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38 #ifndef GMX_FILEIO_GMXFIO_H
39 #define GMX_FILEIO_GMXFIO_H
42 #include "../legacyheaders/typedefs.h"
51 /* Enumerated for different items in files */
53 eitemHEADER, eitemIR, eitemBOX,
54 eitemTOP, eitemX, eitemV, eitemF, eitemNR
57 /* Enumerated for data types in files */
59 eioREAL, eioFLOAT, eioDOUBLE, eioINT, eioINT64,
60 eioUCHAR, eioNUCHAR, eioUSHORT,
61 eioRVEC, eioNRVEC, eioIVEC, eioSTRING, eioNR
64 typedef struct t_fileio t_fileio;
66 extern const char *itemstr[eitemNR];
67 extern const char *comment_str[eitemNR];
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.
83 * If fn is NULL, stdin / stdout will be used for Ascii I/O (TPA type)
84 * mode may be "r", "w", or "a". You should append a "b" to the mode
85 * if you are writing a binary file, but the routine will also
86 * doublecheck it and try to do it if you forgot. This has no effect on
87 * unix, but is important on windows.
90 int gmx_fio_close(t_fileio *fp);
91 /* Close the file corresponding to fp (if not stdio)
92 * The routine will exit when an invalid fio is handled.
93 * Returns 0 on success.
96 int gmx_fio_fp_close(t_fileio *fp);
97 /* Close the file corresponding to fp without closing the FIO entry
98 * Needed e.g. for trxio because the FIO entries are used to store
100 * NOTE that the fp still needs to be properly closed with gmx_fio_close().
101 * The routine will exit when an invalid fio is handled.
102 * Returns 0 on success.
106 /* Open a file, return a stream, record the entry in internal FIO object */
107 FILE* gmx_fio_fopen(const char *fn, const char *mode);
109 /* Close a file previously opened with gmx_fio_fopen.
110 * Do not mix these calls with standard fopen/fclose ones!
111 * Returns 0 on success. */
112 int gmx_fio_fclose(FILE *fp);
116 /********************************************************
117 * Change properties of the open file
118 ********************************************************/
120 void gmx_fio_setprecision(t_fileio *fio, gmx_bool bDouble);
121 /* Select the floating point precision for reading and writing files */
123 char *gmx_fio_getname(t_fileio *fio);
124 /* Return the filename corresponding to the fio index */
126 int gmx_fio_getftp(t_fileio *fio);
127 /* Return the filetype corresponding to the fio index.
128 There is as of now no corresponding setftp function because the file
129 was opened as a specific file type and changing that midway is most
130 likely an evil hack. */
132 void gmx_fio_setdebug(t_fileio *fio, gmx_bool bDebug);
133 /* Set the debug mode */
135 gmx_bool gmx_fio_getdebug(t_fileio *fio);
136 /* Return whether debug mode is on in fio */
138 gmx_bool gmx_fio_getread(t_fileio *fio);
139 /* Return whether read mode is on in fio */
142 void gmx_fio_checktype(t_fileio *fio);
143 /* Check whether the fio is of a sane type */
145 /***************************************************
147 ***************************************************/
149 void gmx_fio_rewind(t_fileio *fio);
150 /* Rewind the tpa file in fio */
152 int gmx_fio_flush(t_fileio *fio);
153 /* Flush the fio, returns 0 on success */
155 int gmx_fio_fsync(t_fileio *fio);
156 /* fsync the fio, returns 0 on success.
157 NOTE: don't use fsync function unless you're absolutely sure you need it
158 because it deliberately interferes with the OS's caching mechanisms and
159 can cause dramatically slowed down IO performance. Some OSes (Linux,
160 for example), may implement fsync as a full sync() point. */
162 gmx_off_t gmx_fio_ftell(t_fileio *fio);
163 /* Return file position if possible */
165 int gmx_fio_seek(t_fileio *fio, gmx_off_t fpos);
166 /* Set file position if possible, quit otherwise */
168 FILE *gmx_fio_getfp(t_fileio *fio);
169 /* Return the file pointer itself */
172 /* Element with information about position in a currently open file.
173 * gmx_off_t should be defined by autoconf if your system does not have it.
174 * If you do not have it on some other platform you do not have largefile
175 * support at all, and you can define it to int (or better, find out how to
176 * enable large files). */
179 char filename[STRLEN];
181 unsigned char chksum[16];
186 int gmx_fio_get_output_file_positions(gmx_file_position_t ** outputfiles,
188 /* Return the name and file pointer positions for all currently open
189 * output files. This is used for saving in the checkpoint files, so we
190 * can truncate output files upon restart-with-appending.
192 * For the first argument you should use a pointer, which will be set to
193 * point to a list of open files.
196 t_fileio *gmx_fio_all_output_fsync(void);
197 /* fsync all open output files. This is used for checkpointing, where
198 we need to ensure that all output is actually written out to
200 This is most important in the case of some networked file systems,
201 where data is not synced with the file server until close() or
202 fsync(), so data could remain in cache for days.
203 Note the caveats reported with gmx_fio_fsync().
205 returns: NULL if no error occurred, or a pointer to the first file that
206 failed if an error occurred
210 int gmx_fio_get_file_md5(t_fileio *fio, gmx_off_t offset,
211 unsigned char digest[]);
214 int xtc_seek_frame(t_fileio *fio, int frame, int natoms);
216 int xtc_seek_time(t_fileio *fio, real time, int natoms, gmx_bool bSeekForwardOnly);
219 /* Add this to the comment string for debugging */
220 void gmx_fio_set_comment(t_fileio *fio, const char *comment);
222 /* Remove previously set comment */
223 void gmx_fio_unset_comment(t_fileio *fio);
228 /********************************************************
230 ********************************************************/
233 /* basic reading & writing */
234 gmx_bool gmx_fio_reade_real(t_fileio *fio, real *item,
235 const char *desc, const char *srcfile, int line);
236 gmx_bool gmx_fio_reade_float(t_fileio *fio, float *item,
237 const char *desc, const char *srcfile, int line);
238 gmx_bool gmx_fio_reade_double(t_fileio *fio, double *item,
239 const char *desc, const char *srcfile, int line);
240 gmx_bool gmx_fio_reade_int(t_fileio *fio, int *item,
241 const char *desc, const char *srcfile, int line);
242 gmx_bool gmx_fio_reade_int64(t_fileio *fio, gmx_int64_t *item,
243 const char *desc, const char *srcfile, int line);
244 gmx_bool gmx_fio_reade_uchar(t_fileio *fio, unsigned char *item,
245 const char *desc, const char *srcfile, int line);
246 gmx_bool gmx_fio_reade_ushort(t_fileio *fio, unsigned short *item,
247 const char *desc, const char *srcfile, int line);
248 gmx_bool gmx_fio_reade_rvec(t_fileio *fio, rvec *item,
249 const char *desc, const char *srcfile, int line);
250 gmx_bool gmx_fio_reade_ivec(t_fileio *fio, ivec *item,
251 const char *desc, const char *srcfile, int line);
252 gmx_bool gmx_fio_reade_string(t_fileio *fio, char *item,
253 const char *desc, const char *srcfile, int line);
255 gmx_bool gmx_fio_writee_real(t_fileio *fio, real item,
256 const char *desc, const char *srcfile, int line);
257 gmx_bool gmx_fio_writee_float(t_fileio *fio, float item,
258 const char *desc, const char *srcfile, int line);
259 gmx_bool gmx_fio_writee_double(t_fileio *fio, double item,
260 const char *desc, const char *srcfile, int line);
261 gmx_bool gmx_fio_writee_int(t_fileio *fio, int item,
262 const char *desc, const char *srcfile, int line);
263 gmx_bool gmx_fio_writee_int64(t_fileio *fio, gmx_int64_t item,
264 const char *desc, const char *srcfile, int line);
265 gmx_bool gmx_fio_writee_uchar(t_fileio *fio, unsigned char item,
266 const char *desc, const char *srcfile, int line);
267 gmx_bool gmx_fio_writee_ushort(t_fileio *fio, unsigned short item,
268 const char *desc, const char *srcfile, int line);
269 gmx_bool gmx_fio_writee_rvec(t_fileio *fio, rvec *item,
270 const char *desc, const char *srcfile, int line);
271 gmx_bool gmx_fio_writee_ivec(t_fileio *fio, ivec *item,
272 const char *desc, const char *srcfile, int line);
273 gmx_bool gmx_fio_writee_string(t_fileio *fio, const char *item,
274 const char *desc, const char *srcfile, int line);
276 /* reading or writing, depending on the file's opening mode string */
277 gmx_bool gmx_fio_doe_real(t_fileio *fio, real *item,
278 const char *desc, const char *srcfile, int line);
279 gmx_bool gmx_fio_doe_float(t_fileio *fio, float *item,
280 const char *desc, const char *srcfile, int line);
281 gmx_bool gmx_fio_doe_double(t_fileio *fio, double *item,
282 const char *desc, const char *srcfile, int line);
283 gmx_bool gmx_fio_doe_gmx_bool(t_fileio *fio, gmx_bool *item,
284 const char *desc, const char *srcfile, int line);
285 gmx_bool gmx_fio_doe_int(t_fileio *fio, int *item,
286 const char *desc, const char *srcfile, int line);
287 gmx_bool gmx_fio_doe_int64(t_fileio *fio, gmx_int64_t *item,
288 const char *desc, const char *srcfile, int line);
289 gmx_bool gmx_fio_doe_uchar(t_fileio *fio, unsigned char *item,
290 const char *desc, const char *srcfile, int line);
291 gmx_bool gmx_fio_doe_ushort(t_fileio *fio, unsigned short *item,
292 const char *desc, const char *srcfile, int line);
293 gmx_bool gmx_fio_doe_rvec(t_fileio *fio, rvec *item,
294 const char *desc, const char *srcfile, int line);
295 gmx_bool gmx_fio_doe_ivec(t_fileio *fio, ivec *item,
296 const char *desc, const char *srcfile, int line);
297 gmx_bool gmx_fio_doe_string(t_fileio *fio, char *item,
298 const char *desc, const char *srcfile, int line);
303 /* array reading & writing */
304 gmx_bool gmx_fio_nreade_real(t_fileio *fio, real *item, int n,
305 const char *desc, const char *srcfile, int line);
306 gmx_bool gmx_fio_nreade_float(t_fileio *fio, float *item, int n,
307 const char *desc, const char *srcfile, int line);
308 gmx_bool gmx_fio_nreade_double(t_fileio *fio, double *item, int n,
309 const char *desc, const char *srcfile, int line);
310 gmx_bool gmx_fio_nreade_int(t_fileio *fio, int *item, int n,
311 const char *desc, const char *srcfile, int line);
312 gmx_bool gmx_fio_nreade_int64(t_fileio *fio, gmx_int64_t *item, int n,
313 const char *desc, const char *srcfile,
315 gmx_bool gmx_fio_nreade_uchar(t_fileio *fio, unsigned char *item, int n,
316 const char *desc, const char *srcfile, int line);
317 gmx_bool gmx_fio_nreade_ushort(t_fileio *fio, unsigned short *item, int n,
318 const char *desc, const char *srcfile, int line);
319 gmx_bool gmx_fio_nreade_rvec(t_fileio *fio, rvec *item, int n,
320 const char *desc, const char *srcfile, int line);
321 gmx_bool gmx_fio_nreade_ivec(t_fileio *fio, ivec *item, int n,
322 const char *desc, const char *srcfile, int line);
323 gmx_bool gmx_fio_nreade_string(t_fileio *fio, char *item[], int n,
324 const char *desc, const char *srcfile, int line);
326 gmx_bool gmx_fio_nwritee_real(t_fileio *fio, const real *item, int n,
327 const char *desc, const char *srcfile, int line);
328 gmx_bool gmx_fio_nwritee_float(t_fileio *fio, const float *item, int n,
329 const char *desc, const char *srcfile, int line);
330 gmx_bool gmx_fio_nwritee_double(t_fileio *fio, const double *item, int n,
331 const char *desc, const char *srcfile, int line);
332 gmx_bool gmx_fio_nwritee_int(t_fileio *fio, const int *item, int n,
333 const char *desc, const char *srcfile, int line);
334 gmx_bool gmx_fio_nwritee_int64(t_fileio *fio,
335 const gmx_int64_t *item, int n,
336 const char *desc, const char *srcfile,
338 gmx_bool gmx_fio_nwritee_uchar(t_fileio *fio, const unsigned char *item, int n,
339 const char *desc, const char *srcfile, int line);
340 gmx_bool gmx_fio_nwritee_ushort(t_fileio *fio, const unsigned short *item, int n,
341 const char *desc, const char *srcfile, int line);
342 gmx_bool gmx_fio_nwritee_rvec(t_fileio *fio, const rvec *item, int n,
343 const char *desc, const char *srcfile, int line);
344 gmx_bool gmx_fio_nwritee_ivec(t_fileio *fio, const ivec *item, int n,
345 const char *desc, const char *srcfile, int line);
346 gmx_bool gmx_fio_nwritee_string(t_fileio *fio, const char *item[], int n,
347 const char *desc, const char *srcfile, int line);
349 gmx_bool gmx_fio_ndoe_real(t_fileio *fio, real *item, int n,
350 const char *desc, const char *srcfile, int line);
351 gmx_bool gmx_fio_ndoe_float(t_fileio *fio, float *item, int n,
352 const char *desc, const char *srcfile, int line);
353 gmx_bool gmx_fio_ndoe_double(t_fileio *fio, double *item, int n,
354 const char *desc, const char *srcfile, int line);
355 gmx_bool gmx_fio_ndoe_gmx_bool(t_fileio *fio, gmx_bool *item, int n,
356 const char *desc, const char *srcfile, int line);
357 gmx_bool gmx_fio_ndoe_int(t_fileio *fio, int *item, int n,
358 const char *desc, const char *srcfile, int line);
359 gmx_bool gmx_fio_ndoe_int64(t_fileio *fio, gmx_int64_t *item, int n,
360 const char *desc, const char *srcfile,
362 gmx_bool gmx_fio_ndoe_uchar(t_fileio *fio, unsigned char *item, int n,
363 const char *desc, const char *srcfile, int line);
364 gmx_bool gmx_fio_ndoe_ushort(t_fileio *fio, unsigned short *item, int n,
365 const char *desc, const char *srcfile, int line);
366 gmx_bool gmx_fio_ndoe_rvec(t_fileio *fio, rvec *item, int n,
367 const char *desc, const char *srcfile, int line);
368 gmx_bool gmx_fio_ndoe_ivec(t_fileio *fio, ivec *item, int n,
369 const char *desc, const char *srcfile, int line);
370 gmx_bool gmx_fio_ndoe_string(t_fileio *fio, char *item[], int n,
371 const char *desc, const char *srcfile, int line);
375 /* convenience macros */
376 #define gmx_fio_read_real(fio, item) gmx_fio_reade_real(fio, &item, (#item), __FILE__, __LINE__)
377 #define gmx_fio_read_float(fio, item) gmx_fio_reade_float(fio, &item, (#item), __FILE__, __LINE__)
378 #define gmx_fio_read_double(fio, item) gmx_fio_reade_double(fio, &item, (#item), __FILE__, __LINE__)
379 #define gmx_fio_read_int(fio, item) gmx_fio_reade_int(fio, &item, (#item), __FILE__, __LINE__)
380 #define gmx_fio_read_int64(fio, item) gmx_fio_reade_int64(fio, &item, (#item), __FILE__, __LINE__)
381 #define gmx_fio_read_uchar(fio, item) gmx_fio_reade_uchar(fio, &item, (#item), __FILE__, __LINE__)
382 #define gmx_fio_read_ushort(fio, item) gmx_fio_reade_ushort(fio, &item, (#item), __FILE__, __LINE__)
383 #define gmx_fio_read_rvec(fio, item) gmx_fio_reade_rvec(fio, item, (#item), __FILE__, __LINE__)
384 #define gmx_fio_read_ivec(fio, item) gmx_fio_reade_ivec(fio, item, (#item), __FILE__, __LINE__)
385 #define gmx_fio_read_string(fio, item) gmx_fio_reade_string(fio, item, (#item), __FILE__, __LINE__)
387 #define gmx_fio_write_real(fio, item) gmx_fio_writee_real(fio, item, (#item), __FILE__, __LINE__)
388 #define gmx_fio_write_float(fio, item) gmx_fio_writee_float(fio, item, (#item), __FILE__, __LINE__)
389 #define gmx_fio_write_double(fio, item) gmx_fio_writee_double(fio, item, (#item), __FILE__, __LINE__)
390 #define gmx_fio_write_int(fio, item) gmx_fio_writee_int(fio, item, (#item), __FILE__, __LINE__)
391 #define gmx_fio_write_int64(fio, item) gmx_fio_writee_int64(fio, item, (#item), __FILE__, __LINE__)
392 #define gmx_fio_write_uchar(fio, item) gmx_fio_writee_uchar(fio, item, (#item), __FILE__, __LINE__)
393 #define gmx_fio_write_ushort(fio, item) gmx_fio_writee_ushort(fio, item, (#item), __FILE__, __LINE__)
394 #define gmx_fio_write_rvec(fio, item) gmx_fio_writee_rvec(fio, item, (#item), __FILE__, __LINE__)
395 #define gmx_fio_write_ivec(fio, item) gmx_fio_writee_ivec(fio, item, (#item), __FILE__, __LINE__)
396 #define gmx_fio_write_string(fio, item) gmx_fio_writee_string(fio, item, (#item), __FILE__, __LINE__)
398 #define gmx_fio_do_real(fio, item) gmx_fio_doe_real(fio, &item, (#item), __FILE__, __LINE__)
399 #define gmx_fio_do_float(fio, item) gmx_fio_doe_float(fio, &item, (#item), __FILE__, __LINE__)
400 #define gmx_fio_do_double(fio, item) gmx_fio_doe_double(fio, &item, (#item), __FILE__, __LINE__)
401 #define gmx_fio_do_gmx_bool(fio, item) gmx_fio_doe_gmx_bool(fio, &item, (#item), __FILE__, __LINE__)
402 #define gmx_fio_do_int(fio, item) gmx_fio_doe_int(fio, &item, (#item), __FILE__, __LINE__)
403 #define gmx_fio_do_int64(fio, item) gmx_fio_doe_int64(fio, &item, (#item), __FILE__, __LINE__)
404 #define gmx_fio_do_uchar(fio, item) gmx_fio_doe_uchar(fio, &item, (#item), __FILE__, __LINE__)
405 #define gmx_fio_do_ushort(fio, item) gmx_fio_doe_ushort(fio, &item, (#item), __FILE__, __LINE__)
406 #define gmx_fio_do_rvec(fio, item) gmx_fio_doe_rvec(fio, &item, (#item), __FILE__, __LINE__)
407 #define gmx_fio_do_ivec(fio, item) gmx_fio_doe_ivec(fio, &item, (#item), __FILE__, __LINE__)
408 #define gmx_fio_do_string(fio, item) gmx_fio_doe_string(fio, item, (#item), __FILE__, __LINE__)
413 #define gmx_fio_nread_real(fio, item, n) gmx_fio_nreade_real(fio, item, n, (#item), __FILE__, __LINE__)
414 #define gmx_fio_nread_float(fio, item, n) gmx_fio_nreade_float(fio, item, n, (#item), __FILE__, __LINE__)
415 #define gmx_fio_nread_double(fio, item, n) gmx_fio_nreade_double(fio, item, n, (#item), __FILE__, __LINE__)
416 #define gmx_fio_nread_int(fio, item, n) gmx_fio_nreade_int(fio, item, n, (#item), __FILE__, __LINE__)
417 #define gmx_fio_nread_int64(fio, item, n) gmx_fio_nreade_int64(fio, item, n, (#item), __FILE__, __LINE__)
418 #define gmx_fio_nread_uchar(fio, item, n) gmx_fio_nreade_uchar(fio, item, n, (#item), __FILE__, __LINE__)
419 #define gmx_fio_nread_ushort(fio, item, n) gmx_fio_nreade_ushort(fio, item, n, (#item), __FILE__, __LINE__)
420 #define gmx_fio_nread_rvec(fio, item, n) gmx_fio_nreade_rvec(fio, item, n, (#item), __FILE__, __LINE__)
421 #define gmx_fio_nread_ivec(fio, item, n) gmx_fio_nreade_ivec(fio, item, n, (#item), __FILE__, __LINE__)
422 #define gmx_fio_nread_string(fio, item, n) gmx_fio_nreade_string(fio, item, n, (#item), __FILE__, __LINE__)
424 #define gmx_fio_nwrite_real(fio, item, n) gmx_fio_nwritee_real(fio, item, n, (#item), __FILE__, __LINE__)
425 #define gmx_fio_nwrite_float(fio, item, n) gmx_fio_nwritee_float(fio, item, n, (#item), __FILE__, __LINE__)
426 #define gmx_fio_nwrite_double(fio, item, n) gmx_fio_nwritee_double(fio, item, n, (#item), __FILE__, __LINE__)
427 #define gmx_fio_nwrite_int(fio, item, n) gmx_fio_nwritee_int(fio, item, n, (#item), __FILE__, __LINE__)
428 #define gmx_fio_nwrite_int64(fio, item, n) gmx_fio_nwritee_int64(fio, item, n, (#item), __FILE__, __LINE__)
429 #define gmx_fio_nwrite_uchar(fio, item, n) gmx_fio_nwritee_uchar(fio, item, n, (#item), __FILE__, __LINE__)
430 #define gmx_fio_nwrite_ushort(fio, item, n) gmx_fio_nwritee_ushort(fio, item, n, (#item), __FILE__, __LINE__)
431 #define gmx_fio_nwrite_rvec(fio, item, n) gmx_fio_nwritee_rvec(fio, item, n, (#item), __FILE__, __LINE__)
432 #define gmx_fio_nwrite_ivec(fio, item, n) gmx_fio_nwritee_ivec(fio, item, n, (#item), __FILE__, __LINE__)
433 #define gmx_fio_nwrite_string(fio, item, n) gmx_fio_nwritee_string(fio, item, n, (#item), __FILE__, __LINE__)
435 #define gmx_fio_ndo_real(fio, item, n) gmx_fio_ndoe_real(fio, item, n, (#item), __FILE__, __LINE__)
436 #define gmx_fio_ndo_float(fio, item, n) gmx_fio_ndoe_float(fio, item, n, (#item), __FILE__, __LINE__)
437 #define gmx_fio_ndo_double(fio, item, n) gmx_fio_ndoe_double(fio, item, n, (#item), __FILE__, __LINE__)
438 #define gmx_fio_ndo_gmx_bool(fio, item, n) gmx_fio_ndoe_gmx_bool(fio, item, n, (#item), __FILE__, __LINE__)
439 #define gmx_fio_ndo_int(fio, item, n) gmx_fio_ndoe_int(fio, item, n, (#item), __FILE__, __LINE__)
440 #define gmx_fio_ndo_int64(fio, item, n) gmx_fio_ndoe_int64(fio, item, n, (#item), __FILE__, __LINE__)
441 #define gmx_fio_ndo_uchar(fio, item, n) gmx_fio_ndoe_uchar(fio, item, n, (#item), __FILE__, __LINE__)
442 #define gmx_fio_ndo_ushort(fio, item, n) gmx_fio_ndoe_ushort(fio, item, n, (#item), __FILE__, __LINE__)
443 #define gmx_fio_ndo_rvec(fio, item, n) gmx_fio_ndoe_rvec(fio, item, n, (#item), __FILE__, __LINE__)
444 #define gmx_fio_ndo_ivec(fio, item, n) gmx_fio_ndoe_ivec(fio, item, n, (#item), __FILE__, __LINE__)
445 #define gmx_fio_ndo_string(fio, item, n) gmx_fio_ndoe_string(fio, item, n, (#item), __FILE__, __LINE__)