item, n, (#item), __FILE__, __LINE__)
417 #define gmx_fio_nread_string(fio, item, n) gmx_fio_nreade_string(fio, item, n, (#item), __FILE__, __LINE__)
419 #define gmx_fio_nwrite_real(fio, item, n) gmx_fio_nwritee_real(fio, item, n, (#item), __FILE__, __LINE__)
420 #define gmx_fio_nwrite_float(fio, item, n) gmx_fio_nwritee_float(fio, item, n, (#item), __FILE__, __LINE__)
421 #define gmx_fio_nwrite_double(fio, item, n) gmx_fio_nwritee_double(fio, item, n, (#item), __FILE__, __LINE__)
422 #define gmx_fio_nwrite_int(fio, item, n) gmx_fio_nwritee_int(fio, item, n, (#item), __FILE__, __LINE__)
423 #define gmx_fio_nwrite_int64(fio, item, n) gmx_fio_nwritee_int64(fio, item, n, (#item), __FILE__, __LINE__)
424 #define gmx_fio_nwrite_uchar(fio, item, n) gmx_fio_nwritee_uchar(fio, item, n, (#item), __FILE__, __LINE__)
425 #define gmx_fio_nwrite_ushort(fio, item, n) gmx_fio_nwritee_ushort(fio, item, n, (#item), __FILE__, __LINE__)
426 #define gmx_fio_nwrite_rvec(fio, item, n) gmx_fio_nwritee_rvec(fio, item, n, (#item), __FILE__, __LINE__)
427 #define gmx_fio_nwrite_ivec(fio, item, n) gmx_fio_nwritee_ivec(fio, item, n, (#item), __FILE__, __LINE__)
428 #define gmx_fio_nwrite_string(fio, item, n) gmx_fio_nwritee_string(fio, item, n, (#item), __FILE__, __LINE__)
430 #define gmx_fio_ndo_real(fio, item, n) gmx_fio_ndoe_real(fio, item, n, (#item), __FILE__, __LINE__)
431 #define gmx_fio_ndo_float(fio, item, n) gmx_fio_ndoe_float(fio, item, n, (#item), __FILE__, __LINE__)
432 #define gmx_fio_ndo_double(fio, item, n) gmx_fio_ndoe_double(fio, item, n, (#item), __FILE__, __LINE__)
433 #define gmx_fio_ndo_gmx_bool(fio, item, n) gmx_fio_ndoe_gmx_bool(fio, item, n, (#item), __FILE__, __LINE__)
434 #define gmx_fio_ndo_int(fio, item, n) gmx_fio_ndoe_int(fio, item, n, (#item), __FILE__, __LINE__)
435 #define gmx_fio_ndo_int64(fio, item, n) gmx_fio_ndoe_int64(fio, item, n, (#item), __FILE__, __LINE__)
436 #define gmx_fio_ndo_uchar(fio, item, n) gmx_fio_ndoe_uchar(fio, item, n, (#item), __FILE__, __LINE__)
437 #define gmx_fio_ndo_ushort(fio, item, n) gmx_fio_ndoe_ushort(fio, item, n, (#item), __FILE__, __LINE__)
438 #define gmx_fio_ndo_rvec(fio, item, n) gmx_fio_ndoe_rvec(fio, item, n, (#item), __FILE__, __LINE__)
439 #define gmx_fio_ndo_ivec(fio, item, n) gmx_fio_ndoe_ivec(fio, item, n, (#item), __FILE__, __LINE__)
440 #define gmx_fio_ndo_string(fio, item, n) gmx_fio_ndoe_string(fio, item, n, (#item), __FILE__, __LINE__)