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43 #include "visibility.h"
52 /* Enumerated for different items in files */
53 enum { eitemHEADER, eitemIR, eitemBOX,
54 eitemTOP, eitemX, eitemV, eitemF, eitemNR };
56 /* Enumerated for data types in files */
57 enum { eioREAL, eioFLOAT, eioDOUBLE, eioINT, eioGMX_LARGE_INT,
58 eioUCHAR, eioNUCHAR, eioUSHORT,
59 eioRVEC, eioNRVEC, eioIVEC, eioSTRING, eioNR };
61 typedef struct t_fileio t_fileio;
63 extern const char *itemstr[eitemNR];
64 extern const char *comment_str[eitemNR];
66 /* NOTE ABOUT THREAD SAFETY:
68 The functions are all thread-safe, provided that two threads don't
69 do something silly like closing the same file, or one thread
70 accesses a file that has been closed by another.
73 /********************************************************
75 ********************************************************/
77 t_fileio *gmx_fio_open(const char *fn,const char *mode);
78 /* Open a new file for reading or writing.
79 * The file type will be deduced from the file name.
80 * If fn is NULL, stdin / stdout will be used for Ascii I/O (TPA type)
81 * mode may be "r", "w", or "a". You should append a "b" to the mode
82 * if you are writing a binary file, but the routine will also
83 * doublecheck it and try to do it if you forgot. This has no effect on
84 * unix, but is important on windows.
87 int gmx_fio_close(t_fileio *fp);
88 /* Close the file corresponding to fp (if not stdio)
89 * The routine will exit when an invalid fio is handled.
90 * Returns 0 on success.
93 int gmx_fio_fp_close(t_fileio *fp);
94 /* Close the file corresponding to fp without closing the FIO entry
95 * Needed e.g. for trxio because the FIO entries are used to store
97 * NOTE that the fp still needs to be properly closed with gmx_fio_close().
98 * The routine will exit when an invalid fio is handled.
99 * Returns 0 on success.
103 /* Open a file, return a stream, record the entry in internal FIO object */
105 FILE* gmx_fio_fopen(const char *fn,const char *mode);
107 /* Close a file previously opened with gmx_fio_fopen.
108 * Do not mix these calls with standard fopen/fclose ones!
109 * Returns 0 on success. */
111 int gmx_fio_fclose(FILE *fp);
115 /********************************************************
116 * Change properties of the open file
117 ********************************************************/
119 void gmx_fio_setprecision(t_fileio *fio,gmx_bool bDouble);
120 /* Select the floating point precision for reading and writing files */
122 char *gmx_fio_getname(t_fileio *fio);
123 /* 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. */
133 void gmx_fio_setdebug(t_fileio *fio,gmx_bool bDebug);
134 /* Set the debug mode */
136 gmx_bool gmx_fio_getdebug(t_fileio *fio);
137 /* Return whether debug mode is on in fio */
139 gmx_bool gmx_fio_getread(t_fileio *fio);
140 /* Return whether read mode is on in fio */
143 void gmx_fio_checktype(t_fileio *fio);
144 /* Check whether the fio is of a sane type */
146 /***************************************************
148 ***************************************************/
150 void gmx_fio_rewind(t_fileio *fio);
151 /* Rewind the tpa file in fio */
154 int gmx_fio_flush(t_fileio *fio);
155 /* Flush the fio, returns 0 on success */
157 int gmx_fio_fsync(t_fileio *fio);
158 /* fsync the fio, returns 0 on success.
159 NOTE: don't use fsync function unless you're absolutely sure you need it
160 because it deliberately interferes with the OS's caching mechanisms and
161 can cause dramatically slowed down IO performance. Some OSes (Linux,
162 for example), may implement fsync as a full sync() point. */
165 gmx_off_t gmx_fio_ftell(t_fileio *fio);
166 /* Return file position if possible */
169 int gmx_fio_seek(t_fileio *fio,gmx_off_t fpos);
170 /* Set file position if possible, quit otherwise */
173 FILE *gmx_fio_getfp(t_fileio *fio);
174 /* Return the file pointer itself */
177 XDR *gmx_fio_getxdr(t_fileio *fio);
178 /* Return the file pointer itself */
184 /* Element with information about position in a currently open file.
185 * gmx_off_t should be defined by autoconf if your system does not have it.
186 * If you do not have it on some other platform you do not have largefile
187 * support at all, and you can define it to int (or better, find out how to
188 * enable large files). */
191 char filename[STRLEN];
193 unsigned char chksum[16];
200 int gmx_fio_check_file_position(t_fileio *fio);
201 /* Check if the file position is out of the range of off_t.
202 * The result is stored along with the other file data of fio.
205 int gmx_fio_get_output_file_positions(gmx_file_position_t ** outputfiles,
207 /* Return the name and file pointer positions for all currently open
208 * output files. This is used for saving in the checkpoint files, so we
209 * can truncate output files upon restart-with-appending.
211 * For the first argument you should use a pointer, which will be set to
212 * point to a list of open files.
215 t_fileio *gmx_fio_all_output_fsync(void);
216 /* fsync all open output files. This is used for checkpointing, where
217 we need to ensure that all output is actually written out to
219 This is most important in the case of some networked file systems,
220 where data is not synced with the file server until close() or
221 fsync(), so data could remain in cache for days.
222 Note the caveats reported with gmx_fio_fsync().
224 returns: NULL if no error occurred, or a pointer to the first file that
225 failed if an error occurred
229 int gmx_fio_get_file_md5(t_fileio *fio, gmx_off_t offset,
230 unsigned char digest[]);
233 int xtc_seek_frame(t_fileio *fio, int frame, int natoms);
236 int xtc_seek_time(t_fileio *fio, real time, int natoms,gmx_bool bSeekForwardOnly);
239 /* Add this to the comment string for debugging */
240 void gmx_fio_set_comment(t_fileio *fio, const char *comment);
242 /* Remove previously set comment */
243 void gmx_fio_unset_comment(t_fileio *fio);
248 /********************************************************
250 ********************************************************/
253 /* basic reading & writing */
254 gmx_bool gmx_fio_reade_real(t_fileio *fio, real *item,
255 const char *desc, const char *srcfile, int line);
256 gmx_bool gmx_fio_reade_float(t_fileio *fio, float *item,
257 const char *desc, const char *srcfile, int line);
258 gmx_bool gmx_fio_reade_double(t_fileio *fio, double *item,
259 const char *desc, const char *srcfile, int line);
260 gmx_bool gmx_fio_reade_int(t_fileio *fio, int *item,
261 const char *desc, const char *srcfile, int line);
262 gmx_bool gmx_fio_reade_gmx_large_int(t_fileio *fio, gmx_large_int_t *item,
263 const char *desc, const char *srcfile, int line);
264 gmx_bool gmx_fio_reade_uchar(t_fileio *fio, unsigned char *item,
265 const char *desc, const char *srcfile, int line);
266 gmx_bool gmx_fio_reade_ushort(t_fileio *fio, unsigned short *item,
267 const char *desc, const char *srcfile, int line);
268 gmx_bool gmx_fio_reade_rvec(t_fileio *fio, rvec *item,
269 const char *desc, const char *srcfile, int line);
270 gmx_bool gmx_fio_reade_ivec(t_fileio *fio, ivec *item,
271 const char *desc, const char *srcfile, int line);
272 gmx_bool gmx_fio_reade_string(t_fileio *fio, char *item,
273 const char *desc, const char *srcfile, int line);
275 gmx_bool gmx_fio_writee_real(t_fileio *fio, real item,
276 const char *desc, const char *srcfile, int line);
277 gmx_bool gmx_fio_writee_float(t_fileio *fio, float item,
278 const char *desc, const char *srcfile, int line);
279 gmx_bool gmx_fio_writee_double(t_fileio *fio, double item,
280 const char *desc, const char *srcfile, int line);
281 gmx_bool gmx_fio_writee_int(t_fileio *fio, int item,
282 const char *desc, const char *srcfile, int line);
283 gmx_bool gmx_fio_writee_gmx_large_int(t_fileio *fio, gmx_large_int_t item,
284 const char *desc, const char *srcfile, int line);
285 gmx_bool gmx_fio_writee_uchar(t_fileio *fio, unsigned char item,
286 const char *desc, const char *srcfile, int line);
287 gmx_bool gmx_fio_writee_ushort(t_fileio *fio, unsigned short item,
288 const char *desc, const char *srcfile, int line);
289 gmx_bool gmx_fio_writee_rvec(t_fileio *fio, rvec *item,
290 const char *desc, const char *srcfile, int line);
291 gmx_bool gmx_fio_writee_ivec(t_fileio *fio, ivec *item,
292 const char *desc, const char *srcfile, int line);
293 gmx_bool gmx_fio_writee_string(t_fileio *fio, const char *item,
294 const char *desc, const char *srcfile, int line);
296 /* reading or writing, depending on the file's opening mode string */
297 gmx_bool gmx_fio_doe_real(t_fileio *fio, real *item,
298 const char *desc, const char *srcfile, int line);
299 gmx_bool gmx_fio_doe_float(t_fileio *fio, float *item,
300 const char *desc, const char *srcfile, int line);
301 gmx_bool gmx_fio_doe_double(t_fileio *fio, double *item,
302 const char *desc, const char *srcfile, int line);
303 gmx_bool gmx_fio_doe_gmx_bool(t_fileio *fio, gmx_bool *item,
304 const char *desc, const char *srcfile, int line);
305 gmx_bool gmx_fio_doe_int(t_fileio *fio, int *item,
306 const char *desc, const char *srcfile, int line);
307 gmx_bool gmx_fio_doe_gmx_large_int(t_fileio *fio, gmx_large_int_t *item,
308 const char *desc, const char *srcfile, int line);
309 gmx_bool gmx_fio_doe_uchar(t_fileio *fio, unsigned char *item,
310 const char *desc, const char *srcfile, int line);
311 gmx_bool gmx_fio_doe_ushort(t_fileio *fio, unsigned short *item,
312 const char *desc, const char *srcfile, int line);
313 gmx_bool gmx_fio_doe_rvec(t_fileio *fio, rvec *item,
314 const char *desc, const char *srcfile, int line);
315 gmx_bool gmx_fio_doe_ivec(t_fileio *fio, ivec *item,
316 const char *desc, const char *srcfile, int line);
317 gmx_bool gmx_fio_doe_string(t_fileio *fio, char *item,
318 const char *desc, const char *srcfile, int line);
323 /* array reading & writing */
324 gmx_bool gmx_fio_nreade_real(t_fileio *fio, real *item, int n,
325 const char *desc, const char *srcfile, int line);
326 gmx_bool gmx_fio_nreade_float(t_fileio *fio, float *item, int n,
327 const char *desc, const char *srcfile, int line);
328 gmx_bool gmx_fio_nreade_double(t_fileio *fio, double *item, int n,
329 const char *desc, const char *srcfile, int line);
330 gmx_bool gmx_fio_nreade_int(t_fileio *fio, int *item, int n,
331 const char *desc, const char *srcfile, int line);
332 gmx_bool gmx_fio_nreade_gmx_large_int(t_fileio *fio, gmx_large_int_t *item, int n,
333 const char *desc, const char *srcfile,
335 gmx_bool gmx_fio_nreade_uchar(t_fileio *fio, unsigned char *item, int n,
336 const char *desc, const char *srcfile, int line);
337 gmx_bool gmx_fio_nreade_ushort(t_fileio *fio, unsigned short *item, int n,
338 const char *desc, const char *srcfile, int line);
339 gmx_bool gmx_fio_nreade_rvec(t_fileio *fio, rvec *item, int n,
340 const char *desc, const char *srcfile, int line);
341 gmx_bool gmx_fio_nreade_ivec(t_fileio *fio, ivec *item, int n,
342 const char *desc, const char *srcfile, int line);
343 gmx_bool gmx_fio_nreade_string(t_fileio *fio, char *item[], int n,
344 const char *desc, const char *srcfile, int line);
346 gmx_bool gmx_fio_nwritee_real(t_fileio *fio, const real *item, int n,
347 const char *desc, const char *srcfile, int line);
348 gmx_bool gmx_fio_nwritee_float(t_fileio *fio, const float *item, int n,
349 const char *desc, const char *srcfile, int line);
350 gmx_bool gmx_fio_nwritee_double(t_fileio *fio, const double *item, int n,
351 const char *desc, const char *srcfile, int line);
352 gmx_bool gmx_fio_nwritee_int(t_fileio *fio, const int *item, int n,
353 const char *desc, const char *srcfile, int line);
354 gmx_bool gmx_fio_nwritee_gmx_large_int(t_fileio *fio,
355 const gmx_large_int_t *item, int n,
356 const char *desc, const char *srcfile,
358 gmx_bool gmx_fio_nwritee_uchar(t_fileio *fio, const unsigned char *item, int n,
359 const char *desc, const char *srcfile, int line);
360 gmx_bool gmx_fio_nwritee_ushort(t_fileio *fio, const unsigned short *item, int n,
361 const char *desc, const char *srcfile, int line);
362 gmx_bool gmx_fio_nwritee_rvec(t_fileio *fio, const rvec *item, int n,
363 const char *desc, const char *srcfile, int line);
364 gmx_bool gmx_fio_nwritee_ivec(t_fileio *fio, const ivec *item, int n,
365 const char *desc, const char *srcfile, int line);
366 gmx_bool gmx_fio_nwritee_string(t_fileio *fio, const char *item[], int n,
367 const char *desc, const char *srcfile, int line);
369 gmx_bool gmx_fio_ndoe_real(t_fileio *fio, real *item, int n,
370 const char *desc, const char *srcfile, int line);
371 gmx_bool gmx_fio_ndoe_float(t_fileio *fio, float *item, int n,
372 const char *desc, const char *srcfile, int line);
373 gmx_bool gmx_fio_ndoe_double(t_fileio *fio, double *item, int n,
374 const char *desc, const char *srcfile, int line);
375 gmx_bool gmx_fio_ndoe_gmx_bool(t_fileio *fio, gmx_bool *item, int n,
376 const char *desc, const char *srcfile, int line);
377 gmx_bool gmx_fio_ndoe_int(t_fileio *fio, int *item, int n,
378 const char *desc, const char *srcfile, int line);
379 gmx_bool gmx_fio_ndoe_gmx_large_int(t_fileio *fio, gmx_large_int_t *item, int n,
380 const char *desc, const char *srcfile,
382 gmx_bool gmx_fio_ndoe_uchar(t_fileio *fio, unsigned char *item, int n,
383 const char *desc, const char *srcfile, int line);
384 gmx_bool gmx_fio_ndoe_ushort(t_fileio *fio, unsigned short *item, int n,
385 const char *desc, const char *srcfile, int line);
386 gmx_bool gmx_fio_ndoe_rvec(t_fileio *fio, rvec *item, int n,
387 const char *desc, const char *srcfile, int line);
388 gmx_bool gmx_fio_ndoe_ivec(t_fileio *fio, ivec *item, int n,
389 const char *desc, const char *srcfile, int line);
390 gmx_bool gmx_fio_ndoe_string(t_fileio *fio, char *item[], int n,
391 const char *desc, const char *srcfile, int line);
395 /* convenience macros */
396 #define gmx_fio_read_real(fio, item) gmx_fio_reade_real(fio, &item, (#item), __FILE__, __LINE__)
397 #define gmx_fio_read_float(fio, item) gmx_fio_reade_float(fio, &item, (#item), __FILE__, __LINE__)
398 #define gmx_fio_read_double(fio, item) gmx_fio_reade_double(fio, &item, (#item), __FILE__, __LINE__)
399 #define gmx_fio_read_int(fio, item) gmx_fio_reade_int(fio, &item, (#item), __FILE__, __LINE__)
400 #define gmx_fio_read_gmx_large_int(fio, item) gmx_fio_reade_gmx_large_int(fio, &item, (#item), __FILE__, __LINE__)
401 #define gmx_fio_read_uchar(fio, item) gmx_fio_reade_uchar(fio, &item, (#item), __FILE__, __LINE__)
402 #define gmx_fio_read_ushort(fio, item) gmx_fio_reade_ushort(fio, &item, (#item), __FILE__, __LINE__)
403 #define gmx_fio_read_rvec(fio, item) gmx_fio_reade_rvec(fio, item, (#item), __FILE__, __LINE__)
404 #define gmx_fio_read_ivec(fio, item) gmx_fio_reade_ivec(fio, item, (#item), __FILE__, __LINE__)
405 #define gmx_fio_read_string(fio, item) gmx_fio_reade_string(fio, item, (#item), __FILE__, __LINE__)
407 #define gmx_fio_write_real(fio, item) gmx_fio_writee_real(fio, item, (#item), __FILE__, __LINE__)
408 #define gmx_fio_write_float(fio, item) gmx_fio_writee_float(fio, item, (#item), __FILE__, __LINE__)
409 #define gmx_fio_write_double(fio, item) gmx_fio_writee_double(fio, item, (#item), __FILE__, __LINE__)
410 #define gmx_fio_write_int(fio, item) gmx_fio_writee_int(fio, item, (#item), __FILE__, __LINE__)
411 #define gmx_fio_write_gmx_large_int(fio, item) gmx_fio_writee_gmx_large_int(fio, item, (#item), __FILE__, __LINE__)
412 #define gmx_fio_write_uchar(fio, item) gmx_fio_writee_uchar(fio, item, (#item), __FILE__, __LINE__)
413 #define gmx_fio_write_ushort(fio, item) gmx_fio_writee_ushort(fio, item, (#item), __FILE__, __LINE__)
414 #define gmx_fio_write_rvec(fio, item) gmx_fio_writee_rvec(fio, item, (#item), __FILE__, __LINE__)
415 #define gmx_fio_write_ivec(fio, item) gmx_fio_writee_ivec(fio, item, (#item), __FILE__, __LINE__)
416 #define gmx_fio_write_string(fio, item) gmx_fio_writee_string(fio, item, (#item), __FILE__, __LINE__)
418 #define gmx_fio_do_real(fio, item) gmx_fio_doe_real(fio, &item, (#item), __FILE__, __LINE__)
419 #define gmx_fio_do_float(fio, item) gmx_fio_doe_float(fio, &item, (#item), __FILE__, __LINE__)
420 #define gmx_fio_do_double(fio, item) gmx_fio_doe_double(fio, &item, (#item), __FILE__, __LINE__)
421 #define gmx_fio_do_gmx_bool(fio, item) gmx_fio_doe_gmx_bool(fio, &item, (#item), __FILE__, __LINE__)
422 #define gmx_fio_do_int(fio, item) gmx_fio_doe_int(fio, &item, (#item), __FILE__, __LINE__)
423 #define gmx_fio_do_gmx_large_int(fio, item) gmx_fio_doe_gmx_large_int(fio, &item, (#item), __FILE__, __LINE__)
424 #define gmx_fio_do_uchar(fio, item) gmx_fio_doe_uchar(fio, &item, (#item), __FILE__, __LINE__)
425 #define gmx_fio_do_ushort(fio, item) gmx_fio_doe_ushort(fio, &item, (#item), __FILE__, __LINE__)
426 #define gmx_fio_do_rvec(fio, item) gmx_fio_doe_rvec(fio, &item, (#item), __FILE__, __LINE__)
427 #define gmx_fio_do_ivec(fio, item) gmx_fio_doe_ivec(fio, &item, (#item), __FILE__, __LINE__)
428 #define gmx_fio_do_string(fio, item) gmx_fio_doe_string(fio, item, (#item), __FILE__, __LINE__)
433 #define gmx_fio_nread_real(fio, item, n) gmx_fio_nreade_real(fio, item, n, (#item), __FILE__, __LINE__)
434 #define gmx_fio_nread_float(fio, item, n) gmx_fio_nreade_float(fio, item, n, (#item), __FILE__, __LINE__)
435 #define gmx_fio_nread_double(fio, item, n) gmx_fio_nreade_double(fio, item, n, (#item), __FILE__, __LINE__)
436 #define gmx_fio_nread_int(fio, item, n) gmx_fio_nreade_int(fio, item, n, (#item), __FILE__, __LINE__)
437 #define gmx_fio_nread_gmx_large_int(fio, item, n) gmx_fio_nreade_gmx_large_int(fio, item, n, (#item), __FILE__, __LINE__)
438 #define gmx_fio_nread_uchar(fio, item, n) gmx_fio_nreade_uchar(fio, item, n, (#item), __FILE__, __LINE__)
439 #define gmx_fio_nread_ushort(fio, item, n) gmx_fio_nreade_ushort(fio, item, n, (#item), __FILE__, __LINE__)
440 #define gmx_fio_nread_rvec(fio, item, n) gmx_fio_nreade_rvec(fio, item, n, (#item), __FILE__, __LINE__)
441 #define gmx_fio_nread_ivec(fio, item, n) gmx_fio_nreade_ivec(fio, item, n, (#item), __FILE__, __LINE__)
442 #define gmx_fio_nread_string(fio, item, n) gmx_fio_nreade_string(fio, item, n, (#item), __FILE__, __LINE__)
444 #define gmx_fio_nwrite_real(fio, item, n) gmx_fio_nwritee_real(fio, item, n, (#item), __FILE__, __LINE__)
445 #define gmx_fio_nwrite_float(fio, item, n) gmx_fio_nwritee_float(fio, item, n, (#item), __FILE__, __LINE__)
446 #define gmx_fio_nwrite_double(fio, item, n) gmx_fio_nwritee_double(fio, item, n, (#item), __FILE__, __LINE__)
447 #define gmx_fio_nwrite_int(fio, item, n) gmx_fio_nwritee_int(fio, item, n, (#item), __FILE__, __LINE__)
448 #define gmx_fio_nwrite_gmx_large_int(fio, item, n) gmx_fio_nwritee_gmx_large_int(fio, item, n, (#item), __FILE__, __LINE__)
449 #define gmx_fio_nwrite_uchar(fio, item, n) gmx_fio_nwritee_uchar(fio, item, n, (#item), __FILE__, __LINE__)
450 #define gmx_fio_nwrite_ushort(fio, item, n) gmx_fio_nwritee_ushort(fio, item, n, (#item), __FILE__, __LINE__)
451 #define gmx_fio_nwrite_rvec(fio, item, n) gmx_fio_nwritee_rvec(fio, item, n, (#item), __FILE__, __LINE__)
452 #define gmx_fio_nwrite_ivec(fio, item, n) gmx_fio_nwritee_ivec(fio, item, n, (#item), __FILE__, __LINE__)
453 #define gmx_fio_nwrite_string(fio, item, n) gmx_fio_nwritee_string(fio, item, n, (#item), __FILE__, __LINE__)
455 #define gmx_fio_ndo_real(fio, item, n) gmx_fio_ndoe_real(fio, item, n, (#item), __FILE__, __LINE__)
456 #define gmx_fio_ndo_float(fio, item, n) gmx_fio_ndoe_float(fio, item, n, (#item), __FILE__, __LINE__)
457 #define gmx_fio_ndo_double(fio, item, n) gmx_fio_ndoe_double(fio, item, n, (#item), __FILE__, __LINE__)
458 #define gmx_fio_ndo_gmx_bool(fio, item, n) gmx_fio_ndoe_gmx_bool(fio, item, n, (#item), __FILE__, __LINE__)
459 #define gmx_fio_ndo_int(fio, item, n) gmx_fio_ndoe_int(fio, item, n, (#item), __FILE__, __LINE__)
460 #define gmx_fio_ndo_gmx_large_int(fio, item, n) gmx_fio_ndoe_gmx_large_int(fio, item, n, (#item), __FILE__, __LINE__)
461 #define gmx_fio_ndo_uchar(fio, item, n) gmx_fio_ndoe_uchar(fio, item, n, (#item), __FILE__, __LINE__)
462 #define gmx_fio_ndo_ushort(fio, item, n) gmx_fio_ndoe_ushort(fio, item, n, (#item), __FILE__, __LINE__)
463 #define gmx_fio_ndo_rvec(fio, item, n) gmx_fio_ndoe_rvec(fio, item, n, (#item), __FILE__, __LINE__)
464 #define gmx_fio_ndo_ivec(fio, item, n) gmx_fio_ndoe_ivec(fio, item, n, (#item), __FILE__, __LINE__)
465 #define gmx_fio_ndo_string(fio, item, n) gmx_fio_ndoe_string(fio, item, n, (#item), __FILE__, __LINE__)